Human Gene BRD9 (uc003jbq.3)
  Description: Homo sapiens bromodomain containing 9 (BRD9), transcript variant 1, mRNA.
Transcript (Including UTRs)
   Position: hg19 chr5:863,850-892,939 Size: 29,090 Total Exon Count: 16 Strand: -
Coding Region
   Position: hg19 chr5:864,583-892,772 Size: 28,190 Coding Exon Count: 16 

Page IndexSequence and LinksUniProtKB CommentsPrimersGenetic AssociationsCTD
Gene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther Species
GO AnnotationsmRNA DescriptionsOther NamesModel InformationMethods
Data last updated at UCSC: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr5:863,850-892,939)mRNA (may differ from genome)Protein (597 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
GeneNetworkH-INVHGNCHPRDLynxMGI
neXtProtOMIMPubMedUniProtKBBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: BRD9_HUMAN
DESCRIPTION: RecName: Full=Bromodomain-containing protein 9; AltName: Full=Rhabdomyosarcoma antigen MU-RMS-40.8;
FUNCTION: May play a role in chromatin remodeling and regulation of transcription.
SUBUNIT: Binds acetylated histone H3 (in vitro).
DOMAIN: Bromo domains mediate interaction with histones that have acetylated lysine residues at specific positions.
SIMILARITY: Contains 1 bromo domain.
SEQUENCE CAUTION: Sequence=BAB15565.1; Type=Erroneous initiation;

-  Primer design for this transcript
 

Primer3Plus can design qPCR Primers that straddle exon-exon-junctions, which amplify only cDNA, not genomic DNA.
Click here to load the transcript sequence and exon structure into Primer3Plus

Exonprimer can design one pair of Sanger sequencing primers around every exon, located in non-genic sequence.
Click here to open Exonprimer with this transcript

To design primers for a non-coding sequence, zoom to a region of interest and select from the drop-down menu: View > In External Tools > Primer3


-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): BRD9
CDC HuGE Published Literature: BRD9

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene

+  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: 19.28 RPKM in Testis
Total median expression: 496.51 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 -95.20167-0.570 Picture PostScript Text
3' UTR -288.52733-0.394 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
IPR021900 - DUF3512

Pfam Domains:
PF00439 - Bromodomain
PF12024 - Domain of unknown function (DUF3512)

SCOP Domains:
47370 - Bromodomain

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


ModBase Predicted Comparative 3D Structure on Q9H8M2
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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 orthologNo orthologGenome BrowserNo orthologNo orthologNo ortholog
Gene Details     
Gene Sorter     
  Ensembl   
  Protein Sequence   
  Alignment   

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0003676 nucleic acid binding
GO:0005515 protein binding
GO:0070577 lysine-acetylated histone binding

Biological Process:
GO:0006325 chromatin organization
GO:0006351 transcription, DNA-templated
GO:0006355 regulation of transcription, DNA-templated
GO:0008150 biological_process

Cellular Component:
GO:0005575 cellular_component


-  Descriptions from all associated GenBank mRNAs
  LF384935 - JP 2014500723-A/192438: Polycomb-Associated Non-Coding RNAs.
AK125518 - Homo sapiens cDNA FLJ43530 fis, clone PLACE6020145.
AY358630 - Homo sapiens clone DNA119537 LAVS3040 (UNQ3040) mRNA, complete cds.
AK026830 - Homo sapiens cDNA: FLJ23177 fis, clone LNG10649.
DQ248311 - Homo sapiens rhabdomyosarcoma antigen MU-RMS-40.8 mRNA, partial cds, alternatively spliced.
AK024392 - Homo sapiens cDNA FLJ14330 fis, clone PLACE4000261, weakly similar to PEREGRIN.
BC041590 - Homo sapiens bromodomain containing 9, mRNA (cDNA clone MGC:52166 IMAGE:5428011), complete cds.
BC007217 - Homo sapiens cDNA clone IMAGE:2958041.
AK023503 - Homo sapiens cDNA FLJ13441 fis, clone PLACE1002775, weakly similar to PEREGRIN.
BX648703 - Homo sapiens mRNA; cDNA DKFZp686L0539 (from clone DKFZp686L0539).
LF332010 - JP 2014500723-A/139513: Polycomb-Associated Non-Coding RNAs.
JD137175 - Sequence 118199 from Patent EP1572962.
JD216464 - Sequence 197488 from Patent EP1572962.
JD487866 - Sequence 468890 from Patent EP1572962.
JD063751 - Sequence 44775 from Patent EP1572962.
JD109252 - Sequence 90276 from Patent EP1572962.
JD223879 - Sequence 204903 from Patent EP1572962.
JD497226 - Sequence 478250 from Patent EP1572962.
AK297573 - Homo sapiens cDNA FLJ58589 complete cds, highly similar to Bromodomain-containing protein 9.
JD076827 - Sequence 57851 from Patent EP1572962.
JD080185 - Sequence 61209 from Patent EP1572962.
JD044875 - Sequence 25899 from Patent EP1572962.
AK299157 - Homo sapiens cDNA FLJ58253 complete cds, highly similar to Bromodomain-containing protein 9.
JD080184 - Sequence 61208 from Patent EP1572962.
JD063628 - Sequence 44652 from Patent EP1572962.
JD056533 - Sequence 37557 from Patent EP1572962.
EU446522 - Synthetic construct Homo sapiens clone IMAGE:100069803; IMAGE:100011731; FLH257040.01L bromodomain containing 9 (BRD9) gene, encodes complete protein.
LF332009 - JP 2014500723-A/139512: Polycomb-Associated Non-Coding RNAs.
JD371131 - Sequence 352155 from Patent EP1572962.
AL833925 - Homo sapiens mRNA; cDNA DKFZp434D0711 (from clone DKFZp434D0711).
AK301987 - Homo sapiens cDNA FLJ61450 complete cds, highly similar to Bromodomain-containing protein 9.
CU692000 - Synthetic construct Homo sapiens gateway clone IMAGE:100022500 5' read BRD9 mRNA.
JD411760 - Sequence 392784 from Patent EP1572962.
JD173325 - Sequence 154349 from Patent EP1572962.
JD080007 - Sequence 61031 from Patent EP1572962.
JD418344 - Sequence 399368 from Patent EP1572962.
JD435885 - Sequence 416909 from Patent EP1572962.
JD100643 - Sequence 81667 from Patent EP1572962.
JD162756 - Sequence 143780 from Patent EP1572962.
AY211916 - Homo sapiens sarcoma antigen NY-SAR-29 mRNA, partial cds.
LF332004 - JP 2014500723-A/139507: Polycomb-Associated Non-Coding RNAs.
LF332003 - JP 2014500723-A/139506: Polycomb-Associated Non-Coding RNAs.
LF332002 - JP 2014500723-A/139505: Polycomb-Associated Non-Coding RNAs.
LF332001 - JP 2014500723-A/139504: Polycomb-Associated Non-Coding RNAs.
JD111895 - Sequence 92919 from Patent EP1572962.
MA620512 - JP 2018138019-A/192438: Polycomb-Associated Non-Coding RNAs.
MA567587 - JP 2018138019-A/139513: Polycomb-Associated Non-Coding RNAs.
MA567586 - JP 2018138019-A/139512: Polycomb-Associated Non-Coding RNAs.
MA567581 - JP 2018138019-A/139507: Polycomb-Associated Non-Coding RNAs.
MA567580 - JP 2018138019-A/139506: Polycomb-Associated Non-Coding RNAs.
MA567579 - JP 2018138019-A/139505: Polycomb-Associated Non-Coding RNAs.
MA567578 - JP 2018138019-A/139504: Polycomb-Associated Non-Coding RNAs.

-  Other Names for This Gene
  Alternate Gene Symbols: A6NFY8, B4DMQ2, B4DR93, BRD9_HUMAN, NM_023924, NP_076413, Q2XUS1, Q6UWU9, Q8IUS4, Q9H5Q5, Q9H7R9, Q9H8M2, UNQ3040/PRO9856
UCSC ID: uc003jbq.3
RefSeq Accession: NM_023924
Protein: Q9H8M2 (aka BRD9_HUMAN)
CCDS: CCDS34127.2

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_023924.4
exon count: 16CDS single in 3' UTR: no RNA size: 2699
ORF size: 1794CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 3788.00frame shift in genome: no % Coverage: 99.81
has start codon: yes stop codon in genome: no # of Alignments: 1
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.