Inquiry on transcript variant nomenclatue

[Labanca,Estefania]

Hello,

 

we are analyzing transcript variant expression of FGFR1.

In the UCSC genome browser, we get IDs of the type: “uc003xlu.2”

We did an analysis on transcript variant last year, using ucsc IDS. we now want to look at other variants. However, the variant ID doesn’t match to the current list of ucsc genes. it does almost match, except for the last number eg: in our analysis we had “uc003xlu.2”, now that oIDne doesn’t not appear, but we do find “uc003xlu.3”.

 

Therefore,

I. is the last number an updated version of a previous version, same transcript variant? Or how can we find that ID? can you explain the discrepancies we are encountering?

ii. why is there more than one transcript variant with the same number (eq: 13) with different IDs of the type  “uc003lbx.1” (i.e. uc003lbx.1, uc003lbw.2, uc003lbt.1, uc003lbx.1, uc003lbs.2, uc003lbr.2, uc003lwf.3. plase see image below

 

Thanks in advance

Sincerely,

 

-- 

Estefania Labanca, PhD

Postdoctoral Fellow

Genitourinary Medical Oncology- Research   

The University of Texas MD Anderson Cancer Center

 

 

 

 

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[Gerardo Perez]

Hi Dr. Labanca,

Thank you for your question about transcript variant nomenclature.

With every release of the UCSC Genes track, a new gene set is built. A transcript is assigned an accession ID that ends with the suffix ".1" when the transcript was not in the previous release of UCSC Genes. For example, uc003lbx.1 and uc003lbt.1, the suffix ".1" indicates that this is the first version of the transcript.

If the transcript is not identical to any transcript in the previous release but it overlaps a similar transcript with a compatible structure, the previous accession is re-used with the version number incremented. For example, the transcript version number uc003xlu.2 increments to uc003xlu.3.

If the transcript is identical to some transcript in the previous release of UCSC Genes, the accession is re-used with the same version number. For example, uc003lbx.1 transcript version would be re-used as uc003lbx.1 in the new release if the transcripts are identical.

For more information on the UCSC Genes build process, please review the track description page for the UCSC Genes track: http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=knownGene

We drop transcripts from a new gene set built when there is no longer enough evidence to include them in the gene model. If you would like to view the gene model information about your particular older transcript, you can use the Table Browser to query the knownGeneOldX tables, where X is a particular version of the gene set.

To query this table, navigate to the Table Browser (http://genome.ucsc.edu/cgi-bin/hgTables) and make the following selections:

1. clade: Mammal

genome: Human

assembly: Feb. 2009 (GRCh37/hg19)

group: All Tables

database: hg19

table: knownGeneOld5

2. Next to "identifiers", click "paste list", and enter your list of ID's, such as uc003xlu.2

3. Click "Get output" to view transcript information for your list of genes

I hope this is helpful. Please include gen...@soe.ucsc.edu in any replies to ensure visibility by the team. All messages sent to that address are archived on our public forum. If your question includes sensitive information, you may send it instead to genom...@soe.ucsc.edu.

Gerardo Perez
UCSC Genomics Institute

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[Labanca,Estefania]

Thank you very much for the detailed reply. I believe this clarifies our concerns to continue our analysis.

We’ll contact you if we have further questions

 

Best regards,

 

Estefania

 

 

From: Gerardo Perez <gpe...@ucsc.edu>
Date: Thursday, December 17, 2020 at 6:16 PM
To: "Labanca,Estefania" <ELab...@mdanderson.org>
Cc: "gen...@soe.ucsc.edu" <gen...@soe.ucsc.edu>, Juan Bizzotto <juananton...@gmail.com>
Subject: [EXT] Re: [genome] Inquiry on transcript variant nomenclatue

 

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