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@kimrutherford @github-actions
kimrutherford authored and github-actions[bot] committed Nov 19, 2023
1 parent d8ea9a9 commit 165cb96
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Showing 12 changed files with 10,344 additions and 10,328 deletions.
9,947 changes: 4,976 additions & 4,971 deletions data/alleles.tsv
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2 changes: 1 addition & 1 deletion data/chromosome1.contig
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Expand Up @@ -37121,7 +37121,7 @@ FT /db_xref="PMID:21511999"
FT CDS complement(join(2310386..2310517,2310561..2311571,2311694..2311891))
FT /colour=2
FT /primary_name="crb3"
FT /product="Rix1 complex WD repeat subunit Crb3"
FT /product="rixosome complex WD repeat subunit Crb3"
FT /systematic_id="SPAC13G7.08c"
FT /db_xref="SPD:24/24D08"
FT /controlled_curation="term=WD repeat protein;
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18 changes: 12 additions & 6 deletions data/chromosome2.contig
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Expand Up @@ -23947,6 +23947,8 @@ FT cdc2L (cdc2 left) in PMID:16453669, name not added as
FT potentially misleading; date=20150429"
FT /controlled_curation="term=human H2AZ1 and H2AZ2 ortholog;
FT date=20191128"
FT /controlled_curation="term=name description, Pseudo
FT HisTone; date=20231115"
FT 5'UTR complement(1503062..1503444)
FT /systematic_id="SPBC11B10.10c"
FT /db_xref="PMID:30566651"
Expand Down Expand Up @@ -45998,7 +46000,7 @@ FT condition=FYECO:0000126; during=GO:0072690;
FT score=165.883000; db_xref=PMID:30566651"
FT CDS join(2840857..2840897,2840935..2840966,2841006..2841105,2841168..2841221,2841268..2842314,2842387..2842411)
FT /colour=2
FT /product="bouquet formation protein Bqt4"
FT /product="integral nuclear inner membrane protein Bqt4"
FT /primary_name="bqt4"
FT /db_xref="SPD:45/45A08"
FT /systematic_id="SPBC19C7.10"
Expand Down Expand Up @@ -46029,6 +46031,8 @@ FT annotation_extension=during(GO:0006995),
FT during(GO:0071444); qualifier=increased;
FT evidence=ECO:0000058; db_xref=PMID:19948484;
FT date=20150925"
FT /controlled_curation="term=name description, BouQueT
FT formation protein; date=20231115"
FT lncRNA complement(2841054..2841750)
FT /db_xref="PMID:29914874"
FT /systematic_id="SPNCRNA.5846"
Expand Down Expand Up @@ -55377,7 +55381,8 @@ FT /product="non-coding RNA"
FT CDS complement(join(3394350..3395222,3395281..3395310,3395356..3395700))
FT /colour=2
FT /primary_name="php5"
FT /product="CCAAT-binding factor complex subunit Php5"
FT /product="CCAAT-binding factor complex histone fold
FT subunit Php5"
FT /db_xref="SPD:40/40D11"
FT /systematic_id="SPBC3B8.02"
FT /controlled_curation="term=orthologous to S. cerevisiae
Expand Down Expand Up @@ -67866,9 +67871,9 @@ FT /feature_source="evidence=ECO:0000309; source=SO:0001238;
FT condition=FYECO:0000126; during=GO:0072690;
FT score=88.238300; db_xref=PMID:30566651"
FT CDS join(4167588..4167661,4167716..4167754,4167820..4167893,4167944..4171485)
FT /colour=7
FT /product="ER ubiquitin-protein ligase E3 Doa10
FT (predicted)"
FT /colour=2
FT /product="ER and nuclear envelope ubiquitin-protein ligase
FT E3 Doa10"
FT /db_xref="SPD:39/39D05"
FT /synonym="ssm4"
FT /primary_name="doa10"
Expand Down Expand Up @@ -70911,7 +70916,8 @@ FT /systematic_id="SPBC16C6.12c"
FT /db_xref="PMID:21511999"
FT CDS complement(4352663..4354075)
FT /colour=2
FT /product="rRNA processing protein Las1"
FT /product="rixosome complex/ Las1 complex endonuclease
FT Las1"
FT /primary_name="las1"
FT /db_xref="SPD:21/21G08"
FT /systematic_id="SPBC16C6.12c"
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10 changes: 5 additions & 5 deletions data/chromosome3.contig
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Expand Up @@ -6109,7 +6109,7 @@ FT /systematic_id="SPCC4G3.18"
FT /db_xref="PMID:21511999"
FT CDS complement(435937..438423)
FT /colour=2
FT /product="Rix1 complex armadillo-type fold Rix1"
FT /product="rixosome complex armadillo-type fold Rix1"
FT /db_xref="SPD:28/28H12"
FT /systematic_id="SPCC4G3.18"
FT /controlled_curation="term=orthologous to S. cerevisiae
Expand Down Expand Up @@ -11736,7 +11736,7 @@ FT /systematic_id="SPCC1393.05"
FT /db_xref="PMID:21511999"
FT CDS complement(join(804627..805627,805678..805800,805849..805921,805965..806009))
FT /colour=2
FT /product="Rix1 complex armadillo-type fold Ipi1"
FT /product="rixosome complex armadillo-type fold Ipi1"
FT /db_xref="SPD:21/21D08"
FT /systematic_id="SPCC1393.06c"
FT /controlled_curation="term=orthologous to S. cerevisiae
Expand Down Expand Up @@ -27844,7 +27844,7 @@ FT condition=FYECO:0000126; during=GO:0072690;
FT score=36.495300; db_xref=PMID:30566651"
FT CDS 1900504..1914657
FT /colour=2
FT /product="midasin, Mdn1"
FT /product="rixosome complex midasin subunit Mdn1"
FT /db_xref="SPD:50/50A03"
FT /systematic_id="SPCC737.08"
FT /controlled_curation="term=sequence feature, coiled-coil;
Expand Down Expand Up @@ -31916,8 +31916,8 @@ FT score=5.846520; db_xref=PMID:30566651"
FT CDS join(2183807..2183840,2183918..2186094)
FT /colour=2
FT /primary_name="grc3"
FT /product="polynucleotide 5'-hydroxyl-kinase Grc3
FT (predicted)"
FT /product="rixosome coplex/Las1 complex polynucleotide
FT 5'-hydroxyl-kinase Grc3"
FT /db_xref="SPD:28/28C02"
FT /systematic_id="SPCC830.03"
FT /controlled_curation="term=orthologous to S. cerevisiae
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16 changes: 8 additions & 8 deletions results/allele_auto_fix.tsv
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@@ -1,13 +1,13 @@
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
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
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-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-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-17 rpb1-CTD-P3A(r2-r29-2) CTD-P3A(r2-r29-2) amino_acid_insertion_and_mutation amino_acid_mutation type_error CTD-P3A(r2-r29-2) amino_acid_mutation:CTD PMID:32282918,PMID:33579781,PMID:34389684
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-6 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-119 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-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-12 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-32 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-19 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-14 clr4-alpha-mut KRRKR58NEHG amino_acid_mutation amino_acid_deletion_and_mutation type_error KRRKR58NEHG amino_acid_deletion_and_mutation:multiple_aa PMID:22727667
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-3 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
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