IGV tracks gene annotation

Question

[bitpir]

Hi there, I'm trying to visualize a reference genome in IGV and annotate the genes using a custom made GFF file. The snapshot of the IGV looks something like this. I am particularly curious about the pink labeled track. The GFF for the pink track looks something like this:

NC_023010.2 glimmer cds 5011 3686 3.08 - 1 orf00005;

NC_023010.2 glimmer cds 5052 5264 0.82 + 2 orf00006;

NC_023010.2 glimmer cds 5637 6800 3.11 + 2 orf00007;

As you can see, orf00005 is labeled differently. Does anyone know why this is so? Is that partial gene?

Thanks for the help!

Answer 1

[h.mon]

Probably IGV doesn't like the Glimmer gff, as it does not conform to the specification:

Columns 4 & 5: "start" and "end"

[...] Start is always less than or equal to end.

For orf00005, start > end.

[bitpir]

Hmm, I don't think that's the problem because there are other orfs that go in reverse direction too (HSP_RS15385). I found this answer from another site (https://biology.stackexchange.com/questions/68431/clarification-on-refseq-genes-track-on-igv) The thinner line is supposed to be untranslated region. Now I have to figure out why it is so while other tracks are considered translated region.

[h.mon]

Orfs that "go in reverse direction" has nothing to do with the start and end coordinates, this is an indication of strand:

Column 7: "strand"

The strand of the feature. + for positive strand (relative to the landmark), - for minus strand, and . for features that are not stranded. In addition, ? can be used for features whose strandedness is relevant, but unknown.

The feature you indicated (HISP_RS15385) is on minus strand, as orf00005, hence both have left-facing arrows. However, if you look at the gff, its start coordinate is less than the end coordinate ( 36612 < 37661 ):

NC_023010.2 RefSeq  gene    36612   37661   .   -   .   ID=gene-HISP_RS15385;Dbxref=GeneID:23802828;Name=HISP_RS15385;gbkey=Gene;gene_biotype=protein_coding;locus_tag=HISP_RS15385;old_locus_tag=HISP_16005
NC_023010.2 Protein Homology    CDS 36612   37661   .   -   0ID=cds35;Parent=gene-HISP_RS15385;Dbxref=Genbank:WP_014030602.1,GeneID:23802828;Name=WP_014030602.1;gbkey=CDS;inference=COORDINATES: similar to AA sequence:RefSeq:WP_014030602.1;product=radical SAM protein;protein_id=WP_014030602.1;transl_table=11

[bitpir]

I see! Got it, thank you so much for pointing out. That's really weird that Glimmer GFF has that kind of format. I'll check again with the formatting with that file. Thanks!