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‎data/alleles.tsv

+5,263-5,261
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‎data/chromosome1.contig

+5-4
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@@ -22167,7 +22167,8 @@ FT /db_xref="PMID:21511999"
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FT CDS complement(join(1412062..1412214,1412262..1412792,1412836..1413237,1413276..1413410,1413449..1415062))
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FT /colour=7
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FT /primary_name="fft1"
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FT /product="SMARCAD1 family ATPase Fft1 (predicted)"
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FT /product="histone chaperone/ATP-dependent chromatin
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FT remodeller, SMARCAD1 family Fft1 (predicted)"
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FT /systematic_id="SPAC20G8.08c"
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FT /db_xref="SPD:47/47F12"
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FT /controlled_curation="term=DEAD/DEAH box helicase;
@@ -33520,7 +33521,8 @@ FT /systematic_id="SPAC25A8.01c"
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FT /db_xref="PMID:21511999"
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FT CDS complement(2098281..2101049)
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FT /colour=2
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FT /product="SMARCAD1 family ATPase Fft3"
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FT /product="histone chaperone/ATP-dependent chromatin
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FT remodeller, SMARCAD1 family Fft3"
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FT /primary_name="fft3"
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FT /synonym="snf2SR"
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FT /systematic_id="SPAC25A8.01c"
@@ -37723,8 +37725,7 @@ FT /db_xref="PMID:21511999"
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FT CDS complement(2346432..2347031)
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FT /colour=2
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FT /synonym="dpb3"
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FT /product=" transcription regulator complex subunit Bur6
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FT (predicted)"
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FT /product="negative cofactor 2 complex subunit Bur6"
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FT /systematic_id="SPAC17G8.03c"
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FT /db_xref="SPD:06/06F04"
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FT /controlled_curation="term=histone fold;

‎data/chromosome2.contig

+5-4
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@@ -39601,8 +39601,8 @@ FT score=218.846000; db_xref=PMID:30566651"
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FT CDS join(2452052..2452181,2452319..2456757)
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FT /colour=2
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FT /primary_name="pst1"
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FT /product="Clr6 and Rpd3L histone deacetylase complex
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FT subunit Pst1"
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FT /product="Clr6 I prime and Rpd3L histone deacetylase
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FT complex subunit Pst1"
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FT /synonym="SPBC21D10.01c"
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FT /db_xref="SPD:48/48G08"
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FT /systematic_id="SPBC12C2.10c"
@@ -50441,7 +50441,7 @@ FT /db_xref="EMBL:AU009008"
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FT /systematic_id="SPBC30D10.02"
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FT CDS complement(join(3093811..3094253,3094293..3094335))
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FT /colour=7
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FT /product="transcription regulator Ncb2 (predicted)"
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FT /product="negative cofactor 2 complex subunit Ncb2"
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FT /primary_name="ncb2"
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FT /db_xref="SPD:34/34D11"
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FT /systematic_id="SPBC30D10.02"
@@ -60986,7 +60986,8 @@ FT /product="non-coding RNA"
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FT CDS complement(3738975..3740933)
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FT /colour=2
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FT /primary_name="ash2"
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FT /product="Ash2-trithorax family protein"
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FT /product="Set1C complex and Lid2 complex subunit
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FT Ash2-trithorax family"
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FT /db_xref="SPD:27/27A10"
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FT /systematic_id="SPBC13G1.08c"
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FT /controlled_curation="term=zinc finger protein;

‎data/chromosome3.contig

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@@ -2529,7 +2529,8 @@ FT /systematic_id="SPCC1235.05c"
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FT CDS complement(183023..186877)
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FT /colour=7
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FT /primary_name="fft2"
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FT /product="SMARCAD1 family ATPase Fft2 (predicted)"
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FT /product="histone chaperone/ATP-dependent chromatin
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FT remodeller SMARCAD1 family Fft2 (predicted)"
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FT /db_xref="SPD:39/39D02"
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FT /systematic_id="SPCC1235.05c"
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FT /controlled_curation="term=DEAD/DEAH box helicase;
@@ -28668,7 +28669,8 @@ FT /db_xref="PMID:21511999"
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FT CDS complement(join(1976023..1976263,1976348..1976436))
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FT /colour=2
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FT /primary_name="sdc1"
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FT /product="Lid2 complex Dpy-30 domain subunit Sdc1"
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FT /product="Set1C complex and Lid2 complex subunit, Dpy-30
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FT domain Sdc1"
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FT /db_xref="SPD:03/03C06"
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FT /systematic_id="SPCC18.11c"
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FT /controlled_curation="term=orthologous to S. cerevisiae

‎data/genome.pickle

181 Bytes
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‎results/allele_auto_fix.tsv

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Original file line numberDiff line numberDiff line change
@@ -1,13 +1,13 @@
11
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
2-
SPAC140.02 SPAC140.02:allele-8 gar2::ura4+ gar2::ura4+ disruption gar2::ura4 syntax_error gar2::ura4+ disruption:usual PMID:7596817,PMID:9211982
3-
SPAC18G6.02c SPAC18G6.02c:allele-26 chp1-alpha-mut1 KKRKK71NEHG amino_acid_mutation amino_acid_deletion_and_mutation type_error KKRKK71NEHG amino_acid_deletion_and_mutation:multiple_aa PMID:22727667
4-
SPAC23C4.19 SPAC23C4.19:allele-18 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
5-
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
6-
SPAC977.10 SPAC977.10:allele-105 nhe1-REL6 EIEKSIYE390QSSGNSHIKE amino_acid_mutation amino_acid_insertion_and_mutation type_error EIEKSIYE390QSSGNSHIKE amino_acid_insertion_and_mutation:multiple_aa PMID:30996236
2+
SPAC140.02 SPAC140.02:allele-3 gar2::ura4+ gar2::ura4+ disruption gar2::ura4 syntax_error gar2::ura4+ disruption:usual PMID:7596817,PMID:9211982
3+
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
4+
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
5+
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
6+
SPAC977.10 SPAC977.10:allele-112 nhe1-REL6 EIEKSIYE390QSSGNSHIKE amino_acid_mutation amino_acid_insertion_and_mutation type_error EIEKSIYE390QSSGNSHIKE amino_acid_insertion_and_mutation:multiple_aa PMID:30996236
77
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
8-
SPBC28F2.12 SPBC28F2.12:allele-50 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
9-
SPBC28F2.12 SPBC28F2.12:allele-60 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
8+
SPBC28F2.12 SPBC28F2.12:allele-58 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
9+
SPBC28F2.12 SPBC28F2.12:allele-15 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
1010
SPBC3H7.13 SPBC3H7.13:allele-2 csc1::ura4+ csc1::ura4+ disruption csc1::ura4 syntax_error csc1::ura4+ disruption:usual PMID:23874188
11-
SPBC428.08c SPBC428.08c:allele-28 clr4-alpha-mut KRRKR58NEHG amino_acid_mutation amino_acid_deletion_and_mutation type_error KRRKR58NEHG amino_acid_deletion_and_mutation:multiple_aa PMID:22727667
12-
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
11+
SPBC428.08c SPBC428.08c:allele-26 clr4-alpha-mut KRRKR58NEHG amino_acid_mutation amino_acid_deletion_and_mutation type_error KRRKR58NEHG amino_acid_deletion_and_mutation:multiple_aa PMID:22727667
12+
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
1313
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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