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

Gene ID: 322248, updated on 27-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 DNA binding activity. Acts upstream of or within endocardium morphogenesis. Predicted to be located in nucleus. 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 BAF chromatin remodeling complex subunit E1). [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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