set3 (SPAC22E12.11c)


Gene Standard Nameset3 Characterisation Statuspublished
Systematic IDSPAC22E12.11c Feature Typeprotein coding
Synonyms Name Description
Producthistone lysine methyltransferase Set3 Product Size859aa, 94.89 kDa
Genomic Location Chromosome I, 5043440-5039546 (3895nt); CDS:5042481-5039902 (2580nt)

Ensembl Gene Location
GO Molecular Function
Term IDTerm NameEvidenceWith/FromReferenceCount
GO:0018024histone-lysine N-methyltransferase activityTASPMID:155502438
GO:0019787small conjugating protein ligase activityISMIPR001965GO_REF:0000024105
GO:0008270zinc ion bindingIEAIPR001965GO_REF:0000002248
GO Biological Process
Term IDTerm NameEvidenceWith/FromReferenceCount
GO:0006338chromatin remodelingIPIGO:0034967PMID:19040720156
GO:0034968histone lysine methylationTASPMID:1555024311
GO:0018022peptidyl-lysine methylationTASPMID:1555024312
GO Cellular Component
Term IDTerm NameEvidenceWith/FromReferenceCount
GO:0070210Rpd3L-Expanded complexIDAPMID:1904072015
GO:0034967Set3 complexIDAPMID:190407204
GO:0005634nucleusIDAPMID:168233722730
Fission Yeast Phenotype Ontology

Population Phenotype

Term IDTerm NameEvidenceAlleleExpressionConditionReferenceCount
FYPO:0002617sensitive to sodium butyrateCell growth assayset3ΔNullPECO:0000201, PECO:0000005, PECO:0000142PMID:2386193793
expressivity FYPO_EXT:0000003
FYPO:0000086sensitive to tacrolimusCell growth assayset3ΔNullPECO:0000201, PECO:0000005, PECO:0000142PMID:2185027179
expressivity FYPO_EXT:0000003
FYPO:0002546sensitive to trichostatin ACell growth assayset3ΔNullPECO:0000201, PECO:0000005, PECO:0000142PMID:2386193739
expressivity FYPO_EXT:0000002
FYPO:0000115sensitive to valproic acidCell growth assayset3ΔNullPECO:0000201, PECO:0000005, PECO:0000142PMID:23861937154
expressivity FYPO_EXT:0000002
FYPO:0002060viable vegetative cell populationMicroscopyset3ΔNullPECO:0000005, PECO:0000137PMID:236978063755
Microscopyset3ΔNullPMID:20473289

Cell Phenotype

Term IDTerm NameEvidenceAlleleExpressionConditionReferenceCount
FYPO:0001510viable vegetative cell, abnormal cell shape, normal cell sizeMicroscopyset3ΔNullPECO:0000137, PECO:0000004PMID:23697806215
expressivity FYPO_EXT:0000003
penetrance FYPO_EXT:0000001
expressivity FYPO_EXT:0000003Microscopyset3ΔNullPECO:0000137, PECO:0000005PMID:23697806
penetrance FYPO_EXT:0000001
Transcript
Ensembl transcript structure with UTRs, exons and introns

Exons

Exon Start End
150434405039546

UTRs

Region Start End Reference
three_prime_UTR50399015039546PMID:21511999
five_prime_UTR50434405042482PMID:21511999
Protein Features

Graphical View

Ensembl protein image with mapped locations of structural domains

Protein Families and Domains

Feature ID Database InterPro Description Start End Count
PF00628 Pfam IPR019787 Zinc finger, PHD-finger 5 50 16
PF00856 Pfam IPR001214 SET domain 227 332 12
SM00249 SMART IPR001965 Zinc finger, PHD-type 5 49 19
SM00317 SMART IPR001214 SET domain 215 343 11
PS50280 Prosite Profiles IPR001214 SET domain 210 337 13
PS01359 Prosite Patterns IPR019786 Zinc finger, PHD-type, conserved site 6 48 19
PTHR16286 HMMPANTHER 1 399 1
G3DSA:3.30.40.10 Gene3D IPR013083 2 51 84
G3DSA:2.170.270.10 Gene3D 227 341 8
SSF82199 SuperFamily 149 338 13
SSF57903 SuperFamily IPR011011 2 52 25
Low complexity (SEG) seg 730 743
Low complexity (SEG) seg 664 680
Low complexity (SEG) seg 549 562
Low complexity (SEG) seg 413 431
Low complexity (SEG) seg 359 369
Low complexity (SEG) seg 117 131
Low complexity (SEG) seg 68 89

View domain organization at Pfam

Manually Curated Family or Sub-families

Term IDTerm NameReferenceCount
PBO:0000137zinc finger proteinTemporary processing gif - replaced by AJAX with count of genes annotated with the term PBO:0000137
PBO:0000447zf-PHD fingerTemporary processing gif - replaced by AJAX with count of genes annotated with the term PBO:0000447
PBO:0001327SET domainTemporary processing gif - replaced by AJAX with count of genes annotated with the term PBO:0001327

Protein Properties

Ave. residue weight 110.46 Da
Charge 39.50
Isoelectric point 9.76
Molecular weight 94.89 kDa
Number of residues 859
Modifications

Protein Modifications

Term IDTerm NameEvidenceResidueReferenceCount
MOD:00696phosphorylated residuePMID:182575171192
PMID:19547744
Sequence
Gene Expression

Quantitative Gene Expression

Protein Level

Molecules/Cell (average)DuringConditionScaleEvidenceReference
NDduring cell quiescence following G1 arrest due to nitrogen limitationPECO:0000005,
PECO:0000014,
PECO:0000127
population_wideexperimental evidencePMID:23101633
223.33during GO:0072690PECO:0000005,
PECO:0000014
population_wideexperimental evidencePMID:23101633

RNA Level

Molecules/Cell (average)DuringConditionScaleEvidenceReference
2.1during cell quiescence following G1 arrest due to nitrogen limitationPECO:0000005,
PECO:0000014,
PECO:0000127
population_wideexperimental evidencePMID:23101633
4.4during GO:0072690PECO:0000005,
PECO:0000014
population_wideexperimental evidencePMID:23101633
Species Distribution
DescriptionQualifierReferenceCount
predominantly single copy (one to one)3080
conserved in fungi4564
conserved in eukaryotes4482
conserved in metazoa3419
conserved in vertebrates3394
conserved in eukaryotes only2485
Orthologs

Manually curated orthologous groups

SpeciesGeneDescriptionLinksCount

Orthologs in Compara


Genetic Interactions

Source: BioGRID

Gene Product Evidence Reference
med20mediator complex subunit Med20 Negative GeneticPMID:18818364
pnk1DNA kinase/phosphatase Pnk1 Negative GeneticPMID:18818364
yaf9YEATS family histone acetyltransferase subunit Yaf9 Negative GeneticPMID:18818364
mph1dual specificity protein kinase Mph1 Positive GeneticPMID:22681890
bdc1bromodomain containing protein 1, Bdc1 Negative GeneticPMID:18818364
Negative GeneticPMID:22681890
liz1pantothenate transporter Liz1 Negative GeneticPMID:22681890
elp5elongator complex subunit Elp5 (predicted) Negative GeneticPMID:18818364
SPAC694.04cconserved eukaryotic protein Negative GeneticPMID:22681890
usp102U1 snRNP-associated protein Usp102 Negative GeneticPMID:22681890
pef1Pho85/PhoA-like cyclin-dependent kinase Pef1 Negative GeneticPMID:18818364
Negative GeneticPMID:22681890
SPCC16C4.106-phosphogluconolactonase (predicted) Negative GeneticPMID:22681890
sec28coatomer epsilon subunit (predicted) Negative GeneticPMID:18818364
dbr1RNA lariat debranching enzyme Dbr1 Negative GeneticPMID:18818364
Negative GeneticPMID:22681890
mms19Dos2 silencing complex subunit Mms19 Negative GeneticPMID:18818364
Negative GeneticPMID:22681890
uap2U2 snRNP-associated protein Uap2 Negative GeneticPMID:22681890
ash2Ash2-trithorax family protein Negative GeneticPMID:18818364
Negative GeneticPMID:22681890
dad2DASH complex subunit Dad2 Negative GeneticPMID:18818364
Negative GeneticPMID:22681890
pmc5mediator complex subunit Pmc5 Negative GeneticPMID:18818364
sap10splicing factor 3B Negative GeneticPMID:22681890
git3G-protein coupled receptor Git3 Negative GeneticPMID:22681890
swc5Swr1 complex subunit Swc5 Negative GeneticPMID:18818364
ccr4CCR4-Not complex subunit Ccr4 (predicted) Negative GeneticPMID:18818364
swc2Swr1 complex complex subunit Swc2 Negative GeneticPMID:18818364
Negative GeneticPMID:22681890
hip4histone promoter control protein Hip4 Negative GeneticPMID:18818364
Negative GeneticPMID:22681890
spc34DASH complex subunit Spc34 Negative GeneticPMID:18818364
ryh1GTPase Ryh1 Negative GeneticPMID:18818364
Negative GeneticPMID:22681890
SPAC30.02celongator complex associated protein Kti2 (predicted) Negative GeneticPMID:22681890
dep1Sds3-like family protein Dep1 Negative GeneticPMID:22681890
ssp2serine/threonine protein kinase Ssp2 Negative GeneticPMID:22681890
lsc1Lsk1 associated cyclin Negative GeneticPMID:22681890
rsc1RSC complex subunit Rsc1 Negative GeneticPMID:18818364
fft3SMARCAD1 family ATP-dependent DNA helicase Fft3 Negative GeneticPMID:18818364
Negative GeneticPMID:22681890
dam1DASH complex subunit Dam1 Negative GeneticPMID:22681890
duo1DASH complex subunit Duo1 Negative GeneticPMID:22681890
gpa2heterotrimeric G protein alpha-2 subunit Gpa2 Negative GeneticPMID:22681890
caf1CCR4-Not complex CAF1 family ribonuclease subunit Caf1 Negative GeneticPMID:18818364
cwf19complexed with Cdc5 protein Cwf19 Negative GeneticPMID:22681890
ccr1NADPH-cytochrome p450 reductase Negative GeneticPMID:22681890
elp4elongator complex subunit Elp4 (predicted) Negative GeneticPMID:18818364
pab2poly(A) binding protein Pab2 Negative GeneticPMID:18818364
Negative GeneticPMID:22681890
fbh1DNA helicase I Positive GeneticPMID:18818364
atd1aldehyde dehydrogenase (predicted) Negative GeneticPMID:22681890
rxt2histone deacetylase complex subunit Rxt2 Negative GeneticPMID:22681890
Phenotypic EnhancementPMID:19547744
SPAC18G6.13sequence orphan Negative GeneticPMID:22681890
imp1importin alpha Negative GeneticPMID:22681890
dad4DASH complex subunit Dad4 Negative GeneticPMID:22681890
asp1inositol hexakisphosphate kinase/inositol pyrophosphate synthase (predicted) Negative GeneticPMID:22681890
wdr21WD repeat protein, human WDR21 family Positive GeneticPMID:22681890
atp11F1-ATPase chaperone Atp11 (predicted) Positive GeneticPMID:22681890
clr3histone deacetylase (class II) Clr3 Negative GeneticPMID:18818364
Negative GeneticPMID:22681890
bdf2BET family double bromodomain protein Bdf2 Negative GeneticPMID:18818364
Negative GeneticPMID:22681890
srb10cyclin-dependent protein Srb mediator subunit kinase Srb10 Positive GeneticPMID:22681890
cwf15complexed with Cdc5 protein Cwf15 Negative GeneticPMID:22681890
ccq1telomere maintenance protein Ccq1 Negative GeneticPMID:22681890
SPBC1861.05pseudouridine-metabolizing bifunctional protein (predicted) Positive GeneticPMID:22681890
par1protein phosphatase regulatory subunit Par1 Negative GeneticPMID:18818364
Negative GeneticPMID:22681890
tsc1hamartin Negative GeneticPMID:22681890
med7mediator complex subunit Med7 Negative GeneticPMID:22681890
air1zinc knuckle TRAMP complex subunit Air1 Negative GeneticPMID:18818364
SPCC162.11curidine kinase/uracil phosphoribosyltransferase (predicted) Positive GeneticPMID:18818364
saf5splicing factor Negative GeneticPMID:22681890
arp6actin-like protein Arp6 Negative GeneticPMID:18818364
Negative GeneticPMID:22681890
sgf29SAGA complex subunit Sgf29 Positive GeneticPMID:18818364
Positive GeneticPMID:22681890
elp2elongator complex subunit Elp2 (predicted) Negative GeneticPMID:22681890
rnc1RNA-binding protein that suppresses calcineurin deletion Rnc1 Negative GeneticPMID:18818364
Negative GeneticPMID:22681890
pht1histone H2A variant H2A.Z, Pht1 Negative GeneticPMID:18818364
Negative GeneticPMID:22681890
prp4serine/threonine protein kinase Prp4 Negative GeneticPMID:22681890
set1histone lysine methyltransferase Set1 Negative GeneticPMID:18818364
cay1cactin, spliceosome complex subunit (predicted) Negative GeneticPMID:18818364
iwr1RNA polymerase II nuclear import protein Iwr1 (predicted) Negative GeneticPMID:18818364
png2ING family homolog Png2 Negative GeneticPMID:18818364
Negative GeneticPMID:22681890
rok1ATP-dependent RNA helicase Rok1 (predicted) Negative GeneticPMID:18818364
Negative GeneticPMID:22681890
clp1Cdc14-related protein phosphatase Clp1/Flp1 Phenotypic EnhancementPMID:22347452
SPAC824.04WD repeat protein (predicted) Negative GeneticPMID:18818364
Negative GeneticPMID:22681890
apq12nuclear membrane organization protein Apq12 (predicted) Negative GeneticPMID:22681890
pdp1PWWP domain protein Pdp1 Negative GeneticPMID:18818364
spc19DASH complex subunit Spc19 Negative GeneticPMID:22681890
snt2Lid2 complex subunit Snt2 Negative GeneticPMID:18818364
Negative GeneticPMID:22681890
arp42SWI/SNF and RSC complex subunit Arp42 Negative GeneticPMID:18818364
Negative GeneticPMID:22681890
ppk21serine/threonine protein kinase Ppk21 Negative GeneticPMID:22681890
ngg1SAGA complex subunit Ngg1 Positive GeneticPMID:18818364
SPBC8D2.16cDUF171 family protein Positive GeneticPMID:18818364
reb1RNA polymerase I transcription termination factor Reb1 Negative GeneticPMID:18818364
cdc15extended Fer/CIP4 (EFC) domain protein Cdc15 Synthetic Growth DefectPMID:22347452
Synthetic Lethality
vps71Swr1 complex subunit Vps71 Negative GeneticPMID:18818364
rud3Golgi matrix protein Rud3 (predicted) Negative GeneticPMID:22681890
swc3Swr1 complex subunit Swc3 Negative GeneticPMID:22681890
scs7sphingosine hydroxylase Scs7 Positive GeneticPMID:18818364
cti6histone deacetylase complex subunit Cti6 Negative GeneticPMID:22681890
dad1DASH complex subunit Dad1 Negative GeneticPMID:18818364
Negative GeneticPMID:22681890
swd3WD repeat protein Swd3 Negative GeneticPMID:22681890
SPCC1223.01ubiquitin-protein ligase E3 (predicted) Positive GeneticPMID:18818364
sds23PP2A-type phosphatase inhibitor Sds23/Moc1 Negative GeneticPMID:22681890
lsk1P-TEFb-associated cyclin-dependent protein kinase Lsk1 Phenotypic EnhancementPMID:22347452
gls2glucosidase II Gls2 Negative GeneticPMID:22681890
tcg1single-stranded telomeric binding protein Tgc1 Negative GeneticPMID:22681890
SPBC13E7.03cRNA hairpin binding protein (predicted) Positive GeneticPMID:22681890
SPAC13G6.09SSU-rRNA maturation protein Tsr4 homolog 2 (predicted) Negative GeneticPMID:22681890
mpr1histidine-containing response regulator phosphotransferase Mpr1 Negative GeneticPMID:22681890
SPBC16H5.13WD repeat protein, human WDR7 ortholog Negative GeneticPMID:18818364
Negative GeneticPMID:22681890
ask1DASH complex subunit Ask1 Negative GeneticPMID:18818364
Negative GeneticPMID:22681890
sft1SNARE Sft1 (predicted) Negative GeneticPMID:22681890
alp13MRG family Clr6 histone deacetylase complex subunit Alp13 Negative GeneticPMID:22681890
dsk1SR protein-specific kinase Dsk1 Negative GeneticPMID:18818364
Negative GeneticPMID:22681890
msc1multi-copy suppressor of Chk1 Negative GeneticPMID:18818364
Negative GeneticPMID:22681890
pob3FACT complex subunit Pob3 Negative GeneticPMID:18818364
Negative GeneticPMID:22681890
eri1double-strand siRNA ribonuclease Eri1 Negative GeneticPMID:22681890
sdc1Dpy-30 domain protein Sdc1 Negative GeneticPMID:18818364
Negative GeneticPMID:22681890
arp8actin-like protein, Ino80 complex subunit Arp8 Negative GeneticPMID:18818364
Negative GeneticPMID:22681890
amk2AMP-activated protein kinase beta subunit Amk2 Negative GeneticPMID:18818364
SPCC18.10pyridoxine-pyridoxal-pyridoxamine kinase (predicted) Negative GeneticPMID:18818364
Negative GeneticPMID:22681890
snt1Set3 complex subunit Snt1 Phenotypic EnhancementPMID:22347452
sts5RNB-like protein Positive GeneticPMID:22681890
ssu72phosphoric ester hydrolase Ssu72 (predicted) Negative GeneticPMID:18818364
Negative GeneticPMID:22681890
SPBC36B7.08cnucleosome assembly protein (predicted) Negative GeneticPMID:18818364
Negative GeneticPMID:22681890
Physical Interactions

Source: BioGRID

Gene Product Evidence Reference
hif2Set3 complex subunit Hif2 Affinity Capture-WesternPMID:22347452
hos2histone deacetylase (class I) Hos2 Affinity Capture-WesternPMID:22559741
snt1Set3 complex subunit Snt1 Affinity Capture-WesternPMID:22347452
External References
Database Identifier Description
NBRP SPAC22E12.11c Fission yeast strain database, National BioResource Project (Japan)
YOGY SPAC22E12.11c Retrieval of eukaryotic orthologs (Bähler Lab)
BioGrid SPAC22E12.11c BioGRID Interaction Datasets
Expression Viewer SPAC22E12.11c Cell Cycle Expression Profile (Bähler Lab)
Expression Viewer SPAC22E12.11c Meiosis/Sporulation Expression Profies (Bähler Lab)
Expression Viewer SPAC22E12.11c Pheromone response/mating expression profiles (Bähler Lab)
Expression Viewer SPAC22E12.11c Environmental stress expression profiles (Bähler Lab)
Pomb(A) SPAC22E12.11c Polyadenylation Viewer (Gullerova lab)
pombeTV SPAC22E12.11c Transcriptome Viewer (Bähler Lab)
Cyclebase SPAC22E12.11c Cell Cycle Data
GEO SPAC22E12.11c GEO profiles
PInt SPAC22E12.11c Protein-Protein Interaction Predictor (Bähler Lab)
WikiGene2541899histone lysine methyltransferase Set3
EntrezGene2541899histone lysine methyltransferase Set3
SPD / RIKEN38/38E02Orfeome Localization Data
UniProtKB/SwissProtQ10362SET domain-containing protein 3
ModBaseQ10362Database of comparative protein structure models
StringQ10362Network display of known and predicted interactions and functional associations
RefSeq PeptideNP_594837histone lysine methyltransferase Set3
RefSeq mRNANM_001020266972h- histone lysine methyltransferase Set3 (set3), mRNA
European Nucleotide ArchiveBAA87134ENA Protein Mapping
European Nucleotide ArchiveCAA93898ENA Protein Mapping
UniParcUPI000013A908UniProt Archive

Literature for set3

Search: Europe PMC or PubMed

Release Version: PomBase:21_41 - 24 Feb 2014