 Gene-Chemical Interaction Annotations | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Gene Ontology Annotations |
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Analyze GeneStrainQTL List |
 Gene Annotator (Functional Annotation) unavailable |
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 Variant Visualizer (Genomic Variants) unavailble Variant Visualizer (Genomic Variants) unavailable |
Gene Annotator (Functional Annotation) |
Gene Annotator (Annotation Distribution) |
Variant Visualizer (Genomic Variants) |
 InterViewer (Protein-Protein Interactions) unavailable |
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InterViewer (Protein-Protein Interactions) |
GViewer (Genome Viewer) |
Variant Visualizer (Damaging Variants) |
 Gene Annotator (Annotation Comparison) unavailable |
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Gene Annotator (Annotation Comparison) |
OLGA (Gene List Generator) |
Excel (Download) |
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MOET (Multi-Ontology Enrichement) |
GOLF (Gene-Ortholog Location Finder) |
Gene Ontology AnnotationsDisease AnnotationsGene-Chemical Interaction Annotations
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Gene Ontology AnnotationsBiological Process
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Cellular Component
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Molecular Function
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References - curated| 1. | Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27. |
| 2. | RGD automated data pipeline |
| 3. | RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations |
| 4. | RGD automated import pipeline for gene-chemical interactions |
References - uncuratedGenomics
Comparative Map Data| Topbp1 (Rattus norvegicus - Norway rat) |
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| TOPBP1 (Homo sapiens - human) |
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| Topbp1 (Mus musculus - house mouse) |
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| Topbp1 (Chinchilla lanigera - long-tailed chinchilla) |
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| TOPBP1 (Pan paniscus - bonobo/pygmy chimpanzee) |
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| TOPBP1 (Canis lupus familiaris - dog) |
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| Topbp1 (Ictidomys tridecemlineatus - thirteen-lined ground squirrel) |
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| TOPBP1 (Sus scrofa - pig) |
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Position Markers| D8Rat107 |
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| D8Got170 |
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| RH131225 |
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QTLs in Region (Rnor_6.0)| The following QTLs overlap with this region. |  | Full Report | | CSV | | TAB | | Printer | | Gviewer |
miRNA Target Status
Predicted Target Of
| The detailed report is available here: | | Full Report | | CSV | | TAB | | Printer |
miRNA Target Status data imported from miRGate (http://mirgate.bioinfo.cnio.es/). For more information about miRGate, see PMID:25858286 or access the full paper here. |
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Expression
RNA-SEQ ExpressionHigh: > 1000 TPM value Medium: Between 11 and 1000 TPM
Low: Between 0.5 and 10 TPM Below Cutoff: < 0.5 TPM
| testis | heart | brain | ovary | uterus | skeletal muscle tissue | colon | gastrocnemius | forebrain | hindbrain | lung | spleen | liver | kidney | adrenal gland | thymus | |
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| High | ||||||||||||||||
| Medium | 20 | 26 | 21 | 15 | 4 | 2 | 1 | 22 | 25 | 10 | 11 | 30 | 24 | 6 | 8 | |
| Low | 2 | 17 | 2 | 3 | 1 | 7 | 4 | 1 | 11 | 11 | 2 | |||||
| Below cutoff |
View RNA-SEQ Expression Data
Sequence
Nucleotide Sequences| RefSeq Transcripts | XM_001072207 | (Get FASTA) | NCBI Sequence Viewer | Search GEO for Microarray Profiles |
| XM_006226542 | (Get FASTA) | NCBI Sequence Viewer | Search GEO for Microarray Profiles | |
| XM_006243684 | (Get FASTA) | NCBI Sequence Viewer | Search GEO for Microarray Profiles | |
| XM_008757855 | (Get FASTA) | NCBI Sequence Viewer | Search GEO for Microarray Profiles | |
| XM_008757856 | (Get FASTA) | NCBI Sequence Viewer | Search GEO for Microarray Profiles | |
| XM_008766589 | (Get FASTA) | NCBI Sequence Viewer | Search GEO for Microarray Profiles | |
| XM_236578 | (Get FASTA) | NCBI Sequence Viewer | Search GEO for Microarray Profiles | |
| GenBank Nucleotide | AABR07071365 | (Get FASTA) | NCBI Sequence Viewer | Search GEO for Microarray Profiles |
| AABR07073442 | (Get FASTA) | NCBI Sequence Viewer | Search GEO for Microarray Profiles | |
| AAHX01056794 | (Get FASTA) | NCBI Sequence Viewer | Search GEO for Microarray Profiles | |
| AAHX01056795 | (Get FASTA) | NCBI Sequence Viewer | Search GEO for Microarray Profiles | |
| CH473954 | (Get FASTA) | NCBI Sequence Viewer | Search GEO for Microarray Profiles |
Reference Sequences
| RefSeq Acc Id: | XM_001072207 ⟹ XP_001072207 | |||||||||
| RefSeq Status: | ||||||||||
| Type: | CODING | |||||||||
| Position: |
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| Sequence: |
GAGGCGTTGCGTCCGCTCGTTTGGCGCGAAAGTCGGTTCCTGGTCTTGGCCCTTCCGGGTACTGhide sequence |
| RefSeq Acc Id: | XM_006226542 ⟹ XP_006226604 | |||||||||
| RefSeq Status: | ||||||||||
| Type: | CODING | |||||||||
| Position: |
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| Sequence: |
GTGTGTCCCAAGAGCTGAACATCCAGTTTATAATATGATTATGTCTGACATAACTATATCTTGThide sequence |
| RefSeq Acc Id: | XM_006243684 ⟹ XP_006243746 | ||||||||||||||
| RefSeq Status: | |||||||||||||||
| Type: | CODING | ||||||||||||||
| Position: |
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| Sequence: |
AGAGGCGTTGCGTCCGCTCGTTTGGCGCGAAAGTCGGTTCCTGGTCTTGGCCCTTCCGGGTACThide sequence |
| RefSeq Acc Id: | XM_008757855 ⟹ XP_008756077 | |||||||||
| RefSeq Status: | ||||||||||
| Type: | CODING | |||||||||
| Position: |
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| Sequence: |
CCCAGCCGCCGTCCTGCCGGCCGCGCGCCTCCCGACTTGGTGCCCGTGGGCCCTCGGGCTCCAChide sequence |
| RefSeq Acc Id: | XM_008757856 ⟹ XP_008756078 | |||||||||
| RefSeq Status: | ||||||||||
| Type: | CODING | |||||||||
| Position: |
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| Sequence: |
AGAGGCGTTGCGTCCGCTCGTTTGGCGCGAAAGTCGGTTCCTGGTCTTGGCCCTTCCGGGTACThide sequence |
| RefSeq Acc Id: | XM_008766589 ⟹ XP_008764811 | |||||||||
| RefSeq Status: | ||||||||||
| Type: | CODING | |||||||||
| Position: |
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| Sequence: |
CCCAGCCGCCGTCCTGCCGGCCGCGCGCCTCCCGACTTGGTGCCCGTGGGCCCTCGGGCTCCAChide sequence |
| RefSeq Acc Id: | XM_236578 ⟹ XP_236578 | |||||||||||||||||||
| RefSeq Status: | ||||||||||||||||||||
| Type: | CODING | |||||||||||||||||||
| Position: |
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| Sequence: |
GAGGCGTTGCGTCCGCTCGTTTGGCGCGAAAGTCGGTTCCTGGTCTTGGCCCTTCCGGGTACTGhide sequence |
Protein Sequences| Protein RefSeqs | XP_001072207 | (Get FASTA) | NCBI Sequence Viewer |
| XP_006226604 | (Get FASTA) | NCBI Sequence Viewer | |
| XP_006243746 | (Get FASTA) | NCBI Sequence Viewer | |
| XP_008756077 | (Get FASTA) | NCBI Sequence Viewer | |
| XP_008756078 | (Get FASTA) | NCBI Sequence Viewer | |
| XP_008764811 | (Get FASTA) | NCBI Sequence Viewer | |
| XP_236578 | (Get FASTA) | NCBI Sequence Viewer | |
| GenBank Protein | EDL77383 | (Get FASTA) | NCBI Sequence Viewer |
Reference Sequences
| RefSeq Acc Id: | XP_001072207 ⟸ XM_001072207 |
| - Peptide Label: | isoform X3 |
| - Sequence: |
MSRNDQEPFFVKFLKSSDNSECFFKALESIKELQSEEYLQVITDEEALRIKENDKSLYICDRFShide sequence |
| RefSeq Acc Id: | XP_236578 ⟸ XM_236578 |
| - Peptide Label: | isoform X2 |
| - Sequence: |
MSRNDQEPFFVKFLKSSDNSECFFKALESIKELQSEEYLQVITDEEALRIKENDKSLYICDRFShide sequence |
| RefSeq Acc Id: | XP_006226604 ⟸ XM_006226542 |
| - Peptide Label: | isoform X4 |
| - Sequence: |
MEEVHKYVQMMGGRVYRDLNVSVTHLIAGEVGSKKYLVAANLKKPILLPAWIKTLWEKSQEKKIhide sequence |
| RefSeq Acc Id: | XP_006243746 ⟸ XM_006243684 |
| - Peptide Label: | isoform X1 |
| - Sequence: |
MSRNDQEPFFVKFLKSSDNSECFFKALESIKELQSEEYLQVITDEEALRIKENDKSLYICDRFShide sequence |
| RefSeq Acc Id: | XP_008756078 ⟸ XM_008757856 |
| - Peptide Label: | isoform X1 |
| - Sequence: |
MSRNDQEPFFVKFLKSSDNSECFFKALESIKELQSEEYLQVITDEEALRIKENDKSLYICDRFShide sequence |
| RefSeq Acc Id: | XP_008756077 ⟸ XM_008757855 |
| - Peptide Label: | isoform X3 |
| - Sequence: |
MSRNDQEPFFVKFLKSSDNSECFFKALESIKELQSEEYLQVITDEEALRIKENDKSLYICDRFShide sequence |
| RefSeq Acc Id: | XP_008764811 ⟸ XM_008766589 |
| - Peptide Label: | isoform X1 |
| - Sequence: |
MSRNDQEPFFVKFLKSSDNSECFFKALESIKELQSEEYLQVITDEEALRIKENDKSLYICDRFShide sequence |
TranscriptomePromoters| RGD ID: | 13696231 | |||||||||
| Promoter ID: | EPDNEW_R6755 | |||||||||
| Type: | initiation region | |||||||||
| Name: | Topbp1_1 | |||||||||
| Description: | DNA topoisomerase II binding protein 1 | |||||||||
| SO ACC ID: | SO:0000170 | |||||||||
| Source: | EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/) | |||||||||
| Experiment Methods: | Single-end sequencing. | |||||||||
| Position: |
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Strain Variation
Strain Sequence Variants (Rnor 6.0)
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Damaging VariantsAssembly: Rnor_6.0
| Chromosome | Start Pos | End Pos | Reference Nucleotide | Variant Nucleotide | Variant Type | Strain |
| 8 | 111791644 | 111791645 | T | C | snv | WKY/N (MCW), WKY/NCrl (RGD), GK/Ox (RGD), SHRSP/Gcrc (RGD), SHR/NHsd (RGD) |
| 8 | 111825422 | 111825423 | C | A | snv | GK/Ox (RGD), WKY/NCrl (RGD), SHRSP/Gcrc (RGD), WKY/N (MCW), LEW/Crl (RGD), SHR/NHsd (RGD), LEW/NCrlBR (RGD), WKY/NHsd (RGD), WKY/Gcrc (RGD) |
Assembly: RGSC_v3.4
| Chromosome | Start Pos | End Pos | Reference Nucleotide | Variant Nucleotide | Variant Type | Strain |
| 8 | 108317487 | 108317488 | T | C | snv | GK/Ox (ICL), SHRSP/Gcrc (MDC), SHRSP/Gcrc (ICL), SHR/OlaIpcv (ICL), SHR/OlaIpcv (ICL), SHR/NHsd (ICL), WKY/NHsd (ICL), WKY/N (KNAW), WKY/Gcrc (ICL), LCR/2Mco (UMich), SHR/OlaIpcv (KNAW), WKY/NCrl (ICL) |
Additional Information
External Database Links| Database | Acc Id | Source(s) |
| AGR Gene | RGD:1562949 | AgrOrtholog |
| Ensembl Genes | ENSRNOG00000009789 | ENTREZGENE, UniProtKB/TrEMBL |
| Ensembl Protein | ENSRNOP00000013265 | ENTREZGENE, UniProtKB/TrEMBL |
| Ensembl Transcript | ENSRNOT00000013265 | ENTREZGENE, UniProtKB/TrEMBL |
| Gene3D-CATH | 3.40.50.10190 | UniProtKB/TrEMBL |
| InterPro | BRCT | UniProtKB/TrEMBL |
| BRCT_dom_sf | UniProtKB/TrEMBL | |
| NCBI Gene | 315969 | ENTREZGENE |
| Pfam | BRCT | UniProtKB/TrEMBL |
| PTCB-BRCT | UniProtKB/TrEMBL | |
| PhenoGen | Topbp1 | PhenoGen |
| PROSITE | BRCT | UniProtKB/TrEMBL |
| SMART | BRCT | UniProtKB/TrEMBL |
| Superfamily-SCOP | BRCT | UniProtKB/TrEMBL |
| UniProt | D3ZRG0_RAT | UniProtKB/TrEMBL |
Nomenclature History| Date | Current Symbol | Current Name | Previous Symbol | Previous Name | Description | Reference | Status |
|---|---|---|---|---|---|---|---|
| 2017-08-16 | Topbp1 | DNA topoisomerase II binding protein 1 | Topbp1 | topoisomerase (DNA) II binding protein 1 | Nomenclature updated to reflect human and mouse nomenclature | 1299863 | APPROVED |
| 2008-07-28 | Topbp1 | topoisomerase (DNA) II binding protein 1 | Topbp1 | topoisomerase (DNA) II beta binding protein | Nomenclature updated to reflect human and mouse nomenclature | 1299863 | APPROVED |
| 2008-03-03 | Topbp1 | topoisomerase (DNA) II beta binding protein | RGD1562949_predicted | similar to mKIAA0259 protein (predicted) | Nomenclature updated to reflect human and mouse nomenclature | 1299863 | APPROVED |
| 2006-03-07 | RGD1562949_predicted | similar to mKIAA0259 protein (predicted) | LOC315969 | similar to mKIAA0259 protein | Symbol and Name status set to approved | 1299863 | APPROVED |
| 2006-02-09 | LOC315969 | similar to mKIAA0259 protein | Symbol and Name status set to provisional | 70820 | PROVISIONAL |
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| More on Topbp1 | |
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Alliance Gene |
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NCBI Gene |
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Ensembl Gene |
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JBrowse: rn5 rn6 |
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NCBI Genome Data Viewer |
| RGD Object Information | |
| RGD ID: | 1562949 |
| Created: | 2006-02-09 |
| Species: | Rattus norvegicus |
| Last Modified: | 2019-10-16 |
| Status: | ACTIVE |
