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 binding831
Annotation ExtensionEvidenceWith/FromReference
transcription corepressor activity12
Annotation ExtensionEvidenceWith/FromReference
GO Biological Process
Term NameCount
cellular protein localization550
Annotation ExtensionEvidenceWith/FromReference
cellular response to nitrogen starvation86
Annotation ExtensionEvidenceWith/FromReference
chromatin modification219
Annotation ExtensionEvidenceWith/FromReference
chromatin silencing at centromere56
Annotation ExtensionEvidenceWith/FromReference
chromatin silencing at silent mating-type cassette33
Annotation ExtensionEvidenceWith/FromReference
DNA replication-independent nucleosome assembly12
Annotation ExtensionEvidenceWith/FromReference
mitotic sister chromatid segregation192
Annotation ExtensionEvidenceWith/FromReference
negative regulation of transcription from RNA polymerase II promoter79
Annotation ExtensionEvidenceWith/FromReference
regulation of G2/M transition of mitotic cell cycle63
Annotation ExtensionEvidenceWith/FromReference
GO Cellular Component
Term NameCount
cytosol2315
Annotation ExtensionEvidenceWith/FromReference
HIR complex4
Annotation ExtensionEvidenceWith/FromReference
nuclear chromatin283
Annotation ExtensionEvidenceWith/FromReference
nucleus2740
Annotation ExtensionEvidenceWith/FromReference
Fission Yeast Phenotype Ontology
Gene Deletion Viability: Viable

Population Phenotype

Term IDTerm NameEvidenceAlleleExpressionConditionReferenceCount
FYPO:0002060viable vegetative cell populationMicroscopyslm9ΔNullPMID:204732893759
Microscopyslm9ΔNullPECO:0000005, PECO:0000137PMID:23697806

Cell Phenotype

Term IDTerm NameEvidenceAlleleExpressionConditionReferenceCount
FYPO:0000059abnormal mitotic cell cycleMicroscopyslm9ΔNullPECO:0000005, PECO:0000137PMID:23697806686
FYPO:0000623abnormal positive regulation of transcription14
has_regulation_target hht3Quantitative PCRslm9ΔNullPMID:17452352
has_regulation_target hhf1Quantitative PCRslm9ΔNullPMID:17452352
has_regulation_target hht1Quantitative PCRslm9ΔNullPMID:17452352
has_regulation_target hta1Quantitative PCRslm9ΔNullPMID:17452352
has_regulation_target hta2Quantitative PCRslm9ΔNullPMID:17452352
has_regulation_target hht2Quantitative PCRslm9ΔNullPMID:17452352
has_regulation_target hhf2Quantitative PCRslm9ΔNullPMID:17452352
has_regulation_target hhf3Quantitative PCRslm9ΔNullPMID:17452352
FYPO:0001122elongated vegetative cellMicroscopyslm9ΔNullPMID:10835386685
FYPO:0001492viable elongated vegetative cell221
penetrance FYPO_EXT:0000001Microscopyslm9ΔNullPECO:0000005, PECO:0000137PMID:23697806
Transcript
Ensembl transcript structure with UTRs, exons and introns

Exons

Exon Start End
130154063018155

UTRs

Region Coordinates Reference
five_prime_UTR3015406..3015537PMID:21511999
three_prime_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
PF00400 Pfam IPR001680 WD40 repeat 175 212 104
PF00400 Pfam IPR001680 WD40 repeat 273 313 104
PF07569 Pfam IPR011494 TUP1-like enhancer of split 528 743 2
SM00320 SMART IPR001680 WD40 repeat 319 356 112
SM00320 SMART IPR001680 WD40 repeat 267 313 112
SM00320 SMART IPR001680 WD40 repeat 173 212 112
SM00320 SMART IPR001680 WD40 repeat 46 92 112
PS00678 Prosite Patterns IPR019775 WD40 repeat, conserved site 300 314 65
PS50294 Prosite Profiles IPR017986 WD40-repeat-containing domain 180 221 104
PS50082 Prosite Profiles IPR001680 WD40 repeat 180 215 100
PTHR13831:SF0 HMMPANTHER 172 803 2
PTHR13831 HMMPANTHER 172 803 2
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 164 376 145
2.130.10.10 Gene3D IPR015943 WD40/YVTN repeat-like-containing domain 20 130 145
SSF50978 SuperFamily IPR017986 WD40-repeat-containing domain 174 357 135
SSF50978 SuperFamily IPR017986 WD40-repeat-containing domain 16 134 135

View domain organization at Pfam

Manually Curated Family or Sub-families

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
Isoelectric point 7.33
Molecular weight 90.43 kDa
Number of residues 807
Modifications

Protein Modifications

Term IDTerm NameEvidenceResidueReferenceCount
MOD:00046O-phospho-L-serineexperimental evidenceS421PMID:217125471670
present during mitotic M phase
present during mitotic M phaseexperimental evidenceS422PMID:21712547
present during mitotic M phaseexperimental evidenceS406PMID:21712547
present during mitotic M phaseexperimental evidenceS425PMID:21712547
present during mitotic M phaseexperimental evidenceS418PMID:21712547
experimental evidenceS406PMID:24763107
present during mitotic M phaseexperimental evidenceS398PMID:21712547
experimental evidenceS765PMID:24763107
experimental evidenceS422PMID:24763107
MOD:00696phosphorylated residueNASPMID:195477441922
Sequence
Gene Expression

Quantitative Gene Expression

Protein Level

Molecules/Cell (average)ExtensionConditionScaleEvidenceReference
1707during GO:0072690PECO:0000126,
PECO:0000005
single_cellmass spectrometry evidencePMID:24763107
103.33during GO:0072690PECO:0000005,
PECO:0000014
population_wideexperimental evidencePMID:23101633
NDduring cell quiescence following G1 arrest due to nitrogen limitationPECO:0000005,
PECO:0000014,
PECO:0000127
population_wideexperimental evidencePMID:23101633

RNA Level

Molecules/Cell (average)ExtensionConditionScaleEvidenceReference
1.1during GO:0072690PECO:0000005,
PECO:0000014
population_wideexperimental evidencePMID:23101633
0.4during cell quiescence following G1 arrest due to nitrogen limitationPECO:0000005,
PECO:0000014,
PECO:0000127
population_wideexperimental evidencePMID:23101633
Misc
DescriptionQualifierReferenceCount
deletion mutant expression profiling PMID:1962028278
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
Species Distribution
DescriptionQualifierReferenceCount
predominantly single copy (one to one)3092
conserved in fungi4600
conserved in eukaryotes4514
conserved in metazoa3425
conserved in vertebrates3400
conserved in eukaryotes only2497
Orthologs

Manually curated orthologous groups

SpeciesGeneDescriptionLinksCount

Orthologs in Compara


Physical Interactions

Source: BioGRID

View all interactions in esyN
View the HCPIN interactions in esyN

Gene Product Evidence Reference
pss1heat shock protein Pss1 Affinity Capture-MSPMID:20976105
cct6chaperonin-containing T-complex zeta subunit Cct6 Affinity Capture-MSPMID:20976105
hsp90Hsp90 chaperone Affinity Capture-MSPMID:20976105
rad2414-3-3 protein Rad24 Affinity Capture-MSPMID:20976105
nda3tubulin beta Nda3 Affinity Capture-MSPMID:20976105
cct4chaperonin-containing T-complex delta subunit Cct4 Affinity Capture-MSPMID:20976105
trs1cytoplasmic threonine-tRNA ligase Trs1 (predicted) Affinity Capture-MSPMID:20976105
mts419S proteasome regulatory subunit Mts4 Affinity Capture-MSPMID:20976105
dfr1dihydrofolate reductase/ serine hydrolase family fusion protein Dfr1 Affinity Capture-MSPMID:20976105
gpd1glycerol-3-phosphate dehydrogenase Gpd1 Affinity Capture-MSPMID:20976105
cct8chaperonin-containing T-complex theta subunit Cct8 Affinity Capture-MSPMID:20976105
cdc48AAA family ATPase involved in ubiquitin-mediated protein degradation Cdc48 Affinity Capture-MSPMID:20976105
vma2V-type ATPase V1 subunit B Affinity Capture-MSPMID:20976105
rpt119S proteasome regulatory subunit Rpt1 (predicted) Affinity Capture-MSPMID:20976105
hip1hira protein, histone chaperone Hip1 Affinity Capture-MSPMID:20976105
Affinity Capture-MSPMID:16428807
Affinity Capture-WesternPMID:15121850
ura1carbamoyl-phosphate synthase (glutamine hydrolyzing), aspartate carbamoyltransferase Ura1 Affinity Capture-MSPMID:20976105
rpt319S proteasome regulatory subunit Rpt3 (predicted) Affinity Capture-MSPMID:20976105
ilv1acetolactate synthase catalytic subunit Affinity Capture-MSPMID:20976105
cts1CTP synthase Cts1 (predicted) Affinity Capture-MSPMID:20976105
SPBC365.16conserved protein Affinity Capture-MSPMID:20976105
lys4homocitrate synthase Affinity Capture-MSPMID:20976105
ade1phosphoribosylamine-glycine ligase/phosphoribosylformylglycinamidine cyclo-ligase Affinity Capture-MSPMID:20976105
slm9hira protein Slm9 Affinity Capture-MSPMID:20976105
SPCC1827.06caspartate semialdehyde dehydrogenase (predicted) Affinity Capture-MSPMID:20976105
tef3translation elongation factor eEF3 Affinity Capture-MSPMID:20976105
rpt419S proteasome regulatory subunit Rpt4 (predicted) Affinity Capture-MSPMID:20976105
sir1sulfite reductase Sir1 Affinity Capture-MSPMID:20976105
hip3HIRA interacting protein Hip3 Affinity Capture-MSPMID:20976105
Affinity Capture-WesternPMID:16428807
Affinity Capture-MS
rpt219S proteasome regulatory subunit Rpt2 Affinity Capture-MSPMID:20976105
cia1histone chaperone Cia1 Affinity Capture-MSPMID:21211723
hip4histone promoter control protein Hip4 Affinity Capture-MSPMID:20976105
Affinity Capture-Western
atb2tubulin alpha 2 Affinity Capture-MSPMID:20976105
vrs2mitochondrial valine-tRNA ligase Vrs2/Vas2 Affinity Capture-MSPMID:20976105
pgk1phosphoglycerate kinase Pgk1 (predicted) Affinity Capture-MSPMID:20976105
anc1mitochondrial adenine nucleotide carrier Anc1 Affinity Capture-MSPMID:20976105
ssa1heat shock protein Ssa1 (predicted) Affinity Capture-MSPMID:20976105
cct1chaperonin-containing T-complex alpha subunit Cct1 Affinity Capture-MSPMID:20976105
fba1fructose-bisphosphate aldolase Fba1 Affinity Capture-MSPMID:20976105
rvb1AAA family ATPase Rvb1 Affinity Capture-MSPMID:20976105
gus1cytoplasmic glutamate-tRNA ligase gus1 (predicted) Affinity Capture-MSPMID:20976105
atp2F1-ATPase beta subunit Atp2 Affinity Capture-MSPMID:20976105
rpt519S proteasome regulatory subunit Rpt5 (predicted) Affinity Capture-MSPMID:20976105
Genetic Interactions

Source: BioGRID

View these interactions in esyN

Gene Product Evidence Reference
res2MBF transcription factor complex subunit Res2 Synthetic Growth DefectPMID:18931302
rik1silencing protein Rik1 Synthetic Growth DefectPMID:18931302
set1histone lysine methyltransferase Set1 Synthetic Growth DefectPMID:18931302
hos2histone deacetylase (class I) Hos2 Synthetic Growth DefectPMID:18931302
cdr1NIM1 family serine/threonine protein kinase Cdr1/Nim1 Phenotypic EnhancementPMID:10835386
cdr2serine/threonine protein kinase Cdr2 Phenotypic EnhancementPMID:10835386
cul3cullin 3 Synthetic Growth DefectPMID:18931302
mmd1deoxyhypusine hydroxylase (predicted) Synthetic Growth DefectPMID:18931302
pof9F-box protein Pof9 Synthetic Growth DefectPMID:18931302
swd1Set1C complex subunit Swd1 Phenotypic SuppressionPMID:19547744
cdc25M phase inducer tyrosine phosphatase Cdc25 Synthetic Growth DefectPMID:9843572
Phenotypic SuppressionPMID:10835386
pmt3SUMO Synthetic Growth DefectPMID:18931302
ctf18RFC-like complex subunit Ctf18 Synthetic Growth DefectPMID:18931302
ctu1cytosolic thiouridylase subunit Ctu1 Synthetic Growth DefectPMID:18931302
alg6glucosyltransferase Alg6 Synthetic Growth DefectPMID:18931302
sgf73SAGA complex subunit Sgf73 Synthetic Growth DefectPMID:18931302
ash2Ash2-trithorax family protein Synthetic Growth DefectPMID:18931302
ies2Ino80 complex subunit Ies2 Synthetic Growth DefectPMID:18931302
hst2Sir2 family histone deacetylase Hst2 Synthetic Growth DefectPMID:18931302
swc2Swr1 complex complex subunit Swc2 Synthetic Growth DefectPMID:18931302
mak10NatC N-acetyltransferase complex subunit Mak10 (predicted) Synthetic Growth DefectPMID:18931302
pht1histone H2A variant H2A.Z, Pht1 Synthetic Growth DefectPMID:18931302
pli1SUMO E3 ligase Pli1 Synthetic Growth DefectPMID:18931302
pyp2tyrosine phosphatase Pyp2 Synthetic Growth DefectPMID:18931302
spf1Set1C PHD Finger protein Spf1 Synthetic Growth DefectPMID:18931302
wee1M phase inhibitor protein kinase Wee1 Synthetic Growth DefectPMID:9843572
Phenotypic SuppressionPMID:10835386
spa2GTPase activating protein Spa2 (predicted) Synthetic Growth DefectPMID:18931302
mrc1mediator of replication checkpoint 1 Synthetic Growth DefectPMID:18931302
pof3F-box protein Pof3 Synthetic Growth DefectPMID:18931302
rud3Golgi matrix protein Rud3 (predicted) Synthetic Growth DefectPMID:18931302
fhl1forkhead transcription factor Fhl1 Synthetic Growth DefectPMID:18931302
swi6HP1 family chromodomain protein Swi6 Synthetic Growth DefectPMID:18931302
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)
Cyclebase SPBC15D4.03 Cell Cycle Data
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
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:23_47 - 27 Oct 2014