exo5-D176A D176A invalid_error peptide sequence missing

[ValWood]

@manulera

do you know what this means?

SPBC685.02 SPBC685.02:allele-2 exo5-D176A D176A invalid_error peptide sequence missing
SPBC685.02 SPBC685.02:allele-3 exo5-D207A D207A invalid_error peptide sequence missing

These are correct ly describe as far as I can see. This gene has multiple transcripts, but this is the primary transcript?
I can't see what it might be?

[kimrutherford]

Hi Val. Where are those messages coming from?

This gene has multiple transcripts, but this is the primary transcript?

How are specifying which transcript is the primary transcript?

[manulera]

Hi @kimrutherford sorry I did not see this at the time. The problem here is that multi-transcript genes were handled assuming that the systematic_id qualifier would contain the "transcript id" ( gene systematic id + .1 or .2), and therefore there would be no feature in the genome assigned to the gene systematic id.

That's the case for the annotation of SPAC22A12.08c in chromosome 1, where there is two identical UTRs, one for each transcript:

FT   5'UTR           complement(1172127..1172209)
FT                   /systematic_id="SPAC22A12.08c.1"
FT                   /db_xref="PMID:18641648"
FT                   /db_xref="PMID:20118936"
FT                   /db_xref="PMID:30566651"
FT                   /db_xref="PMID:30566651"
FT                   /feature_source="evidence=ECO:0000309; source=SO:0001238;
FT                   condition=FYECO:0000126; during=GO:0072690; score=63.071;
FT                   db_xref=PMID:30566651"
FT   5'UTR           complement(1172127..1172209)
FT                   /systematic_id="SPAC22A12.08c.2"
FT                   /db_xref="PMID:18641648"
FT                   /db_xref="PMID:20118936"
FT                   /db_xref="PMID:30566651"
FT                   /db_xref="PMID:30566651"
FT                   /feature_source="evidence=ECO:0000309; source=SO:0001238;
FT                   condition=FYECO:0000126; during=GO:0072690; score=63.071;
FT                   db_xref=PMID:30566651"

In SPBC685.02, there is a single one with the "main" systematic id, then the specific part of each transcript:

FT   5'UTR           2772853..2772883
FT                   /systematic_id="SPBC685.02"
FT                   /db_xref="PMID:30566651"
FT                   /feature_source="evidence=ECO:0000309; source=SO:0001238;
FT                   condition=FYECO:0000126; during=GO:0072690;
FT                   score=1.028360; db_xref=PMID:30566651"
FT   CDS             join(2772884..2773046,2773102..2773166,2773317..2774093,2774223..2774447)
FT                   /colour=2
FT                   /primary_name="exo5"
FT                   /product="nuclear single stranded DNA specific 5'-3'
FT                   exodeoxyribonuclease Exo5.1"
FT                   /db_xref="SPD:25/25C04"
FT                   /db_xref="PMID:31563844"
FT                   /systematic_id="SPBC685.02.1"

This is handled at process_systematic_id in genome_functions by testing if systematic_id in genome. The solutions would be:

• Do all genome annotation like in SPAC22A12.08c
• Handle this alternative case testing whether peptide is in the dictionary of that systematic id.

[kimrutherford]

Thanks very much for looking into this!

Do all genome annotation like in SPAC22A12.08c

I think that's the best plan.

Cheers.

[manulera]

[kimrutherford]

I've just changed the ID of the SPBC685.02 5'UTR to "SPBC685.02.1". I'll check on Friday to make sure that fixed things.