Human Gene BRD2 (uc021ywf.1) Description and Page Index
  Description: Homo sapiens bromodomain containing 2 (BRD2), transcript variant 4, mRNA.
RefSeq Summary (NM_001199456): This gene encodes a transcriptional regulator that belongs to the BET (bromodomains and extra terminal domain) family of proteins. This protein associates with transcription complexes and with acetylated chromatin during mitosis, and it selectively binds to the acetylated lysine-12 residue of histone H4 via its two bromodomains. The gene maps to the major histocompatability complex (MHC) class II region on chromosome 6p21.3, but sequence comparison suggests that the protein is not involved in the immune response. This gene has been implicated in juvenile myoclonic epilepsy, a common form of epilepsy that becomes apparent in adolescence. Multiple alternatively spliced variants have been described for this gene. [provided by RefSeq, Dec 2010].
Transcript (Including UTRs)
   Position: hg19 chr6:32,940,861-32,949,282 Size: 8,422 Total Exon Count: 12 Strand: +
Coding Region
   Position: hg19 chr6:32,942,351-32,948,495 Size: 6,145 Coding Exon Count: 11 

Page IndexSequence and LinksUniProtKB CommentsGenetic AssociationsMalaCardsCTD
Gene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther Species
GO AnnotationsmRNA DescriptionsPathwaysOther NamesModel InformationMethods
Data last updated: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr6:32,940,861-32,949,282)mRNA (may differ from genome)Protein (754 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
BioGPSCGAPEnsemblEntrez GeneExonPrimerGeneCards
H-INVHGNCLynxMGIneXtProtOMIM
PubMedReactomeStanford SOURCEUniProtKBWikipedia

-  Comments and Description Text from UniProtKB
  ID: BRD2_HUMAN
DESCRIPTION: RecName: Full=Bromodomain-containing protein 2; AltName: Full=O27.1.1; AltName: Full=Really interesting new gene 3 protein;
FUNCTION: May play a role in spermatogenesis or folliculogenesis (By similarity). Binds hyperacetylated chromatin and plays a role in the regulation of transcription, probably by chromatin remodeling. Regulates transcription of the CCND1 gene. Plays a role in nucleosome assembly.
SUBUNIT: Homodimer. Interacts with E2F1 and with histone H4 acetylated at 'Lys-13'.
SUBCELLULAR LOCATION: Nucleus (Probable). Note=Detected on chromatin and nucleosomes.
DOMAIN: One bromodomain is sufficient for a partial interaction with histone H4 acetylated at 'Lys-13'.
SIMILARITY: Contains 2 bromo domains.
SIMILARITY: Contains 1 NET domain.
SEQUENCE CAUTION: Sequence=AAA68890.1; Type=Erroneous initiation;

-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): BRD2
CDC HuGE Published Literature: BRD2
Positive Disease Associations: Asthma , Heart Rate , photoparoxysmal response , Triglycerides
Related Studies:
  1. Asthma
    Tomomitsu Hirota et al. Nature genetics 2011, Genome-wide association study identifies three new susceptibility loci for adult asthma in the Japanese population., Nature genetics. [PubMed 21804548]
  2. Heart Rate
    , , . [PubMed 0]
  3. photoparoxysmal response
    Lorenz, S. et al. 2006, Association of BRD2 polymorphisms with photoparoxysmal response, Neurosci Lett 2006. [PubMed 16516380]
           more ... click here to view the complete list

-  MalaCards Disease Associations
  MalaCards Gene Search: BRD2
Diseases sorted by gene-association score: epilepsy, generalized, with febrile seizures plus, type 5 (4), prolapse of female genital organ (2), enterocele (2), diverticulitis of colon (1)

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene           more ... click here to view the complete list

+  Common Gene Haplotype Alleles
  Press "+" in the title bar above to open this section.

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 79.27 RPKM in Testis
Total median expression: 2448.63 RPKM



View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
  Press "+" in the title bar above to open this section.

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -65.00158-0.411 Picture PostScript Text
3' UTR -276.38787-0.351 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  InterPro Domains: Graphical view of domain structure
IPR001487 - Bromodomain
IPR018359 - Bromodomain_CS

Pfam Domains:
PF00439 - Bromodomain
PF17035 - Bromodomain extra-terminal - transcription regulation

SCOP Domains:
47370 - Bromodomain

Protein Data Bank (PDB) 3-D Structure
MuPIT help

1X0J
- X-ray MuPIT

2DVQ
- X-ray MuPIT

2DVR
- X-ray MuPIT
To conserve bandwidth, only the images from the first 3 structures are shown.
2DVS - X-ray MuPIT 2DVV - X-ray MuPIT 2E3K - X-ray MuPIT
2G4A - NMR MuPIT 2YDW - X-ray MuPIT 2YEK - X-ray MuPIT
3AQA - X-ray MuPIT 3ONI - X-ray MuPIT 4A9E - X-ray MuPIT
4A9F - X-ray MuPIT 4A9H - X-ray MuPIT 4A9I - X-ray MuPIT
4A9J - X-ray MuPIT 4A9M - X-ray MuPIT 4A9N - X-ray MuPIT
4A9O - X-ray MuPIT 4AKN - X-ray MuPIT 4ALG - X-ray MuPIT
4ALH - X-ray MuPIT


ModBase Predicted Comparative 3D Structure on P25440
FrontTopSide
The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
No orthologGenome BrowserNo orthologNo orthologNo orthologNo ortholog
Gene DetailsGene Details    
Gene SorterGene Sorter    
 RGD    
 Protein Sequence    
 Alignment    

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0003682 chromatin binding
GO:0005515 protein binding
GO:0070577 lysine-acetylated histone binding

Biological Process:
GO:0006325 chromatin organization
GO:0006334 nucleosome assembly
GO:0006351 transcription, DNA-templated
GO:0006355 regulation of transcription, DNA-templated
GO:0006357 regulation of transcription from RNA polymerase II promoter
GO:0007283 spermatogenesis

Cellular Component:
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0005737 cytoplasm
GO:0016607 nuclear speck


-  Descriptions from all associated GenBank mRNAs
  D42040 - Homo sapiens KIAA9001 mRNA, complete cds.
BX648109 - Homo sapiens mRNA; cDNA DKFZp686E1432 (from clone DKFZp686E1432).
AK056504 - Homo sapiens cDNA FLJ31942 fis, clone NT2RP7006717, highly similar to Mus musculus Ring3 mRNA.
AL832722 - Homo sapiens mRNA; cDNA DKFZp313H139 (from clone DKFZp313H139).
M80613 - Human homolog of Drosophila female sterile homeotic mRNA, complete cds.
X62083 - H.sapiens mRNA for Drosophila female sterile homeotic (FSH) homologue.
BC007715 - Homo sapiens bromodomain containing 2, mRNA (cDNA clone IMAGE:4302993), partial cds.
BC001885 - Homo sapiens bromodomain containing 2, mRNA (cDNA clone IMAGE:3544244), with apparent retained intron.
BC000477 - Homo sapiens bromodomain containing 2, mRNA (cDNA clone IMAGE:2961647).
BC063840 - Homo sapiens bromodomain containing 2, mRNA (cDNA clone MGC:74927 IMAGE:6181728), complete cds.
AB384868 - Synthetic construct DNA, clone: pF1KB3863, Homo sapiens BRD2 gene for bromodomain-containing protein 2, complete cds, without stop codon, in Flexi system.
BX647233 - Homo sapiens mRNA; cDNA DKFZp686N0336 (from clone DKFZp686N0336).
S78771 - NAT=CpG island-associated gene [human, mRNA, 1741 nt].
AK024312 - Homo sapiens cDNA FLJ14250 fis, clone OVARC1001244, highly similar to H.sapiens mRNA for Drosophila female sterile homeotic (FSH) homologue.
JD197345 - Sequence 178369 from Patent EP1572962.
JD404005 - Sequence 385029 from Patent EP1572962.
JD389260 - Sequence 370284 from Patent EP1572962.
JD132469 - Sequence 113493 from Patent EP1572962.
JD205027 - Sequence 186051 from Patent EP1572962.
JD438748 - Sequence 419772 from Patent EP1572962.
JD092769 - Sequence 73793 from Patent EP1572962.
JD278908 - Sequence 259932 from Patent EP1572962.
JD475169 - Sequence 456193 from Patent EP1572962.
JD357581 - Sequence 338605 from Patent EP1572962.
JD393830 - Sequence 374854 from Patent EP1572962.
JD490179 - Sequence 471203 from Patent EP1572962.
JD124295 - Sequence 105319 from Patent EP1572962.
JD359059 - Sequence 340083 from Patent EP1572962.

-  Biochemical and Signaling Pathways
  Reactome (by CSHL, EBI, and GO)

Protein P25440 (Reactome details) participates in the following event(s):

R-HSA-8951977 Acetylated RUNX3 binds to BRD2
R-HSA-8952069 HDAC4 deacetylates RUNX3
R-HSA-8952058 CCND1 binds RUNX3 and displaces EP300
R-HSA-8952062 CCND1 recruits HDAC4 to RUNX3
R-HSA-8952081 RUNX proteins bind the p14-ARF promoter at the CDKN2A locus
R-HSA-8951936 RUNX3 regulates p14-ARF
R-HSA-8878159 Transcriptional regulation by RUNX3
R-HSA-212436 Generic Transcription Pathway
R-HSA-73857 RNA Polymerase II Transcription
R-HSA-74160 Gene expression (Transcription)

-  Other Names for This Gene
  Alternate Gene Symbols: A2AAU0, B0S7P0, B1AZT1, BRD2_HUMAN, KIAA9001, NM_001199456, NP_001186385, O00699, O00700, P25440, Q15310, Q5STC9, Q6P3U2, Q969U4, RING3
UCSC ID: uc021ywf.1
RefSeq Accession: NM_001199456
Protein: P25440 (aka BRD2_HUMAN)
CCDS: CCDS56421.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_001199456.1
exon count: 12CDS single in 3' UTR: no RNA size: 3210
ORF size: 2265CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 4635.00frame shift in genome: no % Coverage: 100.00
has start codon: yes stop codon in genome: no # of Alignments: 7
has end codon: yes retained intron: no # AT/AC introns 0
selenocysteine: no end bleed into intron: 0# strange splices: 0
Click here for a detailed description of the fields of the table above.

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.