Topbp1 (DNA topoisomerase II binding protein 1) - Rat Genome Database
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Gene: Topbp1 (DNA topoisomerase II binding protein 1) Rattus norvegicus
Analyze
Symbol: Topbp1
Name: DNA topoisomerase II binding protein 1
RGD ID: 1562949
Description: Predicted to have identical protein binding activity. Predicted to be involved in DNA replication initiation; mitotic G2/M transition checkpoint; and response to ionizing radiation. Predicted to localize to actin cytoskeleton; nucleus; and plasma membrane. Orthologous to human TOPBP1 (DNA topoisomerase II binding protein 1); INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; acrylamide; bisphenol A.
Type: protein-coding
RefSeq Status: MODEL
Also known as: DNA topoisomerase 2-binding protein 1; LOC315969; RGD1562949; similar to mKIAA0259 protein; topoisomerase (DNA) II beta binding protein; topoisomerase (DNA) II binding protein 1
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: Rnor_6.0 - RGSC Genome Assembly v6.0
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rnor_6.08111,790,655 - 111,835,224 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl8111,790,678 - 111,827,151 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.08111,182,214 - 111,226,726 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.48108,316,569 - 108,360,753 (+)NCBIRGSC3.4rn4RGSC3.4
Celera8103,263,981 - 103,308,109 (+)NCBICelera
Cytogenetic Map8q32NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

Molecular Function

References

Additional References at PubMed
PMID:12773567   PMID:14718568   PMID:17006541   PMID:17696610   PMID:21659603   PMID:22549958   PMID:31904090  


Genomics

Comparative Map Data
Topbp1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rnor_6.08111,790,655 - 111,835,224 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl8111,790,678 - 111,827,151 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.08111,182,214 - 111,226,726 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.48108,316,569 - 108,360,753 (+)NCBIRGSC3.4rn4RGSC3.4
Celera8103,263,981 - 103,308,109 (+)NCBICelera
Cytogenetic Map8q32NCBI
TOPBP1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl3133,598,175 - 133,662,380 (-)EnsemblGRCh38hg38GRCh38
GRCh383133,600,238 - 133,661,968 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh373133,319,449 - 133,380,762 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 363134,802,177 - 134,863,380 (-)NCBINCBI36hg18NCBI36
Build 343134,802,184 - 134,863,388NCBI
Celera3131,746,550 - 131,807,847 (-)NCBI
Cytogenetic Map3q22.1NCBI
HuRef3130,698,929 - 130,760,396 (-)NCBIHuRef
CHM1_13133,282,831 - 133,344,118 (-)NCBICHM1_1
Topbp1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm399103,182,351 - 103,227,627 (+)NCBIGRCm39mm39
GRCm389103,305,167 - 103,350,428 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl9103,305,215 - 103,350,428 (+)EnsemblGRCm38mm10GRCm38
MGSCv379103,207,657 - 103,252,758 (+)NCBIGRCm37mm9NCBIm37
MGSCv369103,163,477 - 103,208,578 (+)NCBImm8
Celera9102,854,061 - 102,901,479 (+)NCBICelera
Cytogenetic Map9F1NCBI
Topbp1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049555014,908,137 - 4,976,453 (+)EnsemblChiLan1.0
ChiLan1.0NW_0049555014,907,687 - 4,974,995 (+)NCBIChiLan1.0ChiLan1.0
TOPBP1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.13138,143,287 - 138,204,163 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl3138,143,893 - 138,203,363 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v03130,667,998 - 130,729,569 (-)NCBIMhudiblu_PPA_v0panPan3
TOPBP1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1 Ensembl2330,516,125 - 30,578,108 (-)EnsemblCanFam3.1canFam3CanFam3.1
CanFam3.12330,517,172 - 30,578,664 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
Topbp1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
SpeTri2.0NW_0049365296,788,713 - 6,841,824 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
TOPBP1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1374,766,426 - 74,846,793 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11374,768,251 - 74,846,377 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21382,197,685 - 82,230,216 (+)NCBISscrofa10.2Sscrofa10.2susScr3
TOPBP1
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11556,679,333 - 56,740,773 (+)NCBI
ChlSab1.1 Ensembl1556,679,426 - 56,741,566 (+)Ensembl
Topbp1
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046247309,916,717 - 9,994,666 (-)NCBI

Position Markers
D8Rat107  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.08111,800,214 - 111,800,427NCBIRnor6.0
Rnor_5.08111,191,793 - 111,192,006UniSTSRnor5.0
RGSC_v3.48108,325,793 - 108,326,123RGDRGSC3.4
RGSC_v3.48108,325,875 - 108,326,088UniSTSRGSC3.4
RGSC_v3.18108,345,248 - 108,345,578RGD
Celera8103,273,349 - 103,273,556UniSTS
Cytogenetic Map8q32UniSTS
SHRSP x BN Map866.2399UniSTS
SHRSP x BN Map866.2399RGD
D8Got170  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.08111,799,957 - 111,800,435NCBIRnor6.0
Rnor_6.08111,800,139 - 111,800,435NCBIRnor6.0
Rnor_5.08111,191,536 - 111,192,014UniSTSRnor5.0
Rnor_5.08111,191,718 - 111,192,014UniSTSRnor5.0
RGSC_v3.48108,325,799 - 108,326,096RGDRGSC3.4
RGSC_v3.48108,325,800 - 108,326,096UniSTSRGSC3.4
RGSC_v3.18108,345,254 - 108,345,551RGD
Celera8103,273,274 - 103,273,564UniSTS
Cytogenetic Map8q32UniSTS
RH 2.0 Map8888.8RGD
RH131225  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.08111,834,575 - 111,834,767NCBIRnor6.0
Rnor_5.08111,226,418 - 111,226,610UniSTSRnor5.0
RGSC_v3.48108,360,445 - 108,360,637UniSTSRGSC3.4
Celera8103,307,460 - 103,307,652UniSTS
Cytogenetic Map8q32UniSTS
RH 3.4 Map81158.0UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1581557Eae16Experimental allergic encephalomyelitis QTL 163.8nervous system integrity trait (VT:0010566)experimental autoimmune encephalomyelitis incidence/prevalence measurement (CMO:0001046)89531047119211942Rat
631650Stl6Serum triglyceride level QTL 640.0019blood triglyceride amount (VT:0002644)plasma triglyceride level (CMO:0000548)810938911120496129Rat
2316950Scl66Serum cholesterol level QTL 664.1blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)833558764113580387Rat
1554321Bmd3Bone mineral density QTL 37.90.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)844458129118087517Rat
70197BpQTLcluster8Blood pressure QTL cluster 83.482arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)850529480128036471Rat
70197BpQTLcluster8Blood pressure QTL cluster 83.482arterial blood pressure trait (VT:2000000)absolute change in systolic blood pressure (CMO:0000607)850529480128036471Rat
70197BpQTLcluster8Blood pressure QTL cluster 83.482arterial blood pressure trait (VT:2000000)pulse pressure (CMO:0000292)850529480128036471Rat
70197BpQTLcluster8Blood pressure QTL cluster 83.482arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)850529480128036471Rat
1358912Bw51Body weight QTL 512.95body mass (VT:0001259)body weight (CMO:0000012)855435004115812386Rat
2303171Bp331Blood pressure QTL 3315.570.005arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)865717449128033050Rat
631653Bp125Blood pressure QTL 1253.3arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)872849686117849686Rat
631210Bw3Body weight QTL35.9mesenteric fat pad mass (VT:0010427)mesenteric fat pad weight as a percentage of body weight (CMO:0000654)874917593121080545Rat
1300171Bp184Blood pressure QTL 1843.66arterial blood pressure trait (VT:2000000)blood pressure time series experimental set point of the baroreceptor response (CMO:0002593)876103982127182642Rat
9590292Uminl3Urine mineral level QTL 33.620.001urine mineral amount (VT:0015086)urine electrolyte level (CMO:0000593)878805083123805083Rat
8694446Bw170Body weight QTL 17012.070.001retroperitoneal fat pad mass (VT:0010430)retroperitoneal fat pad weight to body weight ratio (CMO:0000635)878805083123805083Rat
8694200Abfw4Abdominal fat weight QTL 49.070.001visceral adipose mass (VT:0010063)abdominal fat pad weight to body weight ratio (CMO:0000095)878805083123805083Rat
8694392Bw161Body weight QTL 1618.060.001body lean mass (VT:0010483)lean tissue morphological measurement (CMO:0002184)878805083123805083Rat
1549909Stresp11Stress response QTL 116.830.0019stress-related behavior trait (VT:0010451)number of approaches toward negative stimulus before onset of defensive burying response (CMO:0001960)880697934125697934Rat
2300181Bmd55Bone mineral density QTL 555.70.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)883894304128894304Rat
61437Cia6Collagen induced arthritis QTL 6joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)889058229132243842Rat
8693654Alc32Alcohol consumption QTL 3220.755drinking behavior trait (VT:0001422)calculated ethanol drink intake rate (CMO:0001615)895319530115625029Rat
2313400Anxrr25Anxiety related response QTL 25aggression-related behavior trait (VT:0015014)tameness/aggressiveness composite score (CMO:0002136)895963141122354314Rat
1358893Bp263Blood pressure QTL 2635.01arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)8100873811133307652Rat
1358903Bp252Blood pressure QTL 25270.0001arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)8100873811133307652Rat
738011Anxrr9Anxiety related response QTL 96.1exploratory behavior trait (VT:0010471)number of entries into a discrete space in an experimental apparatus (CMO:0000960)8102051964133307652Rat
738014Anxrr15Anxiety related response QTL 153.60.005locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)8104682575133307652Rat
2300182Bmd56Bone mineral density QTL 565.4femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)8104682575133307652Rat
724539Cm19Cardiac mass QTL 192.6heart mass (VT:0007028)calculated heart weight (CMO:0000073)8107769005129956433Rat
631217Activ1Activity QTL 115.9voluntary movement trait (VT:0003491)number of photobeam interruptions in an experimental apparatus (CMO:0001517)8110212979116947981Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:22
Count of miRNA genes:21
Interacting mature miRNAs:22
Transcripts:ENSRNOT00000013265
Prediction methods:Miranda, Rnahybrid, Targetscan
Result types:miRGate_prediction

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.


Expression


RNA-SEQ Expression
High: > 1000 TPM value   Medium: Between 11 and 1000 TPM
Low: Between 0.5 and 10 TPM   Below Cutoff: < 0.5 TPM

alimentary part of gastrointestinal system circulatory system endocrine system exocrine system hemolymphoid system hepatobiliary system integumental system musculoskeletal system nervous system renal system reproductive system respiratory system appendage
High
Medium 2 26 44 30 19 30 1 1 68 24 39 10 1
Low 1 17 13 11 11 7 10 6 11 2 1 7
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000013265   ⟹   ENSRNOP00000013265
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl8111,790,678 - 111,827,151 (+)Ensembl
RefSeq Acc Id: XM_001072207   ⟹   XP_001072207
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Celera8103,263,982 - 103,308,109 (+)NCBI
Sequence:
RefSeq Acc Id: XM_006226542   ⟹   XP_006226604
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Celera8103,267,154 - 103,308,109 (+)NCBI
Sequence:
RefSeq Acc Id: XM_006243684   ⟹   XP_006243746
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.08111,790,655 - 111,826,531 (+)NCBI
Rnor_5.08111,182,214 - 111,226,726 (+)NCBI
Sequence:
RefSeq Acc Id: XM_008757855   ⟹   XP_008756077
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Celera8103,264,111 - 103,308,109 (+)NCBI
Sequence:
RefSeq Acc Id: XM_008757856   ⟹   XP_008756078
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Celera8103,263,981 - 103,299,657 (+)NCBI
Sequence:
RefSeq Acc Id: XM_008766589   ⟹   XP_008764811
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.08111,790,785 - 111,826,531 (+)NCBI
Sequence:
RefSeq Acc Id: XM_236578   ⟹   XP_236578
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.08111,790,656 - 111,835,224 (+)NCBI
Rnor_5.08111,182,214 - 111,226,726 (+)NCBI
RGSC_v3.48108,316,569 - 108,360,753 (+)RGD
Sequence:
Reference Sequences
RefSeq Acc Id: XP_001072207   ⟸   XM_001072207
- Peptide Label: isoform X3
- Sequence:
RefSeq Acc Id: XP_236578   ⟸   XM_236578
- Peptide Label: isoform X2
- Sequence:
RefSeq Acc Id: XP_006226604   ⟸   XM_006226542
- Peptide Label: isoform X4
- Sequence:
RefSeq Acc Id: XP_006243746   ⟸   XM_006243684
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: XP_008756078   ⟸   XM_008757856
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: XP_008756077   ⟸   XM_008757855
- Peptide Label: isoform X3
- Sequence:
RefSeq Acc Id: XP_008764811   ⟸   XM_008766589
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: ENSRNOP00000013265   ⟸   ENSRNOT00000013265
Protein Domains
BRCT

Transcriptome

eQTL   View at Phenogen
WGCNA   View at Phenogen
Tissue/Strain Expression   View at Phenogen

Promoters
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:
Rat AssemblyChrPosition (strand)Source
Rnor_6.08111,790,690 - 111,790,750EPDNEW

Strain Variation

Strain Sequence Variants (Rnor 6.0)
ACI/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
ACI/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
ACI/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
BBDP/Wor (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
BN/SsN (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
Buf/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
COP/CrCrl (MCW & UW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
University of Wisconsin (Dr. James Shull)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Charles River Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob) and UW Madison (Dr. James Shull)
F344/NCrl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
F344/NRrrc (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
FHH/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHH/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
FHL/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHL/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
GH/OmrMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
GK/Ox (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LE/Stm (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/Crl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/NCrlBR (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LH/MavRrrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LL/MavRrrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LN/MavRrrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
M520/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
MHS/Gib (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MNS/Gib (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MR/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
SBH/Ygl (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBH/Ygl sequenced by MCW
SBH/Ygl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SBN/Ygl (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBN/Ygl sequenced by MCW
SBN/Ygl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHR/NHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHRSP/Gcrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SR/JrHsd (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Harlan Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SR/JrHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/Jr (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/JrHsdMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SS/JrHsdMcwi (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WAG/Rij (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/Gcrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
WKY/NCrl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/NHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WN/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
Damaging Variants


Assembly: Rnor_6.0
Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
8 111791644 111791645 T C snv SHR/NHsd (RGD), WKY/NCrl (RGD), GK/Ox (RGD), WKY/N (MCW), SHRSP/Gcrc (RGD)
8 111825422 111825423 C A snv SHRSP/Gcrc (RGD), WKY/NCrl (RGD), WKY/Gcrc (RGD), WKY/NHsd (RGD), LEW/NCrlBR (RGD), LEW/Crl (RGD), GK/Ox (RGD), WKY/N (MCW), SHR/NHsd (RGD)


Assembly: RGSC_v3.4
Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
8 108317487 108317488 T C snv SHR/OlaIpcv (ICL), SHRSP/Gcrc (MDC), WKY/N (KNAW), SHR/OlaIpcv (KNAW), GK/Ox (ICL), LCR/2Mco (UMich), SHR/NHsd (ICL), SHRSP/Gcrc (ICL), WKY/Gcrc (ICL), WKY/NHsd (ICL), WKY/NCrl (ICL), SHR/OlaIpcv (ICL)


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1562949 AgrOrtholog
Ensembl Genes ENSRNOG00000009789 Ensembl, 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