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    Smarcd3 SWI/SNF related BAF chromatin remodeling complex subunit D3 [ Mus musculus (house mouse) ]

    Gene ID: 66993, updated on 27-Nov-2024

    Summary

    Official Symbol
    Smarcd3provided by MGI
    Official Full Name
    SWI/SNF related BAF chromatin remodeling complex subunit D3provided by MGI
    Primary source
    MGI:MGI:1914243
    See related
    Ensembl:ENSMUSG00000028949 AllianceGenome:MGI:1914243
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Mus musculus
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
    Also known as
    BAF60C; 1500001J14Rik; 2210409C08Rik
    Summary
    Predicted to enable several functions, including nuclear receptor binding activity; nuclear receptor coactivator activity; and transcription coregulator binding activity. Involved in neural retina development. Acts upstream of or within heart morphogenesis; muscle cell differentiation; and positive regulation of DNA-templated transcription. Located in nucleus. Part of SWI/SNF complex; nBAF complex; and npBAF complex. Is expressed in several structures, including brain; genitourinary system; gut; sensory organ; and spinal cord. Orthologous to human SMARCD3 (SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily d, member 3). [provided by Alliance of Genome Resources, Nov 2024]
    Expression
    Broad expression in genital fat pad adult (RPKM 40.6), CNS E18 (RPKM 30.3) and 23 other tissues See more
    Orthologs
    NEW
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    Genomic context

    See Smarcd3 in Genome Data Viewer
    Location:
    5 A3; 5 11.93 cM
    Exon count:
    17
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCm39 (GCF_000001635.27) 5 NC_000071.7 (24797620..24829649, complement)
    108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 5 NC_000071.6 (24592622..24624456, complement)

    Chromosome 5 - NC_000071.7Genomic Context describing neighboring genes Neighboring gene ATP synthase, H+ transporting, mitochondrial F0 complex, subunit g pseudogene Neighboring gene chondroitin polymerizing factor 2 Neighboring gene microRNA 671 Neighboring gene glycerol-3-phosphate dehydrogenase 1-like pseudogene Neighboring gene STARR-seq mESC enhancer starr_12645 Neighboring gene STARR-positive B cell enhancer mm9_chr5:24180078-24180378 Neighboring gene STARR-positive B cell enhancer ABC_E1298 Neighboring gene STARR-positive B cell enhancer ABC_E11722 Neighboring gene negative regulator of ubiquitin-like proteins 1 Neighboring gene WD repeat domain 86

    Genomic regions, transcripts, and products

    Expression

    • Project title: Mouse ENCODE transcriptome data
    • Description: RNA profiling data sets generated by the Mouse ENCODE project.
    • BioProject: PRJNA66167
    • Publication: PMID 25409824
    • Analysis date: n/a

    Bibliography

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?

    Variation

    Alleles

    Alleles of this type are documented at Mouse Genome Informatics  (MGI)
    • Endonuclease-mediated (2) 
    • Targeted (3)  1 citation

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Gene Ontology Provided by MGI

    Function Evidence Code Pubs
    enables DNA-binding transcription factor binding ISO
    Inferred from Sequence Orthology
    more info
     
    enables chromatin binding IEA
    Inferred from Electronic Annotation
    more info
     
    enables chromatin binding ISO
    Inferred from Sequence Orthology
    more info
     
    enables nuclear receptor binding IEA
    Inferred from Electronic Annotation
    more info
     
    enables nuclear receptor binding ISO
    Inferred from Sequence Orthology
    more info
     
    enables nuclear receptor coactivator activity ISO
    Inferred from Sequence Orthology
    more info
     
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    enables signaling receptor binding IEA
    Inferred from Electronic Annotation
    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 IEA
    Inferred from Electronic Annotation
    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 IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in chromatin remodeling ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in chromatin remodeling NAS
    Non-traceable Author Statement
    more info
    PubMed 
    acts_upstream_of_or_within heart morphogenesis IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    acts_upstream_of_or_within muscle cell differentiation IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in nervous system development IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in neural retina development IEP
    Inferred from Expression Pattern
    more info
    PubMed 
    involved_in nucleosome disassembly IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in nucleosome disassembly ISO
    Inferred from Sequence Orthology
    more info
     
    acts_upstream_of_or_within positive regulation of DNA-templated transcription IDA
    Inferred from Direct Assay
    more info
    PubMed 
    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 IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in positive regulation of G2/M transition of mitotic cell cycle ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in positive regulation of T cell differentiation NAS
    Non-traceable Author Statement
    more info
    PubMed 
    involved_in positive regulation of cell differentiation NAS
    Non-traceable Author Statement
    more info
    PubMed 
    involved_in positive regulation of double-strand break repair NAS
    Non-traceable Author Statement
    more info
    PubMed 
    involved_in positive regulation of myoblast differentiation NAS
    Non-traceable Author Statement
    more info
    PubMed 
    involved_in positive regulation of neuroblast proliferation IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in positive regulation of neuroblast proliferation ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in positive regulation of smooth muscle cell differentiation IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in positive regulation of smooth muscle cell differentiation ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in regulation of G0 to G1 transition NAS
    Non-traceable Author Statement
    more info
    PubMed 
    involved_in regulation of G1/S transition of mitotic cell cycle NAS
    Non-traceable Author Statement
    more info
    PubMed 
    involved_in regulation of mitotic metaphase/anaphase transition NAS
    Non-traceable Author Statement
    more info
    PubMed 
    involved_in regulation of nucleotide-excision repair NAS
    Non-traceable Author Statement
    more info
    PubMed 
    acts_upstream_of_or_within regulation of protein binding 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
     
    involved_in regulation of transcription by RNA polymerase II NAS
    Non-traceable Author Statement
    more info
    PubMed 
    acts_upstream_of_or_within secondary heart field specification IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    Component Evidence Code Pubs
    part_of SWI/SNF complex IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    part_of SWI/SNF complex IDA
    Inferred from Direct Assay
    more info
    PubMed 
    part_of SWI/SNF complex ISO
    Inferred from Sequence Orthology
    more info
     
    part_of SWI/SNF complex NAS
    Non-traceable Author Statement
    more info
    PubMed 
    part_of SWI/SNF superfamily-type complex IDA
    Inferred from Direct Assay
    more info
    PubMed 
    part_of brahma complex NAS
    Non-traceable Author Statement
    more info
    PubMed 
    located_in chromatin ISO
    Inferred from Sequence Orthology
    more info
     
    located_in chromatin NAS
    Non-traceable Author Statement
    more info
    PubMed 
    located_in cytoplasm ISO
    Inferred from Sequence Orthology
    more info
     
    part_of nBAF complex IDA
    Inferred from Direct Assay
    more info
    PubMed 
    part_of nBAF complex NAS
    Non-traceable Author Statement
    more info
    PubMed 
    part_of npBAF complex IDA
    Inferred from Direct Assay
    more info
    PubMed 
    part_of npBAF complex ISO
    Inferred from Sequence Orthology
    more info
     
    part_of npBAF complex NAS
    Non-traceable Author Statement
    more info
    PubMed 
    located_in nucleoplasm ISO
    Inferred from Sequence Orthology
    more info
     
    located_in nucleoplasm TAS
    Traceable Author Statement
    more info
     
    is_active_in nucleus IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    located_in nucleus IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in nucleus ISO
    Inferred from Sequence Orthology
    more info
     

    General protein information

    Preferred Names
    SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily D member 3
    Names
    60 kDa BRG-1/Brm-associated factor subunit C
    BRG1-associated factor 60C
    SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily d, member 3
    mBAF60c

    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_025891.3NP_080167.3  SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily D member 3

      Status: VALIDATED

      Source sequence(s)
      AK005094, AK019064, BC060525
      Consensus CDS
      CCDS19126.1
      UniProtKB/Swiss-Prot
      Q6P9Z1, Q921D3, Q9CX89, Q9DB99
      Related
      ENSMUSP00000030791.8, ENSMUST00000030791.12
      Conserved Domains (3) summary
      COG5531
      Location:179376
      Rsc6; Chromatin remodeling complex protein RSC6, contains SWIB domain [Chromatin structure and dynamics]
      pfam07271
      Location:2767
      Cytadhesin_P30; Cytadhesin P30/P32
      cd17676
      Location:265338
      SWIB_BAF60C; SWIB domain found in BRG1-associated factor 60C (BAF60C) and similar proteins

    RefSeqs of Annotated Genomes: GCF_000001635.27-RS_2024_02

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

    Reference GRCm39 C57BL/6J

    Genomic

    1. NC_000071.7 Reference GRCm39 C57BL/6J

      Range
      24797620..24829649 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_030254770.2XP_030110630.1  SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily D member 3 isoform X5

      UniProtKB/TrEMBL
      A0A0G2JG60
      Related
      ENSMUSP00000143437.2, ENSMUST00000195943.2
      Conserved Domains (2) summary
      COG5531
      Location:150347
      Rsc6; Chromatin remodeling complex protein RSC6, contains SWIB domain [Chromatin structure and dynamics]
      cl38907
      Location:236309
      SWIB-MDM2; SWIB/MDM2 domain family
    2. XM_006535799.1XP_006535862.1  SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily D member 3 isoform X4

      Conserved Domains (2) summary
      COG5531
      Location:150347
      Rsc6; Chromatin remodeling complex protein RSC6, contains SWIB domain [Chromatin structure and dynamics]
      cl38907
      Location:236309
      SWIB-MDM2; SWIB/MDM2 domain family
    3. XM_006535798.4XP_006535861.2  SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily D member 3 isoform X3

      Conserved Domains (4) summary
      COG5531
      Location:166363
      Rsc6; Chromatin remodeling complex protein RSC6, contains SWIB domain [Chromatin structure and dynamics]
      pfam07271
      Location:954
      Cytadhesin_P30; Cytadhesin P30/P32
      pfam13388
      Location:9125
      DUF4106; Protein of unknown function (DUF4106)
      cl38907
      Location:252325
      SWIB-MDM2; SWIB/MDM2 domain family
    4. XM_006535796.5XP_006535859.2  SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily D member 3 isoform X1

      Conserved Domains (4) summary
      COG5531
      Location:166363
      Rsc6; Chromatin remodeling complex protein RSC6, contains SWIB domain [Chromatin structure and dynamics]
      pfam07271
      Location:954
      Cytadhesin_P30; Cytadhesin P30/P32
      pfam13388
      Location:9125
      DUF4106; Protein of unknown function (DUF4106)
      cl38907
      Location:252325
      SWIB-MDM2; SWIB/MDM2 domain family
    5. XM_006535797.5XP_006535860.1  SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily D member 3 isoform X2

      Conserved Domains (2) summary
      COG5531
      Location:179376
      Rsc6; Chromatin remodeling complex protein RSC6, contains SWIB domain [Chromatin structure and dynamics]
      cd17676
      Location:265338
      SWIB_BAF60C; SWIB domain found in BRG1-associated factor 60C (BAF60C) and similar proteins
    6. XM_030254769.2XP_030110629.1  SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily D member 3 isoform X4

      Conserved Domains (2) summary
      COG5531
      Location:150347
      Rsc6; Chromatin remodeling complex protein RSC6, contains SWIB domain [Chromatin structure and dynamics]
      cl38907
      Location:236309
      SWIB-MDM2; SWIB/MDM2 domain family
    7. XM_030254771.2XP_030110631.1  SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily D member 3 isoform X5

      UniProtKB/TrEMBL
      A0A0G2JG60
      Conserved Domains (2) summary
      COG5531
      Location:150347
      Rsc6; Chromatin remodeling complex protein RSC6, contains SWIB domain [Chromatin structure and dynamics]
      cl38907
      Location:236309
      SWIB-MDM2; SWIB/MDM2 domain family

    RNA

    1. XR_003955694.1 RNA Sequence

    2. XR_389749.4 RNA Sequence