slm9 (SPBC15D4.03)


Gene Standard Nameslm9 Characterisation Statuspublished
Systematic IDSPBC15D4.03 Feature Typeprotein coding
Synonyms Name Description
Producthira protein Slm9 Product Size807aa, 90.43 kDa
Genomic Location Chromosome II, 3015406-3018155 (2750nt); CDS:3015538-3017961 (2424nt)

Ensembl Gene Location
GO Molecular Function
Term NameCount
protein binding887
Annotation ExtensionEvidenceWith/FromReference
transcription corepressor activity6
Annotation ExtensionEvidenceWith/FromReference
GO Biological Process
GO Cellular Component
Term NameCount
cytosol2302
Annotation ExtensionEvidenceWith/FromReference
HIR complex4
Annotation ExtensionEvidenceWith/FromReference
nuclear chromatin365
Annotation ExtensionEvidenceWith/FromReference
nucleus2700
Annotation ExtensionEvidenceWith/FromReference
FYPO Single-Allele Phenotypes
Gene Deletion Viability: Viable

Population Phenotype

Term NameGenotypesCount
abolished cell population growth at high temperatureslm9Δ38
abolished cell population growth at low temperatureslm9Δ4
decreased cell population growth at high temperatureslm9Δ178
normal growth on glucose carbon sourceslm9Δ294
normal mating efficiencyslm9Δ30
sensitive to thiabendazoleslm9Δ329
viable vegetative cell populationslm9Δ3850

Cell Phenotype

Term NameGenotypesCount
abnormal mitotic cell cycleslm9Δ894
abnormal positive regulation of transcription21
affecting hhf1slm9Δ
affecting hht1slm9Δ
affecting hta2slm9Δ
affecting hht3slm9Δ
affecting hhf3slm9Δ
affecting hhf2slm9Δ
affecting hht2slm9Δ
affecting hta1slm9Δ
decreased chromatin silencing at centromere outer repeatslm9Δ48
decreased chromatin silencing at silent mating-type cassetteslm9Δ29
decreased level of iron ion starvation-induced proteinsslm9Δ2
decreased protein level during vegetative growth153
affecting hip3slm9Δ
decreased protein localization to nucleus during vegetative growth36
affects localization of hip1slm9Δ
elongated vegetative cellslm9Δ802
increased antisense RNA levelslm9Δ15
increased centromeric outer repeat transcript levelslm9Δ31
increased LTR-derived RNA levelslm9Δ10
increased RNA level during vegetative growth342
affecting SPBC19C7.04cslm9Δ
affecting hsp16slm9Δ
increased subtelomere-derived RNA levelslm9Δ13
increased transposable element-derived small RNA levelslm9Δ10
lagging mitotic chromosomesslm9Δ41
normal protein level during vegetative growth91
affecting hip1slm9Δ
normal RNA level during vegetative growth133
affecting fep1slm9Δ
normal transpositionslm9Δ3
shortened telomeresslm9Δ44
viable elongated vegetative cellslm9Δ325

FYPO Multi-allele Phenotypes

Population Phenotype

Term NameGenotypes
abolished cell population growth at high temperatureslm9Δ, hip1Δ
slm9Δ, hip3Δ
abolished cell population growth at low temperatureslm9Δ, hip1Δ
slm9Δ, hip3Δ
sensitive to thiabendazoleslm9Δ, hip3Δ
slm9Δ, hip1Δ

Cell Phenotype

Term NameGenotypes
increased LTR-derived RNA levelslm9Δ, hip1Δ
slm9Δ, hip3Δ
increased RNA level during vegetative growth
affecting SPBC19C7.04cslm9Δ, hip3Δ
affecting SPBC19C7.04cslm9Δ, hip1Δ
affecting hsp16slm9Δ, hip1Δ
affecting hsp16slm9Δ, hip3Δ
viable elongated vegetative cellslm9Δ, hip3Δ
Target Of
OntologyRelationshipGeneProduct
FYPO affected by mutation in hip1 hira protein, histone chaperone Hip1
FYPO affected by mutation in hip3 HIRA interacting protein Hip3
Transcript
Ensembl transcript structure with UTRs, exons and introns

Transcript Structure

Region Coordinates Reference
Exons3015406..3018155
mRNA3015406..3018155
5' UTR3015406..3015537PMID:21511999
CDS3015538..3017961
3' UTR3017962..3018155PMID: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
PF07569 Pfam IPR011494 TUP1-like enhancer of split 529 743 2
PF00400 Pfam IPR001680 WD40 repeat 175 212 88
SM00320 SMART IPR001680 WD40 repeat 319 356 112
SM00320 SMART IPR001680 WD40 repeat 173 212 112
SM00320 SMART IPR001680 WD40 repeat 46 92 112
SM00320 SMART IPR001680 WD40 repeat 267 313 112
PS50082 Prosite Profiles IPR001680 WD40 repeat 180 215 100
PS50294 Prosite Profiles IPR017986 WD40-repeat-containing domain 180 221 104
PS00678 Prosite Patterns IPR019775 WD40 repeat, conserved site 300 314 65
PTHR13831:SF0 HMMPANTHER 172 801 2
PTHR13831 HMMPANTHER IPR031120 WD repeat HIR1 172 801 2
2.130.10.10 Gene3D IPR015943 WD40/YVTN repeat-like-containing domain 164 376 145
2.130.10.10 Gene3D IPR015943 WD40/YVTN repeat-like-containing domain 473 581 145
2.130.10.10 Gene3D IPR015943 WD40/YVTN repeat-like-containing domain 20 130 145
SSF50978 SuperFamily IPR017986 WD40-repeat-containing domain 16 134 135
SSF50978 SuperFamily IPR017986 WD40-repeat-containing domain 174 357 135

View domain organization at Pfam

Term IDTerm NameReferenceCount
PBO:0000190WD repeat proteinTemporary processing gif - replaced by AJAX with count of genes annotated with the term PBO:0000190

Protein Properties

Ave. residue weight 112.06 Da
Charge 10.50
Codon Adaptation Index 0.38
Isoelectric point 7.33
Molecular weight 90.43 kDa
Number of residues 807
Modifications

Protein Modifications

Term NameResidueCount
O-phospho-L-serine 2289
present during mitotic M phaseS398
present during mitotic M phaseS418
present during mitotic M phaseS406
present during mitotic M phaseS422
present during mitotic M phaseS425
present during mitotic M phaseS421
S398, S406, S408, S421, S422, S425, S765
Annotation ExtensionEvidenceResidueReference
present during mitotic M phase experimental evidence S398 PMID:21712547
present during mitotic M phase experimental evidence S418 PMID:21712547
present during mitotic M phase experimental evidence S406 PMID:21712547
present during mitotic M phase experimental evidence S422 PMID:21712547
present during mitotic M phase experimental evidence S425 PMID:21712547
present during mitotic M phase experimental evidence S421 PMID:21712547
IDA S406 PMID:25720772
IDA S425 PMID:25720772
experimental evidence S765 PMID:24763107
experimental evidence S422 PMID:24763107
IDA S421 PMID:25720772
experimental evidence S406 PMID:24763107
IDA S408 PMID:25720772
IDA S422 PMID:25720772
IDA S398 PMID:25720772
O-phospho-L-threonineT400 1085
Annotation ExtensionEvidenceResidueReference
IDA T400 PMID:25720772
phosphorylated residue 2511
Annotation ExtensionEvidenceResidueReference
IDA PMID:19547744
O-phosphorylated residueS398,S406, S398,S408, S418,S425, S421,S422, S421,S425, S422,S425, T397,S406, T400,S406 2457
Annotation ExtensionEvidenceResidueReference
IDA S398,S408 PMID:25720772
IDA S421,S422 PMID:25720772
IDA S422,S425 PMID:25720772
IDA S398,S406 PMID:25720772
IDA S418,S425 PMID:25720772
IDA T397,S406 PMID:25720772
IDA T400,S406 PMID:25720772
IDA S421,S425 PMID:25720772
Sequence
Gene Expression

Quantitative Gene Expression

View graphical display of gene expression data for slm9 (SPBC15D4.03)

Protein Level

Molecules/Cell (average)ExtensionConditionScaleEvidenceReference
103.33during GO:0072690PECO:0000014,
PECO:0000005
population wideexperimental evidencePMID:23101633
1707during GO:0072690PECO:0000005,
PECO:0000126
single cellmass spectrometry evidencePMID:24763107

RNA Level

Molecules/Cell (average)ExtensionConditionScaleEvidenceReference
1.1during GO:0072690PECO:0000014,
PECO:0000005
population wideexperimental evidencePMID:23101633
0.4during cell quiescence following G1 arrest due to nitrogen limitationPECO:0000127,
PECO:0000014,
PECO:0000005
population wideexperimental evidencePMID:23101633
Misc
DescriptionQualifierReferenceCount
deletion mutant expression profiling PMID:1962028279
target of proteasomeInferred from Physical Interaction PMID:209761053
target of chaperonin-containing T-complexInferred from Physical Interaction PMID:209761051
Miscellaneous Functional Group
DescriptionQualifierReferenceCount
histone chaperone14
Taxonomic Conservation
DescriptionQualifierReferenceCount
predominantly single copy (one to one)3093
conserved in fungi4607
conserved in eukaryotes4517
conserved in metazoa3427
conserved in vertebrates3402
conserved in eukaryotes only2502
Orthologs

Manually curated orthologous groups

SpeciesGeneDescriptionLinksCount

Orthologs in Compara


Physical Interactions

Source: BioGRID

Load genes that interact physically with SPBC15D4.03 into the Query Builder
View all interactions in esyN
View the HCPIN interactions in esyN

Gene Product Evidence Reference
affinity capturesrpt519S proteasome regulatory subunit Rpt5 (predicted) Affinity Capture-MSPMID:20976105
affinity capturescts1CTP synthase Cts1 (predicted) Affinity Capture-MSPMID:20976105
affinity capturesgus1cytoplasmic glutamate-tRNA ligase gus1 (predicted) Affinity Capture-MSPMID:20976105
affinity capturesanc1mitochondrial adenine nucleotide carrier Anc1 Affinity Capture-MSPMID:20976105
affinity capturesura1carbamoyl-phosphate synthase (glutamine hydrolyzing), aspartate carbamoyltransferase Ura1 Affinity Capture-MSPMID:20976105
affinity captureship4histone promoter control protein Hip4 Affinity Capture-MSPMID:20976105
affinity captureship1hira protein, histone chaperone Hip1 Affinity Capture-MSPMID:16428807
affinity capturesmts419S proteasome regulatory subunit Mts4 Affinity Capture-MSPMID:20976105
affinity capturesvrs2mitochondrial valine-tRNA ligase Vrs2/Vas2 Affinity Capture-MSPMID:20976105
affinity capturestef3translation elongation factor eEF3 Affinity Capture-MSPMID:20976105
affinity capturesgpd1glycerol-3-phosphate dehydrogenase Gpd1 Affinity Capture-MSPMID:20976105
affinity capturesslm9hira protein Slm9 Affinity Capture-MSPMID:20976105
affinity capturesrpt219S proteasome regulatory subunit Rpt2 Affinity Capture-MSPMID:20976105
affinity capturesrpt119S proteasome regulatory subunit Rpt1 (predicted) Affinity Capture-MSPMID:20976105
affinity capturesdfr1dihydrofolate reductase/ serine hydrolase family fusion protein Dfr1 Affinity Capture-MSPMID:20976105
affinity captureslys4homocitrate synthase Affinity Capture-MSPMID:20976105
affinity capturessir1sulfite reductase beta subunit Sir1 Affinity Capture-MSPMID:20976105
affinity capturesfba1fructose-bisphosphate aldolase Fba1 Affinity Capture-MSPMID:20976105
affinity capturespgk1phosphoglycerate kinase Pgk1 (predicted) Affinity Capture-MSPMID:20976105
affinity capturesilv1acetolactate synthase catalytic subunit Affinity Capture-MSPMID:20976105
affinity capturescct4chaperonin-containing T-complex delta subunit Cct4 Affinity Capture-MSPMID:20976105
affinity capturesrpt319S proteasome regulatory subunit Rpt3 (predicted) Affinity Capture-MSPMID:20976105
affinity capturesvma2V-type ATPase V1 subunit B Affinity Capture-MSPMID:20976105
affinity capturesrvb1AAA family ATPase Rvb1 Affinity Capture-MSPMID:20976105
affinity capturescct1chaperonin-containing T-complex alpha subunit Cct1 Affinity Capture-MSPMID:20976105
affinity capturespss1heat shock protein Pss1 Affinity Capture-MSPMID:20976105
affinity capturesatp2F1-ATPase beta subunit Atp2 Affinity Capture-MSPMID:20976105
affinity captureshsp90Hsp90 chaperone Affinity Capture-MSPMID:20976105
affinity capturesSPCC1827.06caspartate semialdehyde dehydrogenase (predicted) Affinity Capture-MSPMID:20976105
affinity capturesSPBC365.16conserved protein Affinity Capture-MSPMID:20976105
affinity capturesrpt419S proteasome regulatory subunit Rpt4 (predicted) Affinity Capture-MSPMID:20976105
affinity capturescct6chaperonin-containing T-complex zeta subunit Cct6 Affinity Capture-MSPMID:20976105
affinity capturescdc48AAA family ATPase involved in ubiquitin-mediated protein degradation Cdc48 Affinity Capture-MSPMID:20976105
affinity captureship3HIRA interacting protein Hip3 Affinity Capture-MSPMID:20976105
affinity capturesnda3tubulin beta Nda3 Affinity Capture-MSPMID:20976105
affinity capturescct8chaperonin-containing T-complex theta subunit Cct8 Affinity Capture-MSPMID:20976105
affinity capturestrs1cytoplasmic threonine-tRNA ligase Trs1 (predicted) Affinity Capture-MSPMID:20976105
affinity capturesssa1heat shock protein Ssa1 (predicted) Affinity Capture-MSPMID:20976105
affinity capturesrad2414-3-3 protein Rad24 Affinity Capture-MSPMID:20976105
affinity capturesade1phosphoribosylamine-glycine ligase/phosphoribosylformylglycinamidine cyclo-ligase Affinity Capture-MSPMID:20976105
affinity capturesatb2tubulin alpha 2 Affinity Capture-MSPMID:20976105
affinity captured byhip4histone promoter control protein Hip4 Affinity Capture-WesternPMID:20976105
affinity captured bycia1histone chaperone Cia1 Affinity Capture-MSPMID:21211723
affinity captured byhip1hira protein, histone chaperone Hip1 Affinity Capture-MSPMID:16428807
Genetic Interactions

Source: BioGRID

Load genes that interact genetically with SPBC15D4.03 into the Query Builder
View these interactions in esyN

Gene Product Evidence Reference
synthetic growth defect withpmt3SUMO Synthetic Growth DefectPMID:18931302
synthetic growth defect withwee1M phase inhibitor protein kinase Wee1 Synthetic Growth DefectPMID:9843572
synthetic growth defect withpof9F-box protein Pof9 Synthetic Growth DefectPMID:18931302
synthetic growth defect withsgf73SAGA complex subunit Sgf73 Synthetic Growth DefectPMID:18931302
synthetic growth defect withmmd1deoxyhypusine hydroxylase (predicted) Synthetic Growth DefectPMID:18931302
synthetic growth defect withset1histone lysine methyltransferase Set1 Synthetic Growth DefectPMID:18931302
synthetic growth defect withhos2histone deacetylase (class I) Hos2 Synthetic Growth DefectPMID:18931302
synthetic growth defect withpyp2tyrosine phosphatase Pyp2 Synthetic Growth DefectPMID:18931302
synthetic growth defect withspf1Set1C PHD Finger protein Spf1 Synthetic Growth DefectPMID:18931302
synthetic growth defect withash2Ash2-trithorax family protein Synthetic Growth DefectPMID:18931302
synthetic growth defect withrud3Golgi matrix protein Rud3 (predicted) Synthetic Growth DefectPMID:18931302
synthetic growth defect withswc2Swr1 complex complex subunit Swc2 Synthetic Growth DefectPMID:18931302
synthetic growth defect withcul3cullin 3 Synthetic Growth DefectPMID:18931302
synthetic growth defect withrik1silencing protein Rik1 Synthetic Growth DefectPMID:18931302
synthetic growth defect withalg6glucosyltransferase Alg6 Synthetic Growth DefectPMID:18931302
synthetic growth defect withpli1SUMO E3 ligase Pli1 Synthetic Growth DefectPMID:18931302
synthetic growth defect withcdc25M phase inducer tyrosine phosphatase Cdc25 Synthetic Growth DefectPMID:9843572
synthetic growth defect withpht1histone H2A variant H2A.Z, Pht1 Synthetic Growth DefectPMID:18931302
synthetic growth defect withres2MBF transcription factor complex subunit Res2 Synthetic Growth DefectPMID:18931302
synthetic growth defect withfhl1forkhead transcription factor Fhl1 Synthetic Growth DefectPMID:18931302
synthetic growth defect withswi6HP1 family chromodomain protein Swi6 Synthetic Growth DefectPMID:18931302
synthetic growth defect withies2Ino80 complex subunit Ies2 Synthetic Growth DefectPMID:18931302
synthetic growth defect withpof3F-box protein Pof3 Synthetic Growth DefectPMID:18931302
synthetic growth defect withspa2cell polarity protein Spa2 Synthetic Growth DefectPMID:18931302
synthetic growth defect withmak10NatC N-acetyltransferase complex subunit Mak10 (predicted) Synthetic Growth DefectPMID:18931302
synthetic growth defect withmrc1mediator of replication checkpoint 1 Synthetic Growth DefectPMID:18931302
synthetic growth defect withhst2Sirtuin family histone deacetylase Hst2 Synthetic Growth DefectPMID:18931302
synthetic growth defect withctf18RFC-like complex subunit Ctf18 Synthetic Growth DefectPMID:18931302
synthetic growth defect withctu1cytosolic thiouridylase subunit Ctu1 Synthetic Growth DefectPMID:18931302
rescuesswd1Set1C complex subunit Swd1 Phenotypic SuppressionPMID:19547744
rescued bycdc25M phase inducer tyrosine phosphatase Cdc25 Phenotypic SuppressionPMID:10835386
rescued bywee1M phase inhibitor protein kinase Wee1 Phenotypic SuppressionPMID:10835386
phenotype enhanced bycdr1NIM1 family serine/threonine protein kinase Cdr1/Nim1 Phenotypic EnhancementPMID:10835386
phenotype enhanced bycdr2serine/threonine protein kinase Cdr2 Phenotypic EnhancementPMID:10835386
External References
Database Identifier Description
NBRP SPBC15D4.03 Fission yeast strain database, National BioResource Project (Japan)
YOGY SPBC15D4.03 Retrieval of eukaryotic orthologs (Bähler Lab)
BioGrid SPBC15D4.03 BioGRID Interaction Datasets
Expression Viewer SPBC15D4.03 Cell Cycle Expression Profile (Bähler Lab)
Expression Viewer SPBC15D4.03 Meiosis/Sporulation Expression Profies (Bähler Lab)
Expression Viewer SPBC15D4.03 Pheromone response/mating expression profiles (Bähler Lab)
Expression Viewer SPBC15D4.03 Environmental stress expression profiles (Bähler Lab)
Pomb(A) SPBC15D4.03 Polyadenylation Viewer (Gullerova lab)
pombeTV SPBC15D4.03 Transcriptome Viewer (Bähler Lab)
GEO SPBC15D4.03 GEO profiles
PInt SPBC15D4.03 Protein-Protein Interaction Predictor (Bähler Lab)
PeptideAtlas SPBC15D4.03 Peptides identified in tandem mass spectrometry proteomics experiments
SYSGRO SPBC15D4.03 Fission yeast phenotypic data & analysis
Cyclebase SPBC15D4.03.1 Cell Cycle Data
SPD / RIKEN39/39F12Orfeome Localization Data
UniProtKB/SwissProtO74309Histone transcription regulator slm9
ModBaseO74309Database of comparative protein structure models
STRINGO74309Network display of known and predicted interactions and functional associations
RefSeq PeptideNP_596243hira protein Slm9
RefSeq mRNANM_001022162972h- hira protein Slm9 (slm9), mRNA
European Nucleotide ArchiveCAA20478.1ENA Protein Mapping
UniParcUPI0000135A1CUniProt Archive

Literature for slm9

Search: Europe PMC or PubMed

Release Version: PomBase:30_61 - 12 Sep 2016