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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 4-Nov-2018

Summary

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:HGNC:11098
See related
Ensembl:ENSG00000080503 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]
Expression
Ubiquitous expression in ovary (RPKM 42.5), testis (RPKM 29.4) and 25 other tissues See more
Orthologs

Genomic context

See SMARCA2 in Genome Data Viewer
Location:
9p24.3
Exon count:
38
Annotation release Status Assembly Chr Location
109 current GRCh38.p12 (GCF_000001405.38) 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 uncharacterized LOC105375951 Neighboring gene uncharacterized LOC105375953 Neighboring gene uncharacterized LOC105375952 Neighboring gene uncharacterized LOC107987043 Neighboring gene RNA, U2 small nuclear 25, pseudogene Neighboring gene VISTA enhancer hs1743 Neighboring gene RNA, 7SL, cytoplasmic 592, pseudogene

Genomic regions, transcripts, and products

Expression

  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Jun 15 11:32:44 2016

Bibliography

GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

Phenotypes

Associated conditions

Description Tests
Nicolaides-Baraitser syndrome
MedGen: C1303073 OMIM: 601358 GeneReviews: Nicolaides-Baraitser Syndrome
Compare labs

Copy number response

Description
Copy number response
Haploinsufficency

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

ClinGen Genome Curation Page
Triplosensitivity

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

ClinGen Genome Curation Page

NHGRI GWAS Catalog

Description
A genome-wide association study of chemotherapy-induced alopecia in breast cancer patients.
NHGRI GWA Catalog
Common variants at 1p36 are associated with superior frontal gyrus volume.
NHGRI GWA Catalog
Genome-wide association study combining pathway analysis for typical sporadic amyotrophic lateral sclerosis in Chinese Han populations.
NHGRI GWA Catalog
Identification of risk loci with shared effects on five major psychiatric disorders: a genome-wide analysis.
NHGRI GWA Catalog

HIV-1 interactions

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 Interaction Database

Pathways from BioSystems

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

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 
chromatin binding IEA
Inferred from Electronic Annotation
more info
 
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 IDA
Inferred from Direct Assay
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 
nucleoplasm IDA
Inferred from Direct Assay
more info
 
nucleoplasm TAS
Traceable Author Statement
more info
 
nucleus IDA
Inferred from Direct Assay
more info
PubMed 

General protein information

Preferred Names
probable global transcription activator SNF2L2
Names
ATP-dependent helicase SMARCA2
BAF190B
BRG1-associated factor 190B
SNF2-alpha
SNF2/SWI2-like protein 2
SWI/SNF-related matrix-associated actin-dependent regulator of chromatin a2
brahma homolog
global transcription activator homologous sequence
protein brahma homolog
sucrose nonfermenting 2-like protein 2

NCBI Reference Sequences (RefSeq)

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_032162.2 RefSeqGene

    Range
    39930..218335
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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

    See identical proteins and their annotated locations for 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/Swiss-Prot
    P51531
    UniProtKB/TrEMBL
    B4DSC8, Q8N9Q1
    Related
    ENSP00000371638.1, OTTHUMP00000020970, ENST00000382203.5, OTTHUMT00000051505
    Conserved Domains (10) summary
    cd05516
    Location:13821506
    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 ...
    smart00592
    Location:590632
    BRK; domain in transcription and CHROMO domain helicases
    smart00573
    Location:436508
    HSA; domain in helicases and associated with SANT domains
    cd00046
    Location:744883
    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.
    pfam08430
    Location:40174
    Forkhead_N; Forkhead N-terminal region
    pfam00176
    Location:7271022
    SNF2_N; SNF2 family N-terminal domain
    pfam00271
    Location:10491164
    Helicase_C; Helicase conserved C-terminal domain
    pfam08880
    Location:173207
    QLQ; QLQ
    pfam14619
    Location:12591326
    SnAC; Snf2-ATP coupling, chromatin remodelling complex
    cl02556
    Location:13331419
    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
    Consensus CDS
    CCDS83338.1
    UniProtKB/Swiss-Prot
    P51531
    UniProtKB/TrEMBL
    F6VDE0
    Related
    ENSP00000392081.2, OTTHUMP00000020974, ENST00000450198.6, OTTHUMT00000051510
    Conserved Domains (10) summary
    cd05516
    Location:13241430
    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 ...
    smart00592
    Location:590632
    BRK; domain in transcription and CHROMO domain helicases
    smart00573
    Location:436508
    HSA; domain in helicases and associated with SANT domains
    cd00046
    Location:744872
    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.
    pfam08430
    Location:40174
    Forkhead_N; Forkhead N-terminal region
    pfam00176
    Location:727964
    SNF2_N; SNF2 family N-terminal domain
    pfam00271
    Location:9911106
    Helicase_C; Helicase conserved C-terminal domain
    pfam08880
    Location:173207
    QLQ; QLQ
    pfam14619
    Location:12011268
    SnAC; Snf2-ATP coupling, chromatin remodelling complex
    cl02556
    Location:12751337
    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
    UniProtKB/TrEMBL
    F6T8Q0
    Related
    ENSP00000324770.6, OTTHUMP00000281409, ENST00000324954.10, OTTHUMT00000488360
    Conserved Domains (2) summary
    cd05516
    Location:58164
    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
    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 identical proteins and their annotated locations for 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
    Consensus CDS
    CCDS83339.1
    UniProtKB/TrEMBL
    B4DNT1
    Related
    ENSP00000371620.2, OTTHUMP00000281412, ENST00000382185.6, OTTHUMT00000488367
    Conserved Domains (2) summary
    cd05516
    Location:86192
    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
    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, B4DNT1, Q8N9Q1
    Related
    ENSP00000305411.3, OTTHUMP00000020968, ENST00000302401.8, OTTHUMT00000051503
    Conserved Domains (2) summary
    cd05516
    Location:88194
    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
    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 identical proteins and their annotated locations for 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, Q8N9Q1
    Related
    ENSP00000265773.5, OTTHUMP00000281406, ENST00000349721.7, OTTHUMT00000488355
    Conserved Domains (10) summary
    cd05516
    Location:13821506
    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 ...
    smart00592
    Location:590632
    BRK; domain in transcription and CHROMO domain helicases
    smart00573
    Location:436508
    HSA; domain in helicases and associated with SANT domains
    cd00046
    Location:744883
    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.
    pfam08430
    Location:40174
    Forkhead_N; Forkhead N-terminal region
    pfam00176
    Location:7271022
    SNF2_N; SNF2 family N-terminal domain
    pfam00271
    Location:10491164
    Helicase_C; Helicase conserved C-terminal domain
    pfam08880
    Location:173207
    QLQ; QLQ
    pfam14619
    Location:12591326
    SnAC; Snf2-ATP coupling, chromatin remodelling complex
    cl02556
    Location:13331419
    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 identical proteins and their annotated locations for 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, Q8N9Q1
    Related
    ENSP00000349788.2, OTTHUMP00000281407, ENST00000357248.8, OTTHUMT00000488357
    Conserved Domains (10) summary
    cd05516
    Location:13821488
    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 ...
    smart00592
    Location:590632
    BRK; domain in transcription and CHROMO domain helicases
    smart00573
    Location:436508
    HSA; domain in helicases and associated with SANT domains
    cd00046
    Location:744883
    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.
    pfam08430
    Location:40174
    Forkhead_N; Forkhead N-terminal region
    pfam00176
    Location:7271022
    SNF2_N; SNF2 family N-terminal domain
    pfam00271
    Location:10491164
    Helicase_C; Helicase conserved C-terminal domain
    pfam08880
    Location:173207
    QLQ; QLQ
    pfam14619
    Location:12591326
    SnAC; Snf2-ATP coupling, chromatin remodelling complex
    cl02556
    Location:13331395
    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 109 details...Open this link in a new tab

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

Reference GRCh38.p12 Primary Assembly

Genomic

  1. NC_000009.12 Reference GRCh38.p12 Primary Assembly

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