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smarcb1a SWI/SNF related BAF chromatin remodeling complex subunit B1a [ Danio rerio (zebrafish) ]

Gene ID: 799716, updated on 28-Oct-2024

Summary

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Official Symbol
smarcb1aprovided by ZNC
Official Full Name
SWI/SNF related BAF chromatin remodeling complex subunit B1aprovided by ZNC
Primary source
ZFIN:ZDB-GENE-041114-5
See related
Ensembl:ENSDARG00000033647 AllianceGenome:ZFIN:ZDB-GENE-041114-5
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
zgc:92517
Summary
Predicted to enable DNA binding activity and transcription coactivator activity. Predicted to be involved in chromatin remodeling and regulation of transcription by RNA polymerase II. Predicted to be located in nuclear chromosome. Predicted to be part of brahma complex; nBAF complex; and npBAF complex. Predicted to be active in nucleus. Human ortholog(s) of this gene implicated in Coffin-Siris syndrome 3; central nervous system cancer (multiple); rhabdoid cancer; and schwannomatosis (multiple). Orthologous to human SMARCB1 (SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily b, member 1). [provided by Alliance of Genome Resources, Oct 2024]
Orthologs
all
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Genomic context

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See smarcb1a in Genome Data Viewer
Location:
chromosome: 8
Exon count:
9
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCz11 (GCF_000002035.6) 8 NC_007119.7 (30929704..30944465, complement)
105 previous assembly GRCz10 (GCF_000002035.5) 8 NC_007119.6 (30920472..30935241, complement)

Chromosome 8 - NC_007119.7Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC137496364 Neighboring gene derlin 3 Neighboring gene ral guanine nucleotide dissociation stimulator Neighboring gene prostaglandin E synthase 2-like

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. p53 Pathway Inactivation Drives SMARCB1-deficient p53-wildtype Epithelioid Sarcoma Onset Indicating Therapeutic Vulnerability Through MDM2 Inhibition. Oppel F, et al. Mol Cancer Ther, 2022 Nov 3. PMID 36099437
  2. A network of epigenetic regulators guides developmental haematopoiesis in vivo. Huang HT, et al. Nat Cell Biol, 2013 Dec. PMID 24240475, Free PMC Article
  3. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. Strausberg RL, et al. Proc Natl Acad Sci U S A, 2002 Dec 24. PMID 12477932, Free PMC Article
  4. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Gaudet P, et al. Brief Bioinform, 2011 Sep. PMID 21873635, Free PMC Article

GeneRIFs: Gene References Into Functions

Pathways from PubChem

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General gene information

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Homology

Clone Names

  • MGC92517

Gene Ontology Provided by ZFIN

Function Evidence Code Pubs
enables DNA binding IEA
Inferred from Electronic Annotation
more info
  
enables DNA binding ISS
Inferred from Sequence or Structural Similarity
more info
  
enables transcription coactivator activity IBA
Inferred from Biological aspect of Ancestor
more info
  
Process Evidence Code Pubs
involved_in chromatin remodeling IBA
Inferred from Biological aspect of Ancestor
more info
  
acts_upstream_of_or_within chromatin remodeling IEA
Inferred from Electronic Annotation
more info
  
involved_in regulation of transcription by RNA polymerase II IBA
Inferred from Biological aspect of Ancestor
more info
  
Component Evidence Code Pubs
part_of brahma complex IBA
Inferred from Biological aspect of Ancestor
more info
  
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 nuclear chromosome IEA
Inferred from Electronic Annotation
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
SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily B member 1-A
Names
SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily b, member 1a
SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily B 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_001007296.1 → NP_001007297.1  SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily B member 1-A

    See identical proteins and their annotated locations for NP_001007297.1

    Status: PROVISIONAL

    Source sequence(s)
    BC085668
    UniProtKB/Swiss-Prot
    Q5U379
    Related
    ENSDARP00000049943.7, ENSDART00000049944.9
    Conserved Domains (1) summary
    pfam04855
    Location:169 → 351
    SNF5; SNF5 / SMARCB1 / INI1

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_007119.7 Reference GRCz11 Primary Assembly

    Range
    30929704..30944465 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_005167183.5 → XP_005167240.1  SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily B member 1-A isoform X1

    See identical proteins and their annotated locations for XP_005167240.1

    UniProtKB/TrEMBL
    A0A8M2BEM2, A8WG87
    Related
    ENSDARP00000150055.1, ENSDART00000191717.1
    Conserved Domains (1) summary
    pfam04855
    Location:162 → 344
    SNF5; SNF5 / SMARCB1 / INI1

Reference GRCz11 ALT_DRER_TU_1

Genomic

  1. NW_018394732.1 Reference GRCz11 ALT_DRER_TU_1

    Range
    162395..178512 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein Strain
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q5U379.1 GenPept UniProtKB/Swiss-Prot:Q5U379

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