Extract exon Intron reads from RNA seq data

Question

[AP]

Hello everyone,

I am working with a plant fungi of which I have a DNA sequence. I am trying to make primers for some differentially expressed genes for which I need to know exon-exon junctions. Is there any way I can know the exon intron information of genes I am interested in so that I can easily design the primers.

Many thanks in advance,

Ambika

[GenoMax]

Have you checked to see if there is a gene annotation file available? You should be able to figure the junctions out from that.

[AP]

Genomax, I have a gtf file from augustus. But I am not sure how can I infer information out of that. Can you please tell me if thats the file I need and how can I interpret that file

[GenoMax]

Does the GTF file have entries for exons (and perhaps introns)?

[AP]

It has CDS instead of exons

[GenoMax]

Those 4 are exons of that one gene transcript (g17308.t1) so presumably there are more than one transcript for each gene (g17308)?

[AP]

So these numbers represent the starting and ending position of sequence which are exons. I tried to search for this gene in the file and I just have one transcript (g17308.t1) . So can I say this gene have 4 exons?

[GenoMax]

If that is all blocks then yes. Check what the number following the strand signifies in specifications. I don't recollect off the top of my head.

[AP]

tig00007990     AUGUSTUS        CDS     869652  869790  0.90    +       0       transcript_id "g17308.t1"; gene_id "g17308";
tig00007990     AUGUSTUS        CDS     869843  870931  0.99    +       2       transcript_id "g17308.t1"; gene_id "g17308";
tig00007990     AUGUSTUS        CDS     870982  871333  1.00    +       2       transcript_id "g17308.t1"; gene_id "g17308";
tig00007990     AUGUSTUS        CDS     871385  871442  0.99    +       1       transcript_id "g17308.t1"; gene_id "g17308";

The format looks like this