Support displaying pseudogenic_CDS like a coding sequence #732
Description
Below is an exceprt from a genbank GFF3 of GCA_900002375. This shows CDS attached directly to a pseudogene, which doesn't really work with the sequence ontology, but Artemis does display them in a useful way:.
We need to figure out the "proper" way to represent this using sequence ontology standards and then make sure Apollo also displays the coding sequences in the Linear Apollo Display and Linear Apollo Six Frame Display.
I think this would be represented in an standard GFF3 the same way as a typical gene, but substituting gene->pseudogene, mRNA->pseudogenic_transcript, exon->pseudogenic_exon, and CDS->pseudogenic_CDS.
It should also be evaluated if the default coloring of pseudogene backgrounds is sufficient to visually distinguish the coding-like segments as actually non-coding, or if there should be some additional indicator.
LK023120.2 EMBL pseudogene 922083 930418 . - . ID=gene-PBANKA_0524841;Name=PBANKA_0524841;gbkey=Gene;gene_biotype=pseudogene;locus_tag=PBANKA_0524841;pseudo=true;pseudogene=unknown
LK023120.2 EMBL CDS 930364 930418 . - 0 ID=cds-PBANKA_0524841;Parent=gene-PBANKA_0524841;Note=reticulocyte binding protein%2C putative%2C pseudogene;gbkey=CDS;locus_tag=PBANKA_0524841;pseudo=true;pseudogene=unknown
LK023120.2 EMBL CDS 930177 930236 . - 2 ID=cds-PBANKA_0524841;Parent=gene-PBANKA_0524841;Note=reticulocyte binding protein%2C putative%2C pseudogene;gbkey=CDS;locus_tag=PBANKA_0524841;pseudo=true;pseudogene=unknown
LK023120.2 EMBL CDS 929946 930174 . - 2 ID=cds-PBANKA_0524841;Parent=gene-PBANKA_0524841;Note=reticulocyte binding protein%2C putative%2C pseudogene;gbkey=CDS;locus_tag=PBANKA_0524841;pseudo=true;pseudogene=unknown
LK023120.2 EMBL CDS 929715 929943 . - 1 ID=cds-PBANKA_0524841;Parent=gene-PBANKA_0524841;Note=reticulocyte binding protein%2C putative%2C pseudogene;gbkey=CDS;locus_tag=PBANKA_0524841;pseudo=true;pseudogene=unknown
LK023120.2 EMBL CDS 929523 929712 . - 0 ID=cds-PBANKA_0524841;Parent=gene-PBANKA_0524841;Note=reticulocyte binding protein%2C putative%2C pseudogene;gbkey=CDS;locus_tag=PBANKA_0524841;pseudo=true;pseudogene=unknown
LK023120.2 EMBL CDS 929466 929520 . - 2 ID=cds-PBANKA_0524841;Parent=gene-PBANKA_0524841;Note=reticulocyte binding protein%2C putative%2C pseudogene;gbkey=CDS;locus_tag=PBANKA_0524841;pseudo=true;pseudogene=unknown
LK023120.2 EMBL CDS 929277 929464 . - 1 ID=cds-PBANKA_0524841;Parent=gene-PBANKA_0524841;Note=reticulocyte binding protein%2C putative%2C pseudogene;gbkey=CDS;locus_tag=PBANKA_0524841;pseudo=true;pseudogene=unknown
LK023120.2 EMBL CDS 929262 929275 . - 2 ID=cds-PBANKA_0524841;Parent=gene-PBANKA_0524841;Note=reticulocyte binding protein%2C putative%2C pseudogene;gbkey=CDS;locus_tag=PBANKA_0524841;pseudo=true;pseudogene=unknown
LK023120.2 EMBL CDS 929109 929260 . - 0 ID=cds-PBANKA_0524841;Parent=gene-PBANKA_0524841;Note=reticulocyte binding protein%2C putative%2C pseudogene;gbkey=CDS;locus_tag=PBANKA_0524841;pseudo=true;pseudogene=unknown
LK023120.2 EMBL CDS 929058 929106 . - 1 ID=cds-PBANKA_0524841;Parent=gene-PBANKA_0524841;Note=reticulocyte binding protein%2C putative%2C pseudogene;gbkey=CDS;locus_tag=PBANKA_0524841;pseudo=true;pseudogene=unknown
LK023120.2 EMBL CDS 929040 929056 . - 0 ID=cds-PBANKA_0524841;Parent=gene-PBANKA_0524841;Note=reticulocyte binding protein%2C putative%2C pseudogene;gbkey=CDS;locus_tag=PBANKA_0524841;pseudo=true;pseudogene=unknown
LK023120.2 EMBL CDS 928902 929037 . - 1 ID=cds-PBANKA_0524841;Parent=gene-PBANKA_0524841;Note=reticulocyte binding protein%2C putative%2C pseudogene;gbkey=CDS;locus_tag=PBANKA_0524841;pseudo=true;pseudogene=unknown
LK023120.2 EMBL CDS 928674 928900 . - 0 ID=cds-PBANKA_0524841;Parent=gene-PBANKA_0524841;Note=reticulocyte binding protein%2C putative%2C pseudogene;gbkey=CDS;locus_tag=PBANKA_0524841;pseudo=true;pseudogene=unknown
LK023120.2 EMBL CDS 928641 928672 . - 1 ID=cds-PBANKA_0524841;Parent=gene-PBANKA_0524841;Note=reticulocyte binding protein%2C putative%2C pseudogene;gbkey=CDS;locus_tag=PBANKA_0524841;pseudo=true;pseudogene=unknown
LK023120.2 EMBL CDS 928596 928639 . - 2 ID=cds-PBANKA_0524841;Parent=gene-PBANKA_0524841;Note=reticulocyte binding protein%2C putative%2C pseudogene;gbkey=CDS;locus_tag=PBANKA_0524841;pseudo=true;pseudogene=unknown
LK023120.2 EMBL CDS 928548 928594 . - 0 ID=cds-PBANKA_0524841;Parent=gene-PBANKA_0524841;Note=reticulocyte binding protein%2C putative%2C pseudogene;gbkey=CDS;locus_tag=PBANKA_0524841;pseudo=true;pseudogene=unknown
LK023120.2 EMBL CDS 928404 928546 . - 1 ID=cds-PBANKA_0524841;Parent=gene-PBANKA_0524841;Note=reticulocyte binding protein%2C putative%2C pseudogene;gbkey=CDS;locus_tag=PBANKA_0524841;pseudo=true;pseudogene=unknown
LK023120.2 EMBL CDS 928389 928402 . - 2 ID=cds-PBANKA_0524841;Parent=gene-PBANKA_0524841;Note=reticulocyte binding protein%2C putative%2C pseudogene;gbkey=CDS;locus_tag=PBANKA_0524841;pseudo=true;pseudogene=unknown
LK023120.2 EMBL CDS 928215 928387 . - 0 ID=cds-PBANKA_0524841;Parent=gene-PBANKA_0524841;Note=reticulocyte binding protein%2C putative%2C pseudogene;gbkey=CDS;locus_tag=PBANKA_0524841;pseudo=true;pseudogene=unknown
LK023120.2 EMBL CDS 928074 928213 . - 1 ID=cds-PBANKA_0524841;Parent=gene-PBANKA_0524841;Note=reticulocyte binding protein%2C putative%2C pseudogene;gbkey=CDS;locus_tag=PBANKA_0524841;pseudo=true;pseudogene=unknown
LK023120.2 EMBL CDS 926745 928071 . - 2 ID=cds-PBANKA_0524841;Parent=gene-PBANKA_0524841;Note=reticulocyte binding protein%2C putative%2C pseudogene;gbkey=CDS;locus_tag=PBANKA_0524841;pseudo=true;pseudogene=unknown
LK023120.2 EMBL CDS 922083 926742 . - 1 ID=cds-PBANKA_0524841;Parent=gene-PBANKA_0524841;Note=reticulocyte binding protein%2C putative%2C pseudogene;gbkey=CDS;locus_tag=PBANKA_0524841;pseudo=true;pseudogene=unknown