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    Smarcd3 SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily d, member 3 [ Rattus norvegicus (Norway rat) ]

    Gene ID: 296732, updated on 6-Jun-2024

    Summary

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    Official Symbol
    Smarcd3provided by RGD
    Official Full Name
    SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily d, member 3provided by RGD
    Primary source
    RGD:1311869
    See related
    Ensembl:ENSRNOG00000010077 AllianceGenome:RGD:1311869
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Rattus norvegicus
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
    Summary
    Enables chromatin binding activity. Involved in positive regulation of G2/M transition of mitotic cell cycle and positive regulation of smooth muscle cell differentiation. Located in nucleus. Orthologous to human SMARCD3 (SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily d, member 3). [provided by Alliance of Genome Resources, Apr 2022]
    Expression
    Biased expression in Muscle (RPKM 283.7), Heart (RPKM 144.9) and 6 other tissues See more
    Orthologs
    human mouse all
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    Genomic context

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    See Smarcd3 in Genome Data Viewer
    Location:
    4q11
    Exon count:
    15
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCr8 (GCF_036323735.1) 4 NC_086022.1 (11441142..11472781)
    RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 4 NC_051339.1 (10548693..10580334)
    106 previous assembly Rnor_6.0 (GCF_000001895.5) 4 NC_005103.4 (7076710..7108334)

    Chromosome 4 - NC_086022.1Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC134486541 Neighboring gene glycerol-3-phosphate dehydrogenase 1 like 3 Neighboring gene chondroitin polymerizing factor 2 Neighboring gene microRNA 671 Neighboring gene ATP binding cassette subfamily F member 2

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages
    • Description: 320 RNA samples isolated from 11 organs (adrenal gland, brain, heart, kidney, liver, lung, muscle, spleen, thymus, and testes or uterus) from both sexes of Fischer 344 rats across four developmental stages (2-, 6-, 21-, and 104-weeks-old)
    • BioProject: PRJNA238328
    • Publication: PMID 24510058
    • Analysis date: Mon Jun 6 17:44:12 2016

    Bibliography

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    Related articles in PubMed

    1. TGFβ1-induced Baf60c regulates both smooth muscle cell commitment and quiescence. Sohni A, et al. PLoS One, 2012. PMID 23110084, Free PMC Article
    2. SWI/SNF chromatin remodeling enzymes are associated with cardiac hypertrophy in a genetic rat model of hypertension. Mehrotra A, et al. J Cell Physiol, 2013 Dec. PMID 23702776, Free PMC Article
    3. The mechanism behind BAF60c in myocardial metabolism in rats with heart failure is through the PGC1α-PPARα-mTOR signaling pathway. Chen Q, et al. Biochem Cell Biol, 2022 Apr. PMID 33245682
    4. Canonical Wnt signaling functions in second heart field to promote right ventricular growth. Ai D, et al. Proc Natl Acad Sci U S A, 2007 May 29. PMID 17519332, Free PMC Article
    5. Baf60c is a component of the neural progenitor-specific BAF complex in developing retina. Lamba DA, et al. Dev Dyn, 2008 Oct. PMID 18816825, Free PMC Article

    See all (19) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. The mechanism behind BAF60c in myocardial metabolism in rats with heart failure is through the PGC1alpha-PPARalpha-mTOR signaling pathway.
      Title: The mechanism behind BAF60c in myocardial metabolism in rats with heart failure is through the PGC1α-PPARα-mTOR signaling pathway.
    Submit: New GeneRIF Correction

    General gene information

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    Markers

    Homology

    Gene Ontology Provided by RGD

    Function Evidence Code Pubs
    enables DNA-binding transcription factor binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables chromatin binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables nuclear receptor binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables nuclear receptor coactivator activity ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables signaling receptor binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables transcription coregulator activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables transcription coregulator binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    Process Evidence Code Pubs
    acts_upstream_of_or_within cardiac right ventricle formation ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in chromatin remodeling ISO
    Inferred from Sequence Orthology
    more info
    		  
    acts_upstream_of_or_within heart morphogenesis ISO
    Inferred from Sequence Orthology
    more info
    		  
    acts_upstream_of_or_within muscle cell differentiation ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in neural retina development ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in nucleosome disassembly ISO
    Inferred from Sequence Orthology
    more info
    		  
    acts_upstream_of_or_within positive regulation of DNA-templated transcription ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in positive regulation of DNA-templated transcription ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in positive regulation of G2/M transition of mitotic cell cycle IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in positive regulation of neuroblast proliferation ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in positive regulation of smooth muscle cell differentiation IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in regulation of transcription by RNA polymerase II IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in regulation of transcription by RNA polymerase II ISO
    Inferred from Sequence Orthology
    more info
    		  
    acts_upstream_of_or_within secondary heart field specification ISO
    Inferred from Sequence Orthology
    more info
    		  
    Component Evidence Code Pubs
    part_of SWI/SNF complex IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    part_of SWI/SNF complex ISO
    Inferred from Sequence Orthology
    more info
    		  
    part_of chromatin ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in cytoplasm ISO
    Inferred from Sequence Orthology
    more info
    		  
    part_of nBAF complex ISO
    Inferred from Sequence Orthology
    more info
    		  
    part_of npBAF complex ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in nucleoplasm IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in nucleoplasm ISO
    Inferred from Sequence Orthology
    more info
    		  
    is_active_in nucleus IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in nucleus ISO
    Inferred from Sequence Orthology
    more info
    		  

    General protein information

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    Preferred Names
    SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily D member 3

    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_001011966.1 → NP_001011966.1  SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily D member 3 isoform 1

      See identical proteins and their annotated locations for NP_001011966.1

      Status: VALIDATED

      Source sequence(s)
      BC085349
      UniProtKB/TrEMBL
      A0A8I6A286, F7FMF4, Q5U3Y2
      Related
      ENSRNOP00000061137.1, ENSRNOT00000066598.3
      Conserved Domains (2) summary
      COG5531
      Location:166 → 363
      Rsc6; Chromatin remodeling complex protein RSC6, contains SWIB domain [Chromatin structure and dynamics]
      pfam02201
      Location:249 → 320
      SWIB; SWIB/MDM2 domain

    2. NM_001415835.1 → NP_001402764.1  SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily D member 3 isoform 2

      Status: VALIDATED

      Source sequence(s)
      JAXUCZ010000004
      UniProtKB/TrEMBL
      A0A8I5ZQQ2, A0A8I6A286, A6K534
      Related
      ENSRNOP00000080730.1, ENSRNOT00000115205.1

    RefSeqs of Annotated Genomes: GCF_036323735.1-RS_2024_02

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference GRCr8

    Genomic

    1. NC_086022.1 Reference GRCr8

      Range
      11441142..11472781
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_063285692.1 → XP_063141762.1  SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily D member 3 isoform X3

      UniProtKB/TrEMBL
      A0A8I6A286

    2. XM_039107216.2 → XP_038963144.1  SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily D member 3 isoform X1

      UniProtKB/TrEMBL
      A0A8I6A286
      Conserved Domains (1) summary
      cd17676
      Location:277 → 350
      SWIB_BAF60C; SWIB domain found in BRG1-associated factor 60C (BAF60C) and similar proteins

    3. XM_006235888.5 → XP_006235950.1  SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily D member 3 isoform X2

      UniProtKB/TrEMBL
      A0A8I6A286
      Conserved Domains (2) summary
      COG5531
      Location:179 → 388
      Rsc6; Chromatin remodeling complex protein RSC6, contains SWIB domain [Chromatin structure and dynamics]
      pfam02201
      Location:274 → 345
      SWIB; SWIB/MDM2 domain
    Nucleotide Protein Strain
    Heading Accession and Version

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