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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 21-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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    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

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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