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SMARCC2 SWI/SNF related, matrix associated, actin dependent regulator of chromatin subfamily c member 2 [ Homo sapiens (human) ]

Gene ID: 6601, updated on 18-Nov-2018

Summary

Official Symbol
SMARCC2provided by HGNC
Official Full Name
SWI/SNF related, matrix associated, actin dependent regulator of chromatin subfamily c member 2provided by HGNC
Primary source
HGNC:HGNC:11105
See related
Ensembl:ENSG00000139613 MIM:601734; Vega:OTTHUMG00000170288
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
Rsc8; BAF170; CRACC2
Summary
The protein encoded by this gene is a member of the SWI/SNF family of proteins, whose members display helicase and ATPase activities and which are thought to regulate transcription of certain genes by altering the chromatin structure around those genes. The encoded protein is part of the large ATP-dependent chromatin remodeling complex SNF/SWI and contains a predicted leucine zipper motif typical of many transcription factors. Alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2008]
Expression
Ubiquitous expression in brain (RPKM 28.0), ovary (RPKM 22.4) and 25 other tissues See more
Orthologs

Genomic context

See SMARCC2 in Genome Data Viewer
Location:
12q13.2
Exon count:
29
Annotation release Status Assembly Chr Location
109 current GRCh38.p12 (GCF_000001405.38) 12 NC_000012.12 (56162359..56189574, complement)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 12 NC_000012.11 (56555636..56583351, complement)

Chromosome 12 - NC_000012.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC107987175 Neighboring gene myosin light chain 6B Neighboring gene myosin light chain 6 Neighboring gene uncharacterized LOC107984468 Neighboring gene transfer RNA-Ser (CGA) 4-1

Genomic regions, transcripts, and products

Expression

  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Jun 15 11:32:44 2016

Bibliography

GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

HIV-1 interactions

Protein interactions

Protein Gene Interaction Pubs
Tat tat Most of the components of the SWI2/SNF2 chromatin remodeling complex (BRG1/BRM, BAF250, BAF180, BAF170, BAF155, BAF60a, BAF53A, actin and InI) except BRM, BAF155 and BAF57, are identified to interact with HIV-1 Tat in Jurkat cell PubMed

Go to the HIV-1, Human Interaction Database

Pathways from BioSystems

  • Chromatin modifying enzymes, organism-specific biosystem (from REACTOME)
    Chromatin modifying enzymes, organism-specific biosystemEukaryotic DNA is associated with histone proteins and organized into a complex nucleoprotein structure called chromatin. This structure decreases the accessibility of DNA but also helps to protect i...
  • Chromatin organization, organism-specific biosystem (from REACTOME)
    Chromatin organization, organism-specific biosystemChromatin organization refers to the composition and conformation of complexes between DNA, protein and RNA. It is determined by processes that result in the specification, formation or maintenance o...
  • Glucocorticoid receptor regulatory network, organism-specific biosystem (from Pathway Interaction Database)
    Glucocorticoid receptor regulatory network, organism-specific biosystem
    Glucocorticoid receptor regulatory network
  • RMTs methylate histone arginines, organism-specific biosystem (from REACTOME)
    RMTs methylate histone arginines, organism-specific biosystemArginine methylation is a common post-translational modification; around 2% of arginine residues are methylated in rat liver nuclei (Boffa et al. 1977). Arginine can be methylated in 3 different ways...

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Clone Names

  • DKFZp313D0632

Gene Ontology Provided by GOA

Component Evidence Code Pubs
SWI/SNF complex IDA
Inferred from Direct Assay
more info
PubMed 
nBAF complex ISS
Inferred from Sequence or Structural Similarity
more info
 
npBAF complex ISS
Inferred from Sequence or Structural Similarity
more info
 
nuclear chromatin HDA PubMed 
nucleoplasm IDA
Inferred from Direct Assay
more info
 
nucleoplasm TAS
Traceable Author Statement
more info
 
protein-containing complex HDA PubMed 

General protein information

Preferred Names
SWI/SNF complex subunit SMARCC2
Names
SWI/SNF complex 170 kDa subunit
SWI3-like protein
chromatin remodeling complex BAF170 subunit
mammalian chromatin remodeling complex BRG1-associated factor 170

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.

Genomic

  1. NG_047081.1 RefSeqGene

    Range
    4994..32209
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001130420.2NP_001123892.1  SWI/SNF complex subunit SMARCC2 isoform c

    See identical proteins and their annotated locations for NP_001123892.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) contains an alternate in-frame exon in the central coding region and contains alternate in-frame segment in the 3' coding region, compared to variant 1. The encoded isoform (c), contains a novel internal segment, lacks a segment near the C-terminus, and is shorter than isoform a.
    Source sequence(s)
    AB209006, BM875330, CX165574, HY118539
    Consensus CDS
    CCDS55835.1
    UniProtKB/Swiss-Prot
    Q8TAQ2
    Related
    ENSP00000377591.3, OTTHUMP00000243474, ENST00000394023.7, OTTHUMT00000408459
    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
    cl26386
    Location:10061141
    DNA_pol3_gamma3; DNA polymerase III subunits gamma and tau domain III
    cl26511
    Location:721978
    Neuromodulin_N; Gap junction protein N-terminal region
    cl27154
    Location:379739
    SWIRM; SWIRM domain
  2. NM_001330288.1NP_001317217.1  SWI/SNF complex subunit SMARCC2 isoform d

    Status: REVIEWED

    Description
    Transcript Variant: This variant (4) contains an alternate in-frame exon in the central coding region compared to variant 1. The encoded isoform (d), contains the same N- and C-termini, but is longer than isoform a.
    Source sequence(s)
    AK315153, BC009067, BM875330, CX165574, DA768316, HY118539
    Consensus CDS
    CCDS81698.1
    UniProtKB/Swiss-Prot
    Q8TAQ2
    UniProtKB/TrEMBL
    F8VXC8
    Related
    ENSP00000449396.1, ENST00000550164.5
    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:9991234
    Atrophin-1; Atrophin-1 family
    cl26511
    Location:721978
    Neuromodulin_N; Gap junction protein N-terminal region
    cl27154
    Location:379739
    SWIRM; SWIRM domain
  3. NM_003075.4NP_003066.2  SWI/SNF complex subunit SMARCC2 isoform a

    See identical proteins and their annotated locations for NP_003066.2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) encodes isoform a.
    Source sequence(s)
    AK315153, BC009067, BM875330, CX165574, HY118539
    Consensus CDS
    CCDS8907.1
    UniProtKB/Swiss-Prot
    Q8TAQ2
    UniProtKB/TrEMBL
    A0A024RB22
    Related
    ENSP00000267064.4, OTTHUMP00000243441, ENST00000267064.8, OTTHUMT00000408370
    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:9681203
    Atrophin-1; Atrophin-1 family
    cl26511
    Location:690947
    Neuromodulin_N; Gap junction protein N-terminal region
    cl27154
    Location:379708
    SWIRM; SWIRM domain
  4. NM_139067.3NP_620706.1  SWI/SNF complex subunit SMARCC2 isoform b

    See identical proteins and their annotated locations for NP_620706.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) contains an alternate in-frame exon in the central coding region and uses an alternate in-frame splice site in the 3' coding region, compared to variant 1. The encoded isoform (b), contains a novel internal segment, lacks a segment near the C-terminus, and is shorter than isoform a.
    Source sequence(s)
    AB209006, BM875330, CX165574, HY118539
    Consensus CDS
    CCDS8908.1
    UniProtKB/Swiss-Prot
    Q8TAQ2
    Related
    ENSP00000302919.4, OTTHUMP00000243447, ENST00000347471.8, OTTHUMT00000408379
    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
    cl26511
    Location:721978
    Neuromodulin_N; Gap junction protein N-terminal region
    cl27154
    Location:379739
    SWIRM; SWIRM domain

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109 details...Open this link in a new tab

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

Reference GRCh38.p12 Primary Assembly

Genomic

  1. NC_000012.12 Reference GRCh38.p12 Primary Assembly

    Range
    56162359..56189574 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_017019886.1XP_016875375.1  SWI/SNF complex subunit SMARCC2 isoform X6

  2. XM_017019885.1XP_016875374.1  SWI/SNF complex subunit SMARCC2 isoform X5

  3. XM_017019884.1XP_016875373.1  SWI/SNF complex subunit SMARCC2 isoform X4

  4. XM_005269104.1XP_005269161.1  SWI/SNF complex subunit SMARCC2 isoform X3

    See identical proteins and their annotated locations for XP_005269161.1

    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
  5. XM_005269103.2XP_005269160.1  SWI/SNF complex subunit SMARCC2 isoform X2

    See identical proteins and their annotated locations for XP_005269160.1

    Conserved Domains (5) summary
    COG5259
    Location:379707
    RSC8; RSC chromatin remodeling complex subunit RSC8 [Chromatin structure and dynamics / Transcription]
    pfam04433
    Location:427512
    SWIRM; SWIRM domain
    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
  6. XM_005269102.2XP_005269159.1  SWI/SNF complex subunit SMARCC2 isoform X1

    See identical proteins and their annotated locations for XP_005269159.1

    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
  7. XM_011538693.3XP_011536995.1  SWI/SNF complex subunit SMARCC2 isoform X7

    Conserved Domains (6) summary
    COG5259
    Location:128488
    RSC8; RSC chromatin remodeling complex subunit RSC8 [Chromatin structure and dynamics / Transcription]
    pfam00249
    Location:397422
    Myb_DNA-binding; Myb-like DNA-binding domain
    pfam04433
    Location:176261
    SWIRM; SWIRM domain
    pfam16495
    Location:660726
    SWIRM-assoc_1; SWIRM-associated region 1
    pfam16496
    Location:1169
    SWIRM-assoc_2; SWIRM-associated domain at the N-terminal
    pfam16498
    Location:464528
    SWIRM-assoc_3; SWIRM-associated domain at the C-terminal
  8. XM_017019887.2XP_016875376.1  SWI/SNF complex subunit SMARCC2 isoform X8

RNA

  1. XR_002957374.1 RNA Sequence

  2. XR_002957373.1 RNA Sequence

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