Genomic Positions Of 3'Utrs Of Refseq-Genes

Question

[syrup16g_TO]

Dear all,

I want to get the genomic positions of 3'UTR of RefSeq genes, but I don't know how to get the information about 3'UTR.

e.g. RefSeq_geneID chrXXX:start-end ( 3'UTR position )

Any helps would be much appreciated. Thank you.

[Pierre Lindenbaum]

see Retrieve 3'UTR sequences for a (complete) list of genes using Biomart/UCSC

Answer 1

[dariober]

Hi- if your species is on UCSC Genome Browser, you can download a bed file of 3'UTR positions with:

Go to http://genome.ucsc.edu/cgi-bin/hgTables

Select your specie and assembly; Group: Genes and Gene predictions; Track: RefSeq genes; Output Format: BED; Output file: myutr.bed

-> Get Output

-> Create one BED record per: 3' UTR Exons

-> Get BED

[syrup16g_TO]

Thank you for your reply!

I've succeeded to get that information.