Refgene .gtf including model refseq records (XM, XP, XR_)

[utrr]

hello,

I am looking for a mouse .gtf file based on refseq including model refseqs starting with XP, XM, XR_ .
refgene.gtf I found on UCSC does not include model refseqs.
Althoug mouse.1.rna.fna I found on ncbi includes model refseqs, it gives no information about their loci.

I am wondering if such a file is available or I have to make a .gtf by mapping the fasta file to genome, which I do not want to do.

Thanks

[GenoMax]

You will probably need to make this file but you don't need to do it by mapping.

Assuming that you actually want only model (X*) records you could do this.

$ wget -nc ftp://ftp.ncbi.nlm.nih.gov/gene/DATA/gene2refseq.gz

$ gzip -d gene2refseq.gz

Look at the header line in the resulting gene2refseq file to understand the columns in the file.

$ grep "X" gene2refseq | grep "GRCm38" > mouse_model_ref

Modify result file "mouse_model_ref" into GTF format.

Note: Current file includes GRCm38.p3 reference.

[utrr]

Thank you very much for the answer.
This will do for my purpose.

[utrr]

Hi,

I first thought Genomax's answer has solved my problem.

The gene2refseq file does include model refseqs and their genomic positions and orientaion, but the genomic positions it has are not each refseq's specific position.
Rather, all the refseqs sharing the same gene Symbol seem to have the same positions.

What I would like to know is the transcription start site of all the possible transcript variants.

I am sure NCBI has that kind of information since you can see the exact gene models in the genome browser of NCBI Gene Database like in

http://www.ncbi.nlm.nih.gov/gene/14433

I would be very glad if anyone could give me an answer.

Thanks