updated to last revision

pombase · Jul 21, 2024 · 73d11a6 · 73d11a6
1 parent fe535c2
commit 73d11a6
Show file tree

Hide file tree

Showing 10 changed files with 9,497 additions and 9,501 deletions.
diff --git a/data/alleles.tsv b/data/alleles.tsv
diff --git a/data/chromosome1.contig b/data/chromosome1.contig
@@ -170,7 +170,8 @@ FT                   /systematic_id="SPAC212.04c"
 FT                   /db_xref="PMID:21511999"
 FT   CDS             complement(23589..23978)
 FT                   /colour=8
-FT                   /product="hypothetical protein"
+FT                   /product="Schizosaccharomyces pombe specific protein,
+FT                   ubiquitin related"
 FT                   /systematic_id="SPAC212.03"
 FT                   /db_xref="SPD:41/41B06"
 FT                   /controlled_curation="term=genome organization, telomeric
@@ -4002,8 +4003,8 @@ FT                   /feature_source="evidence=ECO:0000309; source=SO:0001238;
 FT                   condition=FYECO:0000126; during=GO:0072690;
 FT                   score=68.155600; db_xref=PMID:30566651"
 FT   CDS             join(303161..303231,303334..303640,303716..303793,303852..304019)
-FT                   /colour=7
-FT                   /product="serine O-acetyltransferase activity (predicted)"
+FT                   /colour=10
+FT                   /product="O-acetyltransferase activity"
 FT                   /systematic_id="SPAC18B11.09c"
 FT                   /db_xref="SPD:11/11D11"
 FT                   /controlled_curation="term=orthologous to S. cerevisiae
@@ -31842,7 +31843,7 @@ FT                   /db_xref="PMID:29914874"
 FT                   /systematic_id="SPNCRNA.2902"
 FT                   /product="non-coding RNA"
 FT   CDS             2018369..2019349
-FT                   /colour=7
+FT                   /colour=2
 FT                   /product="mitochondrial carrier, coenzyme A, Leu5"
 FT                   /systematic_id="SPAC17H9.08"
 FT                   /db_xref="SPD:14/14B03"
@@ -64016,7 +64017,7 @@ FT                   /feature_source="evidence=ECO:0000309; source=SO:0001238;
 FT                   condition=FYECO:0000126; during=GO:0072690; score=18.2287;
 FT                   db_xref=PMID:30566651"
 FT   CDS             join(4001886..4002860,4002964..4003416,4003467..4003514)
-FT                   /colour=7
+FT                   /colour=10
 FT                   /product="alpha-amylase homolog (predicted)"
 FT                   /systematic_id="SPAC27E2.01"
 FT                   /db_xref="SPD:26/26A07"
@@ -87905,7 +87906,7 @@ FT                   condition=FYECO:0000126; during=GO:0072690; score=4.63058;
 FT                   db_xref=PMID:30566651"
 FT   CDS             5464248..5465060
 FT                   /colour=7
-FT                   /product="serine acetyltransferase (predicted)"
+FT                   /product="serine O-acetyltransferase"
 FT                   /db_xref="KEGG:MAP00272"
 FT                   /db_xref="KEGG:MAP00920"
 FT                   /db_xref="SPD:22/22A09"

diff --git a/data/chromosome2.contig b/data/chromosome2.contig
@@ -6,7 +6,8 @@ FH   Key             Location/Qualifiers
 FH
 FT   CDS             complement(304..693)
 FT                   /systematic_id="SPBC1348.15"
-FT                   /product="Schizosaccharomyces pombe specific protein"
+FT                   /product="Schizosaccharomyces pombe specific protein,
+FT                   ubiquitin related"
 FT                   /controlled_curation="term=genome organization, telomeric
 FT                   duplication; date=20110311"
 FT                   /controlled_curation="term=warning, new gene;
@@ -5825,7 +5826,7 @@ FT   CDS             complement(411120..412634)
 FT                   /EC_number="2.3.1.-"
 FT                   /colour=2
 FT                   /primary_name="cys2"
-FT                   /product="homoserine O-acetyltransferase (predicted)"
+FT                   /product="serine O-acetyltransferase"
 FT                   /db_xref="SPD:44/44H01"
 FT                   /systematic_id="SPBC106.17c"
 FT                   /controlled_curation="term=abhydrolase family;
@@ -6776,7 +6777,7 @@ FT                   PMID:18641648, transcription start or end may not be
 FT                   exact"
 FT   CDS             complement(join(468134..468198,468260..468418,468514..468609,468799..468829))
 FT                   /colour=2
-FT                   /product="peptidyl-prolyl cis-trans isomerase E"
+FT                   /product="splicing factor, RNA binding"
 FT                   /db_xref="SPD:08/08B06"
 FT                   /systematic_id="SPBC428.12c"
 FT                   /controlled_curation="term=rrm RNA recognition motif;
@@ -6795,10 +6796,8 @@ 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,
-FT                   predominantly single copy (one to one); date=20180324"
-FT                   /controlled_curation="term=human PPIE ortholog;
-FT                   db_xref=InterPro:IPR034168; date=20180324"
+FT                   /controlled_curation="term=human PABPC1L2A and PABPC1L2B
+FT                   and SRSF7 ortholog; date=20240716"
 FT   5'UTR           complement(468830..468924)
 FT                   /systematic_id="SPBC428.12c"
 FT                   /db_xref="PMID:30566651"
@@ -55939,7 +55938,7 @@ FT                   /systematic_id="SPBC2G2.03c"
 FT   CDS             complement(join(3441122..3441221,3441272..3441403,3441468..3441529,3441580..3441594))
 FT                   /colour=7
 FT                   /primary_name="sbh1"
-FT                   /product="translocon beta subunit Sbh1 (predicted)"
+FT                   /product="translocon beta subunit, GEF Sbh1"
 FT                   /db_xref="SPD:04/04D01"
 FT                   /systematic_id="SPBC2G2.03c"
 FT                   /controlled_curation="term=orthologous to S. cerevisiae
@@ -70894,8 +70893,8 @@ FT                   /db_xref="EMBL:AU013992"
 FT                   /systematic_id="SPBC1539.03c"
 FT   CDS             complement(4365385..4366767)
 FT                   /EC_number="4.3.2.1"
-FT                   /colour=7
-FT                   /product="argininosuccinate lyase (predicted)"
+FT                   /colour=2
+FT                   /product="argininosuccinate lyase"
 FT                   /db_xref="SPD:32/32H10"
 FT                   /systematic_id="SPBC1539.03c"
 FT                   /controlled_curation="term=orthologous to S. cerevisiae

diff --git a/data/chromosome3.contig b/data/chromosome3.contig
@@ -18593,8 +18593,10 @@ FT                   /product="non-coding RNA"
 FT                   /obsolete_name="SPCC23B6.02c-antisense-1"
 FT   CDS             complement(join(1268158..1268172,1268244..1268564))
 FT                   /colour=7
-FT                   /product="ribosome large subunit export factor"
+FT                   /product="ribosome large subunit export factor, Alb1
+FT                   family, Ecm1"
 FT                   /db_xref="SPD:42/42B10"
+FT                   /primary_name="ecm1"
 FT                   /systematic_id="SPCC23B6.02c"
 FT                   /controlled_curation="term=misc functional group,
 FT                   nucleocytoplasmic shuttling protein; qualifier=predicted;
@@ -20572,7 +20574,7 @@ FT                   /controlled_curation="term=species distribution,
 FT                   Schizosaccharomyces pombe specific; db_xref=PMID:24929437;
 FT                   date=20160317"
 FT                   /note="low complexity gene-free region"
-FT                   /product="Schizosaccharomyces specific protein"
+FT                   /product="Schizosaccharomyces pombe specific protein"
 FT                   /db_xref="SPD:02/02E12"
 FT                   /systematic_id="SPCC622.06c"
 FT   5'UTR           complement(1409185..1409330)

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-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-7	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-94	nhe1-REL6	EIEKSIYE390QSSGNSHIKE	amino_acid_mutation			amino_acid_insertion_and_mutation	type_error			EIEKSIYE390QSSGNSHIKE	amino_acid_insertion_and_mutation:multiple_aa	PMID:30996236
+SPAC18G6.02c	SPAC18G6.02c:allele-23	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-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-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-106	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-11	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-26	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-15	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-57	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-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	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
+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	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-1	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