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    smarcc1a SWI/SNF related BAF chromatin remodeling complex subunit C1a [ Danio rerio (zebrafish) ]

    Gene ID: 403020, updated on 14-Nov-2024

    Summary

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    Official Symbol
    smarcc1aprovided by ZNC
    Official Full Name
    SWI/SNF related BAF chromatin remodeling complex subunit C1aprovided by ZNC
    Primary source
    ZFIN:ZDB-GENE-080514-3
    See related
    Ensembl:ENSDARG00000017397 AllianceGenome:ZFIN:ZDB-GENE-080514-3
    Gene type
    protein coding
    RefSeq status
    MODEL
    Organism
    Danio rerio
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Actinopterygii; Neopterygii; Teleostei; Ostariophysi; Cypriniformes; Danionidae; Danioninae; Danio
    Also known as
    smarcc1
    Summary
    Predicted to enable histone binding activity. Acts upstream of or within definitive hemopoiesis and heart morphogenesis. Located in cytoplasm and nucleus. Is expressed in head; tail bud; and telencephalon. Human ortholog(s) of this gene implicated in hydrocephalus. Orthologous to human SMARCC1 (SWI/SNF related, matrix associated, actin dependent regulator of chromatin subfamily c member 1). [provided by Alliance of Genome Resources, Nov 2024]
    Orthologs
    human mouse all
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    Genomic context

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    See smarcc1a in Genome Data Viewer
    Location:
    chromosome: 16
    Exon count:
    28
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCz11 (GCF_000002035.6) 16 NC_007127.7 (42423530..42461243, complement)
    105 previous assembly GRCz10 (GCF_000002035.5) 16 NC_007127.6 (42519652..42557612, complement)

    Chromosome 16 - NC_007127.7Genomic Context describing neighboring genes Neighboring gene protoporphyrinogen oxidase Neighboring gene chondroitin sulfate proteoglycan 5a Neighboring gene si:ch211-215k15.4 Neighboring gene protein kinase-like domain containing

    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. Nuclear/cytoplasmic transport defects in BBS6 underlie congenital heart disease through perturbation of a chromatin remodeling protein. Scott CA, et al. PLoS Genet, 2017 Jul. PMID 28753627, Free PMC Article
    2. Zebrafish smarcc1a mutants reveal requirements for BAF chromatin remodeling complexes in distinguishing the atrioventricular canal from the cardiac chambers. Auman HJ, et al. Dev Dyn, 2024 Jan. PMID 37083132,
    3. A Toolbox for Efficient Proximity-Dependent Biotinylation in Zebrafish Embryos. Rosenthal SM, et al. Mol Cell Proteomics, 2021. PMID 34332124, 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 (8) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Zebrafish smarcc1a mutants reveal requirements for BAF chromatin remodeling complexes in distinguishing the atrioventricular canal from the cardiac chambers.
      Title: Zebrafish smarcc1a mutants reveal requirements for BAF chromatin remodeling complexes in distinguishing the atrioventricular canal from the cardiac chambers.
    2. We demonstrate that through this interaction, BBS6 modulates the sub-cellular localization of SMARCC1 and find, by transcriptional profiling, similar transcriptional changes following smarcc1a and bbs6 manipulation. Our work identifies a new function for BBS6 in nuclear-cytoplasmic transport, and provides insight into the disease mechanism underlying the congenital heart defects in McKusick-Kaufman syndrome patients.
      Title: Nuclear/cytoplasmic transport defects in BBS6 underlie congenital heart disease through perturbation of a chromatin remodeling protein.
    Submit: New GeneRIF Correction

    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 ZFIN

    Function Evidence Code Pubs
    enables histone binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Process Evidence Code Pubs
    acts_upstream_of_or_within cardiac chamber morphogenesis IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    acts_upstream_of_or_within definitive hemopoiesis IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    acts_upstream_of_or_within heart morphogenesis IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in positive regulation of DNA-templated transcription IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Component Evidence Code Pubs
    part_of SWI/SNF complex IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in cytoplasm IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    part_of nBAF complex IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    part_of npBAF complex IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in nucleus IDA
    Inferred from Direct Assay
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    SWI/SNF complex subunit SMARCC1
    Names
    SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily c, member 1
    SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily c, member 1a

    NCBI Reference Sequences (RefSeq)

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    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_007127.7 Reference GRCz11 Primary Assembly

      Range
      42423530..42461243 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_005158282.5 → XP_005158339.1  SWI/SNF complex subunit SMARCC1 isoform X2

      UniProtKB/TrEMBL
      A0A8M2B4M4
      Conserved Domains (5) summary
      COG5259
      Location:431 → 696
      RSC8; RSC chromatin remodeling complex subunit RSC8 [Chromatin structure and dynamics / Transcription]
      pfam04433
      Location:439 → 524
      SWIRM; SWIRM domain
      pfam16495
      Location:879 → 950
      SWIRM-assoc_1; SWIRM-associated region 1
      pfam16496
      Location:29 → 432
      SWIRM-assoc_2; SWIRM-associated domain at the N-terminal
      pfam16498
      Location:692 → 752
      SWIRM-assoc_3; SWIRM-associated domain at the C-terminal

    2. XM_003200246.6 → XP_003200294.1  SWI/SNF complex subunit SMARCC1 isoform X1

      UniProtKB/TrEMBL
      A0A8M1RJ59, F1Q9K1
      Related
      ENSDARP00000103197.2, ENSDART00000109259.4
      Conserved Domains (5) summary
      COG5259
      Location:439 → 704
      RSC8; RSC chromatin remodeling complex subunit RSC8 [Chromatin structure and dynamics / Transcription]
      pfam04433
      Location:447 → 532
      SWIRM; SWIRM domain
      pfam16495
      Location:887 → 958
      SWIRM-assoc_1; SWIRM-associated region 1
      pfam16496
      Location:29 → 440
      SWIRM-assoc_2; SWIRM-associated domain at the N-terminal
      pfam16498
      Location:700 → 760
      SWIRM-assoc_3; SWIRM-associated domain at the C-terminal
    Nucleotide Protein Strain
    Heading Accession and Version

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