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SMARCA2 SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 2 [ Homo sapiens (human) ]

Gene ID: 6595, updated on 26-Aug-2014
Official Symbol
SMARCA2provided by HGNC
Official Full Name
SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 2provided by HGNC
Primary source
HGNC:11098
See related
Ensembl:ENSG00000080503; HPRD:02483; MIM:600014; Vega:OTTHUMG00000019445
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
BRM; SNF2; SWI2; hBRM; NCBRS; Sth1p; BAF190; SNF2L2; SNF2LA; hSNF2a
Summary
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]
See SMARCA2 in Epigenomics, MapViewer
Location:
9p22.3
Exon count:
38
Annotation release Status Assembly Chr Location
106 current GRCh38 (GCF_000001405.26) 9 NC_000009.12 (2015219..2193624)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 9 NC_000009.11 (2015342..2193624)

Chromosome 9 - NC_000009.12Genomic Context describing neighboring genes Neighboring gene RNA, 5S ribosomal pseudogene 279 Neighboring gene uncharacterized LOC101929228 Neighboring gene uncharacterized LOC102723835 Neighboring gene uncharacterized LOC101930053

GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

Associated conditions

Description Tests
Nicolaides-Baraitser syndrome
MedGen: C1303073 OMIM: 601358 GeneReviews: Not available
Compare labs

Copy number response

Description
Copy number response
Haploinsufficency

No evidence available (Last evaluated (2013-03-27)

ISCA Genome Curation Page
Triplosensitivity

No evidence available (Last evaluated (2013-03-27)

ISCA Genome Curation Page

NHGRI GWAS Catalog

Description
A genome-wide association study of chemotherapy-induced alopecia in breast cancer patients.
NHGRI GWA Catalog
Identification of risk loci with shared effects on five major psychiatric disorders: a genome-wide analysis.
NHGRI GWA Catalog

Protein interactions

Protein Gene Interaction Pubs
Tat tat Brm-type SWI/SNF chromatin remodeling complex is required for the occasional transcriptional elongation of the HIV-1 provirus in the absence of Tat and for the reactivation of proviral expression from HIV-1 latently infected cells PubMed
tat HIV-1 Tat interacts directly with BRM, a DNA-dependent ATPase subunit of the SWI/SNF chromatin-remodeling complex, to activate the HIV-1 LTR, and this interaction is regulated by Tat lysine 50 acetylation PubMed
retropepsin gag-pol Positional proteomics analysis identifies the cleavage of human SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 2 (SMARCA2) at amino acid residues 616-617 by the HIV-1 protease PubMed

Go to the HIV-1, Human Protein Interaction Database

Products Interactant Other Gene Complex Source Pubs Description

Markers

Homology

Clone Names

  • FLJ36757, MGC74511

Gene Ontology Provided by GOA

Function Evidence Code Pubs
ATP binding IEA
Inferred from Electronic Annotation
more info
 
DNA-dependent ATPase activity TAS
Traceable Author Statement
more info
PubMed 
RNA polymerase II transcription coactivator activity IDA
Inferred from Direct Assay
more info
PubMed 
helicase activity IEA
Inferred from Electronic Annotation
more info
 
histone binding IEA
Inferred from Electronic Annotation
more info
 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
transcription coactivator activity TAS
Traceable Author Statement
more info
PubMed 
transcription regulatory region DNA binding IDA
Inferred from Direct Assay
more info
PubMed 
Component Evidence Code Pubs
SWI/SNF complex IDA
Inferred from Direct Assay
more info
PubMed 
intermediate filament cytoskeleton IDA
Inferred from Direct Assay
more info
 
intracellular membrane-bounded organelle IDA
Inferred from Direct Assay
more info
 
nBAF complex ISS
Inferred from Sequence or Structural Similarity
more info
 
npBAF complex ISS
Inferred from Sequence or Structural Similarity
more info
 
nuclear chromatin IDA
Inferred from Direct Assay
more info
PubMed 
NOT nucleolus IDA
Inferred from Direct Assay
more info
 
nucleoplasm TAS
Traceable Author Statement
more info
PubMed 
nucleus IDA
Inferred from Direct Assay
more info
 
Preferred Names
probable global transcription activator SNF2L2
Names
probable global transcription activator SNF2L2
BAF190B
SNF2-alpha
protein brahma homolog
SNF2/SWI2-like protein 2
BRG1-associated factor 190B
ATP-dependent helicase SMARCA2
sucrose nonfermenting 2-like protein 2
global transcription activator homologous sequence
SWI/SNF-related matrix-associated actin-dependent regulator of chromatin a2

RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

Genomic

  1. NG_032162.1 

    Range
    4878..183283
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001289396.1NP_001276325.1  probable global transcription activator SNF2L2 isoform a

    See proteins identical to NP_001276325.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) differs in the 5' UTR, compared to variant 1. Variants 1 and 3 encode the same protein (isoform a).
    Source sequence(s)
    AK094076, AK299683, AL359076, BC066596, BC068252, X72889
    Consensus CDS
    CCDS34977.1
    UniProtKB/TrEMBL
    B4DSC8
    UniProtKB/Swiss-Prot
    P51531
    UniProtKB/TrEMBL
    Q8N9Q1
    Related
    ENSP00000371638, OTTHUMP00000020970, ENST00000382203, OTTHUMT00000051505
    Conserved Domains (10) summary
    cd05516
    Location:13821506
    Blast Score: 502
    Bromo_SNF2L2; Bromodomain, SNF2L2-like subfamily, specific to animals. SNF2L2 (SNF2-alpha) or SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A member 2 is a global transcriptional activator, which cooperates with nuclear hormone ...
    smart00573
    Location:436508
    Blast Score: 243
    HSA; domain in helicases and associated with SANT domains
    cd00046
    Location:744883
    Blast Score: 268
    DEXDc; DEAD-like helicases superfamily. A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
    cd00079
    Location:10401172
    Blast Score: 277
    HELICc; Helicase superfamily c-terminal domain; associated with DEXDc-, DEAD-, and DEAH-box proteins, yeast initiation factor 4A, Ski2p, and Hepatitis C virus NS3 helicases; this domain is found in a wide variety of helicases and helicase related proteins; may ...
    pfam00176
    Location:7271022
    Blast Score: 944
    SNF2_N; SNF2 family N-terminal domain
    pfam07533
    Location:588632
    Blast Score: 175
    BRK; BRK domain
    pfam08430
    Location:40174
    Blast Score: 103
    Fork_head_N; Forkhead N-terminal region
    pfam08880
    Location:172208
    Blast Score: 149
    QLQ; QLQ
    pfam14619
    Location:12591326
    Blast Score: 225
    SnAC; Snf2-ATP coupling, chromatin remodelling complex
    cl02556
    Location:13331419
    Blast Score: 151
    Bromodomain; Bromodomain. Bromodomains are found in many chromatin-associated proteins and in nuclear histone acetyltransferases. They interact specifically with acetylated lysine.
  2. NM_001289397.1NP_001276326.1  probable global transcription activator SNF2L2 isoform c

    Status: REVIEWED

    Description
    Transcript Variant: This variant (4) uses an alternate in-frame splice site and lacks an alternate in-frame exon in the 3' coding region, compared to variant 1. The encoded protein (isoform c) is shorter, compared to isoform a.
    Source sequence(s)
    BC068252, CA313181, D26155
    UniProtKB/Swiss-Prot
    P51531
    Conserved Domains (10) summary
    cd05516
    Location:13241430
    Blast Score: 528
    Bromo_SNF2L2; Bromodomain, SNF2L2-like subfamily, specific to animals. SNF2L2 (SNF2-alpha) or SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A member 2 is a global transcriptional activator, which cooperates with nuclear hormone ...
    smart00573
    Location:436508
    Blast Score: 240
    HSA; domain in helicases and associated with SANT domains
    cd00046
    Location:744872
    Blast Score: 239
    DEXDc; DEAD-like helicases superfamily. A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
    cd00079
    Location:9821114
    Blast Score: 276
    HELICc; Helicase superfamily c-terminal domain; associated with DEXDc-, DEAD-, and DEAH-box proteins, yeast initiation factor 4A, Ski2p, and Hepatitis C virus NS3 helicases; this domain is found in a wide variety of helicases and helicase related proteins; may ...
    pfam00176
    Location:727964
    Blast Score: 712
    SNF2_N; SNF2 family N-terminal domain
    pfam07533
    Location:588632
    Blast Score: 175
    BRK; BRK domain
    pfam08430
    Location:40174
    Blast Score: 103
    Fork_head_N; Forkhead N-terminal region
    pfam08880
    Location:172208
    Blast Score: 149
    QLQ; QLQ
    pfam14619
    Location:12011268
    Blast Score: 223
    SnAC; Snf2-ATP coupling, chromatin remodelling complex
    cl02556
    Location:12751337
    Blast Score: 104
    Bromodomain; Bromodomain. Bromodomains are found in many chromatin-associated proteins and in nuclear histone acetyltransferases. They interact specifically with acetylated lysine.
  3. NM_001289398.1NP_001276327.1  probable global transcription activator SNF2L2 isoform d

    Status: REVIEWED

    Description
    Transcript Variant: This variant (5) differs in the 5' UTR, lacks a portion of the 5' coding region, and initiates translation at an alternate downstream start codon, compared to variant 1. The encoded protein (isoform d) has a shorter and distinct N-terminus, compared to isoform a.
    Source sequence(s)
    AL138755, BI758293, CA313181, CD107405, CD513892, DA084762, DA823500
    Consensus CDS
    CCDS75807.1
    Related
    ENSP00000324770, ENST00000324954
    Conserved Domains (2) summary
    cd05516
    Location:58164
    Blast Score: 493
    Bromo_SNF2L2; Bromodomain, SNF2L2-like subfamily, specific to animals. SNF2L2 (SNF2-alpha) or SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A member 2 is a global transcriptional activator, which cooperates with nuclear hormone ...
    cl02556
    Location:971
    Blast Score: 97
    Bromodomain; Bromodomain. Bromodomains are found in many chromatin-associated proteins and in nuclear histone acetyltransferases. They interact specifically with acetylated lysine.
  4. NM_001289399.1NP_001276328.1  probable global transcription activator SNF2L2 isoform e precursor

    See proteins identical to NP_001276328.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (6) differs in the 5' UTR, lacks a portion of the 5' coding region, and initiates translation at an alternate downstream start codon, compared to variant 1. The encoded protein (isoform e) has a shorter and distinct N-terminus, compared to isoform a.
    Source sequence(s)
    AK298045, CA313181
    UniProtKB/TrEMBL
    B4DNT1
    Related
    ENSP00000371620, OTTHUMP00000020975, ENST00000382185, OTTHUMT00000051511
    Conserved Domains (2) summary
    cd05516
    Location:86192
    Blast Score: 503
    Bromo_SNF2L2; Bromodomain, SNF2L2-like subfamily, specific to animals. SNF2L2 (SNF2-alpha) or SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A member 2 is a global transcriptional activator, which cooperates with nuclear hormone ...
    cl02556
    Location:3799
    Blast Score: 99
    Bromodomain; Bromodomain. Bromodomains are found in many chromatin-associated proteins and in nuclear histone acetyltransferases. They interact specifically with acetylated lysine.
  5. NM_001289400.1NP_001276329.1  probable global transcription activator SNF2L2 isoform f precursor

    Status: REVIEWED

    Description
    Transcript Variant: This variant (7) differs in the 5' UTR, lacks a portion of the 5' coding region, and initiates translation at an alternate downstream start codon, compared to variant 1. The encoded protein (isoform f) has a shorter and distinct N-terminus, compared to isoform a.
    Source sequence(s)
    AK094076, AK298045, CA313181, CD702931
    Consensus CDS
    CCDS75808.1
    UniProtKB/TrEMBL
    B1ALF6
    UniProtKB/TrEMBL
    B4DNT1
    UniProtKB/TrEMBL
    Q8N9Q1
    Related
    ENSP00000305411, OTTHUMP00000020968, ENST00000302401, OTTHUMT00000051503
    Conserved Domains (2) summary
    cd05516
    Location:88194
    Blast Score: 502
    Bromo_SNF2L2; Bromodomain, SNF2L2-like subfamily, specific to animals. SNF2L2 (SNF2-alpha) or SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A member 2 is a global transcriptional activator, which cooperates with nuclear hormone ...
    cl02556
    Location:39101
    Blast Score: 100
    Bromodomain; Bromodomain. Bromodomains are found in many chromatin-associated proteins and in nuclear histone acetyltransferases. They interact specifically with acetylated lysine.
  6. NM_003070.4NP_003061.3  probable global transcription activator SNF2L2 isoform a

    See proteins identical to NP_003061.3

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (a). Variants 1 and 3 encode the same protein (isoform a).
    Source sequence(s)
    AK094076, AL359076, AL558829, BC040029, BC066596, BC068252, X72889
    Consensus CDS
    CCDS34977.1
    UniProtKB/Swiss-Prot
    P51531
    UniProtKB/TrEMBL
    Q56A76
    UniProtKB/TrEMBL
    Q8N9Q1
    Related
    ENSP00000265773, ENST00000349721
    Conserved Domains (10) summary
    cd05516
    Location:13821506
    Blast Score: 502
    Bromo_SNF2L2; Bromodomain, SNF2L2-like subfamily, specific to animals. SNF2L2 (SNF2-alpha) or SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A member 2 is a global transcriptional activator, which cooperates with nuclear hormone ...
    smart00573
    Location:436508
    Blast Score: 243
    HSA; domain in helicases and associated with SANT domains
    cd00046
    Location:744883
    Blast Score: 268
    DEXDc; DEAD-like helicases superfamily. A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
    cd00079
    Location:10401172
    Blast Score: 277
    HELICc; Helicase superfamily c-terminal domain; associated with DEXDc-, DEAD-, and DEAH-box proteins, yeast initiation factor 4A, Ski2p, and Hepatitis C virus NS3 helicases; this domain is found in a wide variety of helicases and helicase related proteins; may ...
    pfam00176
    Location:7271022
    Blast Score: 944
    SNF2_N; SNF2 family N-terminal domain
    pfam07533
    Location:588632
    Blast Score: 175
    BRK; BRK domain
    pfam08430
    Location:40174
    Blast Score: 103
    Fork_head_N; Forkhead N-terminal region
    pfam08880
    Location:172208
    Blast Score: 149
    QLQ; QLQ
    pfam14619
    Location:12591326
    Blast Score: 225
    SnAC; Snf2-ATP coupling, chromatin remodelling complex
    cl02556
    Location:13331419
    Blast Score: 151
    Bromodomain; Bromodomain. Bromodomains are found in many chromatin-associated proteins and in nuclear histone acetyltransferases. They interact specifically with acetylated lysine.
  7. NM_139045.3NP_620614.2  probable global transcription activator SNF2L2 isoform b

    See proteins identical to NP_620614.2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) lacks an alternate in-frame exon in the coding region, compared to variant 1, resulting in a shorter protein (isoform a).
    Source sequence(s)
    AK094076, AL359076, BC040029, BC066596, BC068252, X72889
    Consensus CDS
    CCDS34978.1
    UniProtKB/Swiss-Prot
    P51531
    UniProtKB/TrEMBL
    Q56A76
    UniProtKB/TrEMBL
    Q8N9Q1
    Related
    ENSP00000349788, ENST00000357248
    Conserved Domains (10) summary
    cd05516
    Location:13821488
    Blast Score: 531
    Bromo_SNF2L2; Bromodomain, SNF2L2-like subfamily, specific to animals. SNF2L2 (SNF2-alpha) or SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A member 2 is a global transcriptional activator, which cooperates with nuclear hormone ...
    smart00573
    Location:436508
    Blast Score: 242
    HSA; domain in helicases and associated with SANT domains
    cd00046
    Location:744883
    Blast Score: 268
    DEXDc; DEAD-like helicases superfamily. A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
    cd00079
    Location:10401172
    Blast Score: 277
    HELICc; Helicase superfamily c-terminal domain; associated with DEXDc-, DEAD-, and DEAH-box proteins, yeast initiation factor 4A, Ski2p, and Hepatitis C virus NS3 helicases; this domain is found in a wide variety of helicases and helicase related proteins; may ...
    pfam00176
    Location:7271022
    Blast Score: 943
    SNF2_N; SNF2 family N-terminal domain
    pfam07533
    Location:588632
    Blast Score: 175
    BRK; BRK domain
    pfam08430
    Location:40174
    Blast Score: 103
    Fork_head_N; Forkhead N-terminal region
    pfam08880
    Location:172208
    Blast Score: 148
    QLQ; QLQ
    pfam14619
    Location:12591326
    Blast Score: 225
    SnAC; Snf2-ATP coupling, chromatin remodelling complex
    cl02556
    Location:13331395
    Blast Score: 105
    Bromodomain; Bromodomain. Bromodomains are found in many chromatin-associated proteins and in nuclear histone acetyltransferases. They interact specifically with acetylated lysine.

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 106

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38 Primary Assembly

Genomic

  1. NC_000009.12 

    Range
    2015219..2193624
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate HuRef

Genomic

  1. AC_000141.1 

    Range
    1969117..2147484
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate CHM1_1.1

Genomic

  1. NC_018920.2 

    Range
    2015344..2193714
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)