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manual fixes related to #76
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@manulera
manulera committed Jul 31, 2023
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Showing 2 changed files with 27 additions and 5 deletions.
26 changes: 26 additions & 0 deletions manual_fixes_pombase/description_in_db_doesnt_match.tsv
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systematic_id allele_name allele_description allele_type reference change_description_to change_name_to change_type_to comment_on_change add_synonym add_comment
SPAC23C4.19 spt5-(T1A)7 T1A mutations within the CTR amino_acid_mutation PMID:32496538 CTD-T1A spt5-CTD-T1A
SPBC28F2.12 rpb1-CTD-S7A(5-29) CTD-S7A(5-29) amino_acid_mutation PMID:22771993,PMID:29414789,PMID:30652128 CTD-S7A(r5-r29) rpb1-CTD-S7A(r5-r29)
SPBC28F2.12 rpb1-CTD-T4A(5-29) CTD-T4A(5,29) amino_acid_mutation PMID:29414789,PMID:30282034 CTD-T4A(r5-r29) rpb1-CTD-T4A(r5-r29)
SPAC23C4.19 spt5-CTD-T1A (CTD)T1A amino_acid_mutation PMID:30282034 CTD-T1A
SPBC28F2.12 rpb1-S2A(1-29) All CTD Ser2 mutated to Ala amino_acid_mutation PMID:32282918 CTD-S2A rpb1-CTD-S2A
SPBC28F2.12 rpb1-CTD-S7A CTD-S7A(1-29) amino_acid_mutation PMID:32546512 CTD-S7A
SPBC28F2.12 rpb1-CTD-P3.P3A (CTD)P3A(alternating) amino_acid_insertion_and_mutation PMID:33579781 CTD-P3A(r2-r29-2) rpb1-CTD-P3A(r2-r29-2)
SPBC28F2.12 rpb1-CTD-P6.P6A (CTD)P6A(alternating) amino_acid_mutation PMID:33579781 CTD-P6A(r2-r29-2) rpb1-CTD-P6A(r2-r29-2)
SPBC28F2.12 rpb1-CTD-S5.S5A (CTD)S5A(alternating) amino_acid_mutation PMID:33579781 CTD-S5A(r2-r29-2) rpb1-CTD-S5A(r2-r29-2)
SPBC28F2.12 rpb1-CTD-S5.S5A -CTD-S5.S5A(alternating) amino_acid_mutation PMID:33579781 CTD-S5A(r2-r29-2) rpb1-CTD-S5A(r2-r29-2)
SPBC28F2.12 rpb1-CTD-Y1F (CTD)Y1F amino_acid_mutation PMID:33579781,PMID:33711009 CTD-Y1F
SPBC28F2.12 rpb1-CTD-S2A29 all CTD S2 residues mutated to A amino_acid_mutation PMID:33711009 rpb1-CTD-S2A rpb1-CTD-S2A
SPBC28F2.12 rpb1-CTD-S7A29 all CTD S7 residues mutated to A amino_acid_mutation PMID:33711009 rpb1-CTD-S7A rpb1-CTD-S7A
SPBC28F2.12 rpb1-CTD-T4A29 all CTD T4 residues mutated to A amino_acid_mutation PMID:33711009 rpb1-CTD-T4A rpb1-CTD-T4A
SPBC28F2.12 rpb1-CTD-Y1F29 all CTD Y1 residues mutated to F amino_acid_mutation PMID:33711009 rpb1-CTD-Y1F rpb1-CTD-Y1F
SPCC970.01 swi9-136 E659K nucleotide_mutation PMID:8114734
SPNCRNA.98 srp7-A162 A162 nucleotide_mutation PMID:8390662
SPAC644.06c nim1-Cat aa 1-354 partial_amino_acid_deletion PMID:8515818
SPAC57A10.02 cdr2-S755A-758A S755A,758A amino_acid_mutation PMID:24316795
SPAC20G4.02c Fus1deltaIDR Fus1delta(492-791) partial_amino_acid_deletion PMID:36202103
SPAC20G4.02c fus1delta(492-500) fus1delta(492-500) partial_amino_acid_deletion PMID:36202103
SPAC20G4.02c fus1delta(492-749) fus1delta(492-749) partial_amino_acid_deletion PMID:36202103
SPAC20G4.02c fus1delta(501-749) fus1delta(501-749) partial_amino_acid_deletion PMID:36202103
SPAC20G4.02c fus1delta(501-791) fus1delta(501-791) partial_amino_acid_deletion PMID:36202103
SPBC1A4.03c top2-12KR K1228,K1254,K1255,K1269,K1280,K1284,K1292,K1309,K1376,K1398,K1399,K1437 amino_acid_mutation PMID:28343969
6 changes: 1 addition & 5 deletions manual_fixes_pombase/manual_cannot_fix_new.tsv
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Expand Up @@ -73,9 +73,6 @@ SPBC1718.07c zfs1-S164A,T1645A S164A,T164A amino_acid_mutation PMID:29084823 S16
SPBC8E4.01c pho84-TATA box mutant T-33C,A-32G,T-31C,A-30G,T-29C,A-28G,T-27C,A-26G nucleotide_mutation PMID:29414789 TATATATA-(-184)-CGCGCGCG negative coords in paper refer to the 5UTR, not the transcription start
SPNCRNA.1698 nc-tgp-+5_seb1_bs G521T,T543A,A554T,C569G,C578G nucleotide_mutation PMID:32499400 T543A,G549C,A554T,A560-T,T561A,C570G,G573A,C579G,T582A nucleotide_insertion_and_mutation
SPBC26H8.07c nda3noD U1347A,U1349C nucleotide_mutation PMID:34798057 T803A,T805C Serine 196 codon to Threo
SPAPB1E7.05 gde1-E845A,D847A L1M,E845A,D847A amino_acid_mutation PMID:35012333 E846A,D848A gde1-E846A,D848A
SPAPB1E7.05 gde1-H810A,R811A L1M,H810A,R811A amino_acid_mutation PMID:35012333 H811A,R812A gde1-H811A,R812A
SPAPB1E7.05 gde1-Y21F,K25A,N139A L1M,Y21F,K25A,N139A amino_acid_mutation PMID:35012333 Y22F,K26A,N140A gde1-Y22F,K26A,N140A
SPAPB1E7.05 gde1-R501G,G502V,Y503F,L504T,H505P,L506S,A507R(1-507) 508-1134,R501G,G502V,Y503F,L504T,H505P,L506S,A507R amino_acid_deletion_and_mutation PMID:35012333 510-1136,R503G,G504V,Y505F,L506T,H507P,L508S,A509R gde1-R503G,G504V,Y505F,L506T,H507P,L508S,A509R(1-509)
SPAPB1E7.05 gde1-(met1)E845A,D847A L1M,E845A,D847A amino_acid_mutation PMID:35012333 E846A,D848A gde1-E846A,D848A
SPAPB1E7.05 gde1-(met1)H810A,R811A L1M,H810A,R811A amino_acid_mutation PMID:35012333 H811A,R812A gde1-H811A,R812A
Expand Down Expand Up @@ -145,7 +142,7 @@ SPBC725.16 res1'-D C1085G nucleotide_mutation PMID:26730850 C338G
SPBC725.16 res1'-E C1088G nucleotide_mutation PMID:26730850 C341G
SPBC354.05c sre2-MS+ G772L,N773L,Y775L 1-422,G772L,N773L,Y775L amino_acid_deletion_and_mutation PMID:27655872 1-422,G772L,N773L,Y774L sre2-MS+G772L,N773L,Y774L typo in PomBase
SPBC354.05c sre2-MS+S760L 1-422,E760L amino_acid_deletion_and_mutation PMID:27655872 1-422,S760L typo in PomBase
SPBC19C2.09 sre1-MP C-4865A, A-484T, C-483A, C-480A, A-479T, T-478A, C-528A, A-527T, G-526A, C-523A, A-522T, C-521A nucleotide_mutation PMID:28202541 CACCCCAT-(-528)-ATACCATA,CAGTCCAC-(-485)-ATATCATA
SPBC19C2.09 sre1-MP C-4865A,A-484T,C-483A,C-480A,A-479T,T-478A,C-528A,A-527T,G-526A,C-523A,A-522T,C-521A nucleotide_mutation PMID:28202541 CACCCCAT-(-528)-ATACCATA,CAGTCCAC-(-485)-ATATCATA
SPCC31H12.08c ccr4- H665A amino_acid_mutation PMID:28404620 H664A ccr4-H665A looked into the original cerevisiae paper figure (uses and old gene structure)
SPAC13A11.04c Y96C amino_acid_mutation PMID:29352077 Y95C ubp8-Y95C Error in the paper. Most likely refers to this residue, since the other referred Y residue is correct
SPCC5E4.04 cut1-L739S L379S amino_acid_mutation PMID:29735656 L739S typo in PomBase
Expand All @@ -163,7 +160,6 @@ SPBC215.05 gpd1-G4BS TTACGTCA-329CGGAAGACTCTCCTCCG nucleotide_mutation PMID:2512
SPCC757.07c ctt1-G4BS ATGACGT-435CGGAAGACTCTCCTCCG nucleotide_mutation PMID:25122751 ATGACGT-(-428)-CGGAAGACTCTCCTCCG
SPAC26F1.06 gpm1-R120,121Q R120,121Q amino_acid_mutation PMID:11106417 R120Q,R121Q
SPBC4F6.09 str1-promoter-mut-CYC1-lacZ -870AGATAA-865 ->GCCGTC nucleotide_mutation PMID:12888492 AGATAA-(-870)-GCCGTC
SPBC1734.02c cdc27-R5 1101-CATAAAGAAAAGGAGCCTCTCTTGCCAAAGGAGGAGAAGTTGTCTGAGCAAGCAAAGAGAGAGCGCGATGATCTGAAAAATATTATGCAGCTAGAAGATGAATCAGTATCTACCACTAGCGTTCACGATTCTGAAGATGATAATTTAGATTCTAATAATTTCCAATTGGAAAT nucleotide_insertion PMID:15576681,PMID:15576681 T1101-CATAAAGAAAAGGAGCCTCTCTTGCCAAAGGAGGAGAAGTTGTCTGAGCAAGCAAAGAGAGAGCGCGATGATCTGAAAAATATTATGCAGCTAGAAGATGAATCAGTATCTACCACTAGCGTTCACGATTCTGAAGATGATAATTTAGATTCTAATAATTTCCAATTGGAAAT
SPBC23E6.07c rfc1-47 676-HLGAP amino_acid_insertion PMID:16040599 K676-HLGAP
SPBC23E6.07c rfc1-50 871-VGVPH amino_acid_insertion PMID:16040599 E871-VGVPH
SPAC1D4.12 rad15-P G45D nucleotide_mutation PMID:166019,PMID:7254221,PMID:9658208 amino_acid_mutation
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