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    smarca1 SNF2 related chromatin remodeling ATPase 1 [ Danio rerio (zebrafish) ]

    Gene ID: 559803, updated on 2-Nov-2024

    Summary

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    Official Symbol
    smarca1provided by ZNC
    Official Full Name
    SNF2 related chromatin remodeling ATPase 1provided by ZNC
    Primary source
    ZFIN:ZDB-GENE-070705-296
    See related
    Ensembl:ENSDARG00000012776 AllianceGenome:ZFIN:ZDB-GENE-070705-296
    Gene type
    protein coding
    RefSeq status
    PROVISIONAL
    Organism
    Danio rerio
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Actinopterygii; Neopterygii; Teleostei; Ostariophysi; Cypriniformes; Danionidae; Danioninae; Danio
    Also known as
    si:dkey-148b12.1
    Summary
    Predicted to enable DNA binding activity; chromatin binding activity; and nucleosome array spacer activity. Acts upstream of or within neural plate anterior/posterior regionalization and primitive erythrocyte differentiation. Predicted to be located in chromatin. Predicted to be active in nucleus. Orthologous to human SMARCA1 (SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 1). [provided by Alliance of Genome Resources, Nov 2024]
    Orthologs
    all
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    Genomic context

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    See smarca1 in Genome Data Viewer
    Location:
    chromosome: 5
    Exon count:
    25
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCz11 (GCF_000002035.6) 5 NC_007116.7 (21852714..21888360, complement)
    105 previous assembly GRCz10 (GCF_000002035.5) 5 NC_007116.6 (21348908..21384573, complement)

    Chromosome 5 - NC_007116.7Genomic Context describing neighboring genes Neighboring gene SH2 domain containing 1A duplicate a Neighboring gene uncharacterized LOC137495578 Neighboring gene teneurin transmembrane protein 1 Neighboring gene uncharacterized LOC137495580 Neighboring gene GRB2 associated binding protein 3 Neighboring gene Cdc42 guanine nucleotide exchange factor (GEF) 9a

    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. The Chromatin Remodeling Protein Bptf Promotes Posterior Neuroectodermal Fate by Enhancing Smad2-Activated wnt8a Expression. Ma Y, et al. J Neurosci, 2015 Jun 3. PMID 26041917, Free PMC Article
    2. Efficient identification of CRISPR/Cas9-induced insertions/deletions by direct germline screening in zebrafish. Brocal I, et al. BMC Genomics, 2016 Mar 24. PMID 27009152, Free PMC Article
    3. Large-scale generation and phenotypic characterization of zebrafish CRISPR mutants of DNA repair genes. Shin U, et al. DNA Repair (Amst), 2021 Nov. PMID 34390914
    4. The SARS-CoV-2 receptor and other key components of the Renin-Angiotensin-Aldosterone System related to COVID-19 are expressed in enterocytes in larval zebrafish. Postlethwait JH, et al. Biol Open, 2021 Mar 23. PMID 33757938, Free PMC Article
    5. A network of epigenetic regulators guides developmental haematopoiesis in vivo. Huang HT, et al. Nat Cell Biol, 2013 Dec. PMID 24240475, Free PMC Article

    See all (8) citations in PubMed

    GeneRIFs: Gene References Into Functions

    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
    		  
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    acts_upstream_of_or_within chromatin remodeling IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in heterochromatin formation IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    acts_upstream_of_or_within neural plate anterior/posterior regionalization IGI
    Inferred from Genetic Interaction
    more info
    		 PubMed 
    involved_in positive regulation of transcription by RNA polymerase II IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    acts_upstream_of_or_within primitive erythrocyte differentiation IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    acts_upstream_of_or_within primitive hemopoiesis 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
    probable global transcription activator SNF2L1
    Names
    SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 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.

    mRNA and Protein(s)

    1. NM_001099997.1 → NP_001093467.1  probable global transcription activator SNF2L1

      Status: PROVISIONAL

      Source sequence(s)
      CR848717, CU104724
      UniProtKB/TrEMBL
      A0A8M1NDM3, A5WUY4
      Related
      ENSDARP00000023313.8, ENSDART00000020725.10
      Conserved Domains (7) summary
      PLN03142
      Location:54 → 1033
      PLN03142; Probable chromatin-remodeling complex ATPase chain; Provisional
      cd00046
      Location:163 → 302
      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:829 → 868
      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:444 → 559
      Helicase_C; Helicase conserved C-terminal domain
      pfam09110
      Location:728 → 811
      HAND; HAND
      pfam09111
      Location:883 → 995
      SLIDE; SLIDE
      pfam13892
      Location:44 → 70
      DBINO; DNA-binding 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_007116.7 Reference GRCz11 Primary Assembly

      Range
      21852714..21888360 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_005165157.5 → XP_005165214.1  probable global transcription activator SNF2L1 isoform X1

      UniProtKB/TrEMBL
      A0A8M2BCD5
      Conserved Domains (7) summary
      PLN03142
      Location:54 → 1012
      PLN03142; Probable chromatin-remodeling complex ATPase chain; Provisional
      cd00046
      Location:163 → 302
      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:808 → 847
      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:444 → 559
      Helicase_C; Helicase conserved C-terminal domain
      pfam09110
      Location:707 → 790
      HAND; HAND
      pfam09111
      Location:862 → 974
      SLIDE; SLIDE
      pfam13892
      Location:44 → 70
      DBINO; DNA-binding domain
    Nucleotide Protein Strain
    Heading Accession and Version

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