Human Gene SMARCA2 (ENST00000302401.8) from GENCODE V44
  Description: Homo sapiens SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 2 (SMARCA2), transcript variant 7, mRNA. (from RefSeq NM_001289400)
RefSeq Summary (NM_001289400): 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].
Gencode Transcript: ENST00000302401.8
Gencode Gene: ENSG00000080503.25
Transcript (Including UTRs)
   Position: hg38 chr9:2,158,456-2,193,624 Size: 35,169 Total Exon Count: 8 Strand: +
Coding Region
   Position: hg38 chr9:2,158,976-2,192,739 Size: 33,764 Coding Exon Count: 8 

Page IndexSequence and LinksPrimersMalaCardsCTDRNA-Seq Expression
Microarray ExpressionRNA StructureProtein StructureOther SpeciesGO AnnotationsmRNA Descriptions
Other NamesGeneReviewsMethods
Data last updated at UCSC: 2023-08-18 00:09:47

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr9:2,158,456-2,193,624)mRNA (may differ from genome)Protein (278 aa)
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaAlphaFold
BioGPSEnsemblEntrez GeneExonPrimerGencodeGeneCards
HGNCLynxMalacardsMGImyGene2OMIM
PubMedUniProtKBWikipediaBioGrid CRISPR DB

-  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


-  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

-  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 -136.10520-0.262 Picture PostScript Text
3' UTR -196.00885-0.221 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

ModBase Predicted Comparative 3D Structure on B1ALF6
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
Genome BrowserGenome BrowserNo orthologNo orthologNo orthologNo ortholog
Gene Details     
Gene Sorter     
MGIRGD    
Protein SequenceProtein Sequence    
AlignmentAlignment    

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0016887 ATPase activity

Biological Process:
GO:0006338 chromatin remodeling

Cellular Component:
GO:0016514 SWI/SNF 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.
MB474733 - JP 2019527037-A/1: DIAGNOSTIC AND THERAPEUTIC METHODS FOR CANCER.
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.

-  Other Names for This Gene
  Alternate Gene Symbols: B1ALF6, B1ALF6_HUMAN, ENST00000302401.1, ENST00000302401.2, ENST00000302401.3, ENST00000302401.4, ENST00000302401.5, ENST00000302401.6, ENST00000302401.7, NM_001289400, RP11-48M17.1-001, uc003zhe.1, uc003zhe.2, uc003zhe.3, uc003zhe.4, uc003zhe.5
UCSC ID: ENST00000302401.8
RefSeq Accession: NM_001289400
Protein: B1ALF6 CCDS: CCDS83339.1, CCDS75808.1

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

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