Smarcd3 SWI/SNF related BAF chromatin remodeling complex subunit D3 [Rattus norvegicus (Norway rat)] - Gene

Summary

Official Symbol: Smarcd3provided by RGD
Official Full Name: SWI/SNF related BAF chromatin remodeling complex subunit D3provided by RGD
Primary source: RGD:1311869
See related: EnsemblRapid: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. Predicted to be located in chromatin; cytoplasm; and nucleoplasm. Predicted to be part of SWI/SNF complex; nBAF complex; and npBAF complex. Predicted to be active in nucleus. Orthologous to human SMARCD3 (SWI/SNF related BAF chromatin remodeling complex subunit D3). [provided by Alliance of Genome Resources, Dec 2024]
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

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_086022.1 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

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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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

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

RH138159 (e-PCR)
- UniSTS:220246

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

G33154 (e-PCR)
- UniSTS:67058

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
located_in 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

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)

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, ENSRNOT00000066598.4

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
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

ENSRNOP00000085708.2, ENSRNOT00000116591.2

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

NC_086022.1 Reference GRCr8

Range

11441142..11472781

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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
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

Related

ENSRNOP00000080730.2, ENSRNOT00000115205.2

Conserved Domains (1) summary

cd17676
Location:277 → 350

SWIB_BAF60C; SWIB domain found in BRG1-associated factor 60C (BAF60C) and similar proteins
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