Retrieve gene name and sequence by Transcript ID

Question

[tianlu]

Hi:

I have a long list of Transcript IDs,e.g. NM_001080976,NM_002180,etc. I don't know which program or tool I can use these ID to retrieve the gene name and sequence of these IDs? Thanks!

Answer 1

[mastal511]

You can probably get them with BioMart.

Answer 2

[genecats.ucsc]

You can use the UCSC Genome browser to get this information. Head to the Table Browser: http://genome.ucsc.edu/cgi-bin/hgTables, choose whatever assembly you're interested in (I'm guessing Human hg38 or hg19), use the "paste list" button next to "identifiers (names/accessions):" to paste in your transcript ID's, choose "output format: selected fields from primary and related tables" and then make the following selections:

• hg38.kgXref fields: refseq, geneSymbol
• Linked Tables: check the box next to hg38.knownGeneMrna, scroll down and click "Allow selection from checked tables"
• check the box next to the seq field of the knownGeneMrna table
• Finally click "get output"

You'll have output of the following form:

#hg38.kgXref.geneSymbol hg38.kgXref.refseq  hg38.knownGeneMrna.seq
DSE NM_001080976    GCGGACGACCCACCTT...

Where the first column of each row is your ID and the second column is the corresponding mRNA sequence.

For more information about the UCSC Genome Browser, please feel free to send an email to our mailing list: [e-mail], we love answering questions! We also have a forum here: https://groups.google.com/a/soe.ucsc.edu/forum/#!forum/genome where you can search for questions and answers about how to use the Genome Browser.

Answer 3

[Chirag Parsania]

I found this very useful and very handy to use.

https://biodbnet-abcc.ncifcrf.gov/db/db2db.php

Cheers, Chirag