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smarcb1b SWI/SNF related BAF chromatin remodeling complex subunit B1b [ Danio rerio (zebrafish) ]

Gene ID: 30731, updated on 2-Nov-2024

Summary

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Official Symbol
smarcb1bprovided by ZNC
Official Full Name
SWI/SNF related BAF chromatin remodeling complex subunit B1bprovided by ZNC
Primary source
ZFIN:ZDB-GENE-991008-16
See related
Ensembl:ENSDARG00000011594 AllianceGenome:ZFIN:ZDB-GENE-991008-16
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
fc51b01; smarcb1; wu:fc51b01
Summary
Predicted to enable 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, Nov 2024]
Orthologs
all
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Genomic context

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See smarcb1b in Genome Data Viewer
Location:
chromosome: 21
Exon count:
10
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCz11 (GCF_000002035.6) 21 NC_007132.7 (15601254..15618777)
105 previous assembly GRCz10 (GCF_000002035.5) 21 NC_007132.6 (15505190..15522800)

Chromosome 21 - NC_007132.7Genomic Context describing neighboring genes Neighboring gene si:dkey-11o15.10 Neighboring gene uncharacterized LOC137488790 Neighboring gene matrix metallopeptidase 11b Neighboring gene coiled-coil-helix-coiled-coil-helix domain containing 10

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. Molecular characterization of the zebrafish P2X receptor subunit gene family. Kucenas S, et al. Neuroscience, 2003. PMID 14580944
  3. Somatic mutagenesis with a Sleeping Beauty transposon system leads to solid tumor formation in zebrafish. McGrail M, et al. PLoS One, 2011 Apr 21. PMID 21533036, Free PMC Article
  4. Zebrafish miR-1 and miR-133 shape muscle gene expression and regulate sarcomeric actin organization. Mishima Y, et al. Genes Dev, 2009 Mar 1. PMID 19240126, Free PMC Article
  5. A Toolbox for Efficient Proximity-Dependent Biotinylation in Zebrafish Embryos. Rosenthal SM, et al. Mol Cell Proteomics, 2021. PMID 34332124, Free PMC Article

See all (10) citations in PubMed

GeneRIFs: Gene References Into Functions

Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Clone Names

  • MGC101626

Gene Ontology Provided by ZFIN

Function Evidence Code Pubs
enables DNA binding IEA
Inferred from Electronic Annotation
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 1b
Names
SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily b, member 1b
SWI/SNF-related matrix associated protein

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_131448.1 → NP_571523.1  SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily B member 1b

    See identical proteins and their annotated locations for NP_571523.1

    Status: PROVISIONAL

    Source sequence(s)
    BC083229
    UniProtKB/TrEMBL
    Q5XJR9
    Related
    ENSDARP00000116163.1, ENSDART00000145454.3
    Conserved Domains (1) summary
    pfam04855
    Location:162 → 348
    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_007132.7 Reference GRCz11 Primary Assembly

    Range
    15601254..15618777
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_005161146.4 → XP_005161203.2  SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily B member 1b isoform X1

    Related
    ENSDARP00000157418.1, ENSDART00000180558.1

RNA

  1. XR_011007954.1 RNA Sequence

Nucleotide Protein
Heading Accession and Version

Gene LinkOut

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