Question: Complete exon coordinate for ref seq gene
0
gravatar for fabbri.marco
15 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 • 319 views
ADD COMMENTlink modified 15 months ago • written 15 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 15 months ago by lieven.sterck8.3k

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 15 months ago by genomax87k • written 15 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 15 months ago by genomax87k
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