AntoniasCuratedPapers – PomBase SF Trac Copy

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https://sourceforge.net/apps/trac/pombase/wiki/CuratorTrainingPapers

Papers needing ODA conversions
Papers with WT info or no annotations
AntoniasDoubleMutants
AntoniasRNAmodsandmutants
https://sourceforge.net/apps/trac/pombase/wiki/CuratorTrainingPapers

2900761	Antonia
mat2-P...or mat2-Pc/Pi?	Silenced (waiting for GeneDB to update cassette info so this can be annotated)	IMP mat1-
mat3-M...or mat3-Mc/Mi?	Silenced (waiting for GeneDB to update cassette info so this can be annotated)	IMP mat1-
mat1-Mi	Phenotype: can conjugate but not undergo meiosis/sporulate	allele=Mifs15(del_nt43-129)
mat1-Pi	Phenotype: can conjugate but not undergo meiosis/sporulate	allele=Piop7(del_nt19-357)
mat1-Pc	Phenotype: can't conjugate	allele=Pcop5(del_nt17-480)
mat1-Mc	Phenotype: can't conjugate	allele=Mcop7(del_nt19-546)
mat1-Pc	severe reduction in spore formation	allele=deletion
mat1-Pc	process: required for efficient meiosis	IMP, allele=deletion
mat1-Mc	process: required for efficient meiosis	IMP, allele=deletion
mat1-Pc	expression: constitutively expressed (low levels) (rich media)	IMP, allele=SP272(h+/h- meiotically competent diploid)
mat1-Pc	expression: constitutively expressed (low levels) (rich media)	IMP, allele=SP720(fus1 deletion...capture as WT?)
mat1-Mc	expression: constitutively expressed (low levels) (rich media)	IMP, allele=SP272(h+/h- meiotically competent diploid)
mat1-Mc	expression: constitutively expressed (low levels) (rich media)	IMP, allele=SP720(fus1 deletion...capture as WT?)
mat1-Pi	expression: not expressed (rich media)	IMP, allele=SP272(h+/h- meiotically competent diploid)
mat1-Pi	expression: not expressed (rich media)	IMP, allele=SP720(fus1 deletion...capture as WT?)
mat1-Mi	expression: not expressed (rich media)	IMP, allele=SP272(h+/h- meiotically competent diploid)
mat1-Mi	expression: not expressed (rich media)	IMP, allele=SP720(fus1 deletion...capture as WT?)
All 4 are upregulated in response to nitrogen starvation. In diploid; downregulation at 6h compared to 4h, in haploid; no downregulation

2328719	Antonia
map1	transcription phenotype, target is not upregulated in response to nitrogen starvation	allele=deletion,annotation_extension=has_regulation_target(GeneDB_Spombe:mat1-PC,(strain is H90))
mat1-Pc	positive autoregulation of transcription in response to nitrogen starvation	allele=mat1-Pc-161()
map1	transcription phenotype, target is not expressed in response to nitrogen starvation	allele=deletion,annotation_extension=has_regulation_target(GeneDB_Spombe:mat1-Pm,(strain is H90))
mat1-Pc	transcription phenotype, target is not expressed in response to nitrogen starvation	allele=mat1-Pc-161(),annotation_extension=has_regulation_target(GeneDB_Spombe:mat1-Pm,(strain is H90))
mat1-Pc	low constitutive expression in rich media	allele=H90(fus1 deletion)
mat1-Pm	no constitutive expression in rich media	allele=H90(fus1 deletion)
mat1-Pm	expression in response to nitrogen starvation is dependent on the presence of CL:0002674	annotation_extension=occurs_in(CL:0002675)
mat1-Pc	upregulation in response to nitrogen starvation is not dependent on the presence of CL:0002674	annotation_extension=occurs_in(CL:0002675)
ran1	process: negative regulation of transcription from RNA polymerase II promoter during mitosis (IMP evidence code)	allele=pat1-114,annotation_extension=has_regulation_target(GeneDB_Spombe:mat1-Pm, mat1-Mc and Mat1-Pc

17452352
sequence feature	annotate AACCCT as a GATA transcription factor binding site, seq 5'-ATCA(C/A)AACCCTAACCCT-3'	do we annotate this on the genome sequence?

18077559\|Antonia
ams2 hip1	slow cell growth	allele=dbl mutant

20230746	Antonia
ams2	remove NAS and TAS from artemis
ams2	protein is unstable during G2 and M phase, partially stable during G1 and stable during S
ams2	protein stability: is stable during S phase, level increased
ams2	protein stability: is unstable during G2 phase, level decreased OR possibly only synthesised during S phase?
ams2	protein stability: is unstable during G1/M phase, level increased OR possibly only synthesised during S phase?
ams2	protein stability: is degraded by the SCF ubiquitin ligase pathway

20018864	Antonia
ncs1	promoter region lies in -1-130 region caact esp important
ncs1	promoter for upregulation in response to calcium lies in -101-130 region
ncs1	promoter for basal expression lies in -1-130 region
prz1	binds caact in promoter region of ncs1

19606215	Antonia
cnx1	some confusing data regarding apoptosis. Notes in hardcopy paper	allele=lumenal_cnx1p(aa_del488-560)
cnx1	allele specifications may not be 100% correct

1563351	Antonia
MatPi?	expressed in response to nitrogen starvation and M factor in Pcells	IDA
ste6	MatPi? not expressed during N starvation and in presence of M factor in P cells	allele=deletion
ras1	MatPi? not expressed during N starvation and in presence of M factor in P cells	allele=deletion
ras1	MatPi? expressed during N starvation and in presence of M factor in P cells, not constitutively expressed	allele=ras1val17

7975894	Antonia
promoter element	fig6&7

8314086	Antonia
sxa2	expressed in presence of p-factor
map2	expressed in H- cells

18059475	Antonia
ste11	annotate promoter proximal element FLEX1 and FLEXL1 to ste11, artemis

21960007
mag1	structure PDB ID 3S61	according to authors, does not appear to match however

1448087
pyp2	552 bp 5' UTR

11470243
fas2	increased accumulation of see below	allele=H201(I1276T),annotation_extension=condition(at_high_temperature)
fas2	increased accumulation of see below	allele=H265(Q4Y),annotation_extension=condition(at_high_temperature)
fas2	increased accumulation of see below	allele=H518(I600N),annotation_extension=condition(at_high_temperature)

fas2	decreased accumulation of see below	allele=H201(I1276T),annotation_extension=condition(at_high_temperature)
fas2	decreased accumulation of see below	allele=H265(Q4Y),annotation_extension=condition(at_high_temperature)
fas2	decreased accumulation of see below	allele=H518(I600N),annotation_extension=condition(at_high_temperature)

For the 3 mutants above:
increased accumulation of at high temp: N-monomethyldioleoyl-PE (N-monomethyl-C18:1-C18:1-PE) N,N-dimethyl-C18:1-C18:1-PE N,N-monomethyl-C18:1-C18:1-PE N,N-dimethyl-C16:1-C18:1-PE 1-melissoyl-oleolyl-sn-glycero-3-phosphoethanolamine (C30:0-C18:1-PE) 1-melissoyl-2-oleolyl-sn-glycero-3-phosphocholine (C30:0-C18:1-PC) CHEBI:16337 CHEBI:36711

decreased accumulation of at high temp: (NOT in mutant 518) 1-oleolyl-2-caproyl-sn-glycero-3-phosphocholine (C18:1-C10:0-PC) C18:0-C10:0-PC C18:0-C8:0-PC CHEBI:18303 CHEBI:17517

1448066
-	asked for a term to describe HMW complex. Link to it - GO:0090424

12905027
SPAC3H1.10	MOD requested: cadmium containing modified residue	residue=C173\|

19285552
gpa1	can probably migrate some terms to abnormal decrease in transcription/increase, see what midori says

9191271
mfm1	dbl check annotations, allele descr for phenotype annotation	has_regulation_target(PomBase:SPMTR.02))

8321236	http://oliver0.sysbiol.cam.ac.uk/pombe/curs/169dc6a662075c56/gene/1
frp1	abolished ferric iron reductase activity, not req yet	allele=G-100(W314->opal)
waiting reply from val on paper

7565608	http://oliver0.sysbiol.cam.ac.uk/pombe/curs/07cc7abfbaa6d1b0
rds1	/controlled_curation="term=gene expression, mRNA level; annotation_extension=during(cellular response to adenine starvation); qualifier=increased; evidence=ECO:0000106; db_xref=7565608; date=20120504"

1644306	http://oliver0.sysbiol.cam.ac.uk/pombe/curs/1b8ed217ce984ab5
tnr3/thi1	change FYPO terms so that extension is in term
tnr1	increased RNA level, northern evidence, need to find what this gene is...	allele=tnr1-18(unknown), annotation_extension=assayed_using(SPBC26H8.01), condition=PCO:0000014, annotation_extension=happens_during(GO:0071301)
tnr1	cellular response to vitamin b1 - which gene is this??	IMP
thi2	gene expression: expressed in response to thiamine starvation. repressed in response to thiamine....

/controlled_curation="term=gene expression, mRNA level; annotation_extension=during(GO:0036225); qualifier=increased; evidence=ECO:0000106; db_xref=1644306; date=20120509"
/controlled_curation="term=gene expression, mRNA level; annotation_extension=during(GO:0071301); qualifier=absent; evidence=ECO:0000106; db_xref=1644306; date=20120509"
/controlled_curation="term=gene expression, mRNA level; annotation_extension=in_response_to(CHEBI:16892); qualifier=increased; evidence=ECO:0000106; db_xref=1644306; date=20120509"
/controlled_curation="term=gene expression, mRNA level; annotation_extension=in_response_to(CHEBI:17957); qualifier=decreased; evidence=ECO:0000106; db_xref=1644306; date=20120509"

8675019	http://oliver0.sysbiol.cam.ac.uk/pombe/curs/4b0970d0e5484486/
tnr1	which gene is this? FYPO:0000825 northern ev	allele=tnr1-18(unknown), condition=PCO:0000014, annotation_extension=assayed_using(SPAC17A2.01)

2249257

http://oliver0.sysbiol.cam.ac.uk/pombe/curs/40213c281e540075

/controlled_curation="term=gene expression, mRNA level; annotation_extension=during(cellular response to thiamine starvation); qualifier=increased; evidence=ECO:0000106; db_xref=2249257; date=20120510"

2878925	http://curation.pombase.org/pombe/curs/462720c354cd7b67/
pma mutant	normal ATPase activity	unknown, in vitro
pma mutant	Normal enzyme in vitro response to Dio-9	unknown, in vitro
pma mutant	Normal enzyme in vitro response to DCCD N,N'-dicyclohexylcarbodiimide	unknown, in vitro
pma mutant	Normal enzyme in vitro response to Miconazole	unknown, in vitro
pma mutant	Normal enzyme in vitro response to DES diethylstilbestrol	unknown, in vitro
pma mutant	Normal enzyme in vitro response to Suloctidil	unknown, in vitro
pma mutant	Normal enzyme in vitro response to p-hydroxymercuribenzoate	unknown, in vitro
pma mutant	Normal enzyme in vitro response to protamine sulfate	unknown, in vitro
pma mutant	Normal enzyme in vitro response to decamethylene diguanidine	unknown, in vitro
pma mutant	decreased cellular pH CGA - should this be decreased medium pH?	YE liquid

7898433	http://curation.pombase.org/pombe/curs/5964257cca6cfa69
uvi15	gene expression, change in response to L-canavanine to during the above once the term is in	artemis

10867006

ste11 promoter

8227198
cyr1	decreased cellular cAMP level following glucose stimulus	substrate quantification, glucose/glycerol + glucose added allele=git2-7
cyr1	decreased cellular cAMP level following glucose stimulus	substrate quantification, glucose/glycerol + glucose added, allele=git2-61
cgs2	increased cellular cAMP level following glucose stimulus	substrate quantification, glucose/glycerol + glucose added, allele=cgs2-2
cyr1	normal cellular cAMP level during glucose starvation	substrate quantification, allele=git2-7
cyr1	normal cellular cAMP level during glucose starvation	substrate quantification, allele=git2-61
gpa2	decreased cellular cAMP level during glucose starvation	substrate quantification, allele=git8-60
gpa2	decreased cellular cAMP level following glucose stimulus	substrate quantification, glucose/glycerol + glucose added, allele=git8-60
hsp90	decreased cellular cAMP level following glucose stimulus	substrate quantification, glucose/glycerol + glucose added, allele=git10-201
git1	decreased cellular cAMP level following glucose stimulus	substrate quantification, glucose/glycerol + glucose added, allele=git1-1
git3	decreased cellular cAMP level following glucose stimulus	substrate quantification, glucose/glycerol + glucose added, allele=git3-200
git5	decreased cellular cAMP level following glucose stimulus	substrate quantification, glucose/glycerol + glucose added, allele=git5-75
git7	decreased cellular cAMP level following glucose stimulus	substrate quantification, glucose/glycerol + glucose added, allele=git7-235
git5	increased cellular cAMP level during glucose starvation	substrate quantification, glucose/glycerol, allele=git5-75
pka1	increased cellular cAMP level during glucose starvation	substrate quantification, glucose/glycerol, allele=git6-261

8736869	http://curation.pombase.org/pombe/curs/14f96251db4cbe9b
krp1	decreased or abolished for R102A, same substrate for both annotations? otherwise add in a xenobiotic condition

9418887	http://oliver0.sysbiol.cam.ac.uk/pombe/curs/b6bfec3d1b81e412
krp1	normal protein processing	can I add a assayed_using?

12557275	http://curation.pombase.org/pombe/curs/9569cc1253e3417a
vht1	change IGI annotations to transmembrane transport and transport into cell
vht1	dethiobiotin binding	IGI to cerevisiae

vht1	dethiobiotin import into cell	IMP
vht1	biotin import into cell	IMP
spac1b3.15c	biotin transmembrane transport	NOT, IGI to cerevisiae
spac1b3.15c	dethiobiotin transmembrane transport	NOT, IGI to cerevisiae
REQUEST CELLULAR RESPONSE TO BIOTIN STARVATION

/controlled_curation="term=gene expression, RNA level; annotation_extension=during(cellular response to biotin starvation); qualifier=increased; evidence=ECO:0000106; db_xref=PMID:12557275; date=20121107" /controlled_curation="term=gene expression, RNA level; annotation_extension=during(GO:0072690); qualifier=present; evidence=ECO:0000106; db_xref=PMID:12557275; date=20121107"

mpr1	e6d7e22d7df32487

from M - nothing wrong in this one, but I think if GO makes the name/synonym changes in SF 3584253, the MF annotations could change to GO:0000155 (now 'two-component sensor activity'; I suggested 'phosphorelay sensor kinase activity') https://sourceforge.net/tracker/?func=detail&aid=3584253&group_id=36855&atid=440764

8346915	http://curation.pombase.org/pombe/curs/8699a16a5d40e84b
ade2	search inbox for no need to add substrates if they are implicit in the reaction

10735857	http://curation.pombase.org/pombe/curs/495144e748000da3
ght3	gluconate import (change existing term)	IMP

GHT6 /controlled_curation="term=gene expression, RNA level; annotation_extension=during(GO:0071333); qualifier=present; evidence=ECO:0000106; db_xref=PMID:10735857; date=20121127" /controlled_curation="term=gene expression, RNA level; annotation_extension=during(GO:0009267); qualifier=decreased; evidence=ECO:0000106; db_xref=PMID:10735857; date=20121127" /controlled_curation="term=gene expression, RNA level; annotation_extension=during(GO:0071328); qualifier=decreased; evidence=ECO:0000106; db_xref=PMID:10735857; date=20121127" /controlled_curation="term=gene expression, RNA level; annotation_extension=during(cellular response to D-gluconate); qualifier=present; evidence=ECO:0000106; db_xref=PMID:10735857; date=20121127" /controlled_curation="term=gene expression, RNA level; annotation_extension=during(cellular response to glycerol); qualifier=present; evidence=ECO:0000106; db_xref=PMID:10735857; date=20121127"

GHT5 /controlled_curation="term=gene expression, RNA level; annotation_extension=during(GO:0071333); qualifier=present; evidence=ECO:0000106; db_xref=PMID:10735857; date=20121127" /controlled_curation="term=gene expression, RNA level; annotation_extension=during(GO:0009267); qualifier=present; evidence=ECO:0000106; db_xref=PMID:10735857; date=20121127" /controlled_curation="term=gene expression, RNA level; annotation_extension=during(GO:0071328); qualifier=present; evidence=ECO:0000106; db_xref=PMID:10735857; date=20121127" /controlled_curation="term=gene expression, RNA level; annotation_extension=during(cellular response to D-gluconate); qualifier=present; evidence=ECO:0000106; db_xref=PMID:10735857; date=20121127" /controlled_curation="term=gene expression, RNA level; annotation_extension=during(cellular response to glycerol); qualifier=present; evidence=ECO:0000106; db_xref=PMID:10735857; date=20121127"

GHT2 /controlled_curation="term=gene expression, RNA level; annotation_extension=during(GO:0071333); qualifier=present; evidence=ECO:0000106; db_xref=PMID:10735857; date=20121127" /controlled_curation="term=gene expression, RNA level; annotation_extension=during(GO:0009267); qualifier=present; evidence=ECO:0000106; db_xref=PMID:10735857; date=20121127" /controlled_curation="term=gene expression, RNA level; annotation_extension=during(GO:0071328); qualifier=present; evidence=ECO:0000106; db_xref=PMID:10735857; date=20121127" /controlled_curation="term=gene expression, RNA level; annotation_extension=during(cellular response to D-gluconate); qualifier=present; evidence=ECO:0000106; db_xref=PMID:10735857; date=20121127" /controlled_curation="term=gene expression, RNA level; annotation_extension=during(cellular response to glycerol); qualifier=decreased; evidence=ECO:0000106; db_xref=PMID:10735857; date=20121127"

GHT1 /controlled_curation="term=gene expression, RNA level; annotation_extension=during(GO:0071333); qualifier=absent; evidence=ECO:0000106; db_xref=PMID:10735857; date=20121127" /controlled_curation="term=gene expression, RNA level; annotation_extension=during(GO:0009267); qualifier=present; evidence=ECO:0000106; db_xref=PMID:10735857; date=20121127" /controlled_curation="term=gene expression, RNA level; annotation_extension=during(GO:0071328); qualifier=present; evidence=ECO:0000106; db_xref=PMID:10735857; date=20121127" /controlled_curation="term=gene expression, RNA level; annotation_extension=during(cellular response to D-gluconate); qualifier=increased; evidence=ECO:0000106; db_xref=PMID:10735857; date=20121127" /controlled_curation="term=gene expression, RNA level; annotation_extension=during(cellular response to glycerol); qualifier=present; evidence=ECO:0000106; db_xref=PMID:10735857; date=20121127"

GHT3 /controlled_curation="term=gene expression, RNA level; annotation_extension=during(GO:0071333); qualifier=present; evidence=ECO:0000106; db_xref=PMID:10735857; date=20121127" /controlled_curation="term=gene expression, RNA level; annotation_extension=during(GO:0009267); qualifier=increased; evidence=ECO:0000106; db_xref=PMID:10735857; date=20121127" /controlled_curation="term=gene expression, RNA level; annotation_extension=during(GO:0071328); qualifier=present; evidence=ECO:0000106; db_xref=PMID:10735857; date=20121127" /controlled_curation="term=gene expression, RNA level; annotation_extension=during(cellular response to D-gluconate); qualifier=increased; evidence=ECO:0000106; db_xref=PMID:10735857; date=20121127" /controlled_curation="term=gene expression, RNA level; annotation_extension=during(cellular response to glycerol); qualifier=increased; evidence=ECO:0000106; db_xref=PMID:10735857; date=20121127"

GHT4 /controlled_curation="term=gene expression, RNA level; annotation_extension=during(GO:0071333); qualifier=present; evidence=ECO:0000106; db_xref=PMID:10735857; date=20121127" /controlled_curation="term=gene expression, RNA level; annotation_extension=during(GO:0009267); qualifier=increased; evidence=ECO:0000106; db_xref=PMID:10735857; date=20121127" /controlled_curation="term=gene expression, RNA level; annotation_extension=during(GO:0071328); qualifier=present; evidence=ECO:0000106; db_xref=PMID:10735857; date=20121127" /controlled_curation="term=gene expression, RNA level; annotation_extension=during(cellular response to D-gluconate); qualifier=increased; evidence=ECO:0000106; db_xref=PMID:10735857; date=20121127" /controlled_curation="term=gene expression, RNA level; annotation_extension=during(cellular response to glycerol); qualifier=increased; evidence=ECO:0000106; db_xref=PMID:10735857; date=20121127"=

9135083

http://curation.pombase.org/pombe/curs/6ff4c9edff12167b

http://curation.pombase.org/pombe/curs/42b53662d27d7951
cuf1	change nuclear protein accumulation to nuclear protein accumulation in response to copper

11729194	http://curation.pombase.org/pombe/curs/0e75134c69a78468
pnk1	nucleotide dephosphorylation involved in DNA repair	IMP

12056900	http://curation.pombase.org/pombe/curs/d23920dd53aeb0c5
pnk1	nucleotide dephosphorylation involved in DNA repair	IDA

11349150	http://curation.pombase.org/pombe/curs/0afc32dc747285ae
pot1	viable vegetative cells with circular(ized) chromosomes	deletion, gel
pot1	G-rich strand telomeric DNA binding	IDA

22978652	http://curation.pombase.org/pombe/curs/0afc32dc747285ae
pot1	G-rich strand telomeric DNA binding	IDA, inhibited_by(CHEBI:34653)

8065367	http://curation.pombase.org/pombe/curs/0b84151023ead28b
cut8	viable vegetative cell population should go to "small" colonies	wt op

http://curation.pombase.org/pombe/curs/eef07d879f4207d2 have asked about extensions

http://curation.pombase.org/pombe/curs/e64102699ced97dc

need to talk to Val

http://curation.pombase.org/pombe/curs/8a0da77ab1315722/
txl1	normal level of protein-ubiquitin conjugates	deletion, gel elec
txc1	normal level of protein-ubiquitin conjugates	deletion, gel elec

http://curation.pombase.org/pombe/curs/08562810fce65760#
rad3	decreased level of phosphorylated H2A during S-phase	deletion, chip
swi1	H2A phosphorylation absent at mating type locus during S phase	deletion, chip
swi3	H2A phosphorylation absent at mating type locus during S phase	deletion, chip
swi1	increased level of phosphorylated h2a at rDNA during G2	deletion, chip
swi1	increased level of phosphorylated h2a at rDNA during S phase	deletion, chip
swi1	increased level of phosphorylated h2a at tDNA during S phase	deletion, chip
cds1	increased level of phosphorylated h2a during cellular response to HU	deletion, chip

clr4	decreased level of phosphorylated H2A at centromere otr	deletion, chip
swi6	normal level of phosphorylated H2A at centromere otr	deletion, chip
clr4	normal level of phosphorylated H2A at mating type locus	deletion, chip
swi6	normal level of phosphorylated H2A at mating type locus	deletion, chip
clr4	decreased level of phosphorylated H2A at subtelomere during S phase	deletion, chip
swi6	decreased level of phosphorylated H2A at subtelomere during S-phase	deletion, chip
taz1	normal level of phosphorylated H2A at subtelomere	deletion, chip
clr4	decreased punctate nuclear localization	deletion, micro, assayed_using(PomBase:brc1)
clr4	normal protein localization to rDNA	deletion, chip, assayed_using(PomBase:brc1)
rqh1	increased level of phosphorylated h2a at rDNA	deletion, chip