Human Gene SMARCA2 (uc003zhc.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 1, mRNA.
RefSeq Summary (NM_003070): 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: 34 Strand: +
Coding Region
   Position: hg19 chr9:2,029,023-2,192,739 Size: 163,717 Coding Exon Count: 33 

Page IndexSequence and LinksUniProtKB CommentsGenetic AssociationsMalaCardsCTD
Gene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther Species
GO AnnotationsmRNA DescriptionsPathwaysOther NamesGeneReviewsModel Information
Methods
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 (1590 aa)
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaBioGPS
CGAPEnsemblEntrez GeneExonPrimerGeneCardsGeneNetwork
H-INVHGNCHPRDLynxMGIneXtProt
OMIMPubMedReactomeStanford SOURCETreefamUniProtKB
Wikipedia

-  Comments and Description Text from UniProtKB
  ID: SMCA2_HUMAN
DESCRIPTION: RecName: Full=Probable global transcription activator SNF2L2; EC=3.6.4.-; AltName: Full=ATP-dependent helicase SMARCA2; AltName: Full=BRG1-associated factor 190B; Short=BAF190B; AltName: Full=Protein brahma homolog; Short=hBRM; AltName: Full=SNF2-alpha; AltName: Full=SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A member 2;
FUNCTION: Transcriptional coactivator cooperating with nuclear hormone receptors to potentiate transcriptional activation. Also involved in vitamin D-coupled transcription regulation via its association with the WINAC complex, a chromatin-remodeling complex recruited by vitamin D receptor (VDR), which is required for the ligand-bound VDR-mediated transrepression of the CYP27B1 gene. Belongs to the neural progenitors-specific chromatin remodeling complex (npBAF complex) and the neuron-specific chromatin remodeling complex (nBAF complex). During neural development a switch from a stem/progenitor to a post-mitotic chromatin remodeling mechanism occurs as neurons exit the cell cycle and become committed to their adult state. The transition from proliferating neural stem/progenitor cells to post-mitotic neurons requires a switch in subunit composition of the npBAF and nBAF complexes. As neural progenitors exit mitosis and differentiate into neurons, npBAF complexes which contain ACTL6A/BAF53A and PHF10/BAF45A, are exchanged for homologous alternative ACTL6B/BAF53B and DPF1/BAF45B or DPF3/BAF45C subunits in neuron- specific complexes (nBAF). The npBAF complex is essential for the self-renewal/proliferative capacity of the multipotent neural stem cells. The nBAF complex along with CREST plays a role regulating the activity of genes essential for dendrite growth (By similarity).
SUBUNIT: Component of the BAF complex, which includes at least actin (ACTB), ARID1A, ARID1B/BAF250, SMARCA2, SMARCA4/BRG1/BAF190A, ACTL6A/BAF53, ACTL6B/BAF53B, SMARCE1/BAF57, SMARCC1/BAF155, SMARCC2/BAF170, SMARCB1/SNF5/INI1, and one or more of SMARCD1/BAF60A, SMARCD2/BAF60B, or SMARCD3/BAF60C. In muscle cells, the BAF complex also contains DPF3. Component of the WINAC complex, at least composed of SMARCA2, SMARCA4, SMARCB1, SMARCC1, SMARCC2, SMARCD1, SMARCE1, ACTL6A, BAZ1B/WSTF, ARID1A, SUPT16H, CHAF1A and TOP2B. Binds TOPBP1. Component of neural progenitors- specific chromatin remodeling complex (npBAF complex) composed of at least, ARID1A/BAF250A or ARID1B/BAF250B, SMARCD1/BAF60A, SMARCD3/BAF60C, SMARCA2/BRM/BAF190B, SMARCA4/BRG1/BAF190A, SMARCB1/BAF47, SMARCC1/BAF155, SMARCE1/BAF57, SMARCC2/BAF170, PHF10/BAF45A, ACTL6A/BAF53A and actin. Component of neuron- specific chromatin remodeling complex (nBAF complex) composed of at least, ARID1A/BAF250A or ARID1B/BAF250B, SMARCD1/BAF60A, SMARCD3/BAF60C, SMARCA2/BRM/BAF190B, SMARCA4/BRG1/BAF190A, SMARCB1/BAF47, SMARCC1/BAF155, SMARCE1/BAF57, SMARCC2/BAF170, DPF1/BAF45B, DPF3/BAF45C, ACTL6B/BAF53B and actin. Interacts with PHF10/BAF45A (By similarity).
INTERACTION: O14497:ARID1A; NbExp=3; IntAct=EBI-679562, EBI-637887; Q8NFD5:ARID1B; NbExp=3; IntAct=EBI-679562, EBI-679921; Q07666:KHDRBS1; NbExp=2; IntAct=EBI-679562, EBI-1364; P51608:MECP2; NbExp=4; IntAct=EBI-679562, EBI-1189067;
SUBCELLULAR LOCATION: Nucleus.
PTM: Phosphorylated upon DNA damage, probably by ATM or ATR.
DISEASE: Defects in SMARCA2 are the cause of Nicolaides-Baraitser syndrome (NCBRS) [MIM:601358]. A rare disorder characterized by severe mental retardation with absent or limited speech, seizures, short stature, sparse hair, typical facial characteristics, brachydactyly, prominent finger joints and broad distal phalanges. Some of the features are progressive with time.
SIMILARITY: Belongs to the SNF2/RAD54 helicase family.
SIMILARITY: Contains 1 bromo domain.
SIMILARITY: Contains 1 helicase ATP-binding domain.
SIMILARITY: Contains 1 helicase C-terminal domain.
SIMILARITY: Contains 1 HSA domain.
SIMILARITY: Contains 1 QLQ domain.
WEB RESOURCE: Name=SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 2 (SMARCA2); Note=Leiden Open Variation Database (LOVD); URL="http://grenada.lumc.nl/LOVD2/shared1/home.php?select_db=SMARCA2";

-  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
  InterPro Domains: Graphical view of domain structure
IPR006576 - BRK_domain
IPR001487 - Bromodomain
IPR018359 - Bromodomain_CS
IPR014978 - Gln-Leu-Gln_QLQ
IPR013999 - HAS_subgr
IPR014012 - Helicase/SANT-assoc_DNA-bd
IPR014001 - Helicase_ATP-bd
IPR001650 - Helicase_C
IPR006562 - HSA
IPR000330 - SNF2_N

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

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

2DAT
- NMR MuPIT


ModBase Predicted Comparative 3D Structure on P51531
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:0000166 nucleotide binding
GO:0001105 RNA polymerase II transcription coactivator activity
GO:0003677 DNA binding
GO:0003682 chromatin binding
GO:0003713 transcription coactivator activity
GO:0004386 helicase activity
GO:0005515 protein binding
GO:0005524 ATP binding
GO:0008094 DNA-dependent ATPase activity
GO:0016787 hydrolase activity
GO:0016817 hydrolase activity, acting on acid anhydrides
GO:0016887 ATPase activity
GO:0042393 histone binding
GO:0044212 transcription regulatory region DNA binding

Biological Process:
GO:0000122 negative regulation of transcription from RNA polymerase II promoter
GO:0006338 chromatin remodeling
GO:0006351 transcription, DNA-templated
GO:0006355 regulation of transcription, DNA-templated
GO:0006357 regulation of transcription from RNA polymerase II promoter
GO:0006366 transcription from RNA polymerase II promoter
GO:0007286 spermatid development
GO:0007399 nervous system development
GO:0008285 negative regulation of cell proliferation
GO:0030308 negative regulation of cell growth
GO:0045892 negative regulation of transcription, DNA-templated
GO:0045893 positive regulation of transcription, DNA-templated
GO:0045944 positive regulation of transcription from RNA polymerase II promoter

Cellular Component:
GO:0000790 nuclear chromatin
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0016514 SWI/SNF complex
GO:0043231 intracellular membrane-bounded organelle
GO:0045111 intermediate filament cytoskeleton
GO:0071564 npBAF complex
GO:0071565 nBAF complex


-  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: B1ALG3, B1ALG4, BAF190B, BRM, D3DRH4, D3DRH5, NM_003070, NP_003061, P51531, SMCA2_HUMAN, SNF2A, SNF2L2
UCSC ID: uc003zhc.3
RefSeq Accession: NM_003070
Protein: P51531 (aka SMCA2_HUMAN or SN22_HUMAN)
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_003070.3
exon count: 34CDS single in 3' UTR: no RNA size: 5758
ORF size: 4773CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 9433.50frame shift in genome: no % Coverage: 99.97
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.