wiki:MidoriCuratedPapers

transferred from CuratorTrainingPapers

Quick fixes

Short wait for whatever's needed, so add to existing sessions

Multiple mutations, thorny extensions, etc.

Longer-term, so may require new curation sessions

21813639
mcb1-chk1 genetic interactionalleles OP-mcb1+chk1-deletion, mcb1-D2+chk1-deletion; mcb1-D22+chk1-deletion
mcb1-rad3 genetic interactionalleles OP-mcb1+rad3-deletion, mcb1-D2+rad3-deletion; mcb1-D22+rad3-deletion


20929775
hht1,hht2,hht3 all 3 T3A (triple mutant), sgo2deletiongenetic interaction synthetic lethal
hht1,hht2,hht3, hta1,hta2 all 3 H3 T3A, both H2 S121A (quintuple mutant)genetic interaction synthetic lethal
genetic interactionhrk1, swi6"asynthetic"; check for old same-pathway GO IGI
hht1,hht2,hht3all 3 T3A (triple mutant)genetic interaction "asynthetic" with hrk1deletion
Hrk1-Bir1physical interactionBIR domain of Bir1 (Pfam:PF00653)
hrk1 bub1 genetic interactionalleles hrk1 deletion; bub1-KD (kinase dead, K762R,D900N)
hrk1 sgo2 genetic interactionalleles both deletion
pds5 bub1 genetic interactionalleles pds5 deletion; bub1-KD (kinase dead, K762R,D900N)
pds5 sgo2 genetic interactionalleles both deletion
swi6 sgo2 genetic interactionalleles both deletion


PMID:6887244 long-term note
additional note3 of 13 cold-sensitive mutants curated; if someone can figure out what genes the other 10 correspond to, we can annotate a few more phenotypes


PMID:7865880
other stuffmis2, mis7, mis8, mis9 all apparently uncloned, so don't know which gene they correspond to
mis2 ?geneFYPO:786 ev: plasmid maint assayallele=mis2-87(unknown),condition=PCO:0000005,condition=PCO:0000004 | allele=mis2-197(unknown),condition=PCO:0000004
mis7 ?geneFYPO:786 ev: plasmid maint assayallele=mis7-322(unknown),condition=PCO:0000005
mis8 ?geneFYPO:786 ev: plasmid maint assayallele=mis8-341(unknown),condition=PCO:0000005,condition=PCO:0000004
mis9 ?geneFYPO:786 ev: plasmid maint assayallele=mis9-356(unknown),condition=PCO:0000005


PMID:8631307
cdc21-M68(unknown) mcm4 C-terminus overexpression [note: says overexp piece from BamHI site to end, but the only BamHI site I saw looks too close to N-term to yield fragment in fig 1 gelfypo:2061


PMID:9383050lots of mcm2 alleles done with one on chromosome, another on plasmid (cells otherwise haploid)
mcm2 allele on chromosome/allele on plasmidFYPO ID, high tempFYPO ID, normal temp (32, semi-restrictive)
cdc19-P1/mcm2+fypo:47 normal cell growthfypo:47
cdc19-P1/mcm2-M1fypo:49 inviablefypo:49, fypo:299 microcolony formation, fypo:5 abn. cell morph.
cdc19-P1/mcm2-M2fypo:49fypo:49, fypo:299, fypo:5
cdc19-P1/mcm2-M3fypo:49fypo:49, fypo:299, fypo:5
cdc19-P1/mcm2-M5fypo:49fypo:49, fypo:299, fypo:5
cdc19-P1/mcm2-M6fypo:49fypo:47
cdc19-P1/mcm2-M7fypo:47fypo:46 slow cell growth
cdc19-P1/mcm2-M8fypo:49fypo:46
cdc19-P1/mcm2-M9fypo:49fypo:49, fypo:299, fypo:5
cdc19-P1/mcm2-M10fypo:49fypo:49, fypo:299, fypo:5
cdc19-P1/cdc19-P1fypo:49n/a
cdc19-P1/nda1-KM376fypo:47n/a
cdc19-P1/mcm2-D1fypo:47fypo:47
cdc19-P1/mcm2-D2fypo:47fypo:47
cdc19-P1/mcm2-D3fypo:47fypo:47
cdc19-P1/mcm2-D4fypo:49fypo:49, fypo:299, fypo:5
cdc19-P1/mcm2-D6fypo:49fypo:46
cdc19-P1/mcm2-D7fypo:49fypo:49, fypo:299, fypo:5
cdc19-P1/mcm2-D8fypo:49fypo:46
cdc19-P1/mcm2-D9fypo:49fypo:47
cdc19-P1/mcm2-D10fypo:49fypo:46
wt or deletion setviable at 32dg? (with mcm2 allele of interest overexpressed)
chromosome/plasmidfypo ID, normal temp
mcm2+/mcm2-M1fypo:47
mcm2+/mcm2-M2fypo:47
mcm2+/mcm2-M3fypo:47
mcm2+/mcm2-M5fypo:47
mcm2+/mcm2-M6fypo:47
mcm2+/mcm2-M7fypo:47
mcm2+/mcm2-M8fypo:47
mcm2+/mcm2-M9fypo:47
mcm2+/mcm2-M10fypo:47
mcm2+/mcm2-D1fypo:47
mcm2+/mcm2-D2fypo:47
mcm2+/mcm2-D3fypo:47
mcm2+/mcm2-D4fypo:47
mcm2+/mcm2-D6fypo:47
mcm2+/mcm2-D7fypo:47
mcm2+/mcm2-D8fypo:47
mcm2+/mcm2-D9fypo:47
mcm2+/mcm2-D10fypo:47
mcm2delta/mcm2+fypo:47
mcm2delta/mcm2-M6fypo:49
mcm2delta/mcm2-M7fypo:47
mcm2delta/mcm2-M8fypo:49
mcm2delta/cdc19-P1fypo:47
mcm2delta/mcm2-D1fypo:47
mcm2delta/mcm2-D2fypo:47
mcm2delta/mcm2-D3fypo:47
gene expression complexities
mcm2-M7, D1, D2, D3 and wt alleleslevel of expression from plasmid with nmt promoter much higher with cdc19-P1 on chromosome than with mcm2+ on chr
Mcm2 protein nearly same throughout cell cycle; modest decrease in G2could use artemis gene exp syntax, but don't have a "throughout cell cycle" GO term or extension
ordinary double mutant phenotypes
mcm2 cdc19-P1, mcm4+ overexpslow growth; fypo:150; fypo:614 facsnormal temp
mcm2 cdc19-P1, mcm5+ overexpslow growth; fypo:150; fypo:614 facsnormal temp
mcm2 cdc19-P1, mcm6+ overexpslow growth; fypo:150; fypo:614 facsnormal temp
mcm2 cdc19-P1, cdc6 poldelta-ts1slow cell growth, elong cells, curved cells; normal temp 25 or 29; at 32 dg branched cells, t-shaped cells, inviable high temp (tho 32 is top of PCO "normal" range)
mcm2 cdc19-P1, cdc1-7slow cell growth, elong cells, curved cells; normal temp 25 or 29; at 32 dg branched cells, t-shaped cells, inviable high temp (tho 32 is top of PCO "normal" range)
mcm2 cdc19-P1, cdc18-K46inviable high temp (done at 32, top of PCO "normal" range)


PMID:9658174
annotated physical interactionsno change throughout cell cycle
negative resultno physical interaction between Mcms and Cdc18


PMID:9705504
mcm3-mcm5 phys int "tight"what to do about interaction strength/affinity?


PMID:9914167
mcm2 cdc19-P1FYPO:1386 change 'other' evidence to staining when in ECO
mcm*delta::his3+ (* = 2, 4, 5, or 6)deletion phenotype is that of haploid spore derived from mcm*delta::his3+/mcm*+ diploid; detected protein presumed to be residual from diploid
mcm2delta::his3+/mcm2(cdc19-P1) diploidcouldn't construct; hypothesize that ts mcm2 haploinsufficient
mcm4delta::his3+/mcm4(cdc21-M68) constructed & sporulated at 36dgmcm4delta::his3+ spores: DNA synthesis abolished (didn't enter S phase); 75% abnormal nuclear or cell division


PMID:19168988
note: SPAPB2B4.04c has pmc1 as synonym (used in the paper); documented allele synonyms
multi-way genetic interactionoverexp pmr1+ sup (SPAPB2B4.04cdelta,cta5delta fypo:98)
gene expressionpmr1+ > SPAPB2B4.04c+ > cta5+ during veg growth GO:0072690, but nothing else shown (e.g. change upon stimulus/during GO BP); one measurement


PMID:10409743
hsk1 gene expboth mRNA and protein "relatively constant throughout cell cycle"
dfp1 C-term del, exact residues not specifiedinviable; no further data
Dfp1 "hyperphosphorylated" in presence of HU


PMID:10411894
Dfp1 "hyperphosphorylated" in presence of HUrequires Cds1 kinase


PMID:10490657
lots of Mcm2 & Mcm6 in unspecified "soluble" fractionthroughout cell cycle


PMID:10588642
GFP-beta-galactosidase + SV40 NLSnucleus
GFP-beta-galactosidase + mcm2-M9 residues 5-10 (mutated NLS1)cytoplasm
GFP-beta-galactosidase + Mcm2 residues 114-118 (NLS2)cytoplasm


PMID:11606526
Cdc23 protein loc"insoluble"


PMID:2544292
identified two 5' utrs, starting at -249 and -214; in Artemis they would be: 
FT   5'UTR           complement(3175099..3175313)
FT                   /systematic_id="SPBC776.02c"
FT                   /db_xref="PMID:2544292"
FT   5'UTR           complement(3175099..3175348)
FT                   /systematic_id="SPBC776.02c"
FT                   /db_xref="PMID:2544292"
PMID:2544292 cont'dheadmelting genetic interactions (1st 4 phenotypes entered)
cdc25-22 wee1-6 dis2+ overexpts (unlike cdc25 wee1 double mutant)
cdc25-22 wee1-50 dis2+ overexpts
cdc25-22 cdc2-1w dis2+ overexpts
cdc25-22 cdc2-3w dis2+ overexpts
cdc25-r22 sup3-5,r36 ade6-704ade prototroph
cdc25-r22 sup3-5,r36 ade6-704 dis2+ overexpade prototroph
wee 1-6 cdc25-r22 sup3-5,r36 ade6-704ade auxotroph
wee 1-6 cdc25-r22 sup3-5,r36 ade6-704 dis2+ overexpade auxotroph
cdc2-3w cdc25-r22 sup3-5,r36 ade6-704ade auxotroph
cdc2-3w cdc25-r22 sup3-5,r36 ade6-704 dis2+ overexpade auxotroph
relevant background from a cited paper:
sup3-5,r36 ade6-704ade auxotroph
cdc25-rr43 sup3-5,r36 ade6-704ade prototroph
sup3-5,r36 is an opal nonsense suppressor tRNA; ade6-704 has an opal nonsense mutation to suppress


PMID:11973289
mcm4,6,7 alleles all also tested in presence of corresponding ts (mcm4-M68, mcm6-268, mcm7-98) at high tempmight not be worth annotating, since it doesn't add new info (and there are lots, so it would be a pain)


PMID:1849107
cyr1/git2 intragenic complementation - groupsgit2-7, git2-110, git2-266, git2-18, git2-68, git2-216, git2-226, git2-210
compl. groupgit2-61, git2-29, git2-83


PMID:1883874
phenotypes entered for epistasis
epistasisste6delta gpa1delta (aka sar1delta) (technically both disruptions) same phenotypes as gpa1delta alone
epistasisras1delta gpa11delta (technically both disruptions) same phenotypes as ras1delta alone


PMID:10655214
orc2deltafypo:614 (facs; high temp) in germinating orc2delta spores from orp2-2/orc2delta::ura4 diploid (note difference from orc2delta phenotype if diploid was orc2+/orc2delta::ura4
orc2deltacut (micr; high temp) if from from orp2-2/orc2delta::ura4 diploid as above
orc2deltaabnormal repl checkpoint fypo:173 (micr; high temp, +HU) if from from orp2-2/orc2delta::ura4 diploid as above


PMID:2170029
dis2 gene expactivity constant throughout cell cycle (have annotated constant protein level)
ppa2 gene expactivity constant throughout cell cycle (didn't look at protein)


PMID:3870979
need way to represent h* designation in genotype
ran1 pat1-114 in h90 fypo:761 glucose minimal medium std temp (followed by apparently normal sporulation)
pat1-114 in h-normal absence of conjugation minimal? (it's PMA) std temp
pat1-114 in h-normal absence of sporulation PMA std temp
pat1-114 + mei2::LEU2 in h90 normal conj micr


PMID:7588609
epistasisrep2+ overexp no effect on res2delta


PMID:23260662
need seq feature with ID
mat1-Msmt-0 "deletion of 263 bp distal to mat1"; also see PMID:8431959
mat1-SS2 deletes 111-bp centromere-distal segment 1152-1262 as they've defined cassette (PMID:21423720)fypo:3091 a_u lsd1 chip
double mutants
mat1-Msmt-0 lsd1-E918abol GO:0011000 fypo:3084


PMID:16772338
pending outcome of ​chado 433could add myp2 protein binding go:5515 ipi with chs2 (if it won't be inferred somewhere)


PMID:18256290
pending outcome of ​chado 433could add rho1 protein binding go:5515 ipi with pxl1 (if it won't be inferred somewhere)
double mutantsin some cases "high temp" is a fudge for higher vs. lower within PECO "standard" range


PMID:7969124
srp54 allele combinationsdiploids, wt on one chromosome, mutant on high-copy plasmid
srp54+/T248S decr veg gr fypo:1355 min med; expr low at low temp (growth normal at std or high temp)
srp54+/T248K decr veg gr fypo:1355 min med; expr high at low temp, expr low at high temp (growth normal at std temp)
srp54+/T248R decr veg gr fypo:1355 min med; expr high at low temp, expr low at high temp (growth normal at std temp)
srp54+/T248Ndecr veg gr fypo:1355 min med; expr low at high or low temp (growth normal at std temp)
srp54+/R194Q decr veg gr fypo:1355 min med; expr high at high or low temp (growth normal at std temp)
srp54+/R194L decr veg gr fypo:1355 min med; expr high at high or low temp (growth normal at std temp)
srp54+/R194H decr veg gr fypo:1355 min med; expr low at low temp, expr high at high temp (growth normal at std temp)
srp54+/D190Ndecr veg gr fypo:1355 min med; expr low at low temp (growth normal at std or high temp)
srp54+/D138Ndecr veg gr fypo:1355 min med; expr low at low temp, expr high at high temp (growth normal at std temp)
srp54+/K114R decr veg gr fypo:1355 min med; expr high at high or low temp (growth normal at std temp)
srp54+/K114G decr veg gr fypo:1355 min med; expr low at low temp, expr high at high temp (growth normal at std temp)
srp54+/Q110G decr veg gr fypo:1355 min med; expr high at low temp, expr low at high temp (growth normal at std temp)
srp54+/Q110E decr veg gr fypo:1355 min med; expr high at high temp (growth normal at std or low temp)
srp54+/Q110R decr veg gr fypo:1355 min med; expr low at high or low temp (growth normal at std temp)
srp54+/Q110Kdecr veg gr fypo:1355 min med; expr low at high or low temp (growth normal at std temp)


PMID:10079327
srp54 allele combinationsdiploids, wt on one chromosome, mutant on high-copy plasmid
srp54+/R194A,H195Adecr veg gr fypo:1355 min med; expr high at high or low temp (growth normal at std temp)
srp54+/E277A,H278Adecr veg gr fypo:1355 min med; expr high at high temp (growth normal at std or low temp)
srp54+/K314A,K315Adecr veg gr fypo:1355 min med; expr high at high temp (growth normal at std or low temp)
srp54+/K428A,K429Adecr veg gr fypo:1355 min med; expr high at high temp (growth normal at std or low temp)


Stored additional specificity for evidence (in case we ever want to go back and "upgrade")

PMID:7865880mis5-268(unknown), PCO:0000004FYPO:217PFGE
PMID:8895665orc1 cdc30-4(unknown)FYPO:0000217PFGE
PMID:8838655mcm2FYPO:0000217PFGE
PMID:8838655mcm2FYPO:0001133PFGE
PMID:8838655mcm5FYPO:0000217PFGE
PMID:8838655mcm5FYPO:0001133PFGE
PMID:9914167mcm2 cdc19-P1FYPO:848PFGE
PMID:11606526mcm7-98FYPO:0000848PFGE
PMID:7628438ssp1 allelesFYPO: normal chr morphPFGE

Community Curation sessions I've reviewed

PMID:23677513 fdeaa8d994824f8c
can also add myh1 chromatin binding in_presence_of phleomycin ChEBI:75044


PMID:23427262
Nuf2-Alp7C fusion + ndc80-NH12(nearly) normal veg cell pop growth; normal chromosome seg (fig 6)
ndc80-NH12/ndc80-21 heterozygous diploidsensitive to high temp, but not as severe as either homozygous diploid (fig 7)


PMID:24081329
nab2::kanMX6 rpl3001::kanMX6same pre-mRNA level as rpl3001 single mutant a_u rpl3002 (epistasis)
nab2::kanMX6 rrp6::ura4+same pre-mRNA & mRNA levels as rrp6- alone (epistasis) a_u rpl3002


Last modified 5 years ago Last modified on Sep 1, 2015, 3:36:58 PM