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    Smarcc2 SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily c, member 2 [ Mus musculus (house mouse) ]

    Gene ID: 68094, updated on 31-Jan-2019

    Summary

    Official Symbol
    Smarcc2provided by MGI
    Official Full Name
    SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily c, member 2provided by MGI
    Primary source
    MGI:MGI:1915344
    See related
    Ensembl:ENSMUSG00000025369
    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
    5930405J04Rik
    Expression
    Ubiquitous expression in CNS E14 (RPKM 85.9), whole brain E14.5 (RPKM 78.9) and 28 other tissues See more
    Orthologs

    Genomic context

    See Smarcc2 in Genome Data Viewer
    Location:
    10; 10 D3
    Exon count:
    29
    Annotation release Status Assembly Chr Location
    106 current GRCm38.p4 (GCF_000001635.24) 10 NC_000076.6 (128459236..128490583)
    Build 37.2 previous assembly MGSCv37 (GCF_000001635.18) 10 NC_000076.5 (127896292..127927230)

    Chromosome 10 - NC_000076.6Genomic Context describing neighboring genes Neighboring gene nuclear encoded tRNA serine 2 (anticodon CGA) Neighboring gene microRNA 8105 Neighboring gene myosin, light polypeptide 6, alkali, smooth muscle and non-muscle Neighboring gene myosin, light polypeptide 6B

    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 FunctionsWhat's a GeneRIF?

    Variation

    Alleles

    Alleles of this type are documented at Mouse Genome Informatics  (MGI)

    Pathways from BioSystems

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Homology

    Gene Ontology Provided by MGI

    Function Evidence Code Pubs
    DNA binding IEA
    Inferred from Electronic Annotation
    more info
     
    chromatin binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    Process Evidence Code Pubs
    chromatin organization IEA
    Inferred from Electronic Annotation
    more info
     
    chromatin remodeling ISO
    Inferred from Sequence Orthology
    more info
     
    negative regulation of transcription by RNA polymerase II IGI
    Inferred from Genetic Interaction
    more info
    PubMed 
    negative regulation of transcription, DNA-templated ISO
    Inferred from Sequence Orthology
    more info
     
    nervous system development IEA
    Inferred from Electronic Annotation
    more info
     
    nucleosome disassembly ISO
    Inferred from Sequence Orthology
    more info
     
    positive regulation of transcription, DNA-templated ISO
    Inferred from Sequence Orthology
    more info
     
    regulation of transcription from RNA polymerase II promoter involved in forebrain neuron fate commitment IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    Component Evidence Code Pubs
    SWI/SNF complex IDA
    Inferred from Direct Assay
    more info
    PubMed 
    SWI/SNF complex ISO
    Inferred from Sequence Orthology
    more info
     
    nBAF complex IDA
    Inferred from Direct Assay
    more info
    PubMed 
    npBAF complex IDA
    Inferred from Direct Assay
    more info
    PubMed 
    nucleoplasm ISO
    Inferred from Sequence Orthology
    more info
     
    nucleus IEA
    Inferred from Electronic Annotation
    more info
     

    General protein information

    Preferred Names
    SWI/SNF complex subunit SMARCC2
    Names
    BAF170
    BRG1-associated factor 170
    SWI/SNF complex 170 kDa subunit
    SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily C member 2

    NCBI Reference Sequences (RefSeq)

    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_001114096.1NP_001107568.1  SWI/SNF complex subunit SMARCC2 isoform 2

      See identical proteins and their annotated locations for NP_001107568.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) has an additional in-frame exon in the central coding region and lacks an in-frame segment in the 3' coding region, compared to variant 1. The resulting isoform (2) is shorter and has an additional segment in the central region but lacks an internal segment in the C-terminal region, compared to isoform 1.
      Source sequence(s)
      AI463326, AK146971, BC058720, CB248220
      Consensus CDS
      CCDS48726.1
      UniProtKB/Swiss-Prot
      Q6PDG5
      UniProtKB/TrEMBL
      Q3UID0
      Related
      ENSMUSP00000096734.3, ENSMUST00000099131.10
      Conserved Domains (5) summary
      pfam16495
      Location:911977
      SWIRM-assoc_1; SWIRM-associated region 1
      pfam16496
      Location:4420
      SWIRM-assoc_2; SWIRM-associated domain at the N-terminal
      pfam16498
      Location:715779
      SWIRM-assoc_3; SWIRM-associated domain at the C-terminal
      cl26407
      Location:719874
      IF-2; Translation-initiation factor 2
      cl27154
      Location:379739
      SWIRM; SWIRM domain
    2. NM_001114097.1NP_001107569.1  SWI/SNF complex subunit SMARCC2 isoform 1

      See identical proteins and their annotated locations for NP_001107569.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) encodes the longest isoform (1).
      Source sequence(s)
      AI463326, BC058720, BC062102, CB248220
      Consensus CDS
      CCDS48727.1
      UniProtKB/Swiss-Prot
      Q6PDG5
      Related
      ENSMUSP00000100868.2, ENSMUST00000105235.9
      Conserved Domains (6) summary
      pfam16495
      Location:880946
      SWIRM-assoc_1; SWIRM-associated region 1
      pfam16496
      Location:4420
      SWIRM-assoc_2; SWIRM-associated domain at the N-terminal
      pfam16498
      Location:684748
      SWIRM-assoc_3; SWIRM-associated domain at the C-terminal
      cl26464
      Location:9631202
      Atrophin-1; Atrophin-1 family
      cl26511
      Location:690926
      Neuromodulin_N; Gap junction protein N-terminal region
      cl27154
      Location:379708
      SWIRM; SWIRM domain
    3. NM_198160.2NP_937803.1  SWI/SNF complex subunit SMARCC2 isoform 3

      See identical proteins and their annotated locations for NP_937803.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (3) lacks an in-frame segment in the 3' coding region, compared to variant 1. The resulting isoform (3) is shorter and lacks an internal segment in the C-terminal region, compared to isoform 1.
      Source sequence(s)
      AI463326, BC058720, CB248220
      Consensus CDS
      CCDS24278.1
      UniProtKB/Swiss-Prot
      Q6PDG5
      Related
      ENSMUSP00000026433.7, ENSMUST00000026433.8
      Conserved Domains (5) summary
      pfam16495
      Location:880946
      SWIRM-assoc_1; SWIRM-associated region 1
      pfam16496
      Location:4420
      SWIRM-assoc_2; SWIRM-associated domain at the N-terminal
      pfam16498
      Location:684748
      SWIRM-assoc_3; SWIRM-associated domain at the C-terminal
      cl26407
      Location:688843
      IF-2; Translation-initiation factor 2
      cl27154
      Location:379708
      SWIRM; SWIRM domain

    RefSeqs of Annotated Genomes: Mus musculus Annotation Release 106

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference GRCm38.p4 C57BL/6J

    Genomic

    1. NC_000076.6 Reference GRCm38.p4 C57BL/6J

      Range
      128459236..128490583
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_006514020.3XP_006514083.1  SWI/SNF complex subunit SMARCC2 isoform X1

      Conserved Domains (6) summary
      pfam16495
      Location:911977
      SWIRM-assoc_1; SWIRM-associated region 1
      pfam16496
      Location:4420
      SWIRM-assoc_2; SWIRM-associated domain at the N-terminal
      pfam16498
      Location:715779
      SWIRM-assoc_3; SWIRM-associated domain at the C-terminal
      cl26464
      Location:9941233
      Atrophin-1; Atrophin-1 family
      cl26511
      Location:721957
      Neuromodulin_N; Gap junction protein N-terminal region
      cl27154
      Location:379739
      SWIRM; SWIRM domain
    2. XM_006514023.3XP_006514086.1  SWI/SNF complex subunit SMARCC2 isoform X4

      Conserved Domains (5) summary
      COG5259
      Location:379739
      RSC8; RSC chromatin remodeling complex subunit RSC8 [Chromatin structure and dynamics / Transcription]
      pfam04433
      Location:427512
      SWIRM; SWIRM domain
      pfam16495
      Location:911977
      SWIRM-assoc_1; SWIRM-associated region 1
      pfam16496
      Location:4420
      SWIRM-assoc_2; SWIRM-associated domain at the N-terminal
      pfam16498
      Location:715779
      SWIRM-assoc_3; SWIRM-associated domain at the C-terminal
    3. XM_006514024.3XP_006514087.1  SWI/SNF complex subunit SMARCC2 isoform X5

      Conserved Domains (5) summary
      COG5259
      Location:379738
      RSC8; RSC chromatin remodeling complex subunit RSC8 [Chromatin structure and dynamics / Transcription]
      pfam04433
      Location:427512
      SWIRM; SWIRM domain
      pfam16495
      Location:910976
      SWIRM-assoc_1; SWIRM-associated region 1
      pfam16496
      Location:4420
      SWIRM-assoc_2; SWIRM-associated domain at the N-terminal
      pfam16498
      Location:714778
      SWIRM-assoc_3; SWIRM-associated domain at the C-terminal
    4. XM_006514021.3XP_006514084.1  SWI/SNF complex subunit SMARCC2 isoform X2

      Conserved Domains (6) summary
      COG5259
      Location:379738
      RSC8; RSC chromatin remodeling complex subunit RSC8 [Chromatin structure and dynamics / Transcription]
      pfam04433
      Location:427512
      SWIRM; SWIRM domain
      pfam15621
      Location:11391232
      PROL5-SMR; Proline-rich submaxillary gland androgen-regulated family
      pfam16495
      Location:910976
      SWIRM-assoc_1; SWIRM-associated region 1
      pfam16496
      Location:4420
      SWIRM-assoc_2; SWIRM-associated domain at the N-terminal
      pfam16498
      Location:714778
      SWIRM-assoc_3; SWIRM-associated domain at the C-terminal
    5. XM_006514022.3XP_006514085.1  SWI/SNF complex subunit SMARCC2 isoform X3

      Conserved Domains (6) summary
      pfam16495
      Location:879945
      SWIRM-assoc_1; SWIRM-associated region 1
      pfam16496
      Location:4420
      SWIRM-assoc_2; SWIRM-associated domain at the N-terminal
      pfam16498
      Location:683747
      SWIRM-assoc_3; SWIRM-associated domain at the C-terminal
      cl26464
      Location:9621201
      Atrophin-1; Atrophin-1 family
      cl26511
      Location:689925
      Neuromodulin_N; Gap junction protein N-terminal region
      cl27154
      Location:379707
      SWIRM; SWIRM domain
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