Gene added and removed twice at the same date
Closed this issue · 4 comments
kimrutherford commented
Hi Manu.
I wanted to check that this isn't a problem. This gene is added twice on the same date/revision and then removed twice at the same date/revision:
20080222 - 2008-02-22 II SPBC21C3.07c CDS removed complement(join(3807827..3807891,3807946..3808607,3808665..3808795))
20080222 - 2008-02-22 II SPBC21C3.07c CDS removed complement(join(3807920..3808607,3808665..3808795)) Solexa transread data; added two 3’ exons
20080123 - 2008-01-23 II SPBC21C3.07c CDS added complement(join(3807714..3807783,3807831..3807891,3807946..3808607,3808665..3808795))
20080123 - 2008-01-23 II SPBC21C3.07c CDS added complement(join(3807827..3807891,3807946..3808607,3808665..3808795))
manulera commented
Yes, that's correct, see a chunk of the embl file in 20080123
FT CDS complement(join(3807827..3807891,3807946..3808607,3808665..3808795))
FT /GO="aspect=F; term=actin filament binding;
FT GOid=GO:0051015; evidence=ISS; db_xref=PMID:17072883;
FT with=SGD:S000005765; date=20050603"
FT /GO="aspect=F; term=S-adenosylmethionine-dependent
FT methyltransferase activity; GOid=GO:0008757; evidence=ISS;
FT db_xref=PMID:17072883; with=SGD:S000005765; date=20050603"
FT /GO="aspect=P; term=actin cytoskeleton organization and
FT biogenesis; GOid=GO:0030036; evidence=ISS;
FT db_xref=PMID:17072883; with=SGD:S000005765; date=20050603"
FT /GO="aspect=C; term=actin filament; GOid=GO:0005884;
FT evidence=ISS; db_xref=PMID:17072883; with=SGD:S000005765;
FT date=20050603"
FT /colour=7
FT /controlled_curation="term=conserved eukaryotic protein;
FT date=20070115"
FT /controlled_curation="term=similar to S. cerevisiae
FT YOR239W; date=19700101"
FT /gene="SPBC21C3.07c"
FT /product="actin binding methyltransferase (predicted)"
FT /systematic_id="SPBC21C3.07c"
FT /fasta_file="%uniprot:fasta/chromosome2.contig.seq.04364.out"
FT CDS complement(join(3807920..3808607,3808665..3808795))
FT /GO="aspect=F; term=actin filament binding;
FT GOid=GO:0051015; evidence=ISS; db_xref=PMID:17072883;
FT with=SGD:S000005765; date=20050603"
FT /GO="aspect=F; term=S-adenosylmethionine-dependent
FT methyltransferase activity; GOid=GO:0008757; evidence=ISS;
FT db_xref=PMID:17072883; with=SGD:S000005765; date=20050603"
FT /GO="aspect=P; term=actin cytoskeleton organization and
FT biogenesis; GOid=GO:0030036; evidence=ISS;
FT db_xref=PMID:17072883; with=SGD:S000005765; date=20050603"
FT /GO="aspect=C; term=actin filament; GOid=GO:0005884;
FT evidence=ISS; db_xref=PMID:17072883; with=SGD:S000005765;
FT date=20050603"
FT /colour=7
FT /controlled_curation="term=conserved eukaryotic protein;
FT date=20070115"
FT /controlled_curation="term=similar to S. cerevisiae
FT YOR239W; date=19700101"
FT /fasta_file="fasta/chromosome2.contig.seq.03822.out"
FT /gene="SPBC21C3.07c"
FT /product="actin binding methyltransferase (predicted)"
FT /systematic_id="SPBC21C3.07c"
manulera commented
This is the log for that one:
revision user date chromosome systematic_id primary_name feature_type added_or_removed value db_xref pombase_reference pombase_comments
8650 kmr44 2023-01-12 II SPBC21C3.07c 5'UTR added complement(3808796..3808853) PMID:30566651
8650 kmr44 2023-01-12 II SPBC21C3.07c 5'UTR removed complement(3808796..3808991) PMID:21511999
20110324 - 2011-03-24 II SPBC21C3.07c 3'UTR added complement(3807091..3807713)
20110324 - 2011-03-24 II SPBC21C3.07c 5'UTR added complement(3808796..3808991)
20080222 - 2008-02-22 II SPBC21C3.07c CDS removed complement(join(3807827..3807891,3807946..3808607,3808665..3808795))
20080222 - 2008-02-22 II SPBC21C3.07c CDS removed complement(join(3807920..3808607,3808665..3808795)) Solexa transread data; added two 3’ exons
20080123 - 2008-01-23 II SPBC21C3.07c CDS added complement(join(3807714..3807783,3807831..3807891,3807946..3808607,3808665..3808795))
20080123 - 2008-01-23 II SPBC21C3.07c CDS added complement(join(3807827..3807891,3807946..3808607,3808665..3808795))
20071219 - 2007-12-19 II SPBC21C3.07c CDS added complement(join(3807920..3808607,3808665..3808795)) Solexa intron data; removed final exon, not supported by data
20071219 - 2007-12-19 II SPBC21C3.07c CDS removed complement(join(3807714..3807783,3807963..3808607,3808665..3808795))
manulera commented
The file with changes only:
results/only_modified_coordinates_comments_no_type_change.tsv
kimrutherford commented
The isn't a problem now. See: pombase/website#1993 (comment)