updated to last revision

pombase · Jan 15, 2025 · 218b2b9 · 218b2b9
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Showing 12 changed files with 17,924 additions and 17,921 deletions.
diff --git a/data/alleles.tsv b/data/alleles.tsv
diff --git a/data/chromosome1.contig b/data/chromosome1.contig
@@ -13088,7 +13088,13 @@ FT                   in fungi; date=20160209"
 FT                   /controlled_curation="term=species distribution, no
 FT                   apparent S. cerevisiae ortholog; date=20160209"
 FT                   /controlled_curation="term=species distribution, conserved
-FT                   in fungi only; date=20170902"
+FT                   in eukaryotes; date=20250109"
+FT                   /controlled_curation="term=species distribution, conserved
+FT                   in eukaryotes only; date=20250109"
+FT                   /controlled_curation="term=species distribution, conserved
+FT                   in metazoa; date=20250109"
+FT                   /controlled_curation="term=species distribution, conserved
+FT                   in vertebrates; date=20250109"
 FT   5'UTR           complement(928444..928670)
 FT                   /systematic_id="SPAC1687.14c"
 FT                   /db_xref="PMID:30566651"
@@ -35738,9 +35744,8 @@ FT                   /product="mitotic spindle checkpoint ubiquitin ligase
 FT                   Dma1"
 FT                   /systematic_id="SPAC17G8.10c"
 FT                   /controlled_curation="term=subunit composition,
-FT                   homomeric(2), RING domain-dependent;
-FT                   cv=subunit_composition; db_xref=PMID:22669973;
-FT                   date=20130124"
+FT                   homomeric(2); cv=subunit_composition;
+FT                   db_xref=PMID:22669973; date=20130124"
 FT                   /controlled_curation="term=ubiquitin-protein ligase E3;
 FT                   date=20060726"
 FT                   /controlled_curation="term=zinc finger protein;
@@ -35757,8 +35762,6 @@ FT                   /controlled_curation="term=species distribution, conserved
 FT                   in metazoa; date=20081110"
 FT                   /controlled_curation="term=species distribution, conserved
 FT                   in eukaryotes; date=20090202"
-FT                   /controlled_curation="term=subunit composition,
-FT                   homomeric(2); db_xref=PMID:22669973; date=20130321"
 FT                   /controlled_curation="term=name description, Defective in
 FT                   Mitotic Arrest; db_xref=PMID:8978687; date=20161006"
 FT                   /controlled_curation="term=species distribution, conserved
@@ -44747,7 +44750,7 @@ FT                   in fungi; date=20081110"
 FT                   /controlled_curation="term=species distribution, conserved
 FT                   in bacteria; date=20170210"
 FT                   /controlled_curation="term=subunit composition,
-FT                   tetrameric(1); db_xref=PMID:32981237; date=20201105"
+FT                   homomeric(4); db_xref=PMID:32981237; date=20201105"
 FT                   /synonym="mns2"
 FT   3'UTR           2918135..2920278
 FT                   /systematic_id="SPAC513.05"
@@ -65537,9 +65540,9 @@ FT                   /controlled_curation="term=species distribution, conserved
 FT                   in metazoa; date=20240209"
 FT                   /controlled_curation="term=species distribution, conserved
 FT                   in vertebrates; date=20240209"
-FT                   /controlled_curation="term=subunit composition, dimeric;
-FT                   cv=subunit_composition; db_xref=PMID:36423630;
-FT                   date=20080417"
+FT                   /controlled_curation="term=subunit composition,
+FT                   homomeric(2); cv=subunit_composition;
+FT                   db_xref=PMID:36423630; date=20080417"
 FT                   /db_xref="SPD:17/17A05"
 FT                   /synonym="fkbp40"
 FT   lncRNA          4327312..4328339
@@ -78100,7 +78103,7 @@ FT                   in fungi; date=20081110"
 FT                   /controlled_curation="term=species distribution, conserved
 FT                   in eukaryotes only; date=20081110"
 FT                   /controlled_curation="term=subunit composition,
-FT                   homotetrameric; db_xref=PMID:15601865; date=20230706"
+FT                   homomeric(4); db_xref=PMID:15601865; date=20230706"
 FT   3'UTR           complement(5133784..5135422)
 FT                   /systematic_id="SPAC29A4.07"
 FT                   /db_xref="PMID:21511999"

diff --git a/data/chromosome2.contig b/data/chromosome2.contig
@@ -40332,8 +40332,6 @@ FT                   /controlled_curation="term=subunit composition,
 FT                   homomeric(2); db_xref=PMID:23273429; date=20130801"
 FT                   /controlled_curation="term=subunit composition,
 FT                   homomeric(6); db_xref=PMID:23273429; date=20130801"
-FT                   /controlled_curation="term=subunit composition,
-FT                   homomeric(16); db_xref=PMID:18543332; date=20230706"
 FT   5'UTR           complement(2660922..2660992)
 FT                   /systematic_id="SPBC3E7.02c"
 FT                   /db_xref="PMID:30566651"
@@ -43018,10 +43016,6 @@ FT                   db_xref=PMID:2668944; date=20130930"
 FT                   /controlled_curation="term=species distribution, conserved
 FT                   in eukaryotes; date=20081110"
 FT                   /controlled_curation="term=species distribution, conserved
-FT                   in metazoa; date=20081110"
-FT                   /controlled_curation="term=species distribution, conserved
-FT                   in vertebrates; date=20081110"
-FT                   /controlled_curation="term=species distribution, conserved
 FT                   in fungi; date=20081110"
 FT                   /controlled_curation="term=species distribution, conserved
 FT                   in eukaryotes only; date=20081110"
@@ -49608,8 +49602,7 @@ FT                   /db_xref="EMBL:AU008736"
 FT                   /systematic_id="SPBC19F8.04c"
 FT   CDS             complement(3234821..3235513)
 FT                   /colour=10
-FT                   /product="mitochondrial nuclease Lcl3, implicated in DNA
-FT                   repair (predicted)"
+FT                   /product="mitochondrial protein Lcl3"
 FT                   /db_xref="SPD:08/08A12"
 FT                   /systematic_id="SPBC19F8.04c"
 FT                   /controlled_curation="term=species distribution, conserved
@@ -49618,6 +49611,12 @@ FT                   /controlled_curation="term=species distribution,
 FT                   predominantly single copy (one to one); date=20081110"
 FT                   /controlled_curation="term=species distribution, conserved
 FT                   in bacteria; date=20090706"
+FT                   /controlled_curation="term=species distribution, conserved
+FT                   in eukaryotes; date=20250113"
+FT                   /controlled_curation="term=species distribution, conserved
+FT                   in metazoa; date=20250113"
+FT                   /controlled_curation="term=species distribution, conserved
+FT                   in vertebrsates; date=20250113"
 FT                   /primary_name="lcl3"
 FT   5'UTR           complement(3235514..3235753)
 FT                   /systematic_id="SPBC19F8.04c"
@@ -62414,8 +62413,8 @@ FT                   in metazoa; date=20240209"
 FT                   /controlled_curation="term=species distribution, conserved
 FT                   in vertebrates; date=20240209"
 FT                   /controlled_curation="term=subunit composition,
-FT                   pentameric; cv=subunit_composition; db_xref=PMID:36423630;
-FT                   date=20080417"
+FT                   homomeric(5); cv=subunit_composition;
+FT                   db_xref=PMID:36423630; date=20080417"
 FT   lncRNA          complement(4065448..4065718)
 FT                   /db_xref="PMID:29914874"
 FT                   /systematic_id="SPNCRNA.6420"
@@ -63298,7 +63297,7 @@ FT                   in eukaryotes only; date=20081110"
 FT                   /controlled_curation="term=species distribution,
 FT                   predominantly single copy (one to one); date=20081110"
 FT                   /controlled_curation="term=subunit composition,
-FT                   homodimeric; db_xref=PMID:31366733; date=20190923"
+FT                   homomeric(2); db_xref=PMID:31366733; date=20190923"
 FT   lncRNA          4128246..4128529
 FT                   /db_xref="PMID:29914874"
 FT                   /systematic_id="SPNCRNA.6445"

diff --git a/data/chromosome3.contig b/data/chromosome3.contig
@@ -1406,8 +1406,9 @@ FT                   in eukaryotes; date=20140815"
 FT                   /controlled_curation="term=misc, biased repeat containing
 FT                   protein - 6 copies of 'WKKAREEDKAE' repeat and 6 copies of
 FT                   a smaller 'WRNSMDE' repeat; date=20140822"
-FT                   /controlled_curation="term=name description, transmission
-FT                   distorting killer; db_xref=PMID:39485795; date=20250101"
+FT                   /controlled_curation="term=name description,
+FT                   transmission-distorting killer; db_xref=PMID:39485795;
+FT                   date=20250101"
 FT                   /controlled_curation="term=subunit composition,
 FT                   homomeric(4); annotation_extension=during(GO:0072690);
 FT                   db_xref=PMID:39485800; date=20250108"

diff --git a/data/genome.pickle b/data/genome.pickle
diff --git a/results/allele_auto_fix.tsv b/results/allele_auto_fix.tsv
@@ -1,14 +1,14 @@
 systematic_id	allele_id	allele_name	allele_description	allele_type	change_description_to	change_name_to	change_type_to	auto_fix_comment	sequence_error	solution_index	allele_parts	rules_applied	reference
-SPAC140.02	SPAC140.02:allele-3	gar2::ura4+	gar2::ura4+	disruption	gar2::ura4			syntax_error			gar2::ura4+	disruption:usual	PMID:7596817,PMID:9211982
+SPAC140.02	SPAC140.02:allele-4	gar2::ura4+	gar2::ura4+	disruption	gar2::ura4			syntax_error			gar2::ura4+	disruption:usual	PMID:7596817,PMID:9211982
 SPAC18G6.02c	SPAC18G6.02c:allele-10	chp1-alpha-mut1	KKRKK71NEHG	amino_acid_mutation			amino_acid_deletion_and_mutation	type_error			KKRKK71NEHG	amino_acid_deletion_and_mutation:multiple_aa	PMID:22727667
-SPAC23C4.19	SPAC23C4.19:allele-22	spt5-CTD-T1E(7)	801-990,S800SGSKEPAWNSGSGSKEPAWNSGSGSKEPAWNSGSGSKEPAWNSGSGSKEPAWNSGSGSKEPAWNSGSGSKEPAWNSGS	amino_acid_insertion_and_mutation			amino_acid_insertion_and_deletion	type_error			801-990|S800SGSKEPAWNSGSGSKEPAWNSGSGSKEPAWNSGSGSKEPAWNSGSGSKEPAWNSGSGSKEPAWNSGSGSKEPAWNSGS	partial_amino_acid_deletion:multiple_aa|amino_acid_insertion:standard	PMID:32366382
+SPAC23C4.19	SPAC23C4.19:allele-24	spt5-CTD-T1E(7)	801-990,S800SGSKEPAWNSGSGSKEPAWNSGSGSKEPAWNSGSGSKEPAWNSGSGSKEPAWNSGSGSKEPAWNSGSGSKEPAWNSGS	amino_acid_insertion_and_mutation			amino_acid_insertion_and_deletion	type_error			801-990|S800SGSKEPAWNSGSGSKEPAWNSGSGSKEPAWNSGSGSKEPAWNSGSGSKEPAWNSGSGSKEPAWNSGSGSKEPAWNSGS	partial_amino_acid_deletion:multiple_aa|amino_acid_insertion:standard	PMID:32366382
 SPAC56E4.04c	SPAC56E4.04c:allele-4	cut6-1	L1910S	amino_acid_mutation	L1877S			old_coords_fix, revision 8148: complement(join(1246095..1252807,1253430..1253559))	L1910		L1910S	amino_acid_mutation:single_aa	PMID:37792890
-SPAC977.10	SPAC977.10:allele-46	nhe1-REL6	EIEKSIYE390QSSGNSHIKE	amino_acid_mutation			amino_acid_insertion_and_mutation	type_error			EIEKSIYE390QSSGNSHIKE	amino_acid_insertion_and_mutation:multiple_aa	PMID:30996236
-SPBC215.05	SPBC215.05:allele-2	gpd1-G4BS	TTACGTCA(-324)CGGAAGACTCTCCTCCG	nucleotide_mutation			nucleotide_insertion_and_mutation	type_error			TTACGTCA(-324)CGGAAGACTCTCCTCCG	nucleotide_insertion_and_mutation:multiple_nt	PMID:25122751
-SPBC28F2.12	SPBC28F2.12:allele-4	rpb1-CTD-S2A(r1-r12)delta(r13-r29)	CTD-S2A(r1-r12)delta(r13-r29)	amino_acid_deletion_and_mutation	CTD-S2A(r1-r12),delta(r13-r29)			syntax_error			CTD-S2A(r1-r12)delta(r13-r29)	amino_acid_deletion_and_mutation:CTD	PMID:22144909
+SPAC977.10	SPAC977.10:allele-78	nhe1-REL6	EIEKSIYE390QSSGNSHIKE	amino_acid_mutation			amino_acid_insertion_and_mutation	type_error			EIEKSIYE390QSSGNSHIKE	amino_acid_insertion_and_mutation:multiple_aa	PMID:30996236
+SPBC215.05	SPBC215.05:allele-3	gpd1-G4BS	TTACGTCA(-324)CGGAAGACTCTCCTCCG	nucleotide_mutation			nucleotide_insertion_and_mutation	type_error			TTACGTCA(-324)CGGAAGACTCTCCTCCG	nucleotide_insertion_and_mutation:multiple_nt	PMID:25122751
+SPBC28F2.12	SPBC28F2.12:allele-51	rpb1-CTD-S2A(r1-r12)delta(r13-r29)	CTD-S2A(r1-r12)delta(r13-r29)	amino_acid_deletion_and_mutation	CTD-S2A(r1-r12),delta(r13-r29)			syntax_error			CTD-S2A(r1-r12)delta(r13-r29)	amino_acid_deletion_and_mutation:CTD	PMID:22144909
 SPBC28F2.12	SPBC28F2.12:allele-50	rpb1-CTD-S2A(r5-r29)S7A(r5-r29)	CTD-S2A(r5-r29)S7A(r5-r29)	amino_acid_mutation	CTD-S2A(r5-r29),S7A(r5-r29)			syntax_error			CTD-S2A(r5-r29)S7A(r5-r29)	amino_acid_mutation:CTD	PMID:22771993
 SPBC3H7.13	SPBC3H7.13:allele-2	csc1::ura4+	csc1::ura4+	disruption	csc1::ura4			syntax_error			csc1::ura4+	disruption:usual	PMID:23874188
-SPBC428.08c	SPBC428.08c:allele-6	clr4-alpha-mut	KRRKR58NEHG	amino_acid_mutation			amino_acid_deletion_and_mutation	type_error			KRRKR58NEHG	amino_acid_deletion_and_mutation:multiple_aa	PMID:22727667
+SPBC428.08c	SPBC428.08c:allele-18	clr4-alpha-mut	KRRKR58NEHG	amino_acid_mutation			amino_acid_deletion_and_mutation	type_error			KRRKR58NEHG	amino_acid_deletion_and_mutation:multiple_aa	PMID:22727667
 SPCC285.07c	SPCC285.07c:allele-2	wtf18-2D366NN	D366N,D366DN	amino_acid_insertion_and_mutation	D47N,D47DN			multi_shift_fix	D366|D366	0	D366N|D366DN	amino_acid_mutation:single_aa|amino_acid_insertion:standard	PMID:30475921
 SPCC285.07c	SPCC285.07c:allele-2	wtf18-2D366NN	D366N,D366DN	amino_acid_insertion_and_mutation	D58DN,D58N			multi_shift_fix	D366|D366	1	D366N|D366DN	amino_acid_mutation:single_aa|amino_acid_insertion:standard	PMID:30475921
 SPCC285.07c	SPCC285.07c:allele-2	wtf18-2D366NN	D366N,D366DN	amino_acid_insertion_and_mutation	D79N,D79DN			multi_shift_fix	D366|D366	2	D366N|D366DN	amino_acid_mutation:single_aa|amino_acid_insertion:standard	PMID:30475921
@@ -17,5 +17,5 @@ SPCC285.07c	SPCC285.07c:allele-2	wtf18-2D366NN	D366N,D366DN	amino_acid_insertion
 SPCC285.07c	SPCC285.07c:allele-2	wtf18-2D366NN	D366N,D366DN	amino_acid_insertion_and_mutation	D282N,D282DN			multi_shift_fix	D366|D366	5	D366N|D366DN	amino_acid_mutation:single_aa|amino_acid_insertion:standard	PMID:30475921
 SPCC285.07c	SPCC285.07c:allele-2	wtf18-2D366NN	D366N,D366DN	amino_acid_insertion_and_mutation	D286N,D286DN			multi_shift_fix	D366|D366	6	D366N|D366DN	amino_acid_mutation:single_aa|amino_acid_insertion:standard	PMID:30475921
 SPCC285.07c	SPCC285.07c:allele-2	wtf18-2D366NN	D366N,D366DN	amino_acid_insertion_and_mutation	D356N,D356DN			multi_shift_fix	D366|D366	7	D366N|D366DN	amino_acid_mutation:single_aa|amino_acid_insertion:standard	PMID:30475921
-SPCC757.07c	SPCC757.07c:allele-2	ctt1-G4BS	ATGACGT(-428)CGGAAGACTCTCCTCCG	nucleotide_mutation			nucleotide_insertion_and_mutation	type_error			ATGACGT(-428)CGGAAGACTCTCCTCCG	nucleotide_insertion_and_mutation:multiple_nt	PMID:25122751
+SPCC757.07c	SPCC757.07c:allele-3	ctt1-G4BS	ATGACGT(-428)CGGAAGACTCTCCTCCG	nucleotide_mutation			nucleotide_insertion_and_mutation	type_error			ATGACGT(-428)CGGAAGACTCTCCTCCG	nucleotide_insertion_and_mutation:multiple_nt	PMID:25122751
 SPNCRNA.1712	SPNCRNA.1712:allele-2	nc-pho1-dual-PAS-mut	ATTTTT-342-CTCGAG,AATAAA-568-GGCGGG	nucleotide_mutation	ATTTTT342CTCGAG,AATAAA568GGCGGG			syntax_error			ATTTTT-342-CTCGAG|AATAAA-568-GGCGGG	nucleotide_mutation:multiple_nt|nucleotide_mutation:multiple_nt	PMID:30355770,PMID:36882296