[Genome] annotation from CDS and mRNA coordinates

[Brooke Rhead]

Hello Ram Vinay,

The Table Browser is the tool to use to extract information from the 
Genome Browser databases.  To get to it, use the "Tables" link (in the 
blue bar at the top of the web page).

You can use the Table Browser to upload a list of genes of interest and 
then download data for just those genes.  To do this, choose the genome 
and assembly you are interested in.  Choose "group: Genes and gene 
prediction tracks".  The track you choose will depend on which gene 
dataset you would like to get information from (e.g., RefSeq Genes or 
Ensembl Genes).  Then, for "table:", use the table at the top of the 
drop-down menu list (e.g., refGene or ensGene).  Be sure to choose 
"region: genome".

Now you can paste or upload your list of genes in the "identifiers 
(names/accessions):" section.  The gene names must be in the correct 
format for the track/table you have chosen, usually an accession number. 
  To see an example of the format your selected table uses, click the 
"describe table schema" button and look at the 'name' field of the table.

The output format you choose depends on what information you are looking 
for.  If you are only interested in coordinates of the genes (including 
the transcription start and stop coordinates and the CDS start and stop 
coordinates), you can choose to output "all fields from selected table" 
or "selected fields from primary and related tables".  If you would like 
the coordinate information in BED format (read more about BED format 
here: http://genome.ucsc.edu/FAQ/FAQformat#format1 ), choose to output 
the data as a custom track, and then use the "get custom track in file" 
button.  Alternatively, if you are interested in obtaining the sequence 
for these regions, use the "sequence" output format.  Note that if you 
choose to output the genomic sequence, there are additional formatting 
options available for the untranslated regions and CDS regions.

I hope this information is useful to you.  If you have further 
questions, please do not hesitate to contact the list again.

--
Brooke Rhead
UCSC Genome Bioinformatics Group


ram vinay wrote:
> Dear collogue,
> 
> I am a research scolor from India, I want to get annotation from CDS and
> mRNA coordinates along with Gene coordinates
> for a gene or multiple genes.please let me know from which page of UCSC
> Genome Browser I can get.
> 
> For this help I shall be more greatful, and looking forward.
> 
> 
> thank tou,
> Ram Vinay Pandey
> India
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