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

    Gene ID: 363002, updated on 9-Dec-2024

    Summary

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    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, Dec 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

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    See Smarcd1 in Genome Data Viewer
    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_086025.1Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC134479572 Neighboring gene acid sensing ion channel subunit 1 Neighboring gene glycerol-3-phosphate dehydrogenase 1 Neighboring gene cytochrome c oxidase assembly factor COX14

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • 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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    Related articles in PubMed

    1. Hyperlipidaemia impairs the circadian clock and physiological homeostasis of vascular smooth muscle cells via the suppression of Smarcd1. Chen S, et al. J Pathol, 2014 Jun. PMID 24615205
    2. BAF60a mediates critical interactions between nuclear receptors and the BRG1 chromatin-remodeling complex for transactivation. Hsiao PW, et al. Mol Cell Biol, 2003 Sep. PMID 12917342, Free PMC Article
    3. The spectrum of SWI/SNF mutations, ubiquitous in human cancers. Shain AH, et al. PLoS One, 2013. PMID 23355908, Free PMC Article
    4. Fanconi anemia protein, FANCA, associates with BRG1, a component of the human SWI/SNF complex. Otsuki T, et al. Hum Mol Genet, 2001 Nov 1. PMID 11726552
    5. Purification and biochemical heterogeneity of the mammalian SWI-SNF complex. Wang W, et al. EMBO J, 1996 Oct 1. PMID 8895581, Free PMC Article

    See all (12) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. 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

    Homology

    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)

    1. 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

    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

    1. NC_086025.1 Reference GRCr8

      Range
      132708627..132719167
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_063263961.1 → XP_063120031.1  SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily D member 1 isoform X1

      UniProtKB/TrEMBL
      D3ZBS9
    Nucleotide Protein Strain
    Heading Accession and Version

    Gene LinkOut

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