ctp1 (SPCC338.08)


Gene Standard Namectp1 Characterisation Statuspublished
Systematic IDSPCC338.08 Feature Typeprotein coding
Synonymsmug38, nip1, slr9 Name DescriptionMeiotically Upregulated Gene,
Synthetic Lethal with Rad2 mutant,
Nbs1-Interacting Protein 1
ProductCtIP-related endonuclease Product Size294aa, 33.10 kDa
Genomic Location Chromosome III, 1360260-1358737 (1524nt); CDS:1359819-1358891 (929nt)

Ensembl Gene Location
GO Molecular Function
Term NameCount
DNA binding371
Annotation ExtensionEvidenceWith/FromReference
endonuclease activity75
Annotation ExtensionEvidenceWith/FromReference
single-stranded DNA endodeoxyribonuclease activity7
Annotation ExtensionEvidenceWith/FromReference
GO Biological Process
Term NameCount
DNA damage checkpoint34
Annotation ExtensionEvidenceWith/FromReference
DNA double-strand break processing4
Annotation ExtensionEvidenceWith/FromReference
double-strand break repair via homologous recombination36
Annotation ExtensionEvidenceWith/FromReference
meiotic DNA double-strand break clipping1
Annotation ExtensionEvidenceWith/FromReference
meiotic DNA double-strand break processing2
Annotation ExtensionEvidenceWith/FromReference
meiotic DNA double-strand break resectioning1
Annotation ExtensionEvidenceWith/FromReference
mitotic DNA replication checkpoint19
Annotation ExtensionEvidenceWith/FromReference
response to ionizing radiation1
Annotation ExtensionEvidenceWith/FromReference
GO Cellular Component
Term NameCount
nuclear chromosome487
Annotation ExtensionEvidenceWith/FromReference
FYPO Single-Allele Phenotypes
Gene Deletion Viability: Viable

Population Phenotype

Term NameGenotypesCount
decreased spore germination frequencyctp1-17 (H274L)61
ctp1-11 (Q120H, F232L)
inviable spore populationctp1-9 (C229F)21
ctp1Δ
ctp1-30 (I110N, frameshift at T197 truncating at 208)
ctp1-8 (H160Y, R214*)
ctp1-10 (R201*)
ctp1-6 (D250*)
ctp1-5 (frame shift at W288 truncating at 292)
ctp1-1 (C226Y)
ctp1-25 (G187*)
sensitive to 4-nitroquinoline N-oxidectp1Δ159
sensitive to amphotericin Bctp1Δ69
sensitive to camptothecinctp1-5 (frame shift at W288 truncating at 292)248
ctp1-17 (H274L)
ctp1-9 (C229F)
ctp1-10 (R201*)
ctp1-6 (D250*)
ctp1-25 (G187*)
ctp1Δ
ctp1-8 (H160Y, R214*)
ctp1-30 (I110N, frameshift at T197 truncating at 208)
ctp1-1 (C226Y)
sensitive to cisplatinctp1Δ106
sensitive to clotrimazolectp1Δ107
sensitive to doxorubicinctp1Δ95
sensitive to hydroxyureactp1Δ580
sensitive to ionizing radiation during vegetative growth72
ctp1Δ
sensitive to methyl methanesulfonatectp1-6 (D250*)318
ctp1-30 (I110N, frameshift at T197 truncating at 208)
ctp1-9 (C229F)
ctp1-8 (H160Y, R214*)
ctp1Δ
ctp1-25 (G187*)
ctp1-10 (R201*)
ctp1-1 (C226Y)
ctp1-5 (frame shift at W288 truncating at 292)
sensitive to terbinafinectp1Δ103
sensitive to thiabendazolectp1Δ326
sensitive to UV during vegetative growthctp1Δ151
slow vegetative cell population growth357
viable vegetative cell populationctp1Δ3840

Cell Phenotype

Term NameGenotypesCount
abnormal microtubule cytoskeleton morphology during mitotic interphasectp1Δ186
abnormal mitotic cell cyclectp1Δ877
abnormal mitotic DNA damage checkpointctp1Δ31
abolished meiotic DNA double-strand break clippingctp1Δ1
ctp1-1 (C226Y)
ctp1-17 (H274L)
ctp1-6 (D250*)
decreased intergenic meiotic recombinationctp1-5 (frame shift at W288 truncating at 292)24
ctp1-30 (I110N, frameshift at T197 truncating at 208)
ctp1-8 (H160Y, R214*)
ctp1-6 (D250*)
ctp1Δ
ctp1-25 (G187*)
ctp1-9 (C229F)
decreased intragenic meiotic recombinationctp1-1 (C226Y)30
ctp1-9 (C229F)
ctp1-17 (H274L)
decreased meiotic DNA double-strand break resectioningctp1Δ1
decreased protein phosphorylation during mitotic G2 phase during cellular response to ionizing radiation2
affecting chk1ctp1Δ
elongated vegetative cell793
increased duration of protein localization to double-strand break site1
affects localization of mre11ctp1Δ
increased protein phosphorylation during mitotic G2 phase1
affecting chk1ctp1Δ
normal meiotic DNA double-strand break resectioningctp1-10 (R201*)1
ctp1-25 (G187*)
ctp1-17 (H274L)
ctp1-1 (C226Y)
ctp1-6 (D250*)
viable elongated vegetative cellctp1Δ318
viable vegetative cell with abnormal cell shapectp1Δ700

FYPO Multi-allele Phenotypes

Population Phenotype

Term NameGenotypes
inviable vegetative cell populationctp1Δ, nrm1Δ
Target Of
OntologyRelationshipGeneProduct
FYPO affected by mutation in nrm1 MBF complex corepressor Nrm1
FYPO localization affected by mutation in mre11 Mre11 nuclease
GO localized by mre11 Mre11 nuclease
GO regulated by cdc10 MBF transcription factor complex subunit Cdc10
GO regulated by rep1 MBF transcription factor activator Rep1
GO regulated by rep2 MBF transcription factor activator Rep2
GO substrate of tel1 ATM checkpoint kinase
Transcript
Ensembl transcript structure with UTRs, exons and introns

Transcript Structure

Region Coordinates Reference
Exons1360260..1359127, 1359082..1358737
Intron1359126..1359083
mRNA1360260..1358737
5' UTR1360260..1359820PMID:21511999
CDS1359819..1359127, 1359082..1358891
3' UTR1358890..1358737SPC01163
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
PF08573 Pfam IPR013882 Com1/Ctip family 210 292 1
PTHR15107 HMMPANTHER DNA endonuclease RBBP8-like 54 294 1
Coil ncoils Predicted coiled-coil protein (DUF2205) 16 43 1057

View domain organization at Pfam

Protein Properties

Ave. residue weight 112.59 Da
Charge -6.50
Codon Adaptation Index 0.39
Isoelectric point 5.17
Molecular weight 33.10 kDa
Number of residues 294
Modifications

Protein Modifications

Term NameResidueCount
phosphorylated residue 1931
present during cellular response to DNA damage stimulus
Annotation ExtensionEvidenceResidueReference
present during cellular response to DNA damage stimulus NAS PMID:18378696
IDA PMID:19547744
Sequence
Gene Expression

Qualitative Gene Expression

DescriptionLevelEvidenceReference
RNA levelincreased during GO:0051321experimental evidencePMID:16303567

Quantitative Gene Expression

View graphical display of gene expression data for ctp1 (SPCC338.08)

RNA Level

Molecules/Cell (average)ExtensionConditionScaleEvidenceReference
1.6during GO:0072690PECO:0000014,
PECO:0000005
population wideexperimental evidencePMID:23101633
0.72during cell quiescence following G1 arrest due to nitrogen limitationPECO:0000127,
PECO:0000014,
PECO:0000005
population wideexperimental evidencePMID:23101633
Subunit Composition
DescriptionQualifierReferenceCount
homomeric(2) PMID:1793671053
Misc
DescriptionQualifierReferenceCount
localizes to double-strand breaks PMID:179367101
Warning
DescriptionQualifierReferenceCount
gene structure updated PMID:18378696434
Taxonomic Conservation
DescriptionQualifierReferenceCount
predominantly single copy (one to one)3092
conserved in fungi4606
conserved in eukaryotes4516
conserved in metazoa3424
conserved in vertebrates3399
conserved in eukaryotes only2506
Orthologs

Manually curated orthologous groups

SpeciesGeneDescriptionLinksCount

Orthologs in Compara


Physical Interactions

Source: BioGRID

Load genes that interact physically with SPCC338.08 into the Query Builder
View all interactions in esyN
View the HCPIN interactions in esyN

Gene Product Evidence Reference
(peptide) binds to proteinnbs1Mre11 complex subunit Nbs1 Protein-peptidePMID:19804756
affinity capturesnbs1Mre11 complex subunit Nbs1 Affinity Capture-WesternPMID:20421724
affinity captured bynbs1Mre11 complex subunit Nbs1 Affinity Capture-WesternPMID:19804755
Genetic Interactions

Source: BioGRID

Load genes that interact genetically with SPCC338.08 into the Query Builder
View these interactions in esyN

Gene Product Evidence Reference
synthetic lethal withnrm1MBF complex corepressor Nrm1 Synthetic LethalityPMID:25533348
negative genetic interaction withSPCC126.13chistone deacetylase complex subunit, SAP128 family (predicted) Negative GeneticPMID:22681890
negative genetic interaction witharp8actin-like protein, Ino80 complex subunit Arp8 Negative GeneticPMID:22681890
negative genetic interaction withase1antiparallel microtubule cross-linking factor Ase1 Negative GeneticPMID:22681890
negative genetic interaction withspt2non-specific DNA binding protein Spt2 (predicted) Negative GeneticPMID:22681890
negative genetic interaction withcwf26complexed with Cdc5 protein Cwf26 Negative GeneticPMID:22681890
negative genetic interaction withmug55Cdc20/Fizzy subfamily WD repeat protein Negative GeneticPMID:22681890
negative genetic interaction withclr4histone H3 lysine methyltransferase Clr4 Negative GeneticPMID:22681890
negative genetic interaction withswi6HP1 family chromodomain protein Swi6 Negative GeneticPMID:22681890
negative genetic interaction withcsn2COP9/signalosome complex subunit Csn2 Negative GeneticPMID:22681890
negative genetic interaction withalp13MRG family Clr6 histone deacetylase complex subunit Alp13 Negative GeneticPMID:22681890
negative genetic interaction withraf1CLRC ubiquitin E3 ligase complex specificiy factor Raf1/Dos1 Negative GeneticPMID:22681890
negative genetic interaction withsty1MAP kinase Sty1 Negative GeneticPMID:22681890
negative genetic interaction withcph1Clr6 histone deacetylase associated PHD protein-1 Cph1 Negative GeneticPMID:22681890
negative genetic interaction withprw1Clr6 histone deacetylase complex subunit Prw1 Negative GeneticPMID:22681890
negative genetic interaction withtas3RITS complex subunit 3 Negative GeneticPMID:22681890
negative genetic interaction withpnk1DNA kinase/phosphatase Pnk1 Negative GeneticPMID:22681890
negative genetic interaction withres2MBF transcription factor complex subunit Res2 Negative GeneticPMID:22681890
negative genetic interaction withask1DASH complex subunit Ask1 Negative GeneticPMID:22681890
negative genetic interaction withspc34DASH complex subunit Spc34 Negative GeneticPMID:22681890
negative genetic interaction withpef1Pho85/PhoA-like cyclin-dependent kinase Pef1 Negative GeneticPMID:22681890
negative genetic interaction withdad4DASH complex subunit Dad4 Negative GeneticPMID:22681890
negative genetic interaction withclr3histone deacetylase (class II) Clr3 Negative GeneticPMID:22681890
negative genetic interaction withhrq1RecQ type DNA helicase Hrq1 (predicted) Negative GeneticPMID:22681890
negative genetic interaction withclr1SHREC complex subunit Clr1 Negative GeneticPMID:22681890
negative genetic interaction withhip4histone promoter control protein Hip4 Negative GeneticPMID:22681890
negative genetic interaction withdad3DASH complex subunit Dad3 Negative GeneticPMID:22681890
negative genetic interaction withddb1damaged DNA binding protein Ddb1 Negative GeneticPMID:22681890
negative genetic interaction withmug154conserved fungal protein Negative GeneticPMID:22681890
negative genetic interaction withgcn20AAA family ATPase Gcn20 (predicted) Negative GeneticPMID:22681890
negative genetic interaction withres1MBF transcription factor complex subunit Res1 Negative GeneticPMID:22681890
negative genetic interaction withcph2Clr6 histone deacetylase associated PHD protein-2 Cph2 Negative GeneticPMID:22681890
negative genetic interaction withduo1DASH complex subunit Duo1 Negative GeneticPMID:22681890
negative genetic interaction withswd1Set1C complex subunit Swd1 Negative GeneticPMID:22681890
negative genetic interaction withrad1checkpoint clamp complex protein Rad1 Negative GeneticPMID:22681890
negative genetic interaction withpus1tRNA pseudouridine synthase Lsp1 Negative GeneticPMID:22681890
negative genetic interaction withfin1serine/threonine protein kinase, NIMA related Fin1 Negative GeneticPMID:22681890
negative genetic interaction withexo1exonuclease I Exo1 Negative GeneticPMID:22681890
negative genetic interaction withdam1DASH complex subunit Dam1 Negative GeneticPMID:22681890
negative genetic interaction withraf2Rik1-associated factor Raf2 Negative GeneticPMID:22681890
negative genetic interaction withcsn1COP9/signalosome complex subunit Csn1 Negative GeneticPMID:22681890
negative genetic interaction withkin1microtubule affinity-regulating kinase Kin1 Negative GeneticPMID:22681890
negative genetic interaction withnrm1MBF complex corepressor Nrm1 Negative GeneticPMID:22681890
negative genetic interaction witharp42SWI/SNF and RSC complex subunit Arp42 Negative GeneticPMID:22681890
negative genetic interaction withSPCC126.01cconserved fungal protein Negative GeneticPMID:22681890
negative genetic interaction withrhp14XP-A family homolog Rhp14 Negative GeneticPMID:22681890
negative genetic interaction withset5histone lysine methyltransferase Set5 (predicted) Negative GeneticPMID:22681890
negative genetic interaction withcdt2WD repeat protein Cdt2 Negative GeneticPMID:22681890
negative genetic interaction withfft3SMARCAD1 family ATP-dependent DNA helicase Fft3 Negative GeneticPMID:22681890
positive genetic interaction withrad51RecA family recombinase Rad51/Rhp51 Positive GeneticPMID:22681890
positive genetic interaction withatb2tubulin alpha 2 Positive GeneticPMID:22681890
positive genetic interaction withatp11mitochondrial F1-ATPase chaperone Atp11 (predicted) Positive GeneticPMID:22681890
positive genetic interaction withtom70mitochondrial TOM complex subunit Tom70 (predicted) Positive GeneticPMID:22681890
synthetic growth defect withcrb2DNA repair protein Rad9 homolog Crb2 Synthetic Growth DefectPMID:21098122
synthetic growth defect withhus1checkpoint clamp complex protein Hus1 Synthetic Growth DefectPMID:21098122
synthetic growth defect withhta2histone H2A beta Synthetic Growth DefectPMID:21098122
synthetic growth defect withnbs1Mre11 complex subunit Nbs1 Synthetic Growth DefectPMID:21098122
synthetic growth defect withdcd1deoxycytidylate deaminase (predicted) Synthetic Growth DefectPMID:22927644
phenotype enhanced bypku80Ku domain protein Pku80 Phenotypic EnhancementPMID:21931565
phenotype enhanced bynbs1Mre11 complex subunit Nbs1 Phenotypic EnhancementPMID:21098122
phenotype enhanced byhus1checkpoint clamp complex protein Hus1 Phenotypic EnhancementPMID:21098122
phenotype enhanced bytel1ATM checkpoint kinase Phenotypic EnhancementPMID:21098122
phenotype enhanced bycrb2DNA repair protein Rad9 homolog Crb2 Phenotypic EnhancementPMID:21098122
synthetically rescuesrad3ATR checkpoint kinase Rad3 Synthetic RescuePMID:21098122
rescuesrad3ATR checkpoint kinase Rad3 Phenotypic SuppressionPMID:21098122
rescuestrt1telomerase reverse transcriptase 1 protein Trt1 Phenotypic SuppressionPMID:23335786
rescuestaz1human TRF ortholog Taz1 Phenotypic SuppressionPMID:23335786
synthetically rescued bypku70Ku domain protein Pku70 Synthetic RescuePMID:21931565
synthetically rescued byrad3ATR checkpoint kinase Rad3 Synthetic RescuePMID:21098122
synthetically rescued bypku80Ku domain protein Pku80 Synthetic RescuePMID:21931565
External References
Database Identifier Description
NBRP SPCC338.08 Fission yeast strain database, National BioResource Project (Japan)
YOGY SPCC338.08 Retrieval of eukaryotic orthologs (Bähler Lab)
BioGrid SPCC338.08 BioGRID Interaction Datasets
Expression Viewer SPCC338.08 Cell Cycle Expression Profile (Bähler Lab)
Expression Viewer SPCC338.08 Meiosis/Sporulation Expression Profies (Bähler Lab)
Expression Viewer SPCC338.08 Pheromone response/mating expression profiles (Bähler Lab)
Expression Viewer SPCC338.08 Environmental stress expression profiles (Bähler Lab)
Pomb(A) SPCC338.08 Polyadenylation Viewer (Gullerova lab)
pombeTV SPCC338.08 Transcriptome Viewer (Bähler Lab)
GEO SPCC338.08 GEO profiles
PInt SPCC338.08 Protein-Protein Interaction Predictor (Bähler Lab)
PeptideAtlas SPCC338.08 Peptides identified in tandem mass spectrometry proteomics experiments
SYSGRO SPCC338.08 Fission yeast phenotypic data & analysis
Cyclebase SPCC338.08.1 Cell Cycle Data
SPD / RIKEN11/11D10Orfeome Localization Data
UniProtKB/SwissProtO74986DNA endonuclease ctp1
ModBaseO74986Database of comparative protein structure models
STRINGO74986Network display of known and predicted interactions and functional associations
RefSeq PeptideNP_588159CtIP-related endonuclease
RefSeq mRNANM_001023148972h- CtIP-related endonuclease (ctp1), mRNA

Literature for ctp1

Search: Europe PMC or PubMed

Release Version: PomBase:30_59 - 12 Apr 2016