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    smarce1 SWI/SNF related BAF chromatin remodeling complex subunit E1 [ Danio rerio (zebrafish) ]

    Gene ID: 322248, updated on 9-Dec-2024

    Summary

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    Official Symbol
    smarce1provided by ZNC
    Official Full Name
    SWI/SNF related BAF chromatin remodeling complex subunit E1provided by ZNC
    Primary source
    ZFIN:ZDB-GENE-030131-967
    See related
    Ensembl:ENSDARG00000016871 AllianceGenome:ZFIN:ZDB-GENE-030131-967
    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
    baf57; fb33d02; fb54d11; wu:fb33d02; wu:fb54d11
    Summary
    Predicted to enable nuclear receptor binding activity. Acts upstream of or within endocardium morphogenesis. Predicted to be located in nucleus. Predicted to be part of SWI/SNF complex. Is expressed in telencephalon. Human ortholog(s) of this gene implicated in Coffin-Siris syndrome 5; familial meningioma; and meningioma. Orthologous to human SMARCE1 (SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily e, member 1). [provided by Alliance of Genome Resources, Dec 2024]
    Orthologs
    human mouse all
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    Genomic context

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    See smarce1 in Genome Data Viewer
    Location:
    chromosome: 3
    Exon count:
    11
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCz11 (GCF_000002035.6) 3 NC_007114.7 (34985913..34994988)
    105 previous assembly GRCz10 (GCF_000002035.5) 3 NC_007114.6 (34856360..34865480)

    Chromosome 3 - NC_007114.7Genomic Context describing neighboring genes Neighboring gene integrin, alpha 3a Neighboring gene fatty acid-binding protein, heart-like Neighboring gene carbonic anhydrase Xb Neighboring gene protein kinase C, beta b Neighboring gene calcium channel, voltage-dependent, gamma subunit 3b

    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. smarce1 mutants have a defective endocardium and an increased expression of cardiac transcription factors in zebrafish. Castillo-Robles J, et al. Sci Rep, 2018 Oct 18. PMID 30337622, Free PMC Article
    2. RNA sequencing provides insights into the toxicogenomic response of ZF4 cells to methyl methanesulfonate. Li Z, et al. J Appl Toxicol, 2016 Jan. PMID 26011545
    3. Transcriptional events co-regulated by hypoxia and cold stresses in Zebrafish larvae. Long Y, et al. BMC Genomics, 2015 May 15. PMID 25975375, Free PMC Article
    4. A single-cell resolution developmental atlas of hematopoietic stem and progenitor cell expansion in zebrafish. Xia J, et al. Proc Natl Acad Sci U S A, 2021 Apr 6. PMID 33785593, Free PMC Article
    5. Allele-specific gene expression can underlie altered transcript abundance in zebrafish mutants. White RJ, et al. Elife, 2022 Feb 17. PMID 35175196, Free PMC Article

    See all (12) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Smarce1 binds to cis-regulatory regions of the gata5 gene and is necessary for the recruitment of the BAF complex to these regions.
      Title: smarce1 mutants have a defective endocardium and an increased expression of cardiac transcription factors in zebrafish.
    Submit: New GeneRIF Correction

    Pathways from PubChem

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    General gene information

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    Markers

    Homology

    Gene Ontology Provided by ZFIN

    Function Evidence Code Pubs
    enables DNA binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    Process Evidence Code Pubs
    acts_upstream_of_or_within endocardium morphogenesis IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    Component Evidence Code Pubs
    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 E member 1
    Names
    SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily e, 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_201298.1 → NP_958455.2  SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily E member 1

      See identical proteins and their annotated locations for NP_958455.2

      Status: PROVISIONAL

      Source sequence(s)
      BC044363
      UniProtKB/TrEMBL
      B2GQG3, F6P3C7, Q6NYW7, Q803S1
      Related
      ENSDARP00000112446.2, ENSDART00000121981.3
      Conserved Domains (1) summary
      cd01390
      Location:68 → 129
      HMGB-UBF_HMG-box; HMGB-UBF_HMG-box, class II and III members of the HMG-box superfamily of DNA-binding proteins. These proteins bind the minor groove of DNA in a non-sequence specific fashion and contain two or more tandem HMG boxes. Class II members include non-histone ...

    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_007114.7 Reference GRCz11 Primary Assembly

      Range
      34985913..34994988
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_005163989.5 → XP_005164046.1  SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily E member 1 isoform X1

      UniProtKB/TrEMBL
      A0A8M2BB53
      Conserved Domains (1) summary
      cd01390
      Location:70 → 135
      HMGB-UBF_HMG-box; HMGB-UBF_HMG-box, class II and III members of the HMG-box superfamily of DNA-binding proteins. These proteins bind the minor groove of DNA in a non-sequence specific fashion and contain two or more tandem HMG boxes. Class II members include non-histone ...

    2. XM_005163990.5 → XP_005164047.1  SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily E member 1 isoform X3

      UniProtKB/TrEMBL
      A0A8M2BBH2
      Conserved Domains (1) summary
      cd01390
      Location:70 → 131
      HMGB-UBF_HMG-box; HMGB-UBF_HMG-box, class II and III members of the HMG-box superfamily of DNA-binding proteins. These proteins bind the minor groove of DNA in a non-sequence specific fashion and contain two or more tandem HMG boxes. Class II members include non-histone ...

    3. XM_009299517.4 → XP_009297792.1  SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily E member 1 isoform X2

      UniProtKB/TrEMBL
      A0A8M3AQX7
      Related
      ENSDARP00000024751.7, ENSDART00000011319.8
      Conserved Domains (1) summary
      cd01390
      Location:68 → 133
      HMGB-UBF_HMG-box; HMGB-UBF_HMG-box, class II and III members of the HMG-box superfamily of DNA-binding proteins. These proteins bind the minor groove of DNA in a non-sequence specific fashion and contain two or more tandem HMG boxes. Class II members include non-histone ...

    4. XM_021469404.2 → XP_021325079.1  SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily E member 1 isoform X4

      UniProtKB/TrEMBL
      A0A8M9PJR1
      Conserved Domains (2) summary
      cd01390
      Location:35 → 100
      HMGB-UBF_HMG-box; class II and III members of the HMG-box superfamily of DNA-binding proteins. These proteins bind the minor groove of DNA in a non-sequence specific fashion and contain two or more tandem HMG boxes. Class II members include non-histone chromosomal ...
      cl00478
      Location:281 → 379
      LGT; Prolipoprotein diacylglyceryl transferase

    5. XM_021469407.2 → XP_021325082.1  SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily E member 1 isoform X5

      UniProtKB/TrEMBL
      A0A8M9P4E1
      Conserved Domains (2) summary
      cd01390
      Location:35 → 96
      HMGB-UBF_HMG-box; class II and III members of the HMG-box superfamily of DNA-binding proteins. These proteins bind the minor groove of DNA in a non-sequence specific fashion and contain two or more tandem HMG boxes. Class II members include non-histone chromosomal ...
      cl00478
      Location:277 → 375
      LGT; Prolipoprotein diacylglyceryl transferase
    Nucleotide Protein Strain
    Heading Accession and Version

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