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smarcd3b SWI/SNF related BAF chromatin remodeling complex subunit D3b [ Danio rerio (zebrafish) ]

Gene ID: 562140, updated on 4-Jan-2025

Summary

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Official Symbol
smarcd3bprovided by ZNC
Official Full Name
SWI/SNF related BAF chromatin remodeling complex subunit D3bprovided by ZNC
Primary source
ZFIN:ZDB-GENE-080509-2
See related
Ensembl:ENSDARG00000019969 AllianceGenome:ZFIN:ZDB-GENE-080509-2
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
Summary
Acts upstream of or within cardiac muscle cell differentiation; determination of left/right symmetry; and heart morphogenesis. Is expressed in several structures, including brain; immature eye; margin; notochord; and tail bud. Orthologous to human SMARCD3 (SWI/SNF related BAF chromatin remodeling complex subunit D3). [provided by Alliance of Genome Resources, Jan 2025]
Orthologs
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Genomic context

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See smarcd3b in Genome Data Viewer
Location:
chromosome: 7
Exon count:
16
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCz11 (GCF_000002035.6) 7 NC_007118.7 (41436489..41490002, complement)
105 previous assembly GRCz10 (GCF_000002035.5) 7 NC_007118.6 (41156416..41209985, complement)

Chromosome 7 - NC_007118.7Genomic Context describing neighboring genes Neighboring gene ATP-binding cassette, sub-family F (GCN20), member 2b Neighboring gene chondroitin polymerizing factor 2 Neighboring gene nuclear transcription factor, X-box binding 1 Neighboring gene plexin domain containing 2b

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. Low-level pyrene exposure causes cardiac toxicity in zebrafish (Danio rerio) embryos. Zhang Y, et al. Aquat Toxicol, 2012 Jun 15. PMID 22446823
  2. Assessment of environmentally contaminated sediment using a contact assay with early life stage zebrafish (Danio rerio). Boulanger E, et al. Sci Total Environ, 2019 Apr 1. PMID 31096425
  3. Smarcd3b and Gata5 promote a cardiac progenitor fate in the zebrafish embryo. Lou X, et al. Development, 2011 Aug. PMID 21715426
  4. Smarcd3 regulates the timing of zebrafish myogenesis onset. Ochi H, et al. J Biol Chem, 2008 Feb 8. PMID 18056260
  5. Developmental toxicity and alteration of gene expression in zebrafish embryo exposed to 6-benzylaminopurine. Wang W, et al. Chemosphere, 2019 Oct. PMID 31176896

See all (15) 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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Homology

Gene Ontology Provided by ZFIN

Process Evidence Code Pubs
acts_upstream_of_or_within cardiac muscle cell differentiation IGI
Inferred from Genetic Interaction
more info
 PubMed 
acts_upstream_of_or_within determination of left/right symmetry IMP
Inferred from Mutant Phenotype
more info
 PubMed 
acts_upstream_of_or_within heart morphogenesis IGI
Inferred from Genetic Interaction
more info
 PubMed 

General protein information

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Preferred Names
SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily D member 3b
Names
SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily d, member 3b
smarcd3
smarcd3l

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_001127306.1 → NP_001120778.1  SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily D member 3b

    See identical proteins and their annotated locations for NP_001120778.1

    Status: PROVISIONAL

    Source sequence(s)
    EF552706
    UniProtKB/TrEMBL
    A0A8M1NGY2, B2KL77
    Related
    ENSDARP00000143064.1, ENSDART00000174087.2
    Conserved Domains (2) summary
    COG5531
    Location:172 → 369
    Rsc6; Chromatin remodeling complex protein RSC6, contains SWIB domain [Chromatin structure and dynamics]
    pfam02201
    Location:255 → 326
    SWIB; SWIB/MDM2 domain

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_007118.7 Reference GRCz11 Primary Assembly

    Range
    41436489..41490002 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_005166419.5 → XP_005166476.1  SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily D member 3b isoform X4

    UniProtKB/TrEMBL
    A0A8M2BDZ5
    Conserved Domains (2) summary
    COG5531
    Location:150 → 347
    Rsc6; Chromatin remodeling complex protein RSC6, contains SWIB domain [Chromatin structure and dynamics]
    pfam02201
    Location:233 → 304
    SWIB; SWIB/MDM2 domain

  2. XM_021477564.2 → XP_021333239.1  SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily D member 3b isoform X2

    UniProtKB/TrEMBL
    A0A8M9Q7X8
    Related
    ENSDARP00000015411.10, ENSDART00000006724.12
    Conserved Domains (1) summary
    pfam02201
    Location:289 → 360
    SWIB; SWIB/MDM2 domain

  3. XM_005166417.5 → XP_005166474.1  SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily D member 3b isoform X3

    UniProtKB/TrEMBL
    A0A8M2BDT5
    Conserved Domains (2) summary
    COG5531
    Location:202 → 399
    Rsc6; Chromatin remodeling complex protein RSC6, contains SWIB domain [Chromatin structure and dynamics]
    pfam02201
    Location:285 → 356
    SWIB; SWIB/MDM2 domain

  4. XM_021477563.2 → XP_021333238.1  SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily D member 3b isoform X1

    UniProtKB/TrEMBL
    A0A8M9Q1P6
    Conserved Domains (1) summary
    pfam02201
    Location:311 → 382
    SWIB; SWIB/MDM2 domain
Nucleotide Protein
Heading Accession and Version

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