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 interaction | alleles OP-mcb1+chk1-deletion, mcb1-D2+chk1-deletion; mcb1-D22+chk1-deletion |
mcb1-rad3 genetic interaction | alleles OP-mcb1+rad3-deletion, mcb1-D2+rad3-deletion; mcb1-D22+rad3-deletion |
20929775 | ||
hht1,hht2,hht3 all 3 T3A (triple mutant), sgo2deletion | genetic interaction synthetic lethal | |
hht1,hht2,hht3, hta1,hta2 all 3 H3 T3A, both H2 S121A (quintuple mutant) | genetic interaction synthetic lethal | |
genetic interaction | hrk1, swi6 | "asynthetic"; check for old same-pathway GO IGI |
hht1,hht2,hht3 | all 3 T3A (triple mutant) | genetic interaction "asynthetic" with hrk1deletion |
Hrk1-Bir1 | physical interaction | BIR domain of Bir1 (Pfam:PF00653) |
hrk1 bub1 genetic interaction | alleles hrk1 deletion; bub1-KD (kinase dead, K762R,D900N) | |
hrk1 sgo2 genetic interaction | alleles both deletion | |
pds5 bub1 genetic interaction | alleles pds5 deletion; bub1-KD (kinase dead, K762R,D900N) | |
pds5 sgo2 genetic interaction | alleles both deletion | |
swi6 sgo2 genetic interaction | alleles both deletion |
PMID:6887244 | long-term note |
additional note | 3 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 stuff | mis2, mis7, mis8, mis9 all apparently uncloned, so don't know which gene they correspond to | |
mis2 ?gene | FYPO:786 ev: plasmid maint assay | allele=mis2-87(unknown),condition=PCO:0000005,condition=PCO:0000004 | allele=mis2-197(unknown),condition=PCO:0000004 |
mis7 ?gene | FYPO:786 ev: plasmid maint assay | allele=mis7-322(unknown),condition=PCO:0000005 |
mis8 ?gene | FYPO:786 ev: plasmid maint assay | allele=mis8-341(unknown),condition=PCO:0000005,condition=PCO:0000004 |
mis9 ?gene | FYPO:786 ev: plasmid maint assay | allele=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 gel | fypo:2061 |
PMID:9383050 | lots of mcm2 alleles done with one on chromosome, another on plasmid (cells otherwise haploid) | |
mcm2 allele on chromosome/allele on plasmid | FYPO ID, high temp | FYPO ID, normal temp (32, semi-restrictive) |
cdc19-P1/mcm2+ | fypo:47 normal cell growth | fypo:47 |
cdc19-P1/mcm2-M1 | fypo:49 inviable | fypo:49, fypo:299 microcolony formation, fypo:5 abn. cell morph. |
cdc19-P1/mcm2-M2 | fypo:49 | fypo:49, fypo:299, fypo:5 |
cdc19-P1/mcm2-M3 | fypo:49 | fypo:49, fypo:299, fypo:5 |
cdc19-P1/mcm2-M5 | fypo:49 | fypo:49, fypo:299, fypo:5 |
cdc19-P1/mcm2-M6 | fypo:49 | fypo:47 |
cdc19-P1/mcm2-M7 | fypo:47 | fypo:46 slow cell growth |
cdc19-P1/mcm2-M8 | fypo:49 | fypo:46 |
cdc19-P1/mcm2-M9 | fypo:49 | fypo:49, fypo:299, fypo:5 |
cdc19-P1/mcm2-M10 | fypo:49 | fypo:49, fypo:299, fypo:5 |
cdc19-P1/cdc19-P1 | fypo:49 | n/a |
cdc19-P1/nda1-KM376 | fypo:47 | n/a |
cdc19-P1/mcm2-D1 | fypo:47 | fypo:47 |
cdc19-P1/mcm2-D2 | fypo:47 | fypo:47 |
cdc19-P1/mcm2-D3 | fypo:47 | fypo:47 |
cdc19-P1/mcm2-D4 | fypo:49 | fypo:49, fypo:299, fypo:5 |
cdc19-P1/mcm2-D6 | fypo:49 | fypo:46 |
cdc19-P1/mcm2-D7 | fypo:49 | fypo:49, fypo:299, fypo:5 |
cdc19-P1/mcm2-D8 | fypo:49 | fypo:46 |
cdc19-P1/mcm2-D9 | fypo:49 | fypo:47 |
cdc19-P1/mcm2-D10 | fypo:49 | fypo:46 |
wt or deletion set | viable at 32dg? (with mcm2 allele of interest overexpressed) | |
chromosome/plasmid | fypo ID, normal temp | |
mcm2+/mcm2-M1 | fypo:47 | |
mcm2+/mcm2-M2 | fypo:47 | |
mcm2+/mcm2-M3 | fypo:47 | |
mcm2+/mcm2-M5 | fypo:47 | |
mcm2+/mcm2-M6 | fypo:47 | |
mcm2+/mcm2-M7 | fypo:47 | |
mcm2+/mcm2-M8 | fypo:47 | |
mcm2+/mcm2-M9 | fypo:47 | |
mcm2+/mcm2-M10 | fypo:47 | |
mcm2+/mcm2-D1 | fypo:47 | |
mcm2+/mcm2-D2 | fypo:47 | |
mcm2+/mcm2-D3 | fypo:47 | |
mcm2+/mcm2-D4 | fypo:47 | |
mcm2+/mcm2-D6 | fypo:47 | |
mcm2+/mcm2-D7 | fypo:47 | |
mcm2+/mcm2-D8 | fypo:47 | |
mcm2+/mcm2-D9 | fypo:47 | |
mcm2+/mcm2-D10 | fypo:47 | |
mcm2delta/mcm2+ | fypo:47 | |
mcm2delta/mcm2-M6 | fypo:49 | |
mcm2delta/mcm2-M7 | fypo:47 | |
mcm2delta/mcm2-M8 | fypo:49 | |
mcm2delta/cdc19-P1 | fypo:47 | |
mcm2delta/mcm2-D1 | fypo:47 | |
mcm2delta/mcm2-D2 | fypo:47 | |
mcm2delta/mcm2-D3 | fypo:47 | |
gene expression complexities | ||
mcm2-M7, D1, D2, D3 and wt alleles | level 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 G2 | could 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+ overexp | slow growth; fypo:150; fypo:614 facs | normal temp |
mcm2 cdc19-P1, mcm5+ overexp | slow growth; fypo:150; fypo:614 facs | normal temp |
mcm2 cdc19-P1, mcm6+ overexp | slow growth; fypo:150; fypo:614 facs | normal temp |
mcm2 cdc19-P1, cdc6 poldelta-ts1 | slow 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, cdc1-7 | slow 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-K46 | inviable high temp (done at 32, top of PCO "normal" range) |
PMID:9658174 | |
annotated physical interactions | no change throughout cell cycle |
negative result | no physical interaction between Mcms and Cdc18 |
PMID:9705504 | |
mcm3-mcm5 phys int "tight" | what to do about interaction strength/affinity? |
PMID:9914167 | |
mcm2 cdc19-P1 | FYPO: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) diploid | couldn't construct; hypothesize that ts mcm2 haploinsufficient |
mcm4delta::his3+/mcm4(cdc21-M68) constructed & sporulated at 36dg | mcm4delta::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 interaction | overexp pmr1+ sup (SPAPB2B4.04cdelta,cta5delta fypo:98) |
gene expression | pmr1+ > 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 exp | both mRNA and protein "relatively constant throughout cell cycle" |
dfp1 C-term del, exact residues not specified | inviable; no further data |
Dfp1 "hyperphosphorylated" in presence of HU |
PMID:10411894 | |
Dfp1 "hyperphosphorylated" in presence of HU | requires Cds1 kinase |
PMID:10490657 | |
lots of Mcm2 & Mcm6 in unspecified "soluble" fraction | throughout cell cycle |
PMID:10588642 | |
GFP-beta-galactosidase + SV40 NLS | nucleus |
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'd | headmelting genetic interactions (1st 4 phenotypes entered) |
cdc25-22 wee1-6 dis2+ overexp | ts (unlike cdc25 wee1 double mutant) |
cdc25-22 wee1-50 dis2+ overexp | ts |
cdc25-22 cdc2-1w dis2+ overexp | ts |
cdc25-22 cdc2-3w dis2+ overexp | ts |
cdc25-r22 sup3-5,r36 ade6-704 | ade prototroph |
cdc25-r22 sup3-5,r36 ade6-704 dis2+ overexp | ade prototroph |
wee 1-6 cdc25-r22 sup3-5,r36 ade6-704 | ade auxotroph |
wee 1-6 cdc25-r22 sup3-5,r36 ade6-704 dis2+ overexp | ade auxotroph |
cdc2-3w cdc25-r22 sup3-5,r36 ade6-704 | ade auxotroph |
cdc2-3w cdc25-r22 sup3-5,r36 ade6-704 dis2+ overexp | ade auxotroph |
relevant background from a cited paper: | |
sup3-5,r36 ade6-704 | ade auxotroph |
cdc25-rr43 sup3-5,r36 ade6-704 | ade 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 temp | might 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 - groups | git2-7, git2-110, git2-266, git2-18, git2-68, git2-216, git2-226, git2-210 |
compl. group | git2-61, git2-29, git2-83 |
PMID:1883874 | |
phenotypes entered for epistasis | |
epistasis | ste6delta gpa1delta (aka sar1delta) (technically both disruptions) same phenotypes as gpa1delta alone |
epistasis | ras1delta gpa11delta (technically both disruptions) same phenotypes as ras1delta alone |
PMID:10655214 | |
orc2delta | fypo: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 |
orc2delta | cut (micr; high temp) if from from orp2-2/orc2delta::ura4 diploid as above |
orc2delta | abnormal repl checkpoint fypo:173 (micr; high temp, +HU) if from from orp2-2/orc2delta::ura4 diploid as above |
PMID:2170029 | |
dis2 gene exp | activity constant throughout cell cycle (have annotated constant protein level) |
ppa2 gene exp | activity 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 | |
epistasis | rep2+ 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-E918 | abol GO:0011000 fypo:3084 |
PMID:16772338 | |
pending outcome of chado 433 | could add myp2 protein binding go:5515 ipi with chs2 (if it won't be inferred somewhere) |
PMID:18256290 | |
pending outcome of chado 433 | could add rho1 protein binding go:5515 ipi with pxl1 (if it won't be inferred somewhere) |
double mutants | in some cases "high temp" is a fudge for higher vs. lower within PECO "standard" range |
PMID:7969124 | |
srp54 allele combinations | diploids, 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+/T248N | decr 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+/D190N | decr veg gr fypo:1355 min med; expr low at low temp (growth normal at std or high temp) |
srp54+/D138N | decr 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+/Q110K | decr veg gr fypo:1355 min med; expr low at high or low temp (growth normal at std temp) |
PMID:10079327 | |
srp54 allele combinations | diploids, wt on one chromosome, mutant on high-copy plasmid |
srp54+/R194A,H195A | decr veg gr fypo:1355 min med; expr high at high or low temp (growth normal at std temp) |
srp54+/E277A,H278A | decr veg gr fypo:1355 min med; expr high at high temp (growth normal at std or low temp) |
srp54+/K314A,K315A | decr veg gr fypo:1355 min med; expr high at high temp (growth normal at std or low temp) |
srp54+/K428A,K429A | decr 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:7865880 | mis5-268(unknown), PCO:0000004 | FYPO:217 | PFGE |
PMID:8895665 | orc1 cdc30-4(unknown) | FYPO:0000217 | PFGE |
PMID:8838655 | mcm2 | FYPO:0000217 | PFGE |
PMID:8838655 | mcm2 | FYPO:0001133 | PFGE |
PMID:8838655 | mcm5 | FYPO:0000217 | PFGE |
PMID:8838655 | mcm5 | FYPO:0001133 | PFGE |
PMID:9914167 | mcm2 cdc19-P1 | FYPO:848 | PFGE |
PMID:11606526 | mcm7-98 | FYPO:0000848 | PFGE |
PMID:7628438 | ssp1 alleles | FYPO: normal chr morph | PFGE |
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 diploid | sensitive to high temp, but not as severe as either homozygous diploid (fig 7) |
PMID:24081329 | |
nab2::kanMX6 rpl3001::kanMX6 | same 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