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

Gene ID: 83797, updated on 6-Jun-2024

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
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Genomic context

See Smarcd1 in Genome Data Viewer
Location:
15 F1; 15 56.13 cM
Exon count:
13
Annotation release Status Assembly Chr Location
RS_2024_02 current GRCm39 (GCF_000001635.27) 15 NC_000081.7 (99600175..99611872)
108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 15 NC_000081.6 (99702287..99713995)

Chromosome 15 - NC_000081.7Genomic Context describing neighboring genes Neighboring gene predicted gene, 34880 Neighboring gene acid-sensing ion channel 1 Neighboring gene STARR-seq mESC enhancer starr_39720 Neighboring gene predicted gene, 34939 Neighboring gene ribosomal protein S27 pseudogene Neighboring gene predicted gene 16537 Neighboring gene glycerol-3-phosphate dehydrogenase 1 (soluble) Neighboring gene CapStarr-seq enhancer MGSCv37_chr15:99555871-99556054 Neighboring gene cytochrome c oxidase assembly protein 14

Genomic regions, transcripts, and products

Expression

  • 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

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Variation

Alleles

Alleles of this type are documented at Mouse Genome Informatics  (MGI)
  • Endonuclease-mediated (2) 
  • Targeted (1)  1 citation

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

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
 
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
 
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
 
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 
part_of 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
 

General protein information

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)

  1. NM_001411993.1NP_001398922.1  SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily D member 1 isoform 2

    Status: VALIDATED

    Source sequence(s)
    AC134548
    UniProtKB/TrEMBL
    A0A2R8VKP3
  2. NM_031842.3NP_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
    P70384, Q61466, Q8R0I7
    UniProtKB/TrEMBL
    Q68FH8
    Related
    ENSMUSP00000023759.5, ENSMUST00000023759.6
    Conserved Domains (3) summary
    COG5531
    Location:207408
    Rsc6; Chromatin remodeling complex protein RSC6, contains SWIB domain [Chromatin structure and dynamics]
    pfam02084
    Location:3998
    Bindin
    cd17674
    Location:294370
    SWIB_BAF60A; SWIB domain found in BRG1-associated factor 60A (BAF60A) 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

  1. NC_000081.7 Reference GRCm39 C57BL/6J

    Range
    99600175..99611872
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)