Question: hg19 transcript mapping or exon overlap
0
gravatar for bioguy24
23 months ago by
bioguy24190
Chicago
bioguy24190 wrote:

Is there a tool or script that can map or identify what exon the current version of an hg19 transcript overlaps with? I guess like UCSC genome browser but for just uses the coordinates without visualizing them. Thank you :)

For example.

 Transcript        Exon
 NM_001127222.1     10
ngs • 702 views
ADD COMMENTlink modified 23 months ago by pjalali4610 • written 23 months ago by bioguy24190
1

I'm not sure, but do exon numbers make sense in the context of alternative splicing? There is no unambiguous way to number exons if some are optional.

ADD REPLYlink written 23 months ago by WouterDeCoster38k
1

Do you mean you want to identify all exons of a transcript? If so you can use ucsc table browser (go to ucsc website -> tools -> table browser -> select clade: mammal; genome: human; assembly: hg19; group: genes and gene predictions; leave track and table as default -> either download genome-wide info or upload identifier, in your case NM_001127222 -> hit get output -> exon start and end positions are displayed as one of the default fields)

ADD REPLYlink written 23 months ago by cindyz30

Thank you all for your help :)

ADD REPLYlink written 23 months ago by bioguy24190

WouterDeCoster .....i must talk to yuo...my email: pjalali46@yahoo.com.

ADD REPLYlink written 23 months ago by pjalali4610
4

I have moved your post to a comment. Please use ADD REPLY to answer to earlier reactions.
If you have something to discuss or ask feel free to do it in this forum, we prefer to keep all conversation open so everyone can share their ideas and experience.

ADD REPLYlink written 23 months ago by WouterDeCoster38k
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