Question: Complete exon coordinate for ref seq gene
0
gravatar for fabbri.marco
4 months ago by
fabbri.marco0 wrote:

I have a list of ref-seq genes and I would like to get genome coordinates of all non-overlapping and non-replicated exons for each gene. I am designing a gene panel to detect mutations and I want to be sure to have all exons covered. Any suggestion, how to proceed? thank you Marco

ref-seq exon • 169 views
ADD COMMENTlink modified 4 months ago • written 4 months ago by fabbri.marco0

is that a sizeable list you are talking about? is it from a single species or multiple?

what I'm kinda steering at is can't you simply extract that data from the refseq genome annotation files?

ADD REPLYlink written 4 months ago by lieven.sterck5.8k

In this RefSeq genome annotation file, for example for IL9R we have different exons in different transcripts, some are shared and some unique. I would like to have a single line per gene with the union of exon coordinates:

results:

IL9R chrX
155997580,156002905,156003448,156003676,156004419,156005277,156006082,156007522,156009815,156001407,156002881...
155997787,156003019,156003560,156003855,156004565,156005479,156006188,156007607,156010817,156001508,156003019.

..

starting file:

1775    NM_002186.2 chrX    +   155997580   156010817   155997759   156010409   9   155997580,156002905,156003448,156003676,156004419,156005277,156006082,156007522,156009815,  155997787,156003019,156003560,156003855,156004565,156005479,156006188,156007607,156010817,  0   IL9R    cmpl    cmpl    0,1,1,2,1,0,1,2,0,
1775    NM_176786.1 chrX    +   155997580   156010817   155997743   156009852   9   155997580,156001407,156002881,156003448,156003683,156004448,156005277,156006082,156009815,  155997787,156001508,156003019,156003560,156003855,156004565,156005479,156006188,156010817,  0   IL9R    cmpl    cmpl    0,2,1,1,2,0,0,1,2,

thanks

ADD REPLYlink modified 4 months ago by genomax71k • written 4 months ago by fabbri.marco0

Please use ADD COMMENT/ADD REPLY when responding to existing posts to keep threads logically organized. SUBMIT ANSWER should be used for new answers to original question.

ADD REPLYlink written 4 months ago by genomax71k
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