uc001jiu.2 is contained within an intron of TIMM23 and in the reverse strand so it shouldn't be called TIMM23, it is a different gene?
Valeria -----Original Message----- From: Vanessa Kirkup Swing [mailto:[email protected]] Sent: Thursday, May 26, 2011 11:44 AM To: Vasta, Valeria Cc: [email protected] Subject: Re: [Genome] TIMM23 (uc001jiu.2) Hi Valeria, Please take a look at the track description to see how a transcript is assigned a permanent "uc" accession. In this case, I would assume you are looking at UCSC Genes on hg19 (http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=knownGene). Please keep in mind that this track is generated from gene predictions based on data from RefSeq, Genbank, CCDS and UniProt. Using the table browser to obtain the data for that particular gene symbol you can see that each of the transcripts with "uc" accessions (knownGene.name) each have a different protein ID (which is the UniProt display ID for Known Genes, UniProt accession or RefSeq protein ID for UCSC Genes). #hg19.knownGene.name hg19.knownGene.strand hg19.knownGene.proteinID hg19.kgXref.geneSymbol uc001jin.2 + O14925 TIMM23 uc001jiu.2 - NP_006318 TIMM23 uc010qha.1 + B4DDK6 TIMM23 uc010qhb.1 + TIMM23 uc010qhc.1 + B7ZB25 TIMM23 I hope that this helps to clarify why there are different "uc" identifiers for a particular gene symbol. If you have further questions, please contact the mailing list: [email protected]. Vanessa Kirkup Swing UCSC Genome Bioinformatics Group ----- Original Message ----- From: "Valeria Vasta" <[email protected]> To: [email protected] Sent: Wednesday, May 25, 2011 6:09:09 PM Subject: [Genome] TIMM23 (uc001jiu.2) HELLO THERE ARE TWO TIMM23 annotated and they are in two opposite directions. Can you please let me know about this? thanks Valeria CONFIDENTIALITY NOTICE: This e-mail message, including any attachments, is for the sole use of the intended recipient(s) and may contain confidential and privileged information protected by law. Any unauthorized review, use, disclosure or distribution is prohibited. If you are not the intended recipient, please contact the sender by reply e-mail and destroy all copies of the original message. _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome CONFIDENTIALITY NOTICE: This e-mail message, including any attachments, is for the sole use of the intended recipient(s) and may contain confidential and privileged information protected by law. Any unauthorized review, use, disclosure or distribution is prohibited. If you are not the intended recipient, please contact the sender by reply e-mail and destroy all copies of the original message. _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
