From mcolosimo at mitre.org Mon May 3 12:04:24 2004 From: mcolosimo at mitre.org (Marc Colosimo) Date: Sat Mar 5 14:43:32 2005 Subject: [Biopython-dev] setup.py bug Message-ID: <8C087F81-9D1B-11D8-AA96-000A95A5D8B2@mitre.org> There is a bug in setup.py. I don't know how people got it to work, but on my system I get this (python 2.2.2, Linux): python setup.py build Traceback (most recent call last): File "setup.py", line 392, in ? language="c++" TypeError: __init__() got an unexpected keyword argument 'language' Removing this from: Extension('Bio.KDTree._CKDTree', ["Bio/KDTree/KDTree.C", "Bio/KDTree/KDTree.swig.C"], libraries=["stdc++"] language=["c++"] ), I get the second error at: File "setup.py", line 163, in build_extension if ext.language == "c++": AttributeError: Extension instance has no attribute 'language' If these files are c++, then they should be named correctly (many choices, none with C). Marc From pieter at laeremans.org Mon May 3 13:59:12 2004 From: pieter at laeremans.org (Pieter Laeremans) Date: Sat Mar 5 14:43:32 2005 Subject: [Biopython-dev] Re: How many people on biopython lists? References: <40914EFA.4010809@burnham.org> Message-ID: <87zn8pl7db.fsf@hades.kotnet.org> Iddo Friedberg writes: > Hi, > > Can someone tell me how many subscribers are there on the biopython and > biopython-dev lists? It's for a book chapter.. good PR. > Hello, I think this is extremly difficult to estimate. As there are probably other people like me, who read the mailinglist to a news interface (gmane.org) kind regards, Pieter From bugzilla-daemon at portal.open-bio.org Tue May 4 06:44:45 2004 From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon@portal.open-bio.org) Date: Sat Mar 5 14:43:32 2005 Subject: [Biopython-dev] [Bug 1630] New: Install errors on debian Message-ID: <200405041044.i44AijPg008284@portal.open-bio.org> http://bugzilla.bioperl.org/show_bug.cgi?id=1630 Summary: Install errors on debian Product: Biopython Version: 1.24 Platform: PC OS/Version: Linux Status: NEW Severity: normal Priority: P2 Component: Main Distribution AssignedTo: biopython-dev@biopython.org ReportedBy: david@compbio.dundee.ac.uk I get the following error when trying to install on a debian system. I have tried to find the distutils package to install it but without success. Any hints? % python setup.py build Traceback (most recent call last): File "setup.py", line 31, in ? from distutils.core import setup ImportError: No module named distutils.core ------- You are receiving this mail because: ------- You are the assignee for the bug, or are watching the assignee. From bugzilla-daemon at portal.open-bio.org Tue May 4 07:03:03 2004 From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon@portal.open-bio.org) Date: Sat Mar 5 14:43:32 2005 Subject: [Biopython-dev] [Bug 1630] Install errors on debian Message-ID: <200405041103.i44B33N2008600@portal.open-bio.org> http://bugzilla.bioperl.org/show_bug.cgi?id=1630 hoffman@ebi.ac.uk changed: What |Removed |Added ---------------------------------------------------------------------------- Status|NEW |RESOLVED Resolution| |INVALID ------- Additional Comments From hoffman@ebi.ac.uk 2004-05-04 07:03 ------- Biopython requires Python 2.2 or later. Please install the latest version of Python and try again. Hint: in some distributions there might be a newer version of Python called python2, python2.3, or something similar. ------- You are receiving this mail because: ------- You are the assignee for the bug, or are watching the assignee. From bugzilla-daemon at portal.open-bio.org Tue May 4 08:30:34 2004 From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon@portal.open-bio.org) Date: Sat Mar 5 14:43:32 2005 Subject: [Biopython-dev] [Bug 1630] Install errors on debian Message-ID: <200405041230.i44CUY1K009356@portal.open-bio.org> http://bugzilla.bioperl.org/show_bug.cgi?id=1630 ------- Additional Comments From david@compbio.dundee.ac.uk 2004-05-04 08:30 ------- I am using 2.3.3 % python Python 2.3.3 (#2, Feb 24 2004, 09:29:20) [GCC 3.3.3 (Debian)] on linux2 Type "help", "copyright", "credits" or "license" for more information. >>> ------- You are receiving this mail because: ------- You are the assignee for the bug, or are watching the assignee. From bugzilla-daemon at portal.open-bio.org Tue May 4 08:50:06 2004 From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon@portal.open-bio.org) Date: Sat Mar 5 14:43:32 2005 Subject: [Biopython-dev] [Bug 1630] Install errors on debian Message-ID: <200405041250.i44Co6Rl009455@portal.open-bio.org> http://bugzilla.bioperl.org/show_bug.cgi?id=1630 ------- Additional Comments From diego@conysis.com 2004-05-04 08:50 ------- If you use python2.3, probably, you are working with the testing branch of Debian (sarge). Sarge use python2.3 by default, so that it is no necesary to specify the version. The package python-dev will install python2.3-dev, that has distutils. Just: apt-get install python-dev ------- You are receiving this mail because: ------- You are the assignee for the bug, or are watching the assignee. From mcolosimo at mitre.org Tue May 4 09:14:05 2004 From: mcolosimo at mitre.org (Marc Colosimo) Date: Sat Mar 5 14:43:32 2005 Subject: [Biopython-dev] [Bug 1630] Install errors on debian In-Reply-To: <200405041103.i44B33N2008600@portal.open-bio.org> References: <200405041103.i44B33N2008600@portal.open-bio.org> Message-ID: On May 4, 2004, at 7:03 AM, bugzilla-daemon@portal.open-bio.org wrote: > http://bugzilla.bioperl.org/show_bug.cgi?id=1630 > > hoffman@ebi.ac.uk changed: > > What |Removed |Added > ----------------------------------------------------------------------- > ----- > Status|NEW |RESOLVED > Resolution| |INVALID > > > > ------- Additional Comments From hoffman@ebi.ac.uk 2004-05-04 07:03 > ------- > Biopython requires Python 2.2 or later. Please install the latest > version of > Python and try again. > NO it requires python 2.3. I posted this the other day, I guess I'll submit a bug report. The Disutils with 2.2 do not have Extentions.language. > Hint: in some distributions there might be a newer version of Python > called > python2, python2.3, or something similar. > From hoffman at ebi.ac.uk Tue May 4 09:19:38 2004 From: hoffman at ebi.ac.uk (Michael Hoffman) Date: Sat Mar 5 14:43:32 2005 Subject: [Biopython-dev] [Bug 1630] Install errors on debian In-Reply-To: References: <200405041103.i44B33N2008600@portal.open-bio.org> Message-ID: On Tue, 4 May 2004, Marc Colosimo wrote: > NO it requires python 2.3. I posted this the other day, I guess I'll > submit a bug report. The Disutils with 2.2 do not have > Extentions.language. I remember that e-mail but I thought that was only the CVS version, not the 1.24 release. I consider your previous issue to still be open and was waiting for a response from Brad on that. Either we need to upgrade the requirement to 2.3 or come up with an ever-more-kludgy workaround. -- Michael Hoffman European Bioinformatics Institute From bugzilla-daemon at portal.open-bio.org Tue May 4 09:25:40 2004 From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon@portal.open-bio.org) Date: Sat Mar 5 14:43:32 2005 Subject: [Biopython-dev] [Bug 1631] New: setup.py does not run Message-ID: <200405041325.i44DPepn009713@portal.open-bio.org> http://bugzilla.bioperl.org/show_bug.cgi?id=1631 Summary: setup.py does not run Product: Biopython Version: Not Applicable Platform: PC OS/Version: Linux Status: NEW Severity: trivial Priority: P2 Component: Main Distribution AssignedTo: biopython-dev@biopython.org ReportedBy: mcolosimo@mitre.org setup.py uses fetures of distutils not found in python 2.2 (details below). Therefore, biopython now requires python 2.3 or a newer version of distutils. An easy solution is to change the .C files to correct extention endings (.cpp or .c++ or .cc) python setup.py build Traceback (most recent call last): File "setup.py", line 392, in ? language="c++" TypeError: __init__() got an unexpected keyword argument 'language' Removing this from: Extension('Bio.KDTree._CKDTree', ["Bio/KDTree/KDTree.C", "Bio/KDTree/KDTree.swig.C"], libraries=["stdc++"] language=["c++"] ), I get the second error at: File "setup.py", line 163, in build_extension if ext.language == "c++": AttributeError: Extension instance has no attribute 'language' If these files are c++, then they should be named correctly (many choices, none with .C). ------- You are receiving this mail because: ------- You are the assignee for the bug, or are watching the assignee. From mcolosimo at mitre.org Tue May 4 10:15:51 2004 From: mcolosimo at mitre.org (Marc Colosimo) Date: Sat Mar 5 14:43:32 2005 Subject: [Biopython-dev] [Bug 1630] Install errors on debian In-Reply-To: References: <200405041103.i44B33N2008600@portal.open-bio.org> Message-ID: <8C434506-9DD5-11D8-AA96-000A95A5D8B2@mitre.org> On May 4, 2004, at 9:19 AM, Michael Hoffman wrote: > On Tue, 4 May 2004, Marc Colosimo wrote: > >> NO it requires python 2.3. I posted this the other day, I guess I'll >> submit a bug report. The Disutils with 2.2 do not have >> Extentions.language. > > I remember that e-mail but I thought that was only the CVS version, > not the 1.24 release. Opps, I missed the line on the right of the screen about the version. Mine is with the CVS and I've added it to bugzilla (as we now all know) so that it can be tracked. > I consider your previous issue to still be open > and was waiting for a response from Brad on that. > > Either we need to upgrade the requirement to 2.3 or come up with an > ever-more-kludgy workaround. I think just changing the file name endings is all we have to do. Okay, maybe there is more. I'll send that on the other one. > -- > Michael Hoffman > European Bioinformatics Institute From hoffman at ebi.ac.uk Tue May 4 10:32:04 2004 From: hoffman at ebi.ac.uk (Michael Hoffman) Date: Sat Mar 5 14:43:32 2005 Subject: [Biopython-dev] [Bug 1630] Install errors on debian In-Reply-To: <8C434506-9DD5-11D8-AA96-000A95A5D8B2@mitre.org> References: <200405041103.i44B33N2008600@portal.open-bio.org> <8C434506-9DD5-11D8-AA96-000A95A5D8B2@mitre.org> Message-ID: On Tue, 4 May 2004, Marc Colosimo wrote: > > Either we need to upgrade the requirement to 2.3 or come up with an > > ever-more-kludgy workaround. > > I think just changing the file name endings is all we have to do. Okay, > maybe there is more. I'll send that on the other one. I believe there was a discussion on this last week (two weeks ago?) here. Changing the file name endings won't be enough for platforms that do not use gcc. I know, I have already tried it. :-) -- Michael Hoffman European Bioinformatics Institute From bugzilla-daemon at portal.open-bio.org Tue May 4 10:26:35 2004 From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon@portal.open-bio.org) Date: Sat Mar 5 14:43:32 2005 Subject: [Biopython-dev] [Bug 1631] setup.py does not run Message-ID: <200405041426.i44EQZtS010308@portal.open-bio.org> http://bugzilla.bioperl.org/show_bug.cgi?id=1631 ------- Additional Comments From mcolosimo@mitre.org 2004-05-04 10:26 ------- Diff of setup.py below. Changing the two files to .cpp seems to work (gcc does the correct thing) First, Extension('Bio.KDTree._CKDTree', ["Bio/KDTree/KDTree.cpp", "Bio/KDTree/KDTree.swig.cpp"], libraries=["stdc++"] ) has to be moved since this requires Numeric. I do not have Numeric so maybe some one could try these changes. Index: setup.py =============================================================== ==== RCS file: /home/repository/biopython/biopython/setup.py,v retrieving revision 1.86 diff -r1.86 setup.py 154a155,161 > self.extensions.append( > Extension('Bio.KDTree._CKDTree', > ["Bio/KDTree/KDTree.cpp", > "Bio/KDTree/KDTree.swig.cpp"], > libraries=["stdc++"] > ) > ) 163,166c170,173 < if ext.language == "c++": < self.compiler.compiler_so = self.compiler.compiler_cxx < else: < self.compiler.compiler_so = self._original_compiler_so --- > #if ext.language == "c++": > # self.compiler.compiler_so = self.compiler.compiler_cxx > #else: > # self.compiler.compiler_so = self._original_compiler_so 388,393c395 < Extension('Bio.KDTree._CKDTree', < ["Bio/KDTree/KDTree.C", < "Bio/KDTree/KDTree.swig.C"], < libraries=["stdc++"], < language="c++" < ), --- > ------- You are receiving this mail because: ------- You are the assignee for the bug, or are watching the assignee. From bugzilla-daemon at portal.open-bio.org Tue May 4 10:45:56 2004 From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon@portal.open-bio.org) Date: Sat Mar 5 14:43:32 2005 Subject: [Biopython-dev] [Bug 1631] setup.py does not run Message-ID: <200405041445.i44EjuXM010483@portal.open-bio.org> http://bugzilla.bioperl.org/show_bug.cgi?id=1631 thamelry@vub.ac.be changed: What |Removed |Added ---------------------------------------------------------------------------- Status|NEW |RESOLVED Resolution| |FIXED ------- Additional Comments From thamelry@vub.ac.be 2004-05-04 10:45 ------- I've changed the KDTree extensions from .C to .cpp, and updated setup.py. -Thomas ------- You are receiving this mail because: ------- You are the assignee for the bug, or are watching the assignee. From hoffman at ebi.ac.uk Tue May 4 10:59:35 2004 From: hoffman at ebi.ac.uk (Michael Hoffman) Date: Sat Mar 5 14:43:32 2005 Subject: [Biopython-dev] [Bug 1631] setup.py does not run In-Reply-To: <200405041445.i44EjuXM010483@portal.open-bio.org> References: <200405041445.i44EjuXM010483@portal.open-bio.org> Message-ID: On Tue, 4 May 2004 bugzilla-daemon@portal.open-bio.org wrote: > http://bugzilla.bioperl.org/show_bug.cgi?id=1631 > > thamelry@vub.ac.be changed: > > What |Removed |Added > ---------------------------------------------------------------------------- > Status|NEW |RESOLVED > Resolution| |FIXED > > > > ------- Additional Comments From thamelry@vub.ac.be 2004-05-04 10:45 ------- > I've changed the KDTree extensions from .C to .cpp, > and updated setup.py. Please read this thread: http://portal.open-bio.org/pipermail/biopython-dev/2004-April/001927.html This issue was discussed just a couple of weeks ago and changing the extensions will not fix the problem. -- Michael Hoffman European Bioinformatics Institute From chapmanb at uga.edu Tue May 4 07:01:43 2004 From: chapmanb at uga.edu (Brad Chapman) Date: Sat Mar 5 14:43:32 2005 Subject: [Biopython-dev] [Bug 1631] setup.py does not run In-Reply-To: References: <200405041445.i44EjuXM010483@portal.open-bio.org> Message-ID: <20040504110143.GB3375@misterbd.agtec.uga.edu> Hey all; [C++ problems again] Okay, I think I've got this all figured out and just checked a change into setup.py which hopefully deals with all the problems. Let me summarize: 1. Changing .C to .cpp won't fix the problems (as Michael noted), but there is nothing wrong with that. Thomas -- can you please make sure you checked in the new .cpp files (The old .C are gone, but the new ones aren't there -- you might need to do a cvs add). 2. The problem that Marc is noting is that the changes we used to fix the ugly C++ problem in distutils don't stretch back to 2.2. I've added onto these changes and made them even uglier -- but they appear to work now for both 2.2 and 2.3 (once Thomas checks in the new .cpp code). Please check these out and make sure they work for everyone on all platforms. 3. KDTree requires Numeric and should only be installed when Numeric is present. I've fixed this. Okay, I think this is all the problems. Could people please check out the setup.py and test? We'll get this sorted out today -- sorry about all the problems but it is a very complicated issue with the way that distutils seems to poorly handle C++ code. Hopefully these changes fix everything. Thanks for everyone's work on this! Brad From thamelry at binf.ku.dk Tue May 4 11:28:17 2004 From: thamelry at binf.ku.dk (Thomas Hamelryck) Date: Sat Mar 5 14:43:32 2005 Subject: [Biopython-dev] [Bug 1631] setup.py does not run In-Reply-To: References: <200405041445.i44EjuXM010483@portal.open-bio.org> Message-ID: <33175.192.38.112.226.1083684497.squirrel@www.binf.ku.dk> > Please read this thread: > > http://portal.open-bio.org/pipermail/biopython-dev/2004-April/001927.html > > This issue was discussed just a couple of weeks ago and changing the > extensions will not fix the problem. I'm aware of that, but this will at least help people with python 2.2 and gcc, right? -Thomas From chapmanb at uga.edu Tue May 4 07:24:35 2004 From: chapmanb at uga.edu (Brad Chapman) Date: Sat Mar 5 14:43:32 2005 Subject: [Biopython-dev] [Bug 1631] setup.py does not run In-Reply-To: <33175.192.38.112.226.1083684497.squirrel@www.binf.ku.dk> References: <200405041445.i44EjuXM010483@portal.open-bio.org> <33175.192.38.112.226.1083684497.squirrel@www.binf.ku.dk> Message-ID: <20040504112434.GE3375@misterbd.agtec.uga.edu> Hi Thomas; > > Please read this thread: > > > > http://portal.open-bio.org/pipermail/biopython-dev/2004-April/001927.html > > > > This issue was discussed just a couple of weeks ago and changing the > > extensions will not fix the problem. > > I'm aware of that, but this will at least help people with python 2.2 > and gcc, right? Sadly, not really. I've just been digging around into the guts of distutils in 2.2 and the support for any C++ is really non-existent. It basically expects that the C compiler can handle both C and C++ code (which was our major problem with non-portability of C++ code across platforms). The new setup.py is seriously kludgy but tries to take the important bits out of the 2.3 distutils that aren't in 2.2 and use them to resolve the problems. Saying all that -- it is better to have the extensions be "distutils-friendly" so the change is fine. But yeah, the issues are pretty complicated and messy -- hence the complicated and messy changes necessary in setup.py. Brad From thamelry at binf.ku.dk Tue May 4 11:45:32 2004 From: thamelry at binf.ku.dk (Thomas Hamelryck) Date: Sat Mar 5 14:43:32 2005 Subject: [Biopython-dev] [Bug 1631] setup.py does not run In-Reply-To: <20040504110143.GB3375@misterbd.agtec.uga.edu> References: <200405041445.i44EjuXM010483@portal.open-bio.org> <20040504110143.GB3375@misterbd.agtec.uga.edu> Message-ID: <33194.192.38.112.226.1083685532.squirrel@www.binf.ku.dk> > [C++ problems again] And it's all my fault (I think KDTree is the only C++ code in Biopython). Then again, it is good to have this thing fixed for future C++ modules... > 1. Changing .C to .cpp won't fix the problems (as Michael noted), > but there is nothing wrong with that. Thomas -- can you please make > sure you checked in the new .cpp files (The old .C are gone, but the > new ones aren't there -- you might need to do a cvs add). Ooops! Sorry - I've added them again. Everything works now for me, BTW (Mandrake 9.2). -Thomas From chapmanb at uga.edu Tue May 4 07:55:14 2004 From: chapmanb at uga.edu (Brad Chapman) Date: Sat Mar 5 14:43:33 2005 Subject: [Biopython-dev] [Bug 1631] setup.py does not run In-Reply-To: <33194.192.38.112.226.1083685532.squirrel@www.binf.ku.dk> References: <200405041445.i44EjuXM010483@portal.open-bio.org> <20040504110143.GB3375@misterbd.agtec.uga.edu> <33194.192.38.112.226.1083685532.squirrel@www.binf.ku.dk> Message-ID: <20040504115514.GF3375@misterbd.agtec.uga.edu> Hi Thomas; > And it's all my fault (I think KDTree is the only C++ code in Biopython). > Then again, it is good to have this thing fixed for future C++ modules... Yup, I actually just checked in other C++ code (for Affymetrix -- from Harry Zuzan) so you are not the only offender :-). Seriously, it's good to have this fixed; the real shame is that distutils deals with it so badly. > Ooops! Sorry - I've added them again. > Everything works now for me, BTW (Mandrake 9.2). Thanks! I made another couple of fixes -- everything works fine for me with Python2.2 and 2.3 on FreeBSD. Any problems anyone can come up with are more than welcome. Glad to be getting this sorted out. Brad From chapmanb at uga.edu Tue May 4 13:13:53 2004 From: chapmanb at uga.edu (Brad Chapman) Date: Sat Mar 5 14:43:33 2005 Subject: [Biopython-dev] Documentation for Bio.LogisticRegression In-Reply-To: <408BA858.2030207@ims.u-tokyo.ac.jp> References: <408BA858.2030207@ims.u-tokyo.ac.jp> Message-ID: <20040504171353.GF602@misterbd.agtec.uga.edu> Hi Michiel; > Recently I have been using the logistic regression model in > Bio.LogisticRegression to predict transcription factors in bacteria (thanks > Jeff! Great work). Over the weekend, I wrote some documentation for this > module and submitted it to CVS. Sweet. Thanks for this! Documentation. Woooooo. But yeah, I'm okay, really. I just added this to the website documentation. Thanks for the contribution -- if you update it or do other work, the html and pdfs are on biopython.org in /home/websites/biopython.org/docs/cookbook. Thanks again! Brad From chapmanb at uga.edu Tue May 4 13:18:46 2004 From: chapmanb at uga.edu (Brad Chapman) Date: Sat Mar 5 14:43:33 2005 Subject: [Biopython-dev] new biopython modules In-Reply-To: <5F9035D8A446C84C903301CCD5FC8DB4190653@salte0010.wurnet.nl> References: <5F9035D8A446C84C903301CCD5FC8DB4190653@salte0010.wurnet.nl> Message-ID: <20040504171846.GG602@misterbd.agtec.uga.edu> Hello; > I have made a parser and a record module for Fasta/ssearch similarity > search results, similar to those made by Jeff Chang for parsing > blast/recording the results. > Are you interested in it for use in biopython? Definitely. It sounds like the code works and is well tested since you've been using it, and it's especially great if it conforms to the normal way that Biopython parsers and iterators are welcome. You can feel free to send the code to me and I can integrate it into CVS. If you have any tests or documentation, those are definitely always welcome. Thanks for the mail and looking forward to the code. Brad From mcolosimo at mitre.org Tue May 4 18:38:34 2004 From: mcolosimo at mitre.org (Marc Colosimo) Date: Sat Mar 5 14:43:33 2005 Subject: [Biopython-dev] Medline XLM parsers Message-ID: I can't seem to find anything to parse the recent http://www.nlm.nih.gov/databases/dtd/nlmmedline_031101.dtd XML medline files. Also, there doesn't seem to be any handy classes like for the record_parser, which I can send it one record at a time and deal with it. I found the martel stuff, but I would still have to implement my own xml parser to populate a medline record class. Am I missing something here? Marc From jeffrey_chang at stanfordalumni.org Tue May 4 18:43:01 2004 From: jeffrey_chang at stanfordalumni.org (Jeffrey Chang) Date: Sat Mar 5 14:43:33 2005 Subject: [Biopython-dev] Medline XLM parsers In-Reply-To: References: Message-ID: <65F25A5B-9E1C-11D8-91E2-000A956845CE@stanfordalumni.org> Nope. Code that parses the entire MEDLINE record has not been implemented yet, mostly because I've never needed more than a few of the many fields. Jeff On May 4, 2004, at 6:38 PM, Marc Colosimo wrote: > I can't seem to find anything to parse the recent > http://www.nlm.nih.gov/databases/dtd/nlmmedline_031101.dtd XML medline > files. Also, there doesn't seem to be any handy classes like for the > record_parser, which I can send it one record at a time and deal with > it. I found the martel stuff, but I would still have to implement my > own xml parser to populate a medline record class. > > Am I missing something here? > > Marc > > > _______________________________________________ > Biopython-dev mailing list > Biopython-dev@biopython.org > http://biopython.org/mailman/listinfo/biopython-dev From thamelry at binf.ku.dk Wed May 5 05:17:58 2004 From: thamelry at binf.ku.dk (Thomas Hamelryck) Date: Sat Mar 5 14:43:33 2005 Subject: [Biopython-dev] Bio.PDB: structure alignment added In-Reply-To: <20040504112434.GE3375@misterbd.agtec.uga.edu> References: <200405041445.i44EjuXM010483@portal.open-bio.org> <33175.192.38.112.226.1083684497.squirrel@www.binf.ku.dk> <20040504112434.GE3375@misterbd.agtec.uga.edu> Message-ID: <200405051117.58989.thamelry@binf.ku.dk> Hi, A module that maps the residues in two structures onto each other (based on a FASTA alignment file) was added to Bio.PDB. Cheers, -Thomas From thamelry at binf.ku.dk Wed May 5 07:12:13 2004 From: thamelry at binf.ku.dk (Thomas Hamelryck) Date: Sat Mar 5 14:43:33 2005 Subject: [Biopython-dev] Bio.PDB: DSSP In-Reply-To: <20040504115514.GF3375@misterbd.agtec.uga.edu> References: <200405041445.i44EjuXM010483@portal.open-bio.org> <33194.192.38.112.226.1083685532.squirrel@www.binf.ku.dk> <20040504115514.GF3375@misterbd.agtec.uga.edu> Message-ID: <200405051312.13033.thamelry@binf.ku.dk> Added DSSP support (accessibility, secondary structure) to Bio.PDB. -Thomas From mcolosimo at mitre.org Wed May 5 09:23:55 2004 From: mcolosimo at mitre.org (Marc Colosimo) Date: Sat Mar 5 14:43:33 2005 Subject: [Biopython-dev] Medline XLM parsers In-Reply-To: <65F25A5B-9E1C-11D8-91E2-000A956845CE@stanfordalumni.org> References: <65F25A5B-9E1C-11D8-91E2-000A956845CE@stanfordalumni.org> Message-ID: <75905435-9E97-11D8-AA96-000A95A5D8B2@mitre.org> Jeff, Two questions: first, it seem that none of the current xml classes handle the latest release. Is this correct? And second, how would you use those classes to parse and xml document? From my understanding of martel, I would still need to make an xml parser which then makes this seem odd. Thanks, Marc On May 4, 2004, at 6:43 PM, Jeffrey Chang wrote: > Nope. Code that parses the entire MEDLINE record has not been > implemented yet, mostly because I've never needed more than a few of > the many fields. > > Jeff > > > On May 4, 2004, at 6:38 PM, Marc Colosimo wrote: > >> I can't seem to find anything to parse the recent >> http://www.nlm.nih.gov/databases/dtd/nlmmedline_031101.dtd XML >> medline files. Also, there doesn't seem to be any handy classes like >> for the record_parser, which I can send it one record at a time and >> deal with it. I found the martel stuff, but I would still have to >> implement my own xml parser to populate a medline record class. >> >> Am I missing something here? >> >> Marc >> >> >> _______________________________________________ >> Biopython-dev mailing list >> Biopython-dev@biopython.org >> http://biopython.org/mailman/listinfo/biopython-dev > From thamelry at binf.ku.dk Wed May 5 09:29:16 2004 From: thamelry at binf.ku.dk (Thomas Hamelryck) Date: Sat Mar 5 14:43:33 2005 Subject: [Biopython-dev] Bio.PDB: residue depth In-Reply-To: <20040504110143.GB3375@misterbd.agtec.uga.edu> References: <200405041445.i44EjuXM010483@portal.open-bio.org> <20040504110143.GB3375@misterbd.agtec.uga.edu> Message-ID: <200405051529.16278.thamelry@binf.ku.dk> Added a module to calculate the residue depth (average distance of a residue from the molecular surface). The module makes use of Michel Sanner's MSMS program to calculate the surface. -Thomas From jeffrey_chang at stanfordalumni.org Wed May 5 10:32:14 2004 From: jeffrey_chang at stanfordalumni.org (Jeffrey Chang) Date: Sat Mar 5 14:43:33 2005 Subject: [Biopython-dev] Medline XLM parsers In-Reply-To: <75905435-9E97-11D8-AA96-000A95A5D8B2@mitre.org> References: <65F25A5B-9E1C-11D8-91E2-000A956845CE@stanfordalumni.org> <75905435-9E97-11D8-AA96-000A95A5D8B2@mitre.org> Message-ID: <00C81472-9EA1-11D8-8E64-000A956845CE@stanfordalumni.org> Hi Marc, > Two questions: first, it seem that none of the current xml classes > handle the latest release. Is this correct? That's right. There's no parser for the latest release. I haven't looked at the latest format yet, but usually the changes are pretty minor. It should not be too hard to update the nlmmedline_011101_format to handle the latest files. > And second, > how would you use those classes to parse and xml document? From my > understanding of martel, I would still need to make an xml parser > which then makes this seem odd. Yep, Martel is a SAX parser! You'd parse the Martel format the same way as you'd parse an XML file. You have to create a xml.sax.handler.ContentHandler object to receive each of the events you care about. Warning: untested code! :) from xml.sax import handler class MyHandler(handler.ContentHandler): def __init__(self): ... def startElement(self, name, attrs): ... def characters(self, content): ... def endElement(self, name): ... my_content = MyHandler() format = NLMMedlineXML.choose_format(open(filename).read(1000)) parser = format.citation_format.make_parser() parser.setContentHandler(my_content) parser.setErrorHandler(handler.ErrorHandler()) parser.feed(open(filename)) To get the whole record, the startElement, characters, and endElement functions in your content handler has to store all the different elements that appear in the MEDLINE record. Because there are many elements, doing so is a lot of work! It would probably be useful, but I worry about the speed. Martel has to generate function calls for each element, and function calls are slow in Python. If you want to do that for all of MEDLINE, then the little bits of time for function calls add up to some real time. When I've used Martel to parse MEDLINE in the past, I've created specialized content handlers to pull out only the elements I was interested in. You can tell Martel to ignore the rest of the elements (using the "select_names" function), which speeds things up considerably. Jeff From chapmanb at uga.edu Wed May 5 06:32:31 2004 From: chapmanb at uga.edu (Brad Chapman) Date: Sat Mar 5 14:43:33 2005 Subject: [Biopython-dev] COMPASS parsing code In-Reply-To: <200404271245.20940.j.a.casbon@qmul.ac.uk> References: <200404271245.20940.j.a.casbon@qmul.ac.uk> Message-ID: <20040505103231.GD4372@misterbd.agtec.uga.edu> Hi James; > I have written some code for parsing compass results. [...] > I have attached the code, which you might like to include in the biopython > distribution. Thank you! I just checked this code into Bio/Compass/__init__.py. There are a few adjustments based on your points below but basically it is as submitted. Please let me know if I messed anything up. > There are probably a few issues with the code that could make it better: > > * the unit tests use some sample input, file comtest1 and comtest2. These are > just read using open. I have seen someone use test.locate or something like > that, but I'm not sure how that works. If you want to enlighten me, I'll > change it. Biopython has it's own test system in the Tests directory, which allows us to run all of the tests at once. It is documented pretty decently in: http://www.biopython.org/docs/cookbook/biopython_test.html I converted your code over to this system (thanks for using unittest, by the way) and it is located in Tests/test_Compass.py with the input files in Tests/Compass/. > * i have used regular expressions inefficiently, as I'm not sure how you're > supposed to cache them using the _Scanner/_Consumer framework. At the moment > each subroutine compiles an re when called, which can't be good. Again, > please enlighten me to a better way and I will change it. I just made the compiled regular expressions attributes of the _Scanner class. This way they should only be compiled a single time when a class is first instantiated, and then will be used when the functions are called during the scanning. I think this will make things a little more efficient, although I am certainly no regular expressions expert myself. Thanks again for the contribution! Much appreciated. Brad From bugzilla-daemon at portal.open-bio.org Wed May 5 12:49:59 2004 From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon@portal.open-bio.org) Date: Sat Mar 5 14:43:33 2005 Subject: [Biopython-dev] [Bug 1627] "Unexpected end of stream" when parsing Blast results Message-ID: <200405051649.i45Gnx8B023711@portal.open-bio.org> http://bugzilla.bioperl.org/show_bug.cgi?id=1627 chapmanb@arches.uga.edu changed: What |Removed |Added ---------------------------------------------------------------------------- Status|NEW |RESOLVED Resolution| |FIXED ------- Additional Comments From chapmanb@arches.uga.edu 2004-05-05 12:49 ------- Thanks for the report -- I believe this is the same problem that has been reported on the mailist list: http://portal.open-bio.org/pipermail/biopython/2004-April/002008.html http://portal.open-bio.org/pipermail/biopython/2004-March/001903.html To fix, please add format_type = "HTML" to your NCBIWWW.blast call. This is fixed in CVS and will be in the next release so it won't be necessary. I'll mark this as fixed for now -- if it still doesn't work please report back. Thanks again. ------- You are receiving this mail because: ------- You are the assignee for the bug, or are watching the assignee. From bugzilla-daemon at portal.open-bio.org Wed May 5 12:46:18 2004 From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon@portal.open-bio.org) Date: Sat Mar 5 14:43:33 2005 Subject: [Biopython-dev] [Bug 1613] pubmed example doesn't work. corrected example included Message-ID: <200405051646.i45GkI97023676@portal.open-bio.org> http://bugzilla.bioperl.org/show_bug.cgi?id=1613 chapmanb@arches.uga.edu changed: What |Removed |Added ---------------------------------------------------------------------------- Status|NEW |RESOLVED Resolution| |FIXED ------- Additional Comments From chapmanb@arches.uga.edu 2004-05-05 12:46 ------- Thanks for the heads up -- this is fixed in the version in CVS and also in the pdf and HTML on the website. Please do let us know if you find any other errors. ------- You are receiving this mail because: ------- You are the assignee for the bug, or are watching the assignee. From idoerg at burnham.org Wed May 5 15:30:29 2004 From: idoerg at burnham.org (Iddo Friedberg) Date: Sat Mar 5 14:43:33 2005 Subject: [Biopython-dev] Bio.PDB: DSSP In-Reply-To: <200405051312.13033.thamelry@binf.ku.dk> References: <200405041445.i44EjuXM010483@portal.open-bio.org> <33194.192.38.112.226.1083685532.squirrel@www.binf.ku.dk> <20040504115514.GF3375@misterbd.agtec.uga.edu> <200405051312.13033.thamelry@binf.ku.dk> Message-ID: <409940D5.4020207@burnham.org> Cool. There is a Bio.FSSP module. Do you think we should place that under the PDB mudule for good measure? It is totally disjoint from the PDB module, so maybe we should leave it where it is. What do you think? ./I Thomas Hamelryck wrote: > Added DSSP support (accessibility, secondary structure) to Bio.PDB. > > -Thomas > > _______________________________________________ > Biopython-dev mailing list > Biopython-dev@biopython.org > http://biopython.org/mailman/listinfo/biopython-dev > > -- Iddo Friedberg, Ph.D. The Burnham Institute 10901 N. Torrey Pines Rd. La Jolla, CA 92037 USA Tel: +1 (858) 646 3100 x3516 Fax: +1 (858) 713 9930 http://ffas.ljcrf.edu/~iddo From thamelry at binf.ku.dk Wed May 5 15:52:17 2004 From: thamelry at binf.ku.dk (Thomas Hamelryck) Date: Sat Mar 5 14:43:33 2005 Subject: [Biopython-dev] Bio.PDB: DSSP In-Reply-To: <409940D5.4020207@burnham.org> References: <200405041445.i44EjuXM010483@portal.open-bio.org> <33194.192.38.112.226.1083685532.squirrel@www.binf.ku.dk> <20040504115514.GF3375@misterbd.agtec.uga.edu> <200405051312.13033.thamelry@binf.ku.dk> <409940D5.4020207@burnham.org> Message-ID: <33466.80.63.229.248.1083786737.squirrel@www.binf.ku.dk> > Cool. > > There is a Bio.FSSP module. Do you think we should place that under the > PDB mudule for good measure? It is totally disjoint from the PDB > module, so maybe we should leave it where it is. What do you think? FSSP is standalone, so it can stay in Bio.FSSP, I think. There's also some very nice SCOP code around, BTW. I've got a 13 page Bio.PDB FAQ coming up - what I can do is add documentation about the FSSP and SCOP modules so that these 'structural' modules get some more airplay... Cheers, -Thomas From mdehoon at ims.u-tokyo.ac.jp Sat May 8 02:03:15 2004 From: mdehoon at ims.u-tokyo.ac.jp (Michiel Jan Laurens de Hoon) Date: Sat Mar 5 14:43:33 2005 Subject: [Biopython-dev] Re: Work towards getting KDTree compiling In-Reply-To: <20040419162305.GB596@misterbd.agtec.uga.edu> References: <20040419115616.GA12006@misterbd.agtec.uga.edu> <32794.80.63.229.120.1082401950.squirrel@www.binf.ku.dk> <20040419162305.GB596@misterbd.agtec.uga.edu> Message-ID: <409C7823.50902@ims.u-tokyo.ac.jp> Brad Chapman wrote: > Brilliant. It seems simple enough and only requires us to specify > the language as c++ for our included C++ code. +1 from me for keeping > this in the setup.py. > > If people on disparate platforms could give this another test and > let me know if anything breaks that would be great. Especially like > to hear from the ol' Windows folks. For the record, it all works > fine for me on a FreeBSD machine with gcc (but we probably already > knew that :-). > I tried to compile the Biopython in CVS on various platforms to make sure everything works for the upcoming release. Using Python 2.3.3: o) On cygwin, the compilation runs fine. o) On Windows, the compilation of KDTree fails: building 'Bio.KDTree._CKDTree' extension creating build\temp.win32-2.3\Release\bio\kdtree C:\cygwin\bin\cc.exe -Ic:\Python23\include -Ic:\Python23\PC -c Bio/KDTree/KDTree .swig.cpp -o build\temp.win32-2.3\Release\bio\kdtree\kdtree.swig.o error: command 'cc' failed: Invalid argument I am compiling with python setup.py build --compiler=mingw32. The C extensions in Biopython (e.g. Bio.Cluster) compile without problems. This may be a bug in distutils for mingw32 when dealing with C++. o) On SunOS 5.8, the compilation runs fine, using the native cc compiler for the C extensions and the g++ compiler for the C++ extensions. Note that mixing the cc compiler and the g++ compiler may lead to crashes. But at least on SunOS 5.8, no such problems occur when importing KDTree or Affy. o) On Mac OS X, the compilation seems to run fine, but python crashes if one of the C++ modules is imported. The C modules do not cause a crash. I am not sure what causes this crash; the C and C++ compilers are consistent with each other. I am not very familiar with C++ and I'm not sure what to solve this, so I'll limit myself to reporting problems :-). By the way, there is a typing error in setup.py: ... CplusplusExtension('Affy._cel', ['Bio/Affy/celmodule.cc'], language="c++" ), ... It seems that in the first line, that should be 'Bio.Affy._cel', otherwise _cel will end up in the wrong place. --Michiel. -- Michiel de Hoon, Assistant Professor University of Tokyo, Institute of Medical Science Human Genome Center 4-6-1 Shirokane-dai, Minato-ku Tokyo 108-8639 Japan http://bonsai.ims.u-tokyo.ac.jp/~mdehoon From chapmanb at uga.edu Sat May 8 13:35:04 2004 From: chapmanb at uga.edu (Brad Chapman) Date: Sat Mar 5 14:43:33 2005 Subject: [Biopython-dev] Re: Work towards getting KDTree compiling In-Reply-To: <409C7823.50902@ims.u-tokyo.ac.jp> References: <20040419115616.GA12006@misterbd.agtec.uga.edu> <32794.80.63.229.120.1082401950.squirrel@www.binf.ku.dk> <20040419162305.GB596@misterbd.agtec.uga.edu> <409C7823.50902@ims.u-tokyo.ac.jp> Message-ID: <20040508173504.GA77385@evostick.agtec.uga.edu> Hi Michiel; > I tried to compile the Biopython in CVS on various platforms to make sure > everything works for the upcoming release. Sweet. Thanks for doing this -- it will really help to have this widely tested before the release. > o) On Windows, the compilation of KDTree fails: > > building 'Bio.KDTree._CKDTree' extension > creating build\temp.win32-2.3\Release\bio\kdtree > C:\cygwin\bin\cc.exe -Ic:\Python23\include -Ic:\Python23\PC -c > Bio/KDTree/KDTree > .swig.cpp -o build\temp.win32-2.3\Release\bio\kdtree\kdtree.swig.o > error: command 'cc' failed: Invalid argument > > I am compiling with python setup.py build --compiler=mingw32. The C > extensions in Biopython (e.g. Bio.Cluster) compile without problems. > This may be a bug in distutils for mingw32 when dealing with C++. Yeah, I don't really understand the error (Invalid argument seems to imply there is something wrong with the commandline, and I'm not sure what that is), but digging through distutils code it looks like C++ in mingw32 is not really supported. As a complete guess, I tried applying the same changes I used for Python 2.2.x to mingw32 compilation. Will you give the new setup.py a try and see if it improves anything at all? > o) On SunOS 5.8, the compilation runs fine, using the native cc compiler > for the C extensions and the g++ compiler for the C++ extensions. Note that > mixing the cc compiler and the g++ compiler may lead to crashes. But at > least on SunOS 5.8, no such problems occur when importing KDTree or Affy. Does Tests/test_KDTree.py work for you as well? If there are no problems then I say we are all in the clear. Since distutils is really just pulling up the C++ compiler information from the environment, there is really nothing we can do about the cc/g++ conflict -- honestly this is probably a issue where a solaris user has to set CXX to point to the native c++ compiler. > o) On Mac OS X, the compilation seems to run fine, but python crashes if > one of the C++ modules is imported. The C modules do not cause a crash. I > am not sure what causes this crash; the C and C++ compilers are consistent > with each other. Hmmm. How do they crash? Just a core dump? Can you attach gdb and see anything? Also, is this with gcc? What versions? For the record, I'm compiling with gcc version 2.95.4 and 3.3.3 without any problems. Can any other Mac OS people confirm this problem? Any solutions from anyone? > I am not very familiar with C++ and I'm not sure what to solve this, so > I'll limit myself to reporting problems :-). Okay :-). Seriously, this is great -- I don't have access to a lot of systems right now so this is the only way we can really make sure the messy compilation will work across platforms. > By the way, there is a typing error in setup.py: [...] > It seems that in the first line, that should be 'Bio.Affy._cel', otherwise > _cel will end up in the wrong place. Whoops. Thanks. Fixed. Thanks again for the report. Brad From mdehoon at ims.u-tokyo.ac.jp Sun May 9 22:33:11 2004 From: mdehoon at ims.u-tokyo.ac.jp (Michiel Jan Laurens de Hoon) Date: Sat Mar 5 14:43:33 2005 Subject: [Biopython-dev] Re: Work towards getting KDTree compiling In-Reply-To: <20040508173504.GA77385@evostick.agtec.uga.edu> References: <20040419115616.GA12006@misterbd.agtec.uga.edu> <32794.80.63.229.120.1082401950.squirrel@www.binf.ku.dk> <20040419162305.GB596@misterbd.agtec.uga.edu> <409C7823.50902@ims.u-tokyo.ac.jp> <20040508173504.GA77385@evostick.agtec.uga.edu> Message-ID: <409EE9E7.7040807@ims.u-tokyo.ac.jp> Brad Chapman wrote: >>o) On Windows, the compilation of KDTree fails: >> >>building 'Bio.KDTree._CKDTree' extension >>creating build\temp.win32-2.3\Release\bio\kdtree >>C:\cygwin\bin\cc.exe -Ic:\Python23\include -Ic:\Python23\PC -c >>Bio/KDTree/KDTree >>.swig.cpp -o build\temp.win32-2.3\Release\bio\kdtree\kdtree.swig.o >>error: command 'cc' failed: Invalid argument >> >>I am compiling with python setup.py build --compiler=mingw32. The C >>extensions in Biopython (e.g. Bio.Cluster) compile without problems. >>This may be a bug in distutils for mingw32 when dealing with C++. > > > Yeah, I don't really understand the error (Invalid argument seems to > imply there is something wrong with the commandline, and I'm not > sure what that is), but digging through distutils code it looks like > C++ in mingw32 is not really supported. > > As a complete guess, I tried applying the same changes I used for > Python 2.2.x to mingw32 compilation. Will you give the new setup.py > a try and see if it improves anything at all? Sorry, doesn't work. Using Python 2.3.3: building 'Bio.KDTree._CKDTree' extension creating build\temp.win32-2.3\Release\bio\kdtree Traceback (most recent call last): File "setup.py", line 505, in ? data_files=DATA_FILES, File "c:\Python23\lib\distutils\core.py", line 149, in setup dist.run_commands() File "c:\Python23\lib\distutils\dist.py", line 907, in run_commands self.run_command(cmd) File "c:\Python23\lib\distutils\dist.py", line 927, in run_command cmd_obj.run() File "c:\Python23\lib\distutils\command\build.py", line 107, in run self.run_command(cmd_name) File "c:\Python23\lib\distutils\cmd.py", line 333, in run_command self.distribution.run_command(command) File "c:\Python23\lib\distutils\dist.py", line 927, in run_command cmd_obj.run() File "setup.py", line 166, in run build_ext.run(self) File "c:\Python23\lib\distutils\command\build_ext.py", line 269, in run self.build_extensions() File "setup.py", line 171, in build_extensions build_ext.build_extensions(self) File "c:\Python23\lib\distutils\command\build_ext.py", line 395, in build_exte nsions self.build_extension(ext) File "setup.py", line 197, in build_extension build_ext.build_extension(self, ext) File "c:\Python23\lib\distutils\command\build_ext.py", line 460, in build_exte nsion depends=ext.depends) File "c:\Python23\lib\distutils\ccompiler.py", line 695, in compile self._compile(obj, src, ext, cc_args, extra_postargs, pp_opts) File "c:\Python23\lib\distutils\cygwinccompiler.py", line 137, in _compile self.spawn(self.compiler_so + cc_args + [src, '-o', obj] + File "c:\Python23\lib\distutils\ccompiler.py", line 1036, in spawn spawn (cmd, dry_run=self.dry_run) File "c:\Python23\lib\distutils\spawn.py", line 39, in spawn _spawn_nt(cmd, search_path, dry_run=dry_run) File "c:\Python23\lib\distutils\spawn.py", line 72, in _spawn_nt cmd = _nt_quote_args(cmd) File "c:\Python23\lib\distutils\spawn.py", line 62, in _nt_quote_args if string.find(args[i], ' ') != -1: File "C:\Python23\lib\string.py", line 178, in find return s.find(*args) AttributeError: 'NoneType' object has no attribute 'find' >>o) On SunOS 5.8, the compilation runs fine, using the native cc compiler >>for the C extensions and the g++ compiler for the C++ extensions. Note that >>mixing the cc compiler and the g++ compiler may lead to crashes. But at >>least on SunOS 5.8, no such problems occur when importing KDTree or Affy. > > > Does Tests/test_KDTree.py work for you as well? If there are no > problems then I say we are all in the clear. Since distutils is > really just pulling up the C++ compiler information from the > environment, there is really nothing we can do about the cc/g++ > conflict -- honestly this is probably a issue where a solaris user > has to set CXX to point to the native c++ compiler. It works! Allright! Using Python 2.3.3 on SunOS 5.8: anago{mdehoon}8: python -i test_KDTree.py Passed. Passed. Passed. Passed. Passed. Passed. Passed. Passed. Passed. Passed. Passed. Passed. Passed. Passed. Passed. Passed. Passed. Passed. Passed. Passed. >>> >>o) On Mac OS X, the compilation seems to run fine, but python crashes if >>one of the C++ modules is imported. The C modules do not cause a crash. I >>am not sure what causes this crash; the C and C++ compilers are consistent >>with each other. > > > Hmmm. How do they crash? Just a core dump? Can you attach gdb and > see anything? Also, is this with gcc? What versions? For the record, > I'm compiling with gcc version 2.95.4 and 3.3.3 without any > problems. > I'm not sure if this will help much but this is what I get from gdb: >>> from Bio.KDTree import * Reading symbols for shared libraries . done Reading symbols for shared libraries . done Reading symbols for shared libraries . done Reading symbols for shared libraries . done Reading symbols for shared libraries . done Reading symbols for shared libraries . done Reading symbols for shared libraries . done Reading symbols for shared libraries . done Reading symbols for shared libraries . done Reading symbols for shared libraries . done Reading symbols for shared libraries . done Reading symbols for shared libraries bfd_mach_o_scan_read_symtab_symbol: symbol name out of range (399792 >= 5512) . done Program received signal EXC_BAD_ACCESS, Could not access memory. 0x8fe0cc18 in __dyld_is_symbol_coalesced () (gdb) > Can any other Mac OS people confirm this problem? Any solutions from > anyone? The celmodule.cc code in Affy is very short and uses few C++ specific routines. Converting this code to standard C is almost trivial and would more robust than modifying setup.py to handle C++. Converting KDTree would require some more work though. --Michiel. -- Michiel de Hoon, Assistant Professor University of Tokyo, Institute of Medical Science Human Genome Center 4-6-1 Shirokane-dai, Minato-ku Tokyo 108-8639 Japan http://bonsai.ims.u-tokyo.ac.jp/~mdehoon From chapmanb at uga.edu Mon May 10 16:17:22 2004 From: chapmanb at uga.edu (Brad Chapman) Date: Sat Mar 5 14:43:33 2005 Subject: [Biopython-dev] Re: Work towards getting KDTree compiling In-Reply-To: <409EE9E7.7040807@ims.u-tokyo.ac.jp> References: <20040419115616.GA12006@misterbd.agtec.uga.edu> <32794.80.63.229.120.1082401950.squirrel@www.binf.ku.dk> <20040419162305.GB596@misterbd.agtec.uga.edu> <409C7823.50902@ims.u-tokyo.ac.jp> <20040508173504.GA77385@evostick.agtec.uga.edu> <409EE9E7.7040807@ims.u-tokyo.ac.jp> Message-ID: <20040510201722.GC81206@evostick.agtec.uga.edu> Hi Michiel; [mingw32] > >As a complete guess, I tried applying the same changes I used for > >Python 2.2.x to mingw32 compilation. Will you give the new setup.py > >a try and see if it improves anything at all? > > Sorry, doesn't work. Using Python 2.3.3: > > building 'Bio.KDTree._CKDTree' extension > creating build\temp.win32-2.3\Release\bio\kdtree > Traceback (most recent call last): [...] Ugh, that's worse :-). Clearly I have no idea what I am doing with that, so I'll quit messing around. What I did right now was turn off the compilation of C++ extensions with mingw32. I think. Could you please double check it to make sure it works now -- by works, I mean skips the compilation of C++ and finishes okay. We'll have to wait for either better mingw32 support or someone who knows what they are doing to deal with this again. [Sun] > >Does Tests/test_KDTree.py work for you as well? If there are no > >problems then I say we are all in the clear. Since distutils is > >really just pulling up the C++ compiler information from the > >environment, there is really nothing we can do about the cc/g++ > >conflict -- honestly this is probably a issue where a solaris user > >has to set CXX to point to the native c++ compiler. > > It works! Allright! Using Python 2.3.3 on SunOS 5.8: Good stuff. Well, as long as it compiles and works I'm happy. Woo. [Mac OS X] > >Hmmm. How do they crash? Just a core dump? Can you attach gdb and > >see anything? Also, is this with gcc? What versions? For the record, > >I'm compiling with gcc version 2.95.4 and 3.3.3 without any > >problems. > > > > I'm not sure if this will help much but this is what I get from gdb: > > >>> from Bio.KDTree import * > Reading symbols for shared libraries . done > Reading symbols for shared libraries . done > Reading symbols for shared libraries . done > Reading symbols for shared libraries . done > Reading symbols for shared libraries . done > Reading symbols for shared libraries . done > Reading symbols for shared libraries . done > Reading symbols for shared libraries . done > Reading symbols for shared libraries . done > Reading symbols for shared libraries . done > Reading symbols for shared libraries . done > Reading symbols for shared libraries bfd_mach_o_scan_read_symtab_symbol: > symbol name out of range (399792 >= 5512) > . done > > Program received signal EXC_BAD_ACCESS, Could not access memory. > 0x8fe0cc18 in __dyld_is_symbol_coalesced () > (gdb) Bleah. Some kind of memory leak when loading the libraries -- I have zero idea what that means or how to fix it. If it compiles decently, then I'll leave it right now, and just hope that some Mac OS people can come up with a reason/solution for this. Anyone else with OS X can confirm? Otherwise, well -- I have no idea what to do. > The celmodule.cc code in Affy is very short and uses few C++ specific > routines. Converting this code to standard C is almost trivial and would > more robust than modifying setup.py to handle C++. Converting KDTree would > require some more work though. I'd agree in general -- C++ code seems to be a major mess through distutils. I know that Harry Zuzan, the author of the celmodule code, said he prefers to work in C++ previously. I'm not sure what his plans are for expanding this -- right now it appears to be a tradeoff between what he wants to code in and what level of use on various platforms he can expect. Thanks again for all your work on this Michiel. Now I remember why I prefer to just plain code in Python :-). Brad From mdehoon at ims.u-tokyo.ac.jp Mon May 10 21:19:55 2004 From: mdehoon at ims.u-tokyo.ac.jp (Michiel Jan Laurens de Hoon) Date: Sat Mar 5 14:43:33 2005 Subject: [Biopython-dev] Re: Work towards getting KDTree compiling In-Reply-To: <20040510201722.GC81206@evostick.agtec.uga.edu> References: <20040419115616.GA12006@misterbd.agtec.uga.edu> <32794.80.63.229.120.1082401950.squirrel@www.binf.ku.dk> <20040419162305.GB596@misterbd.agtec.uga.edu> <409C7823.50902@ims.u-tokyo.ac.jp> <20040508173504.GA77385@evostick.agtec.uga.edu> <409EE9E7.7040807@ims.u-tokyo.ac.jp> <20040510201722.GC81206@evostick.agtec.uga.edu> Message-ID: <40A02A3B.4090209@ims.u-tokyo.ac.jp> Brad Chapman wrote: > Hi Michiel; > > [mingw32] > >>>As a complete guess, I tried applying the same changes I used for >>>Python 2.2.x to mingw32 compilation. Will you give the new setup.py >>>a try and see if it improves anything at all? >> >>Sorry, doesn't work. Using Python 2.3.3: >> >>building 'Bio.KDTree._CKDTree' extension >>creating build\temp.win32-2.3\Release\bio\kdtree >>Traceback (most recent call last): > > [...] > > Ugh, that's worse :-). Clearly I have no idea what I am doing with > that, so I'll quit messing around. What I did right now was turn off > the compilation of C++ extensions with mingw32. I think. Could you > please double check it to make sure it works now -- by works, I > mean skips the compilation of C++ and finishes okay. We'll have to > wait for either better mingw32 support or someone who knows what > they are doing to deal with this again. > The compilation works, but making the installer with bdist_wininst doesn't: $ /cygdrive/c/Python23/python setup.py build --compiler=mingw32 ... works OK ... $ /cygdrive/c/Python23/python setup.py bdist_wininst running bdist_wininst running build running build_py running build_ext Traceback (most recent call last): File "setup.py", line 511, in ? data_files=DATA_FILES, File "c:\Python23\lib\distutils\core.py", line 149, in setup dist.run_commands() File "c:\Python23\lib\distutils\dist.py", line 907, in run_commands self.run_command(cmd) File "c:\Python23\lib\distutils\dist.py", line 927, in run_command cmd_obj.run() File "c:\Python23\lib\distutils\command\bdist_wininst.py", line 101, in run self.run_command('build') File "c:\Python23\lib\distutils\cmd.py", line 333, in run_command self.distribution.run_command(command) File "c:\Python23\lib\distutils\dist.py", line 927, in run_command cmd_obj.run() File "c:\Python23\lib\distutils\command\build.py", line 107, in run self.run_command(cmd_name) File "c:\Python23\lib\distutils\cmd.py", line 333, in run_command self.distribution.run_command(command) File "c:\Python23\lib\distutils\dist.py", line 927, in run_command cmd_obj.run() File "setup.py", line 166, in run build_ext.run(self) File "c:\Python23\lib\distutils\command\build_ext.py", line 269, in run self.build_extensions() File "setup.py", line 169, in build_extensions self._original_compiler_so = self.compiler.compiler_so AttributeError: MSVCCompiler instance has no attribute 'compiler_so' --Michiel. -- Michiel de Hoon, Assistant Professor University of Tokyo, Institute of Medical Science Human Genome Center 4-6-1 Shirokane-dai, Minato-ku Tokyo 108-8639 Japan http://bonsai.ims.u-tokyo.ac.jp/~mdehoon From chapmanb at uga.edu Tue May 11 11:00:57 2004 From: chapmanb at uga.edu (Brad Chapman) Date: Sat Mar 5 14:43:33 2005 Subject: [Biopython-dev] Re: Work towards getting KDTree compiling In-Reply-To: <40A02A3B.4090209@ims.u-tokyo.ac.jp> References: <20040419115616.GA12006@misterbd.agtec.uga.edu> <32794.80.63.229.120.1082401950.squirrel@www.binf.ku.dk> <20040419162305.GB596@misterbd.agtec.uga.edu> <409C7823.50902@ims.u-tokyo.ac.jp> <20040508173504.GA77385@evostick.agtec.uga.edu> <409EE9E7.7040807@ims.u-tokyo.ac.jp> <20040510201722.GC81206@evostick.agtec.uga.edu> <40A02A3B.4090209@ims.u-tokyo.ac.jp> Message-ID: <20040511150057.GC83225@evostick.agtec.uga.edu> Hi Michiel; [mingw32] > The compilation works, but making the installer with bdist_wininst doesn't: > $ /cygdrive/c/Python23/python setup.py build --compiler=mingw32 > ... > works OK > ... > $ /cygdrive/c/Python23/python setup.py bdist_wininst > running bdist_wininst > running build > running build_py > running build_ext > Traceback (most recent call last): [...] > AttributeError: MSVCCompiler instance has no attribute 'compiler_so' Well, one thing at a time. At least the compilation works :-). Thanks for putting up with this remote debugging process. First thing about your traceback -- it looks like the bdist_wininst is using the Microsoft Visual C++ compiler -- at least that is where the traceback is coming from. Is that, uh, strange, or normal behavior? Secondly, it should support compiling on msvc regardless, so I tried to modify the setup.py to do this. Basically, msvc uses a different interface to specify the compilers, which I tried to take into account. I also disabled C++ compilation on msvc until we have someone with the compiler willing to get it all worked out. Let me know if this fixes things. I'll probably push back the release until these problems are all worked out. Hopefully they are getting there since we get less errors every time :-). If anyone else reading these mails has time, please do check out the current version of CVS and try compiling it on your platform and let me know if there are any errors. This will definitely make life a lot easier after the release. And easier life means more beers. Yay. Brad From mcolosimo at mitre.org Tue May 11 12:04:06 2004 From: mcolosimo at mitre.org (Marc Colosimo) Date: Sat Mar 5 14:43:33 2005 Subject: [Biopython-dev] Re: Work towards getting KDTree compiling In-Reply-To: <20040510201722.GC81206@evostick.agtec.uga.edu> References: <20040419115616.GA12006@misterbd.agtec.uga.edu> <32794.80.63.229.120.1082401950.squirrel@www.binf.ku.dk> <20040419162305.GB596@misterbd.agtec.uga.edu> <409C7823.50902@ims.u-tokyo.ac.jp> <20040508173504.GA77385@evostick.agtec.uga.edu> <409EE9E7.7040807@ims.u-tokyo.ac.jp> <20040510201722.GC81206@evostick.agtec.uga.edu> Message-ID: On May 10, 2004, at 4:17 PM, Brad Chapman wrote: > Hi Michiel; > > [mingw32] > [snip] > > [Sun] > [snip] > > [Mac OS X] >>> Hmmm. How do they crash? Just a core dump? Can you attach gdb and >>> see anything? Also, is this with gcc? What versions? For the record, >>> I'm compiling with gcc version 2.95.4 and 3.3.3 without any >>> problems. >>> >> >> I'm not sure if this will help much but this is what I get from gdb: >> >>>>> from Bio.KDTree import * >> Reading symbols for shared libraries . done >> Reading symbols for shared libraries . done >> Reading symbols for shared libraries . done >> Reading symbols for shared libraries . done >> Reading symbols for shared libraries . done >> Reading symbols for shared libraries . done >> Reading symbols for shared libraries . done >> Reading symbols for shared libraries . done >> Reading symbols for shared libraries . done >> Reading symbols for shared libraries . done >> Reading symbols for shared libraries . done >> Reading symbols for shared libraries >> bfd_mach_o_scan_read_symtab_symbol: >> symbol name out of range (399792 >= 5512) >> . done >> >> Program received signal EXC_BAD_ACCESS, Could not access memory. >> 0x8fe0cc18 in __dyld_is_symbol_coalesced () >> (gdb) > > Bleah. Some kind of memory leak when loading the libraries -- I have > zero idea what that means or how to fix it. If it compiles decently, > then I'll leave it right now, and just hope that some Mac OS people > can come up with a reason/solution for this. Anyone else with OS X > can confirm? > > Otherwise, well -- I have no idea what to do. > With both the Mac and fink version of python, it works fine for me (two different systems, both 10.3.3). Did you install some other odd python package or gcc? From mdehoon at ims.u-tokyo.ac.jp Tue May 11 22:50:43 2004 From: mdehoon at ims.u-tokyo.ac.jp (Michiel Jan Laurens de Hoon) Date: Sat Mar 5 14:43:33 2005 Subject: [Biopython-dev] Re: Work towards getting KDTree compiling In-Reply-To: References: <20040419115616.GA12006@misterbd.agtec.uga.edu> <32794.80.63.229.120.1082401950.squirrel@www.binf.ku.dk> <20040419162305.GB596@misterbd.agtec.uga.edu> <409C7823.50902@ims.u-tokyo.ac.jp> <20040508173504.GA77385@evostick.agtec.uga.edu> <409EE9E7.7040807@ims.u-tokyo.ac.jp> <20040510201722.GC81206@evostick.agtec.uga.edu> Message-ID: <40A19103.1070206@ims.u-tokyo.ac.jp> Marc Colosimo wrote: >>> Program received signal EXC_BAD_ACCESS, Could not access memory. >>> 0x8fe0cc18 in __dyld_is_symbol_coalesced () >>> (gdb) >> >> >> Bleah. Some kind of memory leak when loading the libraries -- I have >> zero idea what that means or how to fix it. If it compiles decently, >> then I'll leave it right now, and just hope that some Mac OS people >> can come up with a reason/solution for this. Anyone else with OS X >> can confirm? >> >> Otherwise, well -- I have no idea what to do. >> > > With both the Mac and fink version of python, it works fine for me (two > different systems, both 10.3.3). Did you install some other odd python > package or gcc? I compiled Python from souce on Mac OS X, using gcc. Personally I don't need to use the KDTree and Affy modules right now, so don't worry too much about it. But other users may run into the same problem. --Michiel. -- Michiel de Hoon, Assistant Professor University of Tokyo, Institute of Medical Science Human Genome Center 4-6-1 Shirokane-dai, Minato-ku Tokyo 108-8639 Japan http://bonsai.ims.u-tokyo.ac.jp/~mdehoon From mdehoon at ims.u-tokyo.ac.jp Thu May 13 02:18:32 2004 From: mdehoon at ims.u-tokyo.ac.jp (Michiel Jan Laurens de Hoon) Date: Sat Mar 5 14:43:33 2005 Subject: [Biopython-dev] Re: Work towards getting KDTree compiling In-Reply-To: <20040511150057.GC83225@evostick.agtec.uga.edu> References: <20040419115616.GA12006@misterbd.agtec.uga.edu> <32794.80.63.229.120.1082401950.squirrel@www.binf.ku.dk> <20040419162305.GB596@misterbd.agtec.uga.edu> <409C7823.50902@ims.u-tokyo.ac.jp> <20040508173504.GA77385@evostick.agtec.uga.edu> <409EE9E7.7040807@ims.u-tokyo.ac.jp> <20040510201722.GC81206@evostick.agtec.uga.edu> <40A02A3B.4090209@ims.u-tokyo.ac.jp> <20040511150057.GC83225@evostick.agtec.uga.edu> Message-ID: <40A31338.2020308@ims.u-tokyo.ac.jp> Brad Chapman wrote: > Well, one thing at a time. At least the compilation works :-). > Thanks for putting up with this remote debugging process. > > First thing about your traceback -- it looks like the bdist_wininst > is using the Microsoft Visual C++ compiler -- at least that is where > the traceback is coming from. Is that, uh, strange, or normal > behavior? That is probably OK. The bdist_wininst command creates an installer from the compiled and linked files (created by the build command), but doesn't do any compiling itself. > Secondly, it should support compiling on msvc regardless, so I tried > to modify the setup.py to do this. Basically, msvc uses a different > interface to specify the compilers, which I tried to take into > account. I also disabled C++ compilation on msvc until we have > someone with the compiler willing to get it all worked out. Sorry, no luck. With the Microsoft Visual C++ compiler, I get the following error when running python setup.py build: C:\Program Files\Microsoft Visual Studio\VC98\BIN\link.exe /DLL /nologo /INCREME NTAL:NO /LIBPATH:c:\Python23\libs /LIBPATH:c:\Python23\PCBuild /EXPORT:initclust er build\temp.win32-2.3\Release\Bio/Cluster/clustermodule.obj build\temp.win32-2 .3\Release\Bio/Cluster/cluster.obj build\temp.win32-2.3\Release\Bio/Cluster/ranl ib.obj build\temp.win32-2.3\Release\Bio/Cluster/com.obj build\temp.win32-2.3\Rel ease\Bio/Cluster/linpack.obj /OUT:build\lib.win32-2.3\Bio\Cluster\cluster.pyd /I MPLIB:build\temp.win32-2.3\Release\Bio/Cluster\cluster.lib ?????? build\temp.win32-2.3\Release\Bio/Cluster\cluster.lib ????????? build\t emp.win32-2.3\Release\Bio/Cluster\cluster.exp ???? Traceback (most recent call last): File "setup.py", line 515, in ? data_files=DATA_FILES, File "c:\Python23\lib\distutils\core.py", line 149, in setup dist.run_commands() File "c:\Python23\lib\distutils\dist.py", line 907, in run_commands self.run_command(cmd) File "c:\Python23\lib\distutils\dist.py", line 927, in run_command cmd_obj.run() File "c:\Python23\lib\distutils\command\build.py", line 107, in run self.run_command(cmd_name) File "c:\Python23\lib\distutils\cmd.py", line 333, in run_command self.distribution.run_command(command) File "c:\Python23\lib\distutils\dist.py", line 927, in run_command cmd_obj.run() File "setup.py", line 166, in run build_ext.run(self) File "c:\Python23\lib\distutils\command\build_ext.py", line 269, in run self.build_extensions() File "setup.py", line 176, in build_extensions build_ext.build_extensions(self) File "c:\Python23\lib\distutils\command\build_ext.py", line 395, in build_exte nsions self.build_extension(ext) File "setup.py", line 202, in build_extension self.compiler.compiler_so = self.compiler.compiler_cxx AttributeError: MSVCCompiler instance has no attribute 'compiler_cxx' For some reason, distutils is looking for a compiler_cxx member even though it is compiling a C module. There was another compilation error with the Bio.PDB.mmCIF.MMCIFlex module. This error does not appear with the mingw32 compiler. Using mingw32, the build command runs correctly (skipping the C++ modules), but the bdist_wininst command fails: $ /cygdrive/c/Python23/python setup.py bdist_wininst running bdist_wininst running build running build_py running build_ext Traceback (most recent call last): File "setup.py", line 515, in ? data_files=DATA_FILES, File "c:\Python23\lib\distutils\core.py", line 149, in setup dist.run_commands() File "c:\Python23\lib\distutils\dist.py", line 907, in run_commands self.run_command(cmd) File "c:\Python23\lib\distutils\dist.py", line 927, in run_command cmd_obj.run() File "c:\Python23\lib\distutils\command\bdist_wininst.py", line 101, in run self.run_command('build') File "c:\Python23\lib\distutils\cmd.py", line 333, in run_command self.distribution.run_command(command) File "c:\Python23\lib\distutils\dist.py", line 927, in run_command cmd_obj.run() File "c:\Python23\lib\distutils\command\build.py", line 107, in run self.run_command(cmd_name) File "c:\Python23\lib\distutils\cmd.py", line 333, in run_command self.distribution.run_command(command) File "c:\Python23\lib\distutils\dist.py", line 927, in run_command cmd_obj.run() File "setup.py", line 166, in run build_ext.run(self) File "c:\Python23\lib\distutils\command\build_ext.py", line 269, in run self.build_extensions() File "setup.py", line 176, in build_extensions build_ext.build_extensions(self) File "c:\Python23\lib\distutils\command\build_ext.py", line 395, in build_exte nsions self.build_extension(ext) File "setup.py", line 202, in build_extension self.compiler.compiler_so = self.compiler.compiler_cxx AttributeError: MSVCCompiler instance has no attribute 'compiler_cxx' Maybe the Microsoft compiler in distutils doesn't support C++? --Michiel. -- Michiel de Hoon, Assistant Professor University of Tokyo, Institute of Medical Science Human Genome Center 4-6-1 Shirokane-dai, Minato-ku Tokyo 108-8639 Japan http://bonsai.ims.u-tokyo.ac.jp/~mdehoon From chapmanb at uga.edu Thu May 13 09:16:31 2004 From: chapmanb at uga.edu (Brad Chapman) Date: Sat Mar 5 14:43:33 2005 Subject: [Biopython-dev] Re: Work towards getting KDTree compiling In-Reply-To: <40A31338.2020308@ims.u-tokyo.ac.jp> References: <32794.80.63.229.120.1082401950.squirrel@www.binf.ku.dk> <20040419162305.GB596@misterbd.agtec.uga.edu> <409C7823.50902@ims.u-tokyo.ac.jp> <20040508173504.GA77385@evostick.agtec.uga.edu> <409EE9E7.7040807@ims.u-tokyo.ac.jp> <20040510201722.GC81206@evostick.agtec.uga.edu> <40A02A3B.4090209@ims.u-tokyo.ac.jp> <20040511150057.GC83225@evostick.agtec.uga.edu> <40A31338.2020308@ims.u-tokyo.ac.jp> Message-ID: <20040513131631.GH83225@evostick.agtec.uga.edu> Hi Michiel; [bsdist_wininst plus msvc] > Sorry, no luck. With the Microsoft Visual C++ compiler, I get the following > error when running python setup.py build: [...] > AttributeError: MSVCCompiler instance has no attribute 'compiler_cxx' [...] > Using mingw32, the build command runs correctly (skipping the C++ modules), > but the bdist_wininst command fails: > $ /cygdrive/c/Python23/python setup.py bdist_wininst [...] > AttributeError: MSVCCompiler instance has no attribute 'compiler_cxx' Thanks for the tracebacks. Grrrr, I am a moron -- my fix to skip compilation on msvc didn't also fix trying to assign a C++ compiler, before skipping the compilation completely. Ugh, my fault. The problem here is that while the semi-standard compiler_so and compiler_cxx attributes are supported on a number of compilers, msvc uses it's own setup (it just has a cc, which I think supports C++ but am not really into testing for right now, so we are just skipping it). But yes, I've checked in yet another change. I am praying that this will finally let everything compile and build windows installers and all those good things, so that I can stop bothering you with this and we can be all good and happy and ready for release time. Thanks again for all your patience on this. Please do let me know if the changes I just committed fix everything for you. Fingers crossed. Brad From pescara at vreme.yubc.net Thu May 13 14:50:31 2004 From: pescara at vreme.yubc.net (IPSI conference) Date: Sat Mar 5 14:43:33 2005 Subject: [Biopython-dev] Invitation to Montenegro and Sweden vip/bb Message-ID: <200405131850.i4DIoVh12364@vreme.yubc.net> Dear Potential Speaker: This is an invitation for you to attend two IPSI BgD multidisciplinary and interdisciplinary conferences, one in Montenegro, and one in Sweden, as follows: Sveti Stefan, MONTENEGRO (arrival: 2.10.2004. departure 9.10.2004.) Keynote: Dr. de Gennes, Nobel Laureate, France Contact: vipforum@internetconferences.net Deadlines: May 31 2004 (abstract) + June 30 2004 (full paper) Stockholm, SWEDEN (arrival: 24.9.2004. departure: 26.9.2004.) Contact: stockholm@internetconferences.net Deadlines: May 15 2004 (abstract) + June 15 2004 (full paper). Keynote: Dr. Dino Karabeg, University of Oslo, Norway If you like to obtain more information on both conferences, please reply to this email. All IPSI BgD conferences are non-profit! They take place in the leading hotels of the world, and are aimed at bringing together the elite of the world science. Topics of interest include, but are not limited to: Internet, Computer Science and Engineering, Management and Business Administration, Education, e-Medicine, Electrical Engineering, Bioengineering, Environment Protection, and e-Economy. Sincerely Yours, Prof. Veljko Milutinovic, Chairman PS - If you plan to submit an abstract/paper, let us know immediately. If you are not able to attend now, but you like to be informed about the future IPSI BgD conferences, please let us know. If you do not like to receive future invitations, let us know, as well! From mdehoon at ims.u-tokyo.ac.jp Thu May 13 22:25:55 2004 From: mdehoon at ims.u-tokyo.ac.jp (Michiel Jan Laurens de Hoon) Date: Sat Mar 5 14:43:33 2005 Subject: [Biopython-dev] Re: Work towards getting KDTree compiling In-Reply-To: <20040513131631.GH83225@evostick.agtec.uga.edu> References: <32794.80.63.229.120.1082401950.squirrel@www.binf.ku.dk> <20040419162305.GB596@misterbd.agtec.uga.edu> <409C7823.50902@ims.u-tokyo.ac.jp> <20040508173504.GA77385@evostick.agtec.uga.edu> <409EE9E7.7040807@ims.u-tokyo.ac.jp> <20040510201722.GC81206@evostick.agtec.uga.edu> <40A02A3B.4090209@ims.u-tokyo.ac.jp> <20040511150057.GC83225@evostick.agtec.uga.edu> <40A31338.2020308@ims.u-tokyo.ac.jp> <20040513131631.GH83225@evostick.agtec.uga.edu> Message-ID: <40A42E33.5070401@ims.u-tokyo.ac.jp> Brad Chapman wrote: > But yes, I've checked in yet another change. I am praying that this > will finally let everything compile and build windows installers and > all those good things, so that I can stop bothering you with this > and we can be all good and happy and ready for release time. The latest version works with Microsoft Visual Studio and the mingw32 compiler. Good job! Some short comments: o) The source in Bio/PDB/mmCIF/lex.yy.c uses some Unix-specific commands from unistd.h. Microsoft's compiler barfs on these, the mingw32 compiler does not. It may be a good idea anyway to check if the mingw32-compiled version actually works. o) Recently I found out that the official Numerical Python version is now numarray. The Numeric module is now unsupported (see http://www.pfdubois.com/numpy). We'll need to decide if Biopython is going over to numarray, or whether to stick with Numeric for now. Some modifications will be needed in the Python and C code if we start using numarray. --Michiel. -- Michiel de Hoon, Assistant Professor University of Tokyo, Institute of Medical Science Human Genome Center 4-6-1 Shirokane-dai, Minato-ku Tokyo 108-8639 Japan http://bonsai.ims.u-tokyo.ac.jp/~mdehoon From thamelry at binf.ku.dk Fri May 14 02:58:20 2004 From: thamelry at binf.ku.dk (Thomas Hamelryck) Date: Sat Mar 5 14:43:33 2005 Subject: [Biopython-dev] Re: Work towards getting KDTree compiling Message-ID: <32793.192.38.114.59.1084517900.squirrel@www.binf.ku.dk> > o) The source in Bio/PDB/mmCIF/lex.yy.c uses some Unix-specific > commands from unistd.h. Microsoft's compiler barfs on these, the > mingw32 compiler does not. It may be a good idea anyway to check if > the mingw32-compiled version actually works. lex.yy.c is a lex-generated file. I presume it will look different when generated on a windows system. lex.yy.c is part of the distribution because (a) not everyone has lex installed and (b) it's not clear to me how to fire up lex from distutils. I have no objections if you want to comment this out in setup.py. > o) Recently I found out that the official Numerical Python version is > now numarray. The Numeric module is now unsupported (see > http://www.pfdubois.com/numpy). We'll need to decide if Biopython is > going over to numarray, or whether to stick with Numeric for now. Some > modifications will be needed in the Python and C code if we start > using numarray. Good point. We should indeed move to numarray, I think, though we might wait some months until numarray is more widely used. Cheers & thanks for the C++ related work, -- Thomas Hamelryck Bioinformatik centret K?benhavn Universitet Universitetsparken 15 Bygning 10 DK-2100 K?benhavn ? Denmark http://www.binf.ku.dk/users/thamelry/ From chapmanb at uga.edu Fri May 14 11:13:59 2004 From: chapmanb at uga.edu (Brad Chapman) Date: Sat Mar 5 14:43:33 2005 Subject: [Biopython-dev] Re: Work towards getting KDTree compiling In-Reply-To: <32793.192.38.114.59.1084517900.squirrel@www.binf.ku.dk> References: <32793.192.38.114.59.1084517900.squirrel@www.binf.ku.dk> Message-ID: <20040514151359.GG86985@evostick.agtec.uga.edu> Michiel and Thomas; > The latest version works with Microsoft Visual Studio and the mingw32 > compiler. Good job! Sweet. Thanks for all your work helping to debug this. That's good enough for me for now -- making a release with what we've got -- and we'll deal with these next problems for the upcoming release. > > o) The source in Bio/PDB/mmCIF/lex.yy.c uses some Unix-specific > > commands from unistd.h. Microsoft's compiler barfs on these, the > > mingw32 compiler does not. It may be a good idea anyway to check if > > the mingw32-compiled version actually works. > > lex.yy.c is a lex-generated file. I presume it will look different when > generated on a windows system. lex.yy.c is part of the distribution > because (a) not everyone has lex installed and (b) it's not clear to me > how to fire up lex from distutils. I have no objections if you want to > comment this out in setup.py. What kind of work would be involved with generating this lex file on Windows? I know next to nothing about lex, but if we could get different copies that work on Windows and Unix then we could again build up the extension in the setup.py file so it would compile on with all compilers. > > o) Recently I found out that the official Numerical Python version is > > now numarray. The Numeric module is now unsupported (see > > http://www.pfdubois.com/numpy). We'll need to decide if Biopython is > > going over to numarray, or whether to stick with Numeric for now. Some > > modifications will be needed in the Python and C code if we start > > using numarray. > > Good point. We should indeed move to numarray, I think, though we might > wait some months until numarray is more widely used. > Cheers & thanks for the C++ related work, I'd agree that a move to numarray makes the most sense. We need to move in the direction development is going. I'd like to make this something we can plan to do soon-ish so it can be tested and ready for the next release. Right now, it looks like the following code would need to be migrated: -> Affy -- Harry -> KDTree -- Thomas -> PDB -- Thomas -> SVDSuperimposer -- Thomas -> Cluster -- Michiel -> Stasitics/lowess -- Michiel -> LogisticRegression -- Jeff? -> MarkovModel -- Jeff? -> NaiveBayes -- Jeff? -> distance -- Jeff? -> kNN -- Jeff? What I really don't want is to make people download both Numeric and numarray to use Biopython, so I'd hope to make a coordinated switch between releases. If we decide to do this, we can split up the tasks and have a go at it. Let me know what people think about this and we can get it coordinated. I'd like to wait at least a week before starting to do it, so we can make sure I didn't mess anything up with the new release that will require a quick fix-it release :-). Brad From jeffrey_chang at stanfordalumni.org Fri May 14 11:47:54 2004 From: jeffrey_chang at stanfordalumni.org (Jeffrey Chang) Date: Sat Mar 5 14:43:33 2005 Subject: [Biopython-dev] Re: Work towards getting KDTree compiling In-Reply-To: <20040514151359.GG86985@evostick.agtec.uga.edu> References: <32793.192.38.114.59.1084517900.squirrel@www.binf.ku.dk> <20040514151359.GG86985@evostick.agtec.uga.edu> Message-ID: <10470869-A5BE-11D8-BF7A-000A956845CE@stanfordalumni.org> On May 14, 2004, at 11:13 AM, Brad Chapman wrote: > I'd agree that a move to numarray makes the most sense. We need to > move in the direction development is going. I'd like to make this > something we can plan to do soon-ish so it can be tested and ready > for the next release. Right now, it looks like the following code > would need to be migrated: > > -> LogisticRegression -- Jeff? > -> MarkovModel -- Jeff? > -> NaiveBayes -- Jeff? > -> distance -- Jeff? > -> kNN -- Jeff? Yes, these are mine, and I can upgrade them to use numarray. > What I really don't want is to make people download both Numeric and > numarray to use Biopython, so I'd hope to make a coordinated switch > between releases. If we decide to do this, we can split up the tasks > and have a go at it. Sure -- let me know the plans! Jeff From thamelry at binf.ku.dk Sat May 15 05:55:24 2004 From: thamelry at binf.ku.dk (Thomas Hamelryck) Date: Sat Mar 5 14:43:33 2005 Subject: [Biopython-dev] Epydoc markup In-Reply-To: <20040514151359.GG86985@evostick.agtec.uga.edu> References: <32793.192.38.114.59.1084517900.squirrel@www.binf.ku.dk> <20040514151359.GG86985@evostick.agtec.uga.edu> Message-ID: <33174.80.63.229.248.1084614924.squirrel@www.binf.ku.dk> Hi Brad, First of all - thanks for shipping 1.30! Nice job! Small remark: I noticed that the Epydoc markup language in the doc strings of the Bio.PDB module is not translated into HTML in the documentation on the website. If I run Epydoc locally everything looks fine, though. Any idea what could be wrong? BTW, is there a way for the Biopython developers to update the documentation on the website directly? Might be useful. Epydoc is a great tool, BTW. It was a very good idea to introduce it, IMO. Cheers, -Thomas From chapmanb at uga.edu Sat May 15 07:16:59 2004 From: chapmanb at uga.edu (Brad Chapman) Date: Sat Mar 5 14:43:33 2005 Subject: [Biopython-dev] Epydoc markup In-Reply-To: <33174.80.63.229.248.1084614924.squirrel@www.binf.ku.dk> References: <32793.192.38.114.59.1084517900.squirrel@www.binf.ku.dk> <20040514151359.GG86985@evostick.agtec.uga.edu> <33174.80.63.229.248.1084614924.squirrel@www.binf.ku.dk> Message-ID: <20040515111659.GB40622@misterbd.agtec.uga.edu> Hi Thomas; > First of all - thanks for shipping 1.30! Nice job! Thanks to you as well -- there has been lots of nice work with the PDB and structure molecules in well. There is some really impressive stuff in there. > Small remark: I noticed that the Epydoc markup language > in the doc strings of the Bio.PDB module is not translated into > HTML in the documentation on the website. If I run Epydoc locally > everything looks fine, though. Any idea what could be wrong? Well, I've been using '--docformat plaintext' when running epydoc. I do like the epydoc markup, but it seems like if something isn't marked up then it can come out looking pretty unreadable. A good example is the Fasta package, in which it munges together all of the information in the header: Classes: Record Holds FASTA sequence data. Iterator Iterates over sequence data in a FASTA file. Dictionary Accesses a FASTA file using a dictionary interface. RecordParser Parses FASTA sequence data into a Record object. SequenceParser Parses FASTA sequence data into a Sequence object. I'm not sure if there is a way to specify specific modules, like yours, which use epydoc and get it to treat them differently. I'll have to look at it a little more. > BTW, > is there a way for the Biopython developers to update the documentation > on the website directly? Might be useful. Hmmm I don't think you account on biopython.org right now. Would you like me to give you one? If so, just send me a separate mail and I'll set you up with your same account name and a temporary password. The details of where things are on the server and how the web pages work are at: http://www.biopython.org/docs/developer/website_technical.html > Epydoc is a great tool, BTW. It was a very good idea to > introduce it, IMO. I think so as well -- I'm glad people are into using it. The output is much more usable and pointing people at it is a great way to get an overview of what's in Biopython. Brad From fsms at users.sourceforge.net Sun May 16 07:01:39 2004 From: fsms at users.sourceforge.net (fsms@users.sourceforge.net) Date: Sat Mar 5 14:43:33 2005 Subject: [Biopython-dev] Restriction analysis package. Message-ID: <40A74A13.5040503@users.sourceforge.net> Hello, I would like to know if you would be interested by a restriction analysis package. The packages create classes for restriction enzymes from Rebase data and allows to use the generated enzymes to search for restriction site and cut the DNA sequence. F. Sohm From chapmanb at uga.edu Sun May 16 14:23:21 2004 From: chapmanb at uga.edu (Brad Chapman) Date: Sat Mar 5 14:43:33 2005 Subject: [Biopython-dev] Restriction analysis package. In-Reply-To: <40A74A13.5040503@users.sourceforge.net> References: <40A74A13.5040503@users.sourceforge.net> Message-ID: <20040516182321.GA53985@misterbd.agtec.uga.edu> Hello; > I would like to know if you would be interested by a restriction > analysis package. > The packages create classes for restriction enzymes from Rebase data and > allows to use the generated enzymes to search for restriction site and > cut the DNA sequence. We would definitely be interested in something like this, and would be happy to see your code. Biopython does already have some work done with Rebase (see Bio/Rebase/__init__.py). Basically, this is a parser and record to hold Rebase information. It would be great if your code either supplemented or surpassed the code we already have. We just want to avoid duplication within Biopython. If you haven't already you might want to take a look at the guide for contributing to Biopython: http://www.biopython.org/docs/developer/contrib.html Thanks for the mail and looking forward to seeing your code! Brad From fsms at users.sourceforge.net Mon May 17 06:27:00 2004 From: fsms at users.sourceforge.net (fsms@users.sourceforge.net) Date: Sat Mar 5 14:43:33 2005 Subject: [Biopython-dev] Restriction analysis package. In-Reply-To: <20040516182321.GA53985@misterbd.agtec.uga.edu> References: <40A74A13.5040503@users.sourceforge.net> <20040516182321.GA53985@misterbd.agtec.uga.edu> Message-ID: <40A89374.8040005@users.sourceforge.net> Brad Chapman wrote: >Hello; > > > >>I would like to know if you would be interested by a restriction >>analysis package. >>The packages create classes for restriction enzymes from Rebase data and >>allows to use the generated enzymes to search for restriction site and >>cut the DNA sequence. >> >> > >We would definitely be interested in something like this, and would >be happy to see your code. Biopython does already have some work >done with Rebase (see Bio/Rebase/__init__.py). Basically, this is >a parser and record to hold Rebase information. It would be great if >your code either supplemented or surpassed the code we already have. >We just want to avoid duplication within Biopython. > >If you haven't already you might want to take a look at the guide >for contributing to Biopython: > >http://www.biopython.org/docs/developer/contrib.html > >Thanks for the mail and looking forward to seeing your code! >Brad > > > Hello, The package is somehow complementary from the Rebase package, without using it though. It allows to download the file in EMBOSS format from Rebase and builds the corresponding enzymes. Each enzyme is a class on its own (I wanted to play with metaclass). Using Seq and MutableSeq as DNA format it is possible to scan for restriction sites and retrieve the corresponding fragments. Other methods are provided to better describe the enzymes (isoschizomers, compatible ends, methylable or not, blunt or overhang and so on ....). The code is part of a python package called Rana (http://sourceforge.net/projects/rana). This package is early alpha and not mature enough to be included in Biopython, moreover I licensed it under GPL. However, the code which deals with the restriction enzymes is more mature (I would say beta). I tested the results it gives against the restriction analysis facilities of EMBOSS for common vectors (pBR322, pGEMs, ...) and it is ok. I will release this part under python license. For the moment, I have removed the class which allows meta-analysis (full restriction analysis, limited to Blunt, ...) as it has not been tested with Biopython DNA objects. The code itself does not follow exactly the Biopython convention for coding (class methods are in lower case with underscore as in Python). But, this was the convention for the whole Rana package. This can be changed eventually. I release a new package in the Rana project (ranaBiopython-0.1) which contains the package to be included in Biopython. I have tested it quickly and it seems to work fine. Simply put the rana folder in the Biopython folder, the package comes with a bunch of enzyme classes from the march or april Rebase release and should work out of the box. If you want to test the update system you will have to edit RanaConfig.py to enter the address of your ftp_proxy and an e-mail address for anonymous ftp connections. The README contains an example of interactive session using the package which should get you started. You can find it at http://sourceforge.net/projects/rana regards SF From chapmanb at uga.edu Tue May 18 06:00:56 2004 From: chapmanb at uga.edu (Brad Chapman) Date: Sat Mar 5 14:43:33 2005 Subject: [Biopython-dev] Restriction analysis package. In-Reply-To: <40A89374.8040005@users.sourceforge.net> References: <40A74A13.5040503@users.sourceforge.net> <20040516182321.GA53985@misterbd.agtec.uga.edu> <40A89374.8040005@users.sourceforge.net> Message-ID: <20040518100056.GA31418@misterbd.agtec.uga.edu> Hi; [...description of Rana package...] [...http://sourceforge.net/projects/rana...] > However, the code which deals with the restriction enzymes is more > mature (I would say beta). I tested the results it gives against the > restriction analysis facilities of EMBOSS for common vectors (pBR322, > pGEMs, ...) and it is ok. I will release this part under python license. > For the moment, I have removed the class which allows meta-analysis > (full restriction analysis, limited to Blunt, ...) as it has not been > tested with Biopython DNA objects. > > The code itself does not follow exactly the Biopython convention for > coding (class methods are in lower case with underscore as in Python). > But, this was the convention for the whole Rana package. This can be > changed eventually. > > I release a new package in the Rana project (ranaBiopython-0.1) which > contains the > package to be included in Biopython. I have tested it quickly and it > seems to work fine. Thanks for putting this together. The code looks very useful and I'd definitely like to see it work towards being included in Biopython, if that's what you'd like. A few comments on it: 1. First, if you'd like to include this in Biopython the code would have to be willing to license the code under the Biopython license. I see different references to the GPL and Python license within your package. I'm not at all the type of person who argues about licensing issues, but we just need to keep the Biopython distribution under one license. 2. The way this is organized right now puts two different types of functionality together -- building the enzyme dictionary by downloading and parsing Rebase, and the actual enzyme dictionary itself. For Biopython, the public functionality you'd want to expose would be the enzyme dictionary and the useful functions you have within that. The downloading and parsing work would be something that you, or another developer, would do on a monthly or whatever basis to keep the enzyme dictionary up to date within Biopython. Thus I'd propose organizing the code like: Bio/Restriction/__init__.py --> The current Restriction.py Bio/Restriction/Restriction_Dictionary.py --> the dictionary Bio/Restriction/_Update/ --> The Update, RanaConfig and RestrictionCompiler code to do the updates and regenerate the dictionary. ranacompiler.py should exist in somewhere like Scripts/restriction to be run, instead of in site-packages. 3. Going along with reorganizing the code base, I'd propose changing the updating scripts a bit. Storing databases and things into site-packages is generally not a good idea, since that is meant for Python code, and also requires the user to mess around with either running scripts as root or changing permissions -- more work then is really necessary. What I'd do is store the Database and Updates information into, say, the current directory where the user runs the scripts. Additionally, the Restriction_Dictionary.py would be generated there. Then, when the updates are done everything gets run and you have a new Restriction_Dictionary.py to copy over and check into CVS. Hopefully these make some sense. I really like the catalyse and search functionality on the enzyme classes -- it's a nice interface design and it would be great to have in Biopython. Please do let me know what you think about the licensing and change proposals and we can keep moving forward towards getting this in Biopython. Thanks again for the work so far! Brad From pierre.monestie at lbri.lionbioscience.com Tue May 18 16:12:50 2004 From: pierre.monestie at lbri.lionbioscience.com (Pierre Monestie) Date: Sat Mar 5 14:43:33 2005 Subject: [Biopython-dev] ipi parser Message-ID: Hello, I'm trying to use the Swissprot parser to parse IPI. I read that the parser should have been fixed for IPI however I get an error on date when I try to parse ipi.HUMAN I get: File "dbupdate/src/python/make_sptofasta.py", line 172, in ? parseandoutput('ipi',it,fl[0],fl[1],fl[2],fl[3],fl[4]) File "dbupdate/src/python/make_sptofasta.py", line 46, in parseandoutput record = it.next() File "/lbri/gen/lib/python2.2/site-packages/Bio/SwissProt/SProt.py", line 166, in next return self._parser.parse(File.StringHandle(data)) File "/lbri/gen/lib/python2.2/site-packages/Bio/SwissProt/SProt.py", line 290, in parse self._scanner.feed(handle, self._consumer) File "/lbri/gen/lib/python2.2/site-packages/Bio/SwissProt/SProt.py", line 333, in feed self._scan_record(uhandle, consumer) File "/lbri/gen/lib/python2.2/site-packages/Bio/SwissProt/SProt.py", line 338, in _scan_record fn(self, uhandle, consumer) File "/lbri/gen/lib/python2.2/site-packages/Bio/SwissProt/SProt.py", line 379, in _scan_dt self._scan_line('DT', uhandle, consumer.date, exactly_one=1) File "/lbri/gen/lib/python2.2/site-packages/Bio/SwissProt/SProt.py", line 360, in _scan_line read_and_call(uhandle, event_fn, start=line_type) File "/lbri/gen/lib/python2.2/site-packages/Bio/ParserSupport.py", line 301, in read_and_call method(line) File "/lbri/gen/lib/python2.2/site-packages/Bio/SwissProt/SProt.py", line 537, in date self.data.created = cols[1], int(self._chomp(cols[3])) ValueError: invalid literal for int(): Human Thanks in advance for your help Pierre Monestie From jeffrey_chang at stanfordalumni.org Tue May 18 17:19:57 2004 From: jeffrey_chang at stanfordalumni.org (Jeffrey Chang) Date: Sat Mar 5 14:43:33 2005 Subject: [Biopython-dev] ipi parser In-Reply-To: References: Message-ID: <1CF58780-A911-11D8-B3CF-000A956845CE@stanfordalumni.org> Hello, These errors are nearly always due to changes in the formats of the records that occur from time to time. Do you have a sample file, or accession number, that I can use to see what's going on? Jeff On May 18, 2004, at 4:12 PM, Pierre Monestie wrote: > Hello, > I'm trying to use the Swissprot parser to parse IPI. I read that the > parser > should have been fixed for IPI however I get an error on date when I > try to > parse ipi.HUMAN > I get: > File "dbupdate/src/python/make_sptofasta.py", line 172, in ? > parseandoutput('ipi',it,fl[0],fl[1],fl[2],fl[3],fl[4]) > File "dbupdate/src/python/make_sptofasta.py", line 46, in > parseandoutput > record = it.next() > File "/lbri/gen/lib/python2.2/site-packages/Bio/SwissProt/SProt.py", > line > 166, in next > return self._parser.parse(File.StringHandle(data)) > File "/lbri/gen/lib/python2.2/site-packages/Bio/SwissProt/SProt.py", > line > 290, in parse > self._scanner.feed(handle, self._consumer) > File "/lbri/gen/lib/python2.2/site-packages/Bio/SwissProt/SProt.py", > line > 333, in feed > self._scan_record(uhandle, consumer) > File "/lbri/gen/lib/python2.2/site-packages/Bio/SwissProt/SProt.py", > line > 338, in _scan_record > fn(self, uhandle, consumer) > File "/lbri/gen/lib/python2.2/site-packages/Bio/SwissProt/SProt.py", > line > 379, in _scan_dt > self._scan_line('DT', uhandle, consumer.date, exactly_one=1) > File "/lbri/gen/lib/python2.2/site-packages/Bio/SwissProt/SProt.py", > line > 360, in _scan_line > read_and_call(uhandle, event_fn, start=line_type) > File "/lbri/gen/lib/python2.2/site-packages/Bio/ParserSupport.py", > line > 301, in read_and_call > method(line) > File "/lbri/gen/lib/python2.2/site-packages/Bio/SwissProt/SProt.py", > line > 537, in date > self.data.created = cols[1], int(self._chomp(cols[3])) > ValueError: invalid literal for int(): Human > > Thanks in advance for your help > Pierre Monestie > > _______________________________________________ > Biopython-dev mailing list > Biopython-dev@biopython.org > http://biopython.org/mailman/listinfo/biopython-dev From chapmanb at uga.edu Wed May 19 05:50:17 2004 From: chapmanb at uga.edu (Brad Chapman) Date: Sat Mar 5 14:43:33 2005 Subject: [Biopython-dev] ipi parser In-Reply-To: <1CF58780-A911-11D8-B3CF-000A956845CE@stanfordalumni.org> References: <1CF58780-A911-11D8-B3CF-000A956845CE@stanfordalumni.org> Message-ID: <20040519095017.GF34051@misterbd.agtec.uga.edu> Hi Pierre and Jeff; Pierre: > >I'm trying to use the Swissprot parser to parse IPI. I read that the > >parser should have been fixed for IPI however I get an error on date > >when I try to parse ipi.HUMAN I get: [...] > >ValueError: invalid literal for int(): Human Jeff: > These errors are nearly always due to changes in the formats of the > records that occur from time to time. Do you have a sample file, or > accession number, that I can use to see what's going on? I took a look at this using the ipi.HUMAN.dat file from ftp://ftp.infobiogen.fr/pub/db/ipi/current/ and was able to reproduce the error. It looks like the problem was that the DT lines are different then expected: DT 01-AUG-2003 (IPI Human rel. 2.22, Created) DT 01-AUG-2003 (IPI Human rel. 2.22, Last sequence update) They've got the 'IPI Human' bit before 'rel.' and SProt tries to get the version information from the third column (which is 'Human') since it normally expects a rational 'Rel.' part only. Also, the versions are now dotted and not just integers, and the third DT line is missing. Finally, some of these IPI files are missing the DE line. I updated the SProt parser to handle this and a patch to Bio/SwissProt/SProt.py is attached. I also updated the tests with an example file, and added an IPI expression to swissprot in the registry so that the FormatIO system can also handle these files. Jeff, let me know if I broke anything or did anything else bad. Pierre, hope this fixes your problem. Brad -------------- next part -------------- ? SProt.diff Index: SProt.py =================================================================== RCS file: /home/repository/biopython/biopython/Bio/SwissProt/SProt.py,v retrieving revision 1.28 retrieving revision 1.29 diff -c -r1.28 -r1.29 *** SProt.py 18 May 2004 13:58:35 -0000 1.28 --- SProt.py 19 May 2004 14:01:33 -0000 1.29 *************** *** 377,386 **** def _scan_dt(self, uhandle, consumer): self._scan_line('DT', uhandle, consumer.date, exactly_one=1) self._scan_line('DT', uhandle, consumer.date, exactly_one=1) ! self._scan_line('DT', uhandle, consumer.date, exactly_one=1) def _scan_de(self, uhandle, consumer): ! self._scan_line('DE', uhandle, consumer.description, one_or_more=1) def _scan_gn(self, uhandle, consumer): self._scan_line('GN', uhandle, consumer.gene_name, any_number=1) --- 377,388 ---- def _scan_dt(self, uhandle, consumer): self._scan_line('DT', uhandle, consumer.date, exactly_one=1) self._scan_line('DT', uhandle, consumer.date, exactly_one=1) ! # IPI doesn't necessarily contain the third line about annotations ! self._scan_line('DT', uhandle, consumer.date, up_to_one=1) def _scan_de(self, uhandle, consumer): ! # IPI can be missing a DE line ! self._scan_line('DE', uhandle, consumer.description, any_number=1) def _scan_gn(self, uhandle, consumer): self._scan_line('GN', uhandle, consumer.gene_name, any_number=1) *************** *** 526,554 **** def date(self, line): uprline = string.upper(line) cols = line.split() if uprline.find("CREATED") >= 0: ! # ws:2001-12-05 prevent e.g. (IPIrel. , created) ! # !no number given! from crashing ! if self._chomp(cols[3]) == '': #<= ! self.data.created = cols[1], 0 #<= ! else: #<= ! self.data.created = cols[1], int(self._chomp(cols[3])) elif uprline.find('LAST SEQUENCE UPDATE') >= 0: ! # ws:2001-12-05 prevent e.g. (IPIrel. , created) ! # !no number given! from crashing ! if self._chomp(cols[3]) == '': #<= ! self.data.sequence_update = cols[1], 0 #<= ! else: #<= ! self.data.sequence_update = cols[1], int(self._chomp(cols[3])) elif uprline.find( 'LAST ANNOTATION UPDATE') >= 0: ! # ws:2001-12-05 prevent e.g. (IPIrel. , created) ! # !no number given! from crashing ! if self._chomp(cols[3]) == '': #<= ! self.data.annotation_update = cols[1], 0 #<= ! else: #<= ! self.data.annotation_update = cols[1], \ ! int(self._chomp(cols[3])) #<= else: raise SyntaxError, "I don't understand the date line %s" % line --- 528,565 ---- def date(self, line): uprline = string.upper(line) + + # find where the version information will be located + # This is needed for when you have cases like IPI where + # the release verison is in a different spot: + # DT 08-JAN-2002 (IPI Human rel. 2.3, Created) + uprcols = uprline.split() + rel_index = -1 + for index in range(len(uprcols)): + if uprcols[index].find("REL.") >= 0: + rel_index = index + assert rel_index >= 0, \ + "Could not find Rel. in DT line: %s" % (line) + version_index = rel_index + 1 + # get the version information cols = line.split() + str_version = self._chomp(cols[version_index]) + # no version number + if str_version == '': + version = 0 + # dot versioned + elif str_version.find(".") >= 0: + version = str_version + # integer versioned + else: + version = int(str_version) + if uprline.find("CREATED") >= 0: ! self.data.created = cols[1], version elif uprline.find('LAST SEQUENCE UPDATE') >= 0: ! self.data.sequence_update = cols[1], version elif uprline.find( 'LAST ANNOTATION UPDATE') >= 0: ! self.data.annotation_update = cols[1], version else: raise SyntaxError, "I don't understand the date line %s" % line From pierre.monestie at lbri.lionbioscience.com Wed May 19 10:21:13 2004 From: pierre.monestie at lbri.lionbioscience.com (Pierre Monestie) Date: Sat Mar 5 14:43:34 2005 Subject: [Biopython-dev] ipi parser In-Reply-To: <1CF58780-A911-11D8-B3CF-000A956845CE@stanfordalumni.org> Message-ID: Here is a small example: ID IPI00387610.1 IPI; PRT; 697 AA. AC IPI00387610; DT 18-NOV-2003 (IPI Rat rel. 1.9, Created) DT 18-NOV-2003 (IPI Rat rel. 1.9, Last sequence update) OS Rattus norvegicus (Rat). OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; OC Mammalia; Eutheria; Rodentia; Sciurognathi; Muridae; Murinae; Rattus. OX NCBI_TaxID=10116; CC -!- CHROMOSOME: 1. DR InterPro; IPR001611; LRR. DR InterPro; IPR007091; LRR_RNinh. DR InterPro; IPR003590; LRR_RNinh_sub. DR InterPro; IPR007111; NACHT_NTPase. DR Pfam; PF05729; NACHT; 1. DR PRINTS; PR00019; LEURICHRPT. DR SMART; SM00368; LRR_RI; 4. DR PROSITE; PS50503; LRR_RI; 1. DR PROSITE; PS50837; NACHT; 1. DR UniParc; UPI000021DDC2; -; -. DR ENSEMBL; ENSRNOP00000030672; ENSRNOG00000021996; M. SQ SEQUENCE 697 AA; 80092 MW; D6C61D8C95F306AF CRC64; PLVLTDSGHS KLYQAHLKKK LTHDYARKFN IKAQDLFKQK FTQDDCDRFE NLLVSKATGK KPHMVFLQGV AGIGKSLMLT KLMLAWSEGI VFQNKFSYIF YFCCQDVKQL KRASLAELIS REWPNASAPT AEILSQPEKL LFIIDSLEVM ECNMSERESE LCDNCTEKQP VSLLLSSLLR RKMLPESSFL ISATPETFEK MEDRIECTNV KIITGFNENN IKMYFRSLFQ DKNRTLEAFS LVRENEQLFN VCQVPVLCWM VATCIKKEIE KGRDPVFICR RTTSLYTTHI FNLFTPQNAQ YPSKKSQDQL QGLCSLAAEG MWTDTFVFSE EALRRNGILD SDIPTLLDRR ILERSKESES CYIFLHPSLQ EVCAAVFYLL KSHLDHPSQD VKSVEALLFT FLKKAKVQWI FLGCFLFGLL HESEQEKLEM FFGHQLSQEI KHQLYQCLET ISVNEELQEQ IDGMKLFYCL FEMEDEAFLM QAMNCMEQIN FVAKDYSDVI VAAYCLKHCS TLKKLSFSTQ NILSEEQEHS YTEKLLICWH HMCSVLISSK DIHVLQVKDT NLNETAFWVL YNHLKYPSCT LKVLVIAACN LSPDDCKVFA SVLISSKMLK HLNLSSNNLD KGISSLCKAL CHPDCILKHL VVRHCLITTS GCQDLAEVLR HNQNLRSLQV SNNKIEDAGV KLLCDAIKQP NCHLENI // ID IPI00187591.2 IPI; PRT; 163 AA. AC IPI00187591; DT 14-MAR-2003 (IPI Rat rel. 1.0, Created) DT 18-NOV-2003 (IPI Rat rel. 1.9, Last sequence update) OS Rattus norvegicus (Rat). OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; OC Mammalia; Eutheria; Rodentia; Sciurognathi; Muridae; Murinae; Rattus. OX NCBI_TaxID=10116; CC -!- CHROMOSOME: 19. DR UniParc; UPI00001CD005; -; -. DR ENSEMBL; ENSRNOP00000023455; ENSRNOG00000016991; M. SQ SEQUENCE 163 AA; 18683 MW; A1998B08C0383825 CRC64; MDALEEESFA LSFSSASDAE FDAVVGCLED IIMDAEFQLL QRSFMDKYYQ EFEDTEENKL TYTPIFNEYI SLVEKYIEEQ LLERIPGFNM AAFTTTLQHH KDEVAGDIFD MLLTFTDFLA FKEMFLDYRA EKEGRGLDLS SGLVVTSLCK SSSTPASQNN LRH // ID IPI00357878.1 IPI; PRT; 690 AA. AC IPI00357878; IPI00201160; DT 02-OCT-2003 (IPI Rat rel. 1.7, Created) DT 02-OCT-2003 (IPI Rat rel. 1.7, Last sequence update) DE SIMILAR TO ARHGEF3 PROTEIN. OS Rattus norvegicus (Rat). OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; OC Mammalia; Eutheria; Rodentia; Sciurognathi; Muridae; Murinae; Rattus. OX NCBI_TaxID=10116; CC -!- CHROMOSOME: 16. DR InterPro; IPR001849; PH. DR InterPro; IPR000219; RhoGEF. DR Pfam; PF00169; PH; 1. DR Pfam; PF00621; RhoGEF; 1. DR SMART; SM00233; PH; 1. DR SMART; SM00325; RhoGEF; 1. DR PROSITE; PS50010; DH_2; 1. DR PROSITE; PS50003; PH_DOMAIN; 1. DR ENSEMBL; ENSRNOP00000019511; ENSRNOG00000014363; -. DR REFSEQ_XP; XP_224588; GI:34876921; M. DR UniParc; UPI00001D0F0F; -; -. SQ SEQUENCE 690 AA; 77882 MW; FAB74E51D05C987B CRC64; MENSENPPVD NRTSVLHPLL RQTTQTQFVH EPFTEGIQMS ALGYLKRKRK QSAQDEDAVS LCSLDISQPA RALLNPQQTL SERWIRDGLS ASSVVWMTER KGEKHYERER PALPVEPGIR SSLLEAVVGV RVAAAGIVEL GPSFTRDFCC RLGSAVTSQR AGPAAAMVAK DYPFYLTVKR ANCSLEAPLG SGVAKDEEPS NKRVKPLSRV TSLANLIPPV KTTPLKRFSQ TLQRSISFRN ESRPDILAPR AWSRNATSSS TKRRDSKLWS ETFDVCVSQV LTAKEIKRQE AIFELSQGEE DLIEDLKLAK KAYHDPMLKL SIMTEQELNQ IFGTLDSLIP LHEDLLSQLR DVRKPDGSTE HVGPILVGWL PCLSSYDSYC SNQVAAKALL DHKKQDHRVQ DFLQRCLESP FSRKLDLWNF LDIPRSRLVK YPLLLREILR HTPNDNPDQQ HLEEAINIIQ GIVAEINTKT GESECRYYKE RLLYLEEGQK DSLIDSSRVL CCHGELKNNR GVKLHVFLFQ EVLVITRAVT HNEQLCYQLY RQPIPVKDLT LEDLQDGEVR LGGSLRGAFS NNERIKNFFR VSFKNGSQSQ THSLQANDTF NKQQWLNCIR QAKETVLSAA GQAGLLDSES LSQSPGTENR ELRGETKLEQ MDQSDSESDC SMDTSEVSLE CERMEQTDAS CANSRPEENV // ID IPI00200253.1 IPI; PRT; 239 AA. AC IPI00200253; DT 14-MAR-2003 (IPI Rat rel. 1.0, Created) DT 14-MAR-2003 (IPI Rat rel. 1.0, Last sequence update) OS Rattus norvegicus (Rat). OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; OC Mammalia; Eutheria; Rodentia; Sciurognathi; Muridae; Murinae; Rattus. OX NCBI_TaxID=10116; CC -!- CHROMOSOME: 5. DR UniParc; UPI0000180879; -; -. DR ENSEMBL; ENSRNOP00000030673; ENSRNOG00000023459; M. SQ SEQUENCE 239 AA; 25891 MW; 68A1110A31C7C4D9 CRC64; MEGTAESQTP DLRDVEGKVG RKTPEGLLRG LRGECDLGTS GDVLLPGASS TGHGLGDKIM ALRMELAYLR AIDVKILQQL VTLNEGIEAV RWLLEERGTL TSHCSSLTSS QYSLTGGSPE RSRRGSWDSL PDTSSTDRLD SVSIGSFLDT VAPRELDEQG HPGPSCPEID WAKVIPSEDR ARTEVDMTST KLGSLTATWK LPGDGLQCGP PEPSEDDSAK QGFEAHWYWG QCQDDVTFL // ID IPI00387612.1 IPI; PRT; 649 AA. AC IPI00387612; DT 18-NOV-2003 (IPI Rat rel. 1.9, Created) DT 18-NOV-2003 (IPI Rat rel. 1.9, Last sequence update) OS Rattus norvegicus (Rat). OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; OC Mammalia; Eutheria; Rodentia; Sciurognathi; Muridae; Murinae; Rattus. OX NCBI_TaxID=10116; CC -!- CHROMOSOME: 8. DR InterPro; IPR005123; 2OG-FeII_Oxy. DR InterPro; IPR001006; ProcolLys_dioxy. DR InterPro; IPR006620; Pro_4_hyd_alph. DR Pfam; PF03171; 2OG-FeII_Oxy; 1. DR ProDom; PD011578; ProcolLys_dioxy; 1. DR SMART; SM00702; P4Hc; 1. DR PROSITE; PS01325; LYS_HYDROXYLASE; 1. DR UniParc; UPI000021DDC3; -; -. DR ENSEMBL; ENSRNOP00000030674; ENSRNOG00000008171; M. SQ SEQUENCE 649 AA; 74530 MW; C780F254E2DA7C58 CRC64; KLLVITVATK ENDGFHRFMN SAKYFNYTVK VLGQGQEWRG GDGMNSIGGG QKVRLMKEAM EHYAGQDDLV ILFTECFDVI FAGGPEELLK KFQKTNHKIV FAADALLWPD KRLADKYPGV HIGKRYLNSG GFIGYAPYIS RLVQQWDLQD NDDDQLFYTK VYIDPLKREA LNITLDHRCK IFQALNGATD EVVLKFENGK SRVKNTFYET LPVAINGNGP TKILLNYFGN YVPNSWTQEN GCALCDFDTI DLSTVDVYPK VTLGVFIEQP TPFLPRFLDL LLTLDYPKEA LRLFVHNSEY SLVSVVGENS SEVTFLANKP SGRKIIAPLV TRHGKLWSNF WGALSPDGYY ARSEDYVDIV QGNRVGIWNV PYMANVYLIQ GKTLRSEMSE RNYFVRDKLD PDMSLCRNAR DMGVFMYISN RHEFGRLIST ANYNTSHLNN DLWQIFENPV DWKEKYINRD YSKIFTENIV EQPCPDVFWF PIFSERACDE LVEEMEHYGK WSGGKHHDSR ISGGYENVPT DDIHMKQIDL ENVWLHFIRE FIAPVTLKVF AGYYTKGFAL LNFVVKYSPE RQRSLRPHHD ASTFTINIAL NNVGEDFQGG GCKFLRYNCS IESPRKGWSF MHPGRLTHLH EGLPVKNGTR YIAVSFIDP // ID IPI00387613.1 IPI; PRT; 232 AA. AC IPI00387613; DT 18-NOV-2003 (IPI Rat rel. 1.9, Created) DT 18-NOV-2003 (IPI Rat rel. 1.9, Last sequence update) OS Rattus norvegicus (Rat). OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; OC Mammalia; Eutheria; Rodentia; Sciurognathi; Muridae; Murinae; Rattus. OX NCBI_TaxID=10116; CC -!- CHROMOSOME: 3. DR InterPro; IPR001921; Ribosomal_7A. DR InterPro; IPR000231; Ribosomal_L30e. DR InterPro; IPR004038; Ribosomal_L7A. DR InterPro; IPR004037; Ribosomal_L7Ae. DR Pfam; PF01248; Ribosomal_L7Ae; 1. DR PRINTS; PR00881; L7ARS6FAMILY. DR PRINTS; PR00882; RIBOSOMALL7A. DR ProDom; PD004495; Ribosomal_L30e; 1. DR UniParc; UPI000021DDC4; -; -. DR ENSEMBL; ENSRNOP00000030675; ENSRNOG00000022075; M. SQ SEQUENCE 232 AA; 26373 MW; 149FE6A502E3EACB CRC64; KKAKGKKVAP APSVVKKQEA KKMVNPLFEK RPENFGIGQD IQPKRDLTCF VKWPRYIRLQ QQRAILYKWL TVPPAINQFT QALDRQTATQ LLKLTHKYRP ETKQEKKQRL LVNTVTTLVE NKKVQLVVIA HDVDPIELVV FLPALCQKMG VPYCITKGKA RLGRLVHRKT STTVTFTQVN SEDKGALAKL VGAIRTNYND RCDEIRRWGG NVLGPKSVAR IAKPEKAKAK EL // ID IPI00400453.1 IPI; PRT; 94 AA. AC IPI00400453; DT 10-FEB-2004 (IPI Rat rel. 1.12, Created) DT 10-FEB-2004 (IPI Rat rel. 1.12, Last sequence update) OS Rattus norvegicus (Rat). OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; OC Mammalia; Eutheria; Rodentia; Sciurognathi; Muridae; Murinae; Rattus. OX NCBI_TaxID=10116; CC -!- CHROMOSOME: 4. DR InterPro; IPR002890; A2M_N. DR Pfam; PF01835; A2M_N; 1. DR UniParc; UPI000023C54E; -; -. DR S/MARt; G000699; A2-Mag; -. DR ENSEMBL; ENSRNOP00000030676; ENSRNOG00000005599; M. SQ SEQUENCE 94 AA; 10505 MW; 92E4AACC068DF138 CRC64; HQAFHVNATV TEEGTGSEFS GSGRIEVERT RNKFLFLKAD SHFRHGIPFF VKVRLVDIKG DPIPNEQVFI KAQEAGYTNA TTTDQHGLAK FSID // ID IPI00387614.1 IPI; PRT; 492 AA. AC IPI00387614; DT 18-NOV-2003 (IPI Rat rel. 1.9, Created) DT 18-NOV-2003 (IPI Rat rel. 1.9, Last sequence update) OS Rattus norvegicus (Rat). OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; OC Mammalia; Eutheria; Rodentia; Sciurognathi; Muridae; Murinae; Rattus. OX NCBI_TaxID=10116; CC -!- CHROMOSOME: 5. DR InterPro; IPR001128; Cytochrome_P450. DR InterPro; IPR002401; EP450I. DR InterPro; IPR008071; EP450_CYP2J. DR PRINTS; PR00463; EP450I. DR PRINTS; PR01688; EP450ICYP2J. DR PRINTS; PR00385; P450. DR PROSITE; PS00086; CYTOCHROME_P450; 1. DR UniParc; UPI000021DDC5; -; -. DR ENSEMBL; ENSRNOP00000030677; ENSRNOG00000009455; M. SQ SEQUENCE 492 AA; 56862 MW; A9AC35466EFF8490 CRC64; ILLLAAVTFL FLADFLKHRR PKNYPPGPWR LPLVGCLFHL DPKQPHLSLQ QFVKKYGNVL SLDFANIPSV VVTGMPLIKE IFTQMEHNFL NRPVTLLRKH LFNKNGLIFS SGQTWKEQRR FALMTLRNFG LGKKSLEQRI QEEAYHLVEA IKDEGGLPFD PHFNINKAVS NIICSVTFGE RFEYHDSQFQ EMLRLLDEAM CLESSMMCQL YNIFPRILQY LPGSHQTLFS NWRKLKLFIS DIIKNHRRDW DPDEPRDFID AFLKEMAKYP DKTTTSFNEE NLICSTLDLF FAGTETTSTT LRWALLCMAL YPEVQEKVQA EIDRVIGQKR AASLADRESM PYTNAVIHEV QRMGNIIPLN VPREVAMDTT LNGFHLPKGT MVLTNLTALH RDPKEWATPD VFNPEHFLEN GQFKKRESFL PFSMECDPSG FFSTGKRACL GEQLARSELF IFFTSLMQKF TFKPPTNEKL SLKFRNGLTL SPVTHRICAV PR // ID IPI00387615.1 IPI; PRT; 752 AA. AC IPI00387615; DT 18-NOV-2003 (IPI Rat rel. 1.9, Created) DT 18-NOV-2003 (IPI Rat rel. 1.9, Last sequence update) OS Rattus norvegicus (Rat). OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; OC Mammalia; Eutheria; Rodentia; Sciurognathi; Muridae; Murinae; Rattus. OX NCBI_TaxID=10116; CC -!- CHROMOSOME: 7. DR InterPro; IPR009146; Groucho_enhance. DR InterPro; IPR005617; TLE_N. DR InterPro; IPR001680; WD40. DR Pfam; PF03920; TLE_N; 1. DR Pfam; PF00400; WD40; 6. DR PRINTS; PR00320; GPROTEINBRPT. DR PRINTS; PR01850; GROUCHOFAMLY. DR ProDom; PD000018; WD40; 1. DR SMART; SM00320; WD40; 6. DR PROSITE; PS00678; WD_REPEATS_1; 1. DR PROSITE; PS50082; WD_REPEATS_2; 3. DR PROSITE; PS50294; WD_REPEATS_REGION; 2. DR UniParc; UPI000021DDC6; -; -. DR ENSEMBL; ENSRNOP00000030679; ENSRNOG00000005874; M. SQ SEQUENCE 752 AA; 81012 MW; 0AE825C2A074F0FB CRC64; PQGSSHLPQQ LKFTTSDSCD RIKDEFQLLQ AQYHSLKLEC DKLASEKSEM QRHYVMYYEM SYGLNIEMHK QAEIVKRLNG ICAQVLPYLS QEHQQQVLGA IERAKQVTAP ELNSIIRVTD SHPTPTLAPQ QQLQAHQLSQ LQALALPLTP LPVGLQPPSL PAVSAGTGLL SLSALGSQTH LSKEDKNGHD GDTHQEDDGE NSSPSPPESL AEEEHPSSRD SNGKQQRAED KNMSGPYDSE EDKSDYNLVV DEDQPSEPPS PATTPCGKAP LCIPARRDLT DSPASLASSL GSPLPRSKDL ALNDLSTGTP ASGSCGPSPP QDSSTPGPSS ASHLCQLATQ PAPPTDSIAL RSPLTLSSPF TSSFSLGSHS TLNGDLSMPG SYVSLHLSPQ VSSSVVYGCS PLMAFESHPH LRGSSISLPS IPGAKPAYSF HVSADGQMQP VPFPSDALVG TGIPRHARQL HTLAHGEVVC AVTISSSTQH VYTGGKGCVK VWDVGQPGSK TPVAQLDCLN RDNYIRSCKL LPDGQSLIVG GEASTLSIWD LAAPTPRIKA ELTSSAPACY ALAISPDAKV CFSCCSDGNI VVWDLQNQAM VRQFQGHTDG ASCIDISDYG TRLWTGGLDN TVRCWDLREG RQLQQHDFSS QIFSLGHCPS QDWLAVGMES SHVEVLHVRK PEKYQLRLHE SCVLSLKFAS CGRWFVSTGK DNLLNAWRTP YGASIFQSKE SSSVLSCDIS RNNKYIVTGS GDKKATVYEV VY // ID IPI00360467.2 IPI; PRT; 630 AA. AC IPI00360467; IPI00187611; IPI00187610; DT 02-OCT-2003 (IPI Rat rel. 1.7, Created) DT 18-NOV-2003 (IPI Rat rel. 1.9, Last sequence update) DE SIMILAR TO DIFFERENTIALLY EXPRESSED IN FDCP 6. OS Rattus norvegicus (Rat). OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; OC Mammalia; Eutheria; Rodentia; Sciurognathi; Muridae; Murinae; Rattus. OX NCBI_TaxID=10116; CC -!- CHROMOSOME: 20. DR InterPro; IPR002048; EF-hand. DR InterPro; IPR001849; PH. DR SMART; SM00233; PH; 1. DR PROSITE; PS50222; EF_HAND_2; 1. DR PROSITE; PS50003; PH_DOMAIN; 1. DR REFSEQ_XP; XP_228031; GI:34852250; -. DR UniParc; UPI000021D4C9; -; -. DR ENSEMBL; ENSRNOP00000000597; ENSRNOG00000000502; M. SQ SEQUENCE 630 AA; 73566 MW; 72BCD6025EA53B3F CRC64; MALRKELLKS IWYAFTALDV EKSGKVSKSQ LKVLSHNLYT VLHIPHDPVA LEEHFRDDDD GPVSSQGYMP YLNKYILDKV EEGAFVKEHF DELCWTLTAK KNYRVEGNGN SLLSNQDAFR LWCLFNFLSE DKYPLIMVPD EVEYLLKKLL GSLSLEMGLG ELEELLAQDA QSAQTSGGLS VWQFLELFNS GRCLRGVGQD SLSMAIQEVY QELIQDVLKQ GYLWKRGHLR RNWTERWFQL QPSCLCYFGS EECKEKRGTI PLDAHCCVEV LPDREGKRCM FCVKTASRTY EMSASDTRQR QEWTAAIQTA IRLQAEGKTS LHKDLKQKRR EQREQRERRR AAKEEELLRL QQLQEEKERK LQELELLQEA QRQAERLLQE EEERRRSQHR ELQQALEGQL REAEQARASM QAEMELKKEE AARQRQRIAE LEEMQERLQE ALQLEVKARR DEEAVRLAQT RLLEEEEEKL KQLMHLKEEQ ERYIERAQQE KQELQQEMAL QSRSLQQAQQ QLEEVRQNRQ RADEDVEAAQ RKLRQASTNV KHWNVQMNRL MHPIEPGDKR PTTSSSFTGF QAPPLARRDS SLKRLTRWGS QGNRTLSANS SEQKSLNGGD ETPILALASQ EEKLDAAPEN // ID IPI00357879.1 IPI; PRT; 221 AA. AC IPI00357879; IPI00200108; DT 02-OCT-2003 (IPI Rat rel. 1.7, Created) DT 02-OCT-2003 (IPI Rat rel. 1.7, Last sequence update) DE SIMILAR TO EVECTIN-2. OS Rattus norvegicus (Rat). OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; OC Mammalia; Eutheria; Rodentia; Sciurognathi; Muridae; Murinae; Rattus. OX NCBI_TaxID=10116; CC -!- CHROMOSOME: 9. DR InterPro; IPR001849; PH. DR Pfam; PF00169; PH; 1. DR SMART; SM00233; PH; 1. DR PROSITE; PS50003; PH_DOMAIN; 1. DR UniParc; UPI00001D015B; -; -. DR REFSEQ_XP; XP_217372; GI:34874919; M. DR ENSEMBL; ENSRNOP00000019419; ENSRNOG00000014162; -. SQ SEQUENCE 221 AA; 24547 MW; 36AD3207014E1C66 CRC64; MAFVKSGWLL RQSTILKRWK KNWFDLWSDG HLIYYDDQTR QSIEDKVHMP VDCINIRTGH ECRDIQPPDG KPRDCLLQIV CRDGKTISLC AESTDDCLAW KFTLQDSRTN TAYVGSAILS EETAVAASPP PYAAYATPTP EVYGYGPYSG AYPAGTQVVY AANGQAYAVP YQYPYAGVYG QQPANQVIIR ERYRDSDSDL ALGMLAGAAT GMALGSLFWV F // ID IPI00357880.1 IPI; PRT; 1180 AA. AC IPI00357880; IPI00202522; IPI00203383; DT 02-OCT-2003 (IPI Rat rel. 1.7, Created) DT 02-OCT-2003 (IPI Rat rel. 1.7, Last sequence update) DE SIMILAR TO RETINOBLASTOMA-ASSOCIATED PROTEIN 140. OS Rattus norvegicus (Rat). OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; OC Mammalia; Eutheria; Rodentia; Sciurognathi; Muridae; Murinae; Rattus. OX NCBI_TaxID=10116; CC -!- CHROMOSOME: 16. DR UniParc; UPI00001D0F10; -; -. DR REFSEQ_XP; XP_224590; GI:34876927; M. DR ENSEMBL; ENSRNOP00000020312; ENSRNOG00000015123; -. SQ SEQUENCE 1180 AA; 133887 MW; CDD0A37B36F836BA CRC64; MVDRYQVQSI CEKGLQVGQS KITVLGSPSM GIYLCRYADL LQANPLEAGA VGDVVIFKIM KGKIKSIYDP LSVKSLESML SKSALDPTPK HECHVSKNAS RITSLLAYRA YELTQYYFYE YGFDEVRRRP RHVCPYAVVS FTYKDDVQTP KFVSLSPEKL DVETVMSIDC LKQKIPSSFF HKDTYVGPNE VLKNGMYCSL YEVVEKTRIG SNMECLLQKL EKEKLVLVKP LGDRGYLFLL SPFQMVSSYD HQTGKSRILH ALFLFQEPRC LIVAQKSVTN TTPLEKHENL PDILKITQFL QFSLIQCRKE FKTINTINFH SVVEKYVSEF FKRGFGSGKR EFFMFSYDSR LDDRKFLYSA PRNKSHIDDC LHTYIYQPEM YQLPIFKLKE LFEENWRRQQ FSPLSDYEGQ EEELNGSKMK FGKRNNSRGE TTEPGQQKSS HSLDYDKDRV KELINLIQCT KKNVGGDPDT EDTKSKNVLK RKLEDLPENM RKFAKTSNSS ENYHPYEEPP QSVGLLGHDP NLRLQQEDAC STGDIHKLYN WISETLANAR HSDAFLTETV NKALGLSSSG TYEELKQKCD YELNPTLDKK ECEQPACTKI ENVHFKDAQS PVLEVDAASG KYPPLLSSSE DPNLINVNHF EECSLCPTVS IEHGLLRQHS KSNDDEETEI HWKLIPITGM KSPGEQLVCP PPAEAFPNDP RVINRERSCD YQFPSSPATD TVKGPTEEED TVAAQEKMNR LSEFIYSKTS KAGVQEFVDG LHEKLNTIII KASAKGVNLP PGVSPNHSHT TTTLSSLGRH VVSISSSDFN SKDLFEPLCS EHLKDNSSNE QYSSSMEVEI NQPHHCKELM LTSDHTVPGD TVLEPTEKEI TKSPSDITIS AQPALSNFIS QLEPEVFNSL VKIMKDVQKN TVKFYIHEEE ESVLCKEIKE YLTKLGNTEC HPDQFLERRS NLDKLLIIIQ NEDIAGFIHK VPGLVTLKKL PCVSFAGVDS LDDVKNHTYN ELFVSGGFIV SDESVLNPEV VTIENDEKDE EDMSLDSGDE ISHIEVFSNV HSEILARETK GSSGTDQKKN IQIELQSSLD VQTSLLEDQT YLIDCDERAP IDRVRSEGEN SNSAEQDAYS DFQAYQNQLK MSHQFSHFNV LTHQTFLGTP YALSSTQSQE NENYFLSAYK NLDTEKSPLS // ID IPI00187615.2 IPI; PRT; 771 AA. AC IPI00187615; DT 14-MAR-2003 (IPI Rat rel. 1.0, Created) DT 18-NOV-2003 (IPI Rat rel. 1.9, Last sequence update) OS Rattus norvegicus (Rat). OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; OC Mammalia; Eutheria; Rodentia; Sciurognathi; Muridae; Murinae; Rattus. OX NCBI_TaxID=10116; CC -!- CHROMOSOME: 5. DR InterPro; IPR007087; Znf_C2H2. DR InterPro; IPR007086; Znf_C2H2_sub. DR PRINTS; PR00048; ZINCFINGER. DR ProDom; PD000003; Znf_C2H2; 23. DR SMART; SM00355; ZnF_C2H2; 27. DR PROSITE; PS00028; ZINC_FINGER_C2H2_1; 27. DR PROSITE; PS50157; ZINC_FINGER_C2H2_2; 27. DR UniParc; UPI000021D4CA; -; -. DR ENSEMBL; ENSRNOP00000009023; ENSRNOG00000006896; M. SQ SEQUENCE 771 AA; 91149 MW; 81172C1F5690FD92 CRC64; HKRTHTGEKP YKCNQCGKAF SQNGHLIIHK RTHTGEKPYE CSQCGKAFTD QSQLRIHKKA HTGEKPYKCN QCDKAFLQNI NLRIHKRAHT GEKPYKCNQC DKAFAQNGHL IIHKRTHTGE KPYECIECGK AFADQSQLRI HRRIHTGEKP YKCNQCDKAF AQHSNLRIHK RTHTGEKPYE CNQCDKAFLQ NINLKIHKKA HTGEKPYKCS ECDKCFGCKG SLRIHQRIHT GEKPYKCSEC DKCFVQQSHL TVHQRIHTGE KPYKCSECDK CFGQQSHRSI HQRIHTGEKP YKCSQCDKHF IQESCLRRHQ RIHTGEKPYK CSECDKCFTV KLTLRSHMRI HTGEKPYKCS ECDKCFGRKG SLRIHQRIHT GEKPYKCSEC DKYFGRKGSL RIHQRIHTGE KPYKCSQCDK RFTQESCLRR HQRIHTGDKP YKCCHECDKC FVSNLSLIIH QRIHTGEKPY KCSQCDKYFA RESCLRRHQR SHSGEKPYKC SQCDKYFAQK YYLSIHQRIH TGEKRYKCSQ CDKYFSQESC LRRHQRIHTG EKPYKCSQCD KYFSQKFHLS IHQRIHTGEK PYKCSECDKC FTEKRTLRNH MRIHTGEKPY KCSECDKCFG RKGSLRIHQR IHTGEKPYKC GECDKCFGQQ SHRSIHQRIH TGEKPYKCSQ CDKHFTQESC LRRHQRIHTG DKPYKCCQCD KYFSQEFYLS IHQRIHTGEK PYKCSECDKC FTEKGTLRNH MRLHTGEKPY KCSECDKSFV QQSHLTVHQR SHTGEKPYKC S // ID IPI00357881.1 IPI; PRT; 487 AA. AC IPI00357881; DT 02-OCT-2003 (IPI Rat rel. 1.7, Created) DT 02-OCT-2003 (IPI Rat rel. 1.7, Last sequence update) DE SIMILAR TO RIKEN CDNA E230015L20 GENE. OS Rattus norvegicus (Rat). OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; OC Mammalia; Eutheria; Rodentia; Sciurognathi; Muridae; Murinae; Rattus. OX NCBI_TaxID=10116; CC -!- CHROMOSOME: 16. DR UniParc; UPI00001D0F11; -; -. DR REFSEQ_XP; XP_224591; GI:34876931; M. DR ENSEMBL; ENSRNOP00000036334; ENSRNOG00000028380; -. SQ SEQUENCE 487 AA; 55620 MW; 0DF05F0036590C28 CRC64; MGNKIKIAKY SLRTKQTGHT LKSTQNTYIG SENLSQKKIS TSDTSQAKRE NSRLTFSSPS TDLCKQYSEK DCLRVQKEIS PTASSIRKTV NTSTDTDPAA KQKPCRKPTA AEGMGSGLVC LTQDQLRQIL MLSVNQGNGS MSLPENGEEV TNEQVALKKK EKEASQKWPD PWKPSEILCE KLQVLERSKE QQRKWIEELN KQVEDDQQRK AEEKLIYSKG EEHDRWAVHF DSFKSHPGSQ SRLSSQLTPQ HLESLCVSPD TQELADVSSV DTPPPAVQVK PSEKEQRARP VMDMSVSHGQ KTNFLRSMTA LLDPAQIEER ERRRQKQLEH QKAITAQVEE NRRKKRLEEE QRRKEEQEEE LRLAREREEM QRQYEEDILK QKHKEEIMTL KTNELFHTMQ RAQELAQRLK QEQRIRELTQ KGHDTSRLIQ NLGAHVDCKA STPVSSSRDT EEAANDTRAA ATSTASPKKD TGVQTVQLAF LLSSYGS // ID IPI00357882.1 IPI; PRT; 688 AA. AC IPI00357882; IPI00201389; DT 02-OCT-2003 (IPI Rat rel. 1.7, Created) DT 02-OCT-2003 (IPI Rat rel. 1.7, Last sequence update) DE SIMILAR TO RHO GUANINE NUCLEOTIDE EXCHANGE FACTOR 4 ISOFORM A. OS Rattus norvegicus (Rat). OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; OC Mammalia; Eutheria; Rodentia; Sciurognathi; Muridae; Murinae; Rattus. OX NCBI_TaxID=10116; CC -!- CHROMOSOME: 9. DR InterPro; IPR001331; GDS_CDC24. DR InterPro; IPR001849; PH. DR InterPro; IPR000219; RhoGEF. DR InterPro; IPR001452; SH3. DR ProDom; PD000066; SH3; 1. DR SMART; SM00233; PH; 1. DR SMART; SM00325; RhoGEF; 1. DR SMART; SM00326; SH3; 1. DR PROSITE; PS00741; DH_1; 1. DR PROSITE; PS50010; DH_2; 1. DR PROSITE; PS50003; PH_DOMAIN; 1. DR PROSITE; PS50002; SH3; 1. DR UniParc; UPI00001D015C; -; -. DR ENSEMBL; ENSRNOP00000018935; ENSRNOG00000014035; -. DR REFSEQ_XP; XP_217374; GI:34874641; M. SQ SEQUENCE 688 AA; 77304 MW; F06F63E8714194D5 CRC64; MSGDPEPRLC GGDAVRDPAG LWLELGAACP GAPRCPSESS GPTSGDLGTS SSSSTGVSPG SDSDSSDVGY GILAVTAKQN PKSQVCVYVS GMPDGTLDAV CAEETGSEED LYEDLHSSGH HYSHPRGGGE QLAINEVPGG WPGVMARPPQ PRRGPTTPGG ALRALLRCNL PPGAQRVVVS AVLALLLISD GSAVCAEALW DHVTMDDQEL GFKAGDVIEV MDATNREWWW GRVVDGEGWF PASFVRLRVN QDEPADDYEA PRAGAGEADD SGPEAQSCKD QMRTNVINEI LSTERDYIKH LRDICEGYVR QCRKREDMFS EEQLRTIFGN IEDIYRCQKA FVKALEQKFN TERPHLSELG ACFLEHQADF QIYSEYCNNH PNACVELSRL TKLSKYVYFF EACRLLQRMI DISLDGFLLT PVQKICKYPL QLAELLKYTH PQHRDFKNVE AALHAMKNVA QLINERKRRL ENIDKIAQWQ SSIEDWEGED LLVRSSELIH SGELTRVTQP QARSQQRMFF LFDRQLIYCK KDLLRRDVLY YKGRLDMDDL EVVDVEDGKD RDLHVSVKNA FRLYCGTTGD SHLLCARKPE QKQRWLKAFA REREQVRLDQ ETGFSITELQ RKQAMLNASK QQATGKPKAV GRPGYLTRHK HPSLPASRPQ QQVLVLAEPR RKPSNFWHSI SRLAPFRK // ID IPI00209391.2 IPI; PRT; 634 AA. AC IPI00209391; DT 14-MAR-2003 (IPI Rat rel. 1.0, Created) DT 06-NOV-2003 (IPI Rat rel. 1.8, Last sequence update) DE SIMILAR TO DNA POLYMERASE ALPHA SUBUNIT III (PRIMASE). OS Rattus norvegicus (Rat). OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; OC Mammalia; Eutheria; Rodentia; Sciurognathi; Muridae; Murinae; Rattus. OX NCBI_TaxID=10116; CC -!- CHROMOSOME: 9. DR InterPro; IPR001917; Aminotrans_II. DR InterPro; IPR006162; Ppantne_S. DR PROSITE; PS00599; AA_TRANSFER_CLASS_2; 1. DR PROSITE; PS00012; PHOSPHOPANTETHEINE; 1. DR SWISS-PROT; O89044; PRI2_RAT; -. DR UniParc; UPI00001D015D; -; -. DR REFSEQ_XP; XP_217375; GI:34874606; M. DR ENSEMBL; ENSRNOP00000016828; ENSRNOG00000012486; -. SQ SEQUENCE 634 AA; 72237 MW; 93FE0875A8CB2A4A CRC64; MKPGGGTSSE RHTWQWKMKA AMLIERGGSH CVRGKADTAS SSPPGTRAAR PIKRAPIKRP KPPEPVTLIL AAAERAAVSA GVSSSLVAGW LKNILRVCLE RRETVGLEAC ELTWWDRVAG GVGWVVKMQF SGRTRKKLRL AGDQRNACYP HSLQFYLQPP TENISLTEFE SLAFDRVKLL KAIENLGVSY VKGTEQYQSK LEAEIRKLKF SYRENLEDEY EPRRRDHISH FILRLAYCQS EDLRRWFIQQ EMDLLRFRFS ILPKDKVQSF LKDTHLHFEA ISDEEKTLRE QDIMASSPSL SGVRWESESV YKVPFADALD LFRGRKVYLE DGFAYVPLKD IVAIILNEFR ATLSKALALT ARSLPAVQSD ERLQPLLSHL SHSYTGQDYS TQKSTGKISL DQIDSLSTKS FPPCMRQLHK ALRENHHLRH GGRMQYGLFL KGIGLTLEQA LQFWKQEFIK GKMDPDKFDK GYSYNIRHSF GKEGKRTDYT PFSCMKIILT NPPSQGDFHG CPFRHSDAEL LKQKMQTYKI PASGISQILD LVKGNHYQVA CQKYFEMTHN VDDCGFSLNH PNQFFFESQR ILTGGKDIKK EASHPETPQH KPSTQKTKDA TSALASLDSS LEMDLEGLED YFSK // ID IPI00357883.1 IPI; PRT; 423 AA. AC IPI00357883; DT 02-OCT-2003 (IPI Rat rel. 1.7, Created) DT 02-OCT-2003 (IPI Rat rel. 1.7, Last sequence update) DE SIMILAR TO 60S RIBOSOMAL PROTEIN L5. OS Rattus norvegicus (Rat). OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; OC Mammalia; Eutheria; Rodentia; Sciurognathi; Muridae; Murinae; Rattus. OX NCBI_TaxID=10116; DR InterPro; IPR005484; Ribosomal_L18p. DR InterPro; IPR005485; Ribosomal_L5euk. DR Pfam; PF00861; Ribosomal_L18p; 1. DR PRINTS; PR00058; RIBOSOMALL5. DR UniParc; UPI00001D0F12; -; -. DR REFSEQ_XP; XP_224593; GI:34877118; M. SQ SEQUENCE 423 AA; 46541 MW; F2586BAAB55BE374 CRC64; MKEMSEYQRR GIHSELMPQA VLGGDPMFCA AIQDSGSILA LGLLNRFGMD KIYEGQVEVT EDEHNVESID CQPGALTSYL DAGLAQTTTG NKVFGAMKGA VDRNLSVPPS TKXLPGYDSE SKELNAERSV SPDTMEDMYK KAHAALXENP VYERKPKREV KXKRXKYPKM SLAQKTDRVA QKMGKIHGLM ETIALLGSQT SASMSALRSS KPATEQSPGP LLTALVRDAK PDLPPYLYSL SVLLHVSFFL LLAFKLKLIC LPVAAIPSHN LNEFCKAGLA DVSDMTDQIL WKHAHWQRGS LGSVSGQRGG CEAYDTGLIL FSFQQQHLHP PSYGCSSNKH WKDENDFSTS PACSGSWLET TGLLLILHSA FKVYCPQGHS AFKGGSCGQG VADTVLCIIY WKQVLAHDED RQETKADNMF NHH // ID IPI00187624.1 IPI; PRT; 570 AA. AC IPI00187624; DT 14-MAR-2003 (IPI Rat rel. 1.0, Created) DT 14-MAR-2003 (IPI Rat rel. 1.0, Last sequence update) OS Rattus norvegicus (Rat). OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; OC Mammalia; Eutheria; Rodentia; Sciurognathi; Muridae; Murinae; Rattus. OX NCBI_TaxID=10116; CC -!- CHROMOSOME: 7. DR UniParc; UPI000017DFCB; -; -. DR ENSEMBL; ENSRNOP00000009027; ENSRNOG00000006822; M. SQ SEQUENCE 570 AA; 67562 MW; 19D3025A34B2711B CRC64; MPPNIKWKEL IKVDPDELPR QEELADKLLI SLSKVEVNEL KNEDQENMIH LFRITQSLMK MKAQEVELAL EEVEKAGEEQ AKFENQLKTK VMKLENELEM AQQSAGGRDT RFLRDEIRQL EKQLEQKDRE LEDMEKELDK EKKVNEQLAL RNEEAENENS KLRRENKRLK KKNEQLRQDI IDYQKQIDSQ KESLLSRRGE DSDYRSQLSK KNYELVQYLD EIQTLTEANE KIEVQNQEMR KNLEESVQEM EKMTDEYNRM KAIVHQTDTV MDQIKKENEH YRLQVRELTD LLKAKDEEDD PVMMAVNAKV EEWKLILSSK DDEIIEYQQM LQSLRGKLKN AQLDADKSNI MALKQERDSQ IKMLTEQVEQ YTKEMEKNTF IIEDLKNELR KDKGTSNIYQ QTHYMKIHSK VQILEEKTKE AERTAELAEA DAREKDKELV EALKRLKDYE SGVYGLEDAV IEIKNYKAQI KIRDGEIEVL TKEINKLEMK INDVLDENEA LRERAGLEPK TMIDLTEFRN SKRVKQQQYR AENQILLKEA SDALLEEERL DLKKNSSNGS RKRQKECSLR // ID IPI00187628.2 IPI; PRT; 682 AA. AC IPI00187628; DT 14-MAR-2003 (IPI Rat rel. 1.0, Created) DT 18-NOV-2003 (IPI Rat rel. 1.9, Last sequence update) OS Rattus norvegicus (Rat). OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; OC Mammalia; Eutheria; Rodentia; Sciurognathi; Muridae; Murinae; Rattus. OX NCBI_TaxID=10116; CC -!- CHROMOSOME: 6. DR InterPro; IPR001849; PH. DR InterPro; IPR002017; Spectrin. DR InterPro; IPR001605; Spectrin_PH. DR PRINTS; PR00683; SPECTRINPH. DR SMART; SM00233; PH; 1. DR SMART; SM00150; SPEC; 4. DR PROSITE; PS50003; PH_DOMAIN; 1. DR PROSITE; PS50083; SPEC_REPEAT; 3. DR UniParc; UPI000021D4CB; -; -. DR ENSEMBL; ENSRNOP00000009028; ENSRNOG00000006911; M. SQ SEQUENCE 682 AA; 77871 MW; 52EEC8501FED4AB4 CRC64; EQIIRLQGQV DKQYAGLKDM AEERRRKLEN MYHLFQLKRE ADDLEQWITE KEMVASSQEM GQDFDHVTML RDKFRDFARE TGAIGQERVD NVNSIIERLI DAGHSEAATI AEWKDGLNDM WADLLELIDT RMQLLAASYD LHRYFYTGTE ILGLIDEKHR ELPEDVGLDA STAESFHRVH TAFERELHLL GVQVQQFQDV ATRLQTAYAG EKADAIQSKE QEVSAAWQAL LDACAGRRAQ LVDTADKFRF FSMVRDLLSW MESIIRQIET QERPRDVSSV ELLLKYHQGI KAEINTRAKN FSTCLELGES LLQRQHQASD EIREKLQQVI SRRQEMNDKW EARSDRLHML LEVCQFSRDA SVAEAWLIAQ EPYLASRDFG HTVDSVEKLI KRHEAFEKST ASWAERFAAL EKPTTVLRPS GGQEGRSYWN GVVLTLTSCS QAGGKGQRKA LLGLKLHEGM LLSCDPEQGE ERGPWPQDLQ PPPLPGHHKD EQEKSVGDER PATEPLFKVL DTPLSEGDEP TTLPAQRDLG HTVQMEGYLG RKHDLEGPNK KASNRSWNNL YCVLRNSQLT FYKDAKNLAL GVPYHGEEPL ALRHAICEIA VNYKKKKHVF KLRLSNGSEW LFHGKDEEEM LLWLQGMSTA INESQSIRVK AQSLPLPSLA GPDASVGKKD KEKRFSFFPK KK // ID IPI00195779.1 IPI; PRT; 160 AA. AC IPI00195779; DT 14-MAR-2003 (IPI Rat rel. 1.0, Created) DT 14-MAR-2003 (IPI Rat rel. 1.0, Last sequence update) DE SIMILAR TO MITOCHONDRIAL RIBOSOMAL PROTEIN L30. OS Rattus norvegicus (Rat). OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; OC Mammalia; Eutheria; Rodentia; Sciurognathi; Muridae; Murinae; Rattus. OX NCBI_TaxID=10116; CC -!- CHROMOSOME: 9. DR UniParc; UPI000017FA74; -; -. DR REFSEQ_XP; XP_217378; GI:27682695; M. DR ENSEMBL; ENSRNOP00000024990; ENSRNOG00000018511; -. SQ SEQUENCE 160 AA; 18411 MW; 3B9D6975466B4B3E CRC64; MAGVLRSVFQ RPPGRLQTVK KGAESLIGTE WIRHKFTRSR IPDKVFQPRP EDHEKYGGDP QNPHKLHIVT RIRSTKRRPY WEKDTIKMLG LQKAHSPQIH KNIPSVNAKL KVVKHLIRIQ PLKLPQGLPT EETMSSTCLK STGELVVQWH LKPVEQEAKS // ID IPI00387616.1 IPI; PRT; 189 AA. AC IPI00387616; DT 18-NOV-2003 (IPI Rat rel. 1.9, Created) DT 18-NOV-2003 (IPI Rat rel. 1.9, Last sequence update) OS Rattus norvegicus (Rat). OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; OC Mammalia; Eutheria; Rodentia; Sciurognathi; Muridae; Murinae; Rattus. OX NCBI_TaxID=10116; CC -!- CHROMOSOME: 1. DR InterPro; IPR000953; Chromo. DR SMART; SM00298; CHROMO; 1. DR UniParc; UPI000021DDC7; -; -. DR ENSEMBL; ENSRNOP00000030680; ENSRNOG00000019585; M. SQ SEQUENCE 189 AA; 20616 MW; CCA0DD2CAE13EFAB CRC64; MAAQGATAAV AATTSGIVGE GEPGPGENTS VEGPARSPGR VSPPTPARGE PEVTVEIGET YLCRRPDSTW HSAEVIQSRV NDQEGREEFY VHYVGFNRRL DEWVDKNRLA LTKTVKDAVQ KNSEKYLSEL AEQPERKITR NQKRKHDEIN HVQKVLAPSL LQGPGVLSGP QQSHSNSHVK SGRVLGCLS // ID IPI00387617.1 IPI; PRT; 572 AA. AC IPI00387617; DT 18-NOV-2003 (IPI Rat rel. 1.9, Created) DT 18-NOV-2003 (IPI Rat rel. 1.9, Last sequence update) OS Rattus norvegicus (Rat). OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; OC Mammalia; Eutheria; Rodentia; Sciurognathi; Muridae; Murinae; Rattus. OX NCBI_TaxID=10116; CC -!- CHROMOSOME: 12. DR InterPro; IPR001909; KRAB. DR InterPro; IPR007087; Znf_C2H2. DR InterPro; IPR007086; Znf_C2H2_sub. DR Pfam; PF01352; KRAB; 1. DR Pfam; PF00096; zf-C2H2; 16. DR PRINTS; PR00048; ZINCFINGER. DR ProDom; PD000003; Znf_C2H2; 17. DR SMART; SM00349; KRAB; 1. DR SMART; SM00355; ZnF_C2H2; 17. DR PROSITE; PS50805; KRAB; 1. DR PROSITE; PS00028; ZINC_FINGER_C2H2_1; 16. DR PROSITE; PS50157; ZINC_FINGER_C2H2_2; 17. DR UniParc; UPI000021DDC8; -; -. DR ENSEMBL; ENSRNOP00000030682; ENSRNOG00000000690; M. SQ SEQUENCE 572 AA; 66334 MW; 0B356C4E3FC0A806 CRC64; DAVTYDDVHV NLTREEWALL DPSQKNLYKD VMLETYWNLT AVGYNWEDRN IEEYCQSSRR HGRCERIHTG EKPYEGIQKG ESSAHHSSLQ MHNIIPVGEK PYKCSQCGKA FSQQSHLQRH KRTHTGEKPY KCDQCGKAFS QQSHLQRHKR THTGEKTYKC DQCGKAFAYP GHLRRHERIH TGEKPYKCNE CGKAFAVSTN LRVHKATHTG VKPYKCNECG KAFAQHRHLQ MHKLTHPGEK TYKCDQCGKS FAYHVFLQMH KVTHTGEKTY KCNQCGKAFA YPSRLRRHER IHTGEKPYKC NECGKAFAFS TNLRVHKATH TGVKPYKCNE CGKAFARHGH LQMLKVTHTG EKTYKCDQCG KAFAYHSYFH VHKRTHTGEK PYECDQCGKA FVSHRYLQVH KRTHTGEKPY ECDQCGKAFA HHRNLQVHKR SHTGEKPYEC DQCGKAFVRY EHLQVHKRIH TGEKPYKCSQ CGKAFSQHSH LQGHKRTHHG EKTYKCDQCG KSFAHHVFLQ MHKVTHTGEK TYKCNQCGKA FAYPGHLQRH ESIHTGEKRY KCNECGKAFA FSTNLQIHKA TH // ID IPI00387618.1 IPI; PRT; 122 AA. AC IPI00387618; DT 18-NOV-2003 (IPI Rat rel. 1.9, Created) DT 18-NOV-2003 (IPI Rat rel. 1.9, Last sequence update) OS Rattus norvegicus (Rat). OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; OC Mammalia; Eutheria; Rodentia; Sciurognathi; Muridae; Murinae; Rattus. OX NCBI_TaxID=10116; CC -!- CHROMOSOME: 2. DR UniParc; UPI000021DDC9; -; -. DR ENSEMBL; ENSRNOP00000030683; ENSRNOG00000024052; M. SQ SEQUENCE 122 AA; 13452 MW; 92379F07F64C09DF CRC64; MNDFDTEDLT IAEQRLQHHA DKALTMNNLT FDVIHQGQDL LQYVNEVQAS GKKGPPPCDG HGLCVTTGTR MTINTTASIN EPLPANMGSL KGSAFHLIPH STATLNFMLK KLVLKIFENC FK // ID IPI00387619.1 IPI; PRT; 501 AA. AC IPI00387619; DT 18-NOV-2003 (IPI Rat rel. 1.9, Created) DT 18-NOV-2003 (IPI Rat rel. 1.9, Last sequence update) OS Rattus norvegicus (Rat). OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; OC Mammalia; Eutheria; Rodentia; Sciurognathi; Muridae; Murinae; Rattus. OX NCBI_TaxID=10116; CC -!- CHROMOSOME: 18. DR InterPro; IPR003128; VHP. DR Pfam; PF02209; VHP; 1. DR SMART; SM00153; VHP; 1. DR UniParc; UPI000021DDCA; -; -. DR ENSEMBL; ENSRNOP00000030684; ENSRNOG00000019365; M. SQ SEQUENCE 501 AA; 56490 MW; 3AD925F7CB0F50EE CRC64; SEVWHPICKQ AARAEKKLKV RGLHATFCHS ALRVTLWTCL LPTEPELLLL TSLSFPQHRR TSETSISPPG SSIGSPNRVI CAKVDNEILN YKDLAALPKV KSIYEVQRPN LISYEPHSRY TSDEMLERCG YGEVSRLALS GTLERDKDIY ENLDLRQRRA SSPGYIDSPT YSQQGMSPTF SRSPHHYYRS ALPTPATQPA ATHAASFSAS FNATMSNACF LYASILSGDH CPHAPGPESG RSSPYHSQLD VRSSTPTSYQ APKHFHIPAG ESNIYRKPPI YKRHGDLSTA TKSKTSEDIS QASKYSPAYS PDPYYASESD YWTYHGSPKE PSPSPQDYLG NRDGLTEENM TTARRESLGK LQSGIGRLIL KEEMKARSSS YADPWTPPRS STSNPLISKS ASLPAYRRNG LHRPSHKLLQ EKTNSPTSTK LDMPPFLIYP YELLLVTTRG RNRLPKDVDR TRLERHLSQE EFYQVFGMTI SEFERLALWK RNELKKQARL F // ID IPI00387620.1 IPI; PRT; 302 AA. AC IPI00387620; DT 18-NOV-2003 (IPI Rat rel. 1.9, Created) DT 18-NOV-2003 (IPI Rat rel. 1.9, Last sequence update) OS Rattus norvegicus (Rat). OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; OC Mammalia; Eutheria; Rodentia; Sciurognathi; Muridae; Murinae; Rattus. OX NCBI_TaxID=10116; CC -!- CHROMOSOME: 1. DR InterPro; IPR000276; GPCR_Rhodpsn. DR InterPro; IPR000725; Olfact_receptor. DR InterPro; IPR000731; SSD_5TM. DR PRINTS; PR00237; GPCRRHODOPSN. DR PRINTS; PR00245; OLFACTORYR. DR PROSITE; PS00237; G_PROTEIN_RECEP_F1_1; 1. DR PROSITE; PS50262; G_PROTEIN_RECEP_F1_2; 1. DR PROSITE; PS50156; SSD; 1. DR UniParc; UPI000021DDCB; -; -. DR ENSEMBL; ENSRNOP00000030685; ENSRNOG00000022065; M. SQ SEQUENCE 302 AA; 33269 MW; DB2D939B810EA00C CRC64; MSNVTKITGF ILMGFSDVPE LQTVCGLFFL VMYLAVIMSN FLIITLITLD LKLQTPMYFF LKNLSLLDVL FISVPIPNFF INSITHNNSI SILGCALQVI LMTSFASGDL FVLTAMSYDR YIAICSPLHY EAIMSRSNCV LMAGVSWATG VLFGTLYTAC TFSMPFCGSC VIAQFFCDVP SLLRISCSDT LVVIYTSLGI GVCLGISCFI CVVISYFYIF STVLKIRTTK GQSKAFATCL PHLTVFSVFI ATACFDYLKP PSNTASIADR VFSVLYIVLP PSLNPVIYSL RNTDIKGALR RL // ID IPI00387621.1 IPI; PRT; 493 AA. AC IPI00387621; DT 18-NOV-2003 (IPI Rat rel. 1.9, Created) DT 18-NOV-2003 (IPI Rat rel. 1.9, Last sequence update) OS Rattus norvegicus (Rat). OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; OC Mammalia; Eutheria; Rodentia; Sciurognathi; Muridae; Murinae; Rattus. OX NCBI_TaxID=10116; CC -!- CHROMOSOME: 3. DR InterPro; IPR001909; KRAB. DR InterPro; IPR007087; Znf_C2H2. DR InterPro; IPR007086; Znf_C2H2_sub. DR Pfam; PF01352; KRAB; 1. DR Pfam; PF00096; zf-C2H2; 9. DR PRINTS; PR00048; ZINCFINGER. DR ProDom; PD000003; Znf_C2H2; 12. DR SMART; SM00349; KRAB; 1. DR SMART; SM00355; ZnF_C2H2; 13. DR PROSITE; PS50805; KRAB; 1. DR PROSITE; PS00028; ZINC_FINGER_C2H2_1; 11. DR PROSITE; PS50157; ZINC_FINGER_C2H2_2; 13. DR UniParc; UPI000021DDCC; -; -. DR ENSEMBL; ENSRNOP00000030686; ENSRNOG00000005949; M. SQ SEQUENCE 493 AA; 56939 MW; F46516C858006BB3 CRC64; VVTYDDVHVN FTQEEWALLD PSQKSLYKDV MLETYRNLAA VVILKGMEEV ILGRNPINVI SAVKPFHKAV ISKCIKEHIL EKNPLSVSNV GKPLQVRVVS NSIKEHIRER DPLNVQCDKA FARHSHLQRH QRIHTVEKLY ECNQCGKSFA QNNHFIQHIR THTGKKLYEC KQCNKAFACQ SGLQYHRRTH TGEKPHGCNE CGKTFIYHSY LQIHRRTHTG EKPFECDQCG KAFARNNNLQ VHKTIHTREK LCECKQCGKA ISLVLHRYLQ IHKRTHTGQK SFECNQCGRA FSGNHHLLRH KRIHTGEKPY ECNLCGKDFT RHCSLQTHKR IHTGEKPYEC NQCGKGFVCH SSLKKHKRTH TGEKPYKCSQ CDKAFSSPSG LLYHKRTHNG ERPYECNECG KAFNHNGHLH IHKRTHTGEK PFECDQCGKT FARNNHLLQH KRVHSGEKPY ECKHCGKAFA YYNSLQVHNR THTGEKPYEC NQCGKAFSCT SGL // ID IPI00387622.1 IPI; PRT; 127 AA. AC IPI00387622; DT 18-NOV-2003 (IPI Rat rel. 1.9, Created) DT 18-NOV-2003 (IPI Rat rel. 1.9, Last sequence update) OS Rattus norvegicus (Rat). OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; OC Mammalia; Eutheria; Rodentia; Sciurognathi; Muridae; Murinae; Rattus. OX NCBI_TaxID=10116; CC -!- CHROMOSOME: 7. DR UniParc; UPI000021DDCD; -; -. DR ENSEMBL; ENSRNOP00000030687; ENSRNOG00000026800; M. SQ SEQUENCE 127 AA; 13571 MW; 0BAC8F57BF9AF113 CRC64; PTSAVATLAA SGKLCPLQRA DTSHWNLQSA SQDRTPQAQG REFLSIWGQC SLPLPAIGSP EKSSSRYLKP EFPLGGGKPG KHRSVGLLLF SLRPECSDRL EQSLFNFCAF DTLLRVVGVG RGGSESG // ID IPI00387623.1 IPI; PRT; 482 AA. AC IPI00387623; DT 18-NOV-2003 (IPI Rat rel. 1.9, Created) DT 18-NOV-2003 (IPI Rat rel. 1.9, Last sequence update) OS Rattus norvegicus (Rat). OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; OC Mammalia; Eutheria; Rodentia; Sciurognathi; Muridae; Murinae; Rattus. OX NCBI_TaxID=10116; CC -!- CHROMOSOME: 1. DR InterPro; IPR001695; Lysyl_oxidase. DR InterPro; IPR001190; Srcr_receptor. DR Pfam; PF00530; SRCR; 4. DR PRINTS; PR00258; SPERACTRCPTR. DR ProDom; PD013887; Lysyl_oxidase; 4. DR SMART; SM00202; SR; 4. DR PROSITE; PS00420; SRCR_1; 4. DR PROSITE; PS50287; SRCR_2; 4. DR UniParc; UPI000021DDCE; -; -. DR ENSEMBL; ENSRNOP00000030688; ENSRNOG00000016687; M. SQ SEQUENCE 482 AA; 50559 MW; 365C4E38B6C6A3F0 CRC64; LRLADGPHGC AGRLEVWYSG RWGTVCDDGW DLRDAAVACR VLGCGGALAA PGGAFFGEGT GPVWLSELAC RGSEGQLGIC PHRGWKAHIC SHEEDAGVVC VGQVHPSPCT DKWSSPPRLR LADGPHGCAG RLEVWHGGRW GSVCDDAWDL RDAAVACREL GCGGALAAPG GAFFGEGAGP IILDDLRCRG NETALRFCPA RPWGQHDCHH REDAGAVCDV GHTPGPAGSW PPPASPTAPP EPGPEAGSPQ LRLVAGPSRC SGRLEVWHDG RWGTVCDDSW DMRDSAVVCR ELGCGGPRQP DPAAGRFGWG AGPIWLDDVG CVGTEASLSE CPAASWGKHN CAHNEDVGVT CTEGSLESSQ DPAATPTAGV PVPSGPFRVR LADGPNRCAG RLEVWHAGLW GTVCDDSWDL RDATVACWEL GCGKVRPRVG KTHYGPGTGP IWLDDMGCKG SETSLSDCPS GTWGKHNCDH EEDVVLTCTG TR // ID IPI00187641.2 IPI; PRT; 653 AA. AC IPI00187641; DT 14-MAR-2003 (IPI Rat rel. 1.0, Created) DT 18-NOV-2003 (IPI Rat rel. 1.9, Last sequence update) OS Rattus norvegicus (Rat). OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; OC Mammalia; Eutheria; Rodentia; Sciurognathi; Muridae; Murinae; Rattus. OX NCBI_TaxID=10116; CC -!- CHROMOSOME: 5. DR InterPro; IPR000694; PRO_rich. DR InterPro; IPR002965; P_rich_extensn. DR PRINTS; PR01217; PRICHEXTENSN. DR PROSITE; PS50099; PRO_RICH; 1. DR UniParc; UPI000021D4CC; -; -. DR ENSEMBL; ENSRNOP00000009030; ENSRNOG00000006357; M. SQ SEQUENCE 653 AA; 70620 MW; B19A11088B263BAD CRC64; GLKKRTRKAF GIRKKEKDTD STGSPDRDGM PSPHEPPYHS KAECAREGGK KASKKSNGAP NGFYAEIDWE RYNSPELDEE GYSIRPEEPG YILSLSHKGK HFYSSSESEE EEESHKKFNI KIKPLQSKDV LKNAATVDEL KASIGNIALS PSPVGAIKRN LSSEEVARPR RSTPTPELTS KKPLDDTLAL APLFGPPLES AFDEQKTEVL LDQPEIWGSG QPINPSMESP KLARPFPTGT PPPLPPKAVP ATPPRTGSPL TVATGASSPA RPATPLVPCS STTPPPPPPR PPSRPKLPPG KPGVGDVSRP FSPPIHSSSP PPIAPLARAE STSSISSTNS LSAATTPTVE NEQPSLVWFD RGKFYLTFEG SSRGPSPLTM GAQDTLPVAA AFTETVNAYF KGADPSKCIV KITGEMVLSF PAGITRHFAN NPSPAALTFR VINSSRLEHV LPNPQLLCCD NTQNDANTKE FWVNMPNLMT HLKKVSEQKP QATYYNVDML KYQVSAQGIQ STPLNLAVNW RCEPGSTDLR IDYKYNTDAM TTAVALNNVQ FLVPIDGGVT KLQAVLPPAV WNAEQQRILW KIPDISQKSE NGGVGSLLAR FQLSEGPSKP SPLVVQFTSE GSTLSGCDIE LVGAGYRFSL IKKRFAAGKW IAN // ID IPI00357885.1 IPI; PRT; 1334 AA. AC IPI00357885; IPI00197358; DT 02-OCT-2003 (IPI Rat rel. 1.7, Created) DT 02-OCT-2003 (IPI Rat rel. 1.7, Last sequence update) DE SIMILAR TO TRAF2 AND NCK INTERACTING KINASE, SPLICE VARIANT 4. OS Rattus norvegicus (Rat). OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; OC Mammalia; Eutheria; Rodentia; Sciurognathi; Muridae; Murinae; Rattus. OX NCBI_TaxID=10116; CC -!- CHROMOSOME: 9. DR InterPro; IPR001180; Citron. DR InterPro; IPR000719; Prot_kinase. DR InterPro; IPR002290; Ser_thr_pkinase. DR InterPro; IPR008271; Ser_thr_pkin_AS. DR InterPro; IPR001245; Tyr_pkinase. DR ProDom; PD000001; Prot_kinase; 1. DR SMART; SM00036; CNH; 1. DR SMART; SM00220; S_TKc; 1. DR SMART; SM00219; TyrKc; 1. DR PROSITE; PS50011; PROTEIN_KINASE_DOM; 1. DR PROSITE; PS00108; PROTEIN_KINASE_ST; 1. DR PROSITE; PS50219; ROM_MOTIF; 1. DR ENSEMBL; ENSRNOP00000019180; ENSRNOG00000014013; -. DR REFSEQ_XP; XP_217381; GI:34875652; M. DR UniParc; UPI00001D01D8; -; -. SQ SEQUENCE 1334 AA; 151521 MW; ACFC57D29E448F56 CRC64; MLNAEGRHVK TGQLAAIKVM DVTEDEEEEI KLEINMLKKY SHHRNIATYY GAFIKKSPPG HDDQLWLVME FCGAGSITDL VKNTKGNTLK EDWIAYISRE ILRGLAHLHI HHVIHRDIKG QNVLLTENAE VKLVDFGVSA QLDRTVGRRN TFIGTPYWMA PEVIACDENP DATYDYRSDL WSCGITAIEM AEGAPPLCDM HPMRALFLIP RNPPPRLKSK KWCDHSNTAD WCSALLVCTA GVTTVTLLTG AGTLLVCTAG VTTVTLLTGA EQLLKHPFIR DQPNERQVRI QLKDHIDRTR KKRGEKDETE YEYSGSEEEE EEVPEQEGEP SSIVNVPGES TLRRDFLRLQ QENKERSEAL RRQQLLQEQQ LREQEEYKRQ LLAERQKRIE QQKEQRRRLE EQQRREREAR RQQEREQRRR EQEEKRRLEE LERRRKEEEE RRRAEDEKRR VEREQEYIRR QLEEEQRHLE ILQQQLLQEQ AMLLECRWRE MEEHRQAERL QRQLQQEQAY LLSLQHDHRR PHAQQPPPPQ QQDRSKPSYH APEPKPHYDP ADRAREVEDR FRKTNHSSPE AQAKQTGRGL EPPVPSRSES FSNGNSESVH PALQRPAEPQ DPCPPSRSEG LSQSSDSKSE VPEPTQKAWS RSDSDEVPPR VPVRTTSRSP VLSRRDSPLQ GSGQQNSQAG QRNSTSSIEP RLLWERVEKL VPRPGSGSSS GSSNSGSQPG SHPGSQSGSG ERFRVRSSSK SEGSPSQRLE NAAKKPEDKK EVFRPLKPAV RDLTALAKEL RAVEDVRPPH KVTDYSSSSE ESGTTDEEEE DVEQEGADDS TSGPEDTRAA SSLNLSNGET ESVKTMIVHD DVESEPAMTP SKEGTLIVRQ STVDQKRASH HESNGFAGRI HLLPDLLQQS HSSSTSSTSS SPSSSQPTPT MSPQTPQDKL TANETQSASS TLQKHKSSSS FTPFIDPRLL QISPSSGTTV TSVVGFSCDG LRPEAIRQDP TRKGSVVNVN PTNTRPQSDT PEIRKYKKRF NSEILCAALW GVNLLVGTES GLMLLDRSGQ GKVYPLISRR RFQQMDVLEG LNVLVTISGK KDKLRVYYLS WLRNKILHND PEVEKKQGWT TVGDLEGCVH YKVVKYERIK FLVIALKSSV EVYAWAPKPY HKFMAFKSFG ELVHKPLLVD LTVEEGQRLK VIYGSCAGFH AVDVDSGSVY DIYLPTHIQC TIKPHAIIIL PNTDGMELLV CYEDEGVYVN TYGRITKDVV LQWGEMPTSV AYIRSNQTMG WGEKAIEIRS VETGHLDGVF MHKRAQRLKF LCERNDKVFF ASVRSGGSSQ VYFMTLGRTS LLSW // ID IPI00357886.1 IPI; PRT; 675 AA. AC IPI00357886; IPI00211915; DT 02-OCT-2003 (IPI Rat rel. 1.7, Created) DT 02-OCT-2003 (IPI Rat rel. 1.7, Last sequence update) DE SIMILAR TO ZAP70 PROTEIN. OS Rattus norvegicus (Rat). OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; OC Mammalia; Eutheria; Rodentia; Sciurognathi; Muridae; Murinae; Rattus. OX NCBI_TaxID=10116; CC -!- CHROMOSOME: 9. DR InterPro; IPR000719; Prot_kinase. DR InterPro; IPR002290; Ser_thr_pkinase. DR InterPro; IPR000980; SH2. DR InterPro; IPR001245; Tyr_pkinase. DR InterPro; IPR008266; Tyr_pkinase_AS. DR PRINTS; PR00401; SH2DOMAIN. DR PRINTS; PR00109; TYRKINASE. DR ProDom; PD000001; Prot_kinase; 1. DR ProDom; PD000093; SH2; 2. DR SMART; SM00252; SH2; 2. DR SMART; SM00220; S_TKc; 1. DR SMART; SM00219; TyrKc; 1. DR PROSITE; PS50011; PROTEIN_KINASE_DOM; 1. DR PROSITE; PS00109; PROTEIN_KINASE_TYR; 1. DR PROSITE; PS50001; SH2; 2. DR REFSEQ_XP; XP_217382; GI:34875595; M. DR UniParc; UPI00001D01D9; -; -. DR ENSEMBL; ENSRNOP00000023036; ENSRNOG00000016995; -. SQ SEQUENCE 675 AA; 76346 MW; 8AC560FBD0402391 CRC64; MPDPAAHLPF FYGSISRAEA EEHLKLAGMA DGLFLLRQCL RSLGGYVLSL VHDVRFHHFP IERQLNGTYA IAGGKAHCGP AELCQFYSQD PDGLPCNLRK PCNRPPGLEP QPGVFDCLRD AMVRDYVRQT WKLEEGDLRP GGGSPNNLQT QGDALEQAII SQAPQVEKLI ATTAHERMPW YHSSLTREEA ERKLYSGQQT DGKFLYVGQG DPVDEGPGLK SWEPVTPFPP PFRLRPRKEQ GTYALSLVYG KTVYHYLISQ DKAGKYCIPE GTKFDTLWQL VEYLKLKADG LIYRLKEVCP NSSASAEAAA PTLPAHPSTF TQPHRRIDTL NSDGYTPEPA RLDKPRPMPM DTSVYESPYS DPEELKDKKL FLKRENLLVA DIELGCGNFG SVRQGVYRMR KYDGSFRLGV GIRAEELKQI DVAIKVLKQS TEKADKDEMM REAQIMHQLD NPYIVRLIGV CQAEALMLVM EMAGGGPLHK FLIGKKEEIP VSNVAELLHQ VAMGMKYLEE KNFVHRDLAA RNVLLVNRHY AKISDFGLSK ALGADDSYYT ARSAGKWPLK WYAPECINFR KFSSRSDVWS YGVTMWEAFS YGQKPYKKMK GPEVLDFIKQ GKRMECPPEC PPEMYALMSD CWIYKWEDRP DFVAVEQRMR TYYYSMASRA EGPPQCEQVA EAACG // ID IPI00187642.2 IPI; PRT; 1031 AA. AC IPI00187642; DT 14-MAR-2003 (IPI Rat rel. 1.0, Created) DT 18-NOV-2003 (IPI Rat rel. 1.9, Last sequence update) DE SIMILAR TO RIKEN CDNA 2410141F18. OS Rattus norvegicus (Rat). OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; OC Mammalia; Eutheria; Rodentia; Sciurognathi; Muridae; Murinae; Rattus. OX NCBI_TaxID=10116; CC -!- CHROMOSOME: 5. DR InterPro; IPR003347; TF_JmjC. DR InterPro; IPR003349; TF_JmjN. DR InterPro; IPR002999; Tudor. DR InterPro; IPR001965; Znf_PHD. DR SMART; SM00558; JmjC; 1. DR SMART; SM00545; JmjN; 1. DR SMART; SM00249; PHD; 1. DR SMART; SM00333; TUDOR; 2. DR REFSEQ_XP; XP_216428; GI:34869001; -. DR UniParc; UPI000021D4CD; -; -. DR ENSEMBL; ENSRNOP00000009031; ENSRNOG00000006644; M. SQ SEQUENCE 1031 AA; 117017 MW; 92355727401A48DB CRC64; PVRVRSEQLS PSAEQVFQRF PKPSGEAALS SLSFGWQTSV AIMEVVEVES PLNPSCKIMT FRPSMEEFRE FNKYLAYMES KGAHRAGLAK VIPPKEWKPR QCYDDIDNLL IPAPIQQMVT GQSGLFTQYN IQKKPMTVKE FRQLANSSKY CTPRYLDYED LERKYWKNLT FVAPIYGADI NGSIYDEGVD EWNIARLNTV LDVVEEECGI SIEGVNTPYL YFGMWKTTFA WHTEDMDLYS INYLHFGEPK YAIPPEHGKR LERLAQGFFP SSSQGCDAFL RHKMTLISPS VLKKYGIPFD KITQEAGEFM ITFPYGYHAG FNHGFNCAES TNFATVRWID YGKVAKLCTC RNDMVKISMD IFVKKFQPDR YQIWKQGKDI YTIDHTKPTP ESTPEVKTWL QRRKKLRKAP KSLQGNKSLS KRPKAEEDEE FAEFIGEEVS SPAVCPRHLK VTEKPEKFKL ANIGASSEKE ASDTRIQVDQ SLTNDTKLSG KSCINSSVID EIQPENDTAN AVTSPSTLKK ASDLIPFSHG HITGKESRLL KILQLESPKI PSSLAESNRV LTEGEENDEE GHASNLEPGE VPDALSEERN GLNVPKIIEG QPKTTKSWRH PLGKPPARSP MTLVKQQVAS DEELPEVLSI DEEVEETESW AKPLIHLWQT KSPNFMAEQE YNATVAKMEP NCAICTLLMP YYKPDXSKEE NDSRWETAVN EVVQSGRKTK PIIPEMCFIY SEENVEYSPP NAFLEEDGTS LLISCSKCFV RVHASKSDFP LSRVSECCLC NLRGGALKQT KNNQWAHVIC AVAVPEVRFT NVPERTQIDV DRIPLQRLKL KCIFCRQRVK RVSGACIQCS YGRCPASFHV TCAHAAGVLM EPDDWPYVVN ITCFRHRVNS NVKSKTCEKA ISVGQTVITK HRNTRYYSCR VIDVTSQIFY EVMFDDGSFS RDTFPEDIVS RNCVKLGPPA EGEVIQVKWP DGKLYGAKYL GSNVAYMYQV EFEDGSQIAM KREDIYTLDE ELPKRVKARF VSANDKCYVQ T // ID IPI00387624.1 IPI; PRT; 134 AA. AC IPI00387624; DT 18-NOV-2003 (IPI Rat rel. 1.9, Created) DT 18-NOV-2003 (IPI Rat rel. 1.9, Last sequence update) OS Rattus norvegicus (Rat). OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; OC Mammalia; Eutheria; Rodentia; Sciurognathi; Muridae; Murinae; Rattus. OX NCBI_TaxID=10116; CC -!- CHROMOSOME: 10. DR InterPro; IPR003309; Treg_SCAN. DR SMART; SM00431; LER; 1. DR PROSITE; PS50804; SCAN_BOX; 1. DR UniParc; UPI000021DDCF; -; -. DR ENSEMBL; ENSRNOP00000009032; ENSRNOG00000021872; M. SQ SEQUENCE 134 AA; 15563 MW; 5F03F38428B641DB CRC64; EEEGLMIVKV EDCSWEQEPA QPVNSRESEA CRQRFRQFCY RDAGGPHEAF SQLWELCCRW LRPELNSKEQ ILELLVLEQF LAVLPGEIQA RVRTQHLGSG EEAVALVEDI QNHPLFLKRD GQERCWMSAL PLKL // ID IPI00187645.2 IPI; PRT; 415 AA. AC IPI00187645; DT 14-MAR-2003 (IPI Rat rel. 1.0, Created) DT 18-NOV-2003 (IPI Rat rel. 1.9, Last sequence update) OS Rattus norvegicus (Rat). OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; OC Mammalia; Eutheria; Rodentia; Sciurognathi; Muridae; Murinae; Rattus. OX NCBI_TaxID=10116; CC -!- CHROMOSOME: 2. DR InterPro; IPR001237; Postsynaptic. DR InterPro; IPR001440; TPR. DR Pfam; PF00515; TPR; 7. DR ProDom; PD012428; Postsynaptic; 1. DR SMART; SM00028; TPR; 7. DR PROSITE; PS50005; TPR; 4. DR PROSITE; PS50293; TPR_REGION; 2. DR UniParc; UPI000021D4CE; -; -. DR ENSEMBL; ENSRNOP00000016250; ENSRNOG00000012149; M. SQ SEQUENCE 415 AA; 46242 MW; D746DE3FD41F5BA3 CRC64; MREDHSFHVR YRMEASCLEL ALEGERLCKS GDCRAGVSFF EAAVQVGTED LKTLSAIYSQ LGNAYFYLHD YAKALEYHHH DLTLARTIGD QLGEAKASGN LGNTLKVLGN FDEAIVCCQR HLDISRELND KVGEARALYN LGNVYHAKGK SFGCPGPQDV GEFPEEVRLA LQAAVELYEE NLSLVTALGD RAAQGRAFGN LGNTHYLLGN FRDAVIAHEQ RLLIAKEFGD KAAERRAYSN LGNAYIFLGE FETASEYYRK TLLLARQLKD RAVEAQSCYS LGNTYTLLQD YEKAIEYHLK HLAIAQELKD RIGEGRACWS LGNAYTALGN HDQAMHFAEK HLEISREVGD KSGELTARLN LSDLQMVLGL SYSTNNSMMS ENIEIDGSLH GAGTKLGRRH SMENMELMKL TPEKV // ID IPI00387625.1 IPI; PRT; 379 AA. AC IPI00387625; DT 18-NOV-2003 (IPI Rat rel. 1.9, Created) DT 18-NOV-2003 (IPI Rat rel. 1.9, Last sequence update) OS Rattus norvegicus (Rat). OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; OC Mammalia; Eutheria; Rodentia; Sciurognathi; Muridae; Murinae; Rattus. OX NCBI_TaxID=10116; CC -!- CHROMOSOME: 5. DR InterPro; IPR006548; ELAD_HUD_SF. DR InterPro; IPR002343; Hud_Sxl_RNA. DR InterPro; IPR000504; RNA_rec_mot. DR PRINTS; PR00961; HUDSXLRNA. DR SMART; SM00360; RRM; 3. DR TIGRFAMs; TIGR01661; ELAV_HUD_SF; 1. DR PROSITE; PS50102; RRM; 3. DR PROSITE; PS00030; RRM_RNP_1; 2. DR UniParc; UPI000021DDD0; -; -. DR ENSEMBL; ENSRNOP00000009034; ENSRNOG00000006853; M. SQ SEQUENCE 379 AA; 41453 MW; AA356B035B32A64D CRC64; RRQRDSSERC CRPAARAVGA AAEPQQASVI AAMETQLSNG PTCNNTANGP TTVNNNCSSP VDSGNTEDSK TNLIVNYLPQ NMTQEELKSL FGSIGEIESC KLVRDKITGQ SLGYGFVNYI DPKDAEKAIN TLNGLRLQTK TIKVSYARPS SASIRDANLY VSGLPKTMTQ KELEQLFSQY GRIITSRILV DQVTGISRGV GFIRFDKRIE AEEAIKGLNG QKPPGATEPI TVKFANNPSQ KTNQAILSQL YQSPNRRYPG PLAQQAQRFS RFSPMTIDGM TSLAGINIPG HPGTGWCIFV YNLAPDADES ILWQMFGPFG AVTNVKVIRD FNTNKCKGFG FVTMTNYDEA AMAIASLNGY RLGDRVLQVS FKTNKTHKA // ID IPI00357887.1 IPI; PRT; 392 AA. AC IPI00357887; IPI00206291; IPI00205232; DT 02-OCT-2003 (IPI Rat rel. 1.7, Created) DT 02-OCT-2003 (IPI Rat rel. 1.7, Last sequence update) DE SIMILAR TO LECTIN, MANNOSE-BINDING 2-LIKE. OS Rattus norvegicus (Rat). OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; OC Mammalia; Eutheria; Rodentia; Sciurognathi; Muridae; Murinae; Rattus. OX NCBI_TaxID=10116; CC -!- CHROMOSOME: 9. DR InterPro; IPR000834; Peptidase_M14. DR PROSITE; PS00133; CARBOXYPEPT_ZN_2; 1. DR UniParc; UPI00001D01DA; -; -. DR REFSEQ_XP; XP_217385; GI:34875582; M. DR ENSEMBL; ENSRNOP00000021111; ENSRNOG00000015699; -. SQ SEQUENCE 392 AA; 44443 MW; 0743A36B082732E9 CRC64; MAAAPRPSWW QRWRRRAWAR DGARLLLFLL LLGSGSGPGP LHVRAGQAVE YLKREHSLSK PYQGVGTSSS SLWNLMGNAM VMTQYIRLTP DMQSKQGALW NRVPCFLKDW ELQVHFKIHG QGKKNLHGDG LAIWYTKDRM QPGPVFGNMD KFVGLGVFVD TYPNEEKQHE VMASAHQTLA RCRGKTSITS VFCSVKISGD SGGPLRGHSG LSLRVFPYIS AMVNNGSLSY DHERDGRPTE LGGCTAIVRN IRYDTFLVIR YVKRHLTIMM DIDGRHEWRD CIEMPGVRLP RGYYFGTSSI TGDLSDNHDV ISLKLFELTG VRTPEEEKLH RDVFLPSVDN LKLPEMTEPP TPLSGLALFL IVFFSLVFSV FAIVIGIILY NKWQDHSRKR FY // ID IPI00187650.2 IPI; PRT; 360 AA. AC IPI00187650; IPI00362742; DT 14-MAR-2003 (IPI Rat rel. 1.0, Created) DT 18-NOV-2003 (IPI Rat rel. 1.9, Last sequence update) DE HYPOTHETICAL PROTEIN XP_346743. OS Rattus norvegicus (Rat). OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; OC Mammalia; Eutheria; Rodentia; Sciurognathi; Muridae; Murinae; Rattus. OX NCBI_TaxID=10116; CC -!- CHROMOSOME: 5. DR InterPro; IPR006548; ELAD_HUD_SF. DR InterPro; IPR002343; Hud_Sxl_RNA. DR InterPro; IPR000504; RNA_rec_mot. DR PRINTS; PR00961; HUDSXLRNA. DR SMART; SM00360; RRM; 3. DR TIGRFAMs; TIGR01661; ELAV_HUD_SF; 1. DR PROSITE; PS50102; RRM; 3. DR PROSITE; PS00030; RRM_RNP_1; 2. DR REFSEQ_XP; XP_346744; GI:34869592; -. DR ENSEMBL; ENSRNOP00000009035; ENSRNOG00000006853; M. DR UniParc; UPI0000001765; -; -. SQ SEQUENCE 360 AA; 39577 MW; 780CDD07F2E97D74 CRC64; METQLSNGPT CNNTANGPTT VNNNCSSPVD SGNTEDSKTN LIVNYLPQNM TQEELKSLFG SIGEIESCKL VRDKITGQSL GYGFVNYIDP KDAEKAINTL NGLRLQTKTI KVSYARPSSA SIRDANLYVS GLPKTMTQKE LEQLFSQYGR IITSRILVDQ VTGISRGVGF IRFDKRIEAE EAIKGLNGQK PPGATEPITV KFANNPSQKT NQAILSQLYQ SPNRRYPGPL AQQAQRFRLD NLLNMAYGVK SRFSPMTIDG MTSLAGINIP GHPGTGWCIF VYNLAPDADE SILWQMFGPF GAVTNVKVIR DFNTNKCKGF GFVTMTNYDE AAMAIASLNG YRLGDRVLQV SFKTNKTHKA // ID IPI00187654.2 IPI; PRT; 72 AA. AC IPI00187654; DT 14-MAR-2003 (IPI Rat rel. 1.0, Created) DT 18-NOV-2003 (IPI Rat rel. 1.9, Last sequence update) OS Rattus norvegicus (Rat). OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; OC Mammalia; Eutheria; Rodentia; Sciurognathi; Muridae; Murinae; Rattus. OX NCBI_TaxID=10116; CC -!- CHROMOSOME: 9. DR UniParc; UPI000021D4CF; -; -. DR ENSEMBL; ENSRNOP00000009036; ENSRNOG00000024627; M. SQ SEQUENCE 72 AA; 8701 MW; 2509D815B88E9CE1 CRC64; VCVCVYVYIC IYIYIYIYIY YIMCSVGVHR YIFVSCMYVC MYVCMYVSIY LSIYLSIYLS IYLSNLSIIY VI // ID IPI00187656.2 IPI; PRT; 121 AA. AC IPI00187656; DT 14-MAR-2003 (IPI Rat rel. 1.0, Created) DT 18-NOV-2003 (IPI Rat rel. 1.9, Last sequence update) OS Rattus norvegicus (Rat). OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; OC Mammalia; Eutheria; Rodentia; Sciurognathi; Muridae; Murinae; Rattus. OX NCBI_TaxID=10116; CC -!- CHROMOSOME: 1. DR InterPro; IPR000096; Serum_amyloid_A. DR Pfam; PF00277; SAA; 1. DR PRINTS; PR00306; SERUMAMYLOID. DR ProDom; PD002112; Serum_amyloid_A; 1. DR SMART; SM00197; SAA; 1. DR PROSITE; PS00992; SAA; 1. DR UniParc; UPI000021D4D0; -; -. DR ENSEMBL; ENSRNOP00000016254; ENSRNOG00000012117; M. SQ SEQUENCE 121 AA; 13622 MW; BFDB3D829FB1252C CRC64; MKLLTSLLLC SLTLGVSSSW LSFVKEAYQG TKDMWRAYSD MRKANWKNSD KYFHARGNYD AARRGPGGAW AAKVISDARE GIQRLIGHGA EDSRADQFAN KWGRSGKDPN HFRPAGLPRK Y // ID IPI00357888.1 IPI; PRT; 1167 AA. AC IPI00357888; IPI00214211; DT 02-OCT-2003 (IPI Rat rel. 1.7, Created) DT 02-OCT-2003 (IPI Rat rel. 1.7, Last sequence update) DE SIMILAR TO XPG. OS Rattus norvegicus (Rat). OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; OC Mammalia; Eutheria; Rodentia; Sciurognathi; Muridae; Murinae; Rattus. OX NCBI_TaxID=10116; CC -!- CHROMOSOME: 9. DR InterPro; IPR000513; Exo_N_I. DR InterPro; IPR001044; XPGC_DNA_repair. DR InterPro; IPR006084; XPGC_Rad. DR InterPro; IPR006086; XPG_I. DR InterPro; IPR006085; XPG_N. DR PRINTS; PR00853; XPGRADSUPER. DR PRINTS; PR00066; XRODRMPGMNTG. DR SMART; SM00484; XPGI; 1. DR SMART; SM00485; XPGN; 1. DR TIGRFAMs; TIGR00600; rad2; 1. DR PROSITE; PS50183; 53EXO_I_DOMAIN; 1. DR PROSITE; PS50182; 53EXO_N_DOMAIN; 1. DR PROSITE; PS00841; XPG_1; 1. DR PROSITE; PS00842; XPG_2; 1. DR REFSEQ_XP; XP_217387; GI:34875746; M. DR UniParc; UPI00001D01DB; -; -. DR ENSEMBL; ENSRNOP00000014836; ENSRNOG00000022812; -. SQ SEQUENCE 1167 AA; 130411 MW; 4D8BAB77359437C9 CRC64; MGVQGLWKLL ECSGRPVSPE ALEGKVLAVD ISIWLNQALK GVRDRHGNAI ENAHLLTLFH RLCKLLFFRI RPIFVFDGDA PLLKKQTLAK RRQKKDSASI DSRKTTEKLL KTFLKRQALK TAFRSKRQEG HSGCRHSLDS AVLSVSVNNR GIQREDDIYV LPPLQEEEKH SSEEEDEKQW QARMDQKQAL QEEFFHNPHA IDIESEDFSS LPPEVKHEIL TDMKEFTKRR RTLFEAMPEE SNDFSQYQLK GLLKKNYLNQ HIENVQKEMN QEHSGQIQRQ YEDEGGFLKE VESRRVVAED TSHYILIKGI QGKKVVDVDL ESLPSSSKEH SVSFNLKSSP YEKVKPESEP EATPPSPRTL HAIQVAMLGG SSEEEPESGE GGQSKERSAW ATADAGSISP QTCAAIQRAL DDDEEERMCA SSDNLAVEML LGNGLKQEHA DEVVVKGGGV PLDTASLLPS VTEVEECVAS ASNDKEQTAS THASSTACHP GEVPKETVSP AHVVSEASQI SSECEVAGRP VPLPSAFIET PCSYASGVLS ERELTLAPPI RTHSHQRTSI DPEEPELQNG LCPPKNTCNS SHLSSDDETE GGQNPASKAG STVHVPSEAV GNVENVSSSN AEEHGDFQKT IQLWEMPEAA ARELISAPES LGPVEMESEE SESDGSFIEV QSVISNDELQ IESSEISKHL SEKDAEEPKE TLEEGSPRNT ECLLQDSSDI KAMKEHRKED RGAEDSPDEW QDVNLEELDA LESNLLAEQN SLEAQKQQQD RIAASVTGQM FLESQELLRL FGIPYIQAPM EAEAQCAILD LTDQTSGTIT DDSDIWLFGA RHVYKNFFNK NKFVEYYQYV DFYNQLGLDR NKLINLAYLL GSDYTEGIPT EIELKGRYTG VLQEPLKVGE WWHKAQNNKK AAENPYDTKV KKKLRKLQLT PGFPNPAVAD AYLRPVVDDS RGSFLTFCQR YFGWNRMKTD ESLYPVLKQL NAHQTQLRID SFFRLAQQEK QDAKHIKSHR LSRAVTCMLR KEREETAGEL KKVPETLDKA NGKTQKRSQP NTRETSVPKR RRPSGNGGFL GNSYLSELPQ ESSSEEAEGS SMISAQQRRA AESSNVSCSD LPDLVRDTPH GRDGYMSTSS SSEDGEDKAK AVLVTARPVF GKKKGKLKNM RRRKKKI // ID IPI00187658.2 IPI; PRT; 287 AA. AC IPI00187658; DT 14-MAR-2003 (IPI Rat rel. 1.0, Created) DT 18-NOV-2003 (IPI Rat rel. 1.9, Last sequence update) OS Rattus norvegicus (Rat). OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; OC Mammalia; Eutheria; Rodentia; Sciurognathi; Muridae; Murinae; Rattus. OX NCBI_TaxID=10116; CC -!- CHROMOSOME: 4. DR InterPro; IPR000058; Znf_AN1. DR Pfam; PF01428; zf-AN1; 1. DR SMART; SM00154; ZnF_AN1; 1. DR UniParc; UPI000021D4D1; -; -. DR ENSEMBL; ENSRNOP00000016255; ENSRNOG00000024296; M. SQ SEQUENCE 287 AA; 31225 MW; F2F77B5EB7F14306 CRC64; MARVLSSDPG DNAVLNHHRE PGSHKNRLLS PLLCVAPVSL HNSLVKPQRQ SKCFESGNPS ASTSQNTLRE LDIRTIADSP FSRTARFRGV KVDSPGKRSD VISKVEARDI TEMANKASKE PVGCVNNNGF LASLARSASR DSLHSTRGVG RLRSSGIGLS TNFQHFQDEN IRKSSPQSEP TDFFLSARGI GMNGSNAAAG KRIGESTHHL PPVKAPLQTK KKVTKHCFLC GKKTGLATSF ECRCGNNFCA SHRYAEAHGC TYDYKSTGRR YLQEANPVVN APKLPKI // ID IPI00357889.1 IPI; PRT; 304 AA. AC IPI00357889; IPI00212510; DT 02-OCT-2003 (IPI Rat rel. 1.7, Created) DT 02-OCT-2003 (IPI Rat rel. 1.7, Last sequence update) DE SIMILAR TO 28S RIBOSOMAL PROTEIN S9, MITOCHONDRIAL PRECURSOR (MRP-S9). OS Rattus norvegicus (Rat). OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; OC Mammalia; Eutheria; Rodentia; Sciurognathi; Muridae; Murinae; Rattus. OX NCBI_TaxID=10116; CC -!- CHROMOSOME: 9. DR InterPro; IPR000754; Ribosomal_S9. DR ProDom; PD001627; Ribosomal_S9; 1. DR UniParc; UPI00001D01DC; -; -. DR REFSEQ_XP; XP_217388; GI:34875660; M. DR ENSEMBL; ENSRNOP00000021899; ENSRNOG00000016201; -. SQ SEQUENCE 304 AA; 35140 MW; 522ACFE7CB9CD80B CRC64; MAAPCMSCGR GLSLRLAHAV RANLCQRPGY WTAPAVGWQT GSRSQLLKLI HTTVVTTKKN AQASRQESYT EDFIRKQIEE FNLGKRHLAN MMGEDPETFT EEDIDRAIAY LFPSGLFEKR ARPMMKHPEQ IFPKQRAIQW GEDGRPFHFL FYTGKQSYYS LMHDVYGKVL QLEKHRGPLS ENTESRDLIG SRWLIKEELE EMLVEKLSDQ DYTQFIRLLE KLLTLPCGPA EEDFVQRFRR SVTVQSKKQL IEPVQYDEQG MAFSTSEGRR KSATARVVVY QHGSGKIHVN GVDYLLYFPI LQDR // ID IPI00187662.2 IPI; PRT; 442 AA. AC IPI00187662; DT 14-MAR-2003 (IPI Rat rel. 1.0, Created) DT 18-NOV-2003 (IPI Rat rel. 1.9, Last sequence update) OS Rattus norvegicus (Rat). OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; OC Mammalia; Eutheria; Rodentia; Sciurognathi; Muridae; Murinae; Rattus. OX NCBI_TaxID=10116; CC -!- CHROMOSOME: 1. DR InterPro; IPR008081; FragX_IP. DR Pfam; PF05994; FragX_IP; 1. DR PRINTS; PR01698; CYTOFMRPINTP. DR UniParc; UPI000021D4D2; -; -. DR ENSEMBL; ENSRNOP00000016256; ENSRNOG00000011945; M. SQ SEQUENCE 442 AA; 50864 MW; CC7E035B421517F2 CRC64; MAAQVTLEDA LSNVDLLEEL PLPDQQPCIE PPPSSLLYQP NFNTNFEDRN AFVTGIARYI EQATVHSSMN EMLEEGQEYA VMLYTWRSCS RAIPQVKCNE QPNRVEIYEK TVEVLEPEVT KLMNFMYFQR NAIERFCGEV RRLCHAERRK DFVSEAYLIT LGKFINMFAV LDELKNMKCS VKNDHSAYKR AAQFLRKMAD PQSIQESQNL SMFLANHNKI TQSLQQQLEV ISGYEELLAD IVNLCVDYYE NRMYLTPSEK HMLLKVMGFG LYLMDGSVSN IYKLDAKKRI NLSKIDKYFK QLQVVPLFGD MQIELARYIK TSAHYEENKS RWTCTSSSSS PQYNICEQMI QIREDHMRFI SELARYSNSE VVTGSGRQEA QKTDAEYRKL FDLALQGLQL LSQWSAHVME VVGTAFVTCV DVGVTVTPSC LEVLLLQTLA MS // ID IPI00357890.1 IPI; PRT; 116 AA. AC IPI00357890; IPI00214202; DT 02-OCT-2003 (IPI Rat rel. 1.7, Created) DT 02-OCT-2003 (IPI Rat rel. 1.7, Last sequence update) DE HYPOTHETICAL PROTEIN XP_217389. OS Rattus norvegicus (Rat). OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; OC Mammalia; Eutheria; Rodentia; Sciurognathi; Muridae; Murinae; Rattus. OX NCBI_TaxID=10116; CC -!- CHROMOSOME: 9. DR UniParc; UPI00001CA9D9; -; -. DR REFSEQ_XP; XP_217389; GI:27683137; M. DR ENSEMBL; ENSRNOP00000015490; ENSRNOG00000011591; -. SQ SEQUENCE 116 AA; 12857 MW; A2194141167E73D0 CRC64; MDQHLHTAQQ PLRLGTPQED VFAGPSVESD MIESSLHSIQ KFVPTDYASY TQEHYHFAGK KIIIQESIEN YGTVVWPGVR IATFVVQLSG DKTFCTSVLP ATGHVPSYLC AFATNE // ID IPI00387626.1 IPI; PRT; 508 AA. AC IPI00387626; DT 18-NOV-2003 (IPI Rat rel. 1.9, Created) DT 18-NOV-2003 (IPI Rat rel. 1.9, Last sequence update) OS Rattus norvegicus (Rat). OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; OC Mammalia; Eutheria; Rodentia; Sciurognathi; Muridae; Murinae; Rattus. OX NCBI_TaxID=10116; CC -!- CHROMOSOME: 10. DR InterPro; IPR000048; IQ_region. DR PROSITE; PS50096; IQ; 1. DR UniParc; UPI000021DDD1; -; -. DR ENSEMBL; ENSRNOP00000030691; ENSRNOG00000021425; M. SQ SEQUENCE 508 AA; 55809 MW; 28314F9A16F81C44 CRC64; MSSECLLPYY TAHSYRSMGV FNTSMGNLQR QLYKGGEYDI FKYAPMFESD FIQISKKGEV IDVHNRVRMV TVCIASTSPV LPLPDVMLLA RPAKVCEEHA RRARFIKGRG YKPSKTLELT RLLPLKFVKI SIHDHEKQQL RLKLATGRTF YLQLCPSSDA REDLFCYWEK LVYLLRPPVN SCISNPSIPT ADTSTETKST LVSLARAGTP TSPVSGVISI AATTSKSPGS GQVATGLTGT ASKDQERSES SKAMAVVANI TTESVDVVLA GAASFTSESP SAEGDAYGSP DTGLNVAFAG SITTKGPAED KPEAPLVSTL QSEGYMCERD GSQKVSHTSS ETQKEKRERR ESDRKGSRKS SHHQRTGASR HSSSKDKGRK TSSYRSVSGH GKTREDKKEK GRGSLRDQRH SSSYRSESRT GHKSRKNRPA ASGGFVSKRA TKIRSFFRAF LVRPTLKTEN TSGERGGVDI VTKLVEKQDI ETTVEKSKDL EFSDTMASES MEKIILET // ID IPI00387627.1 IPI; PRT; 62 AA. AC IPI00387627; DT 18-NOV-2003 (IPI Rat rel. 1.9, Created) DT 18-NOV-2003 (IPI Rat rel. 1.9, Last sequence update) OS Rattus norvegicus (Rat). OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; OC Mammalia; Eutheria; Rodentia; Sciurognathi; Muridae; Murinae; Rattus. OX NCBI_TaxID=10116; CC -!- CHROMOSOME: 4. DR InterPro; IPR001762; Disintegrin. DR InterPro; IPR000519; P_trefoil. DR Pfam; PF00200; Disintegrin; 1. DR PRINTS; PR00680; PTREFOIL. DR SMART; SM00050; DISIN; 1. DR PROSITE; PS50214; DISINTEGRIN_2; 1. DR UniParc; UPI000021DDD2; -; -. DR ENSEMBL; ENSRNOP00000030692; ENSRNOG00000022430; M. SQ SEQUENCE 62 AA; 6506 MW; 5D36645C43614602 CRC64; CLVSVPQLLD PPECGNGFIE TGEECDCGTP AECALEGAEC CKKCTLTQDS QCSDGLCCKK CK // ID IPI00387628.1 IPI; PRT; 203 AA. AC IPI00387628; DT 18-NOV-2003 (IPI Rat rel. 1.9, Created) DT 18-NOV-2003 (IPI Rat rel. 1.9, Last sequence update) OS Rattus norvegicus (Rat). OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; OC Mammalia; Eutheria; Rodentia; Sciurognathi; Muridae; Murinae; Rattus. OX NCBI_TaxID=10116; CC -!- CHROMOSOME: 17. DR InterPro; IPR000694; PRO_rich. DR PROSITE; PS50099; PRO_RICH; 1. DR UniParc; UPI000021DDD3; -; -. DR ENSEMBL; ENSRNOP00000030693; ENSRNOG00000027234; M. SQ SEQUENCE 203 AA; 20090 MW; 859B7EEEDFCC3DAE CRC64; MIRGAPAPMA EPPPVIFCHD SPKRVLVSVI RTTPATPPCS SVGEPEPPPP LVPTSPGFSD FMVYPWRWGE NAHNVTLSPG AAGGVVSAGL PAATELPTLR GAPPSSASVA AVSGGEDEEE ASSPDSGHLK VSGSGPRRGA AWGPLTARLG SGAGPGRKIG AAGAVADRTL TSLPRAKTGP LGARLSRDGC GAKAGLRAAG ATG // ID IPI00387629.1 IPI; PRT; 300 AA. AC IPI00387629; DT 18-NOV-2003 (IPI Rat rel. 1.9, Created) DT 18-NOV-2003 (IPI Rat rel. 1.9, Last sequence update) OS Rattus norvegicus (Rat). OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; OC Mammalia; Eutheria; Rodentia; Sciurognathi; Muridae; Murinae; Rattus. OX NCBI_TaxID=10116; CC -!- CHROMOSOME: 1. DR InterPro; IPR007087; Znf_C2H2. DR InterPro; IPR007086; Znf_C2H2_sub. DR Pfam; PF00096; zf-C2H2; 9. DR PRINTS; PR00048; ZINCFINGER. DR ProDom; PD000003; Znf_C2H2; 8. DR SMART; SM00355; ZnF_C2H2; 9. DR PROSITE; PS00028; ZINC_FINGER_C2H2_1; 9. DR PROSITE; PS50157; ZINC_FINGER_C2H2_2; 9. DR UniParc; UPI000021DDD4; -; -. DR ENSEMBL; ENSRNOP00000030694; ENSRNOG00000019416; M. SQ SEQUENCE 300 AA; 34202 MW; C0DFCACA2481A850 CRC64; RRGVRKTPGT LAVRPMGDPL WERRGIDVKN VTCPSVGYRV SKPIRHTGEK PYKCEECGKG FTRASTLLDH QRGHTGNKPY QCGACWKSFC HSSEFNNHIR VHTGEKPYVC EECGKGFSQA SHLLAHQRGH TGEKPYKCST CGKGFSRSSD LNVHCRIHTG EKPYKCERCG KAFSRVSILQ VHQRVHSEDK PYQCSECGKG FSVESHLQAH QRSHTGERPY QCEECGRGFC RASNFLAHRG VHTGEKPYQC DVCGKRFRQR SYLHDHHRIH TGEKPYRCEE CGKVFSWSSY LKAHQRVHTG // ID IPI00387630.1 IPI; PRT; 150 AA. AC IPI00387630; DT 18-NOV-2003 (IPI Rat rel. 1.9, Created) DT 18-NOV-2003 (IPI Rat rel. 1.9, Last sequence update) OS Rattus norvegicus (Rat). OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; OC Mammalia; Eutheria; Rodentia; Sciurognathi; Muridae; Murinae; Rattus. OX NCBI_TaxID=10116; CC -!- CHROMOSOME: 2. DR UniParc; UPI000021DDD5; -; -. DR ENSEMBL; ENSRNOP00000030695; ENSRNOG00000013336; M. SQ SEQUENCE 150 AA; 16830 MW; 2E0D32C009790C2B CRC64; SVVRCLWHPK LNQIMVGTGN GLAKVYYDPN KSQRYFMGMA SEVNNESGIK QNWLIGYTHA LPMFREPRQR STRKQLEKDR LDPLKSHKPE PPVAGPGRGG RVGTHGGTLS SYIVKNIALD KTDDSNPREA ILRHAKAAED NPYWVSPAYS // ID IPI00187671.2 IPI; PRT; 752 AA. AC IPI00187671; DT 14-MAR-2003 (IPI Rat rel. 1.0, Created) DT 18-NOV-2003 (IPI Rat rel. 1.9, Last sequence update) OS Rattus norvegicus (Rat). OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; OC Mammalia; Eutheria; Rodentia; Sciurognathi; Muridae; Murinae; Rattus. OX NCBI_TaxID=10116; CC -!- CHROMOSOME: 3. DR InterPro; IPR000345; CytC_heme_BS. DR InterPro; IPR001680; WD40. DR Pfam; PF00400; WD40; 2. DR SMART; SM00320; WD40; 3. DR PROSITE; PS00190; CYTOCHROME_C; 1. DR PROSITE; PS00678; WD_REPEATS_1; 1. DR PROSITE; PS50082; WD_REPEATS_2; 1. DR PROSITE; PS50294; WD_REPEATS_REGION; 1. DR UniParc; UPI000021D4D3; -; -. DR ENSEMBL; ENSRNOP00000023479; ENSRNOG00000017422; M. SQ SEQUENCE 752 AA; 83784 MW; 63A60DBCF114C23F CRC64; MKVVPEKNAV RILWGRERGT RAMGAQRLLQ ELVEDKTRWM KWEGKRVELP DSPRSTFLLA FSPDRTLLAS THVNHNIYIT EVKTGKCVHS LIGHRRTPWC VTFHPTISGL IASGCLDGEV RIWDLHGGSE SWFTDSNNAI ASLAFHPTAQ LLLIATANEI HFWDWSRREP FAVVKTASEM ERVRLVRFDP LGHYLLTAIV NPSNQQGDDE PEIPIDGTEL SHYRQRALLQ SQPVRRTPLL HNFLHMLSSR SSGIQVGEQS TVQDSATPSP PPPPPQPSTE RPRTSAYIRL RQRVSYPTTV ECCQHPGILC LCSRCAGTRV PSLLPHQDSV PPASARATTP SFSFVQTEPF HPPEQASSTQ QDQGLLNRPS AFSTVQSSTA GNTLRNLSLG PTRRSLGGPL SSHPSRYHRE LAPGLTGSEW TRTVLTLNSR SEVESMPPPR TSASSVSLLS VLRQQEGGSQ ASVYTSATEG RGFPSSGLAT ESDGGNGSSQ NNSGNIRHEL QCDLRRFFLE YDRLQELDQS LSGETPQTQQ AQEMLNNNIE SERPGPSHQP TPHSSENNSN LSRGHLNRCR ACHNLLTFNN DTLRWERTTP NYSSGEASSS WHVSTTFEGM PPSGNQLPPL ERTEGQMPNS SRLELSSSAS SQEERTVGVA FNQETGHWER IYTQSSRSGT VSQEALHQDM PEESSEEDSL RRLSPAAYYA QRMIQYLSRR DSIRQRSMRY QQNRLRSSTS SSSSDNQGPS VEGTDLEFED FE // ID IPI00387631.1 IPI; PRT; 740 AA. AC IPI00387631; IPI00372660; DT 18-NOV-2003 (IPI Rat rel. 1.9, Created) DT 18-NOV-2003 (IPI Rat rel. 1.9, Last sequence update) DE SIMILAR TO DIOXIN INDUCIBLE FACTOR 3. OS Rattus norvegicus (Rat). OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; OC Mammalia; Eutheria; Rodentia; Sciurognathi; Muridae; Murinae; Rattus. OX NCBI_TaxID=10116; CC -!- CHROMOSOME: 10. DR REFSEQ_XP; XP_340866; GI:34872932; -. DR UniParc; UPI000021DDD6; -; -. DR ENSEMBL; ENSRNOP00000030697; ENSRNOG00000027860; M. SQ SEQUENCE 740 AA; 83986 MW; 57FC26E482817D59 CRC64; MARLVAVCRD GEEEFPFERR QIPLYIDDTL TMVMEFPDNV LNLDGHQNNG AQLKQFIQRH SMLKQQDLSI AMVVTSREVL SALSQLVPCV GCRRSVERLF SQLVESGNPA LEPLTVGPKG VLSLTRSCMT DAKKLYTLFY VHGSKLNDMI DAIPKSKKNK RCQLHSLDTH KPKPLGEGSS SSVSSEKLST DKRSSEDHRK DSKCRIIFHY GPFQGTARGC WMDVWELMSQ ECRDEVVLID SSCLLETLET YLRKHRFCTD CKNKVLRAYN ILIGELDCSK EKGYCAALYE GLRCCPHERH IHVCCETDFI AHLLGRAEPE FAGGYERRER HAKTIDIAQE EVLTCLGIHL YERLHRIWQK LRAEEQTWQM LFYLGVDALR KSFEMTVEKV QGISRLEQLC EEFSEEERVR ELKQEKKRQK RKNRRKNKCV CDSPASLHTA DEKAVSQEKE TDFMENSCKA CGSTEDGNTC VEVIVTNENT SCTCPSSGNL LGSPKIKKGM SPHCNGSDCG YSSSMEGSET GSREGSDVAC TEGICNHDEH GEDPCVHHCE DKEDDGDSCV ECWANSEENN TKGKNKKKKK KSKMLKCDEH IQKLGSCITD PGNRETSGNT MHTVFHRDKT KDAHPESCCS TEKGGQPLPW FEHRKNVPQF TEPTEMSFGP DSGKGAKSLV ELLDESECTS DEEIFISQDE IQSFMANNQS FYSNREQYRQ HLKEKFNKYC RLNDHKRPVC SGWLTTAGAN // ID IPI00357891.1 IPI; PRT; 265 AA. AC IPI00357891; IPI00187672; DT 02-OCT-2003 (IPI Rat rel. 1.7, Created) DT 02-OCT-2003 (IPI Rat rel. 1.7, Last sequence update) DE SIMILAR TO HYPOTHETICAL PROTEIN BC015148. OS Rattus norvegicus (Rat). OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; OC Mammalia; Eutheria; Rodentia; Sciurognathi; Muridae; Murinae; Rattus. OX NCBI_TaxID=10116; CC -!- CHROMOSOME: 9. DR InterPro; IPR000379; Ser_estrs. DR PROSITE; PS50187; ESTERASE; 1. DR UniParc; UPI00001D01DD; -; -. DR REFSEQ_XP; XP_217391; GI:34875675; M. DR ENSEMBL; ENSRNOP00000015600; ENSRNOG00000011658; -. SQ SEQUENCE 265 AA; 29328 MW; 7A8098AAB3D4C872 CRC64; MQGDKEFTAV CEGGAVRLDS MSSEGTSGPE VDMNVFPALG CTSVKLKIPF GNKLLDAVCL VPNKNIAYGI ILTHGASGDM NLPHLMSLAS HLASHGFFCL RFTCKGLNIV HRIKAYKAVL NYLKTSGEYK LAGVFLGGRS MGSRAAASVM CHTELDDADD FVRGLICISY PLHHPKQQHK LRDEDLFRIK DPVLFVSGSA DEMCEKNLLE KVAQKMQAPS KIHWIEKANH SMAVKGRSTN DVFKEINTQI LFWIQEITEM DKKCH // ID IPI00199634.2 IPI; PRT; 373 AA. AC IPI00199634; DT 14-MAR-2003 (IPI Rat rel. 1.0, Created) DT 18-NOV-2003 (IPI Rat rel. 1.9, Last sequence update) OS Rattus norvegicus (Rat). OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; OC Mammalia; Eutheria; Rodentia; Sciurognathi; Muridae; Murinae; Rattus. OX NCBI_TaxID=10116; CC -!- CHROMOSOME: 8. DR InterPro; IPR008132; 5HT3_receptor. DR InterPro; IPR008133; 5HT3_receptor_A. DR InterPro; IPR006201; Neur_channel. DR PRINTS; PR01709; 5HT3ARECEPTR. DR PRINTS; PR01708; 5HT3RECEPTOR. DR PRINTS; PR00252; NRIONCHANNEL. DR TIGRFAMs; TIGR00860; LIC; 1. DR PROSITE; PS00236; NEUROTR_ION_CHANNEL; 1. DR UniParc; UPI000021D4D4; -; -. DR ENSEMBL; ENSRNOP00000009041; ENSRNOG00000006595; M. SQ SEQUENCE 373 AA; 42762 MW; 1C03749C9AAB43E5 CRC64; DEKNQVLTTY IWYRQFWTDE FLQWTPEDFD NVTKLSIPTD SIWVPDILIN EFVDVGKSPS IPYVYVHHQG EVQNYKPLQL VTACSLDIYN FPFDVQNCSL TFTSWLHTKK ELGMGWWFLF PVCLRSPKLL SWSQVVIRRR PLFYAVSLLL PSIFLMVVDI VGFCLPPDSG ERVSFKITLL LGYSVFLIIV SDTLPATAIG TPLIGVYFVV CMALLVISLA ETIFIVQLVH KQDLQRPVPD WLRHLVLDRI AWLLCLGEQP MAHRPPATFQ ANKTDDCSGH PTTLFLYSGS LLPAMGNHCS HVGSPQDLEK TSRSRDSPLP PPREASLAVR GLLQELSSIR HSLEKRDEMR EVARDWLRVG YVLDRLLFRI YLL // ID IPI00199381.2 IPI; PRT; 242 AA. AC IPI00199381; DT 14-MAR-2003 (IPI Rat rel. 1.0, Created) DT 18-NOV-2003 (IPI Rat rel. 1.9, Last sequence update) DE SIMILAR TO HYPOTHETICAL PROTEIN FLJ13448. OS Rattus norvegicus (Rat). OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; OC Mammalia; Eutheria; Rodentia; Sciurognathi; Muridae; Murinae; Rattus. OX NCBI_TaxID=10116; CC -!- CHROMOSOME: 9. DR UniParc; UPI00001D0206; -; -. DR REFSEQ_XP; XP_217393; GI:34875875; M. DR ENSEMBL; ENSRNOP00000019391; ENSRNOG00000014456; -. SQ SEQUENCE 242 AA; 27846 MW; EABB9D12A4746C64 CRC64; MIMAARTSQR TLARVASGCR PKSTTVTEAR VRGSARNVRY LAPCGILMNR TLAPWASVLP KEICARTFFR ITTPLVNKRK EYSERRIIGY SMQEMYDVVS GMEDYKHFVP WCKKSDILSR RSGYCKTRLE IGFPPVLERY TSIVTLVKPH LVKASCTDGK LFNHLETVWR FSPGLPGYPR TCTLDFSISF EFRSLLHSQL ATLFFDEVVK QMVAAFERRA CKLYGPETNI PRELMLHEIH HT // ID IPI00187682.1 IPI; PRT; 314 AA. AC IPI00187682; DT 14-MAR-2003 (IPI Rat rel. 1.0, Created) DT 14-MAR-2003 (IPI Rat rel. 1.0, Last sequence update) OS Rattus norvegicus (Rat). OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; OC Mammalia; Eutheria; Rodentia; Sciurognathi; Muridae; Murinae; Rattus. OX NCBI_TaxID=10116; CC -!- CHROMOSOME: 4. DR InterPro; IPR000276; GPCR_Rhodpsn. DR InterPro; IPR000725; Olfact_receptor. DR Pfam; PF00001; 7tm_1; 1. DR PRINTS; PR00237; GPCRRHODOPSN. DR PRINTS; PR00245; OLFACTORYR. DR PROSITE; PS00237; G_PROTEIN_RECEP_F1_1; 1. DR PROSITE; PS50262; G_PROTEIN_RECEP_F1_2; 1. DR UniParc; UPI000017E001; -; -. DR ENSEMBL; ENSRNOP00000016261; ENSRNOG00000012214; M. SQ SEQUENCE 314 AA; 35381 MW; 4FD91206E4833BAF CRC64; MFGNHTSATK FYLVGFPGSE KLHHILFATF CFFYLVTLVG NTVIIVIVCV DKRLQSPMYF FLVHLSILEI LVTTVIVPVM LWGLLLPGIQ VISLAGCVAQ LFLQLALGTT EFSLLGAMAV DRYVAVCNPL RYSVIMNSRT CNSVVIVSWV FGFLYQIWPV YATFHLNYCK SNVLDNFFCD RGQLLKLSCN NTIFIEFILF LMAVFVLFGS LIPTIVSYTY IIATILKIPS ASGRRKAFST CASHFTCVVI GYGCCLFLYV KPKQTQAADY NRVVSLMISI VTPFLNPFIF TLRNDKVIEA LRDGVNRCYH LFKS // ID IPI00357892.1 IPI; PRT; 255 AA. AC IPI00357892; DT 02-OCT-2003 (IPI Rat rel. 1.7, Created) DT 02-OCT-2003 (IPI Rat rel. 1.7, Last sequence update) DE SIMILAR TO AXONEMAL DYNEIN HEAVY CHAIN 7. OS Rattus norvegicus (Rat). OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; OC Mammalia; Eutheria; Rodentia; Sciurognathi; Muridae; Murinae; Rattus. OX NCBI_TaxID=10116; CC -!- CHROMOSOME: 9. DR UniParc; UPI00001CA9F6; -; -. DR REFSEQ_XP; XP_217394; GI:27683329; M. DR ENSEMBL; ENSRNOP00000029647; ENSRNOG00000021645; -. SQ SEQUENCE 255 AA; 29144 MW; 6890EDBEAA00EC94 CRC64; MRRYPTTYTQ SMNTVLVQEM GRFNKLLITI RESCINIQKA IKGLVVMSTE LEEVVSSILN VKIPGMWMGK SYPSLKPLGS YVNDFLARLK FLQQWYEVGP PPVFWLSGFF FTQAFLTGAQ QNYARKFTIP IDLLGFDYEV MDDKEYKNAP EDGVYIHGLF LDGASWNRKT KKLAESHPKV LYDTVPVMWL KPCKKSDIPK RPSYVAPLYK TSERRGTLST TGHSTNFVIA MILPSDQPKE HWIGRGVALL CQLNS // ID IPI00357893.1 IPI; PRT; 426 AA. AC IPI00357893; DT 02-OCT-2003 (IPI Rat rel. 1.7, Created) DT 02-OCT-2003 (IPI Rat rel. 1.7, Last sequence update) DE SIMILAR TO RIKEN CDNA 2610509I15. OS Rattus norvegicus (Rat). OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; OC Mammalia; Eutheria; Rodentia; Sciurognathi; Muridae; Murinae; Rattus. OX NCBI_TaxID=10116; CC -!- CHROMOSOME: 9. DR UniParc; UPI00001D0207; -; -. DR REFSEQ_XP; XP_217395; GI:34875828; M. DR ENSEMBL; ENSRNOP00000032041; ENSRNOG00000028557; -. SQ SEQUENCE 426 AA; 47870 MW; AE6506A80B8C1B13 CRC64; MGQQFVWRLQ SRFSSIRRAS VILQHLRMSK HTETAEVLLE RRGCAGVITL NRPKLLNALS LNMIRQIYPQ LKKWERDPDT FLIIIKGAGG KAFCAGGDIK ALSEAKKAGQ TLSQDLFREE YILNNAIGQQ HRITYSRLNC ISAYTKLHHP VDPVSMCQGI FLRKPEGRTA VRQPDPPQMP CSSAFAFCLK GVGLSVHGQF RVATERSLFA MPETGIGLFP DVGGGYFLPR LQGKLGYFLA LTGFRLKGRD VHRAGIATHF VDSEKLHVLE EELLALKSPS AEDVAGVLES YHAKSKMGQD KSIIFEEHMD KINSCFSANT VEQILENLRQ DGSPFAMEQI KVINKMSPTS LKITLRQLME GSTKTLQEVL TMEYRLTQAC MEGHDFHEGV RAGNGDLYFD QLLLGREIDL DLDIDPERDW IFSTLL // ID IPI00187689.2 IPI; PRT; 145 AA. AC IPI00187689; DT 14-MAR-2003 (IPI Rat rel. 1.0, Created) DT 18-NOV-2003 (IPI Rat rel. 1.9, Last sequence update) OS Rattus norvegicus (Rat). OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; OC Mammalia; Eutheria; Rodentia; Sciurognathi; Muridae; Murinae; Rattus. OX NCBI_TaxID=10116; CC -!- CHROMOSOME: 5. DR InterPro; IPR004931; Pro/parathymosin. DR Pfam; PF03247; Prothymosin; 2. DR UniParc; UPI000021D4D5; -; -. DR ENSEMBL; ENSRNOP00000023480; ENSRNOG00000017437; M. SQ SEQUENCE 145 AA; 15247 MW; 38449C9B2DEA45AF CRC64; TGCSEKPSLH CSVMLCAHCS HLRHPLPPTV SSNADSPAAL SPESSNSTNL TRSIGPPACP TMSDAAVDSS SEITTKDLKE KEAGEEAENG RRAPANGNAQ NEENGEQEAD KDEDEEAEAP AGKPVAEDDE GDDVDTKKQK TDEDD // ID IPI00357894.1 IPI; PRT; 309 AA. AC IPI00357894; IPI00207434; DT 02-OCT-2003 (IPI Rat rel. 1.7, Created) DT 02-OCT-2003 (IPI Rat rel. 1.7, Last sequence update) DE SIMILAR TO HYPOTHETICAL PROTEIN FLJ37953. OS Rattus norvegicus (Rat). OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; OC Mammalia; Eutheria; Rodentia; Sciurognathi; Muridae; Murinae; Rattus. OX NCBI_TaxID=10116; CC -!- CHROMOSOME: 9. DR InterPro; IPR007113; Cupin_region. DR InterPro; IPR003347; TF_JmjC. DR SMART; SM00558; JmjC; 1. DR PROSITE; PS50849; CUPIN; 1. DR UniParc; UPI00001D0208; -; -. DR REFSEQ_XP; XP_217397; GI:34875893; M. DR ENSEMBL; ENSRNOP00000013502; ENSRNOG00000010100; -. SQ SEQUENCE 309 AA; 35811 MW; 25CB40F5510FA96D CRC64; MEHLYPQRKP LVLEGLDLGS CTSKWTVDYL SQVGGTKEVK IHVAAVAQMD FISKNFVYRT LPFNKLVQRA AEETHKEFFI SQDERYYLRS LGEDPRKVRV VDLKQSLKMS DIADIRQQFP SLGEDITFPM FFREEQFFSS VFRISSPGLQ LWTHYDVMDN FLIQVTGKKR ITLFSPRDAQ YLYLSGSKSE VLNIDSPDLD KYPLFPKARR YECSLEAGDV LFIPALWFHN VVSEEFGVGV NVFLKHLPSE CYDTTDTYGN KDPVAASRAM QILDRALKTL AELPEEYRDF YARQMVLRIQ DKAYSKNSE // ID IPI00387632.1 IPI; PRT; 918 AA. AC IPI00387632; IPI00358697; DT 18-NOV-2003 (IPI Rat rel. 1.9, Created) DT 18-NOV-2003 (IPI Rat rel. 1.9, Last sequence update) DE SIMILAR TO WW DOMAIN-CONTAINING PROTEIN 1. OS Rattus norvegicus (Rat). OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; OC Mammalia; Eutheria; Rodentia; Sciurognathi; Muridae; Murinae; Rattus. OX NCBI_TaxID=10116; CC -!- CHROMOSOME: 5. DR InterPro; IPR000008; C2. DR InterPro; IPR000569; HECT. DR InterPro; IPR002349; WW. DR InterPro; IPR001202; WW_Rsp5_WWP. DR PRINTS; PR00403; WWDOMAIN. DR SMART; SM00239; C2; 1. DR SMART; SM00119; HECTc; 1. DR SMART; SM00456; WW; 4. DR PROSITE; PS50004; C2_DOMAIN_2; 1. DR PROSITE; PS50237; HECT; 1. DR PROSITE; PS01159; WW_DOMAIN_1; 4. DR PROSITE; PS50020; WW_DOMAIN_2; 4. DR REFSEQ_XP; XP_342812; GI:34867077; -. DR UniParc; UPI000021DDD7; -; -. DR ENSEMBL; ENSRNOP00000009047; ENSRNOG00000006328; M. SQ SEQUENCE 918 AA; 104600 MW; 92CE12DEA168351B CRC64; MATASPRSDT SDNHSGRLQL KVTVSSAKLK RKKNWFGTAI YTEVIVDGEI KKTAKSSSSS NPKWDEQLIV NVAPQTTLEF RVWSHHTLKA DALLGKATVD LKQVLLTHNR KLEKVKEQLK LSLENKNGIV QTGELTVVLD GLVIEPEAVT NRSSSPPIEI QQNGDAVHEN GDPLTRTTPR LAVEGTIGID NHVSTSTVVP SSCCSHIVNG ENTPSSPPQV ATRPQNTPAP KPLTSEPTSD TVNGESSSVL ADSTSAMGTS LPSEDSTSTS NCTSTTVQEP PVQEPPASSE HSECIPSASA EVGPEARSLI DPDSDSRNNS GFDKVRQPEG CVEPLRPQSG NTNTESLPSG WEQRKDPHGR TYYVDHNTRT TTWERPQPLP PGWERRVDDR GRVYYVDHNT RTTTWQRPTM ESVRNFEQWQ SQRNQLQGAM QQFNQRYLYS ASMLAAENDP YGPLPPGWEK RVDSTDRVYF VNHNTKTTQW EDPRTQGLPN EEPLPEGWEI RYTREGVRYF VDHNTRTTTF KDPRNGKSSV TKGGPQIAYE RSFRWKLAHF RYLCQSNALP SHVKINVSRQ TLFEDSFQQI MALKPYDLRR RLYVIFRGEE GLDYGGLARE WFFLLSHEVL NPMYCLFEYA GKNNYCLQIN PASTINPDHL SYFCFIGRFI AMALFHGKFI DTGFSLPFYK RMLSKKLTIK DLESIDTEFY NSLIWIRDNN IEECGLEMYF SVDMEILGKV TSHDLKLGGS NILVTEENKD EYIGLMTEWR FSRGVQEQTK AFLDGFNEVV PLQWLQYFDE KELEVMLCGM QEVDLADWQR NTVYRHYTRN SKQIIWFWQF VKETDNEVRM RLLQFVTGTC RLPLGGFAEL MGSNGPQKFC IEKVGKDTWL PRSHTCFNRL DLPPYKSYEQ LKEKLLFAIE ETEGFGQE // ID IPI00387633.1 IPI; PRT; 200 AA. AC IPI00387633; DT 18-NOV-2003 (IPI Rat rel. 1.9, Created) DT 18-NOV-2003 (IPI Rat rel. 1.9, Last sequence update) OS Rattus norvegicus (Rat). OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; OC Mammalia; Eutheria; Rodentia; Sciurognathi; Muridae; Murinae; Rattus. OX NCBI_TaxID=10116; CC -!- CHROMOSOME: 1. DR UniParc; UPI000021DDD8; -; -. DR ENSEMBL; ENSRNOP00000023483; ENSRNOG00000017330; M. SQ SEQUENCE 200 AA; 21474 MW; 192C2249F2BD2456 CRC64; MARPSAGRPS ATPPLRRAAA QYLVRVLPAA RGRRWPARAA SHVHVQRAGE RAPQRPHPPR QPHGRQAQAQ PARQQSHRGA AAASSDHRRA QAQEEEEEPP PPATVVAAGA RAIAAKSPVQ PPSGPRRGGG RSGRRTAFSR PPRPFPTRNA KDSSSGFHPV HVQMQEGRSP CPMSGDGEAR EVEERAYTFS VAPPGLIMAE // ID IPI00357896.1 IPI; PRT; 200 AA. AC IPI00357896; DT 02-OCT-2003 (IPI Rat rel. 1.7, Created) DT 02-OCT-2003 (IPI Rat rel. 1.7, Last sequence update) DE SIMILAR TO GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE. OS Rattus norvegicus (Rat). OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; OC Mammalia; Eutheria; Rodentia; Sciurognathi; Muridae; Murinae; Rattus. OX NCBI_TaxID=10116; DR InterPro; IPR000173; GAP_dhdrogenase. DR PRINTS; PR00078; G3PDHDRGNASE. DR PROSITE; PS00071; GAPDH; 1. DR UniParc; UPI00001D020A; -; -. DR REFSEQ_XP; XP_217399; GI:34875883; M. SQ SEQUENCE 200 AA; 21590 MW; EBB2E86D329A0B7E CRC64; MVKVGVNGFG CIWRLVTRVA FCSASGKVEI VAINDPFIDL NYMVYMVQYD STHGKFNSTV KAENGKLVIN GKPITIFQER DPANIKWGDV GAEYVMESTG VFITMEKAGA HLKGGDKRVI ISAPSADAPM FVMGVNHEKY DNPLKIVSNA SCTTNCLAPL AKVIHDNFGI VEGLMTTVHA ITATQPPTLS ISLTIPSQTP // ID IPI00387634.1 IPI; PRT; 188 AA. AC IPI00387634; DT 18-NOV-2003 (IPI Rat rel. 1.9, Created) DT 18-NOV-2003 (IPI Rat rel. 1.9, Last sequence update) OS Rattus norvegicus (Rat). OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; OC Mammalia; Eutheria; Rodentia; Sciurognathi; Muridae; Murinae; Rattus. OX NCBI_TaxID=10116; CC -!- CHROMOSOME: 5. DR InterPro; IPR000719; Prot_kinase. DR InterPro; IPR002290; Ser_thr_pkinase. DR InterPro; IPR008266; Tyr_pkinase_AS. DR Pfam; PF00069; Pkinase; 1. DR ProDom; PD000001; Prot_kinase; 1. DR SMART; SM00220; S_TKc; 1. DR PROSITE; PS50011; PROTEIN_KINASE_DOM; 1. DR PROSITE; PS00109; PROTEIN_KINASE_TYR; 1. DR ENSEMBL; ENSRNOP00000023484; ENSRNOG00000017282; M. DR UniParc; UPI000021DDD9; -; -. SQ SEQUENCE 188 AA; 20919 MW; EEB7BB3967FD85F9 CRC64; YINSGNLEQL LDSNLYLPWT VRVKLAYDIA VGLSYLHFKG IFHRDLTSKN CLIKRDENGY SAVVADFGLA EKIPDASIGS EKLAVVGSPF WMAPEVLRDE PYNEKTCSLT VSSSARSSPA SRLIRTIFPA QRISGWIMML SSTWWETAPQ TSCNSPSTAV ILEAIFTDLL CGRTIFSFLQ GLCLWLTL // ID IPI00187709.1 IPI; PRT; 169 AA. AC IPI00187709; DT 14-MAR-2003 (IPI Rat rel. 1.0, Created) DT 14-MAR-2003 (IPI Rat rel. 1.0, Last sequence update) OS Rattus norvegicus (Rat). OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; OC Mammalia; Eutheria; Rodentia; Sciurognathi; Muridae; Murinae; Rattus. OX NCBI_TaxID=10116; CC -!- CHROMOSOME: 19. DR UniParc; UPI000017E019; -; -. DR ENSEMBL; ENSRNOP00000023486; ENSRNOG00000017482; M. SQ SEQUENCE 169 AA; 18631 MW; E22356951CC6462C CRC64; MPGPRCSAAP DTCRSHRRPG LSELLISPGA VRRRLGRSGR WSFRGLGQET PAAVAAEDTP KRNAAHSPAP ARSRRPDLSR REVSGFSRKR TRAHRRTARS TQRGHSPPGR CPPRSWRPGL DSRGGPLRGF AGHSSPKSRE EWLTTRLPYL SLKAASPSAW NSAWHLATH // ID IPI00209944.1 IPI; PRT; 578 AA. AC IPI00209944; DT 14-MAR-2003 (IPI Rat rel. 1.0, Created) DT 14-MAR-2003 (IPI Rat rel. 1.0, Last sequence update) DE SPLICE ISOFORM REV-ERB-BETA-1 OF Q63504. OS Rattus norvegicus (Rat). OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; OC Mammalia; Eutheria; Rodentia; Sciurognathi; Muridae; Murinae; Rattus. OX NCBI_TaxID=10116; DR UniParc; UPI00001304C8; -; -. DR SWISS-PROT; Q63504-1; NRD2_RAT; M. SQ SEQUENCE 578 AA; 64192 MW; E2E5370D1617AB35 CRC64; MELNAGGVIA YISSSSSASS PASCHSEGSE NSFQSSSSSV PSSPNSSNCD ANGNPKNTDV SSIDGVLKSD RTDCPVKTGK PGAPGMTKSH SGMTKFSGMV LLCKVCGDVA SGFHYGVHAC EGCKGFFRRS IQQNIQYKKC LKNENCSIMR MNRNRCQQCR FKKCLSVGMS RDAVRFGRIP KREKQRMLIE MQSAMKTMMS TQFGGHLQSD TLAEPHEQSV PPAQEQLRPK PQLEQENIKS TPPPSDFAKE EVIGMVTRAH KDTFLYNQEH RENSSESMPP HRGERIPRNV EQYNLNHDHR GGGLHSHFPC SESQQHLSGQ YKGRNMMHYP NGHTVCISNG HCVNFSSAYP QRVCDRIPVG GCSQTESRNS YLCSTGGRMH LVCPMSKSPY VDPQKSGHEI WEEFSMSFTP AVKEVVEFAK RIPGFRDLSQ HDQVNLLKAG TFEVLMVRFA SLFDAKERTV TFLSGKKYSV DDLHSMGAGD LLSSMFEFSE KLNGLQLSDE EMSLFTAVVL VSADRSGIEN VNSVEALQET LIRALRTLIM KNHPNEASIF TKLLLKLPDL RSLNNMHSEE LLAFKVHP // ID IPI00230783.1 IPI; PRT; 383 AA. AC IPI00230783; DT 09-APR-2003 (IPI Rat rel. 1.1, Created) DT 09-APR-2003 (IPI Rat rel. 1.1, Last sequence update) DE SPLICE ISOFORM REV-ERB-BETA-2 OF Q63504. OS Rattus norvegicus (Rat). OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; OC Mammalia; Eutheria; Rodentia; Sciurognathi; Muridae; Murinae; Rattus. OX NCBI_TaxID=10116; DR InterPro; IPR000324; VitD_receptor. DR InterPro; IPR001628; Znf_C4steroid. DR Pfam; PF00105; zf-C4; 1. DR PRINTS; PR00047; STROIDFINGER. DR PRINTS; PR00350; VITAMINDR. DR ProDom; PD000035; Znf_C4steroid; 1. DR SMART; SM00399; ZnF_C4; 1. DR PROSITE; PS00031; NUCLEAR_RECEPTOR; 1. DR UniParc; UPI000002AF96; -; -. DR SWISS-PROT; Q63504-2; NRD2_RAT; M. SQ SEQUENCE 383 AA; 42271 MW; 71C8B3D759D13B35 CRC64; MELNAGGVIA YISSSSSASS PASCHSEGSE NSFQSSSSSV PSSPNSSNCD ANGNPKNTDV SSIDGVLKSD RTDCPVKTGK PGAPGMTKSH SGMTKFSGMV LLCKVCGDVA SGFHYGVHAC EGCKGFFRRS IQQNIQYKKC LKNENCSIMR MNRNRCQQCR FKKCLSVGMS RDAVRFGRIP KREKQRMLIE MQSAMKTMMS TQFGGHLQSD TLAEPHEQSV PPAQEQLRPK PQLEQENIKS TPPPSDFAKE EVIGMVTRAH KDTFLYNQEH RENSSESMPP HRGERIPRNV EQYNLNHDHR GGGLHSHFPC SESQQHLSGQ YKGRNMMHYP NGHTVCISNG HCVNFSSAYP QRVCDRIPVG GCSQTESRNS YLCSTGGRMH LVQ // ID IPI00187712.1 IPI; PRT; 531 AA. AC IPI00187712; DT 14-MAR-2003 (IPI Rat rel. 1.0, Created) DT 14-MAR-2003 (IPI Rat rel. 1.0, Last sequence update) DE MUSCARINIC ACETYLCHOLINE RECEPTOR M5. OS Rattus norvegicus (Rat). OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; OC Mammalia; Eutheria; Rodentia; Sciurognathi; Muridae; Murinae; Rattus. OX NCBI_TaxID=10116; CC -!- CHROMOSOME: 3. DR InterPro; IPR000276; GPCR_Rhodpsn. DR InterPro; IPR000502; M5_receptor. DR InterPro; IPR000995; MusAcC_receptor. DR Pfam; PF00001; 7tm_1; 1. DR PRINTS; PR00237; GPCRRHODOPSN. DR PRINTS; PR00243; MUSCARINICR. DR PRINTS; PR00542; MUSCRINICM5R. DR PROSITE; PS00237; G_PROTEIN_RECEP_F1_1; 1. DR PROSITE; PS50262; G_PROTEIN_RECEP_F1_2; 1. DR UniParc; UPI00001252BF; -; -. DR SWISS-PROT; P08911; ACM5_RAT; M. DR ENSEMBL; ENSRNOP00000008387; ENSRNOG00000006397; -. DR REFSEQ_NP; NP_059058; GI:8393123; -. DR LocusLink; 53949; Chrm5; -. SQ SEQUENCE 531 AA; 60137 MW; 647CE0D5D75A2BB1 CRC64; MEGESYNEST VNGTPVNHQA LERHGLWEVI TIAVVTAVVS LMTIVGNVLV MISFKVNSQL KTVNNYYLLS LACADLIIGI FSMNLYTTYI LMGRWVLGSL ACDLWLALDY VASNASVMNL LVISFDRYFS ITRPLTYRAK RTPKRAGIMI GLAWLVSFIL WAPAILCWQY LVGKRTVPPD ECQIQFLSEP TITFGTAIAA FYIPVSVMTI LYCRIYRETE KRTKDLADLQ GSDSVAEAKK REPAQRTLLR SFFSCPRPSL AQRERNQASW SSSRRSTSTT GKTTQATDLS ADWEKAEQVT TCSSYPSSED EAKPTTDPVF QMVYKSEAKE SPGKESNTQE TKETVVNTRT ENSDYDTPKY FLSPAAAHRL KSQKCVAYKF RLVVKADGTQ ETNNGCRKVK IMPCSFPVSK DPSTKGPDPN LSHQMTKRKR MVLVKERKAA QTLSAILLAF IITWTPYNIM VLVSTFCDKC VPVTLWHLGY WLCYVNSTIN PICYALCNRT FRKTFKLLLL CRWKKKKVEE KLYWQGNSKL P // ID IPI00400455.1 IPI; PRT; 126 AA. AC IPI00400455; DT 10-FEB-2004 (IPI Rat rel. 1.12, Created) DT 10-FEB-2004 (IPI Rat rel. 1.12, Last sequence update) OS Rattus norvegicus (Rat). OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; OC Mammalia; Eutheria; Rodentia; Sciurognathi; Muridae; Murinae; Rattus. OX NCBI_TaxID=10116; CC -!- CHROMOSOME: 6. DR UniParc; UPI000017E01F; -; -. DR ENSEMBL; ENSRNOP00000009051; ENSRNOG00000027670; M. SQ SEQUENCE 126 AA; 14394 MW; 004D5F469EF0F93B CRC64; MAEGDEAARR QQPQQGLRRR RQTSDSSVGV NHVSSTTSLG EDYEDADLVN SDEVMRKPCP VQIVLAHEDD HNFELDEEAL ERILLQEHIR DLNIVVVSVA GAFRKGKSFL LDFMLRYMYN KVNSVF // ID IPI00409505.1 IPI; PRT; 1429 AA. AC IPI00409505; DT 04-MAR-2004 (IPI Rat rel. 1.13, Created) DT 04-MAR-2004 (IPI Rat rel. 1.13, Last sequence update) OS Rattus norvegicus (Rat). OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; OC Mammalia; Eutheria; Rodentia; Sciurognathi; Muridae; Murinae; Rattus. OX NCBI_TaxID=10116; CC -!- CHROMOSOME: 5. DR UniParc; UPI000021D4D6; -; -. DR ENSEMBL; ENSRNOP00000016271; ENSRNOG00000011967; M. SQ SEQUENCE 1429 AA; 158305 MW; 59B3A06F6EB1BB34 CRC64; MDDWHRAFTQ NTLVPPHPQR ARQFGKESTA FQCILKWLDG PLIKQGILDM LSELECHLRV SLFDVTYKHF FGRTWKTTVK PTNQLSKQPP RILFNEPLYF HTTLSHPSIV AVIEVVAEGR KRDGALQVLS CGFGILRIFG NKPESPTSAG QDKRLRLYHG TPRALLHPLL QDPIEQNRYM TMMENCSLQY TLKPHPPLEP AFHLLPENFL ISGLQQIPGL LPPHGDTGDA LRKPRFQKPT TLHLDDLFFT LYPSLEKFEE ELVQLLISDH FREGVGLLDS GTLEVLERRL HVCVHNGLGF VHRPQVVVLV PEMDMTLTRS ASFSRRITAS SKSSSGNQAL VLRSHLRLPE MVNHPSFAIV FQLEYVFNSP SGADGSASSS TSLSSLACMH MVRWAVWNPD LEAGPGKVTL PLQGGVQHNP SRCLVYKVPS ASMSSEEVKQ VESGTIQFHF SLSSDALTEH ANGPRAGRRS TRKALTSPSG TPALAARDLA AIQDSPVGPG LSLSQLAASP QSLASQRSFK PPPQPLDGSQ SPEGPQLQAG SVLESRISHL EADLSQPPFS VQGTPTVEHL QELPFTPLHA PIVVGAQTRS SRSQLSRAAM VLLQSSGFPE ILDARQQPVE AVNPMDPVRF NPQKEESDCL LGNEIVLQFL AFSRAAQDCP GAPWPQTVYF TFQFYRFPPE TTPRLQLVKL DRTGKNGSAS LSHILVHINK DGSFDAGSPG FQLRYMVDPG FLKPGEQRWF AQYLAAQTLQ VDVWDGDSLL LIGSAGIQMK HLLRQGRPAV QVSHELEVVA TEYEQEMMVV SGDVAGFGSV KPIGVHTVVK GRLHLTLANV GHECEPRARG SNALPPSRSR VISNNGASFF SGGSLLIPGG PKRKRVVQAQ KLADVDSELA AMLLTHTRAG QGPQAVGQEA DAVHRRKLER MRLVRLQEAG GDSDSRRISV LARHSVRAQH SRDLQVIDAY RERTKAENIA SVLSQAITTH HTLYATLGTA EFFEFALKNP HNTQHTVAIE IDSPELSIIL DSQEWRYFKE ATGLLTPLEE DMFHLRGSLA PQLYLRPRET AHIPFKFQNF SVGPPAPTQA PAEVISEKDA ESGPHWKCSA MPTKHAKVLF RVETGQLIAV LCLTVEPQPH VVDQVFRFYH PELTFLKKAI RLPPWHTLPG SAPVGMPGED PPVHVRCSDP NVICEAQNVG LGEPRDVFLK VASGPSPEIK DFFVVIYADR WLAVPVQTWQ VCLHSLQRVD VSCVAGQMTR LSLVLRGTQT VRKVRAFTSH PQELKTDPAG VFVLPPHGVQ DLHVGVRPRR AGSRFIHLNL VDVDYHQLVA SWLVCLSCRQ PLISKAFEIT MAAGEGKGAN KRITYTNPYP SRRTYRLHSD RPDLLHFKED SFQVAGGETY TIGLRFLPSG SAGQEEILIY INDQDDKNEE TFCVKVLYQ // ID IPI00187726.2 IPI; PRT; 374 AA. AC IPI00187726; DT 14-MAR-2003 (IPI Rat rel. 1.0, Created) DT 18-NOV-2003 (IPI Rat rel. 1.9, Last sequence update) OS Rattus norvegicus (Rat). OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; OC Mammalia; Eutheria; Rodentia; Sciurognathi; Muridae; Murinae; Rattus. OX NCBI_TaxID=10116; CC -!- CHROMOSOME: 8. DR InterPro; IPR001687; ATP_GTP_A_BS. DR InterPro; IPR000038; GTP_Cell_Div. DR InterPro; IPR008115; Septin7. DR PRINTS; PR01742; SEPTIN7. DR ProDom; PD002565; GTP_Cell_Div; 1. DR PROSITE; PS50101; ATP_GTP_A2; 1. DR UniParc; UPI000021D4D7; -; -. DR ENSEMBL; ENSRNOP00000009055; ENSRNOG00000006545; M. SQ SEQUENCE 374 AA; 43329 MW; C987EC5212D78E8D CRC64; KNLEGYVGFA NLPNQVYRKS VKRGFEFTLM VVGESGLGKS TLINSLFLTD LYSPEYPGPS HRIKKTVQVE QSKVLIKEGG VQLLLTIVDT PGFGDAVDNS NCWQPVIDYI DSKFEDYLNA ESRVNRRQMP DNRVQCCLYF IAPSGHGLKP LDIEFMKRLH EKVNIIPLIA KADTLTPEEC QQFKKQVARI NLHVFQPFLS LIAFITIYNI DRLPLAVVGS NTIIEVNGKR VRGRQYPWGV AEVENGEHCD FTILRNMLIR THMQDLKDVT NNVHYENYRS RKLAAVTYNG VDNNKNKGQL TKSPLAQMEE ERREHVAKMK KMEMEMEQVF EMKVKEKVQK LKDSEAELQR RHEQMKKNLE AQHKELEEKR RQFE // ID IPI00187729.1 IPI; PRT; 218 AA. AC IPI00187729; DT 14-MAR-2003 (IPI Rat rel. 1.0, Created) DT 14-MAR-2003 (IPI Rat rel. 1.0, Last sequence update) OS Rattus norvegicus (Rat). OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; OC Mammalia; Eutheria; Rodentia; Sciurognathi; Muridae; Murinae; Rattus. OX NCBI_TaxID=10116; CC -!- CHROMOSOME: 13. DR InterPro; IPR009263; SERTA. DR Pfam; PF06031; SERTA; 1. DR UniParc; UPI000017E02C; -; -. DR ENSEMBL; ENSRNOP00000009056; ENSRNOG00000006907; M. SQ SEQUENCE 218 AA; 23680 MW; C3A40E7E249DFDAB CRC64; EEGVEGFGTV RSYSLQQESL LDMSLVKLQL CHVLIEPNLC HLVLITSTVP QIEERMCQNG VRHGIAPQSV EWASIDCLVS TEILCHTVRG AEGEHPTSEL EDGLLQSSAS ELPIVGSAQG QRNPQSSLWE MDNAQENRGS LQKSLDQIFE TLENINSSSV EQLSSDVDSY YNLDMLTGMM SGTKSSLCNG LEAPPPPSST CKSGLAELDN IVETLVET // ID IPI00187737.2 IPI; PRT; 105 AA. AC IPI00187737; DT 14-MAR-2003 (IPI Rat rel. 1.0, Created) DT 18-NOV-2003 (IPI Rat rel. 1.9, Last sequence update) OS Rattus norvegicus (Rat). OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; OC Mammalia; Eutheria; Rodentia; Sciurognathi; Muridae; Murinae; Rattus. OX NCBI_TaxID=10116; CC -!- CHROMOSOME: 4. DR UniParc; UPI000021D4D8; -; -. DR ENSEMBL; ENSRNOP00000016275; ENSRNOG00000012165; M. SQ SEQUENCE 105 AA; 11680 MW; 1BB67D432FC8CC77 CRC64; LRTLREALRQ QVAELAFQLG DRARQIKEGI LLLDLLCEEL PEHCTNQPQC NRTEGKHVQR SCVQAHTVAP EPVLPASSRQ STSGSGMTQL DTLSPSDLET TRRMS // ID IPI00187740.1 IPI; PRT; 163 AA. AC IPI00187740; IPI00206581; DT 14-MAR-2003 (IPI Rat rel. 1.0, Created) DT 14-MAR-2003 (IPI Rat rel. 1.0, Last sequence update) DE PEPTIDYL-PROLYL CIS-TRANS ISOMERASE A. OS Rattus norvegicus (Rat). OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; OC Mammalia; Eutheria; Rodentia; Sciurognathi; Muridae; Murinae; Rattus. OX NCBI_TaxID=10116; CC -!- CHROMOSOME: 4. DR InterPro; IPR002130; CSA_PPIase. DR Pfam; PF00160; Pro_isomerase; 1. DR PRINTS; PR00153; CSAPPISMRASE. DR PROSITE; PS00170; CSA_PPIASE_1; 1. DR PROSITE; PS50072; CSA_PPIASE_2; 1. DR UniParc; UPI0000128C93; -; -. DR ENSEMBL; ENSRNOP00000009407; ENSRNOG00000007183; -. DR REFSEQ_NP; NP_058797; GI:8394009; -. DR Superfamily; SSF50891; CSA_PPIase; 1. DR SWISS-PROT; P10111; PPIA_RAT; M. DR LocusLink; 25518; Ppia; -. SQ SEQUENCE 163 AA; 17743 MW; DD16D1C980474414 CRC64; VNPTVFFDIT ADGEPLGRVC FELFADKVPK TAENFRALST GEKGFGYKGS SFHRIIPGFM CQGGDFTRHN GTGGKSIYGE KFEDENFILK HTGPGILSMA NAGPNTNGSQ FFICTAKTEW LDGKHVVFGK VKEGMSIVEA MERFGSRNGK TSKKITISDC GQL // ID IPI00387635.1 IPI; PRT; 643 AA. AC IPI00387635; DT 18-NOV-2003 (IPI Rat rel. 1.9, Created) DT 18-NOV-2003 (IPI Rat rel. 1.9, Last sequence update) OS Rattus norvegicus (Rat). OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; OC Mammalia; Eutheria; Rodentia; Sciurognathi; Muridae; Murinae; Rattus. OX NCBI_TaxID=10116; CC -!- CHROMOSOME: 8. DR InterPro; IPR001909; KRAB. DR InterPro; IPR003309; Treg_SCAN. DR InterPro; IPR007087; Znf_C2H2. DR ProDom; PD000003; Znf_C2H2; 6. DR SMART; SM00349; KRAB; 1. DR SMART; SM00431; LER; 1. DR SMART; SM00355; ZnF_C2H2; 8. DR PROSITE; PS50805; KRAB; 1. DR PROSITE; PS50804; SCAN_BOX; 1. DR PROSITE; PS00028; ZINC_FINGER_C2H2_1; 8. DR PROSITE; PS50157; ZINC_FINGER_C2H2_2; 8. DR UniParc; UPI000017E039; -; -. DR ENSEMBL; ENSRNOP00000009059; ENSRNOG00000006312; M. SQ SEQUENCE 643 AA; 73434 MW; 85E81AC724AB1624 CRC64; MATALELEDQ DLWEEEEEGV LMVKLEDDFT CGPESALQGD DPVLETSHQN FRCFRYQEAS SPREALIRLR ELCHQWLRPE RRTKEQILEL LVLEQFLTVL PGELQSWVRG QRPESGEEAV TLVEGLQKQP RRPRRWVTVH VQGQEVLSEE TLHLGVEPES SNEQQEPTQT LTAEQPHEEA LRSTDLGTLE QESLQHEGER LPLLESEVPV SQHADLPTEQ GSGHPEMVAL LTALSQGLVT FKDVALCFSQ DQWSDLDPTQ KEFYGEYVLE EDCGIVVSLS FPIPRLDDPS QIREEEPQVP GVHESQEPAE PEILSFTYTG DMSEAEEECV EQQDTNKSIL ANTEIHQTPD WEIVIEDNTS RLNERFGTNV SKVNSFTNIR KTMPVHSQSG RQHHCPLCAK SFTCNSHLIR HLRTHTGEKP YKCMECGKSY TRSSHLARHQ KVHKVNTPHK HPPNRKTVDA SQVQSEATTR VEKPYTCDDC GKHFRWTSDL VRHQRTHTGE KPFFCTICGK SFSQKSVLTT HQRIHVGGKP YTCANCGENF SEQKQYLAHR KTHVSEENHL CSECGRSFNH SAAFAKHLKG HASVRNCRCD ECGKSFSRRD HLVRHQRTHT GEKPFTCATC GKSFSRGYHL IRHQRIHTGK TKT // ID IPI00187747.1 IPI; PRT; 184 AA. AC IPI00187747; IPI00196438; DT 14-MAR-2003 (IPI Rat rel. 1.0, Created) DT 14-MAR-2003 (IPI Rat rel. 1.0, Last sequence update) DE RAS-RELATED PROTEIN RAP-1A. OS Rattus norvegicus (Rat). OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; OC Mammalia; Eutheria; Rodentia; Sciurognathi; Muridae; Murinae; Rattus. OX NCBI_TaxID=10116; CC -!- CHROMOSOME: 2. DR InterPro; IPR001806; Ras_trnsfrmng. DR InterPro; IPR005225; Small_GTP. DR Pfam; PF00071; Ras; 1. DR PRINTS; PR00449; RASTRNSFRMNG. DR TIGRFAMs; TIGR00231; small_GTP; 1. DR ENSEMBL; ENSRNOP00000021043; ENSRNOG00000015694; -. DR REFSEQ_XP; XP_215669; GI:27660326; -. DR UniParc; UPI0000001250; -; -. DR SWISS-PROT; P10113; RAPA_HUMAN; M. DR TREMBL; O08813; O08813; -. SQ SEQUENCE 184 AA; 20987 MW; 42C39290C98E0A92 CRC64; MREYKLVVLG SGGVGKSALT VQFVQGIFVE KYDPTIEDSY RKQVEVDCQQ CMLEILDTAG TEQFTAMRDL YMKNGQGFAL VYSITAQSTF NDLQDLREQI LRVKDTEDVP MILVGNKCDL EDERVVGKEQ GQNLARQWCN CAFLESSAKS KINVNEIFYD LVRQINRKTP VEKKKPKKKS CLLL // ID IPI00212760.1 IPI; PRT; 174 AA. AC IPI00212760; DT 14-MAR-2003 (IPI Rat rel. 1.0, Created) DT 14-MAR-2003 (IPI Rat rel. 1.0, Last sequence update) OS Rattus norvegicus (Rat). OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; OC Mammalia; Eutheria; Rodentia; Sciurognathi; Muridae; Murinae; Rattus. OX NCBI_TaxID=10116; CC -!- CHROMOSOME: 9. DR InterPro; IPR009685; MEA1. DR Pfam; PF06910; MEA1; 1. DR UniParc; UPI0000001930; -; -. DR ENSEMBL; ENSRNOP00000023495; ENSRNOG00000017144; M. SQ SEQUENCE 174 AA; 18584 MW; C3B16361635B176F CRC64; MAAVVLGGDT MGPERIFPNQ TEDLGPHQGP TEGTGDWSSE EPEEEQEETG AGPAGYSYQP LNQDPEQEEV ELAPVGEGED GAADIQDRIQ ALGLHLPDPP LESEDEDEEG AAALSSHSSI PMDPEHVELV KRTMAGVSLP APGVPAWARE ISDAQWEDVV QKALQARQAS PAWK // ID IPI00187754.1 IPI; PRT; 344 AA. AC IPI00187754; DT 14-MAR-2003 (IPI Rat rel. 1.0, Created) DT 14-MAR-2003 (IPI Rat rel. 1.0, Last sequence update) DE T-CELL SURFACE ANTIGEN CD2 PRECURSOR. OS Rattus norvegicus (Rat). OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; OC Mammalia; Eutheria; Rodentia; Sciurognathi; Muridae; Murinae; Rattus. OX NCBI_TaxID=10116; CC -!- CHROMOSOME: 2. DR InterPro; IPR008424; CD2. DR InterPro; IPR003599; Ig. DR InterPro; IPR007110; Ig-like. DR Pfam; PF05790; CD2; 1. DR SMART; SM00409; IG; 1. DR REFSEQ_NP; NP_036962; GI:6978627; -. DR ENSEMBL; ENSRNOP00000021268; ENSRNOG00000015821; -. DR Superfamily; SSF48726; Ig-like; 2. DR UniParc; UPI0000127348; -; -. DR SWISS-PROT; P08921; CD2_RAT; M. DR LocusLink; 25299; Cd2; -. SQ SEQUENCE 344 AA; 38414 MW; 41BAED392CE16356 CRC64; MRCKFLGSFF LLFSLSSKGA DCRDSGTVWG ALGHGINLNI PNFQMTDDID EVRWERGSTL VAEFKRKMKP FLKSGAFEIL ANGDLKIKNL TRDDSGTYNV TVYSTNGTRI LDKALDLRIL EMVSKPMIYW ECSNATLTCE VLEGTDVELK LYQGKEHLRS LRQKTMSYQW TNLRAPFKCK AVNRVSQESE MEVVNCPEKG LPLYLIVGVS AGGLLLVFFG ALFIFCICKR KKRNRRRKGE ELEIKASRMS TVERGPKPHS TQASAPASQN PVASQAPPPP GHHLQTPGHR PLPPSHRNRE HQPKKRPPPS GTQVHQQKGP PLPRPRVQPK PPCGSGDVSL PPPN // ID IPI00187768.2 IPI; PRT; 483 AA. AC IPI00187768; DT 14-MAR-2003 (IPI Rat rel. 1.0, Created) DT 18-NOV-2003 (IPI Rat rel. 1.9, Last sequence update) OS Rattus norvegicus (Rat). OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; OC Mammalia; Eutheria; Rodentia; Sciurognathi; Muridae; Murinae; Rattus. OX NCBI_TaxID=10116; CC -!- CHROMOSOME: 4. DR InterPro; IPR001909; KRAB. DR InterPro; IPR007087; Znf_C2H2. DR ProDom; PD000003; Znf_C2H2; 3. DR SMART; SM00349; KRAB; 2. DR SMART; SM00355; ZnF_C2H2; 10. DR PROSITE; PS50805; KRAB; 2. DR PROSITE; PS00028; ZINC_FINGER_C2H2_1; 9. DR PROSITE; PS50157; ZINC_FINGER_C2H2_2; 10. DR UniParc; UPI000021D4D9; -; -. DR ENSEMBL; ENSRNOP00000009063; ENSRNOG00000006925; M. SQ SEQUENCE 483 AA; 56019 MW; 543DB795890D7368 CRC64; FQVLLTFDDV AVCFSDQEWG KLEDWQKELY KHVMRGNYET LVSLDYAISK PEVLSQIEQG KEPCTWRRTG PKVPEVPVDP SPAHSPEQVQ GRKVSLSSPK QREWGLAIYG DISLVFPDPV VWFQVPVTFD DVAVHFSEQE WGNLSEWQKE LYKNVMRGNY ESLVSMDYAI SKPDLMSQME RGERPAMQEQ EDSEEGETPT DPSAVSFICS LCGKSFSRPS HLLRHQRTHT GERPFKCPEC EKSFSEKSKL TNHCRVHSRE RPHACPECGK SFIRKHHLLE HRRIHTGERP YHCAECGKRF TQKHHLLEHQ RAHTGERPYP CTHCAKCFRY KQSLKYHLRT HTGDKERPFS CGECGKGFTR QSKLTEHFRV HSGERPFQCP ECDRSFRLKG QLLSHQRLHT GERPFQCPEC GKSYRVKADM KMHQLLHSGQ MPFSCQCGKG FAKQSKLVEH MRTHTGEKPF QCPKCDKSFR LKAQLLSHQG LHT // ID IPI00187782.2 IPI; PRT; 1099 AA. AC IPI00187782; DT 14-MAR-2003 (IPI Rat rel. 1.0, Created) DT 18-NOV-2003 (IPI Rat rel. 1.9, Last sequence update) OS Rattus norvegicus (Rat). OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; OC Mammalia; Eutheria; Rodentia; Sciurognathi; Muridae; Murinae; Rattus. OX NCBI_TaxID=10116; CC -!- CHROMOSOME: 4. DR InterPro; IPR001060; Cdc15_Fes_CIP4. DR InterPro; IPR000198; RhoGAP. DR InterPro; IPR001452; SH3. DR ProDom; PD000066; SH3; 1. DR SMART; SM00055; FCH; 1. DR SMART; SM00324; RhoGAP; 1. DR SMART; SM00326; SH3; 1. DR PROSITE; PS50133; FCH; 1. DR PROSITE; PS50238; RHOGAP; 1. DR PROSITE; PS50002; SH3; 1. DR UniParc; UPI000021D4DA; -; -. DR ENSEMBL; ENSRNOP00000009066; ENSRNOG00000006509; M. SQ SEQUENCE 1099 AA; 124448 MW; A07EBF0D51D1A976 CRC64; MSSQTKFKKD KEIIAEYEAQ IKEIRTQLVE QFKCLEQQSE SRLQLLQDLQ EFFRRKAEIE LEYSRSLEKL AERFSSKIRS SREHQFKKDQ YLLSPVNCWY LVLHQTRRES RDHATLNDIF MNNVIVRLSQ ISEDVIRLFK KSKEIGLQMH EELLKVTNEL YTVMKTYHMY HAESISAESK LKEAEKQEEK QFNKSGDLSM NLLRHEDRPQ RRSSVKKIEK MKEKRQAKYS ENKLKCTKAR NDYLLNLAAT NAAISKYYIH DVSDLIDCCD LGFHASLART FRTYLSAEYN LETSRHEGLD IIENAVDNLD SRSDKHTVMD MCSQVFCPPL KFEFQPHMGD EVCQVSAQQP VQTELLMRYH QLQSRLATLK IENEEVRKTL DATMQTLQDM LTVEDFDVSD AFQHSRSTES IKSAASETYM SKINIAKRRA NQQETEMFYF TKFKEYVNGS NLITKLQAKH DLLKQTLGEG ERAECGTTRP PCLPPKPQKM RRPRPLSVYS HKLFNGSMEA FIKDSGQAIP LVVESCIRFI NLYGLQQQGI FRVPGSQVEV NDIKNSFERG EDPLVDDQNE RDINSVAGVL KLYFRGLENP LFPKERFQDL ISTIKLENPA DRVHPIQQIL ITLPRVVIVV MRYLFAFLNH LSQYSDENMM DPYNLAICFG PTLMHIPDGQ DPVSCQAHVN EVIKTIIIHH EAIFPSPREL EGPVYEKCMA GGEEYCDSPH SEPGTIDEVD HDNGTEPHTS DEEVEQIEAI AKFDYVGRSP RELSFKKGAS LLLYHRASED WWEGRHNGVD GLIPHQYIVV QDMDDAFSDS LSQKADSEAS SGPLLDDKAS SKNDLQSPTE HISDYGFGGV MGRVRLRSDG AAIPRRRSGG DTHSPPRGLG PSIDTPPRAA ACPSSPHKIP LSRGRIESPE KRRMATFGSA GSINYPDKKA LTEGLSMRST CGSTRHSSLG DHKSLEAEAL AEDIEKTMST ALHELRELER QNTVKQAPDV VLDTLEPLKN PPGPISSEPA SPLHTIVIRD PDAAMRRSSS SSTEMMTTFK PALSARLAGA QLRPPPMRPV RPVVQHRSSS SSSSGVGSPA VTPTEKMFPN SSSDKSGTM // ID IPI00187789.2 IPI; PRT; 98 AA. AC IPI00187789; DT 14-MAR-2003 (IPI Rat rel. 1.0, Created) DT 18-NOV-2003 (IPI Rat rel. 1.9, Last sequence update) OS Rattus norvegicus (Rat). OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; OC Mammalia; Eutheria; Rodentia; Sciurognathi; Muridae; Murinae; Rattus. OX NCBI_TaxID=10116; CC -!- CHROMOSOME: 3. DR UniParc; UPI000021D4DB; -; -. DR ENSEMBL; ENSRNOP00000009068; ENSRNOG00000006884; M. SQ SEQUENCE 98 AA; 11008 MW; C2D5640BC7BC1602 CRC64; MVLAMLGVLY PRAGLSLFLF YLILAGALLR PQPQRSQRSV PEEFSAPLEL LQPLSGLVDD YGLRPKHPRP GGPRPLLSQA QQRKRDGPDM ADYYYDVN // ID IPI00209000.1 IPI; PRT; 4687 AA. AC IPI00209000; DT 14-MAR-2003 (IPI Rat rel. 1.0, Created) DT 14-MAR-2003 (IPI Rat rel. 1.0, Last sequence update) DE SPLICE ISOFORM 1 OF P30427. OS Rattus norvegicus (Rat). OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; OC Mammalia; Eutheria; Rodentia; Sciurognathi; Muridae; Murinae; Rattus. OX NCBI_TaxID=10116; DR UniParc; UPI000013C4C3; -; -. DR SWISS-PROT; P30427-1; PLE1_RAT; M. DR REFSEQ_NP; NP_071796; GI:13540714; -. SQ SEQUENCE 4687 AA; 533540 MW; 9966CAF71B929751 CRC64; MVAGMLMPLD QLRAIYEVLF REGVMVAKKD RRPRSLHPHV PGVTNLQVMR AMTSLKARGL VRETFAWCHF YWYLTNEGID HLRQYLHLPP EIVPASLQRV RRPVAMVMPA RRRSPHVQTM QGPLGCPPKR GPLPAEDPAR EERQVYRRKE REEGAPETPV VSATIVGTLA RPGPEPTPAT DERDRVQKKT STKWVNKHLI KAQRHISDLY EDLRDGHNLI SLLEVLSGDS LPREKGRMRF HKLQNVQIAL DYLRHRQVKL VNIRNDDIAD GNPKLTLGLI WTIILHFKIS DIQVSGQSED MTAKEKLLLW SQRMVEGYQG LRCDNFTTSW RDGRLFNAII HRHKPMLIDM NKVYRQTNLE NLDQAFSVAE RDLGVTRLLD PEDVDVPQPD EKSIITYVSS LYDAMPRVPG AQDGVRANEL QLRWQEYREL VLLLLQWIRH HTAAFEERKF PSSFEEIEIL WCQFLKFKET ELPAKEADKN RSKGIYQSLE GAVQAGQLKI PPGYHPLDVE KEWGKLHVAI LEREKQLRSE FERLECLQRI VSKLQMEAGL CEEQLYQADS LLQSDIRLLA SGKAAQRAGE VERDLDKADG MIRLLFNDVQ TLKDGRHPQG EQMYRRVYRL HERLVAIRTE YNLRLKAGVG APVTQVTLQS TQRRPELEDS TLRYLHDLLA WVEENQRRID GAEWGVDLPS VEAQLGSHRG MHQSIEEFRA KIERARNDES QLSPATRGAY RDCLGRLDLQ YAKLLNSSKA RLRSLESLHG FVAAATKELM WLNEKEEEEV GFDWSDRNTN MAAKKESYSA LMRELEMKEK KIKEIQNTGD RLLREDHPAR PTVESFQAAL QTQWSWMLQL CCCIEAHLKE NTAYFQFFSD VREAEEQLQK LQETLRRKYS CDRSITVTRL EDLLQDAQDE KEQLNEYKGH LSGLAKRAKA IVQLKPRNPA HPVRGHVPLL AVCDYKQVEV TVHKGDQCQL VGPAQPFHWK VLSSSGSEAA VPSVCFLVPP PNQEAQEAVA RLEAQHQALV TLWHQLHVDM KSLLAWQSLN RDIQLIRSWS LVTFRTLKPE EQRQALRNLE LHYQAFLRDS QDAGGFGPED RLVAEREYGS CSRHYQQLLQ SLEQGEQEES RCQRCISELK DIRLQLEACE TRTVHRLRLP LDKDPARECA QRIAEQQKAQ AEVEGLGKGV ARLSAEAEKV LALPEPSPAA PTLRSELELT LGKLEQVRSL SAIYLEKLKT ISLVIRSTQG AEEVLKTHEE HLKEAQAVPA TLQELEVTKA SLKKLRAQAE AQQPVFNTLR DELRGAQEVG ERLQQRHGER DVEVERWRER VTQLLERWQA VLAQTDVRQR ELEQLGRQLR YYRESADPLS SWLQDAKSRQ EQIQAVPIAN SQAAREQLRQ EKALLEEIER HGEKVEECQK FAKQYINAIK DYELQLITYK AQLEPVASPA KKPKVQSGSE SVIQEYVDLR TRYSELTTLT SQYIKFISET LRRMEEEERL AEQQRAEERE RLAEVEAALE KQRQLAEAHA QAKAQAELEA RELQRRMQEE VTRREEAAVD AQQQKRSIQE ELQHLRQSSE AEIQAKAQQV EAAERSRMRI EEEIRVVRLQ LETTERQRGG AEDELQALRA RAEEAEAQKR QAQEEAERLR RQVQDESQRK RQAEAELALR VKAEAEAARE KQRALQALDE LKLQAEEAER WLCQAEAERA RQVQVALETA QRSAEVELQS KRPSFAEKTA QLERTLQEEH VTVTQLREEA ERRAQQQAEA ERAREEAERE LERWQLKANE ALRLRLQAEE VAQQKSLAQA DAEKQKEEAE REARRRGKAE EQAVRQRELA EQELEKQRQL TEGTAQQRLA AEQELIRLRA ETEQGEHQRQ LLEEELARLQ HEATAATQKR QELEAELAKV RAEMEVLLAS KARAEEESRS TSEKSKQRLE AEAGRFRELA EEAARLRALA EEARRHRELA EEDAARQRAE ADGVLTEKLA AISEATRLKT EAEIALKEKE AENERLRRLA EDEAFQRRRL EEQAAQHKAD IEERLAQLRK ASESELERQK GLVEDTLRQR RQVEEEIMAL KASFEKAAAG KAELELELGR IRSNAEDTMR SKELAEQEAA RQRQLAAEEE QRRREAEERV QRSLAAEEEA ARQRKVALEE VERLKAKVEE ARRLRERAEQ ESARQLQLAQ EAAQKRLQAE EKAHAFVVQQ REEELQQTLQ QEQNMLERLR SEAEAARRAA EEAEEAREQA EREAAQSRKQ VEEAERLKQS AEEQAQAQAQ AQAAAEKLRK EAEQEAARRA QAEQAALKQK QAADAEMEKH KKFAEQTLRQ KAQVEQELTT LRLQLEETDH QKSILDEELQ RLKAEVTEAA RQRSQVEEEL FSVRVQMEEL GKLKARIEAE NRALILRDKD NTQRFLEEEA EKMKQVAEEA ARLSVAAQEA ARLRQLAEED LAQQRALAEK MLKEKMQAVQ EATRLKAEAE LLQQQKELAQ EQARRLQADK EQMAQQLVEE TQGFQRTLEA ERQRQLEMSA EAERLKLRMA EMSRAQARAE EDAQRFRKQA EEIGEKLHRT ELATQEKVTL VQTLEIQRQQ SDQDAERLRE AIAELEREKE KLKQEAKLLQ LKSEEMQTVQ QEQILQETQA LQKSFLSEKD SLLQRERFIE QEKAKLEQLF QDEVAKAKQL QEEQQRQQQQ MEQEKQELVA SMEEARRRQR EAEEGVRRKQ EELQRLEQQR QQQEKLLAEE NQRLRERLQR LEEEHRAALA HSEEIATSQA AATKALPNGR DALDGPSMEA EPEYTFEGLR QKVPAQQLQE AGILSMEELQ RLTQGHTTVA ELTQREDVRH YLKGGSSIAG LLLKPTNEKL SVYTALQRQL LSPGTALILL EAQAASGFLL DPVRNRRLTV NEAVKEGVVG PELHHKLLSA ERAVTGYKDP YTGEQISLFQ AMKKDLIVRD HGIRLLEAQI ATGGIIDPVH SHRVPVDVAY QRGYFDEEMN RVLADPSDDT KGFFDPNTHE NLTYLQLLER CVEDPETGLR LLPLTDKAAK GGELVYTDTE ARDVFEKATV SAPFGKFQGK TVTIWEIINS EYFTAEQRRD LLRQFRTGRI TVEKIIKIVI TVVEEHERKG QLCFEGLRAL VPAAELLDSG VISHEVYQQL QRGERSVREV AEADEVRQAL RGTSVIAGVW LEEAGQKLSI YEALRRDLLQ PEVAVALLEA QAGTGHIIDP ATSARLTVDE AVRAGLVGPE MHEKLLSAEK AVTGYRDPYS GQSVSLFQAL KKGLIPREQG LRLLDAQLST GGIVDPSKSH RVPLDVAYAR GYLDKETNRA LTSPRDDARV YLDPSTREPV TYSQLQQRCR SDQLTGLSLL PLSEKAVRAR QEEVYSELQA RETLEKAKVE VPVGGFKGRA LTVWELISSE YFTEEQRQEL LRQFRTGKVT VEKVIKILIT IVEEVETQRQ ERLSFSGLRA PVPASELLAS KILSRTQFEQ LKDGKTSVKD LSEVGSVRTL LQGSGCLAGI YLEDSKEKVT IYEAMRRGLL RASTATLLLE AQAATGFLVD PVRNQRLYVH EAVKAGVVGP ELHEKLLSAE KAVTGYKDPY SGSTISLFQA MKKGLVLRDH AIRLLEAQIA TGGIIDPVHS HRLPVDVAYQ RGYFDEEMNR VLADPSDDTK GFFDPNTHEN LTYLQLLERC VEDPETGLRL LPLRGAEKTE VVETTQVYTE EETRRAFEET QIDIPGGGSH GGSSMSLWEV MQSDMIPEDQ RARLMADFQA GRVTKERMII IIIEIIEKTE IIRQQNLASY DYVRRRLTAE DLYEARIISL ETYNLFREGT KSLREVLEME SAWRYLYGTG SVAGVYLPGS RQTLTIYQAL KKGLLSAEVA RLLLEAQAAT GFLLDPVKGE RLTVDEAVRK GLVGPELHDR LLSAERAVTG YRDPYTEQPI SLFQAMKKEL IPAEEALRLL DAQLATGGIV DPRLGFHLPL EVAYQRGYLN KDTHDQLSEP SEVRSYVDPS TDERLSYTQL LKRCRRDDNS GQMLLPLSDA RKLTFRGLRK QITVEELVRS QVMDEATALQ LQEGLTSIEE VTKNLQKFLE GTSCIAGVFV DATKERLSVY QAMKKGIIRP GTAFELLEAQ AATGYVIDPI KGLKLTVEEA VRMGIVGPEF KDKLLSAERA VTGYKDPYSG KLISLFQAMK KGLILKDHGI RLLEAQIATG GIIDPEESHR LPVEVAYKRG LFDEEMNEIL TDPSDDTKGF FDPNTEENLT YLQLMERCIT DPQTGLCLLP LKEKKRERKT SSKSSVRKRR VVIVDPETGK EMSVYEAYRK GLIDHQTYLE LSEQECEWEE ITISSSDGVV KSMIIDRRSG RQYDIGDAIT KNLIDRSALD QYRAGTLSIT EFADMLSGNA GGFRSRSSSV GSSSSYPISS AVPRTQLASW SDPTEETGPV AGILDTETLE KVSITEAMHR NLVDNITGQR LLEAQACTGG IIDPSTGERF PVTEAVNKGL VDKIMVDRIN LAQKAFCGFE DPRTKTKMSA AQALKKGWLY YEAGQRFLEV QYLTGGLIEP DTPGRVSLDE ALQRGTVDAR TAQKLRDVSA YSKYLTCPKT KLKISYKDAL DRSMVEEGTG LRLLEAAAQS SKGYYSPYSV SGSGSTAGSR TGSRTGSRAG SRRGSFDATG SGFSMTFSSS SYSSSGYGRR YASGPSASLG GPESAVA // ID IPI00230793.1 IPI; PRT; 4544 AA. AC IPI00230793; DT 09-APR-2003 (IPI Rat rel. 1.1, Created) DT 09-APR-2003 (IPI Rat rel. 1.1, Last sequence update) DE SPLICE ISOFORM 3 OF P30427. OS Rattus norvegicus (Rat). OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; OC Mammalia; Eutheria; Rodentia; Sciurognathi; Muridae; Murinae; Rattus. OX NCBI_TaxID=10116; DR InterPro; IPR001715; Calponin-like. DR InterPro; IPR000209; Pept_S8_S53. DR InterPro; IPR001101; Plectin_repeat. DR InterPro; IPR002017; Spectrin. DR SMART; SM00033; CH; 2. DR SMART; SM00250; PLEC; 34. DR SMART; SM00150; SPEC; 6. DR PROSITE; PS50021; CH; 2. DR PROSITE; PS50083; SPEC_REPEAT; 4. DR PROSITE; PS00136; SUBTILASE_ASP; 1. DR UniParc; UPI000002B773; -; -. DR SWISS-PROT; P30427-3; PLE1_RAT; M. SQ SEQUENCE 4544 AA; 517256 MW; 13FFBE5F79240532 CRC64; MEPSGSLFPS LVVVGHVVSL AAVWHWRKGH RQAQDEQDER DRVQKKTSTK WVNKHLIKAQ RHISDLYEDL RDGHNLISLL EVLSGDSLPR EKGRMRFHKL QNVQIALDYL RHRQVKLVNI RNDDIADGNP KLTLGLIWTI ILHFKISDIQ VSGQSEDMTA KEKLLLWSQR MVEGYQGLRC DNFTTSWRDG RLFNAIIHRH KPMLIDMNKV YRQTNLENLD QAFSVAERDL GVTRLLDPED VDVPQPDEKS IITYVSSLYD AMPRVPGAQD GVRANELQLR WQEYRELVLL LLQWIRHHTA AFEERKFPSS FEEIEILWCQ FLKFKETELP AKEADKNRSK GIYQSLEGAV QAGQLKIPPG YHPLDVEKEW GKLHVAILER EKQLRSEFER LECLQRIVSK LQMEAGLCEE QLYQADSLLQ SDIRLLASGK AAQRAGEVER DLDKADGMIR LLFNDVQTLK DGRHPQGEQM YRRVYRLHER LVAIRTEYNL RLKAGVGAPV TQVTLQSTQR RPELEDSTLR YLHDLLAWVE ENQRRIDGAE WGVDLPSVEA QLGSHRGMHQ SIEEFRAKIE RARNDESQLS PATRGAYRDC LGRLDLQYAK LLNSSKARLR SLESLHGFVA AATKELMWLN EKEEEEVGFD WSDRNTNMAA KKESYSALMR ELEMKEKKIK EIQNTGDRLL REDHPARPTV ESFQAALQTQ WSWMLQLCCC IEAHLKENTA YFQFFSDVRE AEEQLQKLQE TLRRKYSCDR SITVTRLEDL LQDAQDEKEQ LNEYKGHLSG LAKRAKAIVQ LKPRNPAHPV RGHVPLLAVC DYKQVEVTVH KGDQCQLVGP AQPFHWKVLS SSGSEAAVPS VCFLVPPPNQ EAQEAVARLE AQHQALVTLW HQLHVDMKSL LAWQSLNRDI QLIRSWSLVT FRTLKPEEQR QALRNLELHY QAFLRDSQDA GGFGPEDRLV AEREYGSCSR HYQQLLQSLE QGEQEESRCQ RCISELKDIR LQLEACETRT VHRLRLPLDK DPARECAQRI AEQQKAQAEV EGLGKGVARL SAEAEKVLAL PEPSPAAPTL RSELELTLGK LEQVRSLSAI YLEKLKTISL VIRSTQGAEE VLKTHEEHLK EAQAVPATLQ ELEVTKASLK KLRAQAEAQQ PVFNTLRDEL RGAQEVGERL QQRHGERDVE VERWRERVTQ LLERWQAVLA QTDVRQRELE QLGRQLRYYR ESADPLSSWL QDAKSRQEQI QAVPIANSQA AREQLRQEKA LLEEIERHGE KVEECQKFAK QYINAIKDYE LQLITYKAQL EPVASPAKKP KVQSGSESVI QEYVDLRTRY SELTTLTSQY IKFISETLRR MEEEERLAEQ QRAEERERLA EVEAALEKQR QLAEAHAQAK AQAELEAREL QRRMQEEVTR REEAAVDAQQ QKRSIQEELQ HLRQSSEAEI QAKAQQVEAA ERSRMRIEEE IRVVRLQLET TERQRGGAED ELQALRARAE EAEAQKRQAQ EEAERLRRQV QDESQRKRQA EAELALRVKA EAEAAREKQR ALQALDELKL QAEEAERWLC QAEAERARQV QVALETAQRS AEVELQSKRP SFAEKTAQLE RTLQEEHVTV TQLREEAERR AQQQAEAERA REEAERELER WQLKANEALR LRLQAEEVAQ QKSLAQADAE KQKEEAEREA RRRGKAEEQA VRQRELAEQE LEKQRQLTEG TAQQRLAAEQ ELIRLRAETE QGEHQRQLLE EELARLQHEA TAATQKRQEL EAELAKVRAE MEVLLASKAR AEEESRSTSE KSKQRLEAEA GRFRELAEEA ARLRALAEEA RRHRELAEED AARQRAEADG VLTEKLAAIS EATRLKTEAE IALKEKEAEN ERLRRLAEDE AFQRRRLEEQ AAQHKADIEE RLAQLRKASE SELERQKGLV EDTLRQRRQV EEEIMALKAS FEKAAAGKAE LELELGRIRS NAEDTMRSKE LAEQEAARQR QLAAEEEQRR REAEERVQRS LAAEEEAARQ RKVALEEVER LKAKVEEARR LRERAEQESA RQLQLAQEAA QKRLQAEEKA HAFVVQQREE ELQQTLQQEQ NMLERLRSEA EAARRAAEEA EEAREQAERE AAQSRKQVEE AERLKQSAEE QAQAQAQAQA AAEKLRKEAE QEAARRAQAE QAALKQKQAA DAEMEKHKKF AEQTLRQKAQ VEQELTTLRL QLEETDHQKS ILDEELQRLK AEVTEAARQR SQVEEELFSV RVQMEELGKL KARIEAENRA LILRDKDNTQ RFLEEEAEKM KQVAEEAARL SVAAQEAARL RQLAEEDLAQ QRALAEKMLK EKMQAVQEAT RLKAEAELLQ QQKELAQEQA RRLQADKEQM AQQLVEETQG FQRTLEAERQ RQLEMSAEAE RLKLRMAEMS RAQARAEEDA QRFRKQAEEI GEKLHRTELA TQEKVTLVQT LEIQRQQSDQ DAERLREAIA ELEREKEKLK QEAKLLQLKS EEMQTVQQEQ ILQETQALQK SFLSEKDSLL QRERFIEQEK AKLEQLFQDE VAKAKQLQEE QQRQQQQMEQ EKQELVASME EARRRQREAE EGVRRKQEEL QRLEQQRQQQ EKLLAEENQR LRERLQRLEE EHRAALAHSE EIATSQAAAT KALPNGRDAL DGPSMEAEPE YTFEGLRQKV PAQQLQEAGI LSMEELQRLT QGHTTVAELT QREDVRHYLK GGSSIAGLLL KPTNEKLSVY TALQRQLLSP GTALILLEAQ AASGFLLDPV RNRRLTVNEA VKEGVVGPEL HHKLLSAERA VTGYKDPYTG EQISLFQAMK KDLIVRDHGI RLLEAQIATG GIIDPVHSHR VPVDVAYQRG YFDEEMNRVL ADPSDDTKGF FDPNTHENLT YLQLLERCVE DPETGLRLLP LTDKAAKGGE LVYTDTEARD VFEKATVSAP FGKFQGKTVT IWEIINSEYF TAEQRRDLLR QFRTGRITVE KIIKIVITVV EEHERKGQLC FEGLRALVPA AELLDSGVIS HEVYQQLQRG ERSVREVAEA DEVRQALRGT SVIAGVWLEE AGQKLSIYEA LRRDLLQPEV AVALLEAQAG TGHIIDPATS ARLTVDEAVR AGLVGPEMHE KLLSAEKAVT GYRDPYSGQS VSLFQALKKG LIPREQGLRL LDAQLSTGGI VDPSKSHRVP LDVAYARGYL DKETNRALTS PRDDARVYLD PSTREPVTYS QLQQRCRSDQ LTGLSLLPLS EKAVRARQEE VYSELQARET LEKAKVEVPV GGFKGRALTV WELISSEYFT EEQRQELLRQ FRTGKVTVEK VIKILITIVE EVETQRQERL SFSGLRAPVP ASELLASKIL SRTQFEQLKD GKTSVKDLSE VGSVRTLLQG SGCLAGIYLE DSKEKVTIYE AMRRGLLRAS TATLLLEAQA ATGFLVDPVR NQRLYVHEAV KAGVVGPELH EKLLSAEKAV TGYKDPYSGS TISLFQAMKK GLVLRDHAIR LLEAQIATGG IIDPVHSHRL PVDVAYQRGY FDEEMNRVLA DPSDDTKGFF DPNTHENLTY LQLLERCVED PETGLRLLPL RGAEKTEVVE TTQVYTEEET RRAFEETQID IPGGGSHGGS SMSLWEVMQS DMIPEDQRAR LMADFQAGRV TKERMIIIII EIIEKTEIIR QQNLASYDYV RRRLTAEDLY EARIISLETY NLFREGTKSL REVLEMESAW RYLYGTGSVA GVYLPGSRQT LTIYQALKKG LLSAEVARLL LEAQAATGFL LDPVKGERLT VDEAVRKGLV GPELHDRLLS AERAVTGYRD PYTEQPISLF QAMKKELIPA EEALRLLDAQ LATGGIVDPR LGFHLPLEVA YQRGYLNKDT HDQLSEPSEV RSYVDPSTDE RLSYTQLLKR CRRDDNSGQM LLPLSDARKL TFRGLRKQIT VEELVRSQVM DEATALQLQE GLTSIEEVTK NLQKFLEGTS CIAGVFVDAT KERLSVYQAM KKGIIRPGTA FELLEAQAAT GYVIDPIKGL KLTVEEAVRM GIVGPEFKDK LLSAERAVTG YKDPYSGKLI SLFQAMKKGL ILKDHGIRLL EAQIATGGII DPEESHRLPV EVAYKRGLFD EEMNEILTDP SDDTKGFFDP NTEENLTYLQ LMERCITDPQ TGLCLLPLKE KKRERKTSSK SSVRKRRVVI VDPETGKEMS VYEAYRKGLI DHQTYLELSE QECEWEEITI SSSDGVVKSM IIDRRSGRQY DIGDAITKNL IDRSALDQYR AGTLSITEFA DMLSGNAGGF RSRSSSVGSS SSYPISSAVP RTQLASWSDP TEETGPVAGI LDTETLEKVS ITEAMHRNLV DNITGQRLLE AQACTGGIID PSTGERFPVT EAVNKGLVDK IMVDRINLAQ KAFCGFEDPR TKTKMSAAQA LKKGWLYYEA GQRFLEVQYL TGGLIEPDTP GRVSLDEALQ RGTVDARTAQ KLRDVSAYSK YLTCPKTKLK ISYKDALDRS MVEEGTGLRL LEAAAQSSKG YYSPYSVSGS GSTAGSRTGS RTGSRAGSRR GSFDATGSGF SMTFSSSSYS SSGYGRRYAS GPSASLGGPE SAVA // ID IPI00230794.1 IPI; PRT; 4558 AA. AC IPI00230794; DT 09-APR-2003 (IPI Rat rel. 1.1, Created) DT 09-APR-2003 (IPI Rat rel. 1.1, Last sequence update) DE SPLICE ISOFORM 4 OF P30427. OS Rattus norvegicus (Rat). OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; OC Mammalia; Eutheria; Rodentia; Sciurognathi; Muridae; Murinae; Rattus. OX NCBI_TaxID=10116; DR InterPro; IPR001715; Calponin-like. DR InterPro; IPR000209; Pept_S8_S53. DR InterPro; IPR001101; Plectin_repeat. DR InterPro; IPR002017; Spectrin. DR Pfam; PF00307; CH; 2. DR Pfam; PF00681; Plectin; 17. DR Pfam; PF00435; Spectrin; 3. DR SMART; SM00033; CH; 2. DR SMART; SM00250; PLEC; 34. DR SMART; SM00150; SPEC; 6. DR PROSITE; PS50021; CH; 2. DR PROSITE; PS50083; SPEC_REPEAT; 4. DR PROSITE; PS00136; SUBTILASE_ASP; 1. DR UniParc; UPI000002B774; -; -. DR SWISS-PROT; P30427-4; PLE1_RAT; M. SQ SEQUENCE 4558 AA; 518238 MW; 40B5E5371A74B56D CRC64; DVSNGSSGSP SPGDTLPWNL GKTQRSRRSG GGSVGNGSVL DPAERAVIRI ADERDRVQKK TSTKWVNKHL IKAQRHISDL YEDLRDGHNL ISLLEVLSGD SLPREKGRMR FHKLQNVQIA LDYLRHRQVK LVNIRNDDIA DGNPKLTLGL IWTIILHFKI SDIQVSGQSE DMTAKEKLLL WSQRMVEGYQ GLRCDNFTTS WRDGRLFNAI IHRHKPMLID MNKVYRQTNL ENLDQAFSVA ERDLGVTRLL DPEDVDVPQP DEKSIITYVS SLYDAMPRVP GAQDGVRANE LQLRWQEYRE LVLLLLQWIR HHTAAFEERK FPSSFEEIEI LWCQFLKFKE TELPAKEADK NRSKGIYQSL EGAVQAGQLK IPPGYHPLDV EKEWGKLHVA ILEREKQLRS EFERLECLQR IVSKLQMEAG LCEEQLYQAD SLLQSDIRLL ASGKAAQRAG EVERDLDKAD GMIRLLFNDV QTLKDGRHPQ GEQMYRRVYR LHERLVAIRT EYNLRLKAGV GAPVTQVTLQ STQRRPELED STLRYLHDLL AWVEENQRRI DGAEWGVDLP SVEAQLGSHR GMHQSIEEFR AKIERARNDE SQLSPATRGA YRDCLGRLDL QYAKLLNSSK ARLRSLESLH GFVAAATKEL MWLNEKEEEE VGFDWSDRNT NMAAKKESYS ALMRELEMKE KKIKEIQNTG DRLLREDHPA RPTVESFQAA LQTQWSWMLQ LCCCIEAHLK ENTAYFQFFS DVREAEEQLQ KLQETLRRKY SCDRSITVTR LEDLLQDAQD EKEQLNEYKG HLSGLAKRAK AIVQLKPRNP AHPVRGHVPL LAVCDYKQVE VTVHKGDQCQ LVGPAQPFHW KVLSSSGSEA AVPSVCFLVP PPNQEAQEAV ARLEAQHQAL VTLWHQLHVD MKSLLAWQSL NRDIQLIRSW SLVTFRTLKP EEQRQALRNL ELHYQAFLRD SQDAGGFGPE DRLVAEREYG SCSRHYQQLL QSLEQGEQEE SRCQRCISEL KDIRLQLEAC ETRTVHRLRL PLDKDPAREC AQRIAEQQKA QAEVEGLGKG VARLSAEAEK VLALPEPSPA APTLRSELEL TLGKLEQVRS LSAIYLEKLK TISLVIRSTQ GAEEVLKTHE EHLKEAQAVP ATLQELEVTK ASLKKLRAQA EAQQPVFNTL RDELRGAQEV GERLQQRHGE RDVEVERWRE RVTQLLERWQ AVLAQTDVRQ RELEQLGRQL RYYRESADPL SSWLQDAKSR QEQIQAVPIA NSQAAREQLR QEKALLEEIE RHGEKVEECQ KFAKQYINAI KDYELQLITY KAQLEPVASP AKKPKVQSGS ESVIQEYVDL RTRYSELTTL TSQYIKFISE TLRRMEEEER LAEQQRAEER ERLAEVEAAL EKQRQLAEAH AQAKAQAELE ARELQRRMQE EVTRREEAAV DAQQQKRSIQ EELQHLRQSS EAEIQAKAQQ VEAAERSRMR IEEEIRVVRL QLETTERQRG GAEDELQALR ARAEEAEAQK RQAQEEAERL RRQVQDESQR KRQAEAELAL RVKAEAEAAR EKQRALQALD ELKLQAEEAE RWLCQAEAER ARQVQVALET AQRSAEVELQ SKRPSFAEKT AQLERTLQEE HVTVTQLREE AERRAQQQAE AERAREEAER ELERWQLKAN EALRLRLQAE EVAQQKSLAQ ADAEKQKEEA EREARRRGKA EEQAVRQREL AEQELEKQRQ LTEGTAQQRL AAEQELIRLR AETEQGEHQR QLLEEELARL QHEATAATQK RQELEAELAK VRAEMEVLLA SKARAEEESR STSEKSKQRL EAEAGRFREL AEEAARLRAL AEEARRHREL AEEDAARQRA EADGVLTEKL AAISEATRLK TEAEIALKEK EAENERLRRL AEDEAFQRRR LEEQAAQHKA DIEERLAQLR KASESELERQ KGLVEDTLRQ RRQVEEEIMA LKASFEKAAA GKAELELELG RIRSNAEDTM RSKELAEQEA ARQRQLAAEE EQRRREAEER VQRSLAAEEE AARQRKVALE EVERLKAKVE EARRLRERAE QESARQLQLA QEAAQKRLQA EEKAHAFVVQ QREEELQQTL QQEQNMLERL RSEAEAARRA AEEAEEAREQ AEREAAQSRK QVEEAERLKQ SAEEQAQAQA QAQAAAEKLR KEAEQEAARR AQAEQAALKQ KQAADAEMEK HKKFAEQTLR QKAQVEQELT TLRLQLEETD HQKSILDEEL QRLKAEVTEA ARQRSQVEEE LFSVRVQMEE LGKLKARIEA ENRALILRDK DNTQRFLEEE AEKMKQVAEE AARLSVAAQE AARLRQLAEE DLAQQRALAE KMLKEKMQAV QEATRLKAEA ELLQQQKELA QEQARRLQAD KEQMAQQLVE ETQGFQRTLE AERQRQLEMS AEAERLKLRM AEMSRAQARA EEDAQRFRKQ AEEIGEKLHR TELATQEKVT LVQTLEIQRQ QSDQDAERLR EAIAELEREK EKLKQEAKLL QLKSEEMQTV QQEQILQETQ ALQKSFLSEK DSLLQRERFI EQEKAKLEQL FQDEVAKAKQ LQEEQQRQQQ QMEQEKQELV ASMEEARRRQ REAEEGVRRK QEELQRLEQQ RQQQEKLLAE ENQRLRERLQ RLEEEHRAAL AHSEEIATSQ AAATKALPNG RDALDGPSME AEPEYTFEGL RQKVPAQQLQ EAGILSMEEL QRLTQGHTTV AELTQREDVR HYLKGGSSIA GLLLKPTNEK LSVYTALQRQ LLSPGTALIL LEAQAASGFL LDPVRNRRLT VNEAVKEGVV GPELHHKLLS AERAVTGYKD PYTGEQISLF QAMKKDLIVR DHGIRLLEAQ IATGGIIDPV HSHRVPVDVA YQRGYFDEEM NRVLADPSDD TKGFFDPNTH ENLTYLQLLE RCVEDPETGL RLLPLTDKAA KGGELVYTDT EARDVFEKAT VSAPFGKFQG KTVTIWEIIN SEYFTAEQRR DLLRQFRTGR ITVEKIIKIV ITVVEEHERK GQLCFEGLRA LVPAAELLDS GVISHEVYQQ LQRGERSVRE VAEADEVRQA LRGTSVIAGV WLEEAGQKLS IYEALRRDLL QPEVAVALLE AQAGTGHIID PATSARLTVD EAVRAGLVGP EMHEKLLSAE KAVTGYRDPY SGQSVSLFQA LKKGLIPREQ GLRLLDAQLS TGGIVDPSKS HRVPLDVAYA RGYLDKETNR ALTSPRDDAR VYLDPSTREP VTYSQLQQRC RSDQLTGLSL LPLSEKAVRA RQEEVYSELQ ARETLEKAKV EVPVGGFKGR ALTVWELISS EYFTEEQRQE LLRQFRTGKV TVEKVIKILI TIVEEVETQR QERLSFSGLR APVPASELLA SKILSRTQFE QLKDGKTSVK DLSEVGSVRT LLQGSGCLAG IYLEDSKEKV TIYEAMRRGL LRASTATLLL EAQAATGFLV DPVRNQRLYV HEAVKAGVVG PELHEKLLSA EKAVTGYKDP YSGSTISLFQ AMKKGLVLRD HAIRLLEAQI ATGGIIDPVH SHRLPVDVAY QRGYFDEEMN RVLADPSDDT KGFFDPNTHE NLTYLQLLER CVEDPETGLR LLPLRGAEKT EVVETTQVYT EEETRRAFEE TQIDIPGGGS HGGSSMSLWE VMQSDMIPED QRARLMADFQ AGRVTKERMI IIIIEIIEKT EIIRQQNLAS YDYVRRRLTA EDLYEARIIS LETYNLFREG TKSLREVLEM ESAWRYLYGT GSVAGVYLPG SRQTLTIYQA LKKGLLSAEV ARLLLEAQAA TGFLLDPVKG ERLTVDEAVR KGLVGPELHD RLLSAERAVT GYRDPYTEQP ISLFQAMKKE LIPAEEALRL LDAQLATGGI VDPRLGFHLP LEVAYQRGYL NKDTHDQLSE PSEVRSYVDP STDERLSYTQ LLKRCRRDDN SGQMLLPLSD ARKLTFRGLR KQITVEELVR SQVMDEATAL QLQEGLTSIE EVTKNLQKFL EGTSCIAGVF VDATKERLSV YQAMKKGIIR PGTAFELLEA QAATGYVIDP IKGLKLTVEE AVRMGIVGPE FKDKLLSAER AVTGYKDPYS GKLISLFQAM KKGLILKDHG IRLLEAQIAT GGIIDPEESH RLPVEVAYKR GLFDEEMNEI LTDPSDDTKG FFDPNTEENL TYLQLMERCI TDPQTGLCLL PLKEKKRERK TSSKSSVRKR RVVIVDPETG KEMSVYEAYR KGLIDHQTYL ELSEQECEWE EITISSSDGV VKSMIIDRRS GRQYDIGDAI TKNLIDRSAL DQYRAGTLSI TEFADMLSGN AGGFRSRSSS VGSSSSYPIS SAVPRTQLAS WSDPTEETGP VAGILDTETL EKVSITEAMH RNLVDNITGQ RLLEAQACTG GIIDPSTGER FPVTEAVNKG LVDKIMVDRI NLAQKAFCGF EDPRTKTKMS AAQALKKGWL YYEAGQRFLE VQYLTGGLIE PDTPGRVSLD EALQRGTVDA RTAQKLRDVS AYSKYLTCPK TKLKISYKDA LDRSMVEEGT GLRLLEAAAQ SSKGYYSPYS VSGSGSTAGS RTGSRTGSRA GSRRGSFDAT GSGFSMTFSS SSYSSSGYGR RYASGPSASL GGPESAVA // ID IPI00187796.1 IPI; PRT; 430 AA. AC IPI00187796; DT 14-MAR-2003 (IPI Rat rel. 1.0, Created) DT 14-MAR-2003 (IPI Rat rel. 1.0, Last sequence update) DE T-KININOGEN II PRECURSOR. OS Rattus norvegicus (Rat). OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; OC Mammalia; Eutheria; Rodentia; Sciurognathi; Muridae; Murinae; Rattus. OX NCBI_TaxID=10116; DR InterPro; IPR000010; Prot_inh_cystat. DR Pfam; PF00031; Cystatin; 3. DR PROSITE; PS00287; CYSTATIN; 2. DR UniParc; UPI000012DF30; -; -. DR SWISS-PROT; P08932; KNT2_RAT; M. SQ SEQUENCE 430 AA; 47524 MW; 43EDF02D1BF55076 CRC64; MKLITILLLC SRLLPSLAQE EGAQELNCND ETVFQAVDTA LKKYNAELES GNQFVLYRVT KGTKKDGAET LYSFKYQIKE GNCSVQSGLT WQDCDFKDAE EAATGECTTT LGKKENKFSV ATQICNITPG KGPKKTEEDL CVGCFQPIPM DSSDLKPVLK HAVEHSNNNT KHTHLFALRE VKSAHSQVVA GMNYKIIYSI VQTNCSKEDF PSLREDCVPL PYGDHGECTG HTHVDIHNTI AGFSQSCDLY PGDDLFSLLP KKCFGCPKNI PVDSPELKEA LGHSIAQLNA QHNHLFYFKI DTVKKATSQV VAGTKYVIEF IARETNCSKQ TNTELTADCE TKHLGQSLNC NANVYMRPWE NKVVPTVRCQ ALDMMISRPP GFSPFRLVQV QETKEGTTRL LNSCEYKGRL SKAGAGPAPD HQAEASTVTP // ID IPI00323989.1 IPI; PRT; 172 AA. AC IPI00323989; IPI00288632; IPI00187806; DT 12-JUN-2003 (IPI Rat rel. 1.3, Created) DT 12-JUN-2003 (IPI Rat rel. 1.3, Last sequence update) DE ODORANT-BINDING PROTEIN PRECURSOR. OS Rattus norvegicus (Rat). OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; OC Mammalia; Eutheria; Rodentia; Sciurognathi; Muridae; Murinae; Rattus. OX NCBI_TaxID=10116; DR InterPro; IPR011038; Calycin. DR InterPro; IPR000566; Lipocln_cytFABP. DR InterPro; IPR002448; Odorant_bndng. DR Pfam; PF00061; Lipocalin; 1. DR PRINTS; PR01173; ODORANTBNDNG. DR PROSITE; PS00213; LIPOCALIN; 1. DR REFSEQ_NP; NP_620258; GI:20302101; -. DR SWISS-PROT; P08937; OBP_RAT; M. DR UniParc; UPI0000130B9B; -; -. DR Superfamily; SSF50814; Calycin; 1. SQ SEQUENCE 172 AA; 19699 MW; 9DAFFDEF67F724DD CRC64; MVKFLLIVLA LGVSCAHHEN LDISPSEVNG DWRTLYIVAD NVEKVAEGGS LRAYFQHMEC GDECQELKII FNVKLDSECQ THTVVGQKHE DGRYTTDYSG RNYFHVLKKT DDIIFFHNVN VDESGRRQCD LVAGKREDLN KAQKQELRKL AEEYNIPNEN TQHLVPTDTC NQ // ID IPI00187808.2 IPI; PRT; 278 AA. AC IPI00187808; DT 14-MAR-2003 (IPI Rat rel. 1.0, Created) DT 18-NOV-2003 (IPI Rat rel. 1.9, Last sequence update) OS Rattus norvegicus (Rat). OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; OC Mammalia; Eutheria; Rodentia; Sciurognathi; Muridae; Murinae; Rattus. OX NCBI_TaxID=10116; CC -!- CHROMOSOME: 19. DR InterPro; IPR000851; Ribosomal_S5. DR InterPro; IPR005711; Ribosomal_S5_e/a. DR TIGRFAMs; TIGR01020; rpsE_arch; 1. DR PROSITE; PS50881; S5_DSRBD; 1. DR UniParc; UPI000021D4DC; -; -. DR ENSEMBL; ENSRNOP00000009072; ENSRNOG00000006900; M. SQ SEQUENCE 278 AA; 30122 MW; 03D5ACB5A7E2989C CRC64; MADDIGAVRR PGGPGGPGLG GQSFRGGFGR AAVLRGCSRS RGRSGGGKAE DREWISVTNL GRLVKDMKIK PLEEIYLFSL PIKESEIIDF LGASKKDEVL KIMPVQKRAG QRTRFKAFVA IGDYNGQVGL GVKCSKDGIR GAIILVKLSI VPVQRGYWGN KIGKPHTVPC KVIGRCGSVL VHLIPDPRGT DIISAPVPKK LLIMAGIDDC YTSSRGCTAT LGNFAKTTFD EISKTSSYLA PDFWKETFTK SLYQEFTDSV KTHTRVSIQR THAPPVVT // ID IPI00187810.2 IPI; PRT; 831 AA. AC IPI00187810; DT 14-MAR-2003 (IPI Rat rel. 1.0, Created) DT 18-NOV-2003 (IPI Rat rel. 1.9, Last sequence update) OS Rattus norvegicus (Rat). OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; OC Mammalia; Eutheria; Rodentia; Sciurognathi; Muridae; Murinae; Rattus. OX NCBI_TaxID=10116; CC -!- CHROMOSOME: 2. DR InterPro; IPR001394; Peptidase_C19. DR InterPro; IPR006615; Pept_C19_N_1. DR InterPro; IPR001607; Znf_UBP. DR Pfam; PF00443; UCH; 2. DR Pfam; PF02148; zf-UBP; 1. DR SMART; SM00695; DUSP; 2. DR SMART; SM00290; ZnF_UBP; 1. DR PROSITE; PS00972; UCH_2_1; 1. DR PROSITE; PS00973; UCH_2_2; 1. DR PROSITE; PS50235; UCH_2_3; 1. DR UniParc; UPI000021D4DD; -; -. DR ENSEMBL; ENSRNOP00000016290; ENSRNOG00000011294; M. SQ SEQUENCE 831 AA; 94317 MW; 66E5FAA7C75927F9 CRC64; KRKKKKTKKM TTFRNHCPHL DSVGEITKED LIQKSHGACQ DCKVRGPNLW ACLENRCSYV GCGESQDHST IHSKKTKHYL TVNLTTLRVW CYACSKEVFL DRKLGTPPSL PHVRQPQQTQ ENSVQDFKIP SNTALKTPLV AVFEDLDIEV EEEDELKARG LTGLKNIGNT CYMNAALQAL SNCPPLTQFF LDCGGLARTD KKPAICKSYL KLMTELWHKS RPGSVVPANL FQGIKTVNPT FRGYSQQDAQ EFLRCLMDLL HEELKEQVME IEEEPQALTS EETVEEEKSQ SDVDFQSCES CSSSSEKGEN ESVSKGGPED STETTMLIQD EEDLEMAKDW QKEKMCNKSN KADSDGEPDK DRDTVCETVD LNSQETVKVQ IHGRASEYIT DVHLNDLSTP QILPSNESVN PRLSASPPKS GNLWPGLTPP HKKAQSSSPK RKKQHKKYRS VISDIFDGTI ISSVQCLTCD RVSDNMYSCE KCKKLRNGVK FCKVQKFPEI LCIHLKRFRH ELMFSTKIST HVSFPLEGLD LQPFLAKDSP AQIVTYDLLS VICHHGTASS GHYIAYCRNN LNNLWYEFDD QSVTEVSEST VQNAEAYVLF YRKSSEEAQR ERRRISNLLN IMEPSLLQFY ISRQWLNKFK TFAEPGPISN NDFLCIHGGI PPRKASYIED LVLMLPQNIW DNLYSRYGGG PAVNHLYICH TCQIEAEKIE KRRKTELEIF IRLNRAFQEE DSPATFYCIS MQWFREWESF VKGKDGDPPG PIDNTKIAVT KCGNVMLKQG ADSGQISEET WNFLQSIYGG GPEVILRPPV VHVDPDALQA EEKIEVETRS L // ID IPI00187823.1 IPI; PRT; 136 AA. AC IPI00187823; DT 14-MAR-2003 (IPI Rat rel. 1.0, Created) DT 14-MAR-2003 (IPI Rat rel. 1.0, Last sequence update) OS Rattus norvegicus (Rat). OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; OC Mammalia; Eutheria; Rodentia; Sciurognathi; Muridae; Murinae; Rattus. OX NCBI_TaxID=10116; CC -!- CHROMOSOME: 8. DR UniParc; UPI000017E081; -; -. DR ENSEMBL; ENSRNOP00000016293; ENSRNOG00000012224; M. SQ SEQUENCE 136 AA; 14877 MW; 06B104FC9B6E3C47 CRC64; MLLVGSYHLS SNPVQISLSA LAFGPHLGPF QPLQGLEDPT GHTLRTFAAV AGPDLPSSID LGHGTNPCTT TEVQVQCWGS RSCVERVLIL WDKPFMFGQL DCIHPFGDFQ LPRLSEEGCQ SDRLLLVDVF CSNSRH // ID IPI00187851.2 IPI; PRT; 1037 AA. AC IPI00187851; IPI00365020; DT 14-MAR-2003 (IPI Rat rel. 1.0, Created) DT 18-NOV-2003 (IPI Rat rel. 1.9, Last sequence update) DE SIMILAR TO RIKEN CDNA 2410141F18. OS Rattus norvegicus (Rat). OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; OC Mammalia; Eutheria; Rodentia; Sciurognathi; Muridae; Murinae; Rattus. OX NCBI_TaxID=10116; CC -!- CHROMOSOME: 5. DR InterPro; IPR003347; TF_JmjC. DR InterPro; IPR003349; TF_JmjN. DR InterPro; IPR002999; Tudor. DR InterPro; IPR001965; Znf_PHD. DR SMART; SM00558; JmjC; 1. DR SMART; SM00545; JmjN; 1. DR SMART; SM00249; PHD; 1. DR SMART; SM00333; TUDOR; 2. DR REFSEQ_XP; XP_216426; GI:34869003; -. DR UniParc; UPI000021D4DE; -; -. DR ENSEMBL; ENSRNOP00000009083; ENSRNOG00000006644; M. SQ SEQUENCE 1037 AA; 118298 MW; C7247CCEC94B848A CRC64; MEVVEVESPL NPSCKIMTFR PSMEEFREFN KYLAYMESKG AHRAGLAKVI PPKEWKPRQC YDDIDNLLIP APIQQMVTGQ SGLFTQYNIQ KKPMTVKEFR QLANSSKYCT PRYLDYEDLE RKYWKNLTFV APIYGADING SIYDEGVDEW NIARLNTVLD VVEEECGISI EGVNTPYLYF GMWKTTFAWH TEDMDLYSIN YLHFGEPKYA IPPEHGKRLE RLAQGFFPSS SQGCDAFLRH KMTLISPSVL KKYGIPFDKI TQEAGEFMIT FPYGYHAGFN HGFNCAESTN FATVRWIDYG KVAKLCTCRN DMVKISMDIF VKKFQPDRYQ IWKQGKDIYT IDHTKPTPES TPEVKTWLQR RKKLRKAPKS LQGNKSLSKR PKAEEDEEFA EFIGEEVSSP AVCPRHLKVT EKPEKFKLAN IGASSEKEAS DTRIQVDQSL TNDTKLSGKS CINSSVIDEI QPENDTANAV TSPSTLKKAS DLIPFSHGHI TGKESRLLKI LQLESPKIPS SLAESNRVLT EGEENDEEGH ASNLEPGEVP DALSEERNGL NVPKIIEGQP KTTKSWRHPL GKPPARSPMT LVKQQVASDE ELPEVLSIDE EVEETESWAK PLIHLWQTKS PNFMAEQEYN ATVAKMEPNC AICTLLMPYY KPDXSKEEND SRWETAVNEV VQSGRKTKPI IPEMCFIYSE ENVEYSPPNA FLEEDGTSLL ISCSKCFVRV HASKKSDFPL SRVSECCLCN LRGGALKQTK NNQWAHVICA VAVPEVRFTN VPERTQIDVD RIPLQRLKLK CIFCRQRVKR VSGACIQCSY GRCPASFHVT CAHAAGVLME PDDWPYVVNI TCFRHRVNSN VKSKTCEKAI SVGQTVITKH RNTRYYSCRV IDVTSQIFYE VMFDDGSFSR DTFPEDIVSR NCVKLGPPAE GEVIQVKWPD GKLYGAKYLG SNVAYMYQVE FEDGSQIAMK REDIYTLDEE LPKRVKARFS TASDMRFEDT FYGADVIQGE RKRQRVLSSR LKNEYVDDPV YRTFLKSSFQ KKCQKRQ // ID IPI00339007.1 IPI; PRT; 318 AA. AC IPI00339007; IPI00210424; IPI00204288; DT 02-SEP-2003 (IPI Rat rel. 1.6, Created) DT 02-SEP-2003 (IPI Rat rel. 1.6, Last sequence update) DE MYELOID-ASSOCIATED DIFFERENTIATION MARKER. OS Rattus norvegicus (Rat). OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; OC Mammalia; Eutheria; Rodentia; Sciurognathi; Muridae; Murinae; Rattus. OX NCBI_TaxID=10116; CC -!- CHROMOSOME: 1. DR InterPro; IPR008253; Marvel. DR Pfam; PF01284; MARVEL; 2. DR UniParc; UPI00001BB8FD; -; -. DR REFSEQ_NP; NP_899161; GI:34328542; M. DR ENSEMBL; ENSRNOP00000022264; ENSRNOG00000016588; -. SQ SEQUENCE 318 AA; 35148 MW; 1FBE25CF36BC2B60 CRC64; MPVTVTRTTI TTTSSSSTTV GSARALTQPL GLLRLLQLVS TCVAFSLVAS VGAWTGPMGN WAMFTWCFCF AVTLIILIEE LGGFQARFPL SWRNFPITFA CYAALFCLSS SIIYPTTYVQ FLPHGRSRDH AIAATTFSCV ACLAYATEVA WTRARPGEIT GYMATVPGLL KVFETFVACI IFAFISEPSL YQQRPALEWC VAVYAICFIL AAVTVLLNLG DCTNMLPIPF PTFLSGLALL SVLLYATAIV LWPLYQFDQR YNSQPRRSMD PSCSRSYVQP NEVCNWDRRL AVSILTGINL LAYVSDLVYS TRLVFVKV // ID IPI00387636.1 IPI; PRT; 101 AA. AC IPI00387636; DT 18-NOV-2003 (IPI Rat rel. 1.9, Created) DT 18-NOV-2003 (IPI Rat rel. 1.9, Last sequence update) OS Rattus norvegicus (Rat). OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; OC Mammalia; Eutheria; Rodentia; Sciurognathi; Muridae; Murinae; Rattus. OX NCBI_TaxID=10116; CC -!- CHROMOSOME: 8. DR UniParc; UPI000021DDDA; -; -. DR ENSEMBL; ENSRNOP00000009093; ENSRNOG00000006942; M. SQ SEQUENCE 101 AA; 10940 MW; AED52DCAA4945531 CRC64; TPVNLAVLKL SEAGVLDKLK NKWWYDKGEC GPKDSGSKDK TSALSLSNVA GVFYILVGGL GLAMLVALIE FCYKSRAEAK RMKLTFSEAI RNKARLSITG S // ID IPI00187885.2 IPI; PRT; 567 AA. AC IPI00187885; DT 14-MAR-2003 (IPI Rat rel. 1.0, Created) DT 18-NOV-2003 (IPI Rat rel. 1.9, Last sequence update) DE SIMILAR TO RIKEN CDNA A930038C07. OS Rattus norvegicus (Rat). OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; OC Mammalia; Eutheria; Rodentia; Sciurognathi; Muridae; Murinae; Rattus. OX NCBI_TaxID=10116; CC -!- CHROMOSOME: 4. DR InterPro; IPR003961; FN_III. DR SMART; SM00060; FN3; 2. DR REFSEQ_XP; XP_231864; GI:34855958; -. DR UniParc; UPI000021D4DF; -; -. DR ENSEMBL; ENSRNOP00000009094; ENSRNOG00000006857; M. SQ SEQUENCE 567 AA; 64617 MW; A59870602D82A471 CRC64; MELLYWCLLC LLLPLTSRTQ KLPTRDEELF QMQIRDKALF HDSSVIPDGA EISSYLFRDT PRRYFFMXEE DXTPLSVTVT PCDAPLEWKL SQELPEESSA DGSGDPEPLD QQKQQMTDVE GTELFSYKGN DVEYFLSSSS PSGLYQLELL STEKDTHFKV YATTTPESDQ PYPDLPYDPR VDVTSIGRTT VTLAWKQSPT ASMLKQPIEY CVVINKEHNF KSLCAAETKM SADDAFMVAP KPGLDFSPFD FAHFGFPTDN LGKDRSFLAK PSPKVGRHVY WRPKVDIKKI CIGSKNIFTV SDLKPNTQYY FDVFMVNTNT NMSTAFVGAF ARTKEEAKQK TVELKDGRVT DVVVKRKGKK FLRFAPVSSH QKVTLFIHSC MDTVQVQVRR DGKLLLSQNV EGIRQFQLRG KPKGKYLIRL KGNKKGASML KILATTRPSK HAFPSLPDDT RIKAFDKLRT CSSVTVAWLG TQERRKFCIY RKEVGGNYSE EQKRRERNQC LGPDTRKKSE KVLCKYFHSQ NLQKAVTTET IRDLQPGKSY LLDVYVVGHG GHSVKYQSKL VKTRKVC // ID IPI00187889.2 IPI; PRT; 452 AA. AC IPI00187889; DT 14-MAR-2003 (IPI Rat rel. 1.0, Created) DT 18-NOV-2003 (IPI Rat rel. 1.9, Last sequence update) OS Rattus norvegicus (Rat). OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; OC Mammalia; Eutheria; Rodentia; Sciurognathi; Muridae; Murinae; Rattus. OX NCBI_TaxID=10116; CC -!- CHROMOSOME: 4. DR InterPro; IPR001909; KRAB. DR InterPro; IPR007087; Znf_C2H2. DR InterPro; IPR007086; Znf_C2H2_sub. DR PRINTS; PR00048; ZINCFINGER. DR ProDom; PD000003; Znf_C2H2; 11. DR SMART; SM00349; KRAB; 1. DR SMART; SM00355; ZnF_C2H2; 12. DR PROSITE; PS50805; KRAB; 1. DR PROSITE; PS00028; ZINC_FINGER_C2H2_1; 12. DR PROSITE; PS50157; ZINC_FINGER_C2H2_2; 12. DR UniParc; UPI000021D4E0; -; -. DR ENSEMBL; ENSRNOP00000009095; ENSRNOG00000006726; M. SQ SEQUENCE 452 AA; 52613 MW; 99E3FC9CCDD5EB25 CRC64; QGPVTLRDVT VEFTKAEWKL LTPAQKSLYK NVMLETYSHL VSVGYRVVKP SMISKLKKGK EPWPLGAEFL RRSCGDKRRT VHDPKARHQE QQAGTARQKG ELAKRQKTPT RHESYDCSKC GKSFCQKSSL LAHQETHTKK SYKCDKCGQA FYKNEDLSIH QKVHTRDKTY PCKECNKIFY HLSSLTRHLR IHAGEKPYEC SQCEKSFYQK PHLTEHQKTH TGEKPFECKE CGKFFYVKAY LLVHQKTHTG EKPFECKECG KFFSQKSHLT VHQRTHTGEK PYKCKECGKL FSRNSHLITH QRTHTGEKPY KCKECGNRFY QKSALTVHQR THTGEKPFEC SKCGKHFYYK SDLTKHERKH TGEKPYECAE CGKSFSVNSV LRLHERTHTG EKPYACEICG KSFSQKSHFV VHQRKHTGEK PYKCQECGKS FIKKSQLTEH QKTHSKKGKT NK // ID IPI00187892.5 IPI; PRT; 385 AA. AC IPI00187892; IPI00187718; DT 14-MAR-2003 (IPI Rat rel. 1.0, Created) DT 06-NOV-2003 (IPI Rat rel. 1.8, Last sequence update) DE RETINOL DEHYDROGENASE 10 (ALL-TRANS). OS Rattus norvegicus (Rat). OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; OC Mammalia; Eutheria; Rodentia; Sciurognathi; Muridae; Murinae; Rattus. OX NCBI_TaxID=10116; CC -!- CHROMOSOME: 5. DR InterPro; IPR002198; ADH_short. DR InterPro; IPR002347; Adh_short_C2. DR PRINTS; PR00081; GDHRDH. DR PRINTS; PR00080; SDRFAMILY. DR PROSITE; PS00061; ADH_SHORT; 1. DR ENSEMBL; ENSRNOP00000009096; ENSRNOG00000006681; M. DR UniParc; UPI000017E0C4; -; -. DR REFSEQ_NP; NP_852143; GI:31324556; -. DR TREMBL; Q80ZF7; Q80ZF7; -. SQ SEQUENCE 385 AA; 42502 MW; 9D6D964AA640C243 CRC64; SGADSGRSLR VRIAVTSAPG ARSWAVWRGE GEDTVLGSCG RGVAMNIVVE FFLVTFKVLW AFVLAAARWL VRPKEKSVAG QVCLITGAGS GLGRLFALEF ARRRALLVLW DINTQSNEET AGMVRHIYRD LEAADAAALQ AGNGEEEILP PCNLQVFTYT CDVGKRENVY LTAERVRKEV GEVSVLVNNA GVVSGHHLLE CPDELIERTM MVNCHAHFWT TKAFLPTMLE INHGHIVTVA SSLGLFSTAG VEDYCASKFG VVGFHESLSH ELKAAEKDGI KTTLVCPYLV DTGMFRGCRI RKEIEPFLPP LKPDYCVKQA MKAILTDQPM ICTPRLMYIV TFMKSILPFE AVVCMYRFLG ADKCMYPFIA QRKQATNNNE AKNGI // ID IPI00363066.2 IPI; PRT; 173 AA. AC IPI00363066; IPI00187897; DT 02-OCT-2003 (IPI Rat rel. 1.7, Created) DT 18-NOV-2003 (IPI Rat rel. 1.9, Last sequence update) DE HYPOTHETICAL PROTEIN XP_346887. OS Rattus norvegicus (Rat). OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; OC Mammalia; Eutheria; Rodentia; Sciurognathi; Muridae; Murinae; Rattus. OX NCBI_TaxID=10116; CC -!- CHROMOSOME: 10. DR InterPro; IPR001878; Znf_CCHC. DR PRINTS; PR00939; C2HCZNFINGER. DR REFSEQ_XP; XP_346888; GI:34870719; -. DR UniParc; UPI000021D4E1; -; -. DR ENSEMBL; ENSRNOP00000009098; ENSRNOG00000006943; M. SQ SEQUENCE 173 AA; 18715 MW; CF9AE93D01586985 CRC64; MATPMHRLIA RRQAEANKQH VRCQKCLEFG HWTYECKGKR KYLHRPSRTA ELKKALKEKE NRLLQQSMGE TNTERKTKKK RRPKSVTSTS SSDSSASESS SESETSASSS SEDSDADGSL SSSSSSSAYS SSSSSSSSSS SSSSDSDSSS SSSSSSSSES SSDDEPPKKR KKK // ID IPI00187899.2 IPI; PRT; 119 AA. AC IPI00187899; DT 14-MAR-2003 (IPI Rat rel. 1.0, Created) DT 18-NOV-2003 (IPI Rat rel. 1.9, Last sequence update) OS Rattus norvegicus (Rat). OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; OC Mammalia; Eutheria; Rodentia; Sciurognathi; Muridae; Murinae; Rattus. OX NCBI_TaxID=10116; CC -!- CHROMOSOME: 4. DR InterPro; IPR001627; Sema. DR Pfam; PF01403; Sema; 1. DR UniParc; UPI000021D4E2; -; -. DR ENSEMBL; ENSRNOP00000009099; ENSRNOG00000023409; M. SQ SEQUENCE 119 AA; 13778 MW; D1B4FC951A2AE551 CRC64; PLFISELLEL NRTSIFQSPF GFLDLHTMLL DEYQERLFVG GRDLVYSLNL ERVSDGYREI YWPSTAVKVE ECIMKGKDAN ECANYVRVLH HYNRTHLLTC ATGAFDPHCA FIRVGHHSE // ID IPI00187901.1 IPI; PRT; 275 AA. AC IPI00187901; DT 14-MAR-2003 (IPI Rat rel. 1.0, Created) DT 14-MAR-2003 (IPI Rat rel. 1.0, Last sequence update) DE FOS-RELATED ANTIGEN 1. OS Rattus norvegicus (Rat). OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; OC Mammalia; Eutheria; Rodentia; Sciurognathi; Muridae; Murinae; Rattus. OX NCBI_TaxID=10116; CC -!- CHROMOSOME: 1. DR InterPro; IPR008917; Euk_transcr_DNA. DR InterPro; IPR000837; Leuzip_Fos. DR InterPro; IPR004827; TF_bZIP. DR Pfam; PF00170; bZIP; 1. DR PRINTS; PR00042; LEUZIPPRFOS. DR SMART; SM00338; BRLZ; 1. DR PROSITE; PS50217; BZIP; 1. DR PROSITE; PS00036; BZIP_BASIC; 1. DR UniParc; UPI000012ABCD; -; -. DR SWISS-PROT; P10158; FRA1_RAT; M. DR ENSEMBL; ENSRNOP00000027891; ENSRNOG00000020552; -. DR Superfamily; SSF47454; Euk_transcr_DNA; 1. DR REFSEQ_NP; NP_037085; GI:6978851; -. DR LocusLink; 25445; Fosl1; -. SQ SEQUENCE 275 AA; 30115 MW; 103726AD5D1FAB2F CRC64; MYRDFGEPGP SSGAGSAYGR PAQPQQAQTQ TVQQQKFHLV PSINAVSGSQ ELQWMVQPHF LGPSGYPRPL TYPQYSPPQP RPGVIRALGP PPGVRRRPCE QISPEEEERR RVRRERNKLA AAKCRNRRKE LTDFLQAETD KLEDEKSGLQ REIEELQKQK ERLELVLEAH RPICKIPEED KKDTGGTSST SGAGSPPGPC RPVPCISLSP GPVLEPEALH TPTLMTTPSL TPFTPSLVFT YPSTPEPCSS AHRKSSSSSG DPSSDPLGSP TLLAL // ID IPI00203121.1 IPI; PRT; 960 AA. AC IPI00203121; DT 14-MAR-2003 (IPI Rat rel. 1.0, Created) DT 14-MAR-2003 (IPI Rat rel. 1.0, Last sequence update) DE SPLICE ISOFORM SEMA Y-L OF Q9WTL3. OS Rattus norvegicus (Rat). OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; OC Mammalia; Eutheria; Rodentia; Sciurognathi; Muridae; Murinae; Rattus. OX NCBI_TaxID=10116; CC -!- CHROMOSOME: 2. DR UniParc; UPI0000135A73; -; -. DR SWISS-PROT; Q9WTL3-1; SM6C_RAT; M. DR REFSEQ_NP; NP_059004; GI:25742793; -. DR ENSEMBL; ENSRNOP00000028652; ENSRNOG00000021101; -. SQ SEQUENCE 960 AA; 102610 MW; C88293C5607E6086 CRC64; MPRAPHSMPL LLLLLLSLPQ AQTAFPQDPI PLLTSDLQGT SPSSWFRGLE DDAVAAELGL DFQRFLTLNR TLLVAARDHV FSFDLQAQEE GEGLVPNKFL TWRSQDMENC AVRGKLTDEC YNYIRVLVPW DSQTLLACGT NSFSPVCRSY GITSLQQEGE ELSGQARCPF DATQSTVAIS AEGSLYSATA ADFQASDAVV YRSLGPQPPL RSAKYDSKWL REPHFVYALE HGDHVYFFFR EVSVEDARLG RVQFSRVARV CKRDMGGSPR ALDRHWTSFL KLRLNCSVPG DSTFYFDVLQ SLTGPVNLHG RSALFGVFTT QTNSIPGSAV CAFYLDDIER GFEGKFKEQR SLDGAWTPVS EDKVPSPRPG SCAGVGAAAL FSSSQDLPDD VLLFIKAHPL LDPAVPPATH QPLLTLTSRA LLTQVAVDGM AGPHRNTTVL FLGSNDGTVL KVLPPGGQSL GPEPIILEEI DAYSHARCSG KRSPRAARRI IGLELDTEGH RLFVAFPGCI VYLSLSRCAR HGACQRSCLA SLDPYCGWHR FRGCVNIRGP GGTDVDLTGN QESMEHGDCQ DGATGSQSGP GDSAYVLLGP GPSPETPSSP SDAHPGPQSS TLGAHTQGVR RDLSPASASR SIPIPLLLAC VAAAFALGAS VSGLLVSCAC RRANRRRSKD IETPGLPRPL SLRSLARLHG GGPEPPPPPK DGDAAQTPQL YTTFLPPPEG GSPPELACLP TPETTPELPV KHLRASGGPW EWNQNGNNAS EGPGRPRGCS AAGGPAPRVL VRPPPPGCPG QEVEVTTLEE LLRYLHGPQP PRKGSEPLAS APFTSRPPAS EPGAALFVDS SPMPRDCVPP LRLDVPPDGK RAAPSGRPAL SAPAPRLGVS GSRRLPFPTH RAPPGLLTRV PSGGPSRYSG GPGRHLLYLG RPDGHRGRSL KRVDVKSPLS PKPPLATPPQ PAPHGSHFNF // ID IPI00230803.1 IPI; PRT; 928 AA. AC IPI00230803; IPI00208019; DT 09-APR-2003 (IPI Rat rel. 1.1, Created) DT 09-APR-2003 (IPI Rat rel. 1.1, Last sequence update) DE SPLICE ISOFORM SEMA Y-S OF Q9WTL3. OS Rattus norvegicus (Rat). OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; OC Mammalia; Eutheria; Rodentia; Sciurognathi; Muridae; Murinae; Rattus. OX NCBI_TaxID=10116; CC -!- CHROMOSOME: 2. DR InterPro; IPR000694; PRO_rich. DR InterPro; IPR001627; Sema. DR SMART; SM00630; Sema; 1. DR PROSITE; PS50099; PRO_RICH; 1. DR UniParc; UPI000002B3CF; -; -. DR SWISS-PROT; Q9WTL3-2; SM6C_RAT; M. DR ENSEMBL; ENSRNOP00000028645; ENSRNOG00000021101; -. SQ SEQUENCE 928 AA; 99521 MW; 386B08143D19FCDC CRC64; MPRAPHSMPL LLLLLLSLPQ AQTAFPQDPI PLLTSDLQGT SPSSWFRGLE DDAVAAELGL DFQRFLTLNR TLLVAARDHV FSFDLQAQEE GEGLVPNKFL TWRSQDMENC AVRGKLTDEC YNYIRVLVPW DSQTLLACGT NSFSPVCRSY GITSLQQEGE ELSGQARCPF DATQSTVAIS AEGSLYSATA ADFQASDAVV YRSLGPQPPL RSAKYDSKWL REPHFVYALE HGDHVYFFFR EVSVEDARLG RVQFSRVARV CKRDMGGSPR ALDRHWTSFL KLRLNCSVPG DSTFYFDVLQ SLTGPVNLHG RSALFGVFTT QTNSIPGSAV CAFYLDDIER GFEGKFKEQR SLDGAWTPVS EDKVPSPRPG SCAGVGAAAL FSSSQDLPDD VLLFIKAHPL LDPAVPPATH QPLLTLTSRA LLTQVAVDGM AGPHRNTTVL FLGSNDGTVL KVLPPGGQSL GPEPIILEEI DAYSHARCSG KRSPRAARRI IGLELDTEGH RLFVAFPGCI VYLSLSRCAR HGACQRSCLA SLDPYCGWHR FRGCVNIRGP GGTDVDLTGN QESMEHGDCQ DGATGSQSGP GDSAYGVRRD LSPASASRSI PIPLLLACVA AAFALGASVS GLLVSCACRR ANRRRSKDIE TPGLPRPLSL RSLARLHGGG PEPPPPPKDG DAAQTPQLYT TFLPPPEGGS PPELACLPTP ETTPELPVKH LRASGGPWEW NQNGNNASEG PGRPRGCSAA GGPAPRVLVR PPPPGCPGQE VEVTTLEELL RYLHGPQPPR KGSEPLASAP FTSRPPASEP GAALFVDSSP MPRDCVPPLR LDVPPDGKRA APSGRPALSA PAPRLGVSGS RRLPFPTHRA PPGLLTRVPS GGPSRYSGGP GRHLLYLGRP DGHRGRSLKR VDVKSPLSPK PPLATPPQPA PHGSHFNF // ID IPI00187925.1 IPI; PRT; 172 AA. AC IPI00187925; DT 14-MAR-2003 (IPI Rat rel. 1.0, Created) DT 14-MAR-2003 (IPI Rat rel. 1.0, Last sequence update) DE ACIDIC PROLINE-RICH PROTEIN PRP25 PRECURSOR. OS Rattus norvegicus (Rat). OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; OC Mammalia; Eutheria; Rodentia; Sciurognathi; Muridae; Murinae; Rattus. OX NCBI_TaxID=10116; CC -!- CHROMOSOME: 4. DR InterPro; IPR006030; Mollsc_rhodpsn_C. DR PRINTS; PR00239; RHODOPSNTAIL. DR UniParc; UPI000013233B; -; -. DR SWISS-PROT; P10164; PRP2_RAT; M. DR ENSEMBL; ENSRNOP00000007180; ENSRNOG00000005395; -. SQ SEQUENCE 172 AA; 17416 MW; F63BFBD05459D6EA CRC64; MLVVLFTAVL LTLSYAQEPG DELQILDQTP NQKPPPPGFP PRPPANGSQQ GPPPQGGPQQ SPLQPGKPQD PPPQGSPQQK PPQPGKPQGP PPPGGPQKKP PQPGKPQGPP PPGGPQKKPP QPGKPQGPTP PGGPQQKPPQ AGKPQGPPPP GGPQQKPPQP GNQQGPPPPG GP // ID IPI00187926.1 IPI; PRT; 23 AA. AC IPI00187926; DT 14-MAR-2003 (IPI Rat rel. 1.0, Created) DT 14-MAR-2003 (IPI Rat rel. 1.0, Last sequence update) DE ACIDIC PROLINE-RICH PROTEIN PRP18 PRECURSOR. OS Rattus norvegicus (Rat). OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; OC Mammalia; Eutheria; Rodentia; Sciurognathi; Muridae; Murinae; Rattus. OX NCBI_TaxID=10116; DR UniParc; UPI0000132333; -; -. DR SWISS-PROT; P10165; PRP1_RAT; M. SQ SEQUENCE 23 AA; 2380 MW; 875B4F61FD056949 CRC64; MLVVLLTAAL LVLSSAHGVD EEV // ID IPI00387637.1 IPI; PRT; 1847 AA. AC IPI00387637; DT 18-NOV-2003 (IPI Rat rel. 1.9, Created) DT 18-NOV-2003 (IPI Rat rel. 1.9, Last sequence update) OS Rattus norvegicus (Rat). OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; OC Mammalia; Eutheria; Rodentia; Sciurognathi; Muridae; Murinae; Rattus. OX NCBI_TaxID=10116; CC -!- CHROMOSOME: 7. DR InterPro; IPR001590; Peptidase_M12B. DR InterPro; IPR006025; Pept_M_Zn_BS. DR InterPro; IPR000884; TSP1. DR SMART; SM00209; TSP1; 11. DR PROSITE; PS50215; ADAM_MEPRO; 1. DR PROSITE; PS50092; TSP1; 10. DR PROSITE; PS00142; ZINC_PROTEASE; 1. DR UniParc; UPI000021DDDB; -; -. DR ENSEMBL; ENSRNOP00000007803; ENSRNOG00000005860; M. SQ SEQUENCE 1847 AA; 206111 MW; 371DDAC8BF46DEBF CRC64; MRVAKWLTGL LCPISLLLTG SWEVRFHPRQ EALVKTLASY EVVTPTRVNE FGDVFPQNRH FSRKKRSSGV PEPPPLRTHY RISAYGQLFQ LNLSADSAFL AAGYTEVHLG TPVPGPGGRS AEPPDLRHCF YRGQVNARED HIAVFSLCGG LMGTFKANDG EYFLEPVLKA DGSEHEDDHN KPHLIYRQEV KRNAFVRSQS HGPCGVSENQ TEKTALPSPS FRNTTGDLNR RKGAVFGLEG ERSRLHSRSK RFLSYPRYVE VMVTADAKMV RHHGQNLQHY VLTLMSIVAA IYKDSSIGNL INIVIVKLVI IHSEQEGPVI SFNAATTLRN FCLWQQSQNV LDDAHPSHHD TAVLITREDI CGAKEKCDTL GLAELGTLCD PSRSCSISEE NGLSAAFTIA HELGHVFNVP HDDSFKCKES GTKHQYHVMA PTLNYHTSPW TWSACSQKHI TEFLDTGHGE CLLDKPNGRT YDLSPQLPGS VYDGNKQCEL MFGPGSQVCP YLKQCRRLWC TSAEGVHKGC RTQHMPLADG TSCGPGMVVS SQGESCIQSF WDEQLLSAVL VAGCHLWSAR GGDGIAGPRN GGRYCVGRRM KFRSCNTDSC PKGKRDFREK QCSDFDGKHF DISGLPPNVR WLPKYSGIAV KDRCKLYCRV AGTTSFYQLK DRVADGTPCG TETNDICVQG LCRQAGCDHV LNSKAKRDKC GVCGGDNSSC QTLAGVFNSA HYGYNVVVKI PAGATNIEIL QHSYSGRPED DNYLALSDTQ GNFLLNGNFV VSMAKKEINI QGAVFEYSGS NNSIERINST DRLEAELVLQ VLCVGNLYNP DVHYIFNIPI EERSNLFSWD PYGPWQDCTK MCQGLHRRKI ACIRKSDRAV VSDQSCSHLP LPLFVTERCN TDCELRWHIT GKSDCSSQCG QGYRTLDVHC MKYSVHKGQT VPVGDQYCGD QLKPPNREPC HGSCVLTRWH YSEWSQCSRS CGGGEKTRES YCVNGFGHRL AERECQELPR VVLGNCNDFP CPGWATSEWS ECPVTCGKGM KQRQVWCQRS EDPVGDDFCD ASTKPESLGP CELRACASWH VGPWGSCTVT CGHGYQVRAV KCVSEILGTV LDDRECPRAS RPSDRQVKEV SMDQKEMLMK QKGYRYCRDA HDGVADELNC AHWARPAEVS LCFSPCGEWQ AGDWSPCSAS CGHGKTTRRV LCVNYHQLVD ESYCDPEGRP VTEQECRLAA CPPSYSRSPS SSEQPSHGPG RNVPLTHKPE ENPDQGVQLS IRGNQWRTGP WGAVSFNSSV LPRLRHFDAD YKPSGGHKLC YSYFQCTQTC GAGVKSRFVI CQFPDGQMAQ EHSCELPKPP SMMQCHLRAC PDDVSWYRGS WKSCSASCGK GIKYREVLCI DQVQRKLEEK YCSHLHKPRT HKPCRSGRCP SWKANKWKEC SVTCGSGVQQ REVYCRLRGT GRVAEDMCEP STRPQVQRPC WHQDCTRYQW TTGDWLDCST SCKKKETYRL VKCVNERNMQ VNESLCDPLT KPVSIKKCRN SHCKYMVVTG DSSQCAGNCG LTYSQRITYC TRIQPPKKNA FHHQLRPVNY GQCPVIPSPQ VYKCDIRSCL RGATWKVGKW SKCSVTCGNG IMERRVACRT ENGWPSDLCL KRLKPDAQKK CYANDCKLLT TCKEIQVTNN ITKDGNYDLN VRGRILKIHC SGMQLENPRE YLPLVKVEDN FSEIYGLRLQ NPYECPFNGS RRADCACEND YPPAGYTVFS KVRVDLASMQ IKTTDLLFSR TLFGKAVPFA TAGDCYSAAR CPQGQFSINL AGTGMKVSST AKWLAQGRYA SVIIHRSQDG TKVYGRCGGF CGKCVPHVST GLPIQVL // ID IPI00324676.2 IPI; PRT; 334 AA. AC IPI00324676; IPI00230805; IPI00194685; DT 12-JUN-2003 (IPI Rat rel. 1.3, Created) DT 06-NOV-2003 (IPI Rat rel. 1.8, Last sequence update) DE HOMEOBOX PROTEIN HOX-A1. OS Rattus norvegicus (Rat). OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; OC Mammalia; Eutheria; Rodentia; Sciurognathi; Muridae; Murinae; Rattus. OX NCBI_TaxID=10116; CC -!- CHROMOSOME: 4. DR InterPro; IPR001356; Homeobox. DR InterPro; IPR000047; HTH_lambrepressr. DR PRINTS; PR00024; HOMEOBOX. DR PRINTS; PR00031; HTHREPRESSR. DR ProDom; PD000010; Homeobox; 1. DR SMART; SM00389; HOX; 1. DR PROSITE; PS00027; HOMEOBOX_1; 1. DR PROSITE; PS50071; HOMEOBOX_2; 1. DR ENSEMBL; ENSRNOP00000007807; ENSRNOG00000005628; M. DR UniParc; UPI000018600D; -; -. DR SWISS-PROT; O08656; HXA1_RAT; -. DR REFSEQ_NP; NP_037207; GI:6981040; -. SQ SEQUENCE 334 AA; 36293 MW; 73DDE151DA4ADDA5 CRC64; MDNARMNSFL EYPILGSGDS GTCSARVYSS DHGITTFQSC AVSANSCGGD DRFLGGRGVQ ITSPHHHHHH HHHPQPATYQ TSGNLGVSYS HSSCGPSYGA QNFSAPYGPY GLNQEADVSG GYPPCAPAVY SGNLSSPMVQ HHHHHQGYAG GTVGSPQYIH HSYGQEHQSL ALATYNNSLS PLHASHQEAC RSPASETSSP AQTFDWMKVK RNPPKTGKVG EYGYVGQPNA VRTNFTTKQL TELEKEFHFN KYLTRARRVE IAASLQLNET QVKIWFQNRR MKQKKREKEG LLPISPATPP GSDEKTEESS EKSSSSPSAP SPASSTSDTL TTSH // ID IPI00387638.1 IPI; PRT; 434 AA. AC IPI00387638; DT 18-NOV-2003 (IPI Rat rel. 1.9, Created) DT 18-NOV-2003 (IPI Rat rel. 1.9, Last sequence update) OS Rattus norvegicus (Rat). OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; OC Mammalia; Eutheria; Rodentia; Sciurognathi; Muridae; Murinae; Rattus. OX NCBI_TaxID=10116; CC -!- CHROMOSOME: 8. DR UniParc; UPI000021DDDC; -; -. DR ENSEMBL; ENSRNOP00000007809; ENSRNOG00000005934; M. SQ SEQUENCE 434 AA; 48136 MW; 6A4887F34628F1C8 CRC64; VSPGDSEAKP LIFTFVPTLR RLPTHIQLAD TSKFLVKIPE EPTDKNPETV NRFEYSDHMT FSCESKEERD QRILDYPSEV SGKNSQRKEF NTKEPQGMQK GDLFKAEYVF IVDSDGEDEA TCRQGEQGPP GATGNIATRP KSLAISSSLA SDVVRPKVRG VDVKVSSHPE IPHGIAPQQK HGQQYKTKSS YKAFAAIPTN TLLLEQKALD EPARTESNSK ASVSDLPVEL CFPAQLRQQT EELCATIDKV LQDSLSMHSS DSPSRPSQTM LGSETIKTPT THPRAAGRET KYANLSSSSS TTSESQLTKP GVIRPVPIKS KLFLKKEEEV YEPNPFSKYL EDSSGLFSEQ DMAIPHKPVS LHPLYQSKLY PPAKSLLRPQ TLSHADCLTP GPFSHLSSFS LRDEQEKSPT LLSQDTYNHP MVTIPEHDTL DSKE // ID IPI00357897.1 IPI; PRT; 245 AA. AC IPI00357897; IPI00190446; DT 02-OCT-2003 (IPI Rat rel. 1.7, Created) DT 02-OCT-2003 (IPI Rat rel. 1.7, Last sequence update) DE SIMILAR TO EXOSOME COMPLEX EXONUCLEASE RRP40 (RIBOSOMAL RNA PROCESSING DE PROTEIN 40) (P10) (CGI-102). OS Rattus norvegicus (Rat). OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; OC Mammalia; Eutheria; Rodentia; Sciurognathi; Muridae; Murinae; Rattus. OX NCBI_TaxID=10116; CC -!- CHROMOSOME: 5. DR InterPro; IPR008994; Nucleic_acid_OB. DR UniParc; UPI00001CF6A5; -; -. DR REFSEQ_XP; XP_233001; GI:34935161; M. DR ENSEMBL; ENSRNOP00000016582; ENSRNOG00000012409; -. DR Superfamily; SSF50249; Nucleic_acid_OB; 1. SQ SEQUENCE 245 AA; 26337 MW; FBFB700F0D0E950B CRC64; MAEVSAGAES VAGCRARAVH KVLNQVVLPG EELVLPDHED ADGLGGPGEQ PLRLNAGARP RLRIVCGPGL RRCGDRLLYV PVKGDHVIGI VVAKSGDIFK VDVGGSEPAS LSYLAFEGAT KRNRPNVQVG DLIYGQCVVA NKDMEPEMVC IDSCGRANGM GVIGQDGLLF KVTLGLIRKL LAPDCEIVQE LGKLYPLEIV FGMNGRIWVK AKTIQQTLIL ANVLEACEHM TTEQRKQIFA RLAES // ID IPI00357898.1 IPI; PRT; 493 AA. AC IPI00357898; IPI00193992; DT 02-OCT-2003 (IPI Rat rel. 1.7, Created) DT 02-OCT-2003 (IPI Rat rel. 1.7, Last sequence update) DE SIMILAR TO RNA POLYMERASE I ASSOCIATED FACTOR (PAF53). OS Rattus norvegicus (Rat). OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; OC Mammalia; Eutheria; Rodentia; Sciurognathi; Muridae; Murinae; Rattus. OX NCBI_TaxID=10116; CC -!- CHROMOSOME: 5. DR UniParc; UPI00001CF6A7; -; -. DR REFSEQ_XP; XP_233004; GI:34935097; M. DR ENSEMBL; ENSRNOP00000029128; ENSRNOG00000012664; -. SQ SEQUENCE 493 AA; 55397 MW; 05063E0EDDB321EC CRC64; MATPDSPGMD GQTGDTETEV LQSARWQYCG EPDDRQKAVL VQFSNGKLQN PGNMRFTLYN STDLVNPRQK CHRILAAETD RLSYVGNNFG TGALKCNTLC RHFVGILNKT SGQMEVYDAE VFNMQPLFAE DSIEHGPPLE NQNKTFRDKL DSCIEAFGST KQKRSLNSRR MNKVGSESLN FTVAKAAESI IDTKGVSALV SDAMQDDLQN DSLYLPPCHA DATKPEDVYR FEDSILADER VSNLQAVMFV HIGRARLCRR VVIVCDVNRC DIQIFSPCPR AASKSHVLDP QPVLSPAEYD ALESPSEAFR KVMSEDILKM VEENSHCSFI IEMLKSLPAD EVQRNRQARS IWFLDALLRF RAQKVIKGKS ALGPGIPHII NTKLLKQFTC LTYNNDSLRN LISSSMKAKI TAYAIILALH INNFQIDLTV LQRDLKLSEK RMIEIARAMR LKISKRKVSL ADGREEDHRL GTLSVPLPPA QTSDRQSKRK KMS // ID IPI00189187.2 IPI; PRT; 670 AA. AC IPI00189187; DT 14-MAR-2003 (IPI Rat rel. 1.0, Created) DT 18-NOV-2003 (IPI Rat rel. 1.9, Last sequence update) DE SIMILAR TO 5930421I10 PROTEIN. OS Rattus norvegicus (Rat). OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; OC Mammalia; Eutheria; Rodentia; Sciurognathi; Muridae; Murinae; Rattus. OX NCBI_TaxID=10116; CC -!- CHROMOSOME: 5. DR InterPro; IPR000210; BTB_POZ. DR InterPro; IPR007087; Znf_C2H2. DR SMART; SM00225; BTB; 1. DR SMART; SM00355; ZnF_C2H2; 2. DR PROSITE; PS50097; BTB; 1. DR PROSITE; PS00028; ZINC_FINGER_C2H2_1; 1. DR PROSITE; PS50157; ZINC_FINGER_C2H2_2; 2. DR UniParc; UPI00001C922E; -; -. DR REFSEQ_XP; XP_233005; GI:27714553; M. DR ENSEMBL; ENSRNOP00000017047; ENSRNOG00000012726; -. SQ SEQUENCE 670 AA; 73378 MW; BA8958D8BA5134DC CRC64; MDFPGHFEQI FQQLNYQRLH GQLCDCVIVV GNRHFKAHRS VLAACSTHFR ALFSVAEGDQ TMNMIQLDSE VVTAEAFAAL IDMMYTSTLM LGESNVMDVL LAASHLHLNS VVKACKHYLT TRTLPMSPPS ERVQEQSARM QRSFMLQQLG LSIVSSALSS SQSGEEPSAP MSSSMRNNLD QRTPFPMRRL HKRKQTVEER ARQRLRSSMD ESAISDVTPE SGPSGVHSRE EFFSPDSLKI VDNPKPDGMA DNQEDSAMMF DRPFGAQEDA QMPSQSDGSA GNMASRATQV ETSFEQEAVA EKGSFQCENP EVGLGEKEHM RVVVKSEPLS SPEPQDEVSD VTSQAEGSES VEVEGVVVSA EKIDLSPESS DRSFSDPQSS TDRVGDIHIL EVTNNLEHKT SFSISNFLNK SRGSNFSTSQ STDDNLPNTT SDCRLEGEAP YLLSPEAGPA GGPSSAPGSH VENPFSEPAD SHFVRPVQEV MGLPCVQTSG YQGEQFGMDF PRSGLGLHSS FSRAMMGSPR GGASNFPYYR RIAPKMPVVT SVRSSQISEN QASSQLMMNG ASSFENGHSS QPGPPQLTRA SADVLSKCKK ALSEHNVLVV EGARKYACKI CCKTFLTLTD CKKHIRVHTG EKPYACLKCG KRFSQSSHLY KHSKTTCLRW QSSNLPSTLL // ID IPI00187975.2 IPI; PRT; 255 AA. AC IPI00187975; DT 14-MAR-2003 (IPI Rat rel. 1.0, Created) DT 18-NOV-2003 (IPI Rat rel. 1.9, Last sequence update) OS Rattus norvegicus (Rat). OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; OC Mammalia; Eutheria; Rodentia; Sciurognathi; Muridae; Murinae; Rattus. OX NCBI_TaxID=10116; CC -!- CHROMOSOME: 4. DR UniParc; UPI000021D4E3; -; -. DR ENSEMBL; ENSRNOP00000007811; ENSRNOG00000005913; M. SQ SEQUENCE 255 AA; 28387 MW; FD346170948BBE1F CRC64; MEDSMDMNMH ALRPQNYLFS CELKPDKDYH FKEDNDENEH QLSLEQLGLG AKDELYIPIV EAEAMKYEGS PVKTQATLKI SVQPTVSLGG FKITPPVVLS LKCGSGPVHI IGQHLVAVEE DAESEDEENV KLLGMSGKRS APGGEEDDDF DEEETEENFP VKKTVGNTTA KSKQNGKDLK PRPPRRVTSP SKKTEKTPKT PKEPSSVEDI KAKMQAHIEK GGSLPKVEAK FINYVNCFQM TDQGAIQDLW QQKKS // ID IPI00357926.2 IPI; PRT; 599 AA. AC IPI00357926; IPI00187976; DT 02-OCT-2003 (IPI Rat rel. 1.7, Created) DT 18-NOV-2003 (IPI Rat rel. 1.9, Last sequence update) DE SIMILAR TO EGF-LIKE-DOMAIN, MULTIPLE 5. OS Rattus norvegicus (Rat). OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; OC Mammalia; Eutheria; Rodentia; Sciurognathi; Muridae; Murinae; Rattus. OX NCBI_TaxID=10116; CC -!- CHROMOSOME: 5. DR InterPro; IPR006209; EGF_like. DR InterPro; IPR006210; IEGF. DR InterPro; IPR002049; Laminin_EGF. DR PRINTS; PR00011; EGFLAMININ. DR SMART; SM00181; EGF; 4. DR SMART; SM00180; EGF_Lam; 5. DR PROSITE; PS00022; EGF_1; 2. DR PROSITE; PS01186; EGF_2; 1. DR PROSITE; PS50027; EGF_LAM; 2. DR PROSITE; PS01248; LAMININ_TYPE_EGF; 5. DR ENSEMBL; ENSRNOP00000007812; ENSRNOG00000005932; M. DR UniParc; UPI000021D4E4; -; -. DR REFSEQ_XP; XP_233047; GI:27714755; -. SQ SEQUENCE 599 AA; 62886 MW; 5731C23822ACFBA2 CRC64; MNGGAERAMR SLPSLGGLAL FCCAAAAAAS AASAGNVTGG GGAEGQVVAS PSPGLREQTS SPFSKAAAPT AQAPRTGPPR TTVHRTGAAT PSAGSPETIP VRTSAQPAAT LFPVVDLSSA TPSEDGHTPT TEPLPSRPAP TTLASTAGQA PTTSVVTTAQ ASSTPGTPTA ESPDRGRNSS RVPPTAPVTE APTPPPPEYM CNCSEVGSLD VKRCNQTTGQ CDCHVGYQGL HCDTCKEGFY LNHTVGLCLP CHCSPRGAVS ILCNSSGNCQ CKLGVTGSMC DQCQDGHYGF GKTGCLPCQC NNRSDSCDVL TGACLNCQEN TKGEHCEECK EGFYQSPDAA RECLRCPCSA VTSTGNCTIE FGALEPTCDQ CKDGYTGQNC NTCENGYYHS DSICLQCECH GHVDPIKTPK ICKPESGECI NCLHNTTGLW CEKCLEGYVR DLQRNCIKQE VIVPTPEGST ILVSNASLTT SVPTPVINST FAPTTLQTIF SVSSSENSTS ALADVSWTQF NIIILTVIII VVVLLMGFVG AVYMYREYQN RKLNAPFWTI ELKEDNISFS SYHDSIPNAD VSGLLEDDAN EVAPNGQLTL TTPIHNYKA // ID IPI00187977.2 IPI; PRT; 605 AA. AC IPI00187977; DT 14-MAR-2003 (IPI Rat rel. 1.0, Created) DT 18-NOV-2003 (IPI Rat rel. 1.9, Last sequence update) OS Rattus norvegicus (Rat). OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; OC Mammalia; Eutheria; Rodentia; Sciurognathi; Muridae; Murinae; Rattus. OX NCBI_TaxID=10116; CC -!- CHROMOSOME: 10. DR UniParc; UPI000021D4E5; -; -. DR ENSEMBL; ENSRNOP00000007813; ENSRNOG00000005606; M. SQ SEQUENCE 605 AA; 67185 MW; 5771BDB3356A0A2D CRC64; MSSLLDRLHA KFNQSRPWSE TIKLVRQVME KRVVMSSGGH QHLVSCLETL QKALKVTSLP AMTDRLESIA RQNGLGSHLS ASGTECYITS DMFYVEVQLD PAGQLCDVKV AHHGENPVSC PELVQQLREK NFDEFSKHLK GLVNLYNLPG DNKLKTKMYL ALQSLEQDLS KMAIMYWKAT NATPLDKILH GSVGYLTPRS GGHLMNMKYY ASPSDLLHDT TASPITLHEK NVPRSLGMNA SVTIEGTSAM YKLPIAPLIM GSHPADNKWT PSFSAVTSAN SVDLPACFFL KFPQPIPVSK AFVQKLQNCT GIPLFETPPT YLPLYELITQ FELSKDPDPL PLNHNMRFYA ALPGQQHCYF LNKDAPLPDG QSLQGTLVSK ITFQHPGRVP LILNMIRHQV AYNTLIGSCV KRTILKEDSP GLLQFEVCPL SESRFSVSFQ HPVNDSLVCV VMDVQDSTHV SCKLYKGLSD ALICTDDFIA KVVQRCMSIP VTMRAIRRKA ETIQADTPAL SLIAETVEDM VKKNLPPASS PGVEEKRQSK PSLGHLPPIQ VYSFSCKDGK DMKSTSTYVL LLDFNVLLLT SSVFGLHVKG LWTKCSDVQE YFIVS // ID IPI00187980.2 IPI; PRT; 444 AA. AC IPI00187980; DT 14-MAR-2003 (IPI Rat rel. 1.0, Created) DT 18-NOV-2003 (IPI Rat rel. 1.9, Last sequence update) OS Rattus norvegicus (Rat). OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; OC Mammalia; Eutheria; Rodentia; Sciurognathi; Muridae; Murinae; Rattus. OX NCBI_TaxID=10116; CC -!- CHROMOSOME: 3. DR InterPro; IPR007087; Znf_C2H2. DR InterPro; IPR007086; Znf_C2H2_sub. DR PRINTS; PR00048; ZINCFINGER. DR ProDom; PD000003; Znf_C2H2; 9. DR SMART; SM00355; ZnF_C2H2; 11. DR PROSITE; PS00028; ZINC_FINGER_C2H2_1; 9. DR PROSITE; PS50157; ZINC_FINGER_C2H2_2; 12. DR UniParc; UPI000021D4E6; -; -. DR ENSEMBL; ENSRNOP00000007815; ENSRNOG00000005949; M. SQ SEQUENCE 444 AA; 51427 MW; 5FD433F0A0AF555E CRC64; EFTQHGKIFA YHSHSQRHQQ IHTGEKSYEG IQYFESFAYH SSIQIHKRTH GGDKPSNCNQ CGKAFTAHSS LKMHKRIHTG EKPDEGNQRG KDVPQHSHLQ QHAGIHTVKC SQSGKDFACY TDLQIRQRTH TAEKAYECNL CGKAFVQHSH LERHGRSHTG EKPYKCNQCG KAFSQSSNLQ VHKRTHTGEK PFECKQCGKA FASQSGLQQH KRTHTGKRPF ECKQCDKAFA RHSHLQRHQR IHTVEKLYEC NQCGKSFAQN NHFIQHIRTH TGKKLYECKQ CNKAFACQSG LQYHRRTHTG EKPHGCNECG KTFIYHSYLQ IHRRTHTGEK PFECDQCGKA FARNNNLQVH KTIHTREKLC ECKQCGKAIC HSSLHVHKRT HAEEKPYECH QYDQAFACES GLLYHKTTHA GERPYGCNKY AKVFVLHSYL RIYKIIHTGE KFFE // ID IPI00187982.2 IPI; PRT; 326 AA. AC IPI00187982; DT 14-MAR-2003 (IPI Rat rel. 1.0, Created) DT 18-NOV-2003 (IPI Rat rel. 1.9, Last sequence update) OS Rattus norvegicus (Rat). OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; OC Mammalia; Eutheria; Rodentia; Sciurognathi; Muridae; Murinae; Rattus. OX NCBI_TaxID=10116; CC -!- CHROMOSOME: 7. DR UniParc; UPI000021D4E7; -; -. DR ENSEMBL; ENSRNOP00000007816; ENSRNOG00000005956; M. SQ SEQUENCE 326 AA; 34856 MW; 6E810120AC690E77 CRC64; MGCSSSALNK AGDSSRSGSG VPSNENSSTV EQNKFCVAQP KPCTPGREAA FRGNAQKESH PPLERPKASV VPTANGVKSY HQLSLANDEI SGKEATDQSR PTKKTEPLVQ GGECELPQPG GKDDTLGTEE VKKDVEARAE VQALPGKAET EPLRMPAERD APGAGEDIEL PQAGTTKFLQ TAENILSLET AQELPPEEAM GRDKQPQVLE AIPKENSSPE IAEGSQSAEN GEKQQLSEAP GEAEQPQVLE IVLRENETPQ MPDGSQLVPT PVMNDSPCEA PDGVRNESQV TRENRVHPVG TAETAAEVEM TREIHPDKEE PHIEGK // ID IPI00387639.1 IPI; PRT; 951 AA. AC IPI00387639; DT 18-NOV-2003 (IPI Rat rel. 1.9, Created) DT 18-NOV-2003 (IPI Rat rel. 1.9, Last sequence update) OS Rattus norvegicus (Rat). OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; OC Mammalia; Eutheria; Rodentia; Sciurognathi; Muridae; Murinae; Rattus. OX NCBI_TaxID=10116; CC -!- CHROMOSOME: 8. DR InterPro; IPR007087; Znf_C2H2. DR SMART; SM00355; ZnF_C2H2; 9. DR PROSITE; PS00028; ZINC_FINGER_C2H2_1; 5. DR PROSITE; PS50157; ZINC_FINGER_C2H2_2; 1. DR UniParc; UPI000021DDDD; -; -. DR ENSEMBL; ENSRNOP00000007818; ENSRNOG00000005842; M. SQ SEQUENCE 951 AA; 105418 MW; 7EAD74BEDB169412 CRC64; NLKMAELFME CEEEELEPWQ KKVKEVEEDD DDEPIFVAEI ASSKPAISNI LNRVNPSSHS RGIKNGILNR GFTASFKPTS QRCPNSASNP VAALPVNFHP ESRSSDSSVI VQPFSKPGYV TNSPRVLSSN PSELLFDLTQ DTGLSHYQGG PTLSIAGLNE TSFLSKRPSG SDISSVNPKK PKPNENISGT DASSVVSSEK SPSVMSLQVV PSQGTNCSSN QSKNGTTFPR ACPKCNIHFN LLDPLKNHMT YCCPDMINNF LGLTKTDNLN SANEAKTLDS EKGKLIMLVN DFYYGKYEGD VQEEQKTHTT FKCFSCLKVL KNNIRFMNHM KHHLELEKQS SESWEKHTTC QHCYRQFPTP FQLQCHIEST HTPHEFSTIC KICELSFETE QILLQHMKDN HKPGEMPYIC QVCNYRSSLF SEVESHFRTS HENTKNLLCP FCLKVIKIAT PYMHHYMKHQ KKGIHRCTKC RLQFLTCKEK MDHKTQHHRT FVKPKQLEGL PPGTKVTIRA SVAPLQSGSS VTPSISASTS TLQLSPPRTE NVTAKNHVKL NTSTPNTTIS DPSKTNEIKS NGSKSKNRSK VSNMQKKQST LSNSNKKSKV NTALRNLRLR RGVHECIECS SEVKDFANHF PTYVHCSFCR YNTSCSKAYV NHMMSFHSNR PSKRYCIFKK HSENLRGISL VCLNCDFLTD VSGLDNMATH LSQHETHTCQ VLVEKVSVCI PTSERLSDVK VLLFQETARH STAEREPGAS HSESKQDKAP PSEDDTGRDA SVCEAAAAAN RERNVTASDT EDVRTSNDVL SRGPEVGTDN MEKEEQAHHT CQEMELKRDQ SSESTDDQSK EHSPTEAELS SEISQDLQLT PEGVGLGQCL RQGEEPESVN SDASEQDSVR LEPLTPSEVL EFEATEVCHS GEDPSASTSD AVSGGTGGSP GGSSPRRAES AADLAGGQEG S // ID IPI00387640.1 IPI; PRT; 78 AA. AC IPI00387640; DT 18-NOV-2003 (IPI Rat rel. 1.9, Created) DT 18-NOV-2003 (IPI Rat rel. 1.9, Last sequence update) OS Rattus norvegicus (Rat). OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; OC Mammalia; Eutheria; Rodentia; Sciurognathi; Muridae; Murinae; Rattus. OX NCBI_TaxID=10116; CC -!- CHROMOSOME: 1. DR UniParc; UPI000021DDDE; -; -. DR ENSEMBL; ENSRNOP00000037904; ENSRNOG00000025894; M. SQ SEQUENCE 78 AA; 9284 MW; AB61069A63C9E67F CRC64; MKKLCAFPLS FLVLKFSLIF CSLTETGCFW RIKNNEDDDG DLRNDCGFVL VANEEITKDR YYKDLIYFRF FLDHLILT // ID IPI00387641.1 IPI; PRT; 323 AA. AC IPI00387641; DT 18-NOV-2003 (IPI Rat rel. 1.9, Created) DT 18-NOV-2003 (IPI Rat rel. 1.9, Last sequence update) DE LIVER REGENERATION-RELATED PROTEIN LRRG07. OS Rattus norvegicus (Rat). OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; OC Mammalia; Eutheria; Rodentia; Sciurognathi; Muridae; Murinae; Rattus. OX NCBI_TaxID=10116; CC -!- CHROMOSOME: 17. DR InterPro; IPR001395; Aldo/ket_red. DR PRINTS; PR00069; ALDKETRDTASE. DR ProDom; PD000288; Aldo/ket_red; 1. DR PROSITE; PS00798; ALDOKETO_REDUCTASE_1; 1. DR PROSITE; PS00062; ALDOKETO_REDUCTASE_2; 1. DR UniParc; UPI000021DDDF; -; -. DR TREMBL; Q7TNW9; Q7TNW9; -. DR REFSEQ_XP; XP_344627; GI:34876593; -. DR ENSEMBL; ENSRNOP00000037905; ENSRNOG00000022588; M. SQ SEQUENCE 323 AA; 37013 MW; 8573AC78E638F951 CRC64; MSSKLHCVKL NDGHFIPALG FGTYKPKEVP KSKSLEAAHL AIDVGYRHID TASAYQVEEE IGQAIQSKIK AGVVKRKDMF ITTKLWCSCF RTEMVRPALE KSLKNLQLDY VDLFLIHYPV PIKSSVDESP LDEKGKFLLD TVDFCDTWEM LEKCKDAGLV KSIGVSNFNH KQLERLLNKP GLKYKPVCNQ VECHLYLNQS KLLDYCKSKD IVLVAYGALG TQRYKEWVDQ NSPVLLDDPI LCDVAKKNKR SPALIALRYL FQRGVVPLAQ SFKENEMREN LQVFEFQLSP EDMKTLDGLN KNFRYLSAEF LADHPEYPFS EEY // ID IPI00387642.1 IPI; PRT; 234 AA. AC IPI00387642; DT 18-NOV-2003 (IPI Rat rel. 1.9, Created) DT 18-NOV-2003 (IPI Rat rel. 1.9, Last sequence update) OS Rattus norvegicus (Rat). OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; OC Mammalia; Eutheria; Rodentia; Sciurognathi; Muridae; Murinae; Rattus. OX NCBI_TaxID=10116; CC -!- CHROMOSOME: 7. DR InterPro; IPR001254; Peptidase_S1. DR InterPro; IPR001314; Peptidase_S1A. DR Pfam; PF00089; Trypsin; 1. DR PRINTS; PR00722; CHYMOTRYPSIN. DR SMART; SM00020; Tryp_SPc; 1. DR PROSITE; PS50240; TRYPSIN_DOM; 1. DR PROSITE; PS00134; TRYPSIN_HIS; 1. DR PROSITE; PS00135; TRYPSIN_SER; 1. DR UniParc; UPI000021DDE0; -; -. DR ENSEMBL; ENSRNOP00000037906; ENSRNOG00000008358; M. SQ SEQUENCE 234 AA; 25694 MW; C9961E0C16105546 CRC64; PALASEIVGG RPAQPHAWPF MVSLQRRGGH FCGATLIARN FVMSAAHCVN GRTKDEVVQV LLGAHSLSSP EPYKHLYDVQ SVVLHPGSRP DSVEDDLMLF KLSHNASLGP HVRPLPLQRE DREVKPGTLC DVAGWGVVTH AGRRPDVLQQ LTVSIMDRNT CNLRTYHDRA ITKNMMCAES NRRDTCRGDS GGPLVCGDAV EAVVTWGSRV CGNRRKPGVF TRVATYVPWI ENVL // ID IPI00387643.1 IPI; PRT; 268 AA. AC IPI00387643; DT 18-NOV-2003 (IPI Rat rel. 1.9, Created) DT 18-NOV-2003 (IPI Rat rel. 1.9, Last sequence update) OS Rattus norvegicus (Rat). OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; OC Mammalia; Eutheria; Rodentia; Sciurognathi; Muridae; Murinae; Rattus. OX NCBI_TaxID=10116; CC -!- CHROMOSOME: 3. DR UniParc; UPI000021DDE1; -; -. DR ENSEMBL; ENSRNOP00000037907; ENSRNOG00000021920; M. SQ SEQUENCE 268 AA; 30046 MW; 3F9AEC7A2F5F3EB3 CRC64; MSLDSPPTLF HLARHTLLME EALAISALEE LPCHLFPELF KGAFTDRHTN VLTAMVSIWP LPCLPVGTLL EEPHLETLKA LLDGLNVQVT QTCNSSCLMT PLETLSITDC PRLLQSDLEC LPRCSNIFKL KHLHMNAILL SDAVSELPGL ILEKVTSTLQ ILELEQCGMR DSHFQALLPA LSKCSQLLKV NFYHNDISLP VLKRLLCHTA NLSQLTQELY PAPLECYEGN NTILKDRFKK LCPELLCFLR TKRLPKKVSF ATNACSQC // ID IPI00387644.1 IPI; PRT; 1096 AA. AC IPI00387644; DT 18-NOV-2003 (IPI Rat rel. 1.9, Created) DT 18-NOV-2003 (IPI Rat rel. 1.9, Last sequence update) OS Rattus norvegicus (Rat). OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; OC Mammalia; Eutheria; Rodentia; Sciurognathi; Muridae; Murinae; Rattus. OX NCBI_TaxID=10116; CC -!- CHROMOSOME: 4. DR InterPro; IPR005036; CBM_21. DR Pfam; PF03370; CBM_21; 1. DR UniParc; UPI000021DDE2; -; -. DR ENSEMBL; ENSRNOP00000037908; ENSRNOG00000021567; M. SQ SEQUENCE 1096 AA; 122129 MW; 751628AD3BF34D33 CRC64; MEPAEVPGQI SKDNFLEVPN LSDSVCEDEE VKATFKPGFS PQPSRRGSES SEDLYLDTPT SASRRVSFAD SLGFSLVSVK EFDCWDLPSV STDFDLTRDV LHTDEYILSP LFDLPSSKEE LMEQLQVQKA VLESAEHLPG STSVKGIIRV LNISFEKLVY VRMSLDDWQT HYDILAEYVP NSCDGETDQF SFKISLVPPY QMDGGKVEFC IRYETSVGTF WSNNNGTNYI LVCQKKTKEP EPVVKPLEEG PSRQIKGCLK VKSSSKEEPL LTPEENKLGT LKFTESYIPT IICSHEDRDD LGANYQHVKD IDKKHDEHNE KELDLMINQR LITSHDEKNT FSTDAVNSTN KAEGSEKKQA RHEIHTDLCR GPLSPSLSAE SSLKRDFYHS RNYSPGNEHG HPPSEEIISD VGAIGSPLGD TSSDELMQLK VCSKEDVDDN ANPAHGSGRL CSSSDQLRAG GLENNEAGIK KTGIKDYKYS HGDSYLEAST SLRESNASYK DEYDKVDDKR EKKTCLGVNE NPGKNFQSIF QNQERQMGCA KISGEGANAN NQDLTTLLSK DTTTNTWAVT VDPSPSTNTN VNWREAGNGT DLERRTTDLG SPRNFSLLTD GYLFQADREK SDSSNSEDRN MNPQHKKNWN VLESQPETRE TETNITKHTK EQAEYKDTWG KRDNSRNLKA TSTEQLFTCQ ETECCELSSL ADHGITEKAQ AVAAYIIKTT LESTPESASA RGKAIIAKLP QETARHDRPI EVKETAFDPH EGRKDDSHYS LCHGDTAGVI HDNDFERESH LDICNVRVDE MEKEKTTSTC SPRKTYDKEK HGIGSVTSID EPSQVITGNQ KATSKLDLHL GVLPTDRAIL SANADLELLQ ELSRRTDFNA VHSAFNSDPG SASQDSSQVY RRCSKKPVPS YGEQKAVINT TLQSVPTKSE YNCHPESEIF GHATSKPEVV FKSSEIIKSG SGGEQGVGPI LQQKEGSLEK SQDPMISINE PLENLDEVRS ENEGLMRSGQ LQCYLGDKGS VSSASATVPT QELQAQGSES LLSISINSKI PYFLLFLIFL ATVYYYDLMI GLAFYLFSLY WLYWEGGRQR ESVKKK // ID IPI00357899.1 IPI; PRT; 769 AA. AC IPI00357899; IPI00190621; DT 02-OCT-2003 (IPI Rat rel. 1.7, Created) DT 02-OCT-2003 (IPI Rat rel. 1.7, Last sequence update) DE SIMILAR TO KIAA1952 PROTEIN. OS Rattus norvegicus (Rat). OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; OC Mammalia; Eutheria; Rodentia; Sciurognathi; Muridae; Murinae; Rattus. OX NCBI_TaxID=10116; CC -!- CHROMOSOME: 5. DR InterPro; IPR008906; HATC. DR InterPro; IPR007087; Znf_C2H2. DR Pfam; PF05699; hATC; 1. DR SMART; SM00355; ZnF_C2H2; 2. DR PROSITE; PS00028; ZINC_FINGER_C2H2_1; 2. DR PROSITE; PS50157; ZINC_FINGER_C2H2_2; 2. DR UniParc; UPI00001CF6E2; -; -. DR REFSEQ_XP; XP_233016; GI:34868457; M. DR ENSEMBL; ENSRNOP00000008770; ENSRNOG00000006719; -. SQ SEQUENCE 769 AA; 85056 MW; 46201B8E259FB192 CRC64; MNQRVPTPQS KLSLVETGNY TCEFCGKQYK YYTPYQEHVA LHAPITGPVK TSISEVRSML NSSWKRTVIC TGPGFLGPQL LHRLQGPSRT ESMTLSGTAP GWEPPEDPDT GSECSHPEVT PSPRFVAAKT QTNQSGKKAP GSVVRCTTLL HRTPPATQTQ TFRTPNSGSP ASKATAAENT FSRRVESKAQ NHFEETNRSS QNSNEPYTCG ACGIQFQFYS NLLEHMQSHA ADNENNITSN QSRSPPAAVE EKWKPQAQRN SANNTTTSSL TPNSVIPEKE RQNIAERLLR VMCADLGALS VVSGKEFLKL AQTLVDSGAR YGAFSVTEIL GNFNTLALKH LPRMYNQVKV KVTCALGSNA CLGIGVTCHS QSVGPDSCYI LTAYQAEGNH IKSYVLGVKG ADIRDSGDLV HHWVQNVLSE FVMSEIRTVY VTDCRVSTSA FSKAGMCLRC SACALNSVVQ SVLSKRTLQA RSMHEVIELL NVCEDLAGST GLAKETFGSL EETSPPPCWN SVTDSLLLVH ERYEQICEFY SRAKKMNLIQ SLNKHLLSNL AAILTPVKQA VIELSNESQP TLQLVLPIYV RLEKLFTAKA NDAGTVSKLC HLFLEALKEN FKVHPAHKVA MILDPQQKLR PVPPYQHEEI ISKVCELINE VKESWAEEAD FEPSAKKARS ATGEHPTAQE DDRLGKNEVY DYLQEPLFQA TPDLFQYWSC VTQKHTKLAK LAFWLLAVPA VGARSGCVNM CEQALLIKRR RLLSPEDMNK LMFLKSNML // ID IPI00357900.1 IPI; PRT; 617 AA. AC IPI00357900; IPI00191570; DT 02-OCT-2003 (IPI Rat rel. 1.7, Created) DT 02-OCT-2003 (IPI Rat rel. 1.7, Last sequence update) DE SIMILAR TO KINESIN FAMILY MEMBER 12. OS Rattus norvegicus (Rat). OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; OC Mammalia; Eutheria; Rodentia; Sciurognathi; Muridae; Murinae; Rattus. OX NCBI_TaxID=10116; CC -!- CHROMOSOME: 5. DR InterPro; IPR001752; kinesin_motor. DR Pfam; PF00225; Kinesin; 1. DR PRINTS; PR00380; KINESINHEAVY. DR SMART; SM00129; KISc; 1. DR PROSITE; PS00411; KINESIN_MOTOR_DOMAIN1; 1. DR PROSITE; PS50067; KINESIN_MOTOR_DOMAIN2; 1. DR UniParc; UPI00001CF6E3; -; -. DR ENSEMBL; ENSRNOP00000010040; ENSRNOG00000007080; -. DR REFSEQ_XP; XP_233017; GI:34868461; M. SQ SEQUENCE 617 AA; 67824 MW; 50994FC21EFCE94B CRC64; MEERGSPDGD PARNLEQGPE GSETPIQVVL RVRPMSTVEL RRGEQSALHC SGTRTLQVSP PGGGPDVAFR FGAVLDGART QEDVFRACGV KRLGELALRG FSCTVFTFGQ TGSGKTYTLT GPPPQAEGVP VPPSLAGIMQ RTFTWLLDRM QHLDSPVTLR ASYLEIYNEQ VQDLLSQGSP RPLPVRWSKA RGFYVEQLRL VECGSLEALM ELLQMGRPFV GLSRRRSSSH TLNQASSRSH ALLTLHISRP TSQQVPPVDL GEPPVGGKLC FVDLAGSEKV AATGSRGQLM LEANSINRSL LALGHCISLL LDPQRKQSHI PFRDSKLTKL LADSLGGRGV TLMSPAVKPP QQVEAELLQL QEENRCLRLQ LDQMYTKAPR VHGARVAWAQ RNLYGMLQEF MLENEKLRKE MRQLRSSRDL AQAEQHVLAQ QIHELERRLL LACSLPQQTS ATVCPCRMTP AASCHVLPPL CYCYHLCPLC RVSLTHWACP WRECHAPQVL EPEAPGHISP SVRPPPWAPP TSPGSAKPPQ ERNHSDWTQT RVLAEMLMGE EVVPSAPPLP AGPSNMPQVL RGGSGIPNQT PRLETLTHQI NSSLNPSQRQ PQPSEDTQSP GQGLSSY // ID IPI00188001.1 IPI; PRT; 364 AA. AC IPI00188001; DT 14-MAR-2003 (IPI Rat rel. 1.0, Created) DT 14-MAR-2003 (IPI Rat rel. 1.0, Last sequence update) OS Rattus norvegicus (Rat). OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; OC Mammalia; Eutheria; Rodentia; Sciurognathi; Muridae; Murinae; Rattus. OX NCBI_TaxID=10116; CC -!- CHROMOSOME: 4. DR InterPro; IPR005817; Wnt. DR InterPro; IPR005816; Wnt_grthfactor. DR PRINTS; PR01349; WNTPROTEIN. DR SMART; SM00097; WNT1; 1. DR UniParc; UPI000017E129; -; -. DR ENSEMBL; ENSRNOP00000007822; ENSRNOG00000005781; M. SQ SEQUENCE 364 AA; 40715 MW; E94BB43BAD740DE6 CRC64; MDRAALLALP SLCALWAAVL SLLPCGTQGN WMWLGIASFG VPEKLGCSGL PLNSRQKELC KRKPYLLPSI REGARLGIQE CRSQFRHERW NCMVATATST QLATAPLFGY ELSSGTKETA FIYAIMAAGL VHSVTRSCSA GNMTECSCDT TLQNSGSASE GWHWGGCSDD VQYGMWFSRK FLDLPVRNTT EKESKVLLAM NLHNNEAGRQ AVAKLMSVDC RCHGVSGSCA VKTCWKTMSS FEKIGYFLKD KYENSIQISD KTKRKMRRRE KDQRQTPILK DDLLYVHKSP NYCVENKKLG IPGTQGRECN RTSGGADGCN LLCCGRGYNT HVVRHVERCE CKFIWCCYVR CRRCESMTDV HTCK // ID IPI00387645.1 IPI; PRT; 369 AA. AC IPI00387645; DT 18-NOV-2003 (IPI Rat rel. 1.9, Created) DT 18-NOV-2003 (IPI Rat rel. 1.9, Last sequence update) OS Rattus norvegicus (Rat). OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; OC Mammalia; Eutheria; Rodentia; Sciurognathi; Muridae; Murinae; Rattus. OX NCBI_TaxID=10116; CC -!- CHROMOSOME: 11. DR UniParc; UPI000021DDE3; -; -. DR ENSEMBL; ENSRNOP00000037911; ENSRNOG00000001776; M. SQ SEQUENCE 369 AA; 38101 MW; 1F5695F73F990682 CRC64; ETRILSKRIP SNFMVVHTIP TGTLAPSDSP RAGMTTVKAG TLSSESSSSS DSSAGVLSSS QALGPDSTTP AKDSVAFSIS HIKLTTCITE IETTITISGT PDASRSPAEA MTALSASEML TLPPSTEAKP VVPKTTSSSG ILSTATTLAL ATTLEGTLPA SGITESEIAV AQTPTSSGTS ATGGTQVTVR RNPLEDTSAL SSETQSHTEV FGTITVPTVA GSTVGEATSL VSSTALDSSL SAVVTTKGSA SSETLTTDNT TNSSFLTGSR PPSLIYSTTA STSERTNVTL TKTTASPKTP MNPAPTAWTR KTTEHDPGIN GGFLLVRLTV ASPKDLTEHV TREKLMHQLR RELHTHMPLV QVSLLSIRR // ID IPI00387646.1 IPI; PRT; 1527 AA. AC IPI00387646; DT 18-NOV-2003 (IPI Rat rel. 1.9, Created) DT 18-NOV-2003 (IPI Rat rel. 1.9, Last sequence update) OS Rattus norvegicus (Rat). OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; OC Mammalia; Eutheria; Rodentia; Sciurognathi; Muridae; Murinae; Rattus. OX NCBI_TaxID=10116; CC -!- CHROMOSOME: 2. DR InterPro; IPR001715; Calponin-like. DR InterPro; IPR003247; CH_type. DR InterPro; IPR000048; IQ_region. DR InterPro; IPR001936; RasGAP. DR InterPro; IPR000593; RasGAP_C. DR InterPro; IPR001202; WW_Rsp5_WWP. DR Pfam; PF00307; CH; 1. DR Pfam; PF00612; IQ; 3. DR Pfam; PF00616; RasGAP; 1. DR Pfam; PF03836; RasGAP_C; 1. DR ProDom; PD001527; CH_type; 1. DR ProDom; PD008735; RasGAP_C; 1. DR SMART; SM00033; CH; 1. DR SMART; SM00015; IQ; 4. DR SMART; SM00323; RasGAP; 1. DR PROSITE; PS50021; CH; 1. DR PROSITE; PS50096; IQ; 4. DR PROSITE; PS50243; RASGAP_CTERM; 1. DR PROSITE; PS00509; RAS_GTPASE_ACTIV_1; 1. DR PROSITE; PS50018; RAS_GTPASE_ACTIV_2; 1. DR PROSITE; PS01159; WW_DOMAIN_1; 1. DR PROSITE; PS50020; WW_DOMAIN_2; 1. DR UniParc; UPI000021DDE4; -; -. DR ENSEMBL; ENSRNOP00000037912; ENSRNOG00000027894; M. SQ SEQUENCE 1527 AA; 173762 MW; D89C8234F2CAC0B5 CRC64; DDRLTAEEMD EQRRQNVAYQ YLCRLEEAKR WMEVCLKEEL PSPVELEESL RNGVLLAKLG HCFAPSVVPL KKIYDMEQLR YQATGLHFRH TDNINFWLSA VAHIGLPSTF LPETTDIYDK KNMPRVIYCI HALSLFLFRL GLAPQIHDLY GKVKFTAEEL SNIASELAKY GLQLPAFSKI GGILANEFSA DEAAVHAAIL AINDAVERGV VEDTLVALQN PNALLGNLRE PLAAVYQELL ALAKMEKAAN ARNHDDGQDQ DIYESCLTQA EIQGHINLAN VLRAVWKINK AIQRGVAADT VKELMCPEAQ LPQVYPFASA VYQQELALLQ KQQQGELDQE ELFVAVEMLS AVVLINRALE AGDACTFWDN LVNPATGLAQ VEEENAQRYF DALVKVQQLR GTHRGFLSWN DLQAAVSQVN AQVQEETDQV LAISLINEAL DQGCPEKTLS ALLLPAAGLE DVSLPVAPRY HHLLVAAKRQ KAQKTGDPGA VLWLEEIRQG VARANEDTNT AQRIALGVAA INQAIKEGKA AQTERVLRNP NVALRGIVPD CAKSYQQALE GAAAKKHRPG DTAFWVPRDM KDGTAYYFHL QTFQGTWERP PSRHLNASHL TWEEIQSVIT KVTAAHDRQL LWKANVGFVI KLQARLRGFL VRQKFAESSH FLRTLLPAVI KIQAHWRGYR QRKTYQERLQ YFKANLNAII TIQAWARMWA ARRQYLRRLR YFQKNVDSVV KIQAFFRARK ARDDYRMLVH ARHPPLSVVR KFAHLLNQSQ EDFSAEAELL RLQEEVVRKI RSNQQLEQDL NLMDIKIGLL VKNRITLQEV VSHCKKLTKK NKEQLSDMMI LDKQKGLKSL SREKRQKLEA YQHLFYLLQT QPIYLAKLIF QMPQNKTTKF MEGVIFSLYN YASNRREAYL LLQLFRTALQ EEIKSKVEQP QDVVTGNPTV VRLVVRFYRN GRGQSALQEI LGKVIQDVLE DRSVSIHTDP VHIYKSWINQ VEAQTGQRSH LPYDVTPEQA LSHSEVQRRL DISLRNLLAM TEKFFVAISS SVDHIPYGIR YMAKVLKTTL ETKFPNATER DIYKASVVGN LLYYRFLNPA VVAPDAFDIV AMAAGSSLAA PQRHALGAVA QLLQHAAAGK VFSGESRHLR ILNGYLEDLH HKFRKFICRA CRVPEPEERF AIDEYSDMVA VAKPMVYITV GELIGTHRLL LEHQDQLAPG HQDPLHQLLE DLGEPPTITD LIVQTWGRIH LSLALWPTLS RPGPQTALSC STKQMLADLI QFHPGDSLEE ILTSSAPREH EEAHHRLMCW RQACDTQKPE PLQRRHSLMA HSLLPLAEKQ QRVLRNLRRL QGLGLVRAND CYQGLVDELA KDICNQRRHR QRRKAEMLRL RATLQGLDAK TIFYEEQGDY YNQYTQACLD HLAPNPRYAL SSGKGKKQPS LHYTAAQLLE KGVLVEIEDL PVSHFRNVIF DITPGDEAGR FAVNAKFLGV DMEKFQLHYQ DLLQLQYEGV AVMKLFNKAK VNVNLLIFLL NKKFLRK // ID IPI00387647.1 IPI; PRT; 128 AA. AC IPI00387647; DT 18-NOV-2003 (IPI Rat rel. 1.9, Created) DT 18-NOV-2003 (IPI Rat rel. 1.9, Last sequence update) OS Rattus norvegicus (Rat). OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; OC Mammalia; Eutheria; Rodentia; Sciurognathi; Muridae; Murinae; Rattus. OX NCBI_TaxID=10116; CC -!- CHROMOSOME: 8. DR InterPro; IPR006907; DUF622. DR Pfam; PF04822; DUF622; 1. DR UniParc; UPI000021DDE5; -; -. DR ENSEMBL; ENSRNOP00000037913; ENSRNOG00000024735; M. SQ SEQUENCE 128 AA; 15217 MW; 7320F15AF35BD455 CRC64; MYSRLRKHFG RVNVDFGQTG VRESRLSSKT NDGQRKVAWG MRKDGRLTSS PGPVVINKEA NTEEQRLIRQ LQSATEERNE LRDLLTYVTE RYRNNSRYIR SNPFYEKLKI KEREVMSLLH NLEMRNIE // ID IPI00387648.1 IPI; PRT; 608 AA. AC IPI00387648; DT 18-NOV-2003 (IPI Rat rel. 1.9, Created) DT 18-NOV-2003 (IPI Rat rel. 1.9, Last sequence update) OS Rattus norvegicus (Rat). OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; OC Mammalia; Eutheria; Rodentia; Sciurognathi; Muridae; Murinae; Rattus. OX NCBI_TaxID=10116; CC -!- CHROMOSOME: 1. DR InterPro; IPR001909; KRAB. DR InterPro; IPR007087; Znf_C2H2. DR Pfam; PF01352; KRAB; 1. DR Pfam; PF00096; zf-C2H2; 16. DR ProDom; PD000003; Znf_C2H2; 13. DR SMART; SM00349; KRAB; 1. DR SMART; SM00355; ZnF_C2H2; 17. DR PROSITE; PS50805; KRAB; 1. DR PROSITE; PS00028; ZINC_FINGER_C2H2_1; 17. DR PROSITE; PS50157; ZINC_FINGER_C2H2_2; 17. DR UniParc; UPI000021DDE6; -; -. DR ENSEMBL; ENSRNOP00000037914; ENSRNOG00000018936; M. SQ SEQUENCE 608 AA; 70217 MW; 75EB549F2E320B4E CRC64; FQGSVTFRDV AVDFSQEEWA CLDATQKVLY RDAMLETYSH LVTVELETGY DAENISPENP INNGKFLKQS IKQLSRTFDF KDSSSSNGPN YSAFHGLKDC QGDADQQITN KEEMPPYTCQ TLAHNIERAY ECKECGKCLG CRSTLTQHQT IHTGEKPYEC KECGKAFRLP QQLTRHQKFH SGEKPFKCNE CGKAFHLPDL LKYHKTIHTG TKPFECRECG KAFNRVSNLV AHRIIHADVK PYECNECGKA FKRRSNLVQH QKIHSDERPF QCKDCGKGFI VLAQLTRHQN IHTGEKLFEC HECGKAFRLP QQLTRHQKSH SGEKPFKCNE CGKAFHLPDL LKYHKTIHTG TKPFECRECG KSFNRVSNLV EHRIIHADVK PYACNQCGKA FKRQKSLMQH QKIHSGERPF QCKDCGKAFI VLSHLTRHQT IHTGEKSFEC NECGKKFRTA THLVMHQTIH TGEKPFECNV CGKAFRLQVY LSEHQKTHIE GKPFKCKLCG SAFRRKYQLN EHYTIHTDEK PYQCKECGKC FRQRSNFTEH QSIHTGNKPF ECKECGKSFR LNTLLIRHQK SHSGERPYEC KECGKAFHLP SELNNHQIVH TSKRPFEC // ID IPI00188017.1 IPI; PRT; 140 AA. AC IPI00188017; DT 14-MAR-2003 (IPI Rat rel. 1.0, Created) DT 14-MAR-2003 (IPI Rat rel. 1.0, Last sequence update) DE RELAXIN 3 PRECURSOR. OS Rattus norvegicus (Rat). OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; OC Mammalia; Eutheria; Rodentia; Sciurognathi; Muridae; Murinae; Rattus. OX NCBI_TaxID=10116; CC -!- CHROMOSOME: 19. DR InterPro; IPR004825; Ins/IGF/relax. DR PROSITE; PS00262; INSULIN; 1. DR SWISS-PROT; Q8BFS3; REL3_RAT; M. DR ENSEMBL; ENSRNOP00000007775; ENSRNOG00000005911; -. DR REFSEQ_NP; NP_733767; GI:24638442; -. DR UniParc; UPI00000EBAB6; -; -. DR LocusLink; 266997; Rln3; -. SQ SEQUENCE 140 AA; 14922 MW; F4B6979756122EDA CRC64; MATRGLLLAS WALLGALVLQ AEARPAPYGV KLCGREFIRA VIFTCGGSRW RRADILAHDP LGEFFADGEA NTDHLASELD EAVGSSEWLA LTKSPQVFYG GRSSWQGSPG VVRGSRDVLA GLSSSCCEWG CSKSQISSLC // ID IPI00357901.1 IPI; PRT; 470 AA. AC IPI00357901; IPI00202044; DT 02-OCT-2003 (IPI Rat rel. 1.7, Created) DT 02-OCT-2003 (IPI Rat rel. 1.7, Last sequence update) DE SIMILAR TO RIKEN CDNA 6330416G13 GENE. OS Rattus norvegicus (Rat). OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; OC Mammalia; Eutheria; Rodentia; Sciurognathi; Muridae; Murinae; Rattus. OX NCBI_TaxID=10116; CC -!- CHROMOSOME: 5. DR UniParc; UPI00001CF6E4; -; -. DR REFSEQ_XP; XP_233020; GI:34868470; M. DR ENSEMBL; ENSRNOP00000011799; ENSRNOG00000008712; -. SQ SEQUENCE 470 AA; 51641 MW; 493421A9F47BC77B CRC64; MACEPPSDPG GAAGPLPTST LGCSTLPQGN PPGWGEELHN GQVLSVLRID NTCAPISFDL RVAEEQLQAW GIQVPAEQYR SLAESALLEP QVRRYIIYNS RPMRLAFAVV FYVLVWANIY STSQMFALGN QWAGVLLATL AAVSLTLTLV LVFERQQRKA NTNTDLRLVA ANGALLRHRV LLGVTDTVEG CQSVIQLWFV YFDLENCVQF LSDHVQEMKR SQESLLRSRL SQLCVVMETG VSPVVERPED LEDSPLLPRT PGPQERPLTQ TELYQLVPEA EPEEMARQLL AVFGGYYTRL LVTSQLPQPM GTRHMDSARI PCPCQLIEVH ILGTGCCPFL ASVSHVGLWV IKCTPDVFLA SYSVLALLNL VAELVAGLAA WMEDTVCCLS RPRDLQLTPQ GKCLTLGSES ETKAPRRRPS FSGASVCRSQ PTCPQYTGEE STSSRCFNLN SNNLQCLQHQ SCHKAGAGTP // ID IPI00357902.1 IPI; PRT; 561 AA. AC IPI00357902; IPI00205217; DT 02-OCT-2003 (IPI Rat rel. 1.7, Created) DT 02-OCT-2003 (IPI Rat rel. 1.7, Last sequence update) DE SIMILAR TO U4/U6 SMALL NUCLEAR RIBONUCLEOPROTEIN PRP4 (U4/U6 SNRNP 60 DE KDA PROTEIN) (WD SPLICING FACTOR PRP4) (HPRP4). OS Rattus norvegicus (Rat). OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; OC Mammalia; Eutheria; Rodentia; Sciurognathi; Muridae; Murinae; Rattus. OX NCBI_TaxID=10116; CC -!- CHROMOSOME: 5. DR InterPro; IPR002016; Peroxidase. DR InterPro; IPR003648; SFM. DR InterPro; IPR001680; WD40. DR Pfam; PF00400; WD40; 7. DR PRINTS; PR00320; GPROTEINBRPT. DR ProDom; PD000018; WD40; 3. DR SMART; SM00500; SFM; 1. DR SMART; SM00320; WD40; 7. DR PROSITE; PS00436; PEROXIDASE_2; 1. DR PROSITE; PS00678; WD_REPEATS_1; 2. DR PROSITE; PS50082; WD_REPEATS_2; 6. DR PROSITE; PS50294; WD_REPEATS_REGION; 1. DR UniParc; UPI00001CF6E5; -; -. DR ENSEMBL; ENSRNOP00000019910; ENSRNOG00000014777; -. DR REFSEQ_XP; XP_233022; GI:34868449; M. SQ SEQUENCE 561 AA; 63208 MW; 18C7729BE1D8C62E CRC64; MTADTWQLPL PRYFATPRAR TGRTRSPWER AVTLRVRAEE EEEEGWGTVT TKTKAPDDLV APVVKKPHIY YGSLEEKERE RLAKGESGIL GKEGLKAGIE AGNINITSGE VFEIEEHISE RQAEVLAEFE RRKRARQINV STDDSEVKAC LRALGEPITL FGEGPAERRE RLRNILSVVG TDALKKTKKD DEKSKKSKEE YQQTWYHEGP NSLKVARLWI ANYSLPRAMK RLEEARLHKE IPETTRTSQM QELHKSLRSL NNFCSQIGDD RPISYCHFSP NSKMLATACW SGLCKLWSVP DCSLLHTLRG HNTNVGAIVF HPKSTVSLDQ KDVNLASCAA DGSVKLWSLD SDEPVADIEG HTVRVARVMW HPSGRFLGTT CYDRSWRLWD LEAQEEILHQ EGHSMGVYDI AFHQDGSLAG TGGLDAFGRV WDLRTGRCIM FLEGHLKEIY GISFSPNGYH IATGSGDNTC KVWDLRQRRC VYTIPAHQNL VTGVKFEPIH GDFLLTGAYD NTAKIWTHPG WSPLKTLAGH EGKVMGLDIS SDGQLIATCS YDRTFKLWMA E // ID IPI00387649.1 IPI; PRT; 403 AA. AC IPI00387649; DT 18-NOV-2003 (IPI Rat rel. 1.9, Created) DT 18-NOV-2003 (IPI Rat rel. 1.9, Last sequence update) OS Rattus norvegicus (Rat). OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; OC Mammalia; Eutheria; Rodentia; Sciurognathi; Muridae; Murinae; Rattus. OX NCBI_TaxID=10116; CC -!- CHROMOSOME: 3. DR InterPro; IPR005016; TMS_TDE. DR Pfam; PF03348; TMS_TDE; 2. DR UniParc; UPI000021DDE7; -; -. DR ENSEMBL; ENSRNOP00000037919; ENSRNOG00000015499; M. SQ SEQUENCE 403 AA; 44551 MW; BAF6EDA8D643AA08 CRC64; SRCPQCYVPT CSATLTVQCS GSGAVYRVCA GTATFHLLQA VLLVRLHSPT SPRAQLHNSF WSLKLLFLLG LCTAAFCIPD EHLFPAWHYI GICGGFTFIL LQLVLITAFA QSWNKNWQTG AAQDCSWFLG VLLATLGFYS MAGVGAVLLF HHYTHPDGCL LNKMLLSLHL CFCGLLSLLS IAPCIRLRQP NSGLLQASII SCYIMYLTFS ALSSRPPETI IFQGQNHTLC LPGQNKMEPQ IPDASVAVFS ASIMYACVLF ACNEASYLAQ LFGPLWIIKV YKYEFQKPSV CFCCPQTVEP EDGQGSRARP ADQETPPAAQ VQSQHLSYSY SGFHFAFFLA SLYVMVTLTN WFSYEEAELE KTFTKGSWAT FWVKVASCWA CVLLYLGLLL APLLAHHSES PPP // ID IPI00387650.1 IPI; PRT; 1306 AA. AC IPI00387650; DT 18-NOV-2003 (IPI Rat rel. 1.9, Created) DT 18-NOV-2003 (IPI Rat rel. 1.9, Last sequence update) OS Rattus norvegicus (Rat). OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; OC Mammalia; Eutheria; Rodentia; Sciurognathi; Muridae; Murinae; Rattus. OX NCBI_TaxID=10116; CC -!- CHROMOSOME: 3. DR InterPro; IPR001440; TPR. DR SMART; SM00028; TPR; 16. DR PROSITE; PS50005; TPR; 4. DR PROSITE; PS50293; TPR_REGION; 3. DR UniParc; UPI000021DDE8; -; -. DR ENSEMBL; ENSRNOP00000007832; ENSRNOG00000005868; M. SQ SEQUENCE 1306 AA; 149833 MW; A9AA3DFE50522210 CRC64; INYYCQERYY HHVLLVASEG MKKYSSDPVF RFYHAYGTLM EGKAQEALRE FEAIKNKQDV SLCSLMALMY VHKMSPNPDR EAILELDTKM KEQRKEAGRK ALYHAGLFLW HIGRHDKARE YIDRMSKMPH DSNEGPILKA WLDITRGKEP YAKKALRYFE EGLQDGNDIF ALLGKVLCLE MRQNYSGALE TVSQIIVNFP SFLPAFEKKM KLQLALQDWD QTVETAQRLL LQDGHNVEAL RMLALYYLCR EGDIEKAAAK LENLGNALDV MEPQNAQLFY KITIAFSRTC GRNQLILQKV QSFLEKAFSL TPQQAEIATE LGYQMILQGK VKEAWKWYRT AMTLNESNIS AVTGLIRCQL IEGQLQDADQ QLEFFSEFQQ SMGRSAELMY LHAVLATKKN NRQEEVINLL NDVVNTHFSH LEDLPLGIQY FEKLNPDFLL EVVNEYLNLC PIQPAGPGQP LSPVLRRCSS VLETIIRSVP GLPQAVFLMA KVKYLSGDTE AAYNNLQHCL EHSPSYAEAH LLMAQVYLSQ DKVQLCSQSL ELCLSYNFNV RDYPLYHLIK AQSQKKMGEV AEAIKTLHMA MNLPGMRRSR ASSKSKHRSE VDGSHRLSIF LELVEVHRLN GEQHEAAKVL QDAIHEFSGT CEELRVTIAN ADLALAQGDT ERALSMLRNV TTEQPYFIEA KEKMADIYLK HRKEKMLYIT CYREIAERMP SPRSFLLLGD AYMNIQEPEE AIVAYEQALN QNPKDGTLAR KIGKALVKTH NYSKAITYYE AALKSGQQNC LCYDLAELLL RLKLYEKAEK VLQHSLAHDP VNELSALMVD GRSQVLLAKV YSKMERPGDA IAALQQAREL QARILKRVQM EQPDAVPSQR HFAAEICAEI AKHSAAQRDY EKAITFYREA LVHCETDSKI MLELAQLYLA QEDLDASLRH CALLLQRDQD NEPATMLMAD LMFRKQDYEQ AVFHLQQLLE RKPDNFMTLS RLIDLLRRCG KLEEVPRFFL MAEKHNSRTK LEPGFQYCKG LHFWYTGEPN DALRHFNKAR KDSDWGQNAL YNMIEICLNP DNETIGGEVF ENLNGDLGTS PEKQESVQLA VRTAEKLLKE LKPQTVQGRL QLRIMENCCL MATKQKSSVE QALNTFTEIA ASEKDHIPAL LGMATAYMIL KQTPKARNQL KRIAKMTWNP IEAEELEKSW LLLADIYIQS AKYDMAEELL KRCLCHNRSC CKAYEYMGYI MEKEQAYTDA AFNYEMAWKH SNQTNPAVGY KLAFNYLKAK RYVDAIDVCH QVLEAHPTYP KIRKDILDKA RASLRP // ID IPI00357903.1 IPI; PRT; 297 AA. AC IPI00357903; IPI00194960; DT 02-OCT-2003 (IPI Rat rel. 1.7, Created) DT 02-OCT-2003 (IPI Rat rel. 1.7, Last sequence update) DE SIMILAR TO PHOSPHOLIPASE A2, GROUP IVB (CYTOSOLIC). OS Rattus norvegicus (Rat). OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; OC Mammalia; Eutheria; Rodentia; Sciurognathi; Muridae; Murinae; Rattus. OX NCBI_TaxID=10116; CC -!- CHROMOSOME: 3. DR InterPro; IPR003347; TF_JmjC. DR SMART; SM00558; JmjC; 1. DR UniParc; UPI00001CF263; -; -. DR REFSEQ_XP; XP_342500; GI:34856719; M. DR ENSEMBL; ENSRNOP00000009820; ENSRNOG00000024997; -. SQ SEQUENCE 297 AA; 33897 MW; 8B4A7098E9BB4D2F CRC64; MAEAALDAVR RALQEFPAAA RDLNVPRVVP YLDEPPSPLC FYRDWVCPNR PCIIRNALQH WPALQKWSFS YLRATVGSTE VSVAVTPDGY ADAVRGDRFV MPAERRLPVS HVLDVLEGQA QHPGVLYVQK QCSNLPTELP QLLSDIESHV PWASESLVHK DHYENLYCVV SGEKHFLLHP PSDRPFIPYN LYTPATYQLT EEGTFRVVDE EAMEKVPWIP LDPLAPDLAR YPSYSQARAL HCTVRAGELL YLPALWFHHV QQSHGCIAVN FWYDMEYDLK YSYFQLMDSL TRAAGLD // ID IPI00188026.1 IPI; PRT; 101 AA. AC IPI00188026; DT 14-MAR-2003 (IPI Rat rel. 1.0, Created) DT 14-MAR-2003 (IPI Rat rel. 1.0, Last sequence update) OS Rattus norvegicus (Rat). OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; OC Mammalia; Eutheria; Rodentia; Sciurognathi; Muridae; Murinae; Rattus. OX NCBI_TaxID=10116; CC -!- CHROMOSOME: 8. DR UniParc; UPI000017E141; -; -. DR ENSEMBL; ENSRNOP00000007837; ENSRNOG00000005961; M. SQ SEQUENCE 101 AA; 11097 MW; 90E04D3053431898 CRC64; MGKHILLLPL GLSLLMSSLL ALQCFRCESF DSTGLCQFGR YKCQTYPGEV CAFVIITTRD GKFVYGNQSC AECNATTVEH GSLIVSTNCF SATPFCNMVH R // ID IPI00357904.1 IPI; PRT; 956 AA. AC IPI00357904; IPI00195919; DT 02-OCT-2003 (IPI Rat rel. 1.7, Created) DT 02-OCT-2003 (IPI Rat rel. 1.7, Last sequence update) DE SIMILAR TO VAM6/VPS39-LIKE, ISOFORM 2. OS Rattus norvegicus (Rat). OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; OC Mammalia; Eutheria; Rodentia; Sciurognathi; Muridae; Murinae; Rattus. OX NCBI_TaxID=10116; CC -!- CHROMOSOME: 3. DR InterPro; IPR001180; Citron. DR Pfam; PF00780; CNH; 1. DR PROSITE; PS50219; ROM_MOTIF; 1. DR UniParc; UPI00001CF264; -; -. DR REFSEQ_XP; XP_342501; GI:34856725; M. DR ENSEMBL; ENSRNOP00000011155; ENSRNOG00000008316; -. SQ SEQUENCE 956 AA; 109687 MW; D32DBB79DCBB5586 CRC64; MHDAFEPVPI LEKLPLQIDC LAAWEEWLLV GTKQGHLLLY RIRKDVGCNR FEVTLEKSNK NFSKKIQQLQ QGMWVIKTAS AMNLSSVLQG SLFSGQHAKI YKVNGDADCD SVVGSEEWEG LTHFPQEERK NNIYVHDLLT FQQITTVSKA KGASLFTCDL QHTETGEEVL RMCVAVRKKL QLYFWKDREF HELQGDFSVP DVPKSMAWCE NSICVGFKRD YYLIRKLSKY ATDTINKKIE EVQISQMPHP NQKLSVQVDA KGSIKELFPT GKQLEPLVAP LADGKVAVGQ DDLTVVLNEE GICTQKCALN WTDIPVAMEH QPPYIVAVLP RYVEIRTLEP RLLVQSIELQ RPRFITSGGS NIIYVASNHF VWRLIPVPMA TQIQQLLQDK QFELALQLAE MKDDSDSEKQ QQIHHIKNLY AFNLFCQKRF DESMQVFAKL GTDPTHVMGL YPDLLPTDYR KQLQYPNPLP TLSGAELEKA HLALIDYLTQ KRSQLVKKLN DSDHQSSTSP LMEGTPTIKS KQKLLQIIDT TLLKCYLHTN VALVAPLLRL ENNHCHIEES EHVLKKAHKY SELIILYEKK GLHEKALQVL VDQSKKANSP LKGHERTVQY LQHLGTENLH LIFSYSIWVL RDFPEDGLKI FTEDLPEVES LPRDRVLNFL IENFKALAIP YLEHIIHVWE ETGTRFHNCL IQLYCEKVQN LMKDYLLSLP TGKSPVPAGE EAGELGESRQ KLLTFLEISS SYDPGRLICD FPFDGERLLE ERALLLGRMG KHEQALFIYV HVLKDTKMAK EYCHKHYDQN KEGNKDVYLS LLRMYLSPPS IHCLGPIKLE LLEPQANLQA ALQVLELHYS KLDTTKAINL LPANTQINDI RIFLEKVLEE NAQKKRFNQV LKNLLHAEFL RVQEERILHQ QVKCIITEEK VCMVCKKKIG NSAFARYPNG VVVHYFCSKE VNSADT // ID IPI00357905.1 IPI; PRT; 113 AA. AC IPI00357905; DT 02-OCT-2003 (IPI Rat rel. 1.7, Created) DT 02-OCT-2003 (IPI Rat rel. 1.7, Last sequence update) DE SIMILAR TO HYPOTHETICAL PROTEIN 9330160A12. OS Rattus norvegicus (Rat). OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; OC Mammalia; Eutheria; Rodentia; Sciurognathi; Muridae; Murinae; Rattus. OX NCBI_TaxID=10116; DR UniParc; UPI00001CF265; -; -. DR REFSEQ_XP; XP_342502; GI:34856727; M. SQ SEQUENCE 113 AA; 12786 MW; F19210F2DF40919D CRC64; METPEKKEIS VEDEAVDKTI FKDCGKIAFY RRQKQQLSKN TTYRASLGSV STEQDSTRFQ ISSEATKVQR NSSKSKRSIF SSQLQFSNCT EEADSNKPRT PGACLPPHLY SIK // ID IPI00357906.1 IPI; PRT; 389 AA. AC IPI00357906; IPI00214130; DT 02-OCT-2003 (IPI Rat rel. 1.7, Created) DT 02-OCT-2003 (IPI Rat rel. 1.7, Last sequence update) DE SIMILAR TO HHM PROTEIN. OS Rattus norvegicus (Rat). OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; OC Mammalia; Eutheria; Rodentia; Sciurognathi; Muridae; Murinae; Rattus. OX NCBI_TaxID=10116; CC -!- CHROMOSOME: 3. DR UniParc; UPI00001CF266; -; -. DR REFSEQ_XP; XP_342503; GI:34856745; M. DR ENSEMBL; ENSRNOP00000015472; ENSRNOG00000011379; -. SQ SEQUENCE 389 AA; 42459 MW; 28B626ED69B47227 CRC64; MCVAGNEMSS SAPEVLGAGS NGLSVWVSSR REAAMASSTT PVSFLAPPLE QLRHLAEELR SLLPRVRVGE AQETAEEFNR EMFWRRLNEA AMKVSGEATV LTTLFSKIPS PSPQETQRIC EQVHIATEEV IAAYYTFPKD QGITLRKLVR NAVLDIVDGT AQLLDALLAA PSQSPENGDL ISCNSVSVAC QQVAEIPKDN KAAALLMLTK SVDLVKDAHE EMEQAVEECD PYCGLLDDSE DNSDSHHNED GVGLPSNRDS YWSEEDQALI TPCLALVRAS RASLKKIRIL VAENGRKDQV AQLDDIVDIS DEISPSVDDL VLSVYPPVCH LTVRITSAKL VSVLIKALEI TKASHVSPQP GDSWIPLLIN AVDHCMDRIK ELTQRAVEL // ID IPI00357907.1 IPI; PRT; 689 AA. AC IPI00357907; IPI00214971; DT 02-OCT-2003 (IPI Rat rel. 1.7, Created) DT 02-OCT-2003 (IPI Rat rel. 1.7, Last sequence update) DE SIMILAR TO ERYTHROCYTE MEMBRANE PROTEIN BAND 4.2. OS Rattus norvegicus (Rat). OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; OC Mammalia; Eutheria; Rodentia; Sciurognathi; Muridae; Murinae; Rattus. OX NCBI_TaxID=10116; CC -!- CHROMOSOME: 3. DR InterPro; IPR002931; Trnsglumase_like. DR SMART; SM00460; TGc; 1. DR UniParc; UPI00001CF267; -; -. DR REFSEQ_XP; XP_342504; GI:34856749; M. DR ENSEMBL; ENSRNOP00000015556; ENSRNOG00000011649; -. SQ SEQUENCE 689 AA; 76501 MW; 15A846FA3A8E394C CRC64; MGQALSIKSC DFHAAENNKE HHTDAISSQH LILRRGQSFT ITLNFRAPAH IFLSALKKVA LIAQTGEQPS KTSKTQAIFP ISSLGDKKGW SAAVVERDAQ HWTISVTTPV DAVIGHYSLL LQVSGKKQYP LGQFTLLFNP WNRDDAVFLQ NEVQRTEYVL NQDGFIYLGT ADCIQEEPWD FGQFERDVMD LSLNLLSVDK QVKDWSQPAH VACIVGALLH ALKKKSVLPI SQTQAAQQGA LLYKRRGSVP ILRQWLTGRG RPVYESQAWV FAAVACTVLR CLGIPARVVT TFDSAQGTNG SLLVDEYYNE EGLQNGEGQR GHIWVFQTSV ECWMNRPDLS PGYDGWQILH PRAPNGVGVL GSCNLVPVKA VKEGDLQLDP AVPELFAAVN ASCVVWKCCE DGKLELTNSN RKNVGNSIST KVVGSDRCED ITQNYKYPEG SLQEKEVLER VQKERMKLGE DTCPPSCEPG DPLHLFLEVP SSQPLRGNGR LSVALINPTD KEKEVELVIA AQALYYNGVL ATGLWRQKQF LMLGPNQVLR LSTSLSFSCF EQNPPENTFL RVTAMARHSH AGFSCFAQED VVISRPNLVI EMPKRATQYQ PLTASVRMHN SLDAPMQNCI ISIFGRGLIH REKRYGLGSV WPGSSLHTQF QFTPTHLGLQ RLTVEVDCDM FQNLTGHRSV LVVAPEVSV // ID IPI00357908.1 IPI; PRT; 590 AA. AC IPI00357908; IPI00213357; DT 02-OCT-2003 (IPI Rat rel. 1.7, Created) DT 02-OCT-2003 (IPI Rat rel. 1.7, Last sequence update) DE SIMILAR TO H63 BREAST CANCER EXPRESSED GENE ISOFORM A. OS Rattus norvegicus (Rat). OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; OC Mammalia; Eutheria; Rodentia; Sciurognathi; Muridae; Murinae; Rattus. OX NCBI_TaxID=10116; CC -!- CHROMOSOME: 3. DR InterPro; IPR000169; Pept_cys_acsite. DR PROSITE; PS00639; THIOL_PROTEASE_HIS; 1. DR UniParc; UPI00001CF269; -; -. DR REFSEQ_XP; XP_342507; GI:34856790; M. DR ENSEMBL; ENSRNOP00000021977; ENSRNOG00000016357; -. SQ SEQUENCE 590 AA; 65470 MW; BEC88CA054696CEE CRC64; MVGFGANRRA GRLPSFVLVV LLVVIVVLAF NYWSISSRHV LLQEEVAELQ GQVQRTEVAR GRLEKRNSDL LLLVDTHKKQ IDQKEADYGR LSSRLQAREG LGKRCEDDKT RSVNWSGVET GGHSLLTAGA ATLRKSRPGP ELEGLSRTPG FECGAEAAAK AGAVAYSFRE SLFSMEGGYR AIFFNHIGAV PKDTVLPKTS TSGSPRPSTP SSMTSGSDLE KSSPPQAPKT CRWMKALLGG SDSLIKEQLA ELRQEFLRQE DQLQDYRKNN TYLVKRLEYE SFQCGQQIKE LRAQHEENIK KLADQFLQEQ KENHKIQSND GKELGRNDHV APKNIPNVPE NDANKNEDPS SNHLPHGKEQ VKRVGDAGMP GVEENDLAKV DDLPAALKKP PVLASQHESH QTISHLLTGQ PLSANMAAGS HLNQNENPST SKQNPSNPLQ HIIPGPNLER EPRIQTDTIK QATKDRANDF HKLKQSKNQL VNTLSLPRVG VNTLIALWNE VCRLVTSDTD FGRFFDENES PVDPQHGSKL ADYNGDDGNV GEYEADKQAE LAYNEEEDGD GGEEDVQDDE XRELQMXPAD YGKQRFSDVL // ID IPI00357909.1 IPI; PRT; 373 AA. AC IPI00357909; DT 02-OCT-2003 (IPI Rat rel. 1.7, Created) DT 02-OCT-2003 (IPI Rat rel. 1.7, Last sequence update) DE SIMILAR TO SHB-LIKE ADAPTER PROTEIN, SHF - HUMAN. OS Rattus norvegicus (Rat). OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; OC Mammalia; Eutheria; Rodentia; Sciurognathi; Muridae; Murinae; Rattus. OX NCBI_TaxID=10116; CC -!- CHROMOSOME: 3. DR InterPro; IPR000980; SH2. DR PRINTS; PR00401; SH2DOMAIN. DR ProDom; PD000093; SH2; 1. DR PROSITE; PS50001; SH2; 1. DR ENSEMBL; ENSRNOP00000033446; ENSRNOG00000028685; -. DR REFSEQ_XP; XP_342508; GI:34856804; M. DR UniParc; UPI00001CF26A; -; -. SQ SEQUENCE 373 AA; 40088 MW; 4E2717485721C2D5 CRC64; MYDRKGYHTA LLQQGGKKRL RHAGSCAPEA VEELQNPGQA GLGSGLDFLC PEWIPVLPAF PAGDSAAAPV LGLSGSSLHA PVQGGGLGLP GAGCGTRSAT EEPLSCLQNR HQLAILEDYA DPFDVQETGE GSGGTSGAAE KVPENDGYME PYEAQKMMAE IRGSKETAVQ PLPLYDTPYE PEDEGASLEG EGAPWPRESR LPEDDERPPE EYDQPWEWKK ERISKAFAVD IKVIKDLPWP PPVGQLDSSP SLPDGDRDIS GPASPLPEPS LEDSSAQFEG SEKNCLSPGR EEKGRLPPRL SAGNPKTAKP LGAEPSSPLG EWTDPALPLE NQVWYHGAIS RTDAENLLRL CKEASYLVRN SESSKNDFSL SLK // > -----Original Message----- > From: biopython-dev-bounces@portal.open-bio.org > [mailto:biopython-dev-bounces@portal.open-bio.org]On Behalf Of Jeffrey > Chang > Sent: Tuesday, May 18, 2004 5:20 PM > To: Pierre Monestie > Cc: biopython-dev@biopython.org > Subject: Re: [Biopython-dev] ipi parser > > > Hello, > > These errors are nearly always due to changes in the formats of the > records that occur from time to time. Do you have a sample file, or > accession number, that I can use to see what's going on? > > Jeff > > > On May 18, 2004, at 4:12 PM, Pierre Monestie wrote: > > > Hello, > > I'm trying to use the Swissprot parser to parse IPI. I read that the > > parser > > should have been fixed for IPI however I get an error on date when I > > try to > > parse ipi.HUMAN > > I get: > > File "dbupdate/src/python/make_sptofasta.py", line 172, in ? > > parseandoutput('ipi',it,fl[0],fl[1],fl[2],fl[3],fl[4]) > > File "dbupdate/src/python/make_sptofasta.py", line 46, in > > parseandoutput > > record = it.next() > > File "/lbri/gen/lib/python2.2/site-packages/Bio/SwissProt/SProt.py", > > line > > 166, in next > > return self._parser.parse(File.StringHandle(data)) > > File "/lbri/gen/lib/python2.2/site-packages/Bio/SwissProt/SProt.py", > > line > > 290, in parse > > self._scanner.feed(handle, self._consumer) > > File "/lbri/gen/lib/python2.2/site-packages/Bio/SwissProt/SProt.py", > > line > > 333, in feed > > self._scan_record(uhandle, consumer) > > File "/lbri/gen/lib/python2.2/site-packages/Bio/SwissProt/SProt.py", > > line > > 338, in _scan_record > > fn(self, uhandle, consumer) > > File "/lbri/gen/lib/python2.2/site-packages/Bio/SwissProt/SProt.py", > > line > > 379, in _scan_dt > > self._scan_line('DT', uhandle, consumer.date, exactly_one=1) > > File "/lbri/gen/lib/python2.2/site-packages/Bio/SwissProt/SProt.py", > > line > > 360, in _scan_line > > read_and_call(uhandle, event_fn, start=line_type) > > File "/lbri/gen/lib/python2.2/site-packages/Bio/ParserSupport.py", > > line > > 301, in read_and_call > > method(line) > > File "/lbri/gen/lib/python2.2/site-packages/Bio/SwissProt/SProt.py", > > line > > 537, in date > > self.data.created = cols[1], int(self._chomp(cols[3])) > > ValueError: invalid literal for int(): Human > > > > Thanks in advance for your help > > Pierre Monestie > > > > _______________________________________________ > > Biopython-dev mailing list > > Biopython-dev@biopython.org > > http://biopython.org/mailman/listinfo/biopython-dev > > _______________________________________________ > Biopython-dev mailing list > Biopython-dev@biopython.org > http://biopython.org/mailman/listinfo/biopython-dev From pierre.monestie at lbri.lionbioscience.com Wed May 19 10:33:13 2004 From: pierre.monestie at lbri.lionbioscience.com (Pierre Monestie) Date: Sat Mar 5 14:43:34 2005 Subject: [Biopython-dev] ipi parser In-Reply-To: <1CF58780-A911-11D8-B3CF-000A956845CE@stanfordalumni.org> Message-ID: Sorry my first message was too long, here is a shorter example: Thanks for the looking at it, Pierre ID IPI00387610.1 IPI; PRT; 697 AA. AC IPI00387610; DT 18-NOV-2003 (IPI Rat rel. 1.9, Created) DT 18-NOV-2003 (IPI Rat rel. 1.9, Last sequence update) OS Rattus norvegicus (Rat). OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; OC Mammalia; Eutheria; Rodentia; Sciurognathi; Muridae; Murinae; Rattus. OX NCBI_TaxID=10116; CC -!- CHROMOSOME: 1. DR InterPro; IPR001611; LRR. DR InterPro; IPR007091; LRR_RNinh. DR InterPro; IPR003590; LRR_RNinh_sub. DR InterPro; IPR007111; NACHT_NTPase. DR Pfam; PF05729; NACHT; 1. DR PRINTS; PR00019; LEURICHRPT. DR SMART; SM00368; LRR_RI; 4. DR PROSITE; PS50503; LRR_RI; 1. DR PROSITE; PS50837; NACHT; 1. DR UniParc; UPI000021DDC2; -; -. DR ENSEMBL; ENSRNOP00000030672; ENSRNOG00000021996; M. SQ SEQUENCE 697 AA; 80092 MW; D6C61D8C95F306AF CRC64; PLVLTDSGHS KLYQAHLKKK LTHDYARKFN IKAQDLFKQK FTQDDCDRFE NLLVSKATGK KPHMVFLQGV AGIGKSLMLT KLMLAWSEGI VFQNKFSYIF YFCCQDVKQL KRASLAELIS REWPNASAPT AEILSQPEKL LFIIDSLEVM ECNMSERESE LCDNCTEKQP VSLLLSSLLR RKMLPESSFL ISATPETFEK MEDRIECTNV KIITGFNENN IKMYFRSLFQ DKNRTLEAFS LVRENEQLFN VCQVPVLCWM VATCIKKEIE KGRDPVFICR RTTSLYTTHI FNLFTPQNAQ YPSKKSQDQL QGLCSLAAEG MWTDTFVFSE EALRRNGILD SDIPTLLDRR ILERSKESES CYIFLHPSLQ EVCAAVFYLL KSHLDHPSQD VKSVEALLFT FLKKAKVQWI FLGCFLFGLL HESEQEKLEM FFGHQLSQEI KHQLYQCLET ISVNEELQEQ IDGMKLFYCL FEMEDEAFLM QAMNCMEQIN FVAKDYSDVI VAAYCLKHCS TLKKLSFSTQ NILSEEQEHS YTEKLLICWH HMCSVLISSK DIHVLQVKDT NLNETAFWVL YNHLKYPSCT LKVLVIAACN LSPDDCKVFA SVLISSKMLK HLNLSSNNLD KGISSLCKAL CHPDCILKHL VVRHCLITTS GCQDLAEVLR HNQNLRSLQV SNNKIEDAGV KLLCDAIKQP NCHLENI // ID IPI00187591.2 IPI; PRT; 163 AA. AC IPI00187591; DT 14-MAR-2003 (IPI Rat rel. 1.0, Created) DT 18-NOV-2003 (IPI Rat rel. 1.9, Last sequence update) OS Rattus norvegicus (Rat). OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; OC Mammalia; Eutheria; Rodentia; Sciurognathi; Muridae; Murinae; Rattus. OX NCBI_TaxID=10116; CC -!- CHROMOSOME: 19. DR UniParc; UPI00001CD005; -; -. DR ENSEMBL; ENSRNOP00000023455; ENSRNOG00000016991; M. SQ SEQUENCE 163 AA; 18683 MW; A1998B08C0383825 CRC64; MDALEEESFA LSFSSASDAE FDAVVGCLED IIMDAEFQLL QRSFMDKYYQ EFEDTEENKL TYTPIFNEYI SLVEKYIEEQ LLERIPGFNM AAFTTTLQHH KDEVAGDIFD MLLTFTDFLA FKEMFLDYRA EKEGRGLDLS SGLVVTSLCK SSSTPASQNN LRH // ID IPI00357878.1 IPI; PRT; 690 AA. AC IPI00357878; IPI00201160; DT 02-OCT-2003 (IPI Rat rel. 1.7, Created) DT 02-OCT-2003 (IPI Rat rel. 1.7, Last sequence update) DE SIMILAR TO ARHGEF3 PROTEIN. OS Rattus norvegicus (Rat). OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; OC Mammalia; Eutheria; Rodentia; Sciurognathi; Muridae; Murinae; Rattus. OX NCBI_TaxID=10116; CC -!- CHROMOSOME: 16. DR InterPro; IPR001849; PH. DR InterPro; IPR000219; RhoGEF. DR Pfam; PF00169; PH; 1. DR Pfam; PF00621; RhoGEF; 1. DR SMART; SM00233; PH; 1. DR SMART; SM00325; RhoGEF; 1. DR PROSITE; PS50010; DH_2; 1. DR PROSITE; PS50003; PH_DOMAIN; 1. DR ENSEMBL; ENSRNOP00000019511; ENSRNOG00000014363; -. DR REFSEQ_XP; XP_224588; GI:34876921; M. DR UniParc; UPI00001D0F0F; -; -. SQ SEQUENCE 690 AA; 77882 MW; FAB74E51D05C987B CRC64; MENSENPPVD NRTSVLHPLL RQTTQTQFVH EPFTEGIQMS ALGYLKRKRK QSAQDEDAVS LCSLDISQPA RALLNPQQTL SERWIRDGLS ASSVVWMTER KGEKHYERER PALPVEPGIR SSLLEAVVGV RVAAAGIVEL GPSFTRDFCC RLGSAVTSQR AGPAAAMVAK DYPFYLTVKR ANCSLEAPLG SGVAKDEEPS NKRVKPLSRV TSLANLIPPV KTTPLKRFSQ TLQRSISFRN ESRPDILAPR AWSRNATSSS TKRRDSKLWS ETFDVCVSQV LTAKEIKRQE AIFELSQGEE DLIEDLKLAK KAYHDPMLKL SIMTEQELNQ IFGTLDSLIP LHEDLLSQLR DVRKPDGSTE HVGPILVGWL PCLSSYDSYC SNQVAAKALL DHKKQDHRVQ DFLQRCLESP FSRKLDLWNF LDIPRSRLVK YPLLLREILR HTPNDNPDQQ HLEEAINIIQ GIVAEINTKT GESECRYYKE RLLYLEEGQK DSLIDSSRVL CCHGELKNNR GVKLHVFLFQ EVLVITRAVT HNEQLCYQLY RQPIPVKDLT LEDLQDGEVR LGGSLRGAFS NNERIKNFFR VSFKNGSQSQ THSLQANDTF NKQQWLNCIR QAKETVLSAA GQAGLLDSES LSQSPGTENR ELRGETKLEQ MDQSDSESDC SMDTSEVSLE CERMEQTDAS CANSRPEENV // > -----Original Message----- > From: Jeffrey Chang [mailto:jeffrey_chang@stanfordalumni.org] > Sent: Tuesday, May 18, 2004 5:20 PM > To: Pierre Monestie > Cc: biopython-dev@biopython.org > Subject: Re: [Biopython-dev] ipi parser > > > Hello, > > These errors are nearly always due to changes in the formats of the > records that occur from time to time. Do you have a sample file, or > accession number, that I can use to see what's going on? > > Jeff > > > On May 18, 2004, at 4:12 PM, Pierre Monestie wrote: > > > Hello, > > I'm trying to use the Swissprot parser to parse IPI. I read that the > > parser > > should have been fixed for IPI however I get an error on date when I > > try to > > parse ipi.HUMAN > > I get: > > File "dbupdate/src/python/make_sptofasta.py", line 172, in ? > > parseandoutput('ipi',it,fl[0],fl[1],fl[2],fl[3],fl[4]) > > File "dbupdate/src/python/make_sptofasta.py", line 46, in > > parseandoutput > > record = it.next() > > File "/lbri/gen/lib/python2.2/site-packages/Bio/SwissProt/SProt.py", > > line > > 166, in next > > return self._parser.parse(File.StringHandle(data)) > > File "/lbri/gen/lib/python2.2/site-packages/Bio/SwissProt/SProt.py", > > line > > 290, in parse > > self._scanner.feed(handle, self._consumer) > > File "/lbri/gen/lib/python2.2/site-packages/Bio/SwissProt/SProt.py", > > line > > 333, in feed > > self._scan_record(uhandle, consumer) > > File "/lbri/gen/lib/python2.2/site-packages/Bio/SwissProt/SProt.py", > > line > > 338, in _scan_record > > fn(self, uhandle, consumer) > > File "/lbri/gen/lib/python2.2/site-packages/Bio/SwissProt/SProt.py", > > line > > 379, in _scan_dt > > self._scan_line('DT', uhandle, consumer.date, exactly_one=1) > > File "/lbri/gen/lib/python2.2/site-packages/Bio/SwissProt/SProt.py", > > line > > 360, in _scan_line > > read_and_call(uhandle, event_fn, start=line_type) > > File "/lbri/gen/lib/python2.2/site-packages/Bio/ParserSupport.py", > > line > > 301, in read_and_call > > method(line) > > File "/lbri/gen/lib/python2.2/site-packages/Bio/SwissProt/SProt.py", > > line > > 537, in date > > self.data.created = cols[1], int(self._chomp(cols[3])) > > ValueError: invalid literal for int(): Human > > > > Thanks in advance for your help > > Pierre Monestie > > > > _______________________________________________ > > Biopython-dev mailing list > > Biopython-dev@biopython.org > > http://biopython.org/mailman/listinfo/biopython-dev From jeffrey_chang at stanfordalumni.org Wed May 19 10:46:03 2004 From: jeffrey_chang at stanfordalumni.org (Jeffrey Chang) Date: Sat Mar 5 14:43:34 2005 Subject: [Biopython-dev] ipi parser In-Reply-To: <20040519095017.GF34051@misterbd.agtec.uga.edu> References: <1CF58780-A911-11D8-B3CF-000A956845CE@stanfordalumni.org> <20040519095017.GF34051@misterbd.agtec.uga.edu> Message-ID: <40474F10-A9A3-11D8-88EB-000A956845CE@stanfordalumni.org> On May 19, 2004, at 5:50 AM, Brad Chapman wrote: > Hi Pierre and Jeff; > > Pierre: >>> I'm trying to use the Swissprot parser to parse IPI. I read that the >>> parser should have been fixed for IPI however I get an error on date >>> when I try to parse ipi.HUMAN I get: > [...] >>> ValueError: invalid literal for int(): Human > > Jeff: >> These errors are nearly always due to changes in the formats of the >> records that occur from time to time. Do you have a sample file, or >> accession number, that I can use to see what's going on? > > I took a look at this using the ipi.HUMAN.dat file from > ftp://ftp.infobiogen.fr/pub/db/ipi/current/ and was able to > reproduce the error. It looks like the problem was that the DT lines > are different then expected: [...] > > I updated the SProt parser to handle this and a patch to > Bio/SwissProt/SProt.py is attached. The code looks good! I've run it on Pierre's file (sent in another email) and it seems to run through correctly and generate the right results. Thanks a lot! Jeff From fsms at users.sourceforge.net Thu May 27 07:20:44 2004 From: fsms at users.sourceforge.net (fsms@users.sourceforge.net) Date: Sat Mar 5 14:43:34 2005 Subject: [Biopython-dev] Restriction analysis package. In-Reply-To: <20040516182321.GA53985@misterbd.agtec.uga.edu> References: <40A74A13.5040503@users.sourceforge.net> <20040516182321.GA53985@misterbd.agtec.uga.edu> Message-ID: <40B5CF0C.5020107@users.sourceforge.net> Hello, Sorry, about the delay, Id to go to a job interview and had not easy access to the net. // > Thanks for putting this together. The code looks very useful and I'd > definitely like to see it work towards being included in Biopython, > if that's what you'd like. A few comments on it: > > 1. First, if you'd like to include this in Biopython the code would > have to be willing to license the code under the Biopython license. > I see different references to the GPL and Python license within your > package. I'm not at all the type of person who argues about > licensing issues, but we just need to keep the Biopython > distribution under one license. > Obviously, I will put the code under Biopython license. I put it under Python for the time being knowing that some people don't like to read GPL code. > 2. The way this is organized right now puts two different types of > functionality together -- building the enzyme dictionary by > downloading and parsing Rebase, and the actual enzyme dictionary > itself. For Biopython, the public functionality you'd want to expose > would be the enzyme dictionary and the useful functions you have > within that. The downloading and parsing work would be something > that you, or another developer, would do on a monthly or whatever > basis to keep the enzyme dictionary up to date within Biopython. > Thus I'd propose organizing the code like: > > Bio/Restriction/__init__.py --> The current Restriction.py > Bio/Restriction/Restriction_Dictionary.py --> the dictionary > Bio/Restriction/_Update/ --> The Update, RanaConfig and > RestrictionCompiler code to do the updates and regenerate the > dictionary. yes and no. I agree with the organisation of the code and I would effectively update the dictionary in Biopython but I think it is important for the end user to be able to update the dictionary on their machine without downloading the full distribution, so this is also a public functionality. Something I would like to implement as well when I have the time is a switch in the ranacompiler.py script to pre-select the supplier(s). If one organisation gets its enzymes from supplier A and B, they may wish not to search the sequences for enzymes of supplier C. > ranacompiler.py should exist in somewhere like Scripts/restriction > to be run, instead of in site-packages. > Yes, the organisation of the package I submitted was quick and dirty to assess if you were interested. I will write a setup.py for the package which will allow the modification. > 3. Going along with reorganizing the code base, I'd propose changing > the updating scripts a bit. Storing databases and things into > site-packages is generally not a good idea, since that is meant > for Python code, and also requires the user to mess around with > either running scripts as root or changing permissions -- more work > then is really necessary. What I'd do is store the Database and > Updates information into, say, the current directory where the user > runs the scripts. Additionally, the Restriction_Dictionary.py would > be generated there. Then, when the updates are done everything gets > run and you have a new Restriction_Dictionary.py to copy over and > check into CVS. > Well, as before I am also in favour of putting the databases, scripts and so on in another directory than site-packages, this was a shortcut. But I am not sure I understand what you propose. The first point is who we want to do the update : 1 ) Should it be done in a centralised way, i.e. in Biopython, and people get the update when they update their CVS. Which means they use CVS for their Biopython installation and that people getting Biopython from the release system rather than CVS will not get frequent updates of the enzyme dictionary. This might not be a problem since Rebase does not change that quickly at least for the most usual enzymes. 2) Another way is to propose an admin scheme. The administrator of the box is in charge of keeping the enzyme dictionary up to date. Then we must provide a script to do that easily. We can then install all the data into a centralised directory something like /var/Biopython/Restriction/ In this case, the script would be run as root when the updates are done and the enzyme dictionary is installed into site-packages since it is a python script after all. 3) The third way is to propose a scheme where everybody can make the update. the directory in which everything is stored is then a /home/user/Biopython/Restriction. The enzyme dictionary is kept and run from the user home directory. There is no problem of permission, since the enzyme will be accessible to the user. Each user will run its personnal version of the enzyme dictionary that will be kept in its own directory. This means Restriction is installed centrally in site-packages/Biopython/Restriction but the enzyme dictionary is not installed when Biopython is installed. The first time a new user run the package, it get to update the dictionary. The script Restriction_Dictionary.py is never installed into site-package. 4) The fourth solution is the current directory scheme. I am personnaly not very keen on this one. My worry with this scheme is that, on machines that are used by several persons, this will ultimately finish by installing several times the same information in different places. That could well be ok on *nix boxes, which restrict what a user can do, but on windows... This will end up into a mess and the scripts are more likely to break if you have several installations of the enzyme dictionary. Another solution here is to use temporary files. My personnal preference would go to a mix of the first and second solution, but I am open to discuss it further. Does not Biopython have a centralised way to keep data centralised ? Something like /var/Biopython. I am sure that this package is not the only one which could benefit from such facility. > Hopefully these make some sense. I really like the catalyse and > search functionality on the enzyme classes -- it's a nice interface > design and it would be great to have in Biopython. > Please do let me know what you think about the licensing and change > proposals and we can keep moving forward towards getting this in > Biopython. Thanks again for the work so far! > > Brad I have had some time when I was away to test a bit further the Restriction package. I have a class to add which allow analysis (i.e where you can specify things as only blunt, or enzymes which cut twice...). I will do the modif over the weekend. (i.e put it under biopython license for a start). The remaining will need a bit more time. Fred From venice at vreme.yubc.net Sat May 29 11:12:35 2004 From: venice at vreme.yubc.net (IPSI-2004) Date: Sat Mar 5 14:43:34 2005 Subject: [Biopython-dev] Invitation to IPSI-2004 Montenegro and IPSI-2004 Stockholm, vip/code Message-ID: <200405291512.i4TFCZQ31909@vreme.yubc.net> Dear Potential Speaker: This is an invitation for you to attend two IPSI BgD multidisciplinary and interdisciplinary conferences, one in Venice, and one in Prague, as follows: IPSI-2004 VENICE Venice, Italy (arrival: 10.11.2004. departure: 14.11.2004.) Deadlines: 15 June 2004 (abstract) + 1 August 2004 (full paper). IPSI-2004 PRAGUE Prague, Czeck Republic (arrival: 11.12.2004. departure: 14.12.2004.). Deadlines: 15 July 2004 (abstract) + 1 September 2004 (full papers) If you like to obtain more information on both conferences, please reply to this email. All IPSI BgD conferences are non-profit! 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