updated to last revision

pombase · Sep 15, 2024 · 00481ce · 00481ce
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Showing 11 changed files with 13,482 additions and 13,468 deletions.
diff --git a/data/alleles.tsv b/data/alleles.tsv
diff --git a/data/chromosome1.contig b/data/chromosome1.contig
@@ -1148,7 +1148,8 @@ FT                   condition=FYECO:0000126; during=GO:0072690;
 FT                   score=96.621400; db_xref=PMID:30566651"
 FT   CDS             106965..107198
 FT                   /systematic_id="SPAC11D3.19"
-FT                   /product="Schizosaccharomyces pombe specific microprotein"
+FT                   /product="Schizosaccharomyces pombe specific microprotein,
+FT                   GPI anchored"
 FT                   /controlled_curation="term=warning, new gene;
 FT                   db_xref=PMID:21511999; date=20110311"
 FT                   /controlled_curation="term=species distribution,
@@ -37972,7 +37973,7 @@ FT                   /product="non-coding RNA"
 FT   CDS             complement(2500613..2501809)
 FT                   /colour=2
 FT                   /primary_name="swd1"
-FT                   /product="Set1C complex WDC repeat subunit Swd1"
+FT                   /product="Set1C complex WD repeat subunit Swd1"
 FT                   /systematic_id="SPAC23H3.05c"
 FT                   /db_xref="SPD:19/19B03"
 FT                   /controlled_curation="term=WD repeat protein;
@@ -38488,7 +38489,7 @@ FT                   db_xref=PMID:30566651"
 FT   CDS             2531453..2532679
 FT                   /colour=2
 FT                   /product="histone H3-H4 chaperone, CAF assembly factor
-FT                   (CAF-1) complex subunit C, Pcf3"
+FT                   (CAF-1) complex WD repeat subunit C, Pcf3"
 FT                   /primary_name="pcf3"
 FT                   /systematic_id="SPAC25H1.06"
 FT                   /db_xref="SPD:22/22B11"
@@ -62186,7 +62187,7 @@ FT                   db_xref=PMID:30566651"
 FT   CDS             join(4119899..4120030,4120126..4120228,4120270..4120512,4120578..4121638)
 FT                   /colour=2
 FT                   /product="histone H3-H4 chaperone, CAF assembly factor
-FT                   (CAF-1) complex subunit B, Pcf2"
+FT                   (CAF-1) complex WD repeat subunit, Pcf2"
 FT                   /primary_name="pcf2"
 FT                   /synonym="cac2"
 FT                   /systematic_id="SPAC26H5.03"
@@ -74747,7 +74748,8 @@ FT                   condition=FYECO:0000126; during=GO:0072690; score=51.117;
 FT                   db_xref=PMID:30566651"
 FT   CDS             4923580..4923891
 FT                   /colour=8
-FT                   /product="Schizosaccharomyces pombe specific protein"
+FT                   /product="Schizosaccharomyces pombe specific protein, GPI
+FT                   anchored"
 FT                   /systematic_id="SPAPB8E5.08"
 FT                   /controlled_curation="term=warning, previously annotated
 FT                   as dubious; date=20120103"
@@ -77728,8 +77730,8 @@ FT                   /db_xref="PMID:21511999"
 FT   CDS             complement(join(5110432..5111536,5111614..5111719,5111790..5111874))
 FT                   /colour=2
 FT                   /primary_name="prw1"
-FT                   /product="histone chaperone, Clr6 and Rpd3L complex
-FT                   subunit Prw1"
+FT                   /product="histone chaperone, Clr6 and Rpd3L complex WD
+FT                   repeat subunit Prw1"
 FT                   /systematic_id="SPAC29A4.18"
 FT                   /db_xref="SPD:23/23C03"
 FT                   /controlled_curation="term=WD repeat protein;
@@ -84086,7 +84088,8 @@ FT                   /systematic_id="SPNCRNA.4509"
 FT                   /product="non-coding RNA"
 FT   CDS             complement(5575193..5575564)
 FT                   /colour=8
-FT                   /product="S. pombe specific protein"
+FT                   /product="Schizosaccharomyces pombe specific protein, GPI
+FT                   anchored"
 FT                   /systematic_id="SPAC750.07c"
 FT                   /controlled_curation="term=genome organization, telomeric
 FT                   duplication; cv=genome_org; date=19700101"

diff --git a/data/chromosome2.contig b/data/chromosome2.contig
@@ -30430,7 +30430,8 @@ FT                   /systematic_id="SPNCRNA.5461"
 FT                   /product="non-coding RNA"
 FT   CDS             2037092..2037394
 FT                   /colour=8
-FT                   /product="Schizosaccharomyces pombe specific protein"
+FT                   /product="Schizosaccharomyces pombe specific protein, GPI
+FT                   anchored"
 FT                   /db_xref="SPD:51/51F08"
 FT                   /systematic_id="SPBC29A3.21"
 FT                   /controlled_curation="term=warning, previously annotated
@@ -48210,7 +48211,8 @@ FT                   /systematic_id="SPBC405.02c"
 FT                   /db_xref="PMID:21511999"
 FT   CDS             complement(3143466..3144809)
 FT                   /colour=12
-FT                   /product="Schizosaccharomyces specific protein"
+FT                   /product="Schizosaccharomyces specific protein, GPI
+FT                   anchored"
 FT                   /synonym="SPBC4C3.01"
 FT                   /db_xref="SPD:20/20G08"
 FT                   /systematic_id="SPBC405.02c"

diff --git a/data/chromosome3.contig b/data/chromosome3.contig
@@ -2592,7 +2592,7 @@ FT                   condition=FYECO:0000126; during=GO:0072690;
 FT                   score=69.328900; db_xref=PMID:30566651"
 FT   CDS             join(194552..194603,194694..195460,195499..195918,195971..196426)
 FT                   /colour=2
-FT                   /product="Set3 complex subunit Hif2"
+FT                   /product="Set3 complex WD repeat subunit Hif2"
 FT                   /primary_name="hif2"
 FT                   /db_xref="SPD:46/46A09"
 FT                   /systematic_id="SPCC1235.09"
@@ -4649,8 +4649,10 @@ FT                   /db_xref="PMID:29914874"
 FT                   /systematic_id="SPNCRNA.6812"
 FT                   /product="non-coding RNA"
 FT   CDS             join(354456..354756,354856..354946,355269..357252)
-FT                   /colour=10
-FT                   /product="DUF1769 family protein"
+FT                   /colour=2
+FT                   /product="plasma membrane
+FT                   phosphatidylinositol-4,5-bisphosphate binding protein
+FT                   Duc1"
 FT                   /synonym="SPCC736.16"
 FT                   /db_xref="SPD:29/29D11"
 FT                   /systematic_id="SPCC594.01"
@@ -4666,6 +4668,8 @@ FT                   /controlled_curation="term=species distribution, conserved
 FT                   in eukaryotes; date=20080202"
 FT                   /controlled_curation="term=name description, Domain of
 FT                   Unknown function protein at the Cortex;  date=20210122"
+FT                   /controlled_curation="term=name description, Domain of
+FT                   Unknown function at the Cortex; db_xref=; date=20240911"
 FT                   /primary_name="duc1"
 FT   3'UTR           357253..357773
 FT                   /systematic_id="SPCC594.01"
@@ -8037,7 +8041,7 @@ FT   CDS             join(584135..584219,584292..584397,584486..585587)
 FT                   /colour=2
 FT                   /primary_name="mis16"
 FT                   /product="histone H4 chaperone, CENP-A recruiting complex
-FT                   CENP-A chaperone Mis16"
+FT                   CENP-A chaperone, WD repeat subunit Mis16"
 FT                   /db_xref="SPD:23/23D08"
 FT                   /systematic_id="SPCC1672.10"
 FT                   /controlled_curation="term=WD repeat protein;
@@ -13666,7 +13670,8 @@ FT                   condition=FYECO:0000126; during=GO:0072690;
 FT                   score=37.385500; db_xref=PMID:30566651"
 FT   CDS             972824..973162
 FT                   /colour=12
-FT                   /product="Schizosaccharomyces specific protein"
+FT                   /product="Schizosaccharomyces specific protein, GPI
+FT                   anchored"
 FT                   /db_xref="SPD:02/02A05"
 FT                   /systematic_id="SPCC1795.12c"
 FT                   /controlled_curation="term=warning, previously annotated
@@ -17887,8 +17892,8 @@ FT                   /systematic_id="SPCC1322.06"
 FT                   /db_xref="PMID:21511999"
 FT   CDS             complement(1300640..1300954)
 FT                   /colour=8
-FT                   /product="Schizosaccharomyces pombe specific protein
-FT                   Mug150"
+FT                   /product="Schizosaccharomyces pombe specific protein, GPI
+FT                   anchored, Mug150"
 FT                   /db_xref="SPD:01/01F07"
 FT                   /primary_name="mug150"
 FT                   /systematic_id="SPCC1322.07c"

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
-SPAC18G6.02c	SPAC18G6.02c:allele-17	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
+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-19	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
-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
+SPAC977.10	SPAC977.10:allele-43	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-8	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-10	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-24	clr4-alpha-mut	KRRKR58NEHG	amino_acid_mutation			amino_acid_deletion_and_mutation	type_error			KRRKR58NEHG	amino_acid_deletion_and_mutation:multiple_aa	PMID:22727667
+SPBC28F2.12	SPBC28F2.12:allele-28	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-30	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
@@ -18,4 +18,4 @@ 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	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-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-12	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
+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