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    Smarcc2 SWI/SNF related BAF chromatin remodeling complex subunit C2 [ Rattus norvegicus (Norway rat) ]

    Gene ID: 685179, updated on 27-Nov-2024

    Summary

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    Official Symbol
    Smarcc2provided by RGD
    Official Full Name
    SWI/SNF related BAF chromatin remodeling complex subunit C2provided by RGD
    Primary source
    RGD:1597704
    See related
    EnsemblRapid:ENSRNOG00000031135 AllianceGenome:RGD:1597704
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Rattus norvegicus
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
    Summary
    Predicted to enable chromatin binding activity and histone binding activity. Involved in negative regulation of DNA-templated transcription. Predicted to be located in nucleoplasm. Predicted to be part of SWI/SNF complex; nBAF complex; and npBAF complex. Human ortholog(s) of this gene implicated in Coffin-Siris syndrome 8. Orthologous to human SMARCC2 (SWI/SNF related, matrix associated, actin dependent regulator of chromatin subfamily c member 2). [provided by Alliance of Genome Resources, Nov 2024]
    Expression
    Biased expression in Brain (RPKM 196.8), Lung (RPKM 173.5) and 9 other tissues See more
    Orthologs
    human mouse all
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    Genomic context

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    See Smarcc2 in Genome Data Viewer
    Location:
    7q11
    Exon count:
    29
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCr8 (GCF_036323735.1) 7 NC_086025.1 (1466223..1494627)
    RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 7 NC_051342.1 (881844..910090)
    106 previous assembly Rnor_6.0 (GCF_000001895.5) 7 NC_005106.4 (2875898..2905463)

    Chromosome 7 - NC_086025.1Genomic Context describing neighboring genes Neighboring gene small nucleolar RNA SNORA55 Neighboring gene transfer RNA serine (anticodon CGA) 1 Neighboring gene uncharacterized LOC120093526 Neighboring gene myosin light chain 6 Neighboring gene myosin light chain 6B like 1

    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. Functional selectivity of recombinant mammalian SWI/SNF subunits. Kadam S, et al. Genes Dev, 2000 Oct 1. PMID 11018012, Free PMC Article
    2. The spectrum of SWI/SNF mutations, ubiquitous in human cancers. Shain AH, et al. PLoS One, 2013. PMID 23355908, Free PMC Article
    3. 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
    4. Purification and biochemical heterogeneity of the mammalian SWI-SNF complex. Wang W, et al. EMBO J, 1996 Oct 1. PMID 8895581, Free PMC Article
    5. Kinetic analysis of npBAF to nBAF switching reveals exchange of SS18 with CREST and integration with neural developmental pathways. Staahl BT, et al. J Neurosci, 2013 Jun 19. PMID 23785148, Free PMC Article

    See all (18) citations in PubMed

    GeneRIFs: Gene References Into Functions

    Pathways from PubChem

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    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Homology

    Gene Ontology Provided by RGD

    Function Evidence Code Pubs
    enables chromatin binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables histone binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in chromatin remodeling ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in negative regulation of DNA-templated transcription IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in negative regulation of DNA-templated transcription ISO
    Inferred from Sequence Orthology
    more info
    		  
    acts_upstream_of_or_within negative regulation of transcription by RNA polymerase II ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in nucleosome disassembly ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in positive regulation of DNA-templated transcription IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in positive regulation of DNA-templated transcription ISO
    Inferred from Sequence Orthology
    more info
    		  
    acts_upstream_of_or_within regulation of transcription by RNA polymerase II ISO
    Inferred from Sequence Orthology
    more info
    		  
    acts_upstream_of transcription by RNA polymerase II 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
    		  
    part_of nBAF complex IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    part_of nBAF complex ISO
    Inferred from Sequence Orthology
    more info
    		  
    part_of npBAF complex IBA
    Inferred from Biological aspect of Ancestor
    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
    		  

    General protein information

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    Preferred Names
    SWI/SNF complex subunit SMARCC2
    Names
    SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily c, member 2

    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_001427252.1 → NP_001414181.1  SWI/SNF complex subunit SMARCC2

      Status: VALIDATED

      Source sequence(s)
      JAXUCZ010000007
      UniProtKB/TrEMBL
      A0A8I6A5E1
      Related
      ENSRNOP00000028244.9, ENSRNOT00000028244.9

    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
      1466223..1494627
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_006240805.5 → XP_006240867.1  SWI/SNF complex subunit SMARCC2 isoform X1

      UniProtKB/TrEMBL
      D4A510
      Conserved Domains (6) summary
      COG5259
      Location:379 → 738
      RSC8; RSC chromatin remodeling complex subunit RSC8 [Chromatin structure and dynamics / Transcription]
      pfam04433
      Location:427 → 512
      SWIRM; SWIRM domain
      pfam15621
      Location:1145 → 1235
      PROL5-SMR; Proline-rich submaxillary gland androgen-regulated family
      pfam16495
      Location:910 → 976
      SWIRM-assoc_1; SWIRM-associated region 1
      pfam16496
      Location:4 → 420
      SWIRM-assoc_2; SWIRM-associated domain at the N-terminal
      pfam16498
      Location:714 → 778
      SWIRM-assoc_3; SWIRM-associated domain at the C-terminal

    2. XM_006240806.5 → XP_006240868.1  SWI/SNF complex subunit SMARCC2 isoform X2

      UniProtKB/TrEMBL
      D4A510
      Conserved Domains (6) summary
      COG5259
      Location:379 → 732
      RSC8; RSC chromatin remodeling complex subunit RSC8 [Chromatin structure and dynamics / Transcription]
      pfam04433
      Location:427 → 512
      SWIRM; SWIRM domain
      pfam15621
      Location:1139 → 1229
      PROL5-SMR; Proline-rich submaxillary gland androgen-regulated family
      pfam16495
      Location:904 → 970
      SWIRM-assoc_1; SWIRM-associated region 1
      pfam16496
      Location:4 → 420
      SWIRM-assoc_2; SWIRM-associated domain at the N-terminal
      pfam16498
      Location:708 → 772
      SWIRM-assoc_3; SWIRM-associated domain at the C-terminal

    3. XM_063264254.1 → XP_063120324.1  SWI/SNF complex subunit SMARCC2 isoform X7

    4. XM_063264255.1 → XP_063120325.1  SWI/SNF complex subunit SMARCC2 isoform X9

    5. XM_006240807.5 → XP_006240869.1  SWI/SNF complex subunit SMARCC2 isoform X4

      UniProtKB/TrEMBL
      D4A510
      Related
      ENSRNOP00000091991.2, ENSRNOT00000097786.2
      Conserved Domains (6) summary
      COG5259
      Location:379 → 707
      RSC8; RSC chromatin remodeling complex subunit RSC8 [Chromatin structure and dynamics / Transcription]
      pfam04433
      Location:427 → 512
      SWIRM; SWIRM domain
      pfam15621
      Location:1114 → 1204
      PROL5-SMR; Proline-rich submaxillary gland androgen-regulated family
      pfam16495
      Location:879 → 945
      SWIRM-assoc_1; SWIRM-associated region 1
      pfam16496
      Location:4 → 420
      SWIRM-assoc_2; SWIRM-associated domain at the N-terminal
      pfam16498
      Location:683 → 747
      SWIRM-assoc_3; SWIRM-associated domain at the C-terminal

    6. XM_039079999.2 → XP_038935927.1  SWI/SNF complex subunit SMARCC2 isoform X5

      UniProtKB/TrEMBL
      D4A510
      Conserved Domains (6) summary
      PTZ00121
      Location:683 → 919
      PTZ00121; MAEBL; Provisional
      COG5259
      Location:379 → 701
      RSC8; RSC chromatin remodeling complex subunit RSC8 [Chromatin structure and dynamics / Transcription]
      pfam06346
      Location:1108 → 1194
      Drf_FH1; Formin Homology Region 1
      pfam16495
      Location:873 → 939
      SWIRM-assoc_1; SWIRM-associated region 1
      pfam16496
      Location:7 → 420
      SWIRM-assoc_2; SWIRM-associated domain at the N-terminal
      pfam16498
      Location:677 → 741
      SWIRM-assoc_3; SWIRM-associated domain at the C-terminal

    7. XM_001055673.8 → XP_001055673.1  SWI/SNF complex subunit SMARCC2 isoform X6

      UniProtKB/TrEMBL
      D4A510
      Conserved Domains (5) summary
      COG5259
      Location:379 → 739
      RSC8; RSC chromatin remodeling complex subunit RSC8 [Chromatin structure and dynamics / Transcription]
      pfam04433
      Location:427 → 512
      SWIRM; SWIRM domain
      pfam16495
      Location:911 → 977
      SWIRM-assoc_1; SWIRM-associated region 1
      pfam16496
      Location:4 → 420
      SWIRM-assoc_2; SWIRM-associated domain at the N-terminal
      pfam16498
      Location:715 → 779
      SWIRM-assoc_3; SWIRM-associated domain at the C-terminal

    8. XM_001055795.8 → XP_001055795.1  SWI/SNF complex subunit SMARCC2 isoform X3

      UniProtKB/TrEMBL
      A0A8I6AGR8, D4A510
      Conserved Domains (6) summary
      COG5259
      Location:379 → 708
      RSC8; RSC chromatin remodeling complex subunit RSC8 [Chromatin structure and dynamics / Transcription]
      pfam04433
      Location:427 → 512
      SWIRM; SWIRM domain
      pfam15621
      Location:1115 → 1205
      PROL5-SMR; Proline-rich submaxillary gland androgen-regulated family
      pfam16495
      Location:880 → 946
      SWIRM-assoc_1; SWIRM-associated region 1
      pfam16496
      Location:4 → 420
      SWIRM-assoc_2; SWIRM-associated domain at the N-terminal
      pfam16498
      Location:684 → 748
      SWIRM-assoc_3; SWIRM-associated domain at the C-terminal

    9. XM_063264256.1 → XP_063120326.1  SWI/SNF complex subunit SMARCC2 isoform X11

    10. XM_001055738.8 → XP_001055738.1  SWI/SNF complex subunit SMARCC2 isoform X10

      UniProtKB/TrEMBL
      D4A510
      Conserved Domains (5) summary
      COG5259
      Location:379 → 708
      RSC8; RSC chromatin remodeling complex subunit RSC8 [Chromatin structure and dynamics / Transcription]
      pfam04433
      Location:427 → 512
      SWIRM; SWIRM domain
      pfam16495
      Location:880 → 946
      SWIRM-assoc_1; SWIRM-associated region 1
      pfam16496
      Location:4 → 420
      SWIRM-assoc_2; SWIRM-associated domain at the N-terminal
      pfam16498
      Location:684 → 748
      SWIRM-assoc_3; SWIRM-associated domain at the C-terminal

    11. XM_039080000.2 → XP_038935928.1  SWI/SNF complex subunit SMARCC2 isoform X8

      UniProtKB/TrEMBL
      D4A510
      Conserved Domains (6) summary
      PTZ00121
      Location:605 → 841
      PTZ00121; MAEBL; Provisional
      COG5259
      Location:263 → 623
      RSC8; RSC chromatin remodeling complex subunit RSC8 [Chromatin structure and dynamics / Transcription]
      pfam06346
      Location:1030 → 1116
      Drf_FH1; Formin Homology Region 1
      pfam16495
      Location:795 → 861
      SWIRM-assoc_1; SWIRM-associated region 1
      pfam16496
      Location:1 → 304
      SWIRM-assoc_2; SWIRM-associated domain at the N-terminal
      pfam16498
      Location:599 → 663
      SWIRM-assoc_3; SWIRM-associated domain at the C-terminal
    Nucleotide Protein Strain
    Heading Accession and Version

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