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SMARCA1 SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 1 [ Homo sapiens (human) ]

Gene ID: 6594, updated on 11-Apr-2024

Summary

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Official Symbol
SMARCA1provided by HGNC
Official Full Name
SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 1provided by HGNC
Primary source
HGNC:HGNC:11097
See related
Ensembl:ENSG00000102038 MIM:300012; AllianceGenome:HGNC:11097
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
SWI; ISWI; SWI2; SNF2L; SNF2L1; SNF2LB; SNF2LT; hSNF2L; NURF140
Summary
This gene encodes a member of the SWI/SNF family of proteins. The encoded protein is an ATPase which is expressed in diverse tissues and contributes to the chromatin remodeling complex that is involved in transcription. The protein may also play a role in DNA damage, growth inhibition and apoptosis of cancer cells. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Sep 2013]
Expression
Broad expression in adrenal (RPKM 46.7), testis (RPKM 43.0) and 22 other tissues See more
Orthologs
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Genomic context

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Location:
Xq25-q26.1
Exon count:
25
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) X NC_000023.11 (129446506..129523490, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) X NC_060947.1 (127765288..127842272, complement)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) X NC_000023.10 (128580483..128657467, complement)

Chromosome X - NC_000023.11Genomic Context describing neighboring genes Neighboring gene ribosomal protein S26 pseudogene 56 Neighboring gene RNA, 5S ribosomal pseudogene 513 Neighboring gene small nucleolar RNA SNORD112 Neighboring gene Sharpr-MPRA regulatory region 13828 Neighboring gene NANOG hESC enhancer GRCh37_chrX:128698883-128699384 Neighboring gene OCRL inositol polyphosphate-5-phosphatase Neighboring gene H3K4me1 hESC enhancer GRCh37_chrX:128734568-128735068 Neighboring gene H3K4me1 hESC enhancer GRCh37_chrX:128735069-128735569 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20975 Neighboring gene H3K4me1 hESC enhancer GRCh37_chrX:128783429-128783930 Neighboring gene H3K4me1 hESC enhancer GRCh37_chrX:128783931-128784430 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29915 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20976 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20977 Neighboring gene apelin

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • 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 Apr 4 07:08:55 2018

Bibliography

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Related articles in PubMed

  1. A pan-cancer bioinformatic analysis of the carcinogenic role of SMARCA1 in human carcinomas. Dai L, et al. PLoS One, 2022. PMID 36126083, Free PMC Article
  2. Frequent involvement of chromatin remodeler alterations in gastric field cancerization. Takeshima H, et al. Cancer Lett, 2015 Feb 1. PMID 25462860
  3. Human SNF2L gene is regulated constitutively and inducibly in neural cells via a cAMP-response element. Xia Y, et al. Yonsei Med J, 2013 May 1. PMID 23549828, Free PMC Article
  4. SWI/SNF chromatin-remodeling factors: multiscale analyses and diverse functions. Euskirchen G, et al. J Biol Chem, 2012 Sep 7. PMID 22952240, Free PMC Article
  5. Singular v dual inhibition of SNF2L and its isoform, SNF2LT, have similar effects on DNA damage but opposite effects on the DNA damage response, cancer cell growth arrest and apoptosis. Ye Y, et al. Oncotarget, 2012 Apr. PMID 22577152, Free PMC Article

See all (96) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. The lncRNA MIR99AHG directs alternative splicing of SMARCA1 by PTBP1 to enable invadopodia formation in colorectal cancer cells.
    Title: The lncRNA MIR99AHG directs alternative splicing of SMARCA1 by PTBP1 to enable invadopodia formation in colorectal cancer cells.
  2. A pan-cancer bioinformatic analysis of the carcinogenic role of SMARCA1 in human carcinomas.
    Title: A pan-cancer bioinformatic analysis of the carcinogenic role of SMARCA1 in human carcinomas.
  3. This is the first report of an interstitial deletion encompassing OCRL and SMARCA1 gene in Lowe syndrome.
    Title: Whole-genome sequencing revealed an interstitial deletion encompassing OCRL and SMARCA1 gene in a patient with Lowe syndrome.
  4. High SNF2L expression is associated with gastric cancer growth and invasion.
    Title: Circular RNA circ-DONSON facilitates gastric cancer growth and invasion via NURF complex dependent activation of transcription factor SOX4.
  5. Data identified SMARCA1 as an interactive protein of DLEU1 in colorectal cancer to regulate cancer cell proliferation.
    Title: LncRNA DLEU1 contributes to colorectal cancer progression via activation of KPNA3.
  6. In one family, four siblings with a psychotic illness and their unaffected mother each carry a novel private missense variant in the SMARCA1 gene on the X chromosome.
    Title: Whole-genome sequencing in multiplex families with psychoses reveals mutations in the SHANK2 and SMARCA1 genes segregating with illness.
  7. Depletion of a chromatin remodeler, SMARCA1, in cancer cell lines promoted their growth.
    Title: Frequent involvement of chromatin remodeler alterations in gastric field cancerization.
  8. The results suggest that the cAMP-response element consensus sequence in the SNF2L proximal promoter most likely confers constitutive activation and regulation by cAMP in neural cells.
    Title: Human SNF2L gene is regulated constitutively and inducibly in neural cells via a cAMP-response element.
  9. The effect of SNF2L depletion on gene expression portray the cell in a state of activated Wnt signaling with increased proliferation and locomotion. High levels of SNF2L expression in normal melanocytes contrast with undetectable expression in melanoma.
    Title: Nucleosome remodeler SNF2L suppresses cell proliferation and migration and attenuates Wnt signaling.
  10. expression profiling analyses revealed that SWI/SNF likely antagonizes Polycomb repressive complex 2, implicating this as one possible mechanism of tumor suppression
    Title: Convergent structural alterations define SWItch/Sucrose NonFermentable (SWI/SNF) chromatin remodeler as a central tumor suppressive complex in pancreatic cancer.
Submit: New GeneRIF Correction See all GeneRIFs (16)

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

Pathways from PubChem

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Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Clone Names

  • FLJ41547, DKFZp686D1623

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables ATP binding IEA
Inferred from Electronic Annotation
more info
  
enables ATP-dependent DNA/DNA annealing activity IDA
Inferred from Direct Assay
more info
 PubMed 
contributes_to ATP-dependent activity, acting on DNA IDA
Inferred from Direct Assay
more info
 PubMed 
contributes_to ATP-dependent chromatin remodeler activity IDA
Inferred from Direct Assay
more info
 PubMed 
enables ATP-dependent chromatin remodeler activity IDA
Inferred from Direct Assay
more info
 PubMed 
enables DNA binding IBA
Inferred from Biological aspect of Ancestor
more info
  
enables RNA polymerase II-specific DNA-binding transcription factor binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables helicase activity IEA
Inferred from Electronic Annotation
more info
  
enables nucleosome binding IEA
Inferred from Electronic Annotation
more info
  
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
Process Evidence Code Pubs
involved_in brain development IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in brain development NAS
Non-traceable Author Statement
more info
 PubMed 
involved_in chromatin remodeling IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in neuron differentiation ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in positive regulation of DNA-templated transcription IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in positive regulation of transcription by RNA polymerase II IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in positive regulation of transcription by RNA polymerase II IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in regulation of DNA-templated transcription IDA
Inferred from Direct Assay
more info
 PubMed 
Component Evidence Code Pubs
part_of ATPase complex IDA
Inferred from Direct Assay
more info
 PubMed 
part_of CERF complex IDA
Inferred from Direct Assay
more info
 PubMed 
part_of CERF complex IPI
Inferred from Physical Interaction
more info
 PubMed 
part_of NURF complex IDA
Inferred from Direct Assay
more info
 PubMed 
part_of NURF complex IPI
Inferred from Physical Interaction
more info
 PubMed 
located_in intracellular membrane-bounded organelle IDA
Inferred from Direct Assay
more info
  
located_in nucleoplasm IDA
Inferred from Direct Assay
more info
  
is_active_in nucleus IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in nucleus IDA
Inferred from Direct Assay
more info
 PubMed 
located_in nucleus NAS
Non-traceable Author Statement
more info
 PubMed 

General protein information

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Preferred Names
probable global transcription activator SNF2L1
Names
ATP-dependent helicase SMARCA1
SNF2-like 1
global transcription activator homologous sequence
nucleosome-remodeling factor subunit SNF2L
sucrose nonfermenting 2-like protein 1

NCBI Reference Sequences (RefSeq)

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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_012526.1 RefSeqGene

    Range
    4994..81978
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001282874.2 → NP_001269803.1  probable global transcription activator SNF2L1 isoform d

    See identical proteins and their annotated locations for NP_001269803.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (4) encodes the longest isoform (d).
    Source sequence(s)
    BC143954, BQ006393, HY043725
    Consensus CDS
    CCDS76019.1
    UniProtKB/TrEMBL
    B7ZLQ5, Q86UA8
    Related
    ENSP00000360162.4, ENST00000371121.5
    Conserved Domains (1) summary
    PLN03142
    Location:87 → 1069
    PLN03142; Probable chromatin-remodeling complex ATPase chain; Provisional

  2. NM_001282875.2 → NP_001269804.1  probable global transcription activator SNF2L1 isoform c

    See identical proteins and their annotated locations for NP_001269804.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) lacks an alternate in-frame exon in the 3' coding region, compared to variant 4. It encodes isoform c, which lacks an internal segment and is shorter, compared to isoform d.
    Source sequence(s)
    BC117447, BC143955, BQ006393, HY043725
    Consensus CDS
    CCDS76018.1
    UniProtKB/TrEMBL
    A0A0A0MRP6, Q86UA8
    Related
    ENSP00000360164.2, ENST00000371123.5
    Conserved Domains (1) summary
    PLN03142
    Location:87 → 1057
    PLN03142; Probable chromatin-remodeling complex ATPase chain; Provisional

  3. NM_001378261.1 → NP_001365190.1  probable global transcription activator SNF2L1 isoform e

    Status: REVIEWED

    Source sequence(s)
    AL022577, AL138745
    UniProtKB/TrEMBL
    Q86UA8
    Conserved Domains (1) summary
    PLN03142
    Location:87 → 1046
    PLN03142; Probable chromatin-remodeling complex ATPase chain; Provisional

  4. NM_001378262.1 → NP_001365191.1  probable global transcription activator SNF2L1 isoform f

    Status: REVIEWED

    Source sequence(s)
    AL022577, AL138745
    UniProtKB/TrEMBL
    Q86UA8
    Related
    ENST00000617310.4
    Conserved Domains (1) summary
    PLN03142
    Location:87 → 1034
    PLN03142; Probable chromatin-remodeling complex ATPase chain; Provisional

  5. NM_001378263.1 → NP_001365192.1  probable global transcription activator SNF2L1 isoform f

    Status: REVIEWED

    Source sequence(s)
    AL022577, AL138745
    UniProtKB/TrEMBL
    Q86UA8
    Conserved Domains (1) summary
    PLN03142
    Location:87 → 1034
    PLN03142; Probable chromatin-remodeling complex ATPase chain; Provisional

  6. NM_001378264.1 → NP_001365193.1  probable global transcription activator SNF2L1 isoform g

    Status: REVIEWED

    Source sequence(s)
    AL022577, AL138745
    UniProtKB/TrEMBL
    Q86UA8
    Conserved Domains (1) summary
    PLN03142
    Location:87 → 1034
    PLN03142; Probable chromatin-remodeling complex ATPase chain; Provisional

  7. NM_003069.5 → NP_003060.2  probable global transcription activator SNF2L1 isoform a

    See identical proteins and their annotated locations for NP_003060.2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) differs in the 3' UTR and uses two alternate splice sites in the 3' coding region, resulting in an early stop codon, compared to variant 4. It encodes isoform a, which has a shorter and distinct C-terminus, compared to isoform d.
    Source sequence(s)
    BC117447, BQ006393, HY043725
    Consensus CDS
    CCDS14612.1
    UniProtKB/Swiss-Prot
    P28370, Q5JV41, Q5JV42
    UniProtKB/TrEMBL
    Q86UA8
    Related
    ENSP00000360163.4, ENST00000371122.8
    Conserved Domains (1) summary
    PLN03142
    Location:87 → 1046
    PLN03142; Probable chromatin-remodeling complex ATPase chain; Provisional

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

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

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000023.11 Reference GRCh38.p14 Primary Assembly

    Range
    129446506..129523490 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060947.1 Alternate T2T-CHM13v2.0

    Range
    127765288..127842272 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

  1. NM_139035.2: Suppressed sequence

    Description
    NM_139035.2: This RefSeq was permanently suppressed because currently there is insufficient support for the transcript and the protein.
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
P28370.2 GenPept UniProtKB/Swiss-Prot:P28370

Gene LinkOut

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