Rbpj (recombination signal binding protein for immunoglobulin kappa J region) - Rat Genome Database
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Gene: Rbpj (recombination signal binding protein for immunoglobulin kappa J region) Rattus norvegicus
Analyze
Symbol: Rbpj
Name: recombination signal binding protein for immunoglobulin kappa J region
RGD ID: 1593096
Description: Predicted to have several functions, including DNA-binding transcription activator activity, RNA polymerase II-specific; RNA polymerase II repressing transcription factor binding activity; and protein N-terminus binding activity. Involved in several processes, including negative regulation of smooth muscle cell apoptotic process; negative regulation of smooth muscle cell migration; and positive regulation of smooth muscle cell proliferation. Localizes to nucleus and protein-DNA complex. Human ortholog(s) of this gene implicated in Adams-Oliver syndrome and dilated cardiomyopathy. Orthologous to human RBPJ (recombination signal binding protein for immunoglobulin kappa J region); PARTICIPATES IN Notch signaling pathway; Notch signaling pathway; Notch signaling pathway; INTERACTS WITH acrylamide; bisphenol A; cadmium dichloride.
Type: protein-coding
RefSeq Status: INFERRED
Also known as: LOC679028; recombining binding protein suppressor of hairless; similar to Recombining binding protein suppressor of hairless (J kappa-recombination signal binding protein) (RBP-J kappa)
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_6.01459,657,738 - 59,865,427 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1459,658,935 - 59,735,450 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01459,785,053 - 59,859,229 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
Celera1456,447,546 - 56,510,235 (-)NCBICelera
Cytogenetic Map14q11NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process
angiogenesis  (ISO)
aortic valve development  (ISO)
arterial endothelial cell fate commitment  (ISO)
artery morphogenesis  (ISO)
atrioventricular canal development  (ISO)
auditory receptor cell fate commitment  (ISO)
B cell differentiation  (ISO)
blood vessel endothelial cell fate specification  (ISO)
blood vessel lumenization  (ISO)
blood vessel remodeling  (ISO)
cardiac left ventricle morphogenesis  (ISO)
cell fate commitment  (ISO)
club cell differentiation  (ISO)
defense response to bacterium  (ISO)
dorsal aorta morphogenesis  (ISO)
endocardium development  (ISO)
endocardium morphogenesis  (ISO)
epidermal cell fate specification  (ISO)
epithelial to mesenchymal transition  (ISO)
epithelial to mesenchymal transition involved in endocardial cushion formation  (ISO)
hair follicle maturation  (ISO)
heart development  (ISO)
hemopoiesis  (ISO)
humoral immune response  (ISO)
inflammatory response to antigenic stimulus  (ISO)
keratinocyte differentiation  (ISO)
labyrinthine layer blood vessel development  (ISO)
myeloid dendritic cell differentiation  (ISO)
negative regulation of cell differentiation  (ISO)
negative regulation of cell population proliferation  (ISO)
negative regulation of cold-induced thermogenesis  (ISO,ISS)
negative regulation of neuron projection development  (IMP)
negative regulation of ossification  (ISO)
negative regulation of smooth muscle cell apoptotic process  (IMP)
negative regulation of smooth muscle cell migration  (IMP)
negative regulation of transcription by RNA polymerase II  (ISO)
negative regulation of transcription, DNA-templated  (ISO)
neuron differentiation  (ISO)
Notch signaling pathway  (IBA,ISO)
outflow tract morphogenesis  (ISO)
pituitary gland development  (ISO)
positive regulation of BMP signaling pathway  (ISO)
positive regulation of canonical Wnt signaling pathway involved in cardiac muscle cell fate commitment  (ISO)
positive regulation of cardiac muscle cell proliferation  (ISO)
positive regulation of cell population proliferation  (ISO)
positive regulation of cell proliferation involved in heart morphogenesis  (ISO)
positive regulation of ephrin receptor signaling pathway  (ISO)
positive regulation of ERBB signaling pathway  (ISO)
positive regulation of gene expression  (ISO)
positive regulation of smooth muscle cell proliferation  (IMP)
positive regulation of transcription by RNA polymerase II  (ISO)
positive regulation of transcription from RNA polymerase II promoter in response to hypoxia  (ISO)
positive regulation of transcription of Notch receptor target  (ISO)
positive regulation of transcription, DNA-templated  (IMP)
pulmonary valve development  (ISO)
regulation of cell population proliferation  (ISO)
regulation of gene expression  (ISO)
regulation of timing of cell differentiation  (ISO)
regulation of transcription by RNA polymerase II  (ISO)
regulation of transcription from RNA polymerase II promoter involved in myocardial precursor cell differentiation  (ISO)
sebaceous gland development  (ISO)
secondary heart field specification  (ISO)
somatic stem cell population maintenance  (ISO)
somitogenesis  (ISO)
ventricular septum morphogenesis  (ISO)
ventricular trabecula myocardium morphogenesis  (ISO)

Cellular Component

Molecular Pathway Annotations     Click to see Annotation Detail View
Notch signaling pathway  (IDA,IEA,ISO)

References

Additional References at PubMed
PMID:9102301   PMID:9111338   PMID:9874765   PMID:10476967   PMID:10713164   PMID:11967543   PMID:12730124   PMID:12794108   PMID:14701881   PMID:15466160   PMID:15509736   PMID:15632090  
PMID:15689374   PMID:16287852   PMID:16510869   PMID:16691198   PMID:17015435   PMID:17079689   PMID:17283045   PMID:17336907   PMID:17392792   PMID:17658278   PMID:17658279   PMID:17685488  
PMID:17938243   PMID:18663143   PMID:19124651   PMID:19154718   PMID:19779553   PMID:20890042   PMID:21102556   PMID:21311046   PMID:21402740   PMID:21493891   PMID:22711842   PMID:22797898  
PMID:23117660   PMID:23303788   PMID:23571214   PMID:23639443   PMID:23913046   PMID:25406395   PMID:26491108   PMID:26951801  


Genomics

Comparative Map Data
Rbpj
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rnor_6.01459,657,738 - 59,865,427 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1459,658,935 - 59,735,450 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01459,785,053 - 59,859,229 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
Celera1456,447,546 - 56,510,235 (-)NCBICelera
Cytogenetic Map14q11NCBI
RBPJ
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl426,163,455 - 26,435,131 (+)EnsemblGRCh38hg38GRCh38
GRCh38426,163,458 - 26,435,131 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh37426,165,077 - 26,436,753 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36425,930,430 - 26,042,376 (+)NCBINCBI36hg18NCBI36
Celera426,771,681 - 26,884,040 (+)NCBI
Cytogenetic Map4p15.2NCBI
HuRef425,659,979 - 25,775,063 (+)NCBIHuRef
CHM1_1426,322,549 - 26,437,875 (+)NCBICHM1_1
Rbpj
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39553,713,121 - 53,814,787 (+)NCBIGRCm39mm39
GRCm38553,555,779 - 53,657,445 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl553,466,152 - 53,657,362 (+)EnsemblGRCm38mm10GRCm38
MGSCv37553,947,018 - 54,048,684 (+)NCBIGRCm37mm9NCBIm37
MGSCv36553,878,593 - 53,944,281 (+)NCBImm8
Celera550,938,216 - 51,041,035 (+)NCBICelera
Cytogenetic Map5C1NCBI
cM Map529.37NCBI
Rbpj
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495544318,783,061 - 18,910,228 (-)EnsemblChiLan1.0
ChiLan1.0NW_00495544318,783,061 - 19,029,441 (-)NCBIChiLan1.0ChiLan1.0
RBPJ
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.1425,996,223 - 26,107,683 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl425,995,263 - 26,107,683 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v0420,719,548 - 20,835,439 (+)NCBIMhudiblu_PPA_v0panPan3
RBPJ
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1 Ensembl384,064,440 - 84,286,360 (-)EnsemblCanFam3.1canFam3CanFam3.1
CanFam3.1384,060,417 - 84,286,008 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
Rbpj
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
SpeTri2.0NW_0049364773,354,336 - 3,445,248 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
RBPJ
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl819,922,779 - 20,166,755 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1819,933,035 - 20,166,746 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2820,306,820 - 20,540,623 (+)NCBISscrofa10.2Sscrofa10.2susScr3
RBPJ
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.12723,911,084 - 24,023,856 (-)NCBI
Rbpj
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046247556,176,497 - 6,298,034 (-)NCBI

Position Markers
D14Got163  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.01459,712,144 - 59,712,283NCBIRnor6.0
Rnor_5.01459,836,103 - 59,836,242UniSTSRnor5.0
RGSC_v3.41462,296,273 - 62,296,412UniSTSRGSC3.4
Celera1456,486,697 - 56,486,835UniSTS
Cytogenetic Map14 RGD
Rbpsuh-rs3  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.054,878,500 - 4,879,123NCBIRnor6.0
Rnor_5.054,847,450 - 4,848,073UniSTSRnor5.0
RGSC_v3.454,664,368 - 4,664,991UniSTSRGSC3.4
Celera55,053,895 - 5,054,518UniSTS
Cytogenetic Map5q11UniSTS
X17459  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.01459,661,351 - 59,661,508NCBIRnor6.0
Rnor_5.01459,787,469 - 59,787,626UniSTSRnor5.0
Celera1456,449,963 - 56,450,120UniSTS
UniSTS:465469  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.01459,662,034 - 59,662,578NCBIRnor6.0
Rnor_5.01459,788,152 - 59,788,696UniSTSRnor5.0
Celera1456,450,646 - 56,451,190UniSTS
Rbpj  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.054,878,905 - 4,879,403NCBIRnor6.0
Rnor_5.054,847,855 - 4,848,353UniSTSRnor5.0
RGSC_v3.454,664,773 - 4,665,271UniSTSRGSC3.4
Celera55,054,300 - 5,054,798UniSTS
Cytogenetic Map5q11UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1581500Renag1Renal agenesis QTL 1kidney development trait (VT:0000527)percentage of study population developing unilateral renal agenesis during a period of time (CMO:0000940)14975643572854397Rat
731183Pia20Pristane induced arthritis QTL 203.55joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)141072926861873323Rat
631839Niddm37Non-insulin dependent diabetes mellitus QTL 373.37blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)1412680424106641756Rat
2313397Coatc1Coat color QTL1coat/hair pigmentation trait (VT:0010463)coat/hair color measurement (CMO:0001808)142018938665189386Rat
10755459Coatc15Coat color QTL 150.01681coat/hair pigmentation trait (VT:0010463)pigmented ventral coat/hair area to total ventral coat/hair area ratio (CMO:0001812)142145756566457565Rat
70187Pancm5Pancreatic morphology QTL 516.7pancreas mass (VT:0010144)pancreas weight to body weight ratio (CMO:0000630)143259392686191589Rat
2324617Coatc2Coat color QTL 20.001coat/hair pigmentation trait (VT:0010463)pigmented coat/hair area to total coat/hair area ratio (CMO:0001810)143303991261783215Rat
1300154Bp189Blood pressure QTL 1893.04arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)143316331673391571Rat
2313048Bss84Bone structure and strength QTL 843.10.0001tibia strength trait (VT:1000284)tibia total energy absorbed before break (CMO:0001736)144031561085315610Rat
2313084Bss83Bone structure and strength QTL 832.90.0001tibia size trait (VT:0100001)tibia midshaft endosteal cross-sectional area (CMO:0001716)144031561085315610Rat
2313089Bss81Bone structure and strength QTL 813.40.0001body length (VT:0001256)body length, nose to rump (CMO:0000079)144031561085315610Rat
2313100Bss82Bone structure and strength QTL 8230.0001tibia size trait (VT:0100001)tibia midshaft cross-sectional area (CMO:0001717)144031561085315610Rat
70214Niddm28Non-insulin dependent diabetes mellitus QTL 284.06blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)144163756980841518Rat
631523Pia13Pristane induced arthritis QTL 133.3joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1442442731108833671Rat
1300136Rf22Renal function QTL 223.9renal blood flow trait (VT:2000006)absolute change in renal vascular resistance (CMO:0001900)1443910761105074364Rat
1549834Scl45Serum cholesterol level QTL 455.8blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)1451818462105074364Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:378
Count of miRNA genes:217
Interacting mature miRNAs:273
Transcripts:ENSRNOT00000071929
Prediction methods:Miranda, 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 3 41 39 23 19 23 8 9 74 35 38 11 8
Low 2 18 18 18 2 3
Below cutoff

Sequence

Nucleotide Sequences
RefSeq Transcripts NM_001106631 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008770190 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008770191 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008770192 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008770193 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017599376 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide AABR07015494 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AABR07015495 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AABR07015496 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AABR07015497 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AABR07015498 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AABR07015499 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AABR07015500 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AABR07015501 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AABR07015502 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AAHX01080124 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AAHX01080125 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AAHX01080126 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AAHX01080127 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CH473963 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Reference Sequences
RefSeq Acc Id: ENSRNOT00000071929   ⟹   ENSRNOP00000065485
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1459,658,935 - 59,735,450 (-)Ensembl
RefSeq Acc Id: NM_001106631   ⟹   NP_001100101
RefSeq Status: INFERRED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01459,658,935 - 59,735,450 (-)NCBI
Rnor_5.01459,785,053 - 59,859,229 (-)NCBI
Celera1456,447,546 - 56,510,235 (-)RGD
Sequence:
RefSeq Acc Id: XM_008770190   ⟹   XP_008768412
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01459,657,738 - 59,736,162 (-)NCBI
Sequence:
RefSeq Acc Id: XM_008770191   ⟹   XP_008768413
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01459,661,510 - 59,735,163 (-)NCBI
Sequence:
RefSeq Acc Id: XM_008770192   ⟹   XP_008768414
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01459,661,510 - 59,711,970 (-)NCBI
Sequence:
RefSeq Acc Id: XM_008770193   ⟹   XP_008768415
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01459,661,510 - 59,735,157 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017599376   ⟹   XP_017454865
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01459,661,510 - 59,865,427 (-)NCBI
Sequence:
Reference Sequences
RefSeq Acc Id: NP_001100101   ⟸   NM_001106631
- UniProtKB: M0R7Q3 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_008768412   ⟸   XM_008770190
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: XP_008768413   ⟸   XM_008770191
- Peptide Label: isoform X3
- Sequence:
RefSeq Acc Id: XP_008768415   ⟸   XM_008770193
- Peptide Label: isoform X4
- Sequence:
RefSeq Acc Id: XP_008768414   ⟸   XM_008770192
- Peptide Label: isoform X4
- Sequence:
RefSeq Acc Id: XP_017454865   ⟸   XM_017599376
- Peptide Label: isoform X2
- Sequence:
RefSeq Acc Id: ENSRNOP00000065485   ⟸   ENSRNOT00000071929
Protein Domains
BTD   LAG1_DNAbind

Transcriptome

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


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)
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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)
FHL/EurMcwi (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
GH/OmrMcwi (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)
GK/Ox (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
LE/Stm (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
LEW/Crl (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
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)
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
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)
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
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)
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
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)
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

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1593096 AgrOrtholog
Ensembl Genes ENSRNOG00000046327 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000065485 ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000071929 ENTREZGENE, UniProtKB/TrEMBL
Gene3D-CATH 2.60.40.10 UniProtKB/TrEMBL
  2.60.40.1450 UniProtKB/TrEMBL
InterPro Beta-trefoil_DNA-bd_dom UniProtKB/TrEMBL
  BTD_sf UniProtKB/TrEMBL
  CLS_fam UniProtKB/TrEMBL
  Ig-like_fold UniProtKB/TrEMBL
  Ig_E-set UniProtKB/TrEMBL
  LAG1_DNA-bd UniProtKB/TrEMBL
  p53-like_TF_DNA-bd UniProtKB/TrEMBL
  RBP-J/Cbf11/Cbf12_DNA-bd_sf UniProtKB/TrEMBL
  RBP-Jkappa_IPT UniProtKB/TrEMBL
KEGG Report rno:679028 UniProtKB/TrEMBL
NCBI Gene 679028 ENTREZGENE
PANTHER PTHR10665 UniProtKB/TrEMBL
Pfam BTD UniProtKB/TrEMBL
  LAG1-DNAbind UniProtKB/TrEMBL
PhenoGen Rbpj PhenoGen
SMART BTD UniProtKB/TrEMBL
  LAG1_DNAbind UniProtKB/TrEMBL
Superfamily-SCOP Beta-trefoil UniProtKB/TrEMBL
  Ig_E-set UniProtKB/TrEMBL
  P53_like_DNA_bnd UniProtKB/TrEMBL
UniGene Rn.3958 ENTREZGENE
UniProt M0R7Q3 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2009-04-14 Rbpj  recombination signal binding protein for immunoglobulin kappa J region  LOC679028  similar to Recombining binding protein suppressor of hairless (J kappa-recombination signal binding protein) (RBP-J kappa)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2006-11-20 LOC679028  similar to Recombining binding protein suppressor of hairless (J kappa-recombination signal binding protein) (RBP-J kappa)      Symbol and Name status set to provisional 70820 PROVISIONAL