Exon numbering convention followed by UCSC

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Rohit Gavval

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Apr 25, 2013, 7:05:19 AM4/25/13

to gen...@soe.ucsc.edu

Hi UCSC,

I am trying to figure out the exon numbering convention followed by UCSC. I understand that RefSeq numbers the exons from 5’-3’. Does UCSC browser follow the same naming convention?

Thanks and Regards,

Rohit Gavval

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Pauline Fujita

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Apr 25, 2013, 3:34:05 PM4/25/13

to Rohit Gavval, gen...@soe.ucsc.edu

Hello Rohit,

This depends where you are looking at the exon numbers. For output from the Table Browser (genome.ucsc.edu/cgi-bin/hgTables) exons will be numbered in order of increasing chromosomal coordinate (not 5' to 3').

However, if you are looking at RefSeq in the browser, and have the next/previous exon navigation arrows turned on (enabled by clicking on the "configure" button below the main browser display - and checking the box at the top), then the exon numbers you will see as you hover your mouse above the next/prev arrow are numbered 5' to 3' to match RefSeq.

Hopefully this clarifies things. If you have further questions please feel free to contact the mailing list again at gen...@soe.ucsc.edu.

Best regards,

Pauline Fujita
UCSC Genome Bioinformatics Group
http://genome.ucsc.edu