tdp1 (SPCP31B10.05)

Gene Standard Nametdp1 ChromosomeIII
Systematic IDSPCP31B10.05 Gene Start529028
Synonyms Gene End531496
Producttyrosyl-DNA phosphodiesterase Tdp1 Gene Length2469
Feature Typeprotein coding CDS Start529173
Name Description CDS End530783
Characterisation Statuspublished CDS Length1611

Ensembl Gene Location
  1. prp11
  2. SPRRNA.24
  3. cwf23
  4. SPCP31B10.02
  5. med31
  6. SPCP31B10.04
  7. tdp1
  8. SPNCRNA.580
  9. mug190
  10. eft202
Fission Yeast Phenotype Ontology

Ontology Graph

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Term IDTerm NameEvidenceAlleleAllele TypeExpressionConditionReference
FYPO:0000085sensitive to camptothecincompetitive growth assay evidencetdp1delta (deletion)deletionPMID:20537132
Cell growth assaytdp1delta (deletion)deletionPMID:19197239
FYPO:0000087sensitive to hydrogen peroxideCell growth assaytdp1delta (deletion)deletionPMID:19197239
FYPO:0000238inviable cell upon G0 to G1 transitionMicroscopytdp1delta (deletion)deletionPECO:0000090PMID:19197239
FYPO:0000245loss of viability in stationary phaseFlow cytometry datatdp1delta (deletion)deletionPECO:0000090PMID:19197239
Cell growth assaytdp1delta (deletion)deletionPECO:0000090PMID:19197239
FYPO:0000262abnormal cellular response to reactive oxygen species during G0 phaseCell growth assaytdp1delta (deletion)deletionPECO:0000090PMID:19197239
FYPO:0000266sensitive to DNA damaging agentscompetitive growth assay evidencetdp1delta (deletion)deletionPMID:20537132
FYPO:0002060viable vegetative cell populationMicroscopytdp1delta (deletion)deletionPMID:20473289
GO Molecular Function

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Term IDTerm NameEvidenceWith/FromReference
GO:0004527exonuclease activityIEAUniProtKB:KW-0269GO_REF:0000037
GO:00170053'-tyrosyl-DNA phosphodiesterase activityIMPPMID:19197239
GO Biological Process

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Term IDTerm NameEvidenceWith/FromReference
GO:0000012single strand break repairIMPPMID:19197239
GO Cellular Component

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Term IDTerm NameEvidenceWith/FromReference
GO:0005634nucleusIDAPMID:16823372
ISOSGD:S000000427GO_REF:0000024
Transcript
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Ensembl transcript structure with UTRs, exons and introns

Exons

Exon Start End
1529028531496

References

Region Start End Reference
three_prime_UTR530784531496PMID:21511999
three_prime_UTR530784531496PMID:21511999
five_prime_UTR529028529172PMID: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
PF06087 IPR010347 Pfam Tyrosyl-DNA phosphodiesterase 220 510 1
PF06087 IPR010347 Pfam Tyrosyl-DNA phosphodiesterase 23 168 1
G3DSA:3.30.870.20 Gene3D 262 518 1
G3DSA:3.30.870.10 Gene3D 20 169 3
G3DSA:3.30.870.10 Gene3D 227 261 3
SSF56024 SuperFamily 227 286 3
SSF56024 SuperFamily 261 534 3
SSF56024 SuperFamily 20 169 3
PTHR12415 IPR010347 hmmpanther Tyrosyl-DNA phosphodiesterase 17 536 1

View domain organization at Pfam

Protein Properties

Ave. residue weight 114.92 Da
Charge 13.00
Isoelectric point 8.45
Molecular weight 61.60 kDa
Number of residues 536
Sequence
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Gene Expression
DescriptionEvidenceDuringConditionRangeAverage per CellReference
antisense transcript detected
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_wide0.98PMID:23101633
experimental evidencecell quiescence following G1 arrest due to nitrogen limitationPECO:0000127,
PECO:0000014,
PECO:0000005		population_wide0.41PMID:23101633
Disease Association
DescriptionQualifierReference
neurological disorders
spinocerebellar ataxia
Species Distribution
DescriptionQualifierReference
predominantly single copy (one to one)
conserved in fungi
conserved in eukaryotes
conserved in metazoa
conserved in vertebrates
conserved in eukaryotes only
Manually curated orthologous groups
SpeciesGeneDescription

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Genetic Interactions

Source: BioGRID

Gene Product Evidence Reference
rad2FEN-1 endonuclease Rad2 Negative GeneticPMID:22681890
get1GET complex subunit Get1 (predicted) Negative GeneticPMID:22681890
Negative GeneticPMID:18818364
swi10DNA repair endonuclease Swi10 Synthetic LethalityPMID:21408210
Synthetic Growth DefectPMID:18931302
nth1DNA endonuclease III Synthetic RescuePMID:22084197
pyp1tyrosine phosphatase Pyp1 Positive GeneticPMID:22681890
rad60DNA repair protein Rad60 Synthetic LethalityPMID:21408210
rad51RecA family recombinase Rad51/Rhp51 Synthetic Growth DefectPMID:21408210
Synthetic Lethality
usp102U1 snRNP-associated protein Usp102 Positive GeneticPMID:22681890
pob3FACT complex subunit Pob3 Negative GeneticPMID:18818364
top1DNA topoisomerase I Synthetic RescuePMID:21408210
SPCC1450.09cphospholipase (predicted) Negative GeneticPMID:22681890
slx8SUMO-targeted ubiquitin-protein ligase E3 Slx8 (predicted) Phenotypic EnhancementPMID:21408210
Synthetic Growth Defect
Synthetic Lethality
SPCC1322.02sequence orphan Negative GeneticPMID:22681890
nse6Smc5-6 complex non-SMC subunit Nse6 Synthetic Growth DefectPMID:18931302
mgr2mitochondrial membrane protein Mgr2 (predicted) Positive GeneticPMID:22681890
nse5Smc5-6 complex non-SMC subunit Nse5 Synthetic Growth DefectPMID:18931302
pnk1DNA kinase/phosphatase Pnk1 Synthetic RescuePMID:22748672
apn2AP-endonuclease Apn2 Dosage LethalityPMID:22084197
Negative GeneticPMID:22681890
Negative GeneticPMID:18818364
Synthetic RescuePMID:22748672
Synthetic Growth Defect
mre11Mre11 nuclease Synthetic Growth DefectPMID:21408210
SPAC19B12.06crhomboid family protease Positive GeneticPMID:22681890
SPBC28F2.11HMG box protein Synthetic Growth DefectPMID:18931302
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External References
Database Identifier Description
NBRP SPCP31B10.05 Fission yeast strain database, National BioResource Project (Japan)
YOGY SPCP31B10.05 Retrieval of eukaryotic orthologs
BioGrid SPCP31B10.05 BioGRID Interaction Datasets
Bähler Lab SPCP31B10.05 Cell Cycle Expression Profile
Bähler Lab SPCP31B10.05 Meiosis/Sporulation Expression Profies
Bähler Lab SPCP31B10.05 Pheromone response/mating expression profiles
Bähler Lab SPCP31B10.05 Environmental stress expression profiles
Bähler Lab SPCP31B10.05 Bähler Lab Transcriptome Viewer
Cyclebase SPCP31B10.05 Cell Cycle Data
PInt SPCP31B10.05 Bähler Lab Protein-Protein Interaction Predictor
Entrez Gene SPCP31B10.05 Entrez Gene
WikiGene2539579tyrosyl-DNA phosphodiesterase Tdp1
EntrezGene2539579tyrosyl-DNA phosphodiesterase Tdp1
SPD / RIKEN45/45D01Orfeome Localization Data
UniProtKB/SwissProtQ9USG9Probable tyrosyl-DNA phosphodiesterase
ModBaseQ9USG9Database of comparative protein structure models
Pfam Protein DomainsQ9USG9Pfam Domain Arrangement
RefSeq PeptideNP_587861tyrosyl-DNA phosphodiesterase Tdp1
RefSeq mRNANM_001022854972h- tyrosyl-DNA phosphodiesterase Tdp1 (tdp1), mRNA
European Nucleotide ArchiveCAB58371ENA Protein Mapping
UniParcUPI0000039A9AUniProt Archive

Literature for tdp1
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Search: UK PMC or PubMed

Release Version: PomBase:18_35 - 11 May 2013