Human Gene SMARCA2 (uc003zhd.3) Description and Page Index
  Description: Homo sapiens SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 2 (SMARCA2), transcript variant 2, mRNA.
RefSeq Summary (NM_139045): The protein encoded by this gene is a member of the SWI/SNF family of proteins and is highly similar to the brahma protein of Drosophila. Members of this family have helicase and ATPase activities and are thought to regulate transcription of certain genes by altering the chromatin structure around those genes. The encoded protein is part of the large ATP-dependent chromatin remodeling complex SNF/SWI, which is required for transcriptional activation of genes normally repressed by chromatin. Alternatively spliced transcript variants encoding different isoforms have been found for this gene, which contains a trinucleotide repeat (CAG) length polymorphism. [provided by RefSeq, Jan 2014].
Transcript (Including UTRs)
   Position: hg19 chr9:2,015,342-2,193,623 Size: 178,282 Total Exon Count: 33 Strand: +
Coding Region
   Position: hg19 chr9:2,029,023-2,192,739 Size: 163,717 Coding Exon Count: 32 

Page IndexSequence and LinksGenetic AssociationsMalaCardsCTDGene Alleles
RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesmRNA Descriptions
PathwaysOther NamesGeneReviewsModel InformationMethods
Data last updated: 2013-06-15

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr9:2,015,342-2,193,623)mRNA (may differ from genome)Protein (1572 aa)
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaBioGPS
CGAPEnsemblEntrez GeneExonPrimerGeneCardsGeneNetwork
H-INVHGNCLynxMGIOMIMPubMed
ReactomeStanford SOURCETreefamUniProtKBWikipedia

-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): SMARCA2
CDC HuGE Published Literature: SMARCA2
Positive Disease Associations: Angiography , Arteries , Body Fat Distribution , Body Weight Changes , Breath Tests , Cholesterol, HDL , Electrocardiography , Erythrocyte Count , Hand Strength , Myocardial Infarction , Stroke , Thyrotropin
Related Studies:
  1. Angiography
    Ramachandran S Vasan et al. BMC medical genetics 2007, Genome-wide association of echocardiographic dimensions, brachial artery endothelial function and treadmill exercise responses in the Framingham Heart Study., BMC medical genetics. [PubMed 17903301]
    In hypothesis-generating GWAS of echocardiography, ETT and BA vascular function in a moderate-sized community-based sample, we identified several SNPs that are candidates for replication attempts and we provide a web-based GWAS resource for the research community.
  2. Arteries
    , , . [PubMed 0]
  3. Body Fat Distribution
    , , . [PubMed 0]
           more ... click here to view the complete list

-  MalaCards Disease Associations
  MalaCards Gene Search: SMARCA2
Diseases sorted by gene-association score: nicolaides-baraitser syndrome* (1692), schimke immunoosseous dysplasia (12), alpha thalassemia-x-linked intellectual disability syndrome (12), gingival disease (10), enamel erosion (9), myoclonic astatic epilepsy (9), tooth erosion (8), epilepsy, familial temporal lobe, 1 (8), root caries (8), coffin-siris syndrome 1 (5), teeth hard tissue disease (5), thalassemias, alpha- (5), borjeson-forssman-lehmann syndrome (4), psychotic disorder (2), schizophrenia (2)
* = Manually curated disease association

-  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: 37.04 RPKM in Ovary
Total median expression: 973.33 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 -27.0099-0.273 Picture PostScript Text
3' UTR -209.90884-0.237 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
  Pfam Domains:
PF00176 - SNF2 family N-terminal domain
PF00271 - Helicase conserved C-terminal domain
PF00439 - Bromodomain
PF04851 - Type III restriction enzyme, res subunit
PF07529 - HSA
PF07533 - BRK domain
PF08880 - QLQ
PF14619 - Snf2-ATP coupling, chromatin remodelling complex

SCOP Domains:
47370 - Bromodomain
52540 - P-loop containing nucleoside triphosphate hydrolases

ModBase Predicted Comparative 3D Structure on P51531-2
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 BrowserGenome BrowserNo orthologGenome BrowserNo ortholog
Gene DetailsGene Details  Gene Details 
Gene SorterGene Sorter  Gene Sorter 
 RGDEnsembl WormBase 
 Protein SequenceProtein Sequence Protein Sequence 
 AlignmentAlignment Alignment 

-  Descriptions from all associated GenBank mRNAs
  BC068252 - Homo sapiens cDNA clone IMAGE:4822434, containing frame-shift errors.
AK296373 - Homo sapiens cDNA FLJ61591 partial cds, highly similar to Probable global transcription activator SNF2L2 (EC 3.6.1.-).
AK299683 - Homo sapiens cDNA FLJ53181 partial cds, highly similar to Probable global transcription activator SNF2L2 (EC 3.6.1.-).
LP955719 - Sequence 1 from Patent WO2017214373.
X72889 - H.sapiens hbrm mRNA.
D26155 - Homo sapiens mRNA for transcriptional activator hSNF2a, complete cds.
AB590966 - Synthetic construct DNA, clone: pFN21AE0797, Homo sapiens SMARCA2 gene for SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 2, without stop codon, in Flexi system.
BC156185 - Synthetic construct Homo sapiens clone IMAGE:100061549, MGC:190022 SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 2 (SMARCA2) mRNA, encodes complete protein.
AY293824 - Homo sapiens SMARCA2 mRNA, partial sequence.
BC040029 - Homo sapiens SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 2, mRNA (cDNA clone IMAGE:5752305), partial cds.
JD426550 - Sequence 407574 from Patent EP1572962.
JD103754 - Sequence 84778 from Patent EP1572962.
JD240986 - Sequence 222010 from Patent EP1572962.
JD059268 - Sequence 40292 from Patent EP1572962.
AK298045 - Homo sapiens cDNA FLJ61143 complete cds, highly similar to Probable global transcription activator SNF2L2 (EC 3.6.1.-).
AK300093 - Homo sapiens cDNA FLJ59976 complete cds, highly similar to Probable global transcription activator SNF2L2 (EC 3.6.1.-).
AK094076 - Homo sapiens cDNA FLJ36757 fis, clone UTERU2018522, highly similar to Human mRNA for transcriptional activator hSNF2a.
AX748443 - Sequence 1968 from Patent EP1308459.
AK308941 - Homo sapiens cDNA, FLJ98982.
BC066596 - Homo sapiens SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 2, mRNA (cDNA clone IMAGE:5753597), **** WARNING: chimeric clone ****.
KJ901751 - Synthetic construct Homo sapiens clone ccsbBroadEn_11145 SMARCA2 gene, encodes complete protein.
KR711126 - Synthetic construct Homo sapiens clone CCSBHm_00020556 SMARCA2 (SMARCA2) mRNA, encodes complete protein.
JD349737 - Sequence 330761 from Patent EP1572962.
JD287741 - Sequence 268765 from Patent EP1572962.
JD433328 - Sequence 414352 from Patent EP1572962.
JD563811 - Sequence 544835 from Patent EP1572962.
JD508823 - Sequence 489847 from Patent EP1572962.
JD246518 - Sequence 227542 from Patent EP1572962.

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

Protein P51531 (Reactome details) participates in the following event(s):

R-HSA-3215448 SWI/SNF chromatin remodelling complex enhances MEP50:PRMT5 methyltransferase activity
R-HSA-8938217 RUNX1 binds the SWI/SNF complex
R-HSA-3214858 RMTs methylate histone arginines
R-HSA-8939243 RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known
R-HSA-3247509 Chromatin modifying enzymes
R-HSA-8878171 Transcriptional regulation by RUNX1
R-HSA-4839726 Chromatin organization
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: BAF190B, BRM, NM_139045, NP_620614, P51531-2, SNF2A, SNF2L2
UCSC ID: uc003zhd.3
RefSeq Accession: NM_139045
Protein: P51531-2, splice isoform of P51531 CCDS: CCDS34977.1, CCDS34978.1

-  GeneReviews for This Gene
  GeneReviews article(s) related to gene SMARCA2:
nbs (Nicolaides-Baraitser Syndrome)

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_139045.2
exon count: 33CDS single in 3' UTR: no RNA size: 5703
ORF size: 4719CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 9325.50frame shift in genome: no % Coverage: 99.98
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.