Smarcd1 SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily d, member 1 [Mus musculus (house mouse)] - Gene

Summary

Official Symbol: Smarcd1provided by MGI
Official Full Name: SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily d, member 1provided by MGI
Primary source: MGI:MGI:1933623
See related: Ensembl:ENSMUSG00000023018 AllianceGenome:MGI:1933623
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: Baf60a; D15Kz1
Summary: Predicted to enable several functions, including chromatin binding activity; molecular adaptor activity; and transcription coregulator activity. Predicted to be involved in epigenetic maintenance of chromatin in transcription-competent conformation; nucleosome disassembly; and regulation of transcription by RNA polymerase II. Predicted to act upstream of or within chromatin organization and nervous system development. Part of SWI/SNF complex; nBAF complex; and npBAF complex. Is expressed in several structures, including central nervous system; dorsal root ganglion; early conceptus; genitourinary system; and retina layer. Human ortholog(s) of this gene implicated in Coffin-Siris syndrome. Orthologous to human SMARCD1 (SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily d, member 1). [provided by Alliance of Genome Resources, Apr 2022]
Expression: Ubiquitous expression in whole brain E14.5 (RPKM 60.6), CNS E14 (RPKM 56.2) and 28 other tissues See more
Orthologs: human all
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Genomic context

Location:: 15 F1; 15 56.13 cM

Exon count:: 13

Annotation release	Status	Assembly	Chr	Location
109	current	GRCm39 (GCF_000001635.27)	15	NC_000081.7 (99600168..99611876)
108.20200622	previous assembly	GRCm38.p6 (GCF_000001635.26)	15	NC_000081.6 (99702287..99713995)

Chromosome 15 - NC_000081.7 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
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?

BAF60a Deficiency in Macrophage Promotes Diet-Induced Obesity and Metabolic Inflammation.
Title: BAF60a Deficiency in Macrophage Promotes Diet-Induced Obesity and Metabolic Inflammation.
SWI/SNF complex subunit BAF60a represses hepatic ureagenesis through a crosstalk between YB-1 and PGC-1alpha.
Title: SWI/SNF complex subunit BAF60a represses hepatic ureagenesis through a crosstalk between YB-1 and PGC-1α.
BAF60a Deficiency in Vascular Smooth Muscle Cells Prevents Abdominal Aortic Aneurysm by Reducing Inflammation and Extracellular Matrix Degradation.
Title: BAF60a Deficiency in Vascular Smooth Muscle Cells Prevents Abdominal Aortic Aneurysm by Reducing Inflammation and Extracellular Matrix Degradation.
BAF60a deficiency uncouples chromatin accessibility and cold sensitivity from white fat browning.
Title: BAF60a deficiency uncouples chromatin accessibility and cold sensitivity from white fat browning.
MITF promoted BAF60A recruitment to melanocyte-specific promoters, and BAF60A was required to promote BRG1 recruitment and chromatin remodeling.
Title: BAF60A mediates interactions between the microphthalmia-associated transcription factor and the BRG1-containing SWI/SNF complex during melanocyte differentiation.
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.
Hepatocyte-specific inactivation of Baf60a reduced bile acid production.
Title: A Diet-Sensitive BAF60a-Mediated Pathway Links Hepatic Bile Acid Metabolism to Cholesterol Absorption and Atherosclerosis.
propose a role for SMARCD1 in restricting pluripotency and activating lineage pathways by regulating H3K27 methylation
Title: Differential association of chromatin proteins identifies BAF60a/SMARCD1 as a regulator of embryonic stem cell differentiation.
hypermethylation-mediated silencing of miR-490-3p reactivates SMARCD1 to confer malignant phenotypes, mechanistically linking H. pylori, chromatin remodeling, and gastric carcinogenesis
Title: Epigenetic silencing of miR-490-3p reactivates the chromatin remodeler SMARCD1 to promote Helicobacter pylori-induced gastric carcinogenesis.
Tbx1 expression increases Baf60a occupation of the Wnt5a gene and enhances its H3K4 monomethylation status, while Baf60a knockdown abolishes the ability of Tbx1 to regulate Wnt5a and other target genes.
Title: Transcriptional control in cardiac progenitors: Tbx1 interacts with the BAF chromatin remodeling complex and regulates Wnt5a.

Submit: New GeneRIF Correction See all GeneRIFs (13)

Variation

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Alleles

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

Targeted (1) 1 citation

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

M25773 (e-PCR)
- UniSTS:124949

AI843610 (e-PCR)
- UniSTS:165964

GDB:4584943 (e-PCR)
- UniSTS:65969

RH124655 (e-PCR)
- UniSTS:161477

Homology

Homologs of the Smarcd1 gene: The Smarcd1 gene is conserved in human, chimpanzee, Rhesus monkey, dog, cow, rat, chicken, zebrafish, fruit fly, mosquito, C.elegans, A.thaliana, rice, and frog.
Orthologs from Annotation Pipeline: 468 organisms have orthologs with human gene Smarcd1
Orthologs

Gene Ontology Provided by MGI

Function	Evidence Code	Pubs
enables chromatin binding	ISO Inferred from Sequence Orthology more info
enables molecular adaptor 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	PubMed

Process	Evidence Code	Pubs
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
involved_in negative regulation of cell differentiation	NAS Non-traceable Author Statement more info	PubMed
acts_upstream_of_or_within nervous system development	IEA Inferred from Electronic Annotation more info
involved_in nucleosome disassembly	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 cell population proliferation	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 stem cell population maintenance	NAS Non-traceable Author Statement more info	PubMed
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
involved_in regulation of transcription by RNA polymerase II	IBA Inferred from Biological aspect of Ancestor more info	PubMed
involved_in regulation of transcription by RNA polymerase II	NAS Non-traceable Author Statement more info	PubMed
involved_in transcription initiation-coupled chromatin remodeling	ISO Inferred from Sequence Orthology more info

Component	Evidence Code	Pubs
part_of GBAF complex	NAS Non-traceable Author Statement more info	PubMed
part_of RSC-type complex	NAS Non-traceable Author Statement more info	PubMed
part_of SWI/SNF complex	IBA Inferred from Biological aspect of Ancestor more info	PubMed
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	NAS Non-traceable Author Statement more info	PubMed
located_in intracellular membrane-bounded organelle	ISO Inferred from Sequence Orthology more info
located_in kinetochore	NAS Non-traceable Author Statement more info	PubMed
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	NAS Non-traceable Author Statement more info	PubMed
located_in nuclear matrix	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	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 1

Names: 60 kDa BRG-1/Brm-associated factor subunit A; BRG1-associated factor 60A; SWI/SNF complex 60 kDa subunit

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_001411993.1 → NP_001398922.1 SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily D member 1 isoform 2

Status: VALIDATED

Source sequence(s)

AC134548
NM_031842.3 → NP_114030.2 SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily D member 1 isoform 1

See identical proteins and their annotated locations for NP_114030.2

Status: VALIDATED

Source sequence(s)

AC134548

Consensus CDS

CCDS37204.1

UniProtKB/Swiss-Prot

Q61466, Q8R0I7

UniProtKB/TrEMBL

A0A6P5R9W0, A0A8C6GKP5, Q68FH8

Related

ENSMUSP00000023759.5, ENSMUST00000023759.6

Conserved Domains (3) summary

COG5531
Location:207 → 408

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

pfam02084
Location:39 → 98

Bindin

cd17674
Location:294 → 370

SWIB_BAF60A; SWIB domain found in BRG1-associated factor 60A (BAF60A) and similar proteins

RefSeqs of Annotated Genomes: Mus musculus Annotation Release 109 details...

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

Reference GRCm39 C57BL/6J

Genomic

NC_000081.7 Reference GRCm39 C57BL/6J

Range

99600168..99611876

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_036159643.1 → XP_036015536.1 SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily D member 1 isoform X1

Conserved Domains (1) summary

cd17674
Location:255 → 331

SWIB_BAF60A; SWIB domain found in BRG1-associated factor 60A (BAF60A) and similar proteins