rad13 (SPBC3E7.08c)

Gene Standard Namerad13 ChromosomeII
Systematic IDSPBC3E7.08c Gene Start2676799
Synonyms Gene End2672990
ProductDNA repair nuclease Rad13 Gene Length3810
Feature Typeprotein coding CDS Start2676357
Name Description CDS End2673019
Characterisation Statuspublished CDS Length3339

Ensembl Gene Location
  1. SPBC3E7.05c
  2. fnx2
  3. SPBC3E7.07c
  4. rad13
  5. SPBC3E7.09
  6. SPNCRNA.1543
  7. fma1
  8. SPBC3E7.11c
  9. cfh4
Fission Yeast Phenotype Ontology

Ontology Graph

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Term IDTerm NameEvidenceAlleleAllele TypeExpressionConditionReference
FYPO:0000102sensitive to cisplatinCell growth assayrad13delta (deletion)deletionNot specifiedPMID:8879272
FYPO:0000266sensitive to DNA damaging agentscompetitive growth assay evidencerad13delta (deletion)deletionPMID:20537132
FYPO:0000268sensitive to UVcompetitive growth assay evidencerad13delta (deletion)deletionPMID:20537132
FYPO:0002060viable vegetative cell populationMicroscopyrad13delta (deletion)deletionPMID:20473289
GO Molecular Function

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Term IDTerm NameEvidenceWith/FromReference
GO:0003697single-stranded DNA bindingIEAIPR001044GO_REF:0000002
GO:0004519endonuclease activityIEAUniProtKB:KW-0255GO_REF:0000037
GO:0046872metal ion bindingIEAUniProtKB:KW-0479GO_REF:0000037
GO Biological Process

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Term IDTerm NameEvidenceWith/FromReference
GO:0006289nucleotide-excision repair
same_pathwayIGIrad16PMID:8709952
GO:0006295nucleotide-excision repair, DNA incision, 3'-to lesionTASPMID:11800554
GO:1901255nucleotide-excision repair involved in interstrand cross-link repairIMPPMID:22064477
GO Cellular Component

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Term IDTerm NameEvidenceWith/FromReference
GO:0005634nucleusIDAPMID:16823372
Transcript
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Ensembl transcript structure with UTRs, exons and introns

Exons

Exon Start End
126767992672990

References

Region Start End Reference
three_prime_UTR26730182672990PMID:21511999
five_prime_UTR26767992676358PMID:21511999
three_prime_UTR26730182672990PMID:21511999
Protein Features
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Graphical View

Ensembl protein image with mapped locations of structural domains

Protein Families and Domains

Feature ID InterPro Database Description Start End All Genes
PF00752 IPR006085 Pfam XPG N-terminal 1 96 5
PF00867 IPR006086 Pfam XPG-I domain 765 849 5
SM00484 IPR006086 SMART XPG-I domain 765 834 4
SM00279 IPR008918 SMART Helix-hairpin-helix motif, class 2 836 869 4
SM00485 IPR006085 SMART XPG N-terminal 1 98 5
PS50330 IPR003903 Prosite Profiles Ubiquitin interacting motif 395 414 6
PS00841 IPR019974 Prosite Patterns XPG N-terminal 70 84 3
PS00842 IPR019974 Prosite Patterns XPG-I domain 768 782 3
G3DSA:3.40.50.1010 Gene3D 1 126 9
G3DSA:3.40.50.1010 Gene3D 716 832 9
G3DSA:1.10.150.20 Gene3D 836 883 14
SSF47807 IPR020045 SuperFamily 912 989 4
SSF47807 IPR020045 SuperFamily 838 877 4
SSF88723 SuperFamily 3 102 10
SSF88723 SuperFamily 731 849 10
PTHR11081:SF1 IPR001044 hmmpanther 2 1024 1
PTHR11081 IPR006084 hmmpanther XPG/Rad2 endonuclease 2 1024 5
Coil ncoils Rabaptin coiled-coil domain 721 756 974
PR00066 IPR001044 PRINTS XPG/Rad2 endonuclease, eukaryotes 2 19 1
PR00066 IPR001044 PRINTS XPG/Rad2 endonuclease, eukaryotes 54 77 1
PR00066 IPR001044 PRINTS XPG/Rad2 endonuclease, eukaryotes 286 310 1
PR00853 IPR006084 PRINTS XPG/Rad2 endonuclease 785 805 4
PR00853 IPR006084 PRINTS XPG/Rad2 endonuclease 72 91 4
PR00853 IPR006084 PRINTS XPG/Rad2 endonuclease 764 781 4
PR00853 IPR006084 PRINTS XPG/Rad2 endonuclease 24 38 4
PR00853 IPR006084 PRINTS XPG/Rad2 endonuclease 839 854 4
TIGR00600 IPR001044 tigrfam XPG/Rad2 endonuclease, eukaryotes 1 1020 1

View domain organization at Pfam

Manually Curated Family or Sub-families

Term IDTerm NameReferenceAll Genes
PBO:0000281XP-G familyTemporary processing gif - replaced by AJAX with count of genes annotated with the term PBO:0000281

Protein Properties

Ave. residue weight 113.61 Da
Charge -36.50
Isoelectric point 4.73
Molecular weight 126.33 kDa
Number of residues 1112
Sequence
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Gene Expression
DescriptionEvidenceDuringConditionRangeAverage per CellReference
protein levelexperimental evidencesingle-celled organism vegetative growth phasePECO:0000005,
PECO:0000014		population_widePMID:23101633
experimental evidencecell quiescence following G1 arrest due to nitrogen limitationPECO:0000005,
PECO:0000014,
PECO:0000127		population_widePMID:23101633
RNA levelexperimental evidencesingle-celled organism vegetative growth phasePECO:0000014,
PECO:0000005		population_wide1.2PMID:23101633
experimental evidencecell quiescence following G1 arrest due to nitrogen limitationPECO:0000127,
PECO:0000014,
PECO:0000005		population_wide0.56PMID:23101633
Disease Association
DescriptionQualifierReference
cancer
Xeroderma pigmentosum
Species Distribution
DescriptionQualifierReference
predominantly single copy (one to one)
conserved in fungi
conserved in eukaryotes
conserved in metazoa
conserved in vertebrates
conserved in archaea
Manually curated orthologous groups
SpeciesGeneDescription

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Genetic Interactions

Source: BioGRID

Gene Product Evidence Reference
srs2ATP-dependent DNA helicase, UvrD subfamily Phenotypic EnhancementPMID:11452021
but1neddylation pathway protein But1 Negative GeneticPMID:22681890
rad2FEN-1 endonuclease Rad2 Synthetic Growth DefectPMID:11800554
Phenotypic EnhancementPMID:9092661
ssb3DNA replication factor A subunit Ssb3 Synthetic Growth DefectPMID:20885790
iwr1RNA polymerase II nuclear import protein Iwr1 (predicted) Positive GeneticPMID:22681890
SPCC162.11curidine kinase/uracil phosphoribosyltransferase (predicted) Positive GeneticPMID:22681890
msh2MutS protein homolog 2 Phenotypic SuppressionPMID:11800554
Synthetic Growth DefectPMID:18931302
nup40nucleoporin Nup40 Positive GeneticPMID:22681890
mus81Holliday junction resolvase subunit Mus81 Phenotypic EnhancementPMID:11073977
cgi121EKC/KEOPS complex subunit Cgi121 (predicted) Negative GeneticPMID:22681890
mph1dual specificity protein kinase Mph1 Positive GeneticPMID:22681890
hst4Sir2 family histone deacetylase Hst4 Synthetic Growth DefectPMID:18344406
mus7DNA repair protein Mus7/Mms22 Synthetic Growth DefectPMID:17307401
sif1Sad1 interacting factor 1 Positive GeneticPMID:22681890
rad8ubiquitin-protein ligase E3 Rad8 Synthetic Growth DefectPMID:8290359
sts5RNB-like protein Positive GeneticPMID:22681890
rhp14XP-A family homolog Rhp14 Synthetic Growth DefectPMID:18931302
dis2serine/threonine protein phosphatase PP1 Synthetic Growth DefectPMID:14765108
rad55RecA family ATPase Rad55/Rhp55 Negative GeneticPMID:22681890
smc6Smc5-6 complex SMC subunit Smc6 Phenotypic EnhancementPMID:8524274
amk2AMP-activated protein kinase beta subunit Amk2 Positive GeneticPMID:22681890
SPBC19F8.02nuclear distribution protein NUDC homolog Negative GeneticPMID:22681890
nth1DNA endonuclease III Synthetic Growth DefectPMID:12675805
Negative GeneticPMID:18818364
pcn1PCNA Synthetic Growth DefectPMID:9563836
csk1cyclin-dependent kinase activating kinase Csk1 Synthetic Growth DefectPMID:18231579
uve1endonuclease Uve1 Phenotypic EnhancementPMID:10390527
Phenotypic EnhancementPMID:10652237
Synthetic Growth DefectPMID:17151242
Phenotypic EnhancementPMID:10480889
Phenotypic SuppressionPMID:22665798
Phenotypic Enhancement
Synthetic Growth DefectPMID:10446227
Phenotypic EnhancementPMID:9092661
mag1DNA-3-methyladenine glycosylase Mag1 Synthetic Growth DefectPMID:10735851
atl1alkyltransferase-like protein Atl1 Phenotypic SuppressionPMID:19516334
mad2spindle checkpoint protein Mad2 Synthetic Growth DefectPMID:18931302
pms1MutL family mismatch-repair protein Pms1 Phenotypic SuppressionPMID:11800554
rad57RecA family ATPase Rad57/Rhp57 Synthetic Growth DefectPMID:18931302
Negative GeneticPMID:18818364
pef1Pho85/PhoA-like cyclin-dependent kinase Pef1 Synthetic Growth DefectPMID:18931302
hrq1RecQ type DNA helicase Hrq1 (predicted) Negative GeneticPMID:22681890
Negative GeneticPMID:18818364
SPBC13E7.08cRNA polymerase II associated Paf1 complex (predicted) Synthetic Growth DefectPMID:18931302
rrp2ATP-dependent DNA helicase (predicted) Negative GeneticPMID:22681890
plc1phosphoinositide phospholipase C Plc1 Phenotypic EnhancementPMID:9613582
swi10DNA repair endonuclease Swi10 Phenotypic SuppressionPMID:11800554
Synthetic Growth Defect
hop1linear element associated protein Hop1 Negative GeneticPMID:22681890
ypa2protein phosphatase type 2A regulator, PTPA family Ypa2 Negative GeneticPMID:22681890
elp2elongator complex subunit Elp2 (predicted) Negative GeneticPMID:22681890
hus1checkpoint clamp complex protein Hus1 Negative GeneticPMID:22681890
sfr1Swi five-dependent recombination repair protein Sfr1 Phenotypic EnhancementPMID:18769921
yam8calcium channel regulatory subunit Yam8 Synthetic Growth DefectPMID:18931302
vip1RNA-binding protein Vip1 Positive GeneticPMID:22681890
fft3fun thirty related protein Fft3 Negative GeneticPMID:22681890
rhp18Rad18 homolog Rhp18 Synthetic Growth DefectPMID:11523791
cut14condensin complex subunit Cut14 Synthetic LethalityPMID:22645654
cut2securin, sister chromatid separation inhibitor Synthetic Growth DefectPMID:15329725
nse4Smc5-6 complex non-SMC subunit Nse4 Synthetic LethalityPMID:15485909
rad2414-3-3 protein Rad24 Phenotypic EnhancementPMID:9613582
nse6Smc5-6 complex non-SMC subunit Nse6 Synthetic Growth DefectPMID:16478984
Synthetic Growth DefectPMID:18931302
mre11Mre11 nuclease Synthetic Growth DefectPMID:7885834
klp3kinesin-like protein Klp3 Negative GeneticPMID:22681890
SPAC1805.14sequence orphan Positive GeneticPMID:22681890
rad31SUMO E1-like activator enzyme Rad31 Phenotypic EnhancementPMID:9092625
rad1checkpoint clamp complex protein Rad1 Negative GeneticPMID:22681890
cnd2condensin complex non-SMC subunit Cnd2 Synthetic Growth DefectPMID:12000964
mms1E3 ubiquitin ligase complex subunit Mms1 (predicted) Synthetic LethalityPMID:21183410
pyp1tyrosine phosphatase Pyp1 Synthetic Growth DefectPMID:18931302
crb2DNA repair protein Rad9 homolog, Rhp9 Synthetic Growth DefectPMID:9153313
rad3ATR checkpoint kinase Rad3 Synthetic Growth DefectPMID:10480889
rhp41DNA repair protein Rhp41 Synthetic Growth DefectPMID:18931302
rad51RecA family recombinase Rad51/Rhp51 Phenotypic EnhancementPMID:8524274
Synthetic RescuePMID:16912194
Negative GeneticPMID:18818364
sap1switch-activating protein Sap1 Synthetic Growth DefectPMID:17151242
SPCC1281.07cglutathione S-transferase (predicted) Positive GeneticPMID:22681890
emc1ER membrane protein complex subunit Emc1 (predicted) Positive GeneticPMID:22681890
rqh1RecQ type DNA helicase Rqh1 Phenotypic EnhancementPMID:9372918
Phenotypic EnhancementPMID:7623848
Phenotypic EnhancementPMID:9092661
nse5Smc5-6 complex non-SMC subunit Nse5 Synthetic Growth DefectPMID:18931302
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External References
Database Identifier Description
NBRP SPBC3E7.08c Fission yeast strain database, National BioResource Project (Japan)
YOGY SPBC3E7.08c Retrieval of eukaryotic orthologs
BioGrid SPBC3E7.08c BioGRID Interaction Datasets
Bähler Lab SPBC3E7.08c Cell Cycle Expression Profile
Bähler Lab SPBC3E7.08c Meiosis/Sporulation Expression Profies
Bähler Lab SPBC3E7.08c Pheromone response/mating expression profiles
Bähler Lab SPBC3E7.08c Environmental stress expression profiles
Bähler Lab SPBC3E7.08c Bähler Lab Transcriptome Viewer
Cyclebase SPBC3E7.08c Cell Cycle Data
PInt SPBC3E7.08c Bähler Lab Protein-Protein Interaction Predictor
Entrez Gene SPBC3E7.08c Entrez Gene
EntrezGene2541051DNA repair nuclease Rad13
Uniprot_genenameRAD13
WikiGene2541051DNA repair nuclease Rad13
SPD / RIKEN34/34A07Orfeome Localization Data
UniProtKB/SwissProtP28706DNA repair protein rad13
ModBaseP28706Database of comparative protein structure models
Pfam Protein DomainsP28706Pfam Domain Arrangement
RefSeq PeptideNP_596095DNA repair nuclease Rad13
RefSeq mRNANM_001022011972h- DNA repair nuclease Rad13 (rad13), mRNA
European Nucleotide ArchiveCAA19011ENA Protein Mapping
European Nucleotide ArchiveCAA47291ENA Protein Mapping
UniParcUPI000013300BUniProt Archive

Literature for rad13
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Search: UK PMC or PubMed

Release Version: PomBase:18_35 - 11 May 2013