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 NameCount
protein binding872
Annotation ExtensionEvidenceWith/FromReference
protein complex scaffold6
Annotation ExtensionEvidenceWith/FromReference
GO Biological Process
Term NameCount
mitotic DNA damage checkpoint30
Annotation ExtensionEvidenceWith/FromReference
mitotic DNA replication checkpoint19
Annotation ExtensionEvidenceWith/FromReference
mitotic DNA replication preinitiation complex assembly4
Annotation ExtensionEvidenceWith/FromReference
replication fork processing22
Annotation ExtensionEvidenceWith/FromReference
GO Cellular Component
Term NameCount
cytosol2302
Annotation ExtensionEvidenceWith/FromReference
DNA replication preinitiation complex18
Annotation ExtensionEvidenceWith/FromReference
mitotic spindle271
Annotation ExtensionEvidenceWith/FromReference
mitotic spindle pole body220
Annotation ExtensionEvidenceWith/FromReference
nuclear chromatin359
Annotation ExtensionEvidenceWith/FromReference
nuclear replication fork65
Annotation ExtensionEvidenceWith/FromReference
nucleus2691
Annotation ExtensionEvidenceWith/FromReference
site of double-strand break50
Annotation ExtensionEvidenceWith/FromReference
FYPO Single-Allele Phenotypes
Gene Deletion Viability: Inviable

Population Phenotype

Term NameGenotypesCount
decreased mating efficiencycut5-T401272
inviable vegetative cell populationcut5-T4011452
rad4Δ
normal growth on glucose carbon sourceK56E (K56E)287
K151A (K151A)
T15V,K56E (T15V, K56E)
R22E (R22E)
K56A (K56A)
T15V (T15V)
K151E (K151E)
R117E (R117E)
T110V (T110V)
normal growth on JM335cut5-T4015
normal growth on tetraplatincut5-T40114
normal growth on triplatin tetranitratecut5-T40111
sensitive to camptothecinT15V (T15V)248
K151E (K151E)
R117E (R117E)
T15V,K56E (T15V, K56E)
K56E (K56E)
K56A (K56A)
K151A (K151A)
T110V (T110V)
sensitive to cisplatincut5-T401106
sensitive to DNA damaging agentscut5-T4017
sensitive to hydroxyureaK56E (K56E)580
cut5-T401
K151E (K151E)
sensitive to ionizing radiation during vegetative growthcut5-T40173
sensitive to JM216cut5-T40110
sensitive to methyl methanesulfonateR22E (R22E)321
K56E (K56E)
T15V (T15V)
K151E (K151E)
K56A (K56A)
T110V (T110V)
K151A (K151A)
R117E (R117E)
sensitive to oxaliplatincut5-T40116
sensitive to UV during vegetative growthT110V (T110V)152
T15V,K56E (T15V, K56E)
K56A (K56A)
K56E (K56E)
R117E (R117E)
K151E (K151E)
R22E (R22E)
K151A (K151A)
T15V (T15V)
cut5-T401
slow vegetative cell population growthcut5-T401361
viable spore populationcut5-T40146

Cell Phenotype

Term NameGenotypesCount
abnormal chromosome morphologycut5-T40125
abnormal mitotic cell cycle regulation during cellular response to hydroxyureacut5-T40114
abolished protein binding130
affecting rad4 and rad9K452E (K452E)
affecting rad4 and cdc23cut5-T401
affecting rad4 and crb2K56E,K151E (K56E, K151E)
abolished protein localization to chromatin at replication origin2
affects localization of sld3cut5-T401
affects localization of drc1cut5-T401
affects localization of cdc23cut5-T401
abolished protein phosphorylation during cellular response to ionizing radiation5
affecting chk1K56E (K56E)
affecting chk1K56A (K56A)
affecting chk1T15V (T15V)
altered DNA level during vegetative growthcut5-T40193
cutcut5-401128
rad4-42 (A132G)
cut5-T401
cut cell with decreased poly(A)+ mRNA export from nucleuscut5-12
cut during cellular response to hydroxyureacut5-T40144
decreased protein localization to chromatin at replication origin10
affects localization of mcm4cut5-T401
decreased protein phosphorylation during cellular response to ionizing radiation9
affecting chk1R117E (R117E)
affecting chk1K151E (K151E)
affecting chk1K151A (K151A)
affecting chk1T110V (T110V)
DNA content decreased during vegetative growthrad4-42 (A132G)11
fragmented nucleuscut5-T40113
increased duration of mitotic S phasecut5-T40123
inviable after spore germination, single or double cell divisionrad4Δ107
inviable after spore germination, without cell division, with abnormal germ tube morphologyrad4Δ153
inviable cell at high temperaturecut5-T40120
inviable vegetative cellrad4Δ1352
loss of punctate nuclear protein localization during cellular response to ionizing radiation4
affects localization of crb2K151E (K151E)
affects localization of crb2K56E (K56E)
normal cell cycle regulation during cellular response to ionizing radiationcut5-T40116
normal meiosiscut5-T401149
normal mitotic cell cycle regulation during cellular response to UVcut5-T40111
normal premeiotic DNA replicationcut5-T40124
normal protein binding77
affecting rad4 and cdc23cut5-T401
affecting drc1 and rad4cut5-T401
normal protein phosphorylation during cellular response to ionizing radiation1
affecting chk1R22E (R22E)
normal spore morphologycut5-T40118
premature mitotic G1 phase entry during cellular response to ionizing radiationK56E (K56E)2
K151E (K151E)

FYPO Multi-allele Phenotypes

Population Phenotype

Term NameGenotypes
decreased vegetative cell population growthcbp1Δ, cut5-T401
inviable vegetative cell populationrad4+, (1-491)
cbp1Δ, cut5-T401
rad4+, (59-648)

Cell Phenotype

Term NameGenotypes
abnormal chromosome morphologycdc10-129 (T429A), cut5-T401
abnormal mitotic cell cycle regulation during cellular response to hydroxyureacdc2-1w (G146D), cut5-T401
cdc17-K42 (E298K), cut5-T401
cdc18-K46, cut5-T401
wee1::ura4+, cut5-T401
wee1+ (wild type), cut5-T401
cdc21-M68, cut5-T401
rad1-1, cut5-T401
wee-115, cut5-T401
cdc2-3w (C67Y), cut5-T401
abnormal negative regulation of mitotic DNA replication initiation resulting in partial rereplicationrum1+ (wild type), cut5-T401
cutcdc10-129 (T429A), cut5-T401
elongated mononucleate vegetative cellcdc25-22 (C532Y), cut5-T401
cdc2-33 (A177T), cut5-T401
cdc13-R9, cut5-T401
normal cell cycle regulation during cellular response to hydroxyureacdc2-33 (A177T), cut5-T401
cdc13-R9, cut5-T401
cdc25-22 (C532Y), cut5-T401
Target Of
OntologyRelationshipGeneProduct
FYPO affected by mutation in cdc23 MCM-associated protein Mcm10
FYPO affected by mutation in crb2 DNA repair protein Rad9 homolog Crb2
FYPO affected by mutation in drc1 replication preinitiation complex assembly protein
FYPO affected by mutation in rad4 BRCT domain protein Rad4
FYPO localization affected by mutation in rad17 RFC related checkpoint protein Rad17
FYPO localization affected by mutation in rad9 checkpoint clamp complex protein Rad9
Transcript
Ensembl transcript structure with UTRs, exons and introns

Transcript Structure

Region Coordinates Reference
Exons1063306..1062796, 1062738..1062631, 1062564..1058646
Intron1062795..1062739, 1062630..1062565
mRNA1063306..1058646
5' UTR1063306..1062862PMID:21511999
CDS1062861..1062796, 1062738..1062631, 1062564..1060792
3' UTR1060791..1058646PMID: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 301 371 6
PF00533 Pfam IPR001357 BRCT domain 395 472 6
PF12738 Pfam IPR001357 BRCT domain 105 167 4
PF12738 Pfam IPR001357 BRCT domain 11 74 4
SM00292 SMART IPR001357 BRCT domain 4 82 10
SM00292 SMART IPR001357 BRCT domain 394 476 10
SM00292 SMART IPR001357 BRCT domain 300 374 10
SM00292 SMART IPR001357 BRCT domain 100 175 10
PS50172 Prosite Profiles IPR001357 BRCT domain 114 185 13
PS50172 Prosite Profiles IPR001357 BRCT domain 298 384 13
PS50172 Prosite Profiles IPR001357 BRCT domain 392 480 13
PS50172 Prosite Profiles IPR001357 BRCT domain 2 75 13
PTHR13561 HMMPANTHER 3 451 3
3.40.50.10190 Gene3D IPR001357 BRCT domain 300 384 13
3.40.50.10190 Gene3D IPR001357 BRCT domain 2 76 13
3.40.50.10190 Gene3D IPR001357 BRCT domain 396 480 13
3.40.50.10190 Gene3D IPR001357 BRCT domain 102 183 13
SSF52113 SuperFamily IPR001357 BRCT domain 78 188 12
SSF52113 SuperFamily IPR001357 BRCT domain 359 480 12
SSF52113 SuperFamily IPR001357 BRCT domain 301 384 12
SSF52113 SuperFamily IPR001357 BRCT domain 4 76 12

View domain organization at Pfam

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
Codon Adaptation Index 0.40
Isoelectric point 8.21
Molecular weight 74.17 kDa
Number of residues 648
Modifications

Protein Modifications

Term NameResidueCount
phosphorylated residue 1932
Annotation ExtensionEvidenceResidueReference
IDA PMID:19547744
Sequence
Gene Expression

Qualitative Gene Expression

DescriptionLevelEvidenceReference
protein levelunchanged during GO:0000278Western blot evidencePMID:7957098
RNA levelunchanged during GO:0000278Northern assay evidencePMID:7957098

Quantitative Gene Expression

View graphical display of gene expression data for rad4 (SPAC23C4.18c)

RNA Level

Molecules/Cell (average)ExtensionConditionScaleEvidenceReference
1during GO:0072690PECO:0000014,
PECO:0000005
population wideexperimental evidencePMID:23101633
0.39during cell quiescence following G1 arrest due to nitrogen limitationPECO:0000127,
PECO:0000014,
PECO:0000005
population wideexperimental evidencePMID:23101633
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 only2505
Orthologs

Manually curated orthologous groups

SpeciesGeneDescriptionLinksCount

Orthologs in Compara


Physical Interactions

Source: BioGRID

Load genes that interact physically with SPAC23C4.18c into the Query Builder
View all interactions in esyN
View the HCPIN interactions in esyN

Gene Product Evidence Reference
affinity captured bycrb2DNA repair protein Rad9 homolog Crb2 Affinity Capture-WesternPMID:14739927
affinity captured byrad9checkpoint clamp complex protein Rad9 Affinity Capture-WesternPMID:15155581
affinity captured byrad26ATRIP, ATR checkpoint kinase regulatory subunit Rad26 Affinity Capture-WesternPMID:16723501
affinity captured bypsf2GINS complex subunit Psf2 Affinity Capture-WesternPMID:22718908
affinity captured bydpb2DNA polymerase epsilon catalytic subunit B, Dpb2 Affinity Capture-WesternPMID:16723501
binds activation domain construct withcrb3WD repeat protein Crb3 Two-hybridPMID:9407031
binds activation domain construct withcrb2DNA repair protein Rad9 homolog Crb2 Two-hybridPMID:9407031
binds activation domain construct withchk1Chk1 protein kinase Two-hybridPMID:16723501
binds activation domain construct withdrc1replication preinitiation complex assembly protein Two-hybridPMID:11937031
binds DNA-binding domain construct withrad9checkpoint clamp complex protein Rad9 Two-hybridPMID:16723501
binds DNA-binding domain construct withsld3DNA replication pre-initiation complex subunit Sld3 Two-hybridPMID:21593208
binds DNA-binding domain construct withcdc23MCM-associated protein Mcm10 Two-hybridPMID:21945095
binds DNA-binding domain construct withdrc1replication preinitiation complex assembly protein Two-hybridPMID:21945095
binds DNA-binding domain construct withchk1Chk1 protein kinase Two-hybridPMID:9407031
binds DNA-binding domain construct withbgs11,3-beta-glucan synthase catalytic subunit Bgs1 Two-hybridPMID:11937031
binds DNA-binding domain construct withcrb3WD repeat protein Crb3 Two-hybridPMID:16723501
co-locates (via crystalisation or NMR) withcrb2DNA repair protein Rad9 homolog Crb2 Co-crystal or NMR structurePMID:24074952
affinity capturesrad17RFC related checkpoint protein Rad17 Affinity Capture-WesternPMID:16723501
affinity captureshsk1Dbf4(Dfp1)-dependent protein kinase Hsk1 Affinity Capture-WesternPMID:21095590
affinity capturesrad3ATR checkpoint kinase Rad3 Affinity Capture-WesternPMID:15155581
affinity capturescdc13G2/M B-type cyclin Cdc13 Affinity Capture-WesternPMID:24074952
affinity capturesdfp1Hsk1-Dfp1 kinase complex regulatory subunit Dfp1 Affinity Capture-WesternPMID:21095590
affinity capturesdpb2DNA polymerase epsilon catalytic subunit B, Dpb2 Affinity Capture-WesternPMID:16723501
affinity capturesrad9checkpoint clamp complex protein Rad9 Affinity Capture-WesternPMID:15155581
affinity captureshus1checkpoint clamp complex protein Hus1 Affinity Capture-WesternPMID:16723501
forms complex withrad9checkpoint clamp complex protein Rad9 Reconstituted ComplexPMID:24663817
forms complex withcdc23MCM-associated protein Mcm10 Reconstituted ComplexPMID:21945095
forms complex withcrb2DNA repair protein Rad9 homolog Crb2 Reconstituted ComplexPMID:9407031
forms complex withcrb3WD repeat protein Crb3 Reconstituted ComplexPMID:9407031
modified byhsk1Dbf4(Dfp1)-dependent protein kinase Hsk1 Biochemical ActivityPMID:21095590
Genetic Interactions

Source: BioGRID

Load genes that interact genetically with SPAC23C4.18c into the Query Builder
View these interactions in esyN

Gene Product Evidence Reference
rescued by overexpression ofdrc1replication preinitiation complex assembly protein Dosage RescuePMID:11937031
rescued by overexpression ofSPCC191.01Schizosaccharomyces specific protein Dosage RescuePMID:17272281
rescued by overexpression ofcrb2DNA repair protein Rad9 homolog Crb2 Dosage RescuePMID:9407031
rescued by overexpression ofcrb3WD repeat protein Crb3 Dosage RescuePMID:16723501
synthetic growth defect withcrb2DNA repair protein Rad9 homolog Crb2 Synthetic Growth DefectPMID:24074952
synthetic growth defect withrad8ubiquitin-protein ligase E3 Rad8 Synthetic Growth DefectPMID:8290359
synthetic growth defect withchk1Chk1 protein kinase Synthetic Growth DefectPMID:16723501
synthetic growth defect withcdc45DNA replication pre-initiation complex subunit Cdc45 Synthetic Growth DefectPMID:11523776
synthetic growth defect withpsf3GINS complex subunit Psf3 Synthetic Growth DefectPMID:16990792
synthetic growth defect withset9histone lysine H3-K20 methyltransferase Set9 Synthetic Growth DefectPMID:16778077
synthetic growth defect withhsk1Dbf4(Dfp1)-dependent protein kinase Hsk1 Synthetic Growth DefectPMID:11027263
synthetic growth defect withmcb1MCM binding protein homolog Mcb1 Synthetic Growth DefectPMID:23322785
synthetic growth defect withrad9checkpoint clamp complex protein Rad9 Synthetic Growth DefectPMID:22761595
rescuesrum1CDK inhibitor Rum1 Phenotypic SuppressionPMID:10388806
rescuesmeu13Tat binding protein 1(TBP-1)-interacting protein (TBPIP) homolog (predicted) Phenotypic SuppressionPMID:14718568
rescuesrad9checkpoint clamp complex protein Rad9 Phenotypic SuppressionPMID:22761595
positive genetic interaction withrpl380160S ribosomal protein L38 (predicted) Positive GeneticPMID:22681890
enhances phenotype ofcdc10MBF transcription factor complex subunit Cdc10 Phenotypic EnhancementPMID:8343962
enhances phenotype ofcds1replication checkpoint kinase Cds1 Phenotypic EnhancementPMID:16723501
enhances phenotype ofset9histone lysine H3-K20 methyltransferase Set9 Phenotypic EnhancementPMID:16778077
enhances phenotype ofmeu13Tat binding protein 1(TBP-1)-interacting protein (TBPIP) homolog (predicted) Phenotypic EnhancementPMID:14718568
phenotype enhanced bycds1replication checkpoint kinase Cds1 Phenotypic EnhancementPMID:24663817
rescued bycdc25M phase inducer tyrosine phosphatase Cdc25 Phenotypic SuppressionPMID:7957098
rescued bycdc13G2/M B-type cyclin Cdc13 Phenotypic SuppressionPMID:7957098
rescued bycdc2cyclin-dependent protein kinase Cdk1/Cdc2 Phenotypic SuppressionPMID:7957098
synthetically rescuesrad17RFC related checkpoint protein Rad17 Synthetic RescuePMID:12865439
synthetically rescuesrad3ATR checkpoint kinase Rad3 Synthetic RescuePMID:12865439
synthetically rescuesrad26ATRIP, ATR checkpoint kinase regulatory subunit Rad26 Synthetic RescuePMID:12865439
negative genetic interaction withspo20sec14 cytosolic factor family, glycerophospholipid-transfer protein Spo20/Sec14 Negative GeneticPMID:22681890
synthetic lethal withmcm4MCM complex subunit Mcm4/Cdc21 Synthetic LethalityPMID:11606526
synthetic lethal withcdc22ribonucleoside reductase large subunit Cdc22 Synthetic LethalityPMID:9268024
synthetic lethal withcdc23MCM-associated protein Mcm10 Synthetic LethalityPMID:11606526
synthetic lethal withdpb4DNA polymerase epsilon subunit Dpb4 Synthetic LethalityPMID:15388803
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)
GEO SPAC23C4.18c GEO profiles
PInt SPAC23C4.18c Protein-Protein Interaction Predictor (Bähler Lab)
PeptideAtlas SPAC23C4.18c Peptides identified in tandem mass spectrometry proteomics experiments
SYSGRO SPAC23C4.18c Fission yeast phenotypic data & analysis
Cyclebase SPAC23C4.18c.1 Cell Cycle Data
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
ePDB4BMCThe European PDB
PDB4BMCPDB
PDBsum4BMCPDBsum
ePDB4BMDThe European PDB
PDB4BMDPDB
PDBsum4BMDPDBsum
ePDB4BU0The European PDB
PDB4BU0PDB
PDBsum4BU0PDBsum
ePDB4BU1The European PDB
PDB4BU1PDB
PDBsum4BU1PDBsum
European Nucleotide ArchiveBAA04048.1ENA Protein Mapping
European Nucleotide ArchiveCAA44548.1ENA Protein Mapping
European Nucleotide ArchiveCAB16889.1ENA Protein Mapping
UniParcUPI0000061AF1UniProt Archive

Literature for rad4

Search: Europe PMC or PubMed

Release Version: PomBase:30_60 - 12 May 2016