Find gene regions (START and END) using gene IDs

Question

[Mahan]

I have a list of gene IDs. I would like to know if there is a way to find the gene regions (START-END) on GRCh37 build? TIA

[Ram]

What have you tried?

Answer 1

[GenoMax]

A hacky answer. Find genes you need from the list.

Get GRCh37 GTF file here: https://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_43/GRCh37_mapping/gencode.v43lift37.basic.annotation.gtf.gz

$ zcat gencode.v43lift37.basic.annotation.gtf.gz | awk -F "\t|;" '{OFS="\t"}{if ($3 == "gene") print $11,$4,$5}' | sed -e 's/gene_name//' -e 's/"//g' > genes_37
$ head genes_37
  DDX11L1       12010   13670
  WASH7P        14404   29570
  MIR1302-2HG   29554   31109
  FAM138A       34554   36081
  OR4G4P        52473   53312

Your genes of interest in a file called id.

$ more id
FAM138A
OR4G4P

Grab the start-stop from genes_37 file.

$ grep -f id -w genes_37 
  FAM138A       34554   36081
  OR4G4P        52473   53312

[Mahan]

Thank you very much! Thats really helpful.