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Smarcd3 SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily d, member 3 [ Mus musculus (house mouse) ]

Gene ID: 66993, updated on 21-Apr-2024

Summary

Official Symbol
Smarcd3provided by MGI
Official Full Name
SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily d, member 3provided 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 chromatin binding activity; nuclear receptor binding activity; and nuclear receptor coactivator activity. Acts upstream of or within several processes, including heart morphogenesis; neural retina development; and positive regulation of transcription, DNA-templated. Located in nucleus. Part of SWI/SNF complex; nBAF complex; and npBAF complex. Is expressed in several structures, including cardiogenic plate; central nervous system; ear; genitourinary system; and skin. 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
Broad expression in genital fat pad adult (RPKM 40.6), CNS E18 (RPKM 30.3) and 23 other tissues See more
Orthologs
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Genomic context

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)
  • Targeted (3)  1 citation
  • Endonuclease-mediated (2) 

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 ISO
Inferred from Sequence Orthology
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 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 IMP
Inferred from Mutant Phenotype
more info
PubMed 
acts_upstream_of_or_within chromatin organization IEA
Inferred from Electronic Annotation
more info
 
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 
acts_upstream_of_or_within 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 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 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 ISO
Inferred from Sequence Orthology
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 
part_of chromatin ISO
Inferred from Sequence Orthology
more info
 
part_of 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
 
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
mBAF60c

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

    See identical proteins and their annotated locations for NP_080167.3

    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