Hi Valeria, I've alerted the engineers who work on the UCSC Genes pipeline to these genes. It is possible that the annotations will change in future builds of UCSC Genes.
-- Brooke Rhead UCSC Genome Bioinformatics Group On 05/26/11 15:42, Vasta, Valeria wrote: > Thanks > > It is confusing to me how the genes called TIMM23 (UCSC positive strand > and refseq reverse strand)(not the TIMM23B) have been annotated with the > same gene name if the exons are not shared and in different strands? > > > -----Original Message----- > From: Brooke Rhead [mailto:[email protected]] > Sent: Thursday, May 26, 2011 3:09 PM > To: Vasta, Valeria > Cc: [email protected] > Subject: Re: [Genome] TIMM23 (uc001jiu.2) > > Hi Valeria, > > In this case it is useful to turn on several gene tracks and compare how > > each of them annotates this region. Here is a session with several gene > > tracks turned on: > > http://genome.ucsc.edu/cgi-bin/hgTracks?hgS_doOtherUser=submit&hgS_other > UserName=Rhead&hgS_otherUserSessionName=mlq4052 > > Not all of the tracks are in agreement (which is not surprising, as they > > all use different methods to annotate genes). It looks like most of the > > tracks call the the gene on the reverse strand TIMM23. Several of them > show another gene, TIMM23B, on the positive strand. The UCSC Genes > annotation of the positive strand gene is much longer than most of the > other tracks, but note that it is displayed in light blue, which means > there is less evidence for it than there is for the one on the reverse > strand, which is displayed in Medium blue. > > The color key for UCSC Genes is: > > * Black -- feature has a corresponding entry in the Protein Data Bank > (PDB) > * Dark blue -- transcript has been reviewed or validated by either the > RefSeq, SwissProt or CCDS staff > * Medium blue -- other RefSeq transcripts > * Light blue -- non-RefSeq transcripts > > I hope this helps you interpret what you are seeing in the Genome > Browser. > > -- > Brooke Rhead > UCSC Genome Bioinformatics Group > > > > On 05/26/11 13:49, Vasta, Valeria wrote: >> 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 > > > 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
