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 IDTerm NameEvidenceWith/FromReferenceCount
GO:0003729mRNA bindingISSPDB:2A1RPMID:1745235929
GO:0046872metal ion bindingIDAPMID:17452359748
GO:0004535poly(A)-specific ribonuclease activityIDAPMID:174523593
GO Biological Process
Term IDTerm NameEvidenceWith/FromReferenceCount
GO:0090503RNA phosphodiester bond hydrolysis, exonucleolyticIDAPMID:1745235921
GO:0000289nuclear-transcribed mRNA poly(A) tail shorteningIDAPMID:174523598
GO:0006357regulation of transcription from RNA polymerase II promoterISOSGD:S000005335GO_REF:0000024262
GO:0006368transcription elongation from RNA polymerase II promoterISOSGD:S000005335GO_REF:000002425
GO Cellular Component
Term IDTerm NameEvidenceWith/FromReferenceCount
GO:0030015CCR4-NOT core complexISOSGD:S000005335PMID:174523598
GO:0005737cytoplasmISOSGD:S000005335GO_REF:00000244204
GO:0005829cytosolIDAPMID:168233722319
GO:0005634nucleusIDAPMID:168233722737
Fission Yeast Phenotype Ontology

Population Phenotype

Term IDTerm NameEvidenceAlleleExpressionConditionReferenceCount
FYPO:0001098sensitive to 4-nitroquinoline N-oxide159
expressivity FYPO_EXT:0000003Cell growth assaycaf1ΔNullPECO:0000137, PECO:0000005PMID:19264558
FYPO:0002642sensitive to amphotericin B69
expressivity FYPO_EXT:0000001Cell growth assaycaf1ΔNullPECO:0000137, PECO:0000005PMID:23738021
FYPO:0000096sensitive to cadmium246
expressivity FYPO_EXT:0000002Cell growth assaycaf1ΔNullPECO:0000102, PECO:0000005, PECO:0000137PMID:18684775
FYPO:0000097sensitive to caffeine99
expressivity FYPO_EXT:0000001Cell growth assaycaf1ΔNullPECO:0000137PMID:19672306
FYPO:0000085sensitive to camptothecin211
expressivity FYPO_EXT:0000003Cell growth assaycaf1ΔNullPECO:0000137, PECO:0000005PMID:19264558
competitive growth assay evidencecaf1ΔNullPMID:20537132
FYPO:0003559sensitive to doxorubicin91
expressivity FYPO_EXT:0000003Cell growth assaycaf1ΔNullPECO:0000137, PECO:0000142PMID:23365689
FYPO:0000087sensitive to hydrogen peroxide124
expressivity FYPO_EXT:0000001Cell growth assaycaf1ΔNullPECO:0000137PMID:19672306
expressivity FYPO_EXT:0000003Cell growth assaycaf1ΔNullPECO:0000102, PECO:0000005, PECO:0000137PMID:18684775
FYPO:0000088sensitive to hydroxyurea513
expressivity FYPO_EXT:0000002Cell growth assaycaf1ΔNullPECO:0000137, PECO:0000005PMID:19264558
FYPO:0000267sensitive to ionizing radiation44
expressivity FYPO_EXT:0000003Cell growth assaycaf1ΔNullPECO:0000137, PECO:0000005PMID:19264558
FYPO:0000089sensitive to methyl methanesulfonate214
expressivity FYPO_EXT:0000003Cell growth assaycaf1ΔNullPECO:0000137, PECO:0000005PMID:19264558
FYPO:0002641sensitive to micafungin116
expressivity FYPO_EXT:0000001Cell growth assaycaf1ΔNullPECO:0000137, PECO:0000005PMID:23738021
FYPO:0000271sensitive to salt stress82
expressivity FYPO_EXT:0000003Cell growth assaycaf1ΔNullPECO:0000207, PECO:0000137, PECO:0000102, PECO:0000005PMID:18684775
FYPO:0002060viable vegetative cell populationMicroscopycaf1ΔNullPMID:204732893751
Microscopycaf1ΔNullPECO:0000005, PECO:0000137PMID:23697806

Cell Phenotype

Term IDTerm NameEvidenceAlleleExpressionConditionReferenceCount
FYPO:0000708decreased mating efficiencyhigh throughput nucleotide sequencing assay evidencecaf1ΔNullPECO:0000015PMID:23950735238
FYPO:0002357normal RNA binding3
affecting ago1Gel electrophoresis evidencecaf1ΔNullPMID:24095277
FYPO:0000647vegetative cell lysisCell growth assaycaf1ΔNullPECO:0000137, PECO:0000005PMID:2373802179
FYPO:0002177viable vegetative cell with normal cell morphology3088
penetrance FYPO_EXT:0000001Microscopycaf1ΔNullPECO:0000005, PECO:0000137PMID:23697806
Transcript
Ensembl transcript structure with UTRs, exons and introns

Exons

Exon Start End
119669331965430
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 HMMPANTHER 1 322 1
3.30.420.10 Gene3D 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
Sequence
Gene Expression

Quantitative Gene Expression

Protein Level

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

RNA Level

Molecules/Cell (average)ExtensionConditionScaleEvidenceReference
2.3during GO:0072690PECO:0000005,
PECO:0000014
population_wideexperimental evidencePMID:23101633
0.53during cell quiescence following G1 arrest due to nitrogen limitationPECO:0000005,
PECO:0000014,
PECO:0000127
population_wideexperimental evidencePMID:23101633
Warning
DescriptionQualifierReferenceCount
gene structure updated PMID:21511999432
Species Distribution
DescriptionQualifierReferenceCount
predominantly single copy (one to one)3092
conserved in fungi4599
conserved in eukaryotes4514
conserved in metazoa3428
conserved in vertebrates3402
conserved in eukaryotes only2498
Orthologs

Manually curated orthologous groups

SpeciesGeneDescriptionLinksCount

Orthologs in Compara


Genetic Interactions

Source: BioGRID

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
mad2spindle 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
pek1MAP kinase kinase Pek1 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
cwf21complexed with Cdc5 protein Cwf21 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
SPBC29A3.09cAAA 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 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
hrd1ubiquitin-protein ligase Hrd1, synviolin family 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
Physical Interactions

Source: BioGRID

Gene Product Evidence Reference
epe1Jmjc domain chromatin associated protein Epe1 Affinity Capture-MSPMID:24013502
suc22ribonucleotide reductase small subunit Suc22 Affinity Capture-WesternPMID:17264117
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
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
PDB2P51PDB
PDBsum2P51PDBsum
ePDB3G0ZThe European PDB
PDB3G0ZPDB
PDBsum3G0ZPDBsum
ePDB3G10The European PDB
PDB3G10PDB
PDBsum3G10PDBsum
European Nucleotide ArchiveCAA21420.2ENA Protein Mapping
UniParcUPI000228F4F2UniProt Archive

Literature for caf1

Search: Europe PMC or PubMed

Release Version: PomBase:23_46 - 30 Aug 2014