caf1 (SPCC18.06c)

Gene Standard Namecaf1 Characterisation Statuspublished
Systematic IDSPCC18.06c Feature Typeprotein coding
Synonymspop2 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 binding747
Annotation ExtensionEvidenceWith/FromReference
mRNA binding29
Annotation ExtensionEvidenceWith/FromReference
poly(A)-specific ribonuclease activity3
Annotation ExtensionEvidenceWith/FromReference
GO Biological Process
Term NameCount
nuclear-transcribed mRNA poly(A) tail shortening9
Annotation ExtensionEvidenceWith/FromReference
RNA phosphodiester bond hydrolysis, exonucleolytic21
Annotation ExtensionEvidenceWith/FromReference
GO Cellular Component
Term NameCount
CCR4-NOT core complex8
Annotation ExtensionEvidenceWith/FromReference
Annotation ExtensionEvidenceWith/FromReference
Annotation ExtensionEvidenceWith/FromReference
Annotation ExtensionEvidenceWith/FromReference
Fission Yeast Phenotype Ontology
Gene Deletion Viability: Viable

Population Phenotype

Term NameAlleleExpressionCount
decreased mating efficiencycaf1ΔNull247
sensitive to 4-nitroquinoline N-oxide159
expressivity FYPO_EXT:0000003caf1ΔNull
sensitive to amphotericin B69
expressivity FYPO_EXT:0000001caf1ΔNull
sensitive to cadmium246
expressivity FYPO_EXT:0000002caf1ΔNull
sensitive to caffeine108
expressivity FYPO_EXT:0000001caf1ΔNull
sensitive to camptothecincaf1ΔNull214
expressivity FYPO_EXT:0000003caf1ΔNull
sensitive to doxorubicin91
expressivity FYPO_EXT:0000003caf1ΔNull
sensitive to hydrogen peroxide137
expressivity FYPO_EXT:0000001caf1ΔNull
expressivity FYPO_EXT:0000003caf1ΔNull
sensitive to hydroxyurea518
expressivity FYPO_EXT:0000002caf1ΔNull
sensitive to ionizing radiation58
expressivity FYPO_EXT:0000003caf1ΔNull
sensitive to methyl methanesulfonate227
expressivity FYPO_EXT:0000003caf1ΔNull
sensitive to micafungin116
expressivity FYPO_EXT:0000001caf1ΔNull
sensitive to salt stress86
expressivity FYPO_EXT:0000003caf1ΔNull
viable vegetative cell populationcaf1ΔNull3781

Cell Phenotype

Term NameAlleleExpressionCount
normal RNA binding3
affecting ago1caf1ΔNull
vegetative cell lysiscaf1ΔNull82
viable vegetative cell with normal cell morphology3092
penetrance FYPO_EXT:0000001caf1ΔNull
Ensembl transcript structure with UTRs, exons and introns


Exon Start End


Region Coordinates Reference
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 26 252 2
PTHR10797:SF0 HMMPANTHER 25 330 1
PTHR10797 HMMPANTHER 25 330 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
Isoelectric point 4.63
Molecular weight 37.53 kDa
Number of residues 335
Gene Expression

Quantitative Gene Expression

Protein Level

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

RNA Level

Molecules/Cell (average)ExtensionConditionScaleEvidenceReference
2.3during GO:0072690PECO:0000005,
population wideexperimental evidencePMID:23101633
0.53during cell quiescence following G1 arrest due to nitrogen limitationPECO:0000005,
population wideexperimental evidencePMID:23101633
gene structure updated PMID:21511999432
Species Distribution
predominantly single copy (one to one)3092
conserved in fungi4604
conserved in eukaryotes4516
conserved in metazoa3432
conserved in vertebrates3407
conserved in eukaryotes only2503

Manually curated orthologous groups


Orthologs in Compara

Physical Interactions

Source: BioGRID

View all interactions in esyN
View the HCPIN interactions in esyN

Gene Product Evidence Reference
red1RNA elimination defective protein Red1 Affinity Capture-MSPMID:24713849
epe1Jmjc domain chromatin associated protein Epe1 Affinity Capture-MSPMID:24013502
mtl1TRAMP complex ATP-dependent RNA helicase (predicted) Affinity Capture-MSPMID:24713849
pir2zf-C2H2 type zinc finger protein, implicated in RNAi (predicted) Affinity Capture-MSPMID:24713849
suc22ribonucleotide reductase small subunit Suc22 Affinity Capture-WesternPMID:17264117
Genetic Interactions

Source: BioGRID

View these interactions in esyN

Gene Product Evidence Reference
pht1histone H2A variant H2A.Z, Pht1 Negative GeneticPMID:18818364
pmc1mediator complex subunit Pmc1 Negative GeneticPMID:18818364
SPBC106.13ubiquitin ligase complex subunit, involved in proteasome-dependent catabolite inactivation of FBPase (predicted) Negative GeneticPMID:18818364
scs7sphingosine hydroxylase Scs7 Positive GeneticPMID:18818364
lsk1P-TEFb-associated cyclin-dependent protein kinase Lsk1 Negative GeneticPMID:18818364
mph1dual specificity protein kinase Mph1 Negative GeneticPMID:18818364
dad1DASH complex subunit Dad1 Negative GeneticPMID:18818364
exo1exonuclease I Exo1 Negative GeneticPMID:18818364
bdc1bromodomain containing protein 1, Bdc1 Negative GeneticPMID:18818364
hos2histone deacetylase (class I) Hos2 Negative GeneticPMID:18818364
ago1argonaute Negative GeneticPMID:18818364
cdm1DNA polymerase delta subunit Cdm1 Negative GeneticPMID:18818364
mad2mitotic spindle checkpoint protein Mad2 Synthetic Growth DefectPMID:22737087
dsk1SR protein-specific kinase Dsk1 Negative GeneticPMID:18818364
aut12autophagy associated protein Aut12 (predicted) Negative GeneticPMID:18818364
rpa12DNA-directed RNA polymerase complex I subunit Rpa12 Negative GeneticPMID:18818364
SPBC56F2.08cRNA-binding protein (predicted) Negative GeneticPMID:18818364
cwf21complexed with Cdc5 protein Cwf21 Negative GeneticPMID:18818364
cho1phosphatidyl-N-methylethanolamine N-methyltransferase (predicted) Negative GeneticPMID:18818364
SPBC839.03cneddylation protein Dcn1 (predicted) Negative GeneticPMID:18818364
elp3elongator complex subunit Elp3 (predicted) Positive GeneticPMID:18818364
SPBC16H5.13WD repeat protein, human WDR7 ortholog Negative GeneticPMID:18818364
gtb1gamma-tubulin Gtb1 Synthetic Growth DefectPMID:22737087
mre11Mre11 nuclease Negative GeneticPMID:18818364
rcd1RNA-binding protein, CCR4-NOT complex subunit Rcd1 Negative GeneticPMID:18818364
raf2Rik1-associated factor Raf2 Negative GeneticPMID:18818364
mug89CDC50 domain protein, implicated in signal transduction (predicted) Negative GeneticPMID:18818364
snf5SWI/SNF complex subunit Snf5 Negative GeneticPMID:18818364
pek1MAP kinase kinase Pek1 Negative GeneticPMID:18818364
rad26ATRIP, ATR checkpoint kinase regulatory subunit Rad26 Synthetic Growth DefectPMID:17264117
pmk1MAP kinase Pmk1 Negative GeneticPMID:18818364
dma1mitotic spindle checkpoint ubiquitin ligase Dma1 Negative GeneticPMID:18818364
tfs1transcription elongation factor TFIIS Negative GeneticPMID:18818364
ask1DASH complex subunit Ask1 Negative GeneticPMID:18818364
hrq1RecQ type DNA helicase Hrq1 (predicted) Negative GeneticPMID:18818364
nup40nucleoporin Nup40 Negative GeneticPMID:18818364
snt2Lid2 complex subunit Snt2 Negative GeneticPMID:18818364
gcn20AAA family ATPase Gcn20 (predicted) Negative GeneticPMID:18818364
gcn5SAGA complex histone acetyltransferase catalytic subunit Gcn5 Negative GeneticPMID:18818364
rad57RecA family ATPase Rad57/Rhp57 Negative GeneticPMID:18818364
ers1RNA-silencing factor Ers1 Negative GeneticPMID:18818364
arp8actin-like protein, Ino80 complex subunit Arp8 Negative GeneticPMID:18818364
mal3EB1 family Mal3 Negative GeneticPMID:18818364
klp6kinesin-like protein Klp6 Negative GeneticPMID:18818364
pmc2mediator complex subunit Pmc2/Med1 Negative GeneticPMID:18818364
mcl1DNA polymerase alpha accessory factor Mcl1 Negative GeneticPMID:18818364
set3histone lysine methyltransferase Set3 Negative GeneticPMID:18818364
erg5C-22 sterol desaturase Erg5 Positive GeneticPMID:18818364
ccr4CCR4-Not complex subunit Ccr4 (predicted) Positive GeneticPMID:18818364
tas3RITS complex subunit 3 Negative GeneticPMID:18818364
rpl160160S ribosomal protein L13/L16 (predicted) Negative GeneticPMID:18818364
rtt109RTT109 family histone lysine acetyltransferase Negative GeneticPMID:18818364
cds1replication checkpoint kinase Cds1 Synthetic Growth DefectPMID:17264117
hif2Set3 complex subunit Hif2 Negative GeneticPMID:18818364
rhp14XP-A family homolog Rhp14 Negative GeneticPMID:18818364
ubp7ubiquitin C-terminal hydrolase Ubp7 Negative GeneticPMID:18818364
hip4histone promoter control protein Hip4 Negative GeneticPMID:18818364
atb2tubulin alpha 2 Negative GeneticPMID:18818364
ngg1SAGA complex subunit Ngg1 Negative GeneticPMID:18818364
vrp1verprolin Positive GeneticPMID:18818364
nup61nucleoporin Nup61 Negative GeneticPMID:18818364
SPBC1685.04Schizosaccharomyces specific protein Negative GeneticPMID:18818364
reb1RNA polymerase I transcription termination factor/ RNA polymerase II transcription factor Reb1 Negative GeneticPMID:18818364
rnc1RNA-binding protein that suppresses calcineurin deletion Rnc1 Negative GeneticPMID:18818364
air1zinc knuckle TRAMP complex subunit Air1 Positive GeneticPMID:18818364
fkbp39FKBP-type peptidyl-prolyl cis-trans isomerase (predicted) Negative GeneticPMID:18818364
pab2poly(A) binding protein Pab2 Negative GeneticPMID:18818364
ssu72phosphoric ester hydrolase Ssu72 (predicted) Negative GeneticPMID:18818364
myp2myosin II heavy chain Myo3 Negative GeneticPMID:18818364
swi6HP1 family chromodomain protein Swi6 Negative GeneticPMID:18818364
ctf18RFC-like complex subunit Ctf18 Negative GeneticPMID:18818364
bun107WD repeat protein, human WDR48 family Bun107 Negative GeneticPMID:18818364
cph1Clr6 histone deacetylase associated PHD protein-1 Cph1 Negative GeneticPMID:18818364
hrd1synviolin family ubiquitin-protein ligase E3, Hrd1 Positive GeneticPMID:18818364
elp2elongator complex subunit Elp2 (predicted) Positive GeneticPMID:18818364
srb11cyclin CycC, Srb mediator subunit Srb11 Negative GeneticPMID:18818364
tip1CLIP170 family protein Tip1 Negative GeneticPMID:18818364
sum2G2/M transition checkpoint protein Sum2 Negative GeneticPMID:18818364
sdh4TIM22 inner membrane protein import complex anchor subunit Tim18 Negative GeneticPMID:18818364
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)
Cyclebase SPCC18.06c Cell Cycle Data
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
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
ePDB2P51The European PDB
ePDB3G0ZThe European PDB
ePDB3G10The European PDB
European Nucleotide ArchiveCAA21420.2ENA Protein Mapping
UniParcUPI000228F4F2UniProt Archive

Literature for caf1

Search: Europe PMC or PubMed

Release Version: PomBase:25_48 - 10 Jan 2015