transcript NM_001013742.3 inconsistency

[Monica]

To whom it may concern:

 

In Saphetor SA (Saphetor.com), we aggregate databases to analyze human variants. We are using ucsc for getting genes and transcripts coordinates. We have created an open and free website where we share this information with the whole community, http://varsome.com.    

 

During one of our controls, we have realized that the refseq transcript NM_001013742.3 is inconsistently defined between the two reference genomes (hg19 and hg38).

 

This is why VarSome shows rs782070555 it as c.3501C>A for hg19 (http://varso.me/Bgy)  and c.3502C>A for hg38 (http://varso.me/Bgz). In particular, it’s the region coordinates of exons that are inconsistent between the two. So while the genomic coordinates are correct, the transcript coordinates, the frame and therefore the amino acid impact, are affected.

 

It appears that the hg38 version is the right one.

 

Our intention is to alert about this problem, and ask you whether you could correct this error in the ucsc database.

 

Looking forward for your feedback.

 

Best regards,

 

Monica

 

 

 

___________________________________________________

 

Monica Albarca Aguilera, PhD.

 

Customer Operations & Quality Assurance Manager

SAPHETOR SA

EPFL Innovation Park, Bâtiment C, 1015, Lausanne, Switzerland.

Main : +41 (0) 21 693 8925

Mobile :+41 (0) 78 733 2361

www.saphetor.com

 

Follow us on twitter @saphetor

 

 

[Cath Tyner]

Hello Monica,

Thank you for using the UCSC Genome Browser and for alerting us to your concern. Please review this very similar previously answered question.

In short, this is a fairly common question - annotation differences for RefSeq Genes are due in part to our historical process of using an alignment program (BLAT) to map RefSeq mRNAs to the reference genome. 

Another reason for differences are due to changes from older to newer assemblies, which the "hg19 diff" red line indicates in this session of the regions you described (new contig in hg38 replacing sequence or filling gaps from hg19). In the past, and currently, we receive sequence instead of coordinates from NCBI, thus our solution never allowed direct mapping. 

The good news is that we will soon be releasing a new track for RefSeq genes which uses direct mapping; this eliminates annotation discrepancies among UCSC and NCBI. This new track will only be available for hg38 and future human assemblies.

Please respond to this list if you have further questions!

Thank you again for your inquiry and for using the UCSC Genome Browser. 

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​Enjoy,​

Cath

Cath
. . .

Cath Tyner

UCSC Genome Browser, Software QA & User Support

UC Santa Cruz Genomics Institute

UCSC Genome Browser

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