Brd3 (bromodomain containing 3) - Rat Genome Database
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Gene: Brd3 (bromodomain containing 3) Rattus norvegicus
Analyze
Symbol: Brd3
Name: bromodomain containing 3
RGD ID: 1308925
Description: Predicted to have chromatin binding activity and lysine-acetylated histone binding activity. Predicted to be involved in regulation of transcription by RNA polymerase II. Orthologous to human BRD3 (bromodomain containing 3); PARTICIPATES IN histone modification pathway; INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; 2,4-dinitrotoluene; 2,6-dinitrotoluene.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: bromodomain-containing protein 3; LOC362092
Orthologs:
Homo sapiens (human) : BRD3 (bromodomain containing 3)  HGNC  Alliance
Mus musculus (house mouse) : Brd3 (bromodomain containing 3)  MGI  Alliance
Chinchilla lanigera (long-tailed chinchilla) : Brd3 (bromodomain containing 3)
Pan paniscus (bonobo/pygmy chimpanzee) : BRD3 (bromodomain containing 3)
Canis lupus familiaris (dog) : BRD3 (bromodomain containing 3)
Ictidomys tridecemlineatus (thirteen-lined ground squirrel) : Brd3 (bromodomain containing 3)
Chlorocebus sabaeus (African green monkey) : BRD3 (bromodomain containing 3)
Heterocephalus glaber (naked mole-rat) : Brd3 (bromodomain containing 3)
more info ...
Latest Assembly: Rnor_6.0 - RGSC Genome Assembly v6.0
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rnor_6.035,995,204 - 6,054,467 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl35,997,315 - 6,054,483 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0311,356,155 - 11,415,329 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.436,369,903 - 6,390,116 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.136,347,707 - 6,425,179 (-)NCBI
Celera35,569,850 - 5,590,130 (-)NCBICelera
Cytogenetic Map3p12NCBI
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

Biological Process

Molecular Function

Molecular Pathway Annotations     Click to see Annotation Detail View
References

Additional References at PubMed
PMID:12477932   PMID:18406326   PMID:22464331   PMID:27105114  


Genomics

Comparative Map Data
Brd3
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rnor_6.035,995,204 - 6,054,467 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl35,997,315 - 6,054,483 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0311,356,155 - 11,415,329 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.436,369,903 - 6,390,116 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.136,347,707 - 6,425,179 (-)NCBI
Celera35,569,850 - 5,590,130 (-)NCBICelera
Cytogenetic Map3p12NCBI
BRD3
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl9134,030,305 - 134,068,535 (-)EnsemblGRCh38hg38GRCh38
GRCh389134,030,305 - 134,068,533 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh379136,895,427 - 136,933,655 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 369135,887,784 - 135,922,913 (-)NCBINCBI36hg18NCBI36
Build 349133,927,516 - 133,962,646NCBI
Celera9107,443,656 - 107,481,364 (-)NCBI
Cytogenetic Map9q34.2NCBI
HuRef9106,393,244 - 106,416,418 (-)NCBIHuRef
CHM1_19137,043,869 - 137,081,779 (-)NCBICHM1_1
Brd3
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39227,335,588 - 27,397,669 (-)NCBI
GRCm38227,445,576 - 27,507,657 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl227,445,579 - 27,507,662 (-)EnsemblGRCm38mm10GRCm38
MGSCv37227,301,101 - 27,331,193 (-)NCBIGRCm37mm9NCBIm37
MGSCv36227,269,799 - 27,309,212 (-)NCBImm8
Celera227,148,111 - 27,178,261 (-)NCBICelera
Cytogenetic Map2A3NCBI
Brd3
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049555133,145,288 - 3,174,370 (-)EnsemblChiLan1.0
ChiLan1.0NW_0049555133,145,267 - 3,164,791 (-)NCBIChiLan1.0ChiLan1.0
BRD3
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.19133,759,096 - 133,782,419 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl9133,759,111 - 133,782,419 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v09105,151,354 - 105,189,754 (-)NCBIMhudiblu_PPA_v0panPan3
BRD3
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1 Ensembl950,288,240 - 50,322,127 (-)EnsemblCanFam3.1canFam3CanFam3.1
CanFam3.1950,290,488 - 50,322,243 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
Brd3
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
SpeTri2.0NW_0049366692,993,284 - 3,023,185 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
BRD3
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1 Ensembl124,089,621 - 4,109,441 (+)Ensembl
ChlSab1.1124,075,123 - 4,112,727 (+)NCBI
Brd3
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046247602,220,019 - 2,247,322 (-)NCBI

Position Markers
D3Mgh16  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.036,000,748 - 6,000,866NCBIRnor6.0
Rnor_5.0311,361,699 - 11,361,817UniSTSRnor5.0
RGSC_v3.436,373,336 - 6,373,454UniSTSRGSC3.4
RGSC_v3.436,373,335 - 6,373,454RGDRGSC3.4
RGSC_v3.136,373,636 - 6,373,754RGD
Celera35,573,283 - 5,573,401UniSTS
Cytogenetic Map3p12UniSTS
RH 3.4 Map316.9UniSTS
RH 3.4 Map316.9RGD
RH133905  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.035,997,469 - 5,997,664NCBIRnor6.0
Rnor_5.0311,358,420 - 11,358,615UniSTSRnor5.0
RGSC_v3.436,370,057 - 6,370,252UniSTSRGSC3.4
Celera35,570,004 - 5,570,199UniSTS
Cytogenetic Map3p12UniSTS
RH 3.4 Map333.2UniSTS
RH136842  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.035,998,042 - 5,998,844NCBIRnor6.0
Rnor_5.0311,358,993 - 11,359,795UniSTSRnor5.0
RGSC_v3.436,370,630 - 6,371,432UniSTSRGSC3.4
Celera35,570,577 - 5,571,379UniSTS
Cytogenetic Map3p12UniSTS
RH 3.4 Map330.0UniSTS
UniSTS:234347  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.036,013,934 - 6,014,147NCBIRnor6.0
Rnor_5.0311,374,885 - 11,375,098UniSTSRnor5.0
RGSC_v3.436,386,453 - 6,386,666UniSTSRGSC3.4
Celera35,586,468 - 5,586,681UniSTS
Cytogenetic Map3p12UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
631679Cm10Cardiac mass QTL 107.340.0001heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)3125786001Rat
70202Alc19Alcohol consumption QTL 192.5drinking behavior trait (VT:0001422)ethanol intake volume to total fluid intake volume ratio (CMO:0001591)3128136884Rat
631545Bp85Blood pressure QTL 853.1arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)3128500807Rat
61468Bp15Blood pressure QTL 154.4blood pressure trait (VT:0000183)diastolic blood pressure (CMO:0000005)3128500807Rat
61468Bp15Blood pressure QTL 154.4blood pressure trait (VT:0000183)systolic blood pressure (CMO:0000004)3128500807Rat
61468Bp15Blood pressure QTL 154.4blood pressure trait (VT:0000183)pulse pressure (CMO:0000292)3128500807Rat
631831Alc8Alcohol consumption QTL 82.7consumption behavior trait (VT:0002069)calculated ethanol drink intake rate (CMO:0001615)3132972944Rat
4889966Bss95Bone structure and strength QTL 954.4tibia area (VT:1000281)tibia-fibula cross-sectional area (CMO:0001718)3137891710Rat
2312664Scl62Serum cholesterol level QTL 620.05blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)3139773425Rat
2290452Scl56Serum cholesterol level QTL 562.26blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)3195176874Rat
1358185Ept6Estrogen-induced pituitary tumorigenesis QTL 66.7pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)35711366000866Rat
2292615Ept17Estrogen-induced pituitary tumorigenesis QTL 176.7pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)35711366000866Rat
1298526Arunc3Aerobic running capacity QTL 32.2exercise endurance trait (VT:0002332)maximum distance run on treadmill (CMO:0001406)3263142133477544Rat
10401810Kidm53Kidney mass QTL 53kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)3263142148562146Rat
70203Gcr2Gastric cancer resistance QTL 22.6stomach morphology trait (VT:0000470)stomach tumor susceptibility score (CMO:0002043)3328592928136884Rat
1358357Srcrtb1Stress Responsive Cort Basal QTL 16.360.002blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)3328592928136884Rat
8693641Alc30Alcohol consumption QTL 3020.739drinking behavior trait (VT:0001422)calculated ethanol drink intake rate (CMO:0001615)3565463925105730Rat
1558654Bw56Body weight QTL 564.50.0000171body mass (VT:0001259)body weight (CMO:0000012)3600074834394365Rat
6893355Bw101Body weight QTL 1010.40.38body mass (VT:0001259)body weight (CMO:0000012)3600074834394365Rat
6893363Bw105Body weight QTL 1052.60.0036body mass (VT:0001259)body weight (CMO:0000012)3600074834394365Rat
70191BpQTLcluster4Blood pressure QTL cluster 43arterial blood pressure trait (VT:2000000)absolute change in mean arterial blood pressure (CMO:0000533)3600074851687917Rat
70191BpQTLcluster4Blood pressure QTL cluster 43arterial blood pressure trait (VT:2000000)absolute change in systolic blood pressure (CMO:0000607)3600074851687917Rat
1558647Cm46Cardiac mass QTL 465.40.0000055heart mass (VT:0007028)heart wet weight (CMO:0000069)3600086634394121Rat
1558650Cm48Cardiac mass QTL 4840.0001heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)3600086634394121Rat
1558657Cm43Cardiac mass QTL 436.60.0000000293heart mass (VT:0007028)heart wet weight (CMO:0000069)3600086634394121Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:156
Count of miRNA genes:129
Interacting mature miRNAs:140
Transcripts:ENSRNOT00000065867
Prediction methods:Microtar, 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 3 34 51 35 19 35 1 4 72 30 41 11 1
Low 9 6 6 6 7 7 2 5 7
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000065867   ⟹   ENSRNOP00000059977
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl35,997,315 - 6,017,597 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000084491   ⟹   ENSRNOP00000073373
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl35,997,872 - 6,054,483 (-)Ensembl
RefSeq Acc Id: NM_001108575   ⟹   NP_001102045
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.035,997,315 - 6,017,597 (-)NCBI
Rnor_5.0311,356,155 - 11,415,329 (-)NCBI
RGSC_v3.436,369,903 - 6,390,116 (-)RGD
Celera35,569,850 - 5,590,130 (-)RGD
Sequence:
RefSeq Acc Id: XM_006233825   ⟹   XP_006233887
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.035,995,204 - 6,025,001 (-)NCBI
Rnor_5.0311,356,155 - 11,415,329 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006233826   ⟹   XP_006233888
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.035,995,204 - 6,054,467 (-)NCBI
Rnor_5.0311,356,155 - 11,415,329 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006233830   ⟹   XP_006233892
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.035,995,204 - 6,025,001 (-)NCBI
Rnor_5.0311,356,155 - 11,415,329 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017591876   ⟹   XP_017447365
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.035,995,204 - 6,024,721 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017591877   ⟹   XP_017447366
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.035,995,204 - 6,024,401 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017591878   ⟹   XP_017447367
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.035,995,204 - 6,019,943 (-)NCBI
Sequence:
Reference Sequences
RefSeq Acc Id: NP_001102045   ⟸   NM_001108575
- UniProtKB: D3ZWU1 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006233888   ⟸   XM_006233826
- Peptide Label: isoform X1
- UniProtKB: B5DF71 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006233892   ⟸   XM_006233830
- Peptide Label: isoform X2
- UniProtKB: D3ZWU1 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006233887   ⟸   XM_006233825
- Peptide Label: isoform X1
- UniProtKB: B5DF71 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_017447365   ⟸   XM_017591876
- Peptide Label: isoform X1
- UniProtKB: B5DF71 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_017447366   ⟸   XM_017591877
- Peptide Label: isoform X1
- UniProtKB: B5DF71 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_017447367   ⟸   XM_017591878
- Peptide Label: isoform X1
- UniProtKB: B5DF71 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000073373   ⟸   ENSRNOT00000084491
RefSeq Acc Id: ENSRNOP00000059977   ⟸   ENSRNOT00000065867
Protein Domains
Bromo   NET

Transcriptome

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

Promoters
RGD ID:13691926
Promoter ID:EPDNEW_R2451
Type:initiation region
Name:Brd3_1
Description:bromodomain containing 3
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_6.036,054,510 - 6,054,570EPDNEW

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)
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
LH/MavRrrc (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
LL/MavRrrc (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
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

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1308925 AgrOrtholog
Ensembl Genes ENSRNOG00000007681 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000059977 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOP00000073373 ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000065867 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOT00000084491 ENTREZGENE, UniProtKB/TrEMBL
Gene3D-CATH 1.20.1270.220 UniProtKB/TrEMBL
  1.20.920.10 UniProtKB/TrEMBL
InterPro Bromo_Brdt_I UniProtKB/TrEMBL
  Bromo_Brdt_II UniProtKB/TrEMBL
  Bromodomain UniProtKB/TrEMBL
  Bromodomain-like_sf UniProtKB/TrEMBL
  Bromodomain_CS UniProtKB/TrEMBL
  NET_dom UniProtKB/TrEMBL
  NET_sf UniProtKB/TrEMBL
KEGG Report rno:362092 UniProtKB/TrEMBL
NCBI Gene 362092 ENTREZGENE
Pfam BET UniProtKB/TrEMBL
  Bromodomain UniProtKB/TrEMBL
PhenoGen Brd3 PhenoGen
PRINTS BROMODOMAIN UniProtKB/TrEMBL
PROSITE BROMODOMAIN_1 UniProtKB/TrEMBL
  BROMODOMAIN_2 UniProtKB/TrEMBL
  NET UniProtKB/TrEMBL
SMART BROMO UniProtKB/TrEMBL
Superfamily-SCOP Bromodomain UniProtKB/TrEMBL
UniGene Rn.16796 ENTREZGENE
UniProt B5DF71 ENTREZGENE, UniProtKB/TrEMBL
  D3ZWU1 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2008-04-30 Brd3  bromodomain containing 3   Brd3_predicted  bromodomain containing 3 (predicted)  'predicted' is removed 2292626 APPROVED
2005-01-12 Brd3_predicted  bromodomain containing 3 (predicted)      Symbol and Name status set to approved 70820 APPROVED