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

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 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, Oct 2024]
Expression: Broad expression in genital fat pad adult (RPKM 40.6), CNS E18 (RPKM 30.3) and 23 other tissues See more
Orthologs: human all
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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_000071.7 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

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Expression

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See details

Project title: Mouse ENCODE transcriptome data 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

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Myofiber Baf60c controls muscle regeneration by modulating Dkk3-mediated paracrine signaling.
Title: Myofiber Baf60c controls muscle regeneration by modulating Dkk3-mediated paracrine signaling.
Smarcd3 is an epigenetic modulator of the metabolic landscape in pancreatic ductal adenocarcinoma.
Title: Smarcd3 is an epigenetic modulator of the metabolic landscape in pancreatic ductal adenocarcinoma.
BAF60c prevents abdominal aortic aneurysm formation through epigenetic control of vascular smooth muscle cell homeostasis.
Title: BAF60c prevents abdominal aortic aneurysm formation through epigenetic control of vascular smooth muscle cell homeostasis.
work revealed functional redundancy between Baf60a and Baf60c in maintaining oxidative and glycolytic metabolism in skeletal myofibers and exercise endurance. Unexpectedly, mice lacking these two factors in skeletal muscle were protected from diet-induced and age-associated metabolic disorders. Transcriptional profiling analysis identified the muscle thermogenic gene program and myokine secretion as key pathways that inte
Title: Uncoupling Exercise Bioenergetics From Systemic Metabolic Homeostasis by Conditional Inactivation of Baf60 in Skeletal Muscle.
These data suggested that Baf60c plays an important role in cardiomyocyte proliferation in heart development and regeneration. This is the first study indicating that Baf60c contributes to the heart regeneration in vertebrates.
Title: Expression analysis of Baf60c during heart regeneration in axolotls and neonatal mice.
postmitotic expression SOD1G93A mutant gene promotes a FAPS phenotype in C2C12 cells, by upregulating HDAC4 protein and preventing the BAF60C-SWI/SNF complex myogenic commitment
Title: Postmitotic Expression of SOD1(G93A) Gene Affects the Identity of Myogenic Cells and Inhibits Myoblasts Differentiation.
regulates the Nodal/Bone Morphogenetic Protein antagonist Cerberus and the Baf60c/Smarcd3 subunit of the Brg1/Brm-associated factors (BAF) chromatin-remodelling complex
Title: The G-protein-coupled receptor APJ is expressed in the second heart field and regulates Cerberus-Baf60c axis in embryonic stem cell cardiomyogenesis.
Overexpression of transcription factors MYOCD and SRF alone or in conjunction with Mesp1 and SMARCD3 enhanced the basal but necessary cardio-inducing effect of the previously reported GATA4, TBX5, and MEF2C.
Title: Transcription factors MYOCD, SRF, Mesp1 and SMARCD3 enhance the cardio-inducing effect of GATA4, TBX5, and MEF2C during direct cellular reprogramming.
MyoD and the SWI/SNF subunit BAF60c interact on the regulatory elements of MyoD-target genes in myoblasts, prior to activation of transcription.
Title: Signal-dependent incorporation of MyoD-BAF60c into Brg1-based SWI/SNF chromatin-remodelling complex.
Baf60c is re-expressed in the Muller glial cells that re-enter the cell cycle after neurotoxic damage
Title: Baf60c is a component of the neural progenitor-specific BAF complex in developing retina.

Submit: New GeneRIF Correction See all GeneRIFs (14)

Variation

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Alleles

Alleles of this type are documented at Mouse Genome Informatics (MGI)

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

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

D7S2157E (e-PCR)
- UniSTS:151151

AW060945 (e-PCR)
- UniSTS:179135

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

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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)

NM_025891.3 → NP_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:179 → 376

Rsc6; Chromatin remodeling complex protein RSC6, contains SWIB domain [Chromatin structure and dynamics]

pfam07271
Location:27 → 67

Cytadhesin_P30; Cytadhesin P30/P32

cd17676
Location:265 → 338

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

NC_000071.7 Reference GRCm39 C57BL/6J

Range

24797620..24829649 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_030254770.2 → XP_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:150 → 347

Rsc6; Chromatin remodeling complex protein RSC6, contains SWIB domain [Chromatin structure and dynamics]

cl38907
Location:236 → 309

SWIB-MDM2; SWIB/MDM2 domain family
XM_006535799.1 → XP_006535862.1 SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily D member 3 isoform X4

Conserved Domains (2) summary

COG5531
Location:150 → 347

Rsc6; Chromatin remodeling complex protein RSC6, contains SWIB domain [Chromatin structure and dynamics]

cl38907
Location:236 → 309

SWIB-MDM2; SWIB/MDM2 domain family
XM_006535798.4 → XP_006535861.2 SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily D member 3 isoform X3

Conserved Domains (4) summary

COG5531
Location:166 → 363

Rsc6; Chromatin remodeling complex protein RSC6, contains SWIB domain [Chromatin structure and dynamics]

pfam07271
Location:9 → 54

Cytadhesin_P30; Cytadhesin P30/P32

pfam13388
Location:9 → 125

DUF4106; Protein of unknown function (DUF4106)

cl38907
Location:252 → 325

SWIB-MDM2; SWIB/MDM2 domain family
XM_006535796.5 → XP_006535859.2 SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily D member 3 isoform X1

Conserved Domains (4) summary

COG5531
Location:166 → 363

Rsc6; Chromatin remodeling complex protein RSC6, contains SWIB domain [Chromatin structure and dynamics]

pfam07271
Location:9 → 54

Cytadhesin_P30; Cytadhesin P30/P32

pfam13388
Location:9 → 125

DUF4106; Protein of unknown function (DUF4106)

cl38907
Location:252 → 325

SWIB-MDM2; SWIB/MDM2 domain family
XM_006535797.5 → XP_006535860.1 SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily D member 3 isoform X2

Conserved Domains (2) summary

COG5531
Location:179 → 376

Rsc6; Chromatin remodeling complex protein RSC6, contains SWIB domain [Chromatin structure and dynamics]

cd17676
Location:265 → 338

SWIB_BAF60C; SWIB domain found in BRG1-associated factor 60C (BAF60C) and similar proteins
XM_030254769.2 → XP_030110629.1 SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily D member 3 isoform X4

Conserved Domains (2) summary

COG5531
Location:150 → 347

Rsc6; Chromatin remodeling complex protein RSC6, contains SWIB domain [Chromatin structure and dynamics]

cl38907
Location:236 → 309

SWIB-MDM2; SWIB/MDM2 domain family
XM_030254771.2 → XP_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:150 → 347

Rsc6; Chromatin remodeling complex protein RSC6, contains SWIB domain [Chromatin structure and dynamics]

cl38907
Location:236 → 309

SWIB-MDM2; SWIB/MDM2 domain family