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Smarcd2 SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily d, member 2 [ Mus musculus (house mouse) ]

Gene ID: 83796, updated on 11-Apr-2024

Summary

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Official Symbol
Smarcd2provided by MGI
Official Full Name
SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily d, member 2provided by MGI
Primary source
MGI:MGI:1933621
See related
Ensembl:ENSMUSG00000078619 AllianceGenome:MGI:1933621
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
Baf60b
Summary
Predicted to enable transcription coregulator activity. Predicted to be involved in nucleosome disassembly and regulation of transcription by RNA polymerase II. Predicted to act upstream of or within chromatin organization. Predicted to be located in nucleoplasm. Predicted to be part of SWI/SNF complex. Predicted to be active in nucleus. Is expressed in several structures, including alimentary system; brain; genitourinary system; integumental system; and sensory organ. Orthologous to human SMARCD2 (SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily d, member 2). [provided by Alliance of Genome Resources, Apr 2022]
Expression
Ubiquitous expression in thymus adult (RPKM 97.9), adrenal adult (RPKM 42.3) and 26 other tissues See more
Orthologs
human all
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Genomic context

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See Smarcd2 in Genome Data Viewer
Location:
11 E1; 11 68.89 cM
Exon count:
13
Annotation release Status Assembly Chr Location
RS_2024_02 current GRCm39 (GCF_000001635.27) 11 NC_000077.7 (106153997..106163810, complement)
108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 11 NC_000077.6 (106263171..106272998, complement)

Chromosome 11 - NC_000077.7Genomic Context describing neighboring genes Neighboring gene DEAD box helicase 42 Neighboring gene STARR-positive B cell enhancer ABC_E597 Neighboring gene FtsJ RNA 2'-O-methyltransferase 3 Neighboring gene protease (prosome, macropain) 26S subunit, ATPase 5 Neighboring gene predicted gene, 23645 Neighboring gene CapStarr-seq enhancer MGSCv37_chr11:106130475-106130662 Neighboring gene STARR-positive B cell enhancer ABC_E598 Neighboring gene STARR-positive B cell enhancer ABC_E3029 Neighboring gene testicular cell adhesion molecule 1 Neighboring gene growth hormone

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • 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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Related articles in PubMed

  1. Cloning and characterization of a novel sequence-specific DNA-binding protein recognizing the negative regulatory element (NRE) region of the HIV-1 long terminal repeat. Calvert I, et al. Gene, 1991 May 30. PMID 2055486
  2. Baf60b-mediated ATM-p53 activation blocks cell identity conversion by sensing chromatin opening. Ji S, et al. Cell Res, 2017 May. PMID 28303890, Free PMC Article
  3. Expression analysis of Baf60c during heart regeneration in axolotls and neonatal mice. Nakamura R, et al. Dev Growth Differ, 2016 May. PMID 27125315
  4. The SWI/SNF protein BAF60b is ubiquitinated through a signalling process involving Rac GTPase and the RING finger protein Unkempt. Lorès P, et al. FEBS J, 2010 Mar. PMID 20148946
  5. SWI/SNF Subunits SMARCA4, SMARCD2 and DPF2 Collaborate in MLL-Rearranged Leukaemia Maintenance. Cruickshank VA, et al. PLoS One, 2015. PMID 26571505, Free PMC Article

See all (59) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Baf60b, a member of the SWI/SNF chromatin remodeling complex, links chromatin opening to ATM activation by facilitating ATM recruitment to the open chromatin regions of a panel of hepatic gene loci.
    Title: Baf60b-mediated ATM-p53 activation blocks cell identity conversion by sensing chromatin opening.
  2. the role of SMARCA4 and the two SWI/SNF subunits SMARCD2/BAF60B and DPF2/BAF45D in leukaemia, was investigated.
    Title: SWI/SNF Subunits SMARCA4, SMARCD2 and DPF2 Collaborate in MLL-Rearranged Leukaemia Maintenance.
  3. the Rac- and Unkempt-dependent process leading to BAF60b ubiquitination takes place in the nuclear compartment
    Title: The SWI/SNF protein BAF60b is ubiquitinated through a signalling process involving Rac GTPase and the RING finger protein Unkempt.
Submit: New GeneRIF Correction

Variation

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Alleles

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

Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Gene Ontology Provided by MGI

Function Evidence Code Pubs
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 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 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 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 
Component Evidence Code Pubs
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 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 bBAF complex NAS
Non-traceable Author Statement
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 kinetochore 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

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Preferred Names
SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily D member 2
Names
60 kDa BRG-1/Brm-associated factor subunit B
BRG1-associated factor 60B

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_001130187.1 → NP_001123659.1  SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily D member 2 isoform 1

    See identical proteins and their annotated locations for NP_001123659.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).
    Source sequence(s)
    AK159259, BB642181, BE853586, DV648475
    Consensus CDS
    CCDS48958.1
    UniProtKB/Swiss-Prot
    B1ARI7, B1ARJ6, Q99JR8
    UniProtKB/TrEMBL
    Q3TXH6
    Related
    ENSMUSP00000021052.10, ENSMUST00000021052.16
    Conserved Domains (2) summary
    COG5531
    Location:230 → 425
    Rsc6; Chromatin remodeling complex protein RSC6, contains SWIB domain [Chromatin structure and dynamics]
    pfam02201
    Location:310 → 381
    SWIB; SWIB/MDM2 domain

  2. NM_031878.2 → NP_114084.2  SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily D member 2 isoform 2

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) differs in the 5' UTR and 5' coding region, compared to variant 1. The resulting isoform (2) has a distinct N-terminus and is shorter than isoform 1.
    Source sequence(s)
    AK159259, BE853586, CO425905, DV648475
    Consensus CDS
    CCDS48957.1
    UniProtKB/TrEMBL
    Q3TXH6
    Related
    ENSMUSP00000102456.2, ENSMUST00000106843.8
    Conserved Domains (2) summary
    COG5531
    Location:183 → 378
    Rsc6; Chromatin remodeling complex protein RSC6, contains SWIB domain [Chromatin structure and dynamics]
    pfam02201
    Location:263 → 334
    SWIB; SWIB/MDM2 domain

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_000077.7 Reference GRCm39 C57BL/6J

    Range
    106153997..106163810 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_006534552.5 → XP_006534615.2  SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily D member 2 isoform X1

    UniProtKB/TrEMBL
    Q3TXH6
    Conserved Domains (3) summary
    TIGR01628
    Location:43 → 161
    PABP-1234; polyadenylate binding protein, human types 1, 2, 3, 4 family
    COG5531
    Location:250 → 445
    Rsc6; Chromatin remodeling complex protein RSC6, contains SWIB domain [Chromatin structure and dynamics]
    cd17675
    Location:327 → 406
    SWIB_BAF60B; SWIB domain found in BRG1-associated factor 60B (BAF60B) and similar proteins
Nucleotide Protein Strain
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q99JR8.2 GenPept UniProtKB/Swiss-Prot:Q99JR8

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