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. 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