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    smarca5 SNF2 related chromatin remodeling ATPase 5 [ Danio rerio (zebrafish) ]

    Gene ID: 282615, updated on 9-Dec-2024

    Summary

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    Official Symbol
    smarca5provided by ZNC
    Official Full Name
    SNF2 related chromatin remodeling ATPase 5provided by ZNC
    Primary source
    ZFIN:ZDB-GENE-021125-1
    See related
    Ensembl:ENSDARG00000052348 AllianceGenome:ZFIN:ZDB-GENE-021125-1
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Danio rerio
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Actinopterygii; Neopterygii; Teleostei; Ostariophysi; Cypriniformes; Danionidae; Danioninae; Danio
    Also known as
    fb26d12; fb49g04; chunp6878; im:7146484; wu:fb26d12; wu:fb49g04; zgc:158434
    Summary
    Predicted to enable DNA binding activity; chromatin binding activity; and nucleosome array spacer activity. Acts upstream of or within cardiac ventricle development; erythrocyte aggregation; and retina development in camera-type eye. Predicted to be located in chromatin. Predicted to be active in nucleus. Is expressed in hematopoietic multipotent progenitor cell and telencephalon. Orthologous to human SMARCA5 (SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 5). [provided by Alliance of Genome Resources, Dec 2024]
    Orthologs
    human mouse all
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    Genomic context

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    See smarca5 in Genome Data Viewer
    Location:
    chromosome: 1
    Exon count:
    24
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCz11 (GCF_000002035.6) 1 NC_007112.7 (52792439..52820954)
    105 previous assembly GRCz10 (GCF_000002035.5) 1 NC_007112.6 (52157701..52186216)

    Chromosome 1 - NC_007112.7Genomic Context describing neighboring genes Neighboring gene wu:fc75a09 Neighboring gene uncharacterized LOC137495829 Neighboring gene PAT1 homolog 1, processing body mRNA decay factor Neighboring gene inositol polyphosphate-4-phosphatase type II B Neighboring gene uncharacterized LOC137495826 Neighboring gene interleukin 15

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: Sequencing the Zebrafish transcriptome from a range of tissues and developmental stages
    • Description: Sequencing the Zebrafish transcriptome from a range of tissues and developmental stages
    • BioProject: PRJEB1986
    • Analysis date: Fri Dec 8 19:48:10 2017

    Bibliography

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    Related articles in PubMed

    1. In vivo activation of a conserved microRNA program induces mammalian heart regeneration. Aguirre A, et al. Cell Stem Cell, 2014 Nov 6. PMID 25517466, Free PMC Article
    2. Transcriptome analysis of the zebrafish atoh7-/- Mutant, lakritz, highlights Atoh7-dependent genetic networks with potential implications for human eye diseases. Covello G, et al. FASEB Bioadv, 2020 Jul. PMID 32676583, Free PMC Article
    3. Gene regulatory networks controlling vertebrate retinal regeneration. Hoang T, et al. Science, 2020 Nov 20. PMID 33004674, Free PMC Article
    4. Beyond the binding site: in vivo identification of tbx2, smarca5 and wnt5b as molecular targets of CNBP during embryonic development. Armas P, et al. PLoS One, 2013. PMID 23667590, Free PMC Article
    5. WRN loss accelerates abnormal adipocyte metabolism in Werner syndrome. Tian Y, et al. Cell Biosci, 2024 Jan 6. PMID 38184705, Free PMC Article

    See all (20) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. The chromatin-remodeling enzyme Smarca5 regulates erythrocyte aggregation via Keap1-Nrf2 signaling.
      Title: The chromatin-remodeling enzyme Smarca5 regulates erythrocyte aggregation via Keap1-Nrf2 signaling.
    2. Smarca5-mediated epigenetic programming facilitates fetal HSPC development in vertebrates.
      Title: Smarca5-mediated epigenetic programming facilitates fetal HSPC development in vertebrates.
    3. CNBP up-regulates tbx2b and smarca5, and down-regulates wnt5b gene expression.
      Title: Beyond the binding site: in vivo identification of tbx2, smarca5 and wnt5b as molecular targets of CNBP during embryonic development.
    Submit: New GeneRIF Correction

    General gene information

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    Markers

    Homology

    Gene Ontology Provided by ZFIN

    Function Evidence Code Pubs
    enables ATP binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables ATP-dependent chromatin remodeler activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables DNA binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables DNA binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables chromatin binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables hydrolase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    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 nucleotide binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    Process Evidence Code Pubs
    acts_upstream_of_or_within cardiac ventricle development IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    acts_upstream_of_or_within chromatin remodeling IEA
    Inferred from Electronic Annotation
    more info
    		  
    acts_upstream_of_or_within erythrocyte aggregation IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in heterochromatin formation IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in positive regulation of transcription by RNA polymerase II IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    acts_upstream_of_or_within retina development in camera-type eye IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    Component Evidence Code Pubs
    located_in chromatin IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    is_active_in nucleus IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in nucleus IEA
    Inferred from Electronic Annotation
    more info
    		  

    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
    actin dependent regulator of chromatin A5
    matrix associated

    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_001081629.2 → NP_001075098.2  SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A member 5

      Status: VALIDATED

      Source sequence(s)
      BC133097, CU550733
      UniProtKB/TrEMBL
      A0A8M1NBR1, A2RUY6, B8A552
      Related
      ENSDARP00000107618.2, ENSDART00000123972.3
      Conserved Domains (6) summary
      PLN03142
      Location:4 → 1030
      PLN03142; Probable chromatin-remodeling complex ATPase chain; Provisional
      cd00046
      Location:183 → 322
      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.
      cd00167
      Location:827 → 865
      SANT; 'SWI3, ADA2, N-CoR and TFIIIB' DNA-binding domains. Tandem copies of the domain bind telomeric DNA tandem repeatsas part of the capping complex. Binding is sequence dependent for repeats which contain the G/C rich motif [C2-3 A (CA)1-6]. The domain is ...
      pfam00271
      Location:465 → 580
      Helicase_C; Helicase conserved C-terminal domain
      pfam09110
      Location:725 → 803
      HAND; HAND
      pfam09111
      Location:880 → 992
      SLIDE; SLIDE

    RefSeqs of Annotated Genomes: GCF_000002035.6-RS_2024_08

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

    Reference GRCz11 Primary Assembly

    Genomic

    1. NC_007112.7 Reference GRCz11 Primary Assembly

      Range
      52792439..52820954
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version

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