Hi Haojam,
I accidently crossed some information from the genome browser and the
table browser. So, in the Table Browser, to get the coding regions, you
will want to check the following functions: Synonymous, nonsense,
missense, frameshift, cds-indel, coding-synonymy-unknown.
Sorry for the confusion.
-
Greg Roe
UCSC Genome Browser
On 1/11/11 2:08 PM, Greg Roe wrote:
> Hi Haojam,
>
> When you go into the filter, I think setting you want for selecting
> coding regions only is function ("func"). For SNP131 on hg19 the
> options look like:
>
> *Function*: Predicted functional role (/each variant may have more than
> one functional role/)
>
> * *Locus Region* - variation within 2000 bases of gene, but not in
> transcript (near-gene-3, near-gene-5)
> * *Coding - Synonymous* - no change in peptide for allele with
> respect to reference assembly (coding-synon)
> * *Coding - Non-Synonymous* - change in peptide for allele with
> respect to reference assembly (nonsense, missense, frameshift,
> cds-indel, coding-synonymy-unknown)
> * *Untranslated* - variation in transcript, but not in coding region
> interval (untranslated-3, untranslated-5)
> * *Intron* - variation in intron, but not in first two or last two
> bases of intron
> * *Splice Site* - variation in first two or last two bases of intron
> (splice-3, splice-5)
> * *Unknown* - no known functional classification
>
> (You can see a complete description of all the options by clicking
> "describe table schema" on the table browser screen, to the right of the
> selected table, and scrolling down about half-way. Just note that
> different SNP versions might have slightly different settings.)
>
> I think you will want to select (if using SNP131) function = "Coding -
> Synonymous" and "Coding Non-Synonymous". Is that what you are looking for?
>
> Just let us know if you have any additional questions.
>
> --
> Greg Roe
> UCSC Genome Browser
>
> On 1/7/11 7:29 PM, 하오잠 로 wrote:
>> Mary Goldman
>> UCSC Bioinformatics Group
>>
>> Dear,
>> I would like to clarify for FILTER option available on the UCSC table
>> browser site. Should I need to click single option only for CLASS field
>> instead of ALL option which is represented with * AND for function fied
>> should I click coding-synon, nonsense, missense, untranslated-3,
>> untranslated-5 only instead of *. If I would like to get information for
>> CoDing Sequences (CDS) only then should I click only for coding-synon,
>> nonsense, missense. I would be glad for your assistance and kindness.
>>
>> Warm regards,
>> Haojam Rocky
>> Seoul National University College of Medicine
>> _______________________________________________
>> Genome maillist - [email protected]
>> https://lists.soe.ucsc.edu/mailman/listinfo/genome
> _______________________________________________
> Genome maillist - [email protected]
> https://lists.soe.ucsc.edu/mailman/listinfo/genome
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