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    SMARCA5 SNF2 related chromatin remodeling ATPase 5 [ Homo sapiens (human) ]

    Gene ID: 8467, updated on 28-Oct-2024

    Summary

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    Official Symbol
    SMARCA5provided by HGNC
    Official Full Name
    SNF2 related chromatin remodeling ATPase 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
    mouse all
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    Genomic context

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    See SMARCA5 in Genome Data Viewer
    Location:
    4q31.21
    Exon count:
    24
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 4 NC_000004.12 (143513702..143557486)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 4 NC_060928.1 (146830915..146874681)
    RS_2024_09 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 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. SMARCA5 methylation and expression in gastric cancer. Gigek CO, et al. Cancer Invest, 2011 Feb. PMID 21261476
    2. The histone H4 tail regulates the conformation of the ATP-binding pocket in the SNF2h chromatin remodeling enzyme. Racki LR, et al. J Mol Biol, 2014 May 15. PMID 24607692, Free PMC Article
    3. The chromatin remodeler ISWI regulates the cellular response to hypoxia: role of FIH. Melvin A, et al. Mol Biol Cell, 2011 Nov. PMID 21900490, Free PMC Article
    4. Human ISWI complexes are targeted by SMARCA5 ATPase and SLIDE domains to help resolve lesion-stalled transcription. Aydin ÖZ, et al. Nucleic Acids Res, 2014 Jul. PMID 24990377, Free PMC Article
    5. Overexpression of SMARCA5 correlates with cell proliferation and migration in breast cancer. Jin Q, et al. Tumour Biol, 2015 Mar. PMID 25377162

    See all (285) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. SMARCA5 reprograms AKR1B1-mediated fructose metabolism to control leukemogenesis.
      Title: SMARCA5 reprograms AKR1B1-mediated fructose metabolism to control leukemogenesis.
    2. 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.
    3. 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.
    4. 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.
    5. Human SMARCA5 is continuously required to maintain nucleosome spacing.
      Title: Human SMARCA5 is continuously required to maintain nucleosome spacing.
    6. 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.
    7. 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.
    8. 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.
    9. 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.
    10. 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.
    Submit: New GeneRIF Correction See all GeneRIFs (57)

    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 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 chromatin binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    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 array spacer activity IBA
    Inferred from Biological aspect of Ancestor
    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 DNA damage response NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    involved_in DNA methylation-dependent heterochromatin formation ISO
    Inferred from Sequence Orthology
    more info
    		  
    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 antiviral innate immune response 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 IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    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 
    located_in chromatin IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    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
    		  
    located_in pericentric heterochromatin EXP
    Inferred from Experiment
    more info
    		 PubMed 
    located_in 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, subfamily a, member 5
    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_2024_08

    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
    Molecular Biology Databases
    Research Materials
    Tools
    Miscellaneous