Hi CXK,
It seems like you are using mm9. If so, in the case of the three items
you listed in your email, these are transcript varients of the same
gene. To get this information, you can use our table browser. Click on
"Tables" on the blue bar on the top of the main page and select the
clade, genome, and assembly for your organism of interest. Then make the
following selections:
group: Genes and Gene Prediction Tracks
track: RefSeq Genes
table: refGene
region: genome (or select "position" & enter your location of interest)
output format: selected fields from primary and related tables
output file: if you would rather have the results saved to a file
instead of displaying in the browser window, enter the name you would
like the output file to have, otherwise, leave blank
file type returned: plain text
Click "get output." Select the fields from the refGene table in which
you are interested. Then scroll down to the "Linked Tables" section and
select "gbCdnaInfo" table and click "Allow Selection From Checked
Tables." Now, scroll back down to the "Linked Tables" section. Select
"description" table and click "Allow Selection From Checked Tables."
From description fields, select "id" and "name." Now scroll up to the
top of the page and click "get output". Now you will have all the fields
from refGene you selected plus the id and description (which often
contains transcript information), like so:
"
223 NM_001145781 chr1 + 157405249 157434924
157405767 157434605 4
157405249,157411786,157414714,157434569,
157405989,157411851,157414811,157434924, 186862 Acbd6 cmpl
cmpl 0,0,2,0, 655185 Mus musculus acyl-Coenzyme A binding
domain containing 6 (Acbd6), transcript variant 2, mRNA.
223 NM_026683 chr1 + 157405249 157419417 157405767
157419357 4 157405249,157411786,157414714,157419327,
157405989,157411851,157414811,157419417, 186853 Acbd6 cmpl
cmpl 0,0,2,0, 655187 Mus musculus acyl-Coenzyme A binding
domain containing 6 (Acbd6), transcript variant 3, mRNA.
223 NM_028250 chr1 + 157405249 157534363 157405767
157534233 8
157405249,157411786,157414714,157448583,157462996,157471998,157524333,157534078,
157405989,157411851,157414811,157448666,157463102,157472088,157524364,157534363,
235893 Acbd6 cmpl cmpl 0,0,2,0,2,0,0,1, 655184 Mus
musculus acyl-Coenzyme A binding domain containing 6 (Acbd6), transcript
variant 1, mRNA.
"
For more information about using the Table Browser see "Using the Table
Browser" by scrolling down past the Table Browser form. It provides
brief descriptions of the Table Browser controls. You can also see the
"User's Guide" at http://genome.ucsc.edu/goldenPath/help/hgTablesHelp.html.
Please don't hesitate to contact the mail list again if you have any
further questions.
Katrina Learned
UCSC Genome Bioinformatics Group
xinkai cao wrote, On 11/09/10 17:59:
> Hi, UCSC
>
> when I read the "refgene" file, I found some lines have the same
> "name2"(seeing below).
>
> "
> 223 NM_001145781 chr1 + 157405249 157434924
> 157405767 157434605 4 157405249,157411786,157414714,157434569,
> 157405989,157411851,157414811,157434924, 186862 Acbd6 cmpl
> cmpl 0,0,2,0,
> 223 NM_026683 chr1 + 157405249 157419417 157405767
> 157419357 4 157405249,157411786,157414714,157419327,
> 157405989,157411851,157414811,157419417, 186853 Acbd6 cmpl
> cmpl 0,0,2,0,
> 223 NM_028250 chr1 + 157405249 157534362 157405767
> 157534233 8
> 157405249,157411786,157414714,157448583,157462996,157471998,157524333,157534078,
> 157405989,157411851,157414811,157448666,157463102,157472088,157524364,157534362,
> 193148 Acbd6 cmpl cmpl 0,0,2,0,2,0,0,1,
> "
> So I want to know whether those lines having the same "name2" are the
> differentive alternative splicing isoforms of one gene? How can I get the
> isoform information of each gene from UCSC?
>
>
> Thanks!
>
> CXK
> _______________________________________________
> Genome maillist - [email protected]
> https://lists.soe.ucsc.edu/mailman/listinfo/genome
>
_______________________________________________
Genome maillist - [email protected]
https://lists.soe.ucsc.edu/mailman/listinfo/genome
