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SMARCA5 SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 5 [ Homo sapiens (human) ]

Gene ID: 8467, updated on 11-Apr-2024

Summary

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Official Symbol
SMARCA5provided by HGNC
Official Full Name
SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 5provided by HGNC
Primary source
HGNC:HGNC:11101
See related
Ensembl:ENSG00000153147 MIM:603375; AllianceGenome:HGNC:11101
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
ISWI; SNF2H; hISWI; hSNF2H; WCRF135
Summary
The protein encoded by this gene is a member of the SWI/SNF family of proteins. 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 protein encoded by this gene is a component of the chromatin remodeling and spacing factor RSF, a facilitator of the transcription of class II genes by RNA polymerase II. The encoded protein is similar in sequence to the Drosophila ISWI chromatin remodeling protein. [provided by RefSeq, Jul 2008]
Expression
Ubiquitous expression in testis (RPKM 25.1), lung (RPKM 17.3) and 25 other tissues See more
Orthologs
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Genomic context

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Location:
4q31.21
Exon count:
24
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 4 NC_000004.12 (143513702..143557486)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 4 NC_060928.1 (146830915..146874681)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 4 NC_000004.11 (144434855..144478639)

Chromosome 4 - NC_000004.12Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21942 Neighboring gene ribosomal protein S2 pseudogene 20 Neighboring gene GRB2 associated binding protein 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21943 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21944 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21945 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr4:144358834-144360033 Neighboring gene ribosomal protein SA pseudogene 36 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21949 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21948 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21947 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21946 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21950 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21951 Neighboring gene SMARCA5 antisense RNA 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21952 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21953 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21954 Neighboring gene GUSB pseudogene 5 Neighboring gene FRAS1 related extracellular matrix 3 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:144621195-144621852

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. Human SMARCA5 is continuously required to maintain nucleosome spacing. Bomber ML, et al. Mol Cell, 2023 Feb 16. PMID 36630954, Free PMC Article
  2. Loss of ISWI ATPase SMARCA5 (SNF2H) in Acute Myeloid Leukemia Cells Inhibits Proliferation and Chromatid Cohesion. Zikmund T, et al. Int J Mol Sci, 2020 Mar 18. PMID 32197313, Free PMC Article
  3. A basic motif anchoring ISWI to nucleosome acidic patch regulates nucleosome spacing. Dao HT, et al. Nat Chem Biol, 2020 Feb. PMID 31819269, Free PMC Article
  4. Circ-SMARCA5 suppresses progression of multiple myeloma by targeting miR-767-5p. Liu H, et al. BMC Cancer, 2019 Oct 10. PMID 31601173, Free PMC Article
  5. Cryo-EM structures of remodeler-nucleosome intermediates suggest allosteric control through the nucleosome. Armache JP, et al. Elife, 2019 Jun 18. PMID 31210637, Free PMC Article

See all (258) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Circular RNA SMARCA5 Promotes a Poor Prognosis and Radiotherapy Resistance for Patients with Hepatocellular Carcinoma.
    Title: Circular RNA SMARCA5 Promotes a Poor Prognosis and Radiotherapy Resistance for Patients with Hepatocellular Carcinoma.
  2. Hyperglycemia-Suppressed SMARCA5 Disrupts Transcriptional Homeostasis to Facilitate Endothelial Dysfunction in Diabetes.
    Title: Hyperglycemia-Suppressed SMARCA5 Disrupts Transcriptional Homeostasis to Facilitate Endothelial Dysfunction in Diabetes.
  3. The RPA-RNF20-SNF2H cascade promotes proper chromosome segregation and homologous recombination repair.
    Title: The RPA-RNF20-SNF2H cascade promotes proper chromosome segregation and homologous recombination repair.
  4. Human SMARCA5 is continuously required to maintain nucleosome spacing.
    Title: Human SMARCA5 is continuously required to maintain nucleosome spacing.
  5. The miR-100-5p Targets SMARCA5 to Regulate the Apoptosis and Intracellular Survival of BCG in Infected THP-1 Cells.
    Title: The miR-100-5p Targets SMARCA5 to Regulate the Apoptosis and Intracellular Survival of BCG in Infected THP-1 Cells.
  6. Long noncoding RNA lncMREF promotes myogenic differentiation and muscle regeneration by interacting with the Smarca5/p300 complex.
    Title: Long noncoding RNA lncMREF promotes myogenic differentiation and muscle regeneration by interacting with the Smarca5/p300 complex.
  7. Circular RNA SMARCA5 functions as an anti-tumor candidate in colon cancer by sponging microRNA-552.
    Title: Circular RNA SMARCA5 functions as an anti-tumor candidate in colon cancer by sponging microRNA-552.
  8. Negative Correlation Between Circular RNA SMARC5 and MicroRNA 432, and Their Clinical Implications in Bladder Cancer Patients.
    Title: Negative Correlation Between Circular RNA SMARC5 and MicroRNA 432, and Their Clinical Implications in Bladder Cancer Patients.
  9. A circular RNA, circSMARCA5, inhibits prostate cancer proliferative, migrative, and invasive capabilities via the miR-181b-5p/miR-17-3p-TIMP3 axis.
    Title: A circular RNA, circSMARCA5, inhibits prostate cancer proliferative, migrative, and invasive capabilities via the miR-181b-5p/miR-17-3p-TIMP3 axis.
  10. MicroRNA miR-100 Decreases Glioblastoma Growth by Targeting SMARCA5 and ErbB3 in Tumor-Initiating Cells.
    Title: MicroRNA miR-100 Decreases Glioblastoma Growth by Targeting SMARCA5 and ErbB3 in Tumor-Initiating Cells.
Submit: New GeneRIF Correction See all GeneRIFs (56)

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

HIV-1 interactions

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Protein interactions

Protein Gene Interaction Pubs
Tat tat The WICH complex, composed of WSTF and SNF2H, are identified to interact with HIV-1 Tat in Jurkat cell PubMed
Vpr vpr HIV-1 Vpr directly binds SNF2H and the Vpr mutant lacking amino acids 71-75 abolishes its binding to SNF2H PubMed

Go to the HIV-1, Human Interaction Database

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

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables ATP binding IDA
Inferred from Direct Assay
more info
 PubMed 
enables ATP hydrolysis activity IDA
Inferred from Direct Assay
more info
 PubMed 
enables ATP-dependent activity, acting on DNA IBA
Inferred from Biological aspect of Ancestor
more info
  
enables ATP-dependent chromatin remodeler activity IDA
Inferred from Direct Assay
more info
 PubMed 
enables ATP-dependent chromatin remodeler activity IMP
Inferred from Mutant Phenotype
more info
 PubMed 
enables DNA binding IBA
Inferred from Biological aspect of Ancestor
more info
  
enables DNA binding IDA
Inferred from Direct Assay
more info
 PubMed 
enables helicase activity IEA
Inferred from Electronic Annotation
more info
  
contributes_to histone binding IDA
Inferred from Direct Assay
more info
 PubMed 
enables histone octamer slider activity IDA
Inferred from Direct Assay
more info
 PubMed 
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 DNA damage response NAS
Non-traceable Author Statement
more info
 PubMed 
involved_in DNA repair IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in DNA-templated transcription initiation IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in cellular response to leukemia inhibitory factor IEA
Inferred from Electronic Annotation
more info
  
involved_in chromatin organization IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in chromatin remodeling IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in chromatin remodeling IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in chromatin remodeling ISO
Inferred from Sequence Orthology
more info
  
involved_in chromatin remodeling NAS
Non-traceable Author Statement
more info
 PubMed 
involved_in heterochromatin formation ISO
Inferred from Sequence Orthology
more info
  
involved_in negative regulation of mitotic chromosome condensation IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in negative regulation of mitotic chromosome condensation IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in negative regulation of transcription by RNA polymerase I ISO
Inferred from Sequence Orthology
more info
  
involved_in nucleosome assembly EXP
Inferred from Experiment
more info
 PubMed 
involved_in nucleosome assembly IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in positive regulation of DNA replication IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in positive regulation of transcription by RNA polymerase I NAS
Non-traceable Author Statement
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 NAS
Non-traceable Author Statement
more info
 PubMed 
involved_in positive regulation of transcription by RNA polymerase III IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in rDNA heterochromatin formation ISO
Inferred from Sequence Orthology
more info
  
involved_in regulation of DNA replication IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in regulation of DNA-templated transcription IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in regulation of transcription by RNA polymerase II TAS
Traceable Author Statement
more info
 PubMed 
Component Evidence Code Pubs
part_of ACF complex IPI
Inferred from Physical Interaction
more info
 PubMed 
part_of B-WICH complex IDA
Inferred from Direct Assay
more info
 PubMed 
part_of CHRAC NAS
Non-traceable Author Statement
more info
 PubMed 
part_of NURF complex IDA
Inferred from Direct Assay
more info
 PubMed 
part_of NoRC complex ISO
Inferred from Sequence Orthology
more info
  
part_of RSF complex IPI
Inferred from Physical Interaction
more info
 PubMed 
part_of WICH complex IDA
Inferred from Direct Assay
more info
 PubMed 
part_of chromatin silencing complex IEA
Inferred from Electronic Annotation
more info
  
located_in condensed chromosome IDA
Inferred from Direct Assay
more info
 PubMed 
located_in fibrillar center IDA
Inferred from Direct Assay
more info
  
colocalizes_with nuclear replication fork IDA
Inferred from Direct Assay
more info
 PubMed 
located_in nucleolus NAS
Non-traceable Author Statement
more info
 PubMed 
located_in nucleoplasm IDA
Inferred from Direct Assay
more info
  
located_in nucleoplasm TAS
Traceable Author Statement
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 ISO
Inferred from Sequence Orthology
more info
  
part_of pericentric heterochromatin EXP
Inferred from Experiment
more info
 PubMed 
part_of pericentric heterochromatin ISO
Inferred from Sequence Orthology
more info
  
is_active_in site of double-strand break IDA
Inferred from Direct Assay
more info
 PubMed 

General protein information

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Preferred Names
SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A member 5
Names
SWI/SNF-related matrix-associated actin-dependent regulator of chromatin A5
sucrose nonfermenting protein 2 homolog
sucrose nonfermenting-like 5

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.

mRNA and Protein(s)

  1. NM_003601.4 → NP_003592.3  SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A member 5

    See identical proteins and their annotated locations for NP_003592.3

    Status: REVIEWED

    Source sequence(s)
    AC099396, AC104685, AC139713
    Consensus CDS
    CCDS3761.1
    UniProtKB/Swiss-Prot
    O60264
    UniProtKB/TrEMBL
    B4DZC0, B7ZAX9
    Related
    ENSP00000283131.3, ENST00000283131.4
    Conserved Domains (1) summary
    PLN03142
    Location:69 → 1012
    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_000004.12 Reference GRCh38.p14 Primary Assembly

    Range
    143513702..143557486
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_047416323.1 → XP_047272279.1  SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A member 5 isoform X1

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060928.1 Alternate T2T-CHM13v2.0

    Range
    146830915..146874681
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054351108.1 → XP_054207083.1  SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A member 5 isoform X1

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
O60264.1 GenPept UniProtKB/Swiss-Prot:O60264

Gene LinkOut

The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

Chemical Information
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