Hi Mark,
I'm not sure why you didn't get any results, but here are the instructions:
In the Table Browser, select:
(your assembly, e.g. Mammal, Human, hg19)
group: Genes and Gene Pred Tracks
track: UCSC Genes
table: knownGene
region: genome
identifiers: (use the paste list button to paste your knownGene IDs -
one ID per line)
output format: selected fields from primary and related tables
click "get output"
Now select the fields you're interested in. I would guess, "name",
"chrom", "exonCount", "exonStarts", "exonEnds".
click "get output"
For example, doing the above steps and pasting in these identifiers:
uc001aaa.3
uc001wrk.3
uc002ovx.2
uc001jix.3
Gives these results:
#name chrom exonCount exonStarts exonEnds
uc001aaa.3 chr1 3 11873,12612,13220,
12227,12721,14409,
uc001jix.3 chr10 8
51748077,51749067,51751435,51754154,51761755,51764444,51767784,51768470,
51748698,51749136,51751504,51754189,51761856,51764480,51767836,51770258,
uc001wrk.3 chr14 11
32030590,32031273,32034219,32068494,32142560,32142689,32256985,32295834,32315676,32319324,32328323,
32030753,32031421,32034254,32068585,32142600,32142780,32257079,32295920,32315797,32319407,32330417,
uc002ovx.2 chr19 6
43671895,43674206,43679366,43680021,43688933,43690493,
43672287,43674290,43679621,43680300,43689299,43690688,
Please let us know if you have any additional questions: [email protected]
-
Greg Roe
UCSC Genome Bioinformatics Group
On 10/17/11 8:21 AM, Mark Consugar wrote:
> UCSC Genome Browser Help:
> I have been trying to find a way to use Gene ID values to obtain exon
> coordinates with the UCSC Table Browser. I found the following e-mail
> links that walked me through the process:
>
> https://lists.soe.ucsc.edu/pipermail/genome/2009-September/019972.html
> https://lists.soe.ucsc.edu/pipermail/genome/2006-November/012212.html
>
> However, using known Gene ID's (confirmed by enetering in NCBI) to test
> the set-up did NOT provide any data. I was wondering if someone could
> please assist me with the above or updated method for getting coordinate
> information using Gene ID's w/o having to go through multiple conversion
> tools...
>
> Thanks!
> Mark Consugar
> Research Manager - Ocular Genomics Institute
> _______________________________________________
> Genome maillist - [email protected]
> https://lists.soe.ucsc.edu/mailman/listinfo/genome
_______________________________________________
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