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    smarcad1a SNF2 related chromatin remodeling ATPase with DExD box 1a [ Danio rerio (zebrafish) ]

    Gene ID: 557875, updated on 28-Oct-2024

    Summary

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    Official Symbol
    smarcad1aprovided by ZNC
    Official Full Name
    SNF2 related chromatin remodeling ATPase with DExD box 1aprovided by ZNC
    Primary source
    ZFIN:ZDB-GENE-050522-499
    See related
    Ensembl:ENSDARG00000014041 AllianceGenome:ZFIN:ZDB-GENE-050522-499
    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
    smarcad1; wu:fi25c01; zgc:113183
    Summary
    Predicted to enable ATP-dependent chromatin remodeler activity. Predicted to be involved in DNA double-strand break processing. Predicted to act upstream of or within DNA repair and chromatin organization. Predicted to be located in site of double-strand break. Is expressed in several structures, including brain; intermediate cell mass of mesoderm; optic vesicle; retina; and tail bud. Human ortholog(s) of this gene implicated in BASAN syndrome and adermatoglyphia. Orthologous to human SMARCAD1 (SWI/SNF-related, matrix-associated actin-dependent regulator of chromatin, subfamily a, containing DEAD/H box 1). [provided by Alliance of Genome Resources, Oct 2024]
    Orthologs
    human mouse all
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    Genomic context

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    See smarcad1a in Genome Data Viewer
    Location:
    chromosome: 8
    Exon count:
    23
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCz11 (GCF_000002035.6) 8 NC_007119.7 (29635968..29652413)
    105 previous assembly GRCz10 (GCF_000002035.5) 8 NC_007119.6 (29626736..29643181)

    Chromosome 8 - NC_007119.7Genomic Context describing neighboring genes Neighboring gene glutamate receptor, ionotropic, delta 2 Neighboring gene atonal bHLH transcription factor 1a Neighboring gene macrophage expressed 1, tandem duplicate 3 Neighboring gene perforin 1.6

    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 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. Macrophage-expressed perforins mpeg1 and mpeg1.2 have an anti-bacterial function in zebrafish. Benard EL, et al. J Innate Immun, 2015. PMID 25247677, Free PMC Article
    2. Loss of smarcad1a accelerates tumorigenesis of malignant peripheral nerve sheath tumors in zebrafish. Han H, et al. Genes Chromosomes Cancer, 2021 Nov. PMID 34296799, Free PMC Article
    3. Proinflammatory Caspase A Activation and an Antiviral State Are Induced by a Zebrafish Perforin after Possible Cellular and Functional Diversification from a Myeloid Ancestor. Varela M, et al. J Innate Immun, 2016. PMID 26087843, Free PMC Article
    4. A network of epigenetic regulators guides developmental haematopoiesis in vivo. Huang HT, et al. Nat Cell Biol, 2013 Dec. PMID 24240475, Free PMC Article
    5. Comprehensive expression map of transcription regulators in the adult zebrafish telencephalon reveals distinct neurogenic niches. Diotel N, et al. J Comp Neurol, 2015 Jun 1. PMID 25556858, Free PMC Article

    See all (9) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Loss of smarcad1a accelerates tumorigenesis of malignant peripheral nerve sheath tumors in zebrafish.
      Title: Loss of smarcad1a accelerates tumorigenesis of malignant peripheral nerve sheath tumors in zebrafish.
    Submit: New GeneRIF Correction

    General gene information

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    Markers

    Homology

    Clone Names

    • MGC113183

    Gene Ontology Provided by ZFIN

    Function Evidence Code Pubs
    enables ATP binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables ATP hydrolysis activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables ATP-dependent chromatin remodeler activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables ATP-dependent chromatin remodeler activity ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    enables DNA binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables helicase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables hydrolase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables nucleotide binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables ubiquitin binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    Process Evidence Code Pubs
    acts_upstream_of_or_within DNA damage response IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in DNA double-strand break processing ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    acts_upstream_of_or_within DNA repair IEA
    Inferred from Electronic Annotation
    more info
    		  
    acts_upstream_of_or_within chromatin organization IEA
    Inferred from Electronic Annotation
    more info
    		  
    Component Evidence Code Pubs
    located_in chromosome IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in nucleus IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in site of double-strand break ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  

    General protein information

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    Preferred Names
    SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A containing DEAD/H box 1A
    Names
    SWI/SNF-related, matrix-associated actin-dependent regulator of chromatin, subfamily a, containing DEAD/H box 1 a
    NP_001018610.2

    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_001020774.2 → NP_001018610.2  SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A containing DEAD/H box 1A

      Status: VALIDATED

      Source sequence(s)
      AL715934, AL728037, BQ262749, CK026399, EB775335, EB909784, EB931438, EB931820, EE686075
      UniProtKB/Swiss-Prot
      B0R061
      UniProtKB/TrEMBL
      A0A8M1N6H2
      Related
      ENSDARP00000085842.5, ENSDART00000091409.7
      Conserved Domains (3) summary
      cd00046
      Location:468 → 610
      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.
      pfam00176
      Location:451 → 734
      SNF2_N; SNF2 family N-terminal domain
      pfam00271
      Location:800 → 914
      Helicase_C; Helicase conserved C-terminal domain

    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_007119.7 Reference GRCz11 Primary Assembly

      Range
      29635968..29652413
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Reference GRCz11 ALT_DRER_TU_1

    Genomic

    1. NW_018394729.1 Reference GRCz11 ALT_DRER_TU_1

      Range
      380588..397033
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Reference GRCz11 ALT_DRER_TU_2

    Genomic

    1. NW_018395274.1 Reference GRCz11 ALT_DRER_TU_2

      Range
      136471..151351
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Suppressed Reference Sequence(s)

    The following Reference Sequences have been suppressed. Explain

    1. NM_001110104.1: Suppressed sequence

      Description
      NM_001110104.1: This RefSeq was permanently suppressed because it is a nonsense-mediated mRNA decay (NMD) candidate.
    Nucleotide Protein Strain
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    B0R061.1 GenPept UniProtKB/Swiss-Prot:B0R061

    Gene LinkOut

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