Where can I download the GTF2.2 format file for mm10?

Question

[Gjain]

Hi Everyone,

I am looking for gene annotation file in the GTF2.2 format. Specifically, I am looking for the 5UTR, CDS and 3UTR annotation for the genes.

Format needed and mentioned in the GTF2.2 readme page (shown below)

140    Twinscan    3UTR          65149    65487    .    -    .    gene_id "140.000"; transcript_id "140.000.1";
140    Twinscan    CDS           71696    71807    .    -    0    gene_id "140.000"; transcript_id "140.000.1";
140    Twinscan    start_codon   73222    73222    .    -    2    gene_id "140.000"; transcript_id "140.000.1";
140    Twinscan    CDS           73222    73222    .    -    0    gene_id "140.000"; transcript_id "140.000.1";
140    Twinscan    5UTR          73223    73504    .    -    .    gene_id "140.000"; transcript_id "140.000.1";`

I have downloaded the current gtf file from Ensembl: ftp://ftp.ensembl.org/pub/release-78/gtf/mus_musculus/

Can someone please point me in the right direction to get the above mentioned features of the genes.

Thanks in advance.

[Devon Ryan]

The Ensembl GTFs are compatible with GTF2.2. If you need the 3UTR and 5UTR lines then you can generate them with either Biomart or the appropriate txdb package in R and a bit of typing.

[Gjain]

Thank you for your answer Devon.

txDB package is a good resource. I was not aware of it.

I was looking at a different place in biomart. But after you suggested, I searched again and found it using the query:

• dataset: Mus musculus genes (GRCm38.p3)
• Filters:None
• Attributes: Ensembl Gene ID, Ensembl Transcript ID, 5'UTR Start, 5'UTR End, 3'UTR Start, 3' UTR End, Transcript Start (bp), Transcript End (bp), Strand, Associated Gene Name, Chromosome Name