Retrieval of chromosomal coordinates of coding sequences (CDS)

Question

[shakeelbiochemist]

I want to retrieve chromosomal positions of coding sequences (CDS) of some genes. I searched 'refseq' database which provides the coordinates CDS according to genes (i.e. CDS1 on gene position 424-562, CDS2 gene position 1026-1921 etc.). Can I obtain these positions according to chromosomal coordinates for a desired assembly (e.g hg19).

Thnaks

[shakeelbiochemist]

Thanks, it works and gives the output.

Answer 1

[Matteo Schiavinato]

The GFF/GTF/GFF3 format has what you need. If you know the gene name or the gene position in the chromosome, grep it from here: ftp://ftp.ensembl.org/pub/release-87/gff3/homo_sapiens/Homo_sapiens.GRCh38.87.gff3.gz

[aham]

and for hg19, you can find GFF3/GTF files from here: https://www.gencodegenes.org/releases/25lift37.html

[Matteo Schiavinato]

Yes shakeelbiochemist, use the version linked by mshakeel, my bad. Coordinates might be different.