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Smarcc2 SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily c, member 2 [ Rattus norvegicus (Norway rat) ]

Gene ID: 685179, updated on 13-Apr-2024

Summary

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Official Symbol
Smarcc2provided by RGD
Official Full Name
SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily c, member 2provided by RGD
Primary source
RGD:1597704
See related
Ensembl: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 transcription, DNA-templated. Predicted to be located in nucleoplasm. Predicted to be part of SWI/SNF complex; nBAF complex; and npBAF complex. Orthologous to human SMARCC2 (SWI/SNF related, matrix associated, actin dependent regulator of chromatin subfamily c member 2). [provided by Alliance of Genome Resources, Apr 2022]
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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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

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

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
    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
    Related
    ENSRNOP00000028244.8
    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
    Related
    ENSRNOP00000091991.1
    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
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