getting protein sequences for a list of UCSC knownGene transcript ids

[Amit Indap]

Hi UCSC Genome Browser Staff,

My browser skills are a bit rusty. Is there a way to get the amino acid sequence(s) for a list of UCSC known gene transcript ids? For example, when I search for uc002zgy and click on it's record, the page has a link to its amino acid

sequence: https://genome.ucsc.edu/cgi-bin/hgGene?hgsid=603166487_LqYFJAIhysI2iWkHd6yxwKKVDttW&hgg_section_links_close=0#links. 

But I have ~50 transcript ids I need to do this for and I don't want to do it manually.

Thanks for your help! 

Amit

[Jairo Navarro Gonzalez]

Dear Amit,

Thank you for using the UCSC Genome Browser and your inquiry.

You can get the protein sequence for all your transcript identifiers by using the Table Browser.
Here is an example using the hg19 assembly.

Step 1: Configure the Table Browser

clade: mammal
genome: Human
assembly: Feb. 2009 (GRCh37/hg19)
group: Genes and Gene Predictions
track: UCSC Genes
table: knownGene
region: genome
output format: sequence

Step 2: Upload or Paste Identifiers

Next to identifiers (names/accessions):, click paste list.

You will be taken to a new page where you will be able to insert your 50 transcript identifiers. 
After entering your identifiers, click submit.

Step 3: Get output

Once back on the main Table Browser page, click get output.
You will be redirected to a new page where you can select protein.
Clicking submit will display the protein sequences for your identifiers.

I hope this is helpful. If you have any further questions, please reply to gen...@soe.ucsc.edu.
All messages sent to that address are archived on a publicly-accessible Google Groups forum.
If your question includes sensitive data, you may send it instead to genom...@soe.ucsc.edu.

Jairo Navarro 
UCSC Genomics Institute

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