SPCC550.03c


Gene Standard NameUnassigned Characterisation Statusbiological_role_inferred
Systematic IDSPCC550.03c Feature Typeprotein coding
Synonyms Name Description
ProductSki complex RNA helicase Ski2 (predicted) Product Size1213aa, 138.03 kDa
Genomic Location Chromosome III, 1191396-1187669 (3728nt); CDS:1191376-1187735 (3642nt)

Ensembl Gene Location
GO Molecular Function
Term IDTerm NameEvidenceWith/FromReferenceCount
GO:0005524ATP bindingIEAUniProtKB-KW:KW-0067GO_REF:0000037558
GO:0003723RNA bindingIEAUniProtKB-KW:KW-0694GO_REF:0000037646
GO:0003724RNA helicase activityISOSGD:S000004390GO_REF:000002441
GO Biological Process
Term IDTerm NameEvidenceWith/FromReferenceCount
GO:0006402mRNA catabolic processISOSGD:S000004390GO_REF:000002471
GO:0070478nuclear-transcribed mRNA catabolic process, 3'-5' exonucleolytic nonsense-mediated decayISOSGD:S000004390GO_REF:000002417
GO:0070481nuclear-transcribed mRNA catabolic process, non-stop decayISOSGD:S000004390GO_REF:000002415
GO:2000765regulation of cytoplasmic translationISOSGD:S000004390GO_REF:000002420
GO Cellular Component
Term IDTerm NameEvidenceWith/FromReferenceCount
GO:0055087Ski complexISOSGD:S000004390GO_REF:00000243
GO:0005737cytoplasmISOSGD:S000004390GO_REF:00000244205
GO:0005829cytosolIDAPMID:168233722315
GO:0005730nucleolusISOSGD:S000004390GO_REF:0000024343
Fission Yeast Phenotype Ontology
Gene Deletion Viability: Viable

Population Phenotype

Term IDTerm NameEvidenceAlleleExpressionConditionReferenceCount
FYPO:0001701sensitive to bortezomib256
expressivity FYPO_EXT:0000001Cell growth assaySPCC550.03cΔNullPECO:0000005, PECO:0000137PMID:21760946
FYPO:0000096sensitive to cadmium246
expressivity FYPO_EXT:0000002Cell growth assaySPCC550.03cΔNullPECO:0000102, PECO:0000005, PECO:0000137PMID:18684775
FYPO:0000271sensitive to salt stress84
expressivity FYPO_EXT:0000003Cell growth assaySPCC550.03cΔNullPECO:0000207, PECO:0000137, PECO:0000102, PECO:0000005PMID:18684775
FYPO:0002060viable vegetative cell populationMicroscopySPCC550.03cΔNullPECO:0000005, PECO:0000137PMID:236978063759
MicroscopySPCC550.03cΔNullPMID:20473289

Cell Phenotype

Term IDTerm NameEvidenceAlleleExpressionConditionReferenceCount
FYPO:0002177viable vegetative cell with normal cell morphology3089
penetrance FYPO_EXT:0000001MicroscopySPCC550.03cΔNullPECO:0000005, PECO:0000137PMID:23697806
Transcript
Ensembl transcript structure with UTRs, exons and introns

Exons

Exon Start End
111913961187669

UTRs

Region Coordinates Reference
five_prime_UTR1191396..1191377PMID:21511999
three_prime_UTR1187734..1187669PMID: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
PF13234 Pfam IPR025696 rRNA-processing arch domain 747 848 3
PF00270 Pfam IPR011545 DNA/RNA helicase, DEAD/DEAH box type, N-terminal 284 430 43
PF08148 Pfam IPR012961 DSH, C-terminal 1033 1213 3
PF00271 Pfam IPR001650 Helicase, C-terminal 617 692 68
SM00490 SMART IPR001650 Helicase, C-terminal 606 692 68
SM00487 SMART IPR014001 Helicase, superfamily 1/2, ATP-binding domain 277 460 69
PS51192 Prosite Profiles IPR014001 Helicase, superfamily 1/2, ATP-binding domain 289 445 69
PS51194 Prosite Profiles IPR001650 Helicase, C-terminal 545 736 69
PTHR11752 HMMPANTHER 36 1213 6
3.40.50.300 Gene3D 535 576 288
3.40.50.300 Gene3D 616 701 288
3.40.50.300 Gene3D 278 454 288
SSF52540 SuperFamily IPR027417 P-loop containing nucleoside triphosphate hydrolase 612 704 294
SSF52540 SuperFamily IPR027417 P-loop containing nucleoside triphosphate hydrolase 295 430 294
SSF52540 SuperFamily IPR027417 P-loop containing nucleoside triphosphate hydrolase 515 572 294
PIRSF005198 PIRSF IPR016438 RNA helicase, ATP-dependent, SK12/DOB1 1 1213 3
Coil ncoils Rabaptin coiled-coil domain 763 791 968

View domain organization at Pfam

Manually Curated Family or Sub-families

Term IDTerm NameReferenceCount
PBO:0000174DEAD/DEAH box helicaseTemporary processing gif - replaced by AJAX with count of genes annotated with the term PBO:0000174

Protein Properties

Ave. residue weight 113.79 Da
Charge 3.50
Isoelectric point 6.72
Molecular weight 138.03 kDa
Number of residues 1213
Modifications

Protein Modifications

Term IDTerm NameEvidenceResidueReferenceCount
MOD:00046O-phospho-L-serineexperimental evidenceS143PMID:217125471670
present during mitotic M phase
experimental evidenceS143PMID:24763107
Sequence
Gene Expression

Quantitative Gene Expression

Protein Level

Molecules/Cell (average)ExtensionConditionScaleEvidenceReference
8449during GO:0000080PECO:0000126,
PECO:0000005
single_cellmass spectrometry evidencePMID:24763107
8279during GO:0000084PECO:0000126,
PECO:0000005
single_cellmass spectrometry evidencePMID:24763107
7505during GO:0000085PECO:0000126,
PECO:0000005
single_cellmass spectrometry evidencePMID:24763107
7902during GO:0000087PECO:0000126,
PECO:0000005
single_cellmass spectrometry evidencePMID:24763107
1068.48during GO:0072690PECO:0000005,
PECO:0000014
population_wideexperimental evidencePMID:23101633
8749during GO:0072690PECO:0000126,
PECO:0000005
single_cellmass spectrometry evidencePMID:24763107
996.6during cell quiescence following G1 arrest due to nitrogen limitationPECO:0000005,
PECO:0000014,
PECO:0000127
population_wideexperimental evidencePMID:23101633

RNA Level

Molecules/Cell (average)ExtensionConditionScaleEvidenceReference
2.1during GO:0072690PECO:0000005,
PECO:0000014
population_wideexperimental evidencePMID:23101633
0.86during cell quiescence following G1 arrest due to nitrogen limitationPECO:0000005,
PECO:0000014,
PECO:0000127
population_wideexperimental evidencePMID:23101633
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


Genetic Interactions

Source: BioGRID

Gene Product Evidence Reference
swd2Set1C complex subunit Swd2.1 Negative GeneticPMID:18818364
ubc6ubiquitin conjugating enzyme Ubc6 (predicted) Negative GeneticPMID:18818364
Negative GeneticPMID:22681890
yaf9YEATS family histone acetyltransferase subunit Yaf9 Negative GeneticPMID:18818364
cdt2WD repeat protein Cdt2 Negative GeneticPMID:22681890
rga3Rho-type GTPase activating protein Rga3 Negative GeneticPMID:22681890
srb7mediator complex subunit Srb7 Negative GeneticPMID:18818364
set1histone lysine methyltransferase Set1 Negative GeneticPMID:18818364
cwf19complexed with Cdc5 protein Cwf19 Negative GeneticPMID:22681890
spn1septin Spn1 Negative GeneticPMID:18818364
pab2poly(A) binding protein Pab2 Negative GeneticPMID:18818364
fbh1DNA helicase I Positive GeneticPMID:18818364
exo2exonuclease II Exo2 Synthetic LethalityPMID:23503588
mug81ATP-dependent RNA helicase Slh1 (predicted) Negative GeneticPMID:18818364
Negative GeneticPMID:22681890
sty1MAP kinase Sty1 Negative GeneticPMID:22681890
fta6Sim4 and Mal2 associated (4 and 2 associated) protein 6 Negative GeneticPMID:22681890
pek1MAP kinase kinase Pek1 Negative GeneticPMID:22681890
toc1Tor complex Tor2 interacting protein 1 Negative GeneticPMID:22681890
hip1hira protein, histone chaperone Hip1 Negative GeneticPMID:18818364
Negative GeneticPMID:22681890
elp3elongator complex subunit Elp3 (predicted) Positive GeneticPMID:18818364
sre2membrane-tethered transcription factor Sre2 Negative GeneticPMID:21504829
Negative GeneticPMID:22681890
caf4CCR4-Not complex subunit Caf4/Mdv1 (predicted) Negative GeneticPMID:22681890
SPBC56F2.08cRNA-binding protein (predicted) Negative GeneticPMID:18818364
SPBC16H5.13WD repeat protein, human WDR7 ortholog Negative GeneticPMID:18818364
laf1clr6 L associated factor 1 Laf1 Positive GeneticPMID:18818364
swd1Set1C complex subunit Swd1 Negative GeneticPMID:22681890
par2protein phosphatase regulatory subunit Par2 Negative GeneticPMID:18818364
vph2endoplasmic reticulum membrane protein involved in assembly of the V-ATPase (predicted) Positive GeneticPMID:22681890
cho1phosphatidyl-N-methylethanolamine N-methyltransferase (predicted) Negative GeneticPMID:18818364
plb1phospholipase B homolog Plb1 Positive GeneticPMID:22681890
ptc3protein phosphatase 2c homolog 3 Positive GeneticPMID:18818364
rap1telomere binding protein Rap1 Negative GeneticPMID:18818364
tma23ribosome biogenesis protein Tma23 (predicted) Positive GeneticPMID:18818364
mug154conserved fungal protein Negative GeneticPMID:22681890
fin1serine/threonine protein kinase, NIMA related Fin1 Positive GeneticPMID:18818364
sck2serine/threonine protein kinase Sck2 Negative GeneticPMID:24463365
cpd1tRNA (m1A) methyltransferase complex catalytic subunit Cpd1 Positive GeneticPMID:18818364
rok1ATP-dependent RNA helicase Rok1 (predicted) Positive GeneticPMID:18818364
msc1multi-copy suppressor of Chk1 Negative GeneticPMID:18818364
atp11F1-ATPase chaperone Atp11 (predicted) Positive GeneticPMID:22681890
SPCC306.07cU3 snoRNP-associated protein Cic1/Utp30 family (predicted) Negative GeneticPMID:22681890
tom70mitochondrial TOM complex subunit Tom70 (predicted) Positive GeneticPMID:22681890
ypa1protein phosphatase type 2A regulator, PTPA family Ypa1 Negative GeneticPMID:22681890
cph2Clr6 histone deacetylase associated PHD protein-2 Cph2 Negative GeneticPMID:22681890
hrp1ATP-dependent DNA helicase Hrp1 Negative GeneticPMID:18818364
rad2514-3-3 protein Rad25 Negative GeneticPMID:22681890
SPBC31F10.10czf-MYND type zinc finger protein Negative GeneticPMID:18818364
hip4histone promoter control protein Hip4 Negative GeneticPMID:18818364
Negative GeneticPMID:22681890
dsc5UBX domain containing protein required for Sre1 cleavage Negative GeneticPMID:22681890
res1MBF transcription factor complex subunit Res1 Negative GeneticPMID:22681890
stn1telomere cap complex subunit Stn1 Negative GeneticPMID:22681890
SPBC21C3.03ABC1 kinase family protein Negative GeneticPMID:22681890
srb11cyclin CycC, Srb mediator subunit Srb11 Negative GeneticPMID:18818364
tea5pseudokinase Tea5 Negative GeneticPMID:22681890
hrd1synviolin family ubiquitin-protein ligase E3, Hrd1 Negative GeneticPMID:18818364
tps1alpha,alpha-trehalose-phosphate synthase Negative GeneticPMID:22681890
luc7U1 snRNP-associated protein Luc7 Negative GeneticPMID:22681890
cyp7cyclophilin family peptidyl-prolyl cis-trans isomerase Cyp7 (predicted) Negative GeneticPMID:18818364
fft3SMARCAD1 family ATP-dependent DNA helicase Fft3 Positive GeneticPMID:18818364
Positive GeneticPMID:22681890
fhl1forkhead transcription factor Fhl1 Negative GeneticPMID:22681890
cbh1CENP-B homolog Cbh1 Negative GeneticPMID:22681890
sum2G2/M transition checkpoint protein Sum2 Negative GeneticPMID:18818364
Negative GeneticPMID:22681890
bdf1Swr1 complex bromodomain subunit Brf1 Negative GeneticPMID:18818364
Physical Interactions

Source: BioGRID

Gene Product Evidence Reference
hhp1serine/threonine protein kinase Hhp1 Affinity Capture-MSPMID:24055157
hhp2serine/threonine protein kinase Hhp2 Affinity Capture-MSPMID:24055157
External References
Database Identifier Description
NBRP SPCC550.03c Fission yeast strain database, National BioResource Project (Japan)
YOGY SPCC550.03c Retrieval of eukaryotic orthologs (Bähler Lab)
BioGrid SPCC550.03c BioGRID Interaction Datasets
Expression Viewer SPCC550.03c Cell Cycle Expression Profile (Bähler Lab)
Expression Viewer SPCC550.03c Meiosis/Sporulation Expression Profies (Bähler Lab)
Expression Viewer SPCC550.03c Pheromone response/mating expression profiles (Bähler Lab)
Expression Viewer SPCC550.03c Environmental stress expression profiles (Bähler Lab)
Pomb(A) SPCC550.03c Polyadenylation Viewer (Gullerova lab)
pombeTV SPCC550.03c Transcriptome Viewer (Bähler Lab)
Cyclebase SPCC550.03c Cell Cycle Data
GEO SPCC550.03c GEO profiles
PInt SPCC550.03c Protein-Protein Interaction Predictor (Bähler Lab)
PeptideAtlas SPCC550.03c Peptides identified in tandem mass spectrometry proteomics experiments
SYSGRO SPCC550.03c Fission yeast phenotypic data & analysis
SPD / RIKEN39/39B10Orfeome Localization Data
UniProtKB/SwissProtO59801Putative ATP-dependent RNA helicase C550.03c
ModBaseO59801Database of comparative protein structure models
STRINGO59801Network display of known and predicted interactions and functional associations
RefSeq PeptideNP_588095Ski complex RNA helicase Ski2 (predicted)
RefSeq mRNANM_001023086972h- Ski complex RNA helicase Ski2 (predicted) (SPCC550.03c), mRNA
European Nucleotide ArchiveCAA19107.1ENA Protein Mapping
UniParcUPI0000069A65UniProt Archive

Literature for SPCC550.03c

Search: Europe PMC or PubMed

Release Version: PomBase:23_47 - 27 Oct 2014