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SMARCB1 Gene

protein-coding   GIFtS: 66
GCID: GC22P024129

SWI/SNF Related, Matrix Associated, Actin Dependent Regulator...


(Previous symbol: SNF5L1)
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Aliases
for SMARCB1 gene

(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, 10fRNAdb, 12H-InvDB, 13NCBI, 14NONCODE, and/or 15RNAdb)
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Aliases
SWI/SNF Related, Matrix Associated, Actin Dependent Regulator Of
Chromatin, Subfamily B, Member 11 2
     SNF52 5
SNF5L11 2 3     SWNTS12 5
INI12 3 5     Homolog-Like 11
Malignant Rhabdoid Tumor Suppressor1 2     Integrase Interactor 11
Integrase Interactor 1 Protein2 3     Sucrose Nonfermenting1
BAF472 3     yeast1
BRG1-Associated Factor 472 3     Sfh1p2
hSNF52 3     Snr12
SNF5 Homolog2 3     hSNFS2
MRD152 5     Sucrose Nonfermenting, Yeast, Homolog-Like 12
RDT2 5     SWI/SNF-Related Matrix-Associated Actin-Dependent Regulator Of Chromatin
Subfamily B Member 12
RTPS12 5     SWI/SNF-Related Matrix-Associated Protein2

External Ids:    HGNC: 111031   Entrez Gene: 65982   Ensembl: ENSG000000999567   OMIM: 6016075   UniProtKB: Q128243   

Export aliases for SMARCB1 gene to outside databases

Previous GC identifers: GC22P020825 GC22P022453 GC22P007117


Summaries
for SMARCB1 gene

(According to Entrez Gene, GeneCards, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
About This Section

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Entrez Gene summary for SMARCB1 Gene:
The protein encoded by this gene is part of a complex that relieves repressive chromatin structures, allowing the
transcriptional machinery to access its targets more effectively. The encoded nuclear protein may also bind to
and enhance the DNA joining activity of HIV-1 integrase. This gene has been found to be a tumor suppressor, and
mutations in it have been associated with malignant rhabdoid tumors. Two transcript variants encoding different
isoforms have been found for this gene. (provided by RefSeq, Jul 2008)

GeneCards Summary for SMARCB1 Gene:
SMARCB1 (SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily b, member 1) is a protein-coding gene. Diseases associated with SMARCB1 include choroid plexus carcinoma, and chromosome 22q deletion. GO annotations related to this gene include Tat protein binding and transcription coactivator activity.

UniProtKB/Swiss-Prot: SNF5_HUMAN, Q12824
Function: Core component of the BAF (hSWI/SNF) complex. This ATP-dependent chromatin-remodeling complex plays
important roles in cell proliferation and differentiation, in cellular antiviral activities and inhibition of
tumor formation. The BAF complex is able to create a stable, altered form of chromatin that constrains fewer
negative supercoils than normal. This change in supercoiling would be due to the conversion of up to one-half of
the nucleosomes on polynucleosomal arrays into asymmetric structures, termed altosomes, each composed of 2
histones octamers. Stimulates in vitro the remodeling activity of SMARCA4/BRG1/BAF190A. Involved in activation of
CSF1 promoter. Belongs to the neural progenitors-specific chromatin remodeling complex (npBAF complex) and the
neuron-specific chromatin remodeling complex (nBAF complex). During neural development a switch from a
stem/progenitor to a post-mitotic chromatin remodeling mechanism occurs as neurons exit the cell cycle and become
committed to their adult state. The transition from proliferating neural stem/progenitor cells to post-mitotic
neurons requires a switch in subunit composition of the npBAF and nBAF complexes. As neural progenitors exit
mitosis and differentiate into neurons, npBAF complexes which contain ACTL6A/BAF53A and PHF10/BAF45A, are
exchanged for homologous alternative ACTL6B/BAF53B and DPF1/BAF45B or DPF3/BAF45C subunits in neuron-specific
complexes (nBAF). The npBAF complex is essential for the self-renewal/proliferative capacity of the multipotent
neural stem cells. The nBAF complex along with CREST plays a role regulating the activity of genes essential for
dendrite growth (By similarity). Plays a key role in cell-cycle control and causes cell cycle arrest in G0/G1.
Also involved in vitamin D-coupled transcription regulation via its association with the WINAC complex, a
chromatin-remodeling complex recruited by vitamin D receptor (VDR), which is required for the ligand-bound
VDR-mediated transrepression of the CYP27B1 gene

Gene Wiki entry for SMARCB1 Gene


Genomic Views
for SMARCB1 gene

(According to GeneLoc and/or HGNC, and/or
Entrez Gene (NCBI build 37),
and/or miRBase,
Genomic Views according to UCSC (hg19) and Ensembl (release 75), Regulatory elements and Epigenetics data according to QIAGEN, and/or SwitchGear Genomics)
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RefSeq DNA sequence:
NC_000022.11  NC_018933.2  NT_011520.13  NT_187633.1  
Regulatory elements:
   Regulatory transcription factor binding sites in the SMARCB1 gene promoter:
         Egr-3   p53   p300   Lmo2   LCR-F1   AREB6   MZF-1   HOXA5   ARP-1   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmid: SMARCB1 promoter sequence
   Search Chromatin IP Primers for SMARCB1

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat SMARCB1


Genomic Location:
Genomic View: UCSC Golden Path with GeneCards custom track

Entrez Gene cytogenetic band: 22q11.23|22q11   Ensembl cytogenetic band:  22q11.23   HGNC cytogenetic band: 22q11.23

SMARCB1 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
SMARCB1 gene location

GeneLoc information about chromosome 22         GeneLoc Exon Structure

GeneLoc location for GC22P024129:  view genomic region     (about GC identifiers)

Start:
 24,129,150 bp from pter      End:
 24,176,705 bp from pter
Size:
 47,556 bases      Orientation:
 plus strand

Proteins
for SMARCB1 gene

(According to 1UniProtKB, HORDE, 2neXtProt, Ensembl, and/or Reactome, Modification sites according to PhosphoSitePlus, Specific Peptides from DME, RefSeq according to NCBI, PDB rendering according to OCA and/or Proteopedia, Recombinant Proteins from EMD Millipore, R&D Systems, GenScript, Enzo Life Sciences, OriGene, Novus Biologicals, Sino Biological, ProSpec, and/or Cloud-Clone Corp.,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, and/or Cloud-Clone Corp., Antibodies by EMD Millipore, R&D Systems, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, LSBio, Abcam, and/or Cloud-Clone Corp.)
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UniProtKB/Swiss-Prot: SNF5_HUMAN, Q12824 (See protein sequence)
Recommended Name: SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily B member 1  
Size: 385 amino acids; 44141 Da
Subunit: Component of the BAF (hSWI/SNF) complex, which includes at least actin (ACTB), ARID1A, ARID1B/BAF250,
SMARCA2, SMARCA4/BRG1/BAF190A, ACTL6A/BAF53, ACTL6B/BAF53B, SMARCE1/BAF57 SMARCC1/BAF155, SMARCC2/BAF170,
SMARCB1/SNF5/INI1, and one or more of SMARCD1/BAF60A, SMARCD2/BAF60B, or SMARCD3/BAF60C. In muscle cells, the BAF
complex also contains DPF3. Component of the WINAC complex, at least composed of SMARCA2, SMARCA4, SMARCB1,
SMARCC1, SMARCC2, SMARCD1, SMARCE1, ACTL6A, BAZ1B/WSTF, ARID1A, SUPT16H, CHAF1A and TOP2B. Binds to
double-stranded DNA. Interacts with MYK and MAEL. Interacts with PPP1R15A. Binds tightly to the human
immunodeficiency virus-type 1 (HIV-1) integrase in vitro and stimulates its DNA-joining activity. Interacts with
human papillomavirus 18 E1 protein to stimulate its viral replication. Interacts with Epstein-Barr virus protein
EBNA-2. Component of neural progenitors-specific chromatin remodeling complex (npBAF complex) composed of at
least, ARID1A/BAF250A or ARID1B/BAF250B, SMARCD1/BAF60A, SMARCD3/BAF60C, SMARCA2/BRM/BAF190B,
SMARCA4/BRG1/BAF190A, SMARCB1/BAF47, SMARCC1/BAF155, SMARCE1/BAF57, SMARCC2/BAF170, PHF10/BAF45A, ACTL6A/BAF53A
and actin. Component of neuron-specific chromatin remodeling complex (nBAF complex) composed of at least,
ARID1A/BAF250A or ARID1B/BAF250B, SMARCD1/BAF60A, SMARCD3/BAF60C, SMARCA2/BRM/BAF190B, SMARCA4/BRG1/BAF190A,
SMARCB1/BAF47, SMARCC1/BAF155, SMARCE1/BAF57, SMARCC2/BAF170, DPF1/BAF45B, DPF3/BAF45C, ACTL6B/BAF53B and actin
(By similarity)
Secondary accessions: O75784 O95474 Q17S11 Q38GA1 Q76N08 Q9UBH2
Alternative splicing: 2 isoforms:  Q12824-1   Q12824-2   

Explore the universe of human proteins at neXtProt for SMARCB1: NX_Q12824

Explore proteomics data for SMARCB1 at MOPED

Post-translational modifications: 

  • Ubiquitination2 at Lys292, Lys324
  • Modification sites at PhosphoSitePlus

    • See SMARCB1 Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

    REFSEQ proteins (2 alternative transcripts): 
    NP_001007469.1  NP_003064.2  

    ENSEMBL proteins: 
     ENSP00000388489   ENSP00000340883   ENSP00000263121   ENSP00000383984   ENSP00000385226  

    SMARCB1 Human Recombinant Protein Products:

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    Novus Biologicals SMARCB1 Proteins
    Novus Biologicals SMARCB1 Lysates
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    Cloud-Clone Corp. Proteins for SMARCB1

    SMARCB1 Antibody Products:

    EMD Millipore Mono- and Polyclonal Antibodies for the study of SMARCB1
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    SMARCB1 Assay Products:

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    Cloud-Clone Corp. ELISAs for SMARCB1
    Cloud-Clone Corp. CLIAs for SMARCB1

    Domains /
    Families
    for SMARCB1 gene

    (According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
    About This Section

    TryGeneCards Plus    		 2 InterPro protein domains:
     IPR006939 SNF5
     IPR017393 SWI_SNF_chromatin_remodel_cplx

    Graphical View of Domain Structure for InterPro Entry Q12824

    ProtoNet protein and cluster: Q12824

    1 Blocks protein domain: IPB006939 SNF5/SMARCB1/INI1

    UniProtKB/Swiss-Prot: SNF5_HUMAN, Q12824
    Similarity: Belongs to the SNF5 family


    SMARCB1 for domains           About GeneDecksing


    Function
    for SMARCB1 gene

    (According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013, inGenious Targeting Laboratory, genOway,
    transcription factor targeting from QIAGEN and/or HOMER, miRNA Gene Targets from miRTarBase, shRNA from OriGene, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, SwitchGear Genomics, Gene Editing from DNA2.0, Clones from OriGene, GenScript, Sino Biological, DNA2.0, and Vector BioLabs, Cell Lines from GenScript, ESI BIO, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
    About This Section

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    Molecular Function:

         UniProtKB/Swiss-Prot Summary: SNF5_HUMAN, Q12824
    Function: Core component of the BAF (hSWI/SNF) complex. This ATP-dependent chromatin-remodeling complex plays
    important roles in cell proliferation and differentiation, in cellular antiviral activities and inhibition of
    tumor formation. The BAF complex is able to create a stable, altered form of chromatin that constrains fewer
    negative supercoils than normal. This change in supercoiling would be due to the conversion of up to one-half of
    the nucleosomes on polynucleosomal arrays into asymmetric structures, termed altosomes, each composed of 2
    histones octamers. Stimulates in vitro the remodeling activity of SMARCA4/BRG1/BAF190A. Involved in activation of
    CSF1 promoter. Belongs to the neural progenitors-specific chromatin remodeling complex (npBAF complex) and the
    neuron-specific chromatin remodeling complex (nBAF complex). During neural development a switch from a
    stem/progenitor to a post-mitotic chromatin remodeling mechanism occurs as neurons exit the cell cycle and become
    committed to their adult state. The transition from proliferating neural stem/progenitor cells to post-mitotic
    neurons requires a switch in subunit composition of the npBAF and nBAF complexes. As neural progenitors exit
    mitosis and differentiate into neurons, npBAF complexes which contain ACTL6A/BAF53A and PHF10/BAF45A, are
    exchanged for homologous alternative ACTL6B/BAF53B and DPF1/BAF45B or DPF3/BAF45C subunits in neuron-specific
    complexes (nBAF). The npBAF complex is essential for the self-renewal/proliferative capacity of the multipotent
    neural stem cells. The nBAF complex along with CREST plays a role regulating the activity of genes essential for
    dendrite growth (By similarity). Plays a key role in cell-cycle control and causes cell cycle arrest in G0/G1.
    Also involved in vitamin D-coupled transcription regulation via its association with the WINAC complex, a
    chromatin-remodeling complex recruited by vitamin D receptor (VDR), which is required for the ligand-bound
    VDR-mediated transrepression of the CYP27B1 gene

         Genatlas biochemistry entry for SMARCB1:
    general transcriptional activator,S cerevisiae SWI/SNF2 related protein,matrix associated,actin-dependent
    regulator of chromatin,subfamily B,member 1,component of the chromatin remodeling complex,preferentially
    expressed in muscle and pancreas,mutated in atypical teratoid and rhabdoid tumors,tumor suppressor gene (see
    TSG22D),frequently deleted in chronic myeloid leukemia

         Gene Ontology (GO): 4 molecular function terms:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0002039p53 binding IPI11950834
    GO:0003713transcription coactivator activity NAS8804307
    GO:0005515protein binding IPI10078207
    GO:0030957Tat protein binding IPI16687403
         
    SMARCB1 for ontologies           About GeneDecksing


    Phenotypes:
         2 GenomeRNAi human phenotypes for SMARCB1:
     Enable proliferation in B-Raf   Wnt reporter downregulated 

         14 MGI mutant phenotypes (inferred from 7 alleles) (MGI details for Smarcb1):
     cardiovascular system  cellular  digestive/alimentary  embryogenesis  growth/size/body 
     hematopoietic system  homeostasis/metabolism  immune system  liver/biliary system  mortality/aging 
     nervous system  reproductive system  tumorigenesis  vision/eye 

    SMARCB1 for phenotypes           About GeneDecksing

    Animal Models:
         MGI mouse knock-outs for SMARCB1: Smarcb1tm1Gvk Smarcb1tm1Sho

       inGenious Targeting Laboratory: Let us create your new Knockout/Knockin mouse model for SMARCB1
       inGenious Targeting Laboratory: Contact us about creating complex and humanized mouse models for SMARCB1

       genOway customized KO model: permanent, tissue-specific or time-controlled inactivation for SMARCB1
       genOway customized Knockin model: humanization, point mutation, expression monitoring, etc. for SMARCB1

    miRNA
    Products:            		miRTarBase miRNAs that target SMARCB1:
    hsa-let-7b-5p (MIRT051937), hsa-mir-192-5p (MIRT004861), hsa-mir-215-5p (MIRT024448), hsa-mir-1 (MIRT023864)

    Block miRNA regulation of human, mouse, rat SMARCB1 using miScript Target Protectors
    Selected qRT-PCR Assays for microRNAs that regulate SMARCB1 (see all 9):
    hsa-miR-4283 hsa-miR-3673 hsa-miR-206 hsa-miR-300 hsa-miR-381 hsa-miR-1 hsa-miR-1284 hsa-miR-661
    SwitchGear 3'UTR luciferase reporter plasmid: SMARCB1 3' UTR sequence
    Inhib. RNA
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    Predesigned siRNA for gene silencing in human, mouse, rat SMARCB1

    Gene Editing
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    Clone
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    OriGene ORF clones in mouse, rat for SMARCB1
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    GenScript: all cDNA clones in your preferred vector (see all 2): SMARCB1 (NM_003073)
    Browse Sino Biological Human cDNA Clones
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    Vector BioLabs ready-to-use adenovirus/AAV for human, mouse, rat SMARCB1

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    In Situ Assay
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         		Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for SMARCB1


    Localization
    for SMARCB1 gene

    (According to UniProtKB, COMPARTMENTS Subcellular localization database, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
    About This Section

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    Subcellular locations from UniProtKB/Swiss-Prot
    SNF5_HUMAN, Q12824: Nucleus
    Subcellular locations from COMPARTMENTS: 

    CompartmentConfidence
    nucleus5
    cytosol2
    cytoskeleton1

    Gene Ontology (GO): Selected cellular component terms (see all 8):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0000228nuclear chromosome IEA--
    GO:0001741XY body IEA--
    GO:0005634nucleus IDA--
    GO:0005654nucleoplasm TAS7801128
    GO:0005730NOT nucleolus IDA--

    SMARCB1 for ontologies           About GeneDecksing


    Pathways & Interactions
    for SMARCB1 gene

    (SuperPaths according to PathCards, Pathways according to R&D Systems, Cell Signaling Technology, KEGG, PharmGKB, BioSystems, Sino Biological, Reactome, Tocris Bioscience, GeneGo (Thomson Reuters), QIAGEN, and/or UniProtKB, Sets of similar genes according to GeneDecks, Interaction Networks according to QIAGEN, and/or STRING, Interactions according to 1UniProtKB, 2MINT, 3I2D, and/or 4STRING, with links to IntAct and Ensembl, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene).
    About This Section

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    SuperPaths for SMARCB1 About   (see all 7)  
    See pathways by source

    SuperPathContained pathways About
    1Transcription Ligand dependent activation of the ESR1 SP pathway
    		Transcription Ligand dependent activation of the ESR1 SP pathway0.37
    		Development Ligand dependent activation of the ESR1 AP 1 pathway0.37
    2AMPK Enzyme Complex Pathway
    		Chromatin Remodeling0.00
    		AMPK Enzyme Complex Pathway
    3PEDF Induced Signaling
    		Glucocorticoid Receptor Signaling0.43
    4TNF-alpha/NF-kB Signaling Pathway
    		TNF-alpha/NF-kB Signaling Pathway
    5Regulation of retinoblastoma protein
    		Regulation of retinoblastoma protein

    Pathways by source                                                                                                                                                                 See SuperPaths
    Show all pathways

    4 Downloadable PowerPoint Slides of GeneGlobe Pathway Central Maps for SMARCB1
        AMPK Enzyme Complex Pathway
    BRCA1 Pathway
    Glucocorticoid Receptor Signaling
    Chromatin Remodeling

    1 Cell Signaling Technology (CST) Pathway for SMARCB1
        Chromatin Regulation / Acetylation

    2 GeneGo (Thomson Reuters) Pathways for SMARCB1
        Transcription Ligand-dependent activation of the ESR1/SP pathway
    Development Ligand-dependent activation of the ESR1/AP-1 pathway

    2 BioSystems Pathways for SMARCB1
        TNF-alpha/NF-kB Signaling Pathway
    Regulation of retinoblastoma protein



    SMARCB1 for pathways           About GeneDecksing

        Pathway & Disease-focused RT2 Profiler PCR Arrays including SMARCB1: 
              HIV Host Response in human mouse rat
              Polycomb & Trithorax Complexes in human mouse rat
              Epigenetic Chromatin Remodeling Factors in human mouse rat

    Interactions:

        GeneGlobe Interaction Network for SMARCB1

    STRING Interaction Network Preview (showing 5 interactants - click image to see 25)

    Selected Interacting proteins for SMARCB1 (Q128241, 2, 3 ENSP000002631214) via UniProtKB, MINT, STRING, and/or I2D (see all 1046)
    InteractantInteraction Details
    GeneCardExternal ID(s)
    E1P067891, 2EBI-7015645,EBI-7015660 MINT-68791 MINT-68801 MINT-68789 MINT-68799 MINT-68792 MINT-68798 MINT-68797 MINT-68793 MINT-68796 MINT-69678 MINT-68800
    SMARCA4P515321, 2, 3, ENSP000003507204EBI-358419,EBI-302489 MINT-6614004 I2D: score=7 STRING: ENSP00000350720
    SMARCD1Q96GM52, 3, ENSP000003784144MINT-7945693 MINT-7947479 I2D: score=7 STRING: ENSP00000378414
    HDAC2Q927692, 3, ENSP000003813314MINT-7945693 MINT-7947479 I2D: score=2 STRING: ENSP00000381331
    NCOR1O753762, 3, ENSP000002687124MINT-7945693 MINT-7947479 I2D: score=2 STRING: ENSP00000268712
    About this table

    Gene Ontology (GO): Selected biological process terms (see all 18):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0001824blastocyst development ----
    GO:0001835blastocyst hatching IEA--
    GO:0006281DNA repair IBA--
    GO:0006337nucleosome disassembly IDA8895581
    GO:0006338chromatin remodeling IDA11726552

    SMARCB1 for ontologies           About GeneDecksing



    Drugs & Compounds
    for SMARCB1 gene

    (Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience, ApexBio, HMDB, BitterDB, and/or Novoseek, Ligands according to IUPHAR, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB)
    About This Section

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    Browse Small Molecules at EMD Millipore
       Browse drugs & compounds from Enzo Life Sciences
      Browse compounds at ApexBio 

    Browse Tocris compounds for SMARCB1 (SNF5)



    Transcripts
    for SMARCB1 gene

    (Secondary structures according to fRNAdb,
    GenBank/EMBL/DDBJ Accessions according to
    Unigene (Build 236 Homo sapiens; Apr 25 2013) or GenBank,
    RefSeq according to Entrez Gene,
    DOTS (version 10), and/or AceView, transcript ids from Ensembl with links to UCSC,
    Conferences by KenesGroup, exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
    siRNAs from OriGene, QIAGEN, shRNA from OriGene, microRNA from QIAGEN, SwitchGear Genomics,
    Tagged/untagged cDNA clones from OriGene, GenScript, DNA2.0, Vector BioLabs, Primers from OriGene, and/or QIAGEN )
    About This Section

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    REFSEQ mRNAs for SMARCB1 gene (2 alternative transcripts): 
    NM_001007468.1  NM_003073.3  

    Unigene Cluster for SMARCB1:

    SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily b, member 1
    Hs.534350  [show with all ESTs]
    Unigene Representative Sequence: NM_003073
    7 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000417137(uc002zyg.2 uc011ajb.1 uc002zye.1 uc002zyf.1 uc010gue.1)
    ENST00000344921(uc002zyc.3 uc002zyd.3) ENST00000263121(uc002zya.3 uc002zyb.3)
    ENST00000407422 ENST00000407082 ENST00000491967 ENST00000477836
    Congresses - knowledge worth sharing:
    European Congress of Clinical Microbiology and Infectious Diseases (ECCMID) 10 - 13 May 2014

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    Selected qRT-PCR Assays for microRNAs that regulate SMARCB1 (see all 9):
    hsa-miR-4283 hsa-miR-3673 hsa-miR-206 hsa-miR-300 hsa-miR-381 hsa-miR-1 hsa-miR-1284 hsa-miR-661
    SwitchGear 3'UTR luciferase reporter plasmid: SMARCB1 3' UTR sequence
    Inhib. RNA
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    OriGene qSTAR qPCR primer pairs in human, mouse for SMARCB1
    Pre-validated RT2 qPCR Primer Assay in human, mouse, rat SMARCB1
      QuantiTect SYBR Green Assays in human, mouse, rat SMARCB1
      QuantiFast Probe-based Assays in human, mouse, rat SMARCB1

    Additional mRNA sequence: 

    AB017523.1 AJ011737.1 AJ011738.1 AK021419.1 AK024025.1 AK299411.1 AK303620.1 AL389878.1 
    AL389881.1 AY207470.1 AY207471.1 AY562997.1 BC117114.1 BC143667.1 CR456581.1 

    Selected DOTS entries (see all 25):

    DT.448910  DT.100802211  DT.100883928  DT.92454292  DT.95260683  DT.100883952  DT.100883943  DT.100802041 
    DT.100883949  DT.100883931  DT.100883944  DT.100667649  DT.100883927  DT.100883941  DT.100034945  DT.100044384 
    DT.100665611  DT.100883937  DT.115675  DT.120671557  DT.120671560  DT.91740860  DT.100801439  DT.92346772 

    Selected AceView cDNA sequences (see all 454):

    BM467954 BQ186720 BE393530 AJ011738 AW001930 BU856651 R53013 BE281546 
    BQ063517 CR624865 BM931937 AY207472 AW769907 AI610780 BM791890 BI114406 
    BE407182 CB159362 BE612477 AW406626 AI687258 AK024025 CR600940 CR620956 

    GeneLoc Exon Structure

    Selected Alternative Splicing Database (ASD) splice patterns (SP) for SMARCB1 (see all 7)    About this scheme

    ExUns: 1a · 1b ^ 2a · 2b ^ 3a · 3b ^ 4a · 4b · 4c ^ 5 ^ 6a · 6b ^ 7a · 7b ^ 8 ^ 9
    SP1:                    -                       -     -           -                                 
    SP2:                    -                             -           -                                 
    SP3:                                            -     -           -                                 
    SP4:                                                  -                                             
    SP5:                    -                                                                           


    ECgene alternative splicing isoforms for SMARCB1

    Expression
    for SMARCB1 gene

    (RNA expression data according to H-InvDB, NONCODE, miRBase, and RNAdb, Expression images according to data from BioGPS, Illumina Human BodyMap, and CGAP SAGE, Sets of similar genes according to GeneDecks, in vivo and in vitro expression data from LifeMap Discovery™, Protein expression images according to data from SPIRE 1MOPED, 2PaxDb, and 3MaxQB, plus additional links to SOURCE, and/or BioGPS, and/or UniProtKB,
    PCR Arrays from QIAGEN, Primers from OriGene, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
    About This Section

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    SMARCB1 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: --
    SMARCB1 Expression
    About this image


    SMARCB1 expression in embryonic tissues and stem cells    About this table
    Data from LifeMap, the Embryonic Development and Stem Cells Database
     selected tissues (see all 8) fully expand
     
     Brain (Nervous System)    fully expand to see all 4 entries
             Cerebral Cortex
     
     Ovary (Reproductive System)    fully expand to see all 2 entries
             Ovarian Mesenchymal Stroma Cells Ovary Interstitium
             Oviduct
     
     Testis (Reproductive System)
             Leydig Cells Testis Interstitium
     
     Trophoblast (Extraembryonic Tissues)
             Trophoblast Cells Trophoblast
     
     Pancreas (Endocrine System)
             Islets of Langerhans
    SMARCB1 Protein expression data from MOPED1, PaxDb2 and MaxQB3:     About this image

    SMARCB1 Protein Expression

    SOURCE GeneReport for Unigene cluster: Hs.534350
        Pathway & Disease-focused RT2 Profiler PCR Arrays including SMARCB1: 
              HIV Host Response in human mouse rat
              Polycomb & Trithorax Complexes in human mouse rat
              Epigenetic Chromatin Remodeling Factors in human mouse rat

    Primer
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    OriGene qSTAR qPCR primer pairs in human, mouse for SMARCB1
    Pre-validated RT2 qPCR Primer Assay in human, mouse, rat SMARCB1
    QuantiTect SYBR Green Assays in human, mouse, rat SMARCB1
    QuantiFast Probe-based Assays in human, mouse, rat SMARCB1
    In Situ
    Assay Products:     
         		Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for SMARCB1

    Orthologs
    for SMARCB1 gene

    (Orthologs according to 1,2HomoloGene (2older version, for species not in 1newer version), 3euGenes, 4SGD , 5MGI Mar 06 2013, with possible further links to Flybase and/or WormBase, and/or 6Ensembl pan taxonomic compara , Gene Trees according to Ensembl and TreeFam)
    About This Section

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    This gene was present in the common ancestor of animals and fungi.

    Orthologs for SMARCB1 gene from Selected species (see all 19)    About this table
    Organism Taxonomic
    classification    		 Gene Description Human
    Similarity    		 Orthology
    Type    		 Details
    mouse
    (Mus musculus)    		 Mammalia Smarcb11 , 5 SWI/SNF related, matrix associated, actin dependent more1, 5 91.26(n)1
    100(a)1    		   10 (38.61 cM)5
    205871  NM_011418.21  NP_035548.11 
     758967695 
    chicken
    (Gallus gallus)    		 Aves MMP111 matrix metallopeptidase 11 (stromelysin 3) 84.68(n)
    96.88(a)    		   769489  NM_001039255.1  NP_001034344.1 
    lizard
    (Anolis carolinensis)    		 Reptilia SMARCB16
    		 SWI/SNF related, matrix associated, actin dependen...
    		 92(a)
    		 1 ↔ 1
    		 AAWZ02039747(53-7541)
    African clawed frog
    (Xenopus laevis)    		 Amphibia Xl.75912 Xenopus laevis transcribed sequence with strong similarity more 77.55(n)    BU916038.1 
    zebrafish
    (Danio rerio)    		 Actinopterygii Dr.161412 Transcribed sequence with strong similarity to protein more 79.59(n)    CK126535.1 
    fruit fly
    (Drosophila melanogaster)    		 Insecta Snr11 , 3 embryonic development (sensu Insecta)
    RNA polymerase more3
    Snf5-related 11    		 65(a)3
    66.21(n)1
    68.29(a)1    		   3 83A43
    406571  NM_169055.21  NP_730935.11 
    worm
    (Caenorhabditis elegans)    		 Secernentea R07E5.33
    snfc-51    		 Snf5 (yeast)3
    snfc-51    		 49(a)3
    54.75(n)1
    54.75(a)1    		   III(4476586-4477873)3
    1755711  NM_065489.41  NP_497890.11 
    baker's yeast
    (Saccharomyces cerevisiae)    		 Saccharomycetes SFH1(YLR321C)4 Component of the RSC chromatin remodeling complex; more   --   12(777864-776584) 851032  NP_013425.1 


    ENSEMBL Gene Tree for SMARCB1 (if available)
    TreeFam Gene Tree for SMARCB1 (if available)

    Paralogs
    for SMARCB1 gene

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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    Genomic Variants
    for SMARCB1 gene

    (SNPs/Variants according to the 1NCBI SNP Database, 2Ensembl, 3PupaSUITE, 4UniProtKB, and DNA2.0, Linkage Disequilibrium by HapMap, Structural Variations(CNVs/InDels/Inversions) from the Database of Genomic Variants, Mutations from the Human Gene Mutation Database (HGMD), the Human Cytochrome P450 Allele Nomenclature Database, and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers, Cancer Mutation PCR Arrays and Assays, and Copy Number PCR Arrays from QIAGEN)
    About This Section

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    Selected SNPs for SMARCB1 (see all 1351)    About this table    
    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance    		Chr 22 posSequence#AA
    Chg    		TypeMore#Allele
    freq    		PopTotal
    sample    		More
    ----------
    VAR_0681794
    		Mental retardation, autosomal dominant 15 (MRD15)4--see VAR_0681792 R H mis40--------
    rs743155131,2
    		Cpathogenic18086735(+) TCGGGC/TAGAAG 4 Q * stg10--------
    rs59966121,2
    		C,F--8084671(+) ctactC/Gggaag 2 -- us2k11Minor allele frequency- G:0.00NA 2
    rs57600121,2
    		C,A,H--8084728(+) gagccA/Cagatc 2 -- us2k14Minor allele frequency- C:0.00NA CSA 7
    rs1391609841,2
    		C--8084794(+) ATAAG-/TAAA  
                TAAAT     		2 -- us2k10--------
    rs1438647931,2
    		C--8084794(+) TAAAT-/TAAA  
                AAATA     		2 -- us2k10--------
    rs7387931,2
    		C,A,H--8084839(+) acctcC/Tgtact 2 -- us2k18Minor allele frequency- T:0.32NA WA EA 368
    rs283825811,2
    		C,F--8084935(+) AGTATA/GAGGAA 2 -- us2k17Minor allele frequency- G:0.15NS CSA WA 290
    rs1912231611,2
    		C--8085108(+) ACCACG/TGTGAG 2 -- us2k10--------
    rs1440208901,2
    		--8085177(+) CCTACC/TTTCCA 2 -- us2k10--------

    HapMap Linkage Disequilibrium report for SMARCB1 (24129150 - 24176705 bp)

    Structural Variations
         Database of Genomic Variants (DGV) Selected variations for SMARCB1 (see all 11):    About this table    
    Variant IDTypeSubtypePubMed ID
    esv2724041CNV Deletion23290073
    dgv4907n71CNV Loss21882294
    nsv914597CNV Loss21882294
    nsv914598CNV Loss21882294
    dgv4908n71CNV Loss21882294
    nsv526567CNV Gain19592680
    dgv4906n71CNV Gain21882294
    nsv829103CNV Gain20364138
    nsv914599CNV Gain21882294
    nsv511075CNV Complex20534489

    Human Gene Mutation Database (HGMD): SMARCB1
    Selected Site Specific Mutation Identification with PCR Assays for SMARCB1 (see all 7):
    Cosmic IdAA Change
    991p.Y47*
    24595p.R53*
    1002p.R40*
    992p.R158*
    29382p.A382fs*5
    3 Site Specific Cancer Mutation PCR Panels containing SMARCB1:
    Cancer Comprehensive Panel 384HT
    Soft Tissue Tumors
    Tumor Suppressor Panel 384HT
    SeqTarget long-range PCR primers for resequencing SMARCB1
    DNA2.0 Custom Variant and Variant Library Synthesis for SMARCB1

    Disorders / Diseases
    for SMARCB1 gene

    (in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Conferences by KenesGroup, Novoseek, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
    About This Section

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    OMIM gene information: 601607   
    OMIM disorders: 609322  614608  162091  
    UniProtKB/Swiss-Prot: SNF5_HUMAN, Q12824
  • Rhabdoid tumor predisposition syndrome 1 (RTPS1) [MIM:609322]: A familial cancer syndrome predisposing to
    renal or extrarenal malignant rhabdoid tumors and to a variety of tumors of the central nervous system, including
    choroid plexus carcinoma, medulloblastoma, and central primitive neuroectodermal tumors. Rhabdoid tumors are the
    most aggressive and lethal malignancies occurring in early childhood. Note=The disease is caused by mutations
    affecting the gene represented in this entry
  • Schwannomatosis (SCHWA) [MIM:162091]: Schwannomas are benign tumors of the peripheral nerve sheath that
    usually occur singly in otherwise normal individuals. Multiple schwannomas in the same individual suggest an
    underlying tumor-predisposition syndrome. The most common such syndrome is NF2. The hallmark of NF2 is the
    development of bilateral vestibular-nerve schwannomas; but two-thirds or more of all NF2-affected individuals
    develop schwannomas in other locations, and dermal schwannomas may precede vestibular tumors in NF2-affected
    children. There have been several reports of individuals with multiple schwannomas who do not show evidence of
    vestibular schwannoma. Clinical report suggests that schwannomatosis is a clinical entity distinct from other
    forms of neurofibromatosis. Note=The disease is caused by mutations affecting the gene represented in this entry
  • Mental retardation, autosomal dominant 15 (MRD15) [MIM:614608]: A disease characterized by multiple
    congenital anomalies and mental retardation. Mental retardation is defined by significantly below average general
    intellectual functioning associated with impairments in adaptive behavior and manifested during the developmental
    period. MRD15 patients manifest developmental delay, hypotonia, absent or hypoplastic fifth finger or toenails, a
    coarse facial appearance, sparse scalp hair, thick eyebrows, and long eyelashes. Additional variable features
    include microcephaly, small cerebellum, seizures, hearing loss, abnormal delayed dentition, hirsutism. Note=The
    disease is caused by mutations affecting the gene represented in this entry

    • Selected diseases for SMARCB1 (see all 82):    
    About MalaCards
    choroid plexus carcinoma    chromosome 22q deletion    rhabdoid predisposition syndrome 1    rhabdoid cancer
    monosomy 22    atypical teratoid rhabdoid tumor    mental retardation, autosomal dominant 15    rhabdoid meningioma
    smarcb1-related coffin-siris syndrome    rhabdoid tumor predisposition syndrome 1    rhabdoid tumors, somatic    rhabdoid tumor
    epithelioid sarcoma    neurilemmomatosis    tumor predisposition syndrome    pleomorphic xanthoastrocytoma
    meningioma    epithelioid malignant peripheral nerve sheath tumor    retroperitoneal leiomyosarcoma    coffin-siris syndrome

    9 diseases from the University of Copenhagen DISEASES database for SMARCB1:
    Rhabdoid cancer     Atypical teratoid rhabdoid tumor     Neurilemmoma     Epithelioid sarcoma
    Choroid plexus carcinoma     Collecting duct carcinoma     Medulloblastoma     Retroperitoneal leiomyosarcoma
    Congenital mesoblastic nephroma

    SMARCB1 for disorders           About GeneDecksing

    Selected Novoseek inferred disease relationships for SMARCB1 gene (see all 27)    About this table

    Disease   -log (P-Val)   Hits   PubMed IDs for Articles with Shared Sentences (# sentences)
    rhabdoid tumor 97 86 15761491 (5), 9892189 (4), 17376508 (4), 16099835 (3) (see all 38)
    sarcoma epithelioid 80.2 17 19318800 (7), 19033866 (2), 19342946 (2), 18327209 (1) (see all 6)
    embryonal tumor 69.1 3 19915490 (1), 15965700 (1), 17063089 (1)
    cns tumors 66.9 5 19915490 (1), 18327209 (1), 17063089 (1), 12429635 (1)
    pediatric brain tumor 59.4 5 17063089 (2), 15105654 (1)
    tumors 55.2 112 17063089 (6), 15892296 (5), 16206192 (4), 16301525 (4) (see all 53)
    medulloblastoma 52.2 3 10914721 (2), 11550309 (1)
    schwannoma 49.7 3 10208879 (2), 18072270 (1)
    monosomy 46.2 4 15892296 (1), 17603804 (1), 20118769 (1), 17377740 (1)
    brain tumors 44.8 5 11484819 (3), 10739763 (2)

    Genetic Association Database (GAD): SMARCB1
    Human Genome Epidemiology (HuGE) Navigator: SMARCB1 (10 documents)

    Export disorders for SMARCB1 gene to outside databases

    Publications
    for SMARCB1 gene

    (in PubMed. Associations of this gene to articles via 1Entrez Gene, 2UniProtKB/Swiss-Prot, 3HGNC, 4GAD, 5PharmGKB, 6HMDB, 7DrugBank, 8UniProtKB/TrEMBL, 9 Novoseek, and/or 10fRNAdb)
    About This Section

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    PubMed articles for SMARCB1 gene, integrated from 10 sources (see all 326):
    (articles sorted by number of sources associating them with SMARCB1)    		    Utopia: connect your pdf to the dynamic
    world of online information

    1. Interaction of E1 and hSNF5 proteins stimulates replication of human papillomavirus DNA. (PubMed id 10365963)1, 2, 3, 9 Lee D.... Choe J. (Nature 1999)
    2. Binding and stimulation of HIV-1 integrase by a human homolog of yeast transcription factor SNF5. (PubMed id 7801128)1, 2, 3, 9 Kalpana G.V.... Goff S.P. (Science 1994)
    3. c-MYC interacts with INI1/hSNF5 and requires the SWI/SNF complex for transactivation function. (PubMed id 10319872)1, 2, 3 Cheng S.-W.... Kalpana G.V. (Nat. Genet. 1999)
    4. Evidence of a four-hit mechanism involving SMARCB1 and NF2 in schwannomatosis-associated schwannomas. (PubMed id 18072270)1, 2, 9 Sestini R.... Papi L. (Hum. Mutat. 2008)
    5. P16INK4a is required for hSNF5 chromatin remodeler-induced cellular senescence in malignant rhabdoid tumor cells. (PubMed id 14604992)1, 2, 9 Oruetxebarria I....Verrijzer C.P. (J. Biol. Chem. 2004)
    6. Germ-line and acquired mutations of INI1 in atypical teratoid and rhabdoid tumors. (PubMed id 9892189)1, 2, 9 Biegel J.A....Fogelgren B. (Cancer Res. 1999)
    7. The mouse ortholog of the human SMARCB1 gene encodes two splice forms. (PubMed id 10208879)1, 2, 9 Bruder C.E.... Kedra D. (Biochem. Biophys. Res. Commun. 1999)
    8. Clinical and molecular features in patients with atypical teratoid rhabdoid tumor or malignant rhabdoid tumor. (PubMed id 19902524)1, 4, 9 Kordes U....Schneppenheim R. (amp 2010)
    9. Spectrum of SMARCB1/INI1 mutations in familial and sporadic rhabdoid tumors. (PubMed id 21108436)1, 4 Eaton K.W....Biegel J.A. (amp 2011)
    10. SMARCB1 mutations are not a common cause of multiple meningiomas. (PubMed id 20472658)1, 4 Hadfield K.D....Evans D.G. (J. Med. Genet. 2010)

    External Searches for SMARCB1 gene

    (in PubMed, OMIM, and NCBI Bookshelf)
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     ANDOR
    Aliases
    Disorders
    Free Text  
      Query String
    		PubMed
    OMIM
    NCBI Bookshelf
      (Note: In FireFox, select the above section and copy using Ctrl-C)

    Genome Databases showing SMARCB1 gene

    (According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
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    Entrez Gene: 6598 HGNC: 11103 AceView: SMARCB1 Ensembl:ENSG00000099956 euGenes: HUgn6598
    ECgene: SMARCB1 H-InvDB: SMARCB1

    Other Databases showing SMARCB1 gene

    (According to HUGE)
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    Specialized Databases showing SMARCB1 gene

    (According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL, and/or others, e.g. Wikipedia and GeneReviews, via UniProtKB/Swiss-Prot)
    About This Section

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    NameDescription
    PharmGKB entry for SMARCB1 Pharmacogenomics, SNPs, Pathways
    ATLAS Chromosomes in Cancer entry for SMARCB1 Genetics and Cytogenetics in Oncology and Haematology
    GeneReviewshttp://www.ncbi.nlm.nih.gov/books/NBK1116/?term=SMARCB1[genesymbol]
    NIEHS-SNPshttp://egp.gs.washington.edu/data/smarcb1/

    Intellectual Property
    for SMARCB1 gene

    (Patent information from GeneIP,
    Licensable technologies from WIS Yeda, Salk, Tufts,
    IP news from LifeMap Sciences, Inc.)
    About This Section

    TryGeneCards Plus    		Patent Information for SMARCB1 gene:
    Search GeneIP for patents involving SMARCB1

    GeneCards and IP:
    Japan Patent Office Licenses GeneCards     European Patent Office Licenses GeneCards     Improving the IP Search



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