Hi Amy, While we do not assist with interpretation of the data displayed on the Genome Browser, two of our developers who are affiliated with MGC had this to say:
"This is a hard call. There are two MGC full-length mRNA that support this 3' end. MGC mRNA underwent a review process independent of the sequences. They both align at 100% identity. However they are from the same library. There are no TransMap cross-species alignments. If I was looking into this, I would also look at conservation and ENCODE RNA-seq data." "I agree. I did look to see if there is any genomic polyA sequence at the 3' end as sometimes there is false priming from these sequences during cloning which could produce a truncated sequence. However, this does not appear to have happened in this case. Also, the MGC clones were not PCR-rescued which may also cause truncation. I agree that looking at other sources of transcriptome data would be useful. Since this MGC clone (there are two cDNAs but they are from the same library so considered as only one piece of evidence) has a polyA tail and polyA signal, it would be considered full-length and RefSeq would consider this to be enough evidence create a RefSeq annotation based on this cDNA." Best, Mary ---------------- Mary Goldman UCSC Genome Bioinformatics Group ----- Original Message ----- From: "Amy Elizabeth Dietrich" <[email protected]> To: "Mary Goldman" <[email protected]> Sent: Thursday, October 28, 2010 10:58:15 AM GMT -08:00 US/Canada Pacific Subject: Re: [Genome] NM_015597.4 Thanks so much for the update. I look forward to hearing from you. Cheers, Amy On Thu, Oct 28, 2010 at 12:18 PM, Mary Goldman < [email protected] > wrote: Hi Amy, We are currently looking into this and will contact you shortly. Thank you for your patience. Best regards, Mary Goldman UCSC Genome Bioinformatics Group ----- Original Message ----- From: "Amy Elizabeth Dietrich" < [email protected] > To: [email protected] Sent: Tuesday, October 26, 2010 8:27:31 AM GMT -08:00 US/Canada Pacific Subject: [Genome] NM_015597.4 Good morning, I am interested in GPSM1 on human chr. 9. Before beginning gene expression experiments, I have been researching the 3 different RefSeq transcripts on the UCSC Browser. According to the GenBank entry, transcript variant NM_015597.4 is derived exclusively, save one bp, from cDNA clone (mRNA) BC009979.1. However, I am unable to locate any ESTs matching the unique 3' end of BC009979.1 by BLASTn (of dbEST), despite the existence that I noted of a putative polyadenylation signal ATTAAA close to the end of the the BCOO9979.1 sequence. I attempted to access the details of this mRNA from the website in the cited 2002 PNAS article (PMID12477932) but parts of that website appear to be down. I am curious about the support for the true existence of this transcript and would really appreciate any help you could give me. Sincerely, Amy Dietrich Amy Dietrich Doctoral Candidate, Dept. of Human and Molecular Genetics Virginia Commonwealth University Virginia Institute for Psychiatric and Behavioral Genetics _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
