[Genome] retrieving genomic information by NP_ accessions

[Archana Thakkapallayil]

Hello Yael,

This task can be accomplished using the Table Browser. The 'protAcc' 
field is located in the 'refLink' table, but you can't get the 5' UTR 
sequence directly using this table. To obtain this information, first 
you need to find out the refGene ID's corresponding to your protein 
accessions and then  get the 5' UTR sequence for your refGenes.

To do this press the "Tables" link in the blue navigation bar across the 
top of the browser window. Then make the following selections in the 
Table Browser:

clade: vertebrate
genome: human
assembly: Mar. 2006
group: Genes and Gene Prediction Tracks
track: RefSeq Genes
table: refLink
click on "filter: create" button and then paste a white-space separated 
list of your protAcc into the textbox "protAcc does match" and then 
click "submit".

Back on the main page, set "output format: selected fields from primary 
and related tables" and hit "get output" button.

On this page check the box for "mrnaAcc" from the refLink table and then 
hit "get output". This gives you the list of refGene id's corresponding 
to your protein accessions.

Now back on the Table Browser, select table "refGene" and region: 
"genome" and then paste the list of your mrna accessions using the 
"paste/upload" list buttons.

choose "output format: sequence" and hit "get output".

select "genomic" and click "submit".

On this page under 'Sequence Retrieval Region Option', check the box for 
"5' UTR Exons" and then click "get sequence".

This gives you the 5' UTR sequence for the refGene ID's corresponding to 
your protein accessions.

I hope this information is helpful to you. Please be sure to write back 
if you need further instruction.

Regards,

Archana
UCSC Genome Bioinformatics Group



Yael Altuvia wrote:
> Hi,
>
> What would be the best way to get genomic sequences (e.g. 5' utrs) for a 
> batch query
> Where the query entries are accessions of protAcc either NP_ or XP_
>
> thanks
> yael
>
>
>
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