Brd9 (bromodomain containing 9) - Rat Genome Database

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Gene: Brd9 (bromodomain containing 9) Rattus norvegicus
Analyze
Symbol: Brd9
Name: bromodomain containing 9
RGD ID: 1307359
Description: Predicted to enable histone reader activity. Predicted to be involved in regulation of transcription by RNA polymerase II. Predicted to be located in nucleoplasm. Predicted to be part of SWI/SNF complex. Predicted to be active in nucleus. Orthologous to human BRD9 (bromodomain containing 9); PARTICIPATES IN SWI/SNF family mediated chromatin remodeling pathway; INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; bisphenol A; DDT.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: bromodomain-containing protein 9; LOC308067
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: GRCr8 - GRCr8 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8131,158,546 - 31,185,812 (-)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl131,158,546 - 31,186,125 (-)EnsemblGRCr8
mRatBN7.2129,329,981 - 29,357,285 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl129,329,985 - 29,357,016 (-)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx129,131,492 - 29,158,404 (-)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.011,670,099 - 1,694,406 (-)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0129,332,117 - 29,359,032 (-)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0131,939,612 - 31,968,120 (-)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl131,939,585 - 31,967,915 (-)Ensemblrn6Rnor6.0
Rnor_5.0133,363,870 - 33,392,557 (-)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.4130,136,722 - 30,165,207 (-)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera127,979,163 - 28,005,985 (-)NCBICelera
RGSC_v3.1130,139,668 - 30,168,125 (-)NCBI
Cytogenetic Map1p11NCBI
JBrowse:




Disease Annotations     Click to see Annotation Detail View

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component
nucleoplasm  (IEA,ISO)
nucleus  (IBA,IEA,ISO)
site of double-strand break  (IEA,ISO)
SWI/SNF complex  (IEA,ISO)

Molecular Function

Molecular Pathway Annotations     Click to see Annotation Detail View
References

References - curated
# Reference Title Reference Citation
1. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
2. ATP-dependent chromatin remodeling: genetics, genomics and mechanisms. Hargreaves DC and Crabtree GR, Cell Res. 2011 Mar;21(3):396-420. doi: 10.1038/cr.2011.32. Epub 2011 Mar 1.
3. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
4. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
5. Comprehensive gene review and curation RGD comprehensive gene curation
Additional References at PubMed
PMID:22464331   PMID:29374058   PMID:36801999  


Genomics

Comparative Map Data
Brd9
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8131,158,546 - 31,185,812 (-)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl131,158,546 - 31,186,125 (-)EnsemblGRCr8
mRatBN7.2129,329,981 - 29,357,285 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl129,329,985 - 29,357,016 (-)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx129,131,492 - 29,158,404 (-)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.011,670,099 - 1,694,406 (-)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0129,332,117 - 29,359,032 (-)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0131,939,612 - 31,968,120 (-)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl131,939,585 - 31,967,915 (-)Ensemblrn6Rnor6.0
Rnor_5.0133,363,870 - 33,392,557 (-)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.4130,136,722 - 30,165,207 (-)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera127,979,163 - 28,005,985 (-)NCBICelera
RGSC_v3.1130,139,668 - 30,168,125 (-)NCBI
Cytogenetic Map1p11NCBI
BRD9
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh385863,741 - 892,801 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl5850,291 - 892,838 (-)Ensemblhg38GRCh38
GRCh375863,856 - 892,916 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 365916,856 - 945,915 (-)NCBIBuild 36Build 36hg18NCBI36
Build 345916,855 - 945,915NCBI
Celera5905,000 - 934,089 (-)NCBICelera
Cytogenetic Map5p15.33NCBI
HuRef5849,539 - 878,480 (-)NCBIHuRef
CHM1_15863,562 - 892,651 (-)NCBICHM1_1
T2T-CHM13v2.05769,793 - 798,853 (-)NCBIT2T-CHM13v2.0
Brd9
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391374,085,920 - 74,109,014 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1374,085,930 - 74,109,014 (+)EnsemblGRCm39 EnsemblGRCm39
GRCm381373,937,801 - 73,960,895 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1373,937,811 - 73,960,895 (+)Ensemblmm10GRCm38
MGSCv371374,075,286 - 74,098,343 (+)NCBIMGSCv37MGSCv37mm9NCBIm37
MGSCv361374,403,882 - 74,426,891 (+)NCBIMGSCv36mm8
Celera1376,267,420 - 76,290,477 (+)NCBICelera
Cytogenetic Map13C1NCBI
cM Map1340.15NCBI
Brd9
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_004955504415,904 - 434,142 (-)Ensembl
ChiLan1.0NW_004955504416,145 - 434,132 (-)NCBIChiLan1.0ChiLan1.0
LOC106634368
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v21101,224,044 - 101,256,647 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan11100,811,456 - 100,845,295 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v01123,920,801 - 123,953,480 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
BRD9
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.13411,541,005 - 11,564,760 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl3411,540,481 - 11,564,536 (+)EnsemblcanFam3CanFam3.1
Dog10K_Boxer_Tasha3416,050,294 - 16,079,372 (+)NCBIDog10K_Boxer_TashaDog10K_Boxer_Tasha
ROS_Cfam_1.03411,441,128 - 11,470,285 (+)NCBIROS_Cfam_1.0ROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl3411,441,122 - 11,470,245 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.13411,491,827 - 11,520,832 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.03411,471,570 - 11,500,766 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.03411,682,516 - 11,711,639 (+)NCBIUU_Cfam_GSD_1.0UU_Cfam_GSD_1.0
LOC101956427
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024407213244,582,573 - 244,602,686 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_004936815748,274 - 763,480 (+)EnsemblSpeTri2.0 Ensembl
SpeTri2.0NW_004936815748,112 - 763,971 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
BRD9
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1679,473,745 - 79,492,635 (+)EnsemblsusScr11Sscrofa11.1
Sscrofa11.11679,473,750 - 79,492,638 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
BRD9
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.14711,862 - 737,174 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl4711,375 - 737,094 (-)EnsemblChlSab1.1 EnsemblchlSab2Vervet-AGM
Vero_WHO_p1.0NW_02366605435,262,826 - 35,288,600 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Brd9
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_004624751421,154 - 439,544 (-)EnsemblHetGla_female_1.0 EnsemblhetGla2HetGla_female_1.0 Ensembl
HetGla 1.0NW_004624751421,945 - 439,146 (-)NCBIHetGla 1.0HetGla 1.0hetGla2

Variants

.
Variants in Brd9
99 total Variants
miRNA Target Status (No longer updated)

Predicted Target Of
Summary Value
Count of predictions:357
Count of miRNA genes:218
Interacting mature miRNAs:252
Transcripts:ENSRNOT00000021000
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.


QTLs in Region (GRCr8)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
631688Hcas2Hepatocarcinoma susceptibility QTL 230.0001liver integrity trait (VT:0010547)liver tumorous lesion number (CMO:0001068)1774611852746118Rat
1357397Bw41Body weight QTL 414.190.0001body mass (VT:0001259)body weight (CMO:0000012)12940927974409279Rat
2313090Bmd69Bone mineral density QTL 694.40.0001tibia mineral mass (VT:1000283)compact volumetric bone mineral density (CMO:0001730)1529322934184556Rat
4889451Eae29Experimental allergic encephalomyelitis QTL 295.51nervous system integrity trait (VT:0010566)experimental autoimmune encephalomyelitis severity score (CMO:0001419)1774612152746121Rat
70179Xhs2X-ray hypersensitivity QTL 23.2intestine integrity trait (VT:0010554)post-insult time to onset of moribundity (CMO:0001896)1143965634Rat
1558642Prcr2Prostate cancer resistance QTL 24.3prostate integrity trait (VT:0010571)area of ventral prostate occupied by tumorous lesions to total ventral prostate area ratio (CMO:0000899)11037949255379492Rat
7421626Bp360Blood pressure QTL 3600.001arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)1694102251941022Rat
1357401Bw43Body weight QTL 433.75body mass (VT:0001259)body weight (CMO:0000012)1690935351909353Rat
2313070Bss52Bone structure and strength QTL 524.40.0001body length (VT:0001256)body length (CMO:0000013)1529322934184556Rat
631494Bp95Blood pressure QTL 95400.0001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)11731537851816258Rat
5684998Bss101Bone structure and strength QTL 1013.6tibia strength trait (VT:1000284)tibia ultimate force (CMO:0001734)1690935351909353Rat
5684999Bss102Bone structure and strength QTL 1025.57e-07tibia strength trait (VT:1000284)tibia stiffness (CMO:0001735)1690935351909353Rat
2302038Pia31Pristane induced arthritis QTL 315.50.001blood autoantibody amount (VT:0003725)serum immunoglobulin M-type rheumatoid factor level relative to an arbitrary reference serum (CMO:0002111)11282049457820494Rat
634353Rends2Renal damage susceptibility QTL 20.05kidney blood vessel morphology trait (VT:0000530)organ lesion measurement (CMO:0000677)12065642065656420Rat
2317755Glom22Glomerulus QTL 223.8urine protein amount (VT:0005160)urine protein level (CMO:0000591)1134184556Rat
1578756Iddm22Insulin dependent diabetes mellitus QTL 222.7blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)12050832665508326Rat
1331785Rf27Renal function QTL 274.643urine sodium amount (VT:0006274)urine sodium level (CMO:0000129)13070837587558729Rat
631508Sald1Serum aldosterone level QTL 13.7blood aldosterone amount (VT:0005346)serum aldosterone level (CMO:0000487)11168446456684464Rat
2313053Bss51Bone structure and strength QTL 513.80.0001tibia length (VT:0004357)tibia length (CMO:0000450)1529322934184556Rat


Expression

RNA-SEQ Expression

alimentary part of gastrointestinal system
appendage
circulatory system
ectoderm
endocrine system
endoderm
exocrine system
hemolymphoid system
hepatobiliary system
integumental system
mesenchyme
mesoderm
musculoskeletal system
nervous system
renal system
reproductive system
respiratory system
sensory system
visual system
16 12 67 165 91 90 59 92 59 6 356 192 11 144 81 92 31 17 17

Sequence


Ensembl Acc Id: ENSRNOT00000021000   ⟹   ENSRNOP00000021000
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl131,158,546 - 31,186,125 (-)Ensembl
mRatBN7.2 Ensembl129,329,985 - 29,357,016 (-)Ensembl
Rnor_6.0 Ensembl131,939,585 - 31,967,915 (-)Ensembl
Ensembl Acc Id: ENSRNOT00000097920   ⟹   ENSRNOP00000087025
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl129,330,147 - 29,356,666 (-)Ensembl
RefSeq Acc Id: NM_001395085   ⟹   NP_001382014
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8131,158,546 - 31,185,581 (-)NCBI
mRatBN7.2129,329,981 - 29,357,021 (-)NCBI
RefSeq Acc Id: NM_001395087   ⟹   NP_001382016
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8131,158,546 - 31,185,581 (-)NCBI
mRatBN7.2129,329,981 - 29,357,021 (-)NCBI
RefSeq Acc Id: NM_001395088   ⟹   NP_001382017
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8131,158,546 - 31,185,581 (-)NCBI
mRatBN7.2129,329,981 - 29,357,021 (-)NCBI
RefSeq Acc Id: NM_001395089   ⟹   NP_001382018
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8131,158,546 - 31,185,581 (-)NCBI
mRatBN7.2129,329,981 - 29,357,021 (-)NCBI
RefSeq Acc Id: NM_001395090   ⟹   NP_001382019
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8131,158,546 - 31,185,581 (-)NCBI
mRatBN7.2129,329,981 - 29,357,021 (-)NCBI
RefSeq Acc Id: XM_006227787   ⟹   XP_006227849
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8131,158,546 - 31,185,812 (-)NCBI
mRatBN7.2129,329,987 - 29,357,285 (-)NCBI
Rnor_6.0131,939,619 - 31,968,120 (-)NCBI
Rnor_5.0133,363,870 - 33,392,557 (-)NCBI
Sequence:
RefSeq Acc Id: XP_006227849   ⟸   XM_006227787
- Peptide Label: isoform X1
- UniProtKB: A6JUV9 (UniProtKB/TrEMBL)
- Sequence:
Ensembl Acc Id: ENSRNOP00000021000   ⟸   ENSRNOT00000021000
Ensembl Acc Id: ENSRNOP00000087025   ⟸   ENSRNOT00000097920
RefSeq Acc Id: NP_001382017   ⟸   NM_001395088
- Peptide Label: isoform 3
- UniProtKB: A6JUV9 (UniProtKB/TrEMBL)
RefSeq Acc Id: NP_001382019   ⟸   NM_001395090
- Peptide Label: isoform 5
RefSeq Acc Id: NP_001382018   ⟸   NM_001395089
- Peptide Label: isoform 4
RefSeq Acc Id: NP_001382014   ⟸   NM_001395085
- Peptide Label: isoform 2
- UniProtKB: A6JUV9 (UniProtKB/TrEMBL)
RefSeq Acc Id: NP_001382016   ⟸   NM_001395087
- Peptide Label: isoform 1
- UniProtKB: D4ACF5 (UniProtKB/TrEMBL),   A6JUW0 (UniProtKB/TrEMBL)
Protein Domains
Bromo

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-D4ACF5-F1-model_v2 AlphaFold D4ACF5 1-597 view protein structure

Transcriptome

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

Promoters
RGD ID:13689563
Promoter ID:EPDNEW_R87
Type:multiple initiation site
Name:Brd9_1
Description:bromodomain containing 9
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_6.0131,967,842 - 31,967,902EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1307359 AgrOrtholog
BioCyc Gene G2FUF-61935 BioCyc
Ensembl Genes ENSRNOG00000015676 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000021000 ENTREZGENE
  ENSRNOT00000021000.9 UniProtKB/TrEMBL
Gene3D-CATH 1.20.920.10 UniProtKB/TrEMBL
InterPro Bromodomain UniProtKB/TrEMBL
  Bromodomain-like_sf UniProtKB/TrEMBL
  Bromodomain_contain_prot UniProtKB/TrEMBL
  DUF3512 UniProtKB/TrEMBL
NCBI Gene 308067 ENTREZGENE
PANTHER BROMODOMAIN CONTAINING PROTEIN UniProtKB/TrEMBL
  BROMODOMAIN-CONTAINING PROTEIN 9 UniProtKB/TrEMBL
Pfam Bromodomain UniProtKB/TrEMBL
  DUF3512 UniProtKB/TrEMBL
PhenoGen Brd9 PhenoGen
PRINTS BROMODOMAIN UniProtKB/TrEMBL
PROSITE BROMODOMAIN_2 UniProtKB/TrEMBL
RatGTEx ENSRNOG00000015676 RatGTEx
SMART BROMO UniProtKB/TrEMBL
Superfamily-SCOP Bromodomain UniProtKB/TrEMBL
UniProt A6JUV9 ENTREZGENE, UniProtKB/TrEMBL
  A6JUW0 ENTREZGENE, UniProtKB/TrEMBL
  D4ACF5 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2008-04-30 Brd9  bromodomain containing 9   Brd9_predicted  bromodomain containing 9 (predicted)  'predicted' is removed 2292626 APPROVED
2005-01-12 Brd9_predicted  bromodomain containing 9 (predicted)      Symbol and Name status set to approved 70820 APPROVED