updated to last revision

pombase · Feb 23, 2025 · f966ba4 · f966ba4
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Showing 11 changed files with 16,848 additions and 16,846 deletions.
diff --git a/data/alleles.tsv b/data/alleles.tsv
diff --git a/data/chromosome1.contig b/data/chromosome1.contig
@@ -28167,16 +28167,16 @@ FT                   /product="D-arabinono-1,4-lactone oxidase (predicted)"
 FT                   /systematic_id="SPAPB1A10.12c"
 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,
 FT                   predominantly single copy (one to one); date=20081110"
 FT                   /controlled_curation="term=species distribution, conserved
 FT                   in fungi; date=20081110"
 FT                   /controlled_curation="term=species distribution, conserved
 FT                   in bacteria; date=20081110"
+FT                   /controlled_curation="term=species distribution, conserved
+FT                   in vertebrates;  date=20250219"
+FT                   /controlled_curation="term=species distribution, conserved
+FT                   in metazoa; date=20250219"
 FT   5'UTR           complement(1886204..1886360)
 FT                   /systematic_id="SPAPB1A10.12c"
 FT                   /db_xref="PMID:30566651"
@@ -37345,8 +37345,7 @@ FT                   /systematic_id="SPAC19A8.14"
 FT                   /db_xref="PMID:21511999"
 FT   CDS             complement(2460340..2460957)
 FT                   /colour=7
-FT                   /product="mitochondrial aminoacyl-tRNA hydrolase Pth2
-FT                   (predicted)"
+FT                   /product="mitochondrial peptidyl-tRNA hydrolase Pth2"
 FT                   /systematic_id="SPAC19A8.14"
 FT                   /controlled_curation="term=species distribution, conserved
 FT                   in eukaryotes; date=20081110"
@@ -44031,9 +44030,8 @@ FT                   /systematic_id="SPNCRNA.3295"
 FT                   /product="non-coding RNA"
 FT   CDS             complement(join(2868517..2869171,2869265..2869377))
 FT                   /colour=7
-FT                   /primary_name="nnt1"
-FT                   /product="nicotinamide N-methyltransferase Nnt1
-FT                   (predicted)"
+FT                   /synonym="nnt1"
+FT                   /product="elongation factor methyltransferase Efm7"
 FT                   /systematic_id="SPAC8F11.09c"
 FT                   /db_xref="SPD:11/11E04"
 FT                   /controlled_curation="term=species distribution, conserved
@@ -44048,6 +44046,7 @@ FT                   /controlled_curation="term=species distribution, conserved
 FT                   in fungi; date=20081110"
 FT                   /controlled_curation="term=species distribution, conserved
 FT                   in eukaryotes only; date=20100820"
+FT                   /primary_name="efm7"
 FT   5'UTR           complement(2869378..2869440)
 FT                   /systematic_id="SPAC8F11.09c"
 FT                   /db_xref="PMID:30566651"
@@ -45940,7 +45939,7 @@ FT                   /obsolete_name="gcv1-antisense-1"
 FT   CDS             3012593..3013756
 FT                   /colour=7
 FT                   /primary_name="gcv1"
-FT                   /product="glycine decarboxylase T subunit (predicted)"
+FT                   /product="glycine cleavage complex subunit T, Gcv1"
 FT                   /synonym="n313"
 FT                   /db_xref="KEGG:MAP00260"
 FT                   /db_xref="KEGG:MAP00670"
@@ -47471,7 +47470,8 @@ FT                   /systematic_id="SPNCRNA.3389"
 FT                   /product="non-coding RNA"
 FT   CDS             join(3109174..3109312,3109606..3110015)
 FT                   /colour=2
-FT                   /product="mitochondrial translation release factor"
+FT                   /product="mitochondrial peptidyl tRNA hydrolase,
+FT                   stalled-ribosome rescue factor srRF1, Pth4"
 FT                   /primary_name="pth4"
 FT                   /systematic_id="SPAC589.11"
 FT                   /db_xref="SPD:41/41F09"

diff --git a/data/chromosome2.contig b/data/chromosome2.contig
@@ -1608,7 +1608,7 @@ FT   CDS             complement(160461..162155)
 FT                   /EC_number="1.16.1.7"
 FT                   /colour=2
 FT                   /primary_name="frp1"
-FT                   /product="plasma membrane ferric-chelate reductase (NADPH)
+FT                   /product="plasma membrane ferric iron reductase (NADPH)
 FT                   Frp1"
 FT                   /db_xref="SPD:35/35C11"
 FT                   /systematic_id="SPBC1683.09c"
@@ -23085,9 +23085,9 @@ FT                   /feature_source="evidence=ECO:0000309; source=SO:0001238;
 FT                   condition=FYECO:0000126; during=GO:0072690;
 FT                   score=214.646000; db_xref=PMID:30566651"
 FT   CDS             join(1536899..1536938,1536988..1537106,1537267..1537806,1537868..1537965,1538088..1538454)
-FT                   /colour=7
+FT                   /colour=2
 FT                   /product="ribosome assembly factor, WD repeat protein
-FT                   Nsa1/Wdr74 (predicted)"
+FT                   Nsa1/Wdr74"
 FT                   /db_xref="SPD:25/25B11"
 FT                   /systematic_id="SPBC83.15"
 FT                   /controlled_curation="term=WD repeat protein;
@@ -43382,8 +43382,7 @@ FT                   condition=FYECO:0000126; during=GO:0072690;
 FT                   score=331.210000; db_xref=PMID:30566651"
 FT   CDS             2848523..2849032
 FT                   /colour=7
-FT                   /product="glycine decarboxylase complex subunit H
-FT                   (predicted)"
+FT                   /product="glycine cleavage complex subunit H, Gcv3"
 FT                   /db_xref="SPD:41/41C12"
 FT                   /systematic_id="SPBP19A11.01"
 FT                   /controlled_curation="term=species distribution, conserved
@@ -47353,7 +47352,7 @@ FT                   condition=FYECO:0000126; during=GO:0072690;
 FT                   score=57.156000; db_xref=PMID:30566651"
 FT   CDS             3089997..3090740
 FT                   /colour=7
-FT                   /product="sepiapterin reductase (predicted)"
+FT                   /product="sepiapterin reductase Nre1"
 FT                   /db_xref="SPD:09/09A08"
 FT                   /systematic_id="SPBC30D10.05c"
 FT                   /controlled_curation="term=species distribution, conserved
@@ -47369,6 +47368,7 @@ FT                   in bacteria; date=20081110"
 FT                   /controlled_curation="term=species distribution,
 FT                   predominantly single copy (one to one); date=20081110"
 FT                   /EC_number="1.1.1.153"
+FT                   /primary_name="nre1"
 FT   3'UTR           3090741..3090914
 FT                   /systematic_id="SPBC30D10.05c"
 FT                   /db_xref="PMID:21511999"
@@ -54302,8 +54302,8 @@ FT                   /systematic_id="SPBC1105.18c"
 FT                   /db_xref="PMID:21511999"
 FT   CDS             complement(3539204..3539692)
 FT                   /colour=2
-FT                   /product="mitochondrial aminoacyl-tRNA hydrolase Pth3
-FT                   (predicted)"
+FT                   /product="mitochondrial peptidyl-tRNA hydrolase,
+FT                   stalled-ribosome rescue factor srRF2, Pth3"
 FT                   /synonym="SPBC887.21c"
 FT                   /db_xref="SPD:50/50B06"
 FT                   /systematic_id="SPBC1105.18c"

diff --git a/data/chromosome3.contig b/data/chromosome3.contig
@@ -1119,10 +1119,10 @@ FT                   condition=FYECO:0000126; during=GO:0072690;
 FT                   score=515.530000; db_xref=PMID:30566651"
 FT   CDS             96721..98001
 FT                   /EC_number="1.10.2.2"
-FT                   /colour=7
+FT                   /colour=2
 FT                   /primary_name="qcr2"
 FT                   /product="ubiquinol-cytochrome-c reductase complex core
-FT                   protein Qcr2 (predicted)"
+FT                   protein Qcr2"
 FT                   /db_xref="SPD:20/20E06"
 FT                   /systematic_id="SPCC613.10"
 FT                   /controlled_curation="term=species distribution, conserved
@@ -22610,6 +22610,8 @@ FT                   /controlled_curation="term=gene expression, RNA level;
 FT                   annotation_extension=in_presence_of(CHEBI:47600);
 FT                   qualifier=increased; evidence=ECO:0000058;
 FT                   db_xref=PMID:22840777; date=20121018"
+FT                   /controlled_curation="term=species distribution, no
+FT                   apparent S. cerevisiae ortholog;  date=20250221"
 FT   lncRNA          complement(1635981..1641464)
 FT                   /db_xref="PMID:29914874"
 FT                   /systematic_id="SPNCRNA.7448"

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-4	gar2::ura4+	gar2::ura4+	disruption	gar2::ura4			syntax_error			gar2::ura4+	disruption:usual	PMID:7596817,PMID:9211982
+SPAC140.02	SPAC140.02:allele-8	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-19	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-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
 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
-SPAC977.10	SPAC977.10:allele-117	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-6	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-13	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-7	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-9	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
+SPAC977.10	SPAC977.10:allele-107	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-10	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-19	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-5	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
+SPNCRNA.1712	SPNCRNA.1712:allele-5	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