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 binding848
protein complex scaffold5
Annotation ExtensionEvidenceWith/FromReference
GO Biological Process
Term NameCount
mitotic DNA damage checkpoint31
Annotation ExtensionEvidenceWith/FromReference
mitotic DNA replication checkpoint16
Annotation ExtensionEvidenceWith/FromReference
mitotic DNA replication preinitiation complex assembly4
Annotation ExtensionEvidenceWith/FromReference
GO Cellular Component
Term NameCount
cytosol2316
Annotation ExtensionEvidenceWith/FromReference
DNA replication preinitiation complex21
Annotation ExtensionEvidenceWith/FromReference
mitotic spindle258
Annotation ExtensionEvidenceWith/FromReference
mitotic spindle pole body216
Annotation ExtensionEvidenceWith/FromReference
nuclear replication fork63
Annotation ExtensionEvidenceWith/FromReference
nucleus2690
Annotation ExtensionEvidenceWith/FromReference
site of double-strand break46
Annotation ExtensionEvidenceWith/FromReference
Fission Yeast Phenotype Ontology
Gene Deletion Viability: Inviable

Population Phenotype

Term NameAlleleExpressionCount
inviable vegetative cell populationrad4ΔNull1427
normal growth on glucose carbon sourceK151A (K151A)Not specified189
K151E (K151E)Not specified
K56A (K56A)Not specified
K56E (K56E)Not specified
R117E (R117E)Not specified
R22E (R22E)Not specified
T110V (T110V)Not specified
T15V (T15V)Not specified
T15V,K56E (T15V, K56E)Not specified
sensitive to camptothecinK151A (K151A)Not specified214
K151E (K151E)Not specified
K56A (K56A)Not specified
K56E (K56E)Not specified
R117E (R117E)Not specified
T110V (T110V)Not specified
T15V (T15V)Not specified
T15V,K56E (T15V, K56E)Not specified
sensitive to DNA damaging agentsrad4tsNot specified7
sensitive to hydroxyureaK151E (K151E)Not specified518
K56E (K56E)Not specified
rad4-11CNot specified
sensitive to ionizing radiation58
expressivity FYPO_EXT:0000002rad4-138
rad4.116Not specified
rad4tsNot specified
sensitive to methyl methanesulfonateK151A (K151A)Not specified227
K151E (K151E)Not specified
K56A (K56A)Not specified
K56E (K56E)Not specified
R117E (R117E)Not specified
expressivity FYPO_EXT:0000003R22E (R22E)Not specified
T110V (T110V)Not specified
T15V (T15V)Not specified
sensitive to UV during vegetative growthcut5-T401Not specified133
K151A (K151A)Not specified
K151E (K151E)Not specified
K56A (K56A)Not specified
K56E (K56E)Not specified
R117E (R117E)Not specified
expressivity FYPO_EXT:0000003R22E (R22E)Not specified
rad4 mutantNot specified
expressivity FYPO_EXT:0000002rad4-138
rad4.116Endogenous
rad4tsNot specified
T110V (T110V)Not specified
T15V (T15V)Not specified
T15V,K56E (T15V, K56E)Not specified
slow vegetative cell population growthrad4tsNot specified88
viable spore populationrad4.116Not specified27

Cell Phenotype

Term NameAlleleExpressionCount
abnormal chromosome morphology18
expressivity FYPO_EXT:0000001cut5-T401Not specified
abnormal mitotic cell cycle regulation during cellular response to hydroxyureacut5-T401Not specified10
rad4-11CNot specified
abolished protein binding68
affecting rad4 and rad9K452E (K452E)Not specified
affecting rad4 and crb2K56E,K151E (K56E, K151E)Not specified
abolished protein phosphorylation during cellular response to ionizing radiation5
affecting chk1K56A (K56A)Not specified
affecting chk1K56E (K56E)Not specified
affecting chk1T15V (T15V)Not specified
advanced mitotic G1 phase entry during cellular response to ionizing radiationK151E (K151E)Not specified2
K56E (K56E)Not specified
cutnot recorded (unrecorded)92
rad4-42 (A132G)Not specified
cut during cellular response to hydroxyureacut5-T401Not specified43
decreased protein phosphorylation during cellular response to ionizing radiation3
affecting chk1K151A (K151A)Not specified
affecting chk1K151E (K151E)Not specified
affecting chk1R117E (R117E)Not specified
affecting chk1T110V (T110V)Not specified
DNA content decreased during vegetative growthrad4-42 (A132G)Not specified8
inviable after spore germination, single or double cell division101
penetrance FYPO_EXT:0000003rad4ΔNull
inviable after spore germination, without cell division, with abnormal germ tube morphology150
penetrance FYPO_EXT:0000001rad4ΔNull
inviable cell at high temperaturerad4.116Endogenous22
inviable vegetative cellrad4ΔNull1268
loss of punctate nuclear protein localization during cellular response to ionizing radiation4
affecting crb2K151E (K151E)Not specified
affecting crb2K56E (K56E)Not specified
normal cell cycle regulation during cellular response to ionizing radiationcut5-T401Not specified15
normal meiosisrad4.116Not specified139
normal mitotic cell cycle regulation during cellular response to UVcut5-T401Not specified6
normal premeiotic DNA replicationrad4.116Not specified16
normal protein phosphorylation during cellular response to ionizing radiation1
affecting chk1R22E (R22E)Not specified
normal spore morphologyrad4.116Not specified5
Target Of
OntologyRelationshipGeneProductReference
FYPO affected by mutation in crb2 DNA repair protein Rad9 homolog, Rhp9 PMID:24074952
FYPO affected by mutation in drc1 replication preinitiation complex assembly protein PMID:11937031
FYPO affected by mutation in rad17 RFC related checkpoint protein Rad17 PMID:22792081
FYPO affected by mutation in rad4 BRCT domain protein Rad4 PMID:24074952
FYPO affected by mutation in rad9 checkpoint clamp complex protein Rad9 PMID:22792081
Transcript
Ensembl transcript structure with UTRs, exons and introns

Exons

Exon Start End
110633061062796
210627381062631
310625641058646

UTRs

Region Coordinates Reference
five_prime_UTR1063306..1062862PMID:21511999
three_prime_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 300 371 8
PF00533 Pfam IPR001357 BRCT domain 395 472 8
SM00292 SMART IPR001357 BRCT domain 300 374 10
SM00292 SMART IPR001357 BRCT domain 4 82 10
SM00292 SMART IPR001357 BRCT domain 100 175 10
SM00292 SMART IPR001357 BRCT domain 394 476 10
PS50172 Prosite Profiles IPR001357 BRCT domain 298 384 13
PS50172 Prosite Profiles IPR001357 BRCT domain 2 75 13
PS50172 Prosite Profiles IPR001357 BRCT domain 392 480 13
PS50172 Prosite Profiles IPR001357 BRCT domain 114 185 13
PTHR13561 HMMPANTHER 3 534 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 102 183 13
3.40.50.10190 Gene3D IPR001357 BRCT domain 396 480 13
SSF52113 SuperFamily IPR001357 BRCT domain 78 188 12
SSF52113 SuperFamily IPR001357 BRCT domain 301 384 12
SSF52113 SuperFamily IPR001357 BRCT domain 4 76 12
SSF52113 SuperFamily IPR001357 BRCT domain 359 480 12

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 NameResidueCount
phosphorylated residue 1922
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: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)3092
conserved in fungi4604
conserved in eukaryotes4516
conserved in metazoa3432
conserved in vertebrates3407
conserved in eukaryotes only2503
Orthologs

Manually curated orthologous groups

SpeciesGeneDescriptionLinksCount

Orthologs in Compara


Physical Interactions

Source: BioGRID

View all interactions in esyN
View the HCPIN interactions in esyN

Gene Product Evidence Reference
crb3WD repeat protein Crb3 Two-hybridPMID:16723501
Reconstituted ComplexPMID:9407031
Two-hybrid
psf2GINS complex subunit Psf2 Affinity Capture-WesternPMID:22718908
cdc23MCM-associated protein Mcm10 Reconstituted ComplexPMID:21945095
Two-hybrid
Two-hybridPMID:22433840
rad17RFC related checkpoint protein Rad17 Affinity Capture-WesternPMID:16723501
chk1Chk1 protein kinase Two-hybridPMID:16723501
Two-hybridPMID:9407031
dfp1Hsk1-Dfp1 kinase complex regulatory subunit Dfp1 Affinity Capture-WesternPMID:21095590
drc1replication preinitiation complex assembly protein Two-hybridPMID:21945095
Two-hybridPMID:21593208
Two-hybridPMID:11937031
rad26ATRIP, ATR checkpoint kinase regulatory subunit Rad26 Affinity Capture-WesternPMID:16723501
rad3ATR checkpoint kinase Rad3 Affinity Capture-WesternPMID:16723501
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
hus1checkpoint clamp complex protein Hus1 Affinity Capture-WesternPMID:16723501
rad9checkpoint clamp complex protein Rad9 Reconstituted ComplexPMID:24074952
Affinity Capture-WesternPMID:15155581
Two-hybridPMID:16723501
Affinity Capture-Western
Reconstituted ComplexPMID:24663817
Affinity Capture-Western
hsk1Dbf4(Dfp1)-dependent protein kinase Hsk1 Biochemical ActivityPMID:21095590
Affinity Capture-Western
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 Co-crystal or NMR structurePMID:24074952
Affinity Capture-Western
Two-hybridPMID:9407031
Reconstituted Complex
Two-hybridPMID:16778077
Two-hybridPMID:15229228
Affinity Capture-WesternPMID:24663817
Reconstituted Complex
Genetic Interactions

Source: BioGRID

View these interactions in esyN

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 H3-K20 methyltransferase Set9 Phenotypic EnhancementPMID:16778077
Synthetic Growth Defect
cdc25M phase inducer tyrosine 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
mcb1MCM binding protein homolog Mcb1 Synthetic Growth DefectPMID:23322785
hsk1Dbf4(Dfp1)-dependent protein kinase Hsk1 Synthetic Growth DefectPMID:11027263
crb2DNA repair protein Rad9 homolog, Rhp9 Synthetic Growth DefectPMID:16778077
Phenotypic EnhancementPMID:24074952
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
cds1replication checkpoint kinase Cds1 Phenotypic EnhancementPMID:16723501
Phenotypic EnhancementPMID:24663817
rad3ATR checkpoint kinase Rad3 Synthetic RescuePMID:12865439
meu13Tat binding protein 1(TBP-1)-interacting protein (TBPIP) homolog (predicted) Phenotypic EnhancementPMID:14718568
Phenotypic Suppression
SPCC191.01Schizosaccharomyces specific protein 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
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)
PeptideAtlas SPAC23C4.18c Peptides identified in tandem mass spectrometry proteomics experiments
SYSGRO SPAC23C4.18c Fission yeast phenotypic data & analysis
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:25_48 - 10 Jan 2015