same hg38 different bp
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Filomena Tiziana Papa
Jul 17, 2015, 1:28:32 PM7/17/15
to gen...@soe.ucsc.edu
Hi,
I found the two versions of my gene
>hg38_knownGene_uc001hln.3 range=chr1:218344334-218444619 5'pad=0 3'pad=0 strand=+ repeatMasking=none
I found the two versions of my gene
>hg38_knownGene_uc001hln.3 range=chr1:218344334-218444619 5'pad=0 3'pad=0 strand=+ repeatMasking=none
>hg38_knownGene_uc001hlm.4 range=chr1:218345235-218444619 5'pad=0 3'pad=0 strand=+ repeatMasking=nonebut they have different 5'UTR (hlm.4 has shorter sequence than hln.3). How is possible if both of them are hg38?
Bests
Filomena 
Matthew Speir
Jul 21, 2015, 11:33:35 AM7/21/15
to Filomena Tiziana Papa, gen...@soe.ucsc.edu
Hi Filomena,
Thank you for your question about the GENCODE Genes track in the UCSC Genome Browser. I believe that you may be confusing genes and transcripts. A single gene can have many associated transcripts. These transcripts can differ in many ways including which exons are included or excluded and their UTR length.
Additionally, as my colleague Luvina noted in her response, transcripts can of do undergo minor changes from one version of a gene prediction track to another. Often times, transcripts are updated as new transcriptional evidence is found or gene prediction methods get better. Note that many transcripts may change from one version of a track to another. For example, on the "Old UCSC Genes" track description page, http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg38&g=knownGeneOld8, it says, "43,681 transcripts are "compatible" with those in the previous set, meaning that the two transcripts show consistent splicing. In most cases, the old and new transcripts differ in the lengths of their UTRs."
The transcript "uc001hln.3" exists in the "Old UCSC Genes" track and it has been replaced in the "GENCODE Genes" track by the transcript "uc001hln.4".
I hope this is helpful. If you have any further questions, please reply to gen...@soe.ucsc.edu. All messages sent to that address are archived on a publicly-accessible Google Groups forum. If your question includes sensitive data, you may send it instead to genom...@soe.ucsc.edu.
Matthew Speir
UCSC Genome Bioinformatics Group
Thank you for your question about the GENCODE Genes track in the UCSC Genome Browser. I believe that you may be confusing genes and transcripts. A single gene can have many associated transcripts. These transcripts can differ in many ways including which exons are included or excluded and their UTR length.
Additionally, as my colleague Luvina noted in her response, transcripts can of do undergo minor changes from one version of a gene prediction track to another. Often times, transcripts are updated as new transcriptional evidence is found or gene prediction methods get better. Note that many transcripts may change from one version of a track to another. For example, on the "Old UCSC Genes" track description page, http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg38&g=knownGeneOld8, it says, "43,681 transcripts are "compatible" with those in the previous set, meaning that the two transcripts show consistent splicing. In most cases, the old and new transcripts differ in the lengths of their UTRs."
The transcript "uc001hln.3" exists in the "Old UCSC Genes" track and it has been replaced in the "GENCODE Genes" track by the transcript "uc001hln.4".
I hope this is helpful. If you have any further questions, please reply to gen...@soe.ucsc.edu. All messages sent to that address are archived on a publicly-accessible Google Groups forum. If your question includes sensitive data, you may send it instead to genom...@soe.ucsc.edu.
Matthew Speir
UCSC Genome Bioinformatics Group
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