caf1 (SPCC18.06c)


Gene Standard Namecaf1 Characterisation Statuspublished
Systematic IDSPCC18.06c Feature Typeprotein coding
Synonyms Name Description
ProductCCR4-Not complex CAF1 family ribonuclease subunit Caf1 Product Size335aa, 37.53 kDa
Genomic Location Chromosome III, 1966933-1965430 (1504nt); CDS:1966846-1965839 (1008nt)

Ensembl Gene Location
GO Molecular Function
Term NameCount
metal ion binding750
Annotation ExtensionEvidenceWith/FromReference
mRNA binding28
Annotation ExtensionEvidenceWith/FromReference
poly(A)-specific ribonuclease activity3
Annotation ExtensionEvidenceWith/FromReference
GO Biological Process
Term NameCount
nuclear-transcribed mRNA poly(A) tail shortening10
Annotation ExtensionEvidenceWith/FromReference
GO Cellular Component
Term NameCount
CCR4-NOT core complex8
Annotation ExtensionEvidenceWith/FromReference
cytoplasm4209
Annotation ExtensionEvidenceWith/FromReference
cytosol2306
Annotation ExtensionEvidenceWith/FromReference
nucleus2690
Annotation ExtensionEvidenceWith/FromReference
FYPO Single-Allele Phenotypes
Gene Deletion Viability: Viable

Population Phenotype

Term NameGenotypesCount
decreased mating efficiencycaf1Δ269
sensitive to 4-nitroquinoline N-oxidecaf1Δ159
sensitive to amphotericin Bcaf1Δ69
sensitive to cadmiumcaf1Δ249
sensitive to caffeine during vegetative growthcaf1Δ110
sensitive to camptothecincaf1Δ227
sensitive to doxorubicincaf1Δ93
sensitive to hydrogen peroxidecaf1Δ153
sensitive to hydroxyureacaf1Δ547
sensitive to ionizing radiation during vegetative growthcaf1Δ67
sensitive to methyl methanesulfonatecaf1Δ250
sensitive to micafungincaf1Δ119
sensitive to salt stresscaf1Δ98
viable vegetative cell populationcaf1Δ3831

Cell Phenotype

Term NameGenotypesCount
normal RNA binding5
affecting ago1caf1Δ
vegetative cell lysiscaf1Δ89
viable vegetative cell with normal cell morphologycaf1Δ3099
Transcript
Ensembl transcript structure with UTRs, exons and introns

Transcript Structure

Region Coordinates Reference
Exons1966933..1965430
5' UTR1966933..1966847PMID:21511999
3' UTR1965838..1965430PMID: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
PF04857 Pfam IPR006941 Ribonuclease CAF1 28 145 2
PF04857 Pfam IPR006941 Ribonuclease CAF1 165 251 2
PTHR10797:SF0 HMMPANTHER 11 327 1
PTHR10797 HMMPANTHER 11 327 1
3.30.420.10 Gene3D IPR012337 Ribonuclease H-like domain 23 276 32
SSF53098 SuperFamily IPR012337 Ribonuclease H-like domain 24 271 34

View domain organization at Pfam

Protein Properties

Ave. residue weight 112.04 Da
Charge -10.50
Codon Adaptation Index 0.36
Isoelectric point 4.63
Molecular weight 37.53 kDa
Number of residues 335
Sequence
Gene Expression

Quantitative Gene Expression

View graphical display of gene expression data for caf1 (SPCC18.06c)

Protein Level

Molecules/Cell (average)ExtensionConditionScaleEvidenceReference
40380during GO:0000080PECO:0000005,
PECO:0000126
single cellmass spectrometry evidencePMID:24763107
37568during GO:0000084PECO:0000005,
PECO:0000126
single cellmass spectrometry evidencePMID:24763107
39137during GO:0000085PECO:0000005,
PECO:0000126
single cellmass spectrometry evidencePMID:24763107
43885during GO:0000087PECO:0000005,
PECO:0000126
single cellmass spectrometry evidencePMID:24763107
11290.16during GO:0072690PECO:0000014,
PECO:0000005
population wideexperimental evidencePMID:23101633
36918during GO:0072690PECO:0000005,
PECO:0000126
single cellmass spectrometry evidencePMID:24763107
1645.22during cell quiescence following G1 arrest due to nitrogen limitationPECO:0000127,
PECO:0000014,
PECO:0000005
population wideexperimental evidencePMID:23101633

RNA Level

Molecules/Cell (average)ExtensionConditionScaleEvidenceReference
2.3during GO:0072690PECO:0000014,
PECO:0000005
population wideexperimental evidencePMID:23101633
0.53during cell quiescence following G1 arrest due to nitrogen limitationPECO:0000127,
PECO:0000014,
PECO:0000005
population wideexperimental evidencePMID:23101633
Warning
DescriptionQualifierReferenceCount
gene structure updated PMID:21511999433
Taxonomic Conservation
DescriptionQualifierReferenceCount
predominantly single copy (one to one)3090
conserved in fungi4604
conserved in eukaryotes4514
conserved in metazoa3422
conserved in vertebrates3397
conserved in eukaryotes only2504
Orthologs

Manually curated orthologous groups

SpeciesGeneDescriptionLinksCount

Orthologs in Compara


Physical Interactions

Source: BioGRID

Load gene that interact physically with SPCC18.06c into the Query Builder
View all interactions in esyN
View the HCPIN interactions in esyN

Gene Product Evidence Reference
affinity captured byred1RNA elimination defective protein Red1 Affinity Capture-MSPMID:24713849
affinity captured bypir2zf-C2H2 type zinc finger protein, implicated in RNAi (predicted) Affinity Capture-MSPMID:24713849
affinity captured bymtl1TRAMP complex ATP-dependent RNA helicase (predicted) Affinity Capture-MSPMID:24713849
affinity captured byepe1Jmjc domain chromatin associated protein Epe1 Affinity Capture-MSPMID:24013502
affinity capturessuc22ribonucleotide reductase small subunit Suc22 Affinity Capture-WesternPMID:17264117
Genetic Interactions

Source: BioGRID

Load gene that interact genetically with SPCC18.06c into the Query Builder
View these interactions in esyN

Gene Product Evidence Reference
negative genetic interaction withrhp14XP-A family homolog Rhp14 Negative GeneticPMID:18818364
negative genetic interaction withcdm1DNA polymerase delta subunit Cdm1 Negative GeneticPMID:18818364
negative genetic interaction withmre11Mre11 nuclease Negative GeneticPMID:18818364
negative genetic interaction withsnf5SWI/SNF complex subunit Snf5 Negative GeneticPMID:18818364
negative genetic interaction withnup61nucleoporin Nup61 Negative GeneticPMID:18818364
negative genetic interaction withexo1exonuclease I Exo1 Negative GeneticPMID:18818364
negative genetic interaction withrpa12DNA-directed RNA polymerase complex I subunit Rpa12 Negative GeneticPMID:18818364
negative genetic interaction withtip1CLIP170 family protein Tip1 Negative GeneticPMID:18818364
negative genetic interaction withmed14mediator complex subunit Med14 Negative GeneticPMID:18818364
negative genetic interaction withraf2Rik1-associated factor Raf2 Negative GeneticPMID:18818364
negative genetic interaction withnup40nucleoporin Nup40 Negative GeneticPMID:18818364
negative genetic interaction withatb2tubulin alpha 2 Negative GeneticPMID:18818364
negative genetic interaction witharp8actin-like protein, Ino80 complex subunit Arp8 Negative GeneticPMID:18818364
negative genetic interaction withngg1SAGA complex subunit Ngg1 Negative GeneticPMID:18818364
negative genetic interaction withmug89CDC50 domain protein, implicated in signal transduction (predicted) Negative GeneticPMID:18818364
negative genetic interaction withmal3EB1 family Mal3 Negative GeneticPMID:18818364
negative genetic interaction withcwf21complexed with Cdc5 protein Cwf21 Negative GeneticPMID:18818364
negative genetic interaction withreb1RNA polymerase I transcription termination factor/ RNA polymerase II transcription factor Reb1 Negative GeneticPMID:18818364
negative genetic interaction withsdh4TIM22 inner membrane protein import complex anchor subunit Tim18 Negative GeneticPMID:18818364
negative genetic interaction withSPBC1685.04Schizosaccharomyces specific protein Negative GeneticPMID:18818364
negative genetic interaction withmph1dual specificity protein kinase Mph1 Negative GeneticPMID:18818364
negative genetic interaction withdsk1SR protein-specific kinase Dsk1 Negative GeneticPMID:18818364
negative genetic interaction withdad1DASH complex subunit Dad1 Negative GeneticPMID:18818364
negative genetic interaction withaut12autophagy associated protein Aut12 (predicted) Negative GeneticPMID:18818364
negative genetic interaction withbdc1bromodomain containing protein 1, Bdc1 Negative GeneticPMID:18818364
negative genetic interaction withmyp2myosin II heavy chain Myo3 Negative GeneticPMID:18818364
negative genetic interaction withbun107WD repeat protein, human WDR48 family Bun107 Negative GeneticPMID:18818364
negative genetic interaction withssu72phosphoric ester hydrolase Ssu72 (predicted) Negative GeneticPMID:18818364
negative genetic interaction withrpl160160S ribosomal protein L13/L16 (predicted) Negative GeneticPMID:18818364
negative genetic interaction withhos2histone deacetylase (class I) Hos2 Negative GeneticPMID:18818364
negative genetic interaction withrtt109RTT109 family histone lysine acetyltransferase Negative GeneticPMID:18818364
negative genetic interaction withtfs1transcription elongation factor TFIIS Negative GeneticPMID:18818364
negative genetic interaction withset3histone lysine methyltransferase Set3 Negative GeneticPMID:18818364
negative genetic interaction withdma1mitotic spindle checkpoint ubiquitin ligase Dma1 Negative GeneticPMID:18818364
negative genetic interaction withcph1Clr6 histone deacetylase associated PHD protein-1 Cph1 Negative GeneticPMID:18818364
negative genetic interaction withask1DASH complex subunit Ask1 Negative GeneticPMID:18818364
negative genetic interaction withers1RNA-silencing factor Ers1 Negative GeneticPMID:18818364
negative genetic interaction withctf18RFC-like complex subunit Ctf18 Negative GeneticPMID:18818364
negative genetic interaction withpuf1pumilio family RNA-binding protein Puf1 (predicted) Negative GeneticPMID:18818364
negative genetic interaction withpab2poly(A) binding protein Pab2 Negative GeneticPMID:18818364
negative genetic interaction withago1argonaute Negative GeneticPMID:18818364
negative genetic interaction withpmc2mediator complex subunit Med1 Negative GeneticPMID:18818364
negative genetic interaction withgid9GID complex subunit Gid9 (predicted) Negative GeneticPMID:18818364
negative genetic interaction withrnc1RNA-binding protein that suppresses calcineurin deletion Rnc1 Negative GeneticPMID:18818364
negative genetic interaction withmcl1DNA polymerase alpha accessory factor Mcl1 Negative GeneticPMID:18818364
negative genetic interaction withfkbp39FKBP-type peptidyl-prolyl cis-trans isomerase (predicted) Negative GeneticPMID:18818364
negative genetic interaction withgcn20AAA family ATPase Gcn20 (predicted) Negative GeneticPMID:18818364
negative genetic interaction withpht1histone H2A variant H2A.Z, Pht1 Negative GeneticPMID:18818364
negative genetic interaction withtas3RITS complex subunit 3 Negative GeneticPMID:18818364
negative genetic interaction withhif2Set3 complex subunit Hif2 Negative GeneticPMID:18818364
negative genetic interaction withubp7ubiquitin C-terminal hydrolase Ubp7 Negative GeneticPMID:18818364
negative genetic interaction withSPBC839.03cneddylation protein Dcn1 (predicted) Negative GeneticPMID:18818364
negative genetic interaction withrad57RecA family ATPase Rad57/Rhp57 Negative GeneticPMID:18818364
negative genetic interaction withsrb11cyclin CycC, Srb mediator subunit Srb11 Negative GeneticPMID:18818364
negative genetic interaction withhip4histone promoter control protein Hip4 Negative GeneticPMID:18818364
negative genetic interaction withpek1MAP kinase kinase Pek1 Negative GeneticPMID:18818364
negative genetic interaction withcho1phosphatidyl-N-dimethylethanolamine N-methyltransferase Negative GeneticPMID:18818364
negative genetic interaction withSPBC16H5.13WD repeat protein, human WDR7 ortholog Negative GeneticPMID:18818364
negative genetic interaction withsum2translation initiation inhibitor (predicted) Negative GeneticPMID:18818364
negative genetic interaction withgcn5SAGA complex histone acetyltransferase catalytic subunit Gcn5 Negative GeneticPMID:18818364
negative genetic interaction withklp6kinesin-like protein Klp6 Negative GeneticPMID:18818364
negative genetic interaction withswi6HP1 family chromodomain protein Swi6 Negative GeneticPMID:18818364
negative genetic interaction withrcd1RNA-binding protein, CCR4-NOT complex subunit Rcd1 Negative GeneticPMID:18818364
negative genetic interaction withsnt2Lid2 complex subunit Snt2 Negative GeneticPMID:18818364
negative genetic interaction withlsk1P-TEFb-associated cyclin-dependent protein kinase Lsk1 Negative GeneticPMID:18818364
negative genetic interaction withpmk1MAP kinase Pmk1 Negative GeneticPMID:18818364
negative genetic interaction withhrq1RecQ type DNA helicase Hrq1 (predicted) Negative GeneticPMID:18818364
positive genetic interaction witherg5C-22 sterol desaturase Erg5 Positive GeneticPMID:18818364
positive genetic interaction withccr4CCR4-Not complex subunit Ccr4 (predicted) Positive GeneticPMID:18818364
positive genetic interaction withscs7sphingosine hydroxylase Scs7 Positive GeneticPMID:18818364
positive genetic interaction withvrp1verprolin Positive GeneticPMID:18818364
positive genetic interaction withair1zinc knuckle TRAMP complex subunit Air1 Positive GeneticPMID:18818364
positive genetic interaction withhrd1synviolin family ubiquitin-protein ligase E3, Hrd1 Positive GeneticPMID:18818364
positive genetic interaction withelp3elongator complex subunit Elp3 (predicted) Positive GeneticPMID:18818364
positive genetic interaction withelp2elongator complex subunit Elp2 (predicted) Positive GeneticPMID:18818364
synthetic growth defect withgtb1gamma-tubulin Gtb1 Synthetic Growth DefectPMID:22737087
synthetic growth defect withcds1replication checkpoint kinase Cds1 Synthetic Growth DefectPMID:17264117
synthetic growth defect withrad26ATRIP, ATR checkpoint kinase regulatory subunit Rad26 Synthetic Growth DefectPMID:17264117
synthetic growth defect withmad2mitotic spindle checkpoint protein Mad2 Synthetic Growth DefectPMID:22737087
External References
Database Identifier Description
NBRP SPCC18.06c Fission yeast strain database, National BioResource Project (Japan)
YOGY SPCC18.06c Retrieval of eukaryotic orthologs (Bähler Lab)
BioGrid SPCC18.06c BioGRID Interaction Datasets
Expression Viewer SPCC18.06c Cell Cycle Expression Profile (Bähler Lab)
Expression Viewer SPCC18.06c Meiosis/Sporulation Expression Profies (Bähler Lab)
Expression Viewer SPCC18.06c Pheromone response/mating expression profiles (Bähler Lab)
Expression Viewer SPCC18.06c Environmental stress expression profiles (Bähler Lab)
Pomb(A) SPCC18.06c Polyadenylation Viewer (Gullerova lab)
pombeTV SPCC18.06c Transcriptome Viewer (Bähler Lab)
GEO SPCC18.06c GEO profiles
PInt SPCC18.06c Protein-Protein Interaction Predictor (Bähler Lab)
PeptideAtlas SPCC18.06c Peptides identified in tandem mass spectrometry proteomics experiments
SYSGRO SPCC18.06c Fission yeast phenotypic data & analysis
Cyclebase SPCC18.06c.1 Cell Cycle Data
SPD / RIKEN14/14F07Orfeome Localization Data
UniProtKB/SwissProtO74856Poly(A) ribonuclease pop2
ModBaseO74856Database of comparative protein structure models
STRINGO74856Network display of known and predicted interactions and functional associations
RefSeq PeptideNP_588385CCR4-Not complex CAF1 family ribonuclease subunit Caf1
RefSeq mRNANM_001023376972h- CCR4-Not complex CAF1 family ribonuclease subunit Caf1 (caf1), mRNA
European Nucleotide ArchiveCU329672ENA EMBL mapping
ePDB2P51The European PDB
PDB2P51PDB
PDBsum2P51PDBsum
ePDB3G0ZThe European PDB
PDB3G0ZPDB
PDBsum3G0ZPDBsum
ePDB3G10The European PDB
PDB3G10PDB
PDBsum3G10PDBsum
European Nucleotide ArchiveCAA21420ENA Protein Mapping
UniParcUPI000228F4F2UniProt Archive

Literature for caf1

Search: Europe PMC or PubMed

Release Version: PomBase:30_57 - 27 Jan 2016