Chromosome 21p arm genes in GRCh38

[Lilit Atanesyan]

Dear Sir/madam,

 

As compared to the GRCh37, there are many more genes indicated on the p-arm of chromosome 21.

However, after carefully looking at them, one can see that these genes (especially those close to telomere) are exactly the same as on the 21q arm, with the same exact sequence.

An example is U2AF1 gene; below a blat search of a sequence form that gene in the GRCh38:

 

BLAT Search Results

   ACTIONS      QUERY           SCORE START  END QSIZE IDENTITY CHRO STRAND  START    END      SPAN

---------------------------------------------------------------------------------------------------

browser details YourSeq           50     1    50    50 100.0%    21   -   43104268  43104317     50

browser details YourSeq           50     1    50    50 100.0%    21   -    6495946   6495995     50

 

 

Is there any finding supporting this?

 

Many thanks for your support and consideration.

With best regards,

Lilit

 

 

Lilit Atanesyan, Ph.D

Research scientist/Product developer

MRC-Holland - Amsterdam, the Netherlands

email: l.ata...@mlpa.com

web: www.mlpa.com

Tel: +31 88  865 7228 new

Fax: +31 88 865 7201 new

 

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[Matthew Speir]

Hi Lilit,

Thank you for your question about these duplicated genes on chr21. The example you provided, U2AF1, falls within a contig that was newly added in hg38. It also happens that this gene is part of a segmental duplication that maps to the other U2AF1 location on chr21. In the following session, you can see the newly added contig at the top in red, the U2AF1 transcripts in various shades of blue in the center, and the segmental duplications track in orange at the bottom: http://genome.ucsc.edu/cgi-bin/hgTracks?hgS_doOtherUser=submit&hgS_otherUserName=Matt%20Speir&hgS_otherUserSessionName=hg38_U2AF1segDup. If you turn on the "Hg19 Diff" and "Segmental Dups" tracks at look at the other genes that you noted were duplicated on the p-arm, you may see a similar situation where the new contigs added in hg38 that are also part of a segmental duplication.

If a prediction in the UCSC Genes track ever looks suspicious to you, I recommend turning on some of the other gene prediction tracks like GENCODE, RefSeq, or CCDS to see if they also contain a similar gene prediction at that position. In the case of both U2AF1 locations on chr21, all of three of these gene prediction tracks contain transcripts similar to those in UCSC Genes. For the UCSC and GENCODE Genes tracks, you can also click on a particular transcript to see more detailed information about it, including transcript support information. The UCSC Genes track includes transcript support information under the section titled "Gene Model Information". GENCODE Genes includes the "Annotation Method" and "Transcript Support Level" fields which detail how the gene prediction was generated and the level of support for a particular transcript.

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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