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 binding863
Annotation ExtensionEvidenceWith/FromReference
protein complex scaffold5
Annotation ExtensionEvidenceWith/FromReference
GO Biological Process
Term NameCount
mitotic DNA damage checkpoint31
Annotation ExtensionEvidenceWith/FromReference
mitotic DNA replication checkpoint17
Annotation ExtensionEvidenceWith/FromReference
mitotic DNA replication preinitiation complex assembly4
Annotation ExtensionEvidenceWith/FromReference
GO Cellular Component
Term NameCount
cytosol2307
Annotation ExtensionEvidenceWith/FromReference
DNA replication preinitiation complex18
Annotation ExtensionEvidenceWith/FromReference
mitotic spindle267
Annotation ExtensionEvidenceWith/FromReference
mitotic spindle pole body216
Annotation ExtensionEvidenceWith/FromReference
nuclear replication fork61
Annotation ExtensionEvidenceWith/FromReference
nucleus2691
Annotation ExtensionEvidenceWith/FromReference
site of double-strand break46
Annotation ExtensionEvidenceWith/FromReference
Fission Yeast Phenotype Ontology
Gene Deletion Viability: Inviable

Single-allele Phenotypes

Population Phenotype

Term NameGenotypesCount
inviable vegetative cell populationcut5-5801444
cut5-T401
rad4Δ
normal growth on glucose carbon sourceK56E (K56E)240
T110V (T110V)
T15V,K56E (T15V, K56E)
K151A (K151A)
K151E (K151E)
K56A (K56A)
R22E (R22E)
T15V (T15V)
R117E (R117E)
normal growth on JM335rad4-1385
normal growth on tetraplatinrad4-13814
normal growth on triplatin tetranitraterad4-13811
sensitive to camptothecinK151E (K151E)225
T15V (T15V)
T110V (T110V)
T15V,K56E (T15V, K56E)
K56E (K56E)
K56A (K56A)
K151A (K151A)
R117E (R117E)
sensitive to cisplatinrad4-13829
sensitive to DNA damaging agentsrad4ts7
sensitive to hydroxyureaK151E (K151E)542
rad4-11C
K56E (K56E)
sensitive to ionizing radiation during vegetative growthcut5-T40164
rad4-138
rad4ts
cut5-580
rad4.116
sensitive to JM216rad4-13810
sensitive to methyl methanesulfonateK56E (K56E)242
K151A (K151A)
T110V (T110V)
R117E (R117E)
R22E (R22E)
T15V (T15V)
K151E (K151E)
K56A (K56A)
sensitive to oxaliplatinrad4-13816
sensitive to UV during vegetative growthcut5-T401143
K56A (K56A)
K151E (K151E)
R117E (R117E)
K151A (K151A)
K56E (K56E)
T15V (T15V)
R22E (R22E)
rad4 mutant
T15V,K56E (T15V, K56E)
rad4-138
rad4ts
cut5-580
T110V (T110V)
rad4.116
slow vegetative cell population growthrad4ts332
viable spore populationrad4.11645

Cell Phenotype

Term NameGenotypesCount
abnormal chromosome morphologycut5-T40122
abnormal mitotic cell cycle regulation during cellular response to hydroxyurearad4-11C12
cut5-T401
abolished protein binding104
affecting rad4 and rad9K452E (K452E)
affecting rad4 and crb2K56E,K151E (K56E, K151E)
abolished protein phosphorylation during cellular response to ionizing radiation5
affecting chk1K56E (K56E)
affecting chk1K56A (K56A)
affecting chk1T15V (T15V)
altered DNA level during vegetative growthcut5-T40175
cutcut5-580115
cut5-401
rad4-42 (A132G)
cut during cellular response to hydroxyureacut5-T40143
decreased protein phosphorylation during cellular response to ionizing radiation8
affecting chk1K151E (K151E)
affecting chk1R117E (R117E)
affecting chk1K151A (K151A)
affecting chk1T110V (T110V)
DNA content decreased during vegetative growthrad4-42 (A132G)11
fragmented nucleuscut5-58012
increased duration of mitotic S phasecut5-T40120
inviable after spore germination, single or double cell divisionrad4Δ105
inviable after spore germination, without cell division, with abnormal germ tube morphologyrad4Δ153
inviable cell at high temperaturerad4.11621
inviable vegetative cellrad4Δ1337
loss of punctate nuclear protein localization during cellular response to ionizing radiation4
affecting crb2K151E (K151E)
affecting crb2K56E (K56E)
normal cell cycle regulation during cellular response to ionizing radiationcut5-T40112
normal meiosisrad4.116148
normal mitotic cell cycle regulation during cellular response to UVcut5-T4018
normal premeiotic DNA replicationrad4.11624
normal protein phosphorylation during cellular response to ionizing radiation1
affecting chk1R22E (R22E)
normal spore morphologyrad4.11614
premature mitotic G1 phase entry during cellular response to ionizing radiationK151E (K151E)2
K56E (K56E)

Multi-allele phenotypes


Cell Phenotype

Term NameGenotypes
abnormal negative regulation of mitotic DNA replication initiation resulting in partial rereplicationrad4.116, rum1+ (wild type)
cutcut5-T401, cdc10-129 (T429A)
Target Of
OntologyRelationshipGeneProduct
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 rad17 RFC related checkpoint protein Rad17
FYPO affected by mutation in rad4 BRCT domain protein Rad4
FYPO 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
PF12738 Pfam IPR001357 BRCT domain 105 167 4
PF12738 Pfam IPR001357 BRCT domain 11 74 4
PF00533 Pfam IPR001357 BRCT domain 301 371 6
PF00533 Pfam IPR001357 BRCT domain 395 472 6
SM00292 SMART IPR001357 BRCT domain 394 476 10
SM00292 SMART IPR001357 BRCT domain 100 175 10
SM00292 SMART IPR001357 BRCT domain 4 82 10
SM00292 SMART IPR001357 BRCT domain 300 374 10
PS50172 Prosite Profiles IPR001357 BRCT domain 114 185 13
PS50172 Prosite Profiles IPR001357 BRCT domain 392 480 13
PS50172 Prosite Profiles IPR001357 BRCT domain 2 75 13
PS50172 Prosite Profiles IPR001357 BRCT domain 298 384 13
PTHR13561 HMMPANTHER 3 451 3
3.40.50.10190 Gene3D IPR001357 BRCT domain 396 480 13
3.40.50.10190 Gene3D IPR001357 BRCT domain 102 183 13
3.40.50.10190 Gene3D IPR001357 BRCT domain 2 76 13
3.40.50.10190 Gene3D IPR001357 BRCT domain 300 384 13
SSF52113 SuperFamily IPR001357 BRCT domain 359 480 12
SSF52113 SuperFamily IPR001357 BRCT domain 78 188 12
SSF52113 SuperFamily IPR001357 BRCT domain 4 76 12
SSF52113 SuperFamily IPR001357 BRCT domain 301 384 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
Isoelectric point 8.21
Molecular weight 74.17 kDa
Number of residues 648
Modifications

Protein Modifications

Term NameResidueCount
phosphorylated residue 1930
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

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)3090
conserved in fungi4604
conserved in eukaryotes4514
conserved in metazoa3421
conserved in vertebrates3396
conserved in eukaryotes only2503
Orthologs

Manually curated orthologous groups

SpeciesGeneDescriptionLinksCount

Orthologs in Compara


Physical Interactions

Source: BioGRID

Load gene 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
binds activation domain construct withcrb3WD repeat protein Crb3 Two-hybridPMID:9407031
binds activation domain construct withcrb2DNA repair protein Rad9 homolog Crb2 Two-hybridPMID:15229228
binds activation domain construct withdrc1replication preinitiation complex assembly protein Two-hybridPMID:11937031
binds activation domain construct withchk1Chk1 protein kinase Two-hybridPMID:16723501
forms complex withcrb2DNA repair protein Rad9 homolog Crb2 Reconstituted ComplexPMID:24074952
forms complex withcdc23MCM-associated protein Mcm10 Reconstituted ComplexPMID:21945095
forms complex withrad9checkpoint clamp complex protein Rad9 Reconstituted ComplexPMID:24663817
forms complex withcrb3WD repeat protein Crb3 Reconstituted ComplexPMID:9407031
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 withsld3DNA replication pre-initiation complex subunit Sld3 Two-hybridPMID:21945095
binds DNA-binding domain construct withbgs11,3-beta-glucan synthase catalytic subunit Bgs1 Two-hybridPMID:11937031
binds DNA-binding domain construct withrad9checkpoint clamp complex protein Rad9 Two-hybridPMID:16723501
binds DNA-binding domain construct withchk1Chk1 protein kinase Two-hybridPMID:9407031
binds DNA-binding domain construct withcrb3WD repeat protein Crb3 Two-hybridPMID:16723501
affinity capturesrad17RFC related checkpoint protein Rad17 Affinity Capture-WesternPMID:16723501
affinity captureshsk1Dbf4(Dfp1)-dependent protein kinase Hsk1 Affinity Capture-WesternPMID:21095590
affinity capturesdpb2DNA polymerase epsilon catalytic subunit B, Dpb2 Affinity Capture-WesternPMID:16723501
affinity captureshus1checkpoint clamp complex protein Hus1 Affinity Capture-WesternPMID:16723501
affinity capturesrad3ATR checkpoint kinase Rad3 Affinity Capture-WesternPMID:16723501
affinity capturesrad9checkpoint clamp complex protein Rad9 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
modified byhsk1Dbf4(Dfp1)-dependent protein kinase Hsk1 Biochemical ActivityPMID:21095590
affinity captured byrad9checkpoint clamp complex protein Rad9 Affinity Capture-WesternPMID:15155581
affinity captured bydpb2DNA polymerase epsilon catalytic subunit B, Dpb2 Affinity Capture-WesternPMID:22718908
affinity captured bypsf2GINS complex subunit Psf2 Affinity Capture-WesternPMID:22718908
affinity captured bycrb2DNA repair protein Rad9 homolog Crb2 Affinity Capture-WesternPMID:24663817
affinity captured byrad26ATRIP, ATR checkpoint kinase regulatory subunit Rad26 Affinity Capture-WesternPMID:16723501
co-locates (via crystalisation or NMR) withcrb2DNA repair protein Rad9 homolog Crb2 Co-crystal or NMR structurePMID:24074952
Genetic Interactions

Source: BioGRID

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

Gene Product Evidence Reference
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
rescued by overexpression ofdrc1replication preinitiation complex assembly protein Dosage RescuePMID:11937031
rescued by overexpression ofcrb2DNA repair protein Rad9 homolog Crb2 Dosage RescuePMID:9407031
rescued by overexpression ofSPCC191.01Schizosaccharomyces specific protein Dosage RescuePMID:17272281
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 withmcb1MCM binding protein homolog Mcb1 Synthetic Growth DefectPMID:23322785
synthetic growth defect withrad9checkpoint clamp complex protein Rad9 Synthetic Growth DefectPMID:22761595
synthetic growth defect withhsk1Dbf4(Dfp1)-dependent protein kinase Hsk1 Synthetic Growth DefectPMID:11027263
synthetic growth defect withcdc45DNA replication pre-initiation complex subunit Cdc45 Synthetic Growth DefectPMID:11523776
synthetic growth defect withrad8ubiquitin-protein ligase E3 Rad8 Synthetic Growth DefectPMID:8290359
synthetic growth defect withset9histone lysine H3-K20 methyltransferase Set9 Synthetic Growth DefectPMID:16778077
synthetic growth defect withchk1Chk1 protein kinase Synthetic Growth DefectPMID:16723501
synthetic growth defect withpsf3GINS complex subunit Psf3 Synthetic Growth DefectPMID:16990792
synthetically rescuesrad17RFC related checkpoint protein Rad17 Synthetic RescuePMID:12865439
synthetically rescuesrad26ATRIP, ATR checkpoint kinase regulatory subunit Rad26 Synthetic RescuePMID:12865439
synthetically rescuesrad3ATR checkpoint kinase Rad3 Synthetic RescuePMID:12865439
positive genetic interaction withrpl380160S ribosomal protein L38 (predicted) Positive GeneticPMID:22681890
synthetic lethal withdpb4DNA polymerase epsilon subunit Dpb4 Synthetic LethalityPMID:15388803
synthetic lethal withcdc22ribonucleoside reductase large subunit Cdc22 Synthetic LethalityPMID:9268024
synthetic lethal withmcm4MCM complex subunit Mcm4/Cdc21 Synthetic LethalityPMID:11606526
synthetic lethal withcdc23MCM-associated protein Mcm10 Synthetic LethalityPMID:11606526
enhances phenotype ofset9histone lysine H3-K20 methyltransferase Set9 Phenotypic EnhancementPMID:16778077
enhances phenotype ofcdc10MBF transcription factor complex subunit Cdc10 Phenotypic EnhancementPMID:8343962
enhances phenotype ofmeu13Tat binding protein 1(TBP-1)-interacting protein (TBPIP) homolog (predicted) Phenotypic EnhancementPMID:14718568
enhances phenotype ofcds1replication checkpoint kinase Cds1 Phenotypic EnhancementPMID:16723501
phenotype enhanced bycds1replication checkpoint kinase Cds1 Phenotypic EnhancementPMID:24663817
rescued bycdc13G2/M B-type cyclin Cdc13 Phenotypic SuppressionPMID:7957098
rescued bycdc2cyclin-dependent protein kinase Cdk1/Cdc2 Phenotypic SuppressionPMID:7957098
rescued bycdc25M phase inducer tyrosine phosphatase Cdc25 Phenotypic SuppressionPMID:7957098
negative genetic interaction withspo20sec14 cytosolic factor family, glycerophospholipid-transfer protein Spo20/Sec14 Negative GeneticPMID:22681890
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
European Nucleotide ArchiveCU329670ENA EMBL mapping
European Nucleotide ArchiveD16627ENA EMBL mapping
European Nucleotide ArchiveX62676ENA EMBL mapping
ePDB4BMCThe European PDB
PDB4BMCPDB
PDBsum4BMCPDBsum
ePDB4BMDThe European PDB
PDB4BMDPDB
PDBsum4BMDPDBsum
ePDB4BU0The European PDB
PDB4BU0PDB
PDBsum4BU0PDBsum
ePDB4BU1The European PDB
PDB4BU1PDB
PDBsum4BU1PDBsum
European Nucleotide ArchiveBAA04048ENA Protein Mapping
European Nucleotide ArchiveBAA04048.1ENA Protein Mapping
European Nucleotide ArchiveCAA44548ENA Protein Mapping
European Nucleotide ArchiveCAA44548.1ENA Protein Mapping
European Nucleotide ArchiveCAB16889ENA Protein Mapping
European Nucleotide ArchiveCAB16889.1ENA Protein Mapping
UniParcUPI0000061AF1UniProt Archive

Literature for rad4

Search: Europe PMC or PubMed

Release Version: PomBase:29_56 - 12 Nov 2015