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smarca4a SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 4a [ Danio rerio (zebrafish) ]

Gene ID: 353295, updated on 21-Dec-2022

Summary

Official Symbol
smarca4aprovided by ZNC
Official Full Name
SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 4aprovided by ZNC
Primary source
ZFIN:ZDB-GENE-030605-1
See related
Ensembl:ENSDARG00000077226 AllianceGenome:ZFIN:ZDB-GENE-030605-1
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
brg1; smarca2; smarca4; wu:fb51a08
Summary
Predicted to enable ATP-dependent activity, acting on DNA and DNA binding activity. Acts upstream of or within several processes, including animal organ development; fin regeneration; and nervous system development. Predicted to be part of SWI/SNF complex. Predicted to be active in nucleus. Is expressed in head; mesoderm; nervous system; pectoral fin; and presumptive neural retina. Human ortholog(s) of this gene implicated in Coffin-Siris syndrome 4; hepatocellular carcinoma; lung non-small cell carcinoma; and rhabdoid cancer. Orthologous to human SMARCA4 (SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 4). [provided by Alliance of Genome Resources, Apr 2022]
Orthologs
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Genomic context

See smarca4a in Genome Data Viewer
Location:
chromosome: 3
Exon count:
34
Annotation release Status Assembly Chr Location
106 current GRCz11 (GCF_000002035.6) 3 NC_007114.7 (19245782..19281878)
105 previous assembly GRCz10 (GCF_000002035.5) 3 NC_007114.6 (19099291..19131507)
103 previous assembly Zv9 (GCF_000002035.4) 3 NC_007114.5 (19067681..19103776)

Chromosome 3 - NC_007114.7Genomic Context describing neighboring genes Neighboring gene relaxin 3a Neighboring gene interleukin 12 receptor, beta 2a, like Neighboring gene low density lipoprotein receptor a Neighboring gene KRI1 homolog

Genomic regions, transcripts, and products

Expression

  • 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

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Pathways from PubChem

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Gene Ontology Provided by ZFIN

Function Evidence Code Pubs
enables ATP binding IEA
Inferred from Electronic Annotation
more info
 
enables ATP-dependent activity, acting on DNA IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
enables DNA binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
enables helicase activity IEA
Inferred from Electronic Annotation
more info
 
enables histone binding 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 transcription factor binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
Process Evidence Code Pubs
acts_upstream_of_or_within cardiac muscle cell proliferation IMP
Inferred from Mutant Phenotype
more info
PubMed 
acts_upstream_of_or_within cell migration involved in heart development IMP
Inferred from Mutant Phenotype
more info
PubMed 
acts_upstream_of_or_within central nervous system development IMP
Inferred from Mutant Phenotype
more info
PubMed 
acts_upstream_of_or_within chromatin remodeling IEA
Inferred from Electronic Annotation
more info
 
acts_upstream_of_or_within embryonic camera-type eye morphogenesis IMP
Inferred from Mutant Phenotype
more info
 
acts_upstream_of_or_within embryonic retina morphogenesis in camera-type eye IMP
Inferred from Mutant Phenotype
more info
PubMed 
acts_upstream_of_or_within embryonic viscerocranium morphogenesis IMP
Inferred from Mutant Phenotype
more info
PubMed 
acts_upstream_of_or_within fin regeneration IMP
Inferred from Mutant Phenotype
more info
PubMed 
acts_upstream_of_or_within heart looping IMP
Inferred from Mutant Phenotype
more info
PubMed 
acts_upstream_of_or_within neural crest cell development IMP
Inferred from Mutant Phenotype
more info
PubMed 
acts_upstream_of_or_within neural crest cell differentiation IMP
Inferred from Mutant Phenotype
more info
PubMed 
acts_upstream_of_or_within neural retina development IMP
Inferred from Mutant Phenotype
more info
PubMed 
acts_upstream_of_or_within neuron differentiation IMP
Inferred from Mutant Phenotype
more info
PubMed 
acts_upstream_of_or_within optic nerve formation IMP
Inferred from Mutant Phenotype
more info
PubMed 
acts_upstream_of_or_within positive regulation of MAPK cascade IMP
Inferred from Mutant Phenotype
more info
 
involved_in positive regulation of transcription by RNA polymerase II IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
acts_upstream_of_or_within regulation of DNA-templated transcription IEA
Inferred from Electronic Annotation
more info
 
acts_upstream_of_or_within retina layer formation IMP
Inferred from Mutant Phenotype
more info
PubMed 
acts_upstream_of_or_within retinal pigment epithelium development IMP
Inferred from Mutant Phenotype
more info
PubMed 
Component Evidence Code Pubs
part_of SWI/SNF complex IEA
Inferred from Electronic Annotation
more info
 
is_active_in nucleus IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
located_in nucleus IEA
Inferred from Electronic Annotation
more info
 

General protein information

Preferred Names
SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 4a; transcription activator BRG1
Names
SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 2
SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 4
brahma protein-like protein 1
brahma-related gene 1
yng
young

NCBI Reference Sequences (RefSeq)

NEW Try the new Transcript table

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_181603.1NP_853634.1  SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 4a

    See identical proteins and their annotated locations for NP_853634.1

    Status: PROVISIONAL

    Source sequence(s)
    AY205256
    UniProtKB/TrEMBL
    F6NKY0, Q7ZSY3
    Related
    ENSDARP00000143385.1, ENSDART00000174668.2
    Conserved Domains (8) summary
    cd05516
    Location:14401545
    Bromo_SNF2L2; Bromodomain, SNF2L2-like subfamily, specific to animals. SNF2L2 (SNF2-alpha) or SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A member 2 is a global transcriptional activator, which cooperates with nuclear hormone ...
    smart00573
    Location:478550
    HSA; domain in helicases and associated with SANT domains
    pfam07533
    Location:630670
    BRK; BRK domain
    pfam08880
    Location:198231
    QLQ; QLQ
    pfam09606
    Location:65378
    Med15; ARC105 or Med15 subunit of Mediator complex non-fungal
    pfam14619
    Location:13011368
    SnAC; Snf2-ATP coupling, chromatin remodelling complex
    cl25732
    Location:388595
    SMC_N; RecF/RecN/SMC N terminal domain
    cl26465
    Location:7621244
    SNF2_N; SNF2 family N-terminal domain

RefSeqs of Annotated Genomes: Danio rerio Annotation Release 106 details...Open this link in a new tab

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
    19245782..19281878
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_021469728.1XP_021325403.1  transcription activator BRG1 isoform X1

    UniProtKB/TrEMBL
    F6NKY0
    Related
    ENSDARP00000120295.1, ENSDART00000134514.2
    Conserved Domains (8) summary
    cd05516
    Location:14401545
    Bromo_SNF2L2; Bromodomain, SNF2L2-like subfamily, specific to animals. SNF2L2 (SNF2-alpha) or SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A member 2 is a global transcriptional activator, which cooperates with nuclear hormone ...
    smart00573
    Location:478550
    HSA; domain in helicases and associated with SANT domains
    pfam07533
    Location:630670
    BRK; BRK domain
    pfam08880
    Location:198231
    QLQ; QLQ
    pfam09606
    Location:65378
    Med15; ARC105 or Med15 subunit of Mediator complex non-fungal
    pfam14619
    Location:13011368
    SnAC; Snf2-ATP coupling, chromatin remodelling complex
    cl25732
    Location:388595
    SMC_N; RecF/RecN/SMC N terminal domain
    cl26465
    Location:7621244
    SNF2_N; SNF2 family N-terminal domain