gtf files for various organism in ucsc

Question

[1769mkc]

This one is for the mouse version mm9 where i could see the gtf files for the respective fasta files and for humans as well but when i look for other species as example Canine there isn't any in when i try to follow the same path structure. Is it there which Im not able to find or we have to look to ensembl or ncbi for the gtf file?

[michael.ante]

Hi,

There is a reference mRNA file available called refMrna.fa.gz. Depending on what you need to do, you can use that directly, or use this approach by h.mon .

[1769mkc]

refMrna.fa.gz this contains the gtf? file i was expecting .gtf extension i will look for it.

[michael.ante]

According to the description here:

refMrna.fa.gz - RefSeq mRNA from the same species as the genome. This sequence data is updated once a week via automatic GenBank updates.

These are mRNA sequences without the introns, therefore you might need to map them back to get a gtf (see link above)

[1769mkc]

thank you for the insight i would give it a try and update