rad4 (SPAC23C4.18c)


Gene Standard Namerad4 Characterisation Statuspublished
Systematic IDSPAC23C4.18c Feature Typeprotein coding
Synonymscut5, dpb11, dre3 Name DescriptionDefect in REplication
ProductBRCT domain protein Rad4 Product Size648aa, 74.17 kDa
Genomic Location Chromosome I, 1063306-1058646 (4661nt); CDS:1062861-1060792 (2070nt)

Ensembl Gene Location
GO Molecular Function
Term IDTerm NameEvidenceWith/FromReferenceCount
GO:0005515protein bindingIPIcrb2PMID:9407031887
IPIcrb3PMID:9407031
IPIrad9PMID:24074952
GO:0032947protein complex scaffoldIDAPMID:240749524
GO Biological Process
Term IDTerm NameEvidenceWith/FromReferenceCount
GO:0071163DNA replication preinitiation complex assemblyIMPPMID:169907924
GO:0044773mitotic DNA damage checkpointIMPPMID:989491240
GO:0033314mitotic DNA replication checkpointIMPPMID:926802422
GO Cellular Component
Term IDTerm NameEvidenceWith/FromReferenceCount
GO:0031261DNA replication preinitiation complexISOSGD:S000003626GO_REF:000002421
GO:0005829cytosol2317
during mitotic anaphaseIDAPMID:16823372
GO:0044732mitotic spindle pole bodyIDAPMID:16823372214
GO:0043596nuclear replication forkISOSGD:S000003626GO_REF:000002463
GO:0005634nucleusIDAPMID:168233722730
GO:0035861site of double-strand breakIDAPMID:2362848143
GO:0005819spindleIDAPMID:16823372273
Fission Yeast Phenotype Ontology

Population Phenotype

Term IDTerm NameEvidenceAlleleExpressionConditionReferenceCount
FYPO:0002061inviable vegetative cell populationMicroscopyrad4ΔNullPMID:204732891309
Microscopyrad4ΔNullPECO:0000005, PECO:0000137PMID:23697806
FYPO:0000266sensitive to DNA damaging agentsCell growth assayrad4tsNot specifiedPMID:9775467
FYPO:0000268sensitive to UV during vegetative growthCell growth assayrad4 mutantNot specifiedPMID:829035982
Cell growth assayrad4.116EndogenousPMID:1762905
Cell growth assayrad4tsNot specifiedPMID:977546
FYPO:0000088sensitive to hydroxyureaCell growth assayrad4-11CNot specifiedPMID:1563349233
FYPO:0000267sensitive to ionizing radiationCell growth assayrad4tsNot specifiedPMID:97754641
Cell growth assayrad4.116Not specifiedPMID:1762905
FYPO:0001234slow vegetative cell population growthCell growth assayrad4tsNot specifiedPECO:0000005PMID:97754640

Cell Phenotype

Term IDTerm NameEvidenceAlleleExpressionConditionReferenceCount
FYPO:0000453DNA content decreased during vegetative growthFlow cytometry datarad4-42 (A132G)Not specifiedPECO:0000229, PECO:0000004PMID:154664216
FYPO:0001933abnormal cell cycle regulation during cellular response to hydroxyureaMicroscopyrad4-11CNot specifiedPECO:0000005PMID:15633495
FYPO:0000229cutMicroscopyrad4-42 (A132G)Not specifiedPECO:0000229, PECO:0000004PMID:1546642183
no_namePMID:8395535
FYPO:0001042inviable after spore germination, single or double cell divisionMicroscopyrad4ΔNullPECO:0000005, PECO:0000137PMID:2369780691
penetrance FYPO_EXT:0000003
FYPO:0000313inviable after spore germination, without cell division, with abnormal germ tube morphologyMicroscopyrad4ΔNullPECO:0000005, PECO:0000137PMID:23697806144
penetrance FYPO_EXT:0000001
FYPO:0001801inviable cell at high temperatureCell growth assayrad4.116EndogenousPMID:176290523
FYPO:0001489inviable vegetative cellCell growth assayrad4ΔNullPMID:1762905934
Transcript
Ensembl transcript structure with UTRs, exons and introns

Exons

Exon Start End
110633061062796
210627381062631
310625641058646

UTRs

Region Start End Reference
three_prime_UTR10607911058646PMID:21511999
five_prime_UTR10633061062862PMID: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
PF00533 Pfam IPR001357 BRCT domain 102 172 8
PF00533 Pfam IPR001357 BRCT domain 300 371 8
PF00533 Pfam IPR001357 BRCT domain 4 75 8
PF00533 Pfam IPR001357 BRCT domain 395 472 8
PF12738 Pfam IPR001357 BRCT domain 105 167 3
SM00292 SMART IPR001357 BRCT domain 4 82 12
SM00292 SMART IPR001357 BRCT domain 100 175 12
SM00292 SMART IPR001357 BRCT domain 300 374 12
SM00292 SMART IPR001357 BRCT domain 394 476 12
PS50172 Prosite Profiles IPR001357 BRCT domain 298 384 13
PS50172 Prosite Profiles IPR001357 BRCT domain 2 75 13
PS50172 Prosite Profiles IPR001357 BRCT domain 114 185 13
PS50172 Prosite Profiles IPR001357 BRCT domain 392 480 13
PTHR13561 HMMPANTHER 1 507 3
G3DSA:3.40.50.10190 Gene3D IPR001357 396 480 12
G3DSA:3.40.50.10190 Gene3D IPR001357 102 183 12
G3DSA:3.40.50.10190 Gene3D IPR001357 2 76 12
G3DSA:3.40.50.10190 Gene3D IPR001357 300 384 12
SSF52113 SuperFamily IPR001357 359 480 12
SSF52113 SuperFamily IPR001357 4 76 12
SSF52113 SuperFamily IPR001357 301 384 12
SSF52113 SuperFamily IPR001357 78 188 12
Low complexity (SEG) seg 227 237

View domain organization at Pfam

Manually Curated Family or Sub-families

Term IDTerm NameReferenceCount
PBO:0000443BRCT domainTemporary processing gif - replaced by AJAX with count of genes annotated with the term PBO:0000443

Protein Properties

Ave. residue weight 114.46 Da
Charge 11.50
Isoelectric point 8.21
Molecular weight 74.17 kDa
Number of residues 648
Modifications

Protein Modifications

Term IDTerm NameEvidenceResidueReferenceCount
MOD:00696phosphorylated residuePMID:195477441192
Sequence
Gene Expression

Quantitative Gene Expression

Protein Level

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

RNA Level

Molecules/Cell (average)DuringConditionScaleEvidenceReference
1during GO:0072690PECO:0000005,
PECO:0000014
population_wideexperimental evidencePMID:23101633
0.39during 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)3080
conserved in fungi4564
conserved in eukaryotes4482
conserved in metazoa3419
conserved in vertebrates3394
conserved in eukaryotes only2485
Orthologs

Manually curated orthologous groups

SpeciesGeneDescriptionLinksCount

Orthologs in Compara


Genetic Interactions

Source: BioGRID

Gene Product Evidence Reference
rad9checkpoint clamp complex protein Rad9 Phenotypic SuppressionPMID:22761595
Synthetic Growth Defect
cdc22ribonucleoside reductase large subunit Cdc22 Synthetic LethalityPMID:9268024
set9histone lysine methyltransferase Set9 Synthetic Growth DefectPMID:16778077
Phenotypic Enhancement
cdc25M phase inducer phosphatase Cdc25 Phenotypic SuppressionPMID:7957098
cdc23MCM-associated protein Mcm10 Synthetic LethalityPMID:11606526
rum1CDK inhibitor Rum1 Phenotypic SuppressionPMID:10388806
psf3GINS complex subunit Psf3 Synthetic Growth DefectPMID:16990792
cdc2cyclin-dependent protein kinase Cdk1/Cdc2 Phenotypic SuppressionPMID:7957098
rad26ATRIP, ATR checkpoint kinase regulatory subunit Rad26 Synthetic RescuePMID:12865439
mcm4MCM complex subunit Mcm4/Cdc21 Synthetic LethalityPMID:11606526
rad3ATR checkpoint kinase Rad3 Synthetic RescuePMID:12865439
hsk1Dbf4(Dfp1)-dependent protein kinase Hsk1 Synthetic Growth DefectPMID:11027263
crb2DNA repair protein Rad9 homolog, Rhp9 Synthetic Growth DefectPMID:16778077
Dosage RescuePMID:9407031
spo20sec14 cytosolic factor family Sec14 Negative GeneticPMID:22681890
cdc45DNA replication pre-initiation complex subunit Cdc45 Synthetic Growth DefectPMID:11523776
crb3WD repeat protein Crb3 Dosage RescuePMID:16723501
rad17RFC related checkpoint protein Rad17 Synthetic RescuePMID:12865439
chk1Chk1 protein kinase Synthetic Growth DefectPMID:16723501
drc1DNA replication checkpoint protein Drc1 Dosage RescuePMID:11937031
cds1replication checkpoint kinase Cds1 Phenotypic EnhancementPMID:16723501
mcb1MCM binding protein homolog Mcb1 (predicted) Synthetic Growth DefectPMID:23322785
meu13Tat binding protein 1(TBP-1)-interacting protein (TBPIP) homolog (predicted) Phenotypic SuppressionPMID:14718568
Phenotypic Enhancement
SPCC191.01sequence orphan Dosage RescuePMID:17272281
cdc10MBF transcription factor complex subunit Cdc10 Phenotypic EnhancementPMID:8343962
dpb4DNA polymerase epsilon subunit Dpb4 Synthetic LethalityPMID:15388803
cdc13G2/M B-type cyclin Cdc13 Phenotypic SuppressionPMID:7957098
rpl380160S ribosomal protein L38 (predicted) Positive GeneticPMID:22681890
rad8ubiquitin-protein ligase E3 Rad8 Synthetic Growth DefectPMID:8290359
Physical Interactions

Source: BioGRID

Gene Product Evidence Reference
crb3WD repeat protein Crb3 Two-hybridPMID:16723501
Affinity Capture-Western
Two-hybridPMID:9407031
Reconstituted Complex
cdc23MCM-associated protein Mcm10 Reconstituted ComplexPMID:21945095
Two-hybridPMID:22433840
rad17RFC related checkpoint protein Rad17 Affinity Capture-WesternPMID:16723501
chk1Chk1 protein kinase Affinity Capture-WesternPMID:16723501
Two-hybrid
Two-hybridPMID:9407031
Reconstituted Complex
dfp1Hsk1-Dfp1 kinase complex regulatory subunit Dfp1 Affinity Capture-WesternPMID:21095590
drc1DNA replication checkpoint protein Drc1 Two-hybridPMID:21945095
Two-hybridPMID:21593208
Two-hybridPMID:11937031
rad3ATR checkpoint kinase Rad3 Affinity Capture-WesternPMID:15155581
cdc13G2/M B-type cyclin Cdc13 Affinity Capture-WesternPMID:24074952
dpb2DNA polymerase epsilon catalytic subunit B, Dpb2 Affinity Capture-WesternPMID:22718908
Affinity Capture-WesternPMID:16723501
Two-hybrid
psf2GINS complex subunit Psf2 Affinity Capture-WesternPMID:22718908
rad9checkpoint clamp complex protein Rad9 Affinity Capture-WesternPMID:16723501
Affinity Capture-WesternPMID:15155581
hsk1Dbf4(Dfp1)-dependent protein kinase Hsk1 Affinity Capture-WesternPMID:21095590
Biochemical Activity
bgs11,3-beta-glucan synthase catalytic subunit Bgs1 Two-hybridPMID:11937031
sld3DNA replication pre-initiation complex subunit Sld3 Two-hybridPMID:21945095
Two-hybridPMID:21593208
crb2DNA repair protein Rad9 homolog, Rhp9 Two-hybridPMID:16778077
Two-hybridPMID:15229228
Reconstituted ComplexPMID:24074952
Co-crystal Structure
External References
Database Identifier Description
NBRP SPAC23C4.18c Fission yeast strain database, National BioResource Project (Japan)
YOGY SPAC23C4.18c Retrieval of eukaryotic orthologs (Bähler Lab)
BioGrid SPAC23C4.18c BioGRID Interaction Datasets
Expression Viewer SPAC23C4.18c Cell Cycle Expression Profile (Bähler Lab)
Expression Viewer SPAC23C4.18c Meiosis/Sporulation Expression Profies (Bähler Lab)
Expression Viewer SPAC23C4.18c Pheromone response/mating expression profiles (Bähler Lab)
Expression Viewer SPAC23C4.18c Environmental stress expression profiles (Bähler Lab)
Pomb(A) SPAC23C4.18c Polyadenylation Viewer (Gullerova lab)
pombeTV SPAC23C4.18c Transcriptome Viewer (Bähler Lab)
Cyclebase SPAC23C4.18c Cell Cycle Data
GEO SPAC23C4.18c GEO profiles
PInt SPAC23C4.18c Protein-Protein Interaction Predictor (Bähler Lab)
WikiGene2543281BRCT domain protein Rad4
EntrezGene2543281BRCT domain protein Rad4
SPD / RIKEN27/27F12Orfeome Localization Data
UniProtKB/SwissProtP32372S-M checkpoint control protein rad4
ModBaseP32372Database of comparative protein structure models
StringP32372Network display of known and predicted interactions and functional associations
RefSeq PeptideNP_593190BRCT domain protein Rad4
RefSeq mRNANM_001018586972h- BRCT domain protein Rad4 (rad4), mRNA
European Nucleotide ArchiveBAA04048ENA Protein Mapping
European Nucleotide ArchiveCAA44548ENA Protein Mapping
European Nucleotide ArchiveCAB16889ENA Protein Mapping
UniParcUPI0000061AF1UniProt Archive

Literature for rad4

Search: Europe PMC or PubMed

Release Version: PomBase:21_41 - 24 Feb 2014