How To Obtain Intron And Utr Info From Gff File?

Question

[Flo]

Hi, I have a gff file like this: (example for one gene)

scaffold_1      JGI     start_codon     6757    6759    .       +       0       name "estExtDG_fgenesh_newKGs_kg.C_10006"
scaffold_1      JGI     exon    6972    7023    .       +       .       name "estExtDG_fgenesh_newKGs_kg.C_10006"; transcriptId 431653
scaffold_1      JGI     CDS     6972    7023    .       +       0       name "estExtDG_fgenesh_newKGs_kg.C_10006"; proteinId 431653; exonNumber 2
scaffold_1      JGI     exon    7099    7169    .       +       .       name "estExtDG_fgenesh_newKGs_kg.C_10006"; transcriptId 431653
scaffold_1      JGI     CDS     7099    7169    .       +       1       name "estExtDG_fgenesh_newKGs_kg.C_10006"; proteinId 431653; exonNumber 3
scaffold_1      JGI     exon    7306    7344    .       +       .       name "estExtDG_fgenesh_newKGs_kg.C_10006"; transcriptId 431653
scaffold_1      JGI     CDS     7306    7344    .       +       0       name "estExtDG_fgenesh_newKGs_kg.C_10006"; proteinId 431653; exonNumber 4
scaffold_1      JGI     exon    8316    8366    .       +       .       name "estExtDG_fgenesh_newKGs_kg.C_10006"; transcriptId 431653
scaffold_1      JGI     CDS     8316    8366    .       +       0       name "estExtDG_fgenesh_newKGs_kg.C_10006"; proteinId 431653; exonNumber 5
scaffold_1      JGI     exon    8741    8785    .       +       .       name "estExtDG_fgenesh_newKGs_kg.C_10006"; transcriptId 431653
scaffold_1      JGI     CDS     8741    8785    .       +       0       name "estExtDG_fgenesh_newKGs_kg.C_10006"; proteinId 431653; exonNumber 6
scaffold_1      JGI     exon    9166    9207    .       +       .       name "estExtDG_fgenesh_newKGs_kg.C_10006"; transcriptId 431653
scaffold_1      JGI     CDS     9166    9207    .       +       0       name "estExtDG_fgenesh_newKGs_kg.C_10006"; proteinId 431653; exonNumber 7
scaffold_1      JGI     exon    9458    9514    .       +       .       name "estExtDG_fgenesh_newKGs_kg.C_10006"; transcriptId 431653
scaffold_1      JGI     CDS     9458    9514    .       +       0       name "estExtDG_fgenesh_newKGs_kg.C_10006"; proteinId 431653; exonNumber 8
scaffold_1      JGI     exon    10143   10229   .       +       .       name "estExtDG_fgenesh_newKGs_kg.C_10006"; transcriptId 431653
scaffold_1      JGI     CDS     10143   10229   .       +       0       name "estExtDG_fgenesh_newKGs_kg.C_10006"; proteinId 431653; exonNumber 9
scaffold_1      JGI     exon    10388   10432   .       +       .       name "estExtDG_fgenesh_newKGs_kg.C_10006"; transcriptId 431653
scaffold_1      JGI     CDS     10388   10432   .       +       0       name "estExtDG_fgenesh_newKGs_kg.C_10006"; proteinId 431653; exonNumber 10
scaffold_1      JGI     exon    10864   11308   .       +       .       name "estExtDG_fgenesh_newKGs_kg.C_10006"; transcriptId 431653
scaffold_1      JGI     CDS     10864   10947   .       +       0       name "estExtDG_fgenesh_newKGs_kg.C_10006"; proteinId 431653; exonNumber 11
scaffold_1      JGI     stop_codon      10945   10947   .       +       0       name "estExtDG_fgenesh_newKGs_kg.C_10006"

I would like to recover the utr and intron positions from this. Any easy way to do this?

Thanks!

[Neilfws]

Are the UTRs annotated in your file? I don't see any in column 3 of your example. If not, you cannot recover them; you can only retrieve intergenic positions.

[brentp]

did you see this: http://biostar.stackexchange.com/questions/11939/is-is-feasible-to-produce-intron-gff-according-to-utr-gff-and-cds-gff

[Flo]

Yes I'm trying with genometools but can't get the utrs Any idea?