Dear UCSC browser; Hello, this is Gue-Su Chang again. I almost figured out my second question as below. I have a question related with it. How can I match the UCSC gene identity name (like "uc007aet.1", "uc007afn.1") to the MGI accession ID (like "MGI:3528744")?
I will greatly appreciate it if you could help me out. Thanks a lot. Best Gue SU -----Original Message----- From: Gue Su Chang [mailto:[email protected]] Sent: Tuesday, July 14, 2009 1:08 PM To: '[email protected]' Subject: A question about UCSC tables Dear UCSC browser; Hello, this is Gue-Su Chang. I am a graduate student at Penn State and I am working with Dr. Pugh in Wartik. May I ask several questions? Recently, I am using the UCSC Table browser to curate known genes from the mouse genome. I chose "UCSC Genes" track and the "knownGene" table. The following lines are a result example I now have. I would like to ask a question about them. ----------------------------------- uc007afy.1 chr1 + 6720131 6851021 6758978 6848681 24 6720131,6727660,6742376,6743074,6758978,6761024,6785466,6792400,6797623,6799 357,6800654,6807683,6810014,6817856,6823643,6832219,6832953,6834201,6834371, 6835651,6838987,6845449,6847380,6848540, 6720321,6727738,6742449,6743117,6759033,6761055,6785657,6793186,6797758,6799 448,6800759,6807877,6810226,6818102,6823759,6832282,6833022,6834264,6834452, 6835873,6839076,6845553,6847524,6851021, Q80TY4 uc007afy.1 uc007afz.1 chr1 + 6720131 6851021 6758978 6848681 23 6720131,6742376,6743074,6758978,6761024,6785466,6792400,6797623,6799357,6800 654,6807683,6810014,6817856,6823643,6832219,6832953,6834201,6834371,6835651, 6838987,6845449,6847380,6848540, 6720321,6742449,6743117,6759033,6761055,6785657,6793186,6797758,6799448,6800 759,6807877,6810226,6818102,6823759,6832282,6833022,6834264,6834452,6835873, 6839076,6845553,6847524,6851021, Q80TY4 uc007afz.1 ----------------------------------- Two questions are here, and it will be greatly appreciated if you could provide answers for me. (1) They are two isoforms of a protein which are processed differently by alternative splicing. Why do they have the same protein ID, like "Q80TY4"? They clearly consist of different exons. (2) I saw their ID names are "uc007afy.1" and "uc007afz.1". I would like to have their common names which are more familar with people. How can I retrieve this kind of information from UCSC? I am looking forward to your kind help. Best regards, Gue Su ---------------------------------------------------------------------- Chang, Gue Su (E-mail: [email protected]) Graduate student IBIOS Graduate Program Option in Bioinformatics and Genomics http://www.huck.psu.edu/IBIOS/ PI: Dr. Frank B. Pugh Center for Eukaryotic Gene Regulation 331 South Frear Pennsylvania State University University Park PA, 16802 http://www.bmb.psu.edu/faculty/pugh/pugh.html ---------------------------------------------------------------------- _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
