updated to last revision

pombase · Nov 13, 2024 · 4ed9d3f · 4ed9d3f
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Showing 12 changed files with 13,550 additions and 11,539 deletions.
diff --git a/data/alleles.tsv b/data/alleles.tsv
diff --git a/data/chromosome1.contig b/data/chromosome1.contig
@@ -6688,8 +6688,8 @@ FT                   condition=FYECO:0000126; during=GO:0072690;
 FT                   score=2.311820; db_xref=PMID:30566651"
 FT   CDS             join(488779..489029,489074..489350)
 FT                   /colour=7
-FT                   /product="TIM23 translocase complex subunit Tim15
-FT                   (predicted)"
+FT                   /product="Protein co-chaperone with a zinc finger motif
+FT                   Zim17"
 FT                   /systematic_id="SPAC24H6.02c"
 FT                   /db_xref="SPD:06/06A11"
 FT                   /controlled_curation="term=zinc finger protein;
@@ -6707,7 +6707,8 @@ 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"
-FT                   /primary_name="tim15"
+FT                   /synonym="tim15"
+FT                   /primary_name="zim17"
 FT   lncRNA          complement(489023..489562)
 FT                   /db_xref="PMID:29914874"
 FT                   /db_xref="PMID:21511999"
@@ -8282,10 +8283,9 @@ FT                   /feature_source="evidence=ECO:0000309; source=SO:0001238;
 FT                   condition=FYECO:0000126; during=GO:0072690;
 FT                   score=76.916600; db_xref=PMID:30566651"
 FT   CDS             588925..590259
-FT                   /colour=7
+FT                   /colour=2
 FT                   /product="sec14 cytosolic factor family,
-FT                   phospholipid-intermembrane transfer protein Csr102
-FT                   (predicted)"
+FT                   phospholipid-intermembrane transfer protein Csr102"
 FT                   /systematic_id="SPAC3H8.02"
 FT                   /db_xref="SPD:20/20F07"
 FT                   /controlled_curation="term=species distribution, conserved
@@ -20212,7 +20212,8 @@ FT                   /db_xref="PMID:21511999"
 FT   CDS             complement(1373066..1374883)
 FT                   /colour=2
 FT                   /primary_name="pof1"
-FT                   /product="F-box/WD repeat protein Pof1"
+FT                   /product="F-box/WD repeat protein, probable hydrogen
+FT                   sulfide sensing ubiquitin ligase adaptor Pof1"
 FT                   /systematic_id="SPAC57A10.05c"
 FT                   /controlled_curation="term=F-box protein; date=19700101"
 FT                   /controlled_curation="term=WD repeat protein;
@@ -25733,7 +25734,7 @@ FT                   db_xref=PMID:30566651"
 FT   CDS             1726009..1728033
 FT                   /colour=2
 FT                   /primary_name="ssc1"
-FT                   /product="mitochondrial (2Fe-2S) cluster assembly
+FT                   /product="mitochondrial [2Fe-2S] cluster assembly
 FT                   chaperone Ssc1"
 FT                   /synonym="ssp1"
 FT                   /systematic_id="SPAC664.11"
@@ -31470,8 +31471,8 @@ FT                   /systematic_id="SPNCRNA.2938"
 FT                   /product="non-coding RNA"
 FT   CDS             complement(2096382..2097785)
 FT                   /colour=7
-FT                   /product="mitochondrial repliratory complex assembly
-FT                   factro/arginine methyltransferase, human NDUFAF7 ortholog"
+FT                   /product="mitochondrial respiratory complex assembly
+FT                   factor/arginine methyltransferase, human NDUFAF7 ortholog"
 FT                   /synonym="SPAC3C7.15c"
 FT                   /systematic_id="SPAC25A8.03c"
 FT                   /db_xref="SPD:01/01A11"
@@ -70558,7 +70559,7 @@ FT                   condition=FYECO:0000126; during=GO:0072690; score=25.5886;
 FT                   db_xref=PMID:30566651"
 FT   CDS             4668874..4669551
 FT                   /colour=2
-FT                   /product="mitochondrial (2Fe-2S) cluster assembly
+FT                   /product="mitochondrial [2Fe-2S] cluster assembly
 FT                   co-chaperone Jac1"
 FT                   /systematic_id="SPAC144.08"
 FT                   /db_xref="SPD:07/07G12"
@@ -74916,8 +74917,8 @@ FT                   /systematic_id="SPAC1B3.04c"
 FT                   /db_xref="PMID:21511999"
 FT   CDS             complement(join(4931313..4931351,4931503..4932927,4933016..4933510))
 FT                   /colour=7
-FT                   /product="mitochondrial elongation factor GTPase Guf1
-FT                   (predicted)"
+FT                   /product="mitochondrial translation elongation factor
+FT                   GTPase Guf1"
 FT                   /systematic_id="SPAC1B3.04c"
 FT                   /db_xref="SPD:27/27E11"
 FT                   /controlled_curation="term=species distribution, conserved

diff --git a/data/chromosome2.contig b/data/chromosome2.contig
@@ -15935,9 +15935,8 @@ FT                   /feature_source="evidence=ECO:0000309; source=SO:0001238;
 FT                   condition=FYECO:0000126; during=GO:0072690;
 FT                   score=28.189200; db_xref=PMID:30566651"
 FT   CDS             join(1102314..1102374,1102420..1103075,1103114..1103683)
-FT                   /colour=10
-FT                   /product="	DUF3844 family transmembrane protein, conserved
-FT                   in fungi"
+FT                   /colour=2
+FT                   /product="vacuolar sorting protein Vps3844"
 FT                   /db_xref="SPD:19/19F11"
 FT                   /systematic_id="SPBC1709.03"
 FT                   /controlled_curation="term=species distribution, no
@@ -15952,6 +15951,7 @@ FT                   /controlled_curation="term=species distribution, conserved
 FT                   in eukaryotes; date=20080202"
 FT                   /controlled_curation="term=warning, gene structure
 FT                   updated; db_xref=PMID:21511999; date=20110311"
+FT                   /primary_name="vps3844"
 FT   3'UTR           complement(1103600..1103769)
 FT                   /systematic_id="SPBC1709.04c"
 FT                   /db_xref="PMID:21511999"
@@ -17623,9 +17623,8 @@ FT                   /systematic_id="SPNCRNA.5064"
 FT                   /product="non-coding RNA"
 FT   CDS             1200661..1201974
 FT                   /EC_number="2.6.1.1"
-FT                   /colour=7
-FT                   /product="mitochondrial aspartate aminotransferase Maa1
-FT                   (predicted)"
+FT                   /colour=2
+FT                   /product="mitochondrial aspartate aminotransferase Maa1"
 FT                   /db_xref="SPD:22/22H05"
 FT                   /systematic_id="SPBC725.01"
 FT                   /controlled_curation="term=species distribution, conserved
@@ -40598,7 +40597,7 @@ FT   CDS             complement(2682390..2683760)
 FT                   /colour=7
 FT                   /primary_name="cfh4"
 FT                   /product="SEL1/TPR repeat protein, chitin synthase
-FT                   regulatory factor Cfh4/ predicted human COA7 ortholog"
+FT                   regulatory factor Cfh4"
 FT                   /obsolete_name="chr1"
 FT                   /db_xref="SPD:21/21C04"
 FT                   /systematic_id="SPBC3E7.12c"
@@ -40611,10 +40610,6 @@ FT                   in fungi; date=20081110"
 FT                   /controlled_curation="term=species distribution, conserved
 FT                   in eukaryotes; date=20080202"
 FT                   /controlled_curation="term=species distribution, conserved
-FT                   in metazoa; date=20180324"
-FT                   /controlled_curation="term=species distribution, conserved
-FT                   in vertebrates; date=20180324"
-FT                   /controlled_curation="term=species distribution, conserved
 FT                   in eukaryotes only; date=20100827"
 FT   lncRNA          2683030..2683289
 FT                   /db_xref="PMID:29914874"
@@ -51763,6 +51758,9 @@ FT                   /controlled_curation="term=species distribution, conserved
 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=warning, there is a gene with
+FT                   the systematic identifier SPBC3B8.10 (ina17);
+FT                   date=20241106"
 FT   lncRNA          complement(3373489..3374317)
 FT                   /db_xref="PMID:29914874"
 FT                   /systematic_id="SPNCRNA.6098"
@@ -52014,6 +52012,9 @@ FT                   /controlled_curation="term=species distribution,
 FT                   predominantly single copy (one to one); date=20081110"
 FT                   /controlled_curation="term=warning, gene structure
 FT                   updated; db_xref=PMID:25883323; date=20221212"
+FT                   /controlled_curation="term=warning, there is a gene with
+FT                   the systematic identifier SPBC3B8.10c (nem1);
+FT                   date=20241106"
 FT                   /primary_name="ina17"
 FT   intron          3391070..3391177
 FT                   /systematic_id="SPBC3B8.10"

diff --git a/data/chromosome3.contig b/data/chromosome3.contig
@@ -17639,10 +17639,9 @@ FT   3'UTR           complement(1277590..1277872)
 FT                   /systematic_id="SPCC23B6.04c"
 FT                   /db_xref="PMID:21511999"
 FT   CDS             complement(1277873..1280899)
-FT                   /colour=7
+FT                   /colour=2
 FT                   /product="meiotic sec14 cytosolic factor family,
-FT                   phospholipid-intermembrane transfer protein Pdr16
-FT                   (predicted)"
+FT                   phospholipid-intermembrane transfer protein Pdr16"
 FT                   /db_xref="SPD:29/29H01"
 FT                   /note="longer than orthologs, possibly a gene fusion"
 FT                   /systematic_id="SPCC23B6.04c"

diff --git a/data/genome.pickle b/data/genome.pickle
diff --git a/results/allele_auto_fix.tsv b/results/allele_auto_fix.tsv
@@ -1,21 +1,21 @@
 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
-SPAC18G6.02c	SPAC18G6.02c:allele-11	chp1-alpha-mut1	KKRKK71NEHG	amino_acid_mutation			amino_acid_deletion_and_mutation	type_error			KKRKK71NEHG	amino_acid_deletion_and_mutation:multiple_aa	PMID:22727667
+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-20	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-8	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
+SPAC56E4.04c	SPAC56E4.04c:allele-5	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-56	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-27	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-34	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
+SPBC28F2.12	SPBC28F2.12:allele-49	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-8	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-7	csc1::ura4+	csc1::ura4+	disruption	csc1::ura4			syntax_error			csc1::ura4+	disruption:usual	PMID:23874188
-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	D47DN,D47N			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	D58N,D58DN			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	D79DN,D79N			multi_shift_fix	D366|D366	2	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	D197DN,D197N			multi_shift_fix	D366|D366	3	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	D219DN,D219N			multi_shift_fix	D366|D366	4	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	D282DN,D282N			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	D286DN,D286N			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	D356DN,D356N			multi_shift_fix	D366|D366	7	D366N|D366DN	amino_acid_mutation:single_aa|amino_acid_insertion:standard	PMID:30475921
-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
+SPBC428.08c	SPBC428.08c:allele-8	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
+SPCC285.07c	SPCC285.07c:allele-2	wtf18-2D366NN	D366N,D366DN	amino_acid_insertion_and_mutation	D197N,D197DN			multi_shift_fix	D366|D366	3	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	D219N,D219DN			multi_shift_fix	D366|D366	4	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	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
 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