question about isoform uc010pch in GRCh37/hg19

[Chen,Rong]

Hi,

I did an RNAseq analysis on some primary leukemia samples and found that this isoform is well expressed and changed significantly after my drug treatment.  

It encodes for an isoform of human Mcl-1.

 

However, this isoform only exist in the older version of the database (GRCh37/hg19), and does not exist in the newer version GRCh38/hg38. The description of this isoform gives conflicting information. It says it encodes the transcript variant 1 of Mcl-1, but the ref sequence linked to variant 3.

https://genome.ucsc.edu/cgi-bin/hgGene?hgg_gene=uc010pch.2&hgg_prot=uc010pch.2&hgg_chrom=chr1&hgg_start=150547026&hgg_end=150552086&hgg_type=knownGene&db=hg19&hgsid=567012451_n8EH2tjSVXoDcsZz4a2cf3OljJhO

The only variant 3 of Mcl-1 that is presented in the GRCh38/hg38 version is uc021oyf.1.  However, this isoform was not picked up by RNAseq in our samples.

 

I would like to know exactly what is the correct refseq for this isoform, why was this isoform dropped in the new database, and what is the relationship of this one and the variant 3 isoform. Your help on these questions is greatly appreciated.

 

Many thanks and warm regards,

 

 

Rong Chen

Assistant Professor

Dept. of Experimental Therapeutics

Univ. of Texas M.D. Anderson Cancer Center

Phone: 713-563-6973

 

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[Jairo Navarro Gonzalez]

Hello Rong,

Thank you for using the UCSC Genome Browser and your question about isoform uc010pch.2 in GRCh37/hg19. I apologize for the late reply.

If I understand the question correctly, you are curious why the RefSeq description in the hgGene page for uc010pch.2 links it to NM_001197320, variant 3. Going to this session, and clicking on the details page for each of the transcripts in the RefSeq track, you can see that NM_021960 is "transcript variant 1", NM_182763 is "transcript variant 2", and NM_001197320 is "transcript variant 3". The isoform uc010pch.2 is clustered with variant 3 even though it's not a perfect match like uc021oyf.1. Our engineers have shared that uc010pch.2 is linked to variant 3 because it is more similar to variant 3 than to the other variants since it has the same number of exons even if they don't completely align.

The hg38 UCSC genes dataset comes from GENCODE, which we have no control over. It looks like uc010pch.2 is built from the mRNA AK304775, which has the same CDS, so you'd have to ask them why AK304775 doesn't count as evidence for an isoform. 
You can contact the GENCODE group about the exclusion of this isoform here: http://www.gencodegenes.org/contact.html.

Thank you again for your inquiry and using the UCSC Genome Browser. 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 forum. If your question includes sensitive data, you may send it instead
to genom...@soe.ucsc.edu.

Jairo Navarro
UCSC Genomics Institute

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