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Change get_data.sh to use latest contig files
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@kimrutherford
kimrutherford committed Oct 25, 2023
1 parent ac4f23a commit 4ec936e
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Showing 6 changed files with 2,926 additions and 2,875 deletions.
169 changes: 94 additions & 75 deletions data/chromosome1.contig
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165 changes: 98 additions & 67 deletions data/chromosome2.contig
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68 changes: 35 additions & 33 deletions data/chromosome3.contig
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Original file line number Diff line number Diff line change
Expand Up @@ -3517,7 +3517,7 @@ FT /systematic_id="SPTF.8"
FT /primary_name="Tf-fragment4"
FT CDS complement(256363..256950)
FT /systematic_id="SPCC794.16"
FT /product="Scizosaccharomyces pombe specific protein"
FT /product="Schizosaccharomyces pombe specific protein"
FT /controlled_curation="term=warning, new gene;
FT date=20230109"
FT /colour=8
Expand Down Expand Up @@ -6981,8 +6981,8 @@ FT condition=FYECO:0000126; during=GO:0072690;
FT score=9.820990; db_xref=PMID:30566651"
FT CDS join(479727..479778,479836..479946,480013..481751)
FT /colour=7
FT /product="CASP family protein involved in Golgi vesicle
FT transport Coy1 (predicted)"
FT /product="CASP family protein, Golgi vesicle transport
FT factor Coy1"
FT /db_xref="SPD:46/46C10"
FT /systematic_id="SPCC364.04c"
FT /controlled_curation="term=orthologous to S. cerevisiae
Expand Down Expand Up @@ -9600,7 +9600,8 @@ FT /systematic_id="SPNCRNA.6959"
FT /product="non-coding RNA"
FT CDS complement(join(651622..651905,651973..652045,652115..652225,652280..652371,652419..652455))
FT /colour=10
FT /product="human leukocyte receptor 1 ortholog"
FT /product="human leukocyte receptor 1 ortholog, implicated
FT in mRNA splicing"
FT /db_xref="SPD:02/02F05"
FT /systematic_id="SPCC5E4.10c"
FT /controlled_curation="term=species distribution, conserved
Expand Down Expand Up @@ -10933,7 +10934,8 @@ FT PMID:18641648, transcription start or end may not be
FT exact"
FT CDS complement(737520..737870)
FT /colour=2
FT /product="telomerase holoenzyme complex subunit Thc1"
FT /product="RRM RNA binding protein involved in snRNA
FT processing Thc1"
FT /db_xref="SPD:02/02C04"
FT /systematic_id="SPCC18B5.09c"
FT /controlled_curation="term=warning, previously annotated
Expand Down Expand Up @@ -11452,8 +11454,7 @@ FT /systematic_id="SPNCRNA.7013"
FT /product="non-coding RNA"
FT CDS complement(767986..770052)
FT /colour=7
FT /product="wybutosine biosynthesis protein Tyw1
FT (predicted)"
FT /product="tRNA wybutosine biosynthesis protein Tyw1"
FT /db_xref="SPD:27/27F11"
FT /systematic_id="SPCC1020.08"
FT /controlled_curation="term=orthologous to S. cerevisiae
Expand Down Expand Up @@ -12354,7 +12355,8 @@ FT /systematic_id="SPCC2H8.05c"
FT /db_xref="PMID:21511999"
FT CDS complement(832347..833000)
FT /colour=12
FT /product="double strand break localizing Dbl1"
FT /product="double strand break localizing Dbl1, implicated
FT in DNA repair"
FT /synonym="SPCC63.01c"
FT /db_xref="SPD:06/06D01"
FT /systematic_id="SPCC2H8.05c"
Expand Down Expand Up @@ -13809,9 +13811,9 @@ FT /db_xref="PMID:29914874"
FT /systematic_id="SPNCRNA.7106"
FT /product="non-coding RNA"
FT CDS complement(918772..919839)
FT /colour=7
FT /product="mitochondrial outer membrane ATPase Msp1/Yta4
FT (predicted)"
FT /colour=2
FT /product="mitochondrial outer membrane dislocase
FT Msp1/Yta4"
FT /db_xref="SPD:16/16D08"
FT /systematic_id="SPCC24B10.10c"
FT /controlled_curation="term=AAA family ATPase;
Expand Down Expand Up @@ -14818,8 +14820,8 @@ FT condition=FYECO:0000126; during=GO:0072690;
FT score=7.316200; db_xref=PMID:30566651"
FT CDS join(981120..981128,981211..981491,981549..984243)
FT /colour=2
FT /product="NuA4 histone acetyltransferase complex subunit
FT Vid21"
FT /product="NuA4 histone acetyltransferase complex scaffold
FT subunit Vid21/Eaf1"
FT /db_xref="SPD:47/47H07"
FT /primary_name="vid21"
FT /systematic_id="SPCC1795.08c"
Expand Down Expand Up @@ -15609,8 +15611,8 @@ FT 3'UTR complement(1030996..1031433)
FT /systematic_id="SPCC825.05c"
FT /db_xref="PMID:21511999"
FT CDS complement(join(1031434..1031901,1031940..1032269,1032329..1032418,1032472..1032489))
FT /colour=7
FT /product="splicing coactivator Srm160 (predicted)"
FT /colour=2
FT /product="splicing coactivator Pwi1"
FT /db_xref="SPD:16/16B08"
FT /systematic_id="SPCC825.05c"
FT /controlled_curation="term=species distribution, no
Expand Down Expand Up @@ -21121,7 +21123,8 @@ FT /product="non-coding RNA"
FT /obsolete_name="tti1-antisense-1"
FT CDS complement(1422550..1425846)
FT /colour=2
FT /product="ASTRA complex subunit, armadillo-type fold Tti1"
FT /product="TTT co-chaperone complex, armadillo-type fold
FT subunit Tti1"
FT /db_xref="SPD:48/48B09"
FT /primary_name="tti1"
FT /systematic_id="SPCC622.13c"
Expand Down Expand Up @@ -21878,10 +21881,6 @@ FT date=19700101"
FT /controlled_curation="term=species distribution, conserved
FT in eukaryotes; date=20081110"
FT /controlled_curation="term=species distribution, conserved
FT in metazoa; date=20081110"
FT /controlled_curation="term=species distribution, conserved
FT in vertebrates; date=20081110"
FT /controlled_curation="term=species distribution, conserved
FT in fungi; date=20081110"
FT /controlled_curation="term=species distribution, conserved
FT in eukaryotes only; date=20081110"
Expand Down Expand Up @@ -23704,7 +23703,8 @@ FT /colour=10
FT /note="region appears to be a duplication of a region of
FT chromosome I cosmid c11D3, region encompasses SPCC777.02 &
FT SPC777.03"
FT /product="nifs homolog, possible cysteine desulfurase"
FT /product="nifs homolog, possible cysteine desulfurase,
FT implicated in iron-sulfur cluster assembly"
FT /db_xref="SPD:44/44A03"
FT /systematic_id="SPCC777.03c"
FT /controlled_curation="term=similar to S. pombe
Expand Down Expand Up @@ -24537,8 +24537,7 @@ FT condition=FYECO:0000126; during=GO:0072690;
FT score=131.636000; db_xref=PMID:30566651"
FT CDS 1651272..1652780
FT /colour=7
FT /product="tRNA(Ser) Um(44) 2'-O-methyltransferasetRNA
FT Trm44 (predicted)"
FT /product="tRNA(Ser) Um(44) 2'-O-methyltransferase Trm44"
FT /db_xref="SPD:40/40E12"
FT /systematic_id="SPCC663.10"
FT /controlled_curation="term=orthologous to S. cerevisiae
Expand Down Expand Up @@ -27368,7 +27367,7 @@ FT score=21.943200; db_xref=PMID:30566651"
FT CDS join(1834613..1834709,1834755..1834952,1835011..1836914)
FT /colour=7
FT /product="ubiquitin-protein ligase E3 involved in rescue
FT of stalled ribosomes (predicted)"
FT of stalled ribosomes Hel2"
FT /synonym="SPCC285.18"
FT /db_xref="SPD:46/46G09"
FT /systematic_id="SPCC1223.01"
Expand Down Expand Up @@ -27396,6 +27395,7 @@ FT /controlled_curation="term=species distribution, conserved
FT in eukaryotes only; date=20081110"
FT /controlled_curation="term=species distribution,
FT predominantly single copy (one to one); date=20081110"
FT /primary_name="hel2"
FT 3'UTR 1836915..1837464
FT /systematic_id="SPCC1223.01"
FT /db_xref="PMID:21511999"
Expand Down Expand Up @@ -29837,11 +29837,11 @@ FT 3'UTR complement(2014584..2014832)
FT /systematic_id="SPCC1906.02c"
FT /db_xref="PMID:21511999"
FT CDS complement(2014833..2016578)
FT /colour=10
FT /product="CUE domain protein Cue3, human ASCC2 ortholog,
FT activating signal cointegrator 1 complex (predicted)"
FT /colour=7
FT /product="RQT complex CUE domain protein, human ASCC2
FT ortholog Rqt3"
FT /db_xref="SPD:36/36A02"
FT /primary_name="cue3"
FT /synonym="cue3"
FT /systematic_id="SPCC1906.02c"
FT /controlled_curation="term=modification, phosphorylated;
FT db_xref=PMID:19547744; evidence=IDA; cv=pt_mod;
Expand All @@ -29864,6 +29864,7 @@ FT /controlled_curation="term=human ASCC2 ortholog;
FT date=20141220"
FT /controlled_curation="term=species distribution, conserved
FT in eukaryotes only; date=20141220"
FT /primary_name="rqt3"
FT lncRNA 2016082..2016332
FT /db_xref="PMID:29914874"
FT /systematic_id="SPNCRNA.7587"
Expand Down Expand Up @@ -31389,7 +31390,7 @@ FT /db_xref="PMID:21511999"
FT CDS complement(join(2117287..2117397,2117451..2117660,2117706..2118895,2118970..2119066,2119138..2119320,2119386..2119418))
FT /colour=2
FT /primary_name="pku70"
FT /product="Ku domain helicase (human XRCC6 ortholog) Pku70"
FT /product="Ku70 (human XRCC6 ortholog) Pku70"
FT /db_xref="SPD:37/37D11"
FT /systematic_id="SPCC126.02c"
FT /controlled_curation="term=subunit composition,
Expand All @@ -31410,6 +31411,7 @@ FT /controlled_curation="term=species distribution, conserved
FT in eukaryotes only; date=20081110"
FT /controlled_curation="term=species distribution,
FT predominantly single copy (one to one); date=20081110"
FT /synonym="ku70"
FT 5'UTR complement(join(2119419..2119559,2119609..2119663))
FT /systematic_id="SPCC126.02c"
FT /db_xref="PMID:30566651"
Expand Down Expand Up @@ -31438,8 +31440,7 @@ FT /EC_number="5.4.99.-"
FT /colour=2
FT /obsolete_name="lps1"
FT /primary_name="pus1"
FT /product="TruA family tRNA/ U2 snRNA pseudouridine
FT synthase Lsp1"
FT /product="tRNA/U2 snRNA pseudouridine synthase Lsp1"
FT /db_xref="SPD:35/35E07"
FT /systematic_id="SPCC126.03"
FT /controlled_curation="term=orthologous to S. cerevisiae
Expand Down Expand Up @@ -31806,7 +31807,7 @@ FT /db_xref="EMBL:AU006812"
FT /systematic_id="SPCC126.13c"
FT CDS complement(join(2140570..2140843,2141011..2141174))
FT /colour=7
FT /product="histone deacetylase complex subunit Sap18"
FT /product=" exon junction complex subunit Sap18"
FT /db_xref="SPD:42/42D07"
FT /systematic_id="SPCC126.13c"
FT /controlled_curation="term=species distribution, no
Expand Down Expand Up @@ -32553,7 +32554,8 @@ FT /systematic_id="SPCC830.05c"
FT /db_xref="PMID:21511999"
FT CDS complement(join(2188535..2190040,2190562..2190729))
FT /colour=2
FT /product="NuA4 histone acetyltransferase complex Epl1"
FT /product="NuA4 histone acetyltransferase core
FT complex-Piccolo HAT module linker protein Epl1"
FT /db_xref="SPD:37/37H06"
FT /primary_name="epl1"
FT /systematic_id="SPCC830.05c"
Expand Down
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