Question: Retrieval of chromosomal coordinates of coding sequences (CDS)
0
gravatar for shakeelbiochemist
2.3 years ago by
Pakistan
shakeelbiochemist0 wrote:

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

cds gene genome • 882 views
ADD COMMENTlink modified 2.3 years ago • written 2.3 years ago by shakeelbiochemist0

Thanks, it works and gives the output.

ADD REPLYlink written 2.3 years ago by shakeelbiochemist0
1
gravatar for Macspider
2.3 years ago by
Macspider2.8k
Vienna - BOKU
Macspider2.8k wrote:

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

ADD COMMENTlink modified 2.3 years ago • written 2.3 years ago by Macspider2.8k
1

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

ADD REPLYlink written 2.3 years ago by aham40

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

ADD REPLYlink written 2.3 years ago by Macspider2.8k
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