Smarcd1 SWI/SNF related BAF chromatin remodeling complex subunit D1 [Rattus norvegicus (Norway rat)] - Gene

Summary

Official Symbol: Smarcd1provided by RGD
Official Full Name: SWI/SNF related BAF chromatin remodeling complex subunit D1provided by RGD
Primary source: RGD:1305406
See related: EnsemblRapid:ENSRNOG00000061572 AllianceGenome:RGD:1305406
Gene type: protein coding
RefSeq status: PROVISIONAL
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 and signaling receptor binding activity. Involved in cellular response to fatty acid. Predicted to be located in nucleoplasm. Predicted to be part of SWI/SNF complex; nBAF complex; and npBAF complex. Predicted to be active in nucleus. Biomarker of familial hyperlipidemia. Human ortholog(s) of this gene implicated in Coffin-Siris syndrome 11. Orthologous to human SMARCD1 (SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily d, member 1). [provided by Alliance of Genome Resources, Nov 2024]
Expression: Biased expression in Brain (RPKM 94.8), Thymus (RPKM 73.0) and 9 other tissues See more
Orthologs: human mouse all
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Genomic context

Location:: 7q36

Exon count:: 14

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCr8 (GCF_036323735.1)	7	NC_086025.1 (132708627..132719167)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	7	NC_051342.1 (130829783..130840323)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	7	NC_005106.4 (141355623..141366725)

Chromosome 7 - NC_086025.1 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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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 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?

Demonstrate that Smarcd1 is a critical node integrating the circadian clock and vascular smooth muscle cell physiological homeostasis.
Title: Hyperlipidaemia impairs the circadian clock and physiological homeostasis of vascular smooth muscle cells via the suppression of Smarcd1.

Submit: New GeneRIF Correction

General gene information

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Markers

AI060178 (e-PCR)
- UniSTS:248833

AI008150 (e-PCR)
- UniSTS:261429

RH128342 (e-PCR)
- UniSTS:211650

RH124655 (e-PCR)
- UniSTS:161477

Gene Ontology Provided by RGD

Function	Evidence Code	Pubs
enables chromatin binding	IDA Inferred from Direct Assay more info	PubMed
enables molecular adaptor activity	ISO Inferred from Sequence Orthology more info
enables signaling receptor binding	IPI Inferred from Physical Interaction more info	PubMed
enables transcription coregulator activity	IBA Inferred from Biological aspect of Ancestor more info

Process	Evidence Code	Pubs
involved_in cellular response to fatty acid	IEP Inferred from Expression Pattern more info	PubMed
involved_in chromatin remodeling	ISO Inferred from Sequence Orthology more info
involved_in nucleosome disassembly	ISO Inferred from Sequence Orthology more info
involved_in regulation of transcription by RNA polymerase II	IBA Inferred from Biological aspect of Ancestor more info
involved_in transcription initiation-coupled chromatin remodeling	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 intracellular membrane-bounded organelle	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

General protein information

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Preferred Names: SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily D member 1

Names: SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily d, member 1

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_001108752.1 → NP_001102222.1 SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily D member 1

See identical proteins and their annotated locations for NP_001102222.1

Status: PROVISIONAL

Source sequence(s)

CH474035

UniProtKB/TrEMBL

A6KCH0, D3ZBS9

Related

ENSRNOP00000075525.3, ENSRNOT00000081195.3

Conserved Domains (1) summary

cd17674
Location:294 → 370

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