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Category   Symbol Source: HGNC EntrezGene Ensembl GeneCards RNA genes CroW21
GIFtS

SMARCB1 Gene

protein-coding   GIFtS: 66
GCID: GC22P024129

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


(Previous symbol: SNF5L1)
Microbiology & Infectious Diseases Congress
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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)
About This Section
Aliases
SWI/SNF Related, Matrix Associated, Actin Dependent Regulator Of
Chromatin, Subfamily B, Member 11 2
     SNF52 5
SNF5L11 2 3     Homolog-Like 11
INI12 3 5     Integrase Interactor 11
Malignant Rhabdoid Tumor Suppressor1 2     Sucrose Nonfermenting1
Integrase Interactor 1 Protein2 3     yeast1
BAF472 3     MRD152
BRG1-Associated Factor 472 3     Sfh1p2
hSNF52 3     Snr12
SNF5 Homolog2 3     hSNFS2
RDT2 5     Sucrose Nonfermenting, Yeast, Homolog-Like 12
RTPS12 5     SWI/SNF-Related Matrix-Associated Actin-Dependent Regulator Of Chromatin
Subfamily B Member 12

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, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
About This Section
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 rhabdoid tumor, and atypical teratoid rhabdoid tumor, and among its related super-pathways are Development Ligand-dependent activation of the ESR1/AP-1 pathway and PGC1Alpha Pathway. 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 73), Regulatory elements and Epigenetics data according to QIAGEN, SABiosciences, and/or SwitchGear Genomics)
About This Section
RefSeq DNA sequence:
NC_000022.10  NT_011520.12  NC_018933.2  
Regulatory elements:
   SABiosciences 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 SABiosciences Chromatin IP Primers for SMARCB1

Epigenetics:
QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays 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 UniProtKB, HORDE, neXtProt, Ensembl, and/or Reactome, Modification sites according to PhosphoSitePlus, Specific Peptides from DME, Protein expression images according to data from SPIRE 1MOPED, 2PaxDb, and 3MAXQB 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., Ontologies according to Gene Ontology Consortium 01 Oct 2013 and Entrez Gene, Antibodies by EMD Millipore, R&D Systems, GenScript, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, LSBio, Abcam, and/or Cloud-Clone Corp.)
About This Section
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)
Subcellular location: Nucleus
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:

  • View modification sites using PhosphoSitePlus
  • View neXtProt modification sites for NX_Q12824

    • SMARCB1 Protein expression data from MOPED1, PaxDb2 and MAXQB3 :    About this image 

    SMARCB1 Protein Expression
    REFSEQ proteins (2 alternative transcripts): 
    NP_001007469.1  NP_003064.2  

    ENSEMBL proteins: 
     ENSP00000388489   ENSP00000340883   ENSP00000263121   ENSP00000383984   ENSP00000385226  

    Human Recombinant Protein Products for SMARCB1: 
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    Novus Biologicals SMARCB1 Proteins
    Novus Biologicals SMARCB1 Lysates
    Browse Sino Biological Recombinant Proteins
    Browse Sino Biological Cell Lysates 
    Browse ProSpec Recombinant Proteins
    Cloud-Clone Corp. Proteins for SMARCB1 

    Gene Ontology (GO): 5/8 cellular component terms (GO ID links to tree view) (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



    SMARCB1 Antibody Products: 
    EMD Millipore Mono- and Polyclonal Antibodies for the study of SMARCB1
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    LSBio Antibodies in human, mouse, rat for SMARCB1 

    Assay Products for SMARCB1: 
    Browse Kits and Assays available from EMD Millipore
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    GenScript Custom Assay Services for SMARCB1
    Browse Enzo Life Sciences for kits & assays
    Cloud-Clone Corp. ELISAs for SMARCB1 
    Cloud-Clone Corp. CLIAs for SMARCB1

    Protein 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
    		 2 InterPro protein domains:
     IPR017393 SWI_SNF_chromatin_remodel_cplx
     IPR006939 SNF5

    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,
    bound targets from SABiosciences, miRNA Gene Targets from miRTarBase, shRNA from OriGene, RNAi from EMD Millipore, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, Gene Editing from DNA2.0, Sirion Biotech, Clones from EMD Millipore, OriGene, SwitchGear Genomics, GenScript, Sino Biological, DNA2.0, Vector BioLabs, and Sirion Biotech, Cell Lines from GenScript, LifeMap BioReagents, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Oct 2013 via Entrez Gene.)
    About This Section
    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 (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0002039p53 binding IPI11950834
    GO:0003713transcription coactivator activity NAS8804307
    GO:0005515protein binding IPI10365963
    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 
     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 - Custom generated mouse model solutions for SMARCB1 
       inGenious Targeting Laboratory - Custom generated inducible mouse model solutions 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-mir-192 (MIRT004861)

    QIAGEN Custom miScript Target Protector blocks miRNA-binding site of human, mouse, rat SMARCB1
    8/9 QIAGEN miScript miRNA 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 RNAi products in human, mouse, rat for SMARCB1
    QIAGEN FlexiTube/FlexiPlate siRNA for gene silencing in human, mouse, rat SMARCB1

    Gene Editing
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    Sirion Biotech Customized adenovirus for overexpression of SMARCB1

    Clone
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                         Customized lentivirus expression plasmids for stable overexpression of SMARCB1 

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


    Pathways & Interactions
    for SMARCB1 gene

    (Pathways according to EMD Millipore, 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 SABiosciences, 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 Oct 2013 via Entrez Gene).
    About This Section

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

    SuperPathContained pathways About
    1Development Ligand-dependent activation of the ESR1/AP-1 pathway
    		Development Ligand-dependent activation of the ESR1/AP-1 pathway0.37
    		Chromatin Remodeling0.30
    		Transcription Ligand-dependent activation of the ESR1/SP pathway0.37
    2PEDF Induced Signaling
    		Glucocorticoid Receptor Signaling0.43
    3TNF-alpha/NF-kB Signaling Pathway
    		TNF-alpha/NF-kB Signaling Pathway
    4Regulation of retinoblastoma protein
    		Regulation of retinoblastoma protein
    5BRCA1 Pathway
    		BRCA1 Pathway

    Pathways by source                                                                                                                                                                 See SuperPaths
    Show all pathways

    2 EMD Millipore Pathways for SMARCB1
        Development Ligand-dependent activation of the ESR1/AP-1 pathway
    Transcription Ligand-dependent activation of the ESR1/SP pathway

    4 Downloadable PowerPoint Slides of QIAGEN 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

    Interactions:

        SABiosciences Gene Network CentralTM Interacting Genes and Proteins Network for SMARCB1

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

    5/914 Interacting proteins for SMARCB1 (Q128241, 2, 3 ENSP000002631214) via UniProtKB, MINT, STRING, and/or I2D (see all 914)
    InteractantInteraction Details
    GeneCardExternal ID(s)
    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
    SMARCA2P515312, 3, ENSP000002657734MINT-7945693 MINT-7894924 I2D: score=2 STRING: ENSP00000265773
    ARID1AO144972, 3, ENSP000003204854MINT-7945693 MINT-7947479 I2D: score=1 STRING: ENSP00000320485
    About this table

    Gene Ontology (GO): 5/18 biological process terms (GO ID links to tree view) (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 HMDB, BitterDB, and/or Novoseek, Ligands according to IUPHAR, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB, with drugs/clinical trials/news search links to CenterWatch)
    About This Section
    Browse Small Molecules at EMD Millipore
    Browse drugs & compounds from Enzo Life Sciences

    Browse Tocris compounds for SMARCB1 (SNF5)

    Search CenterWatch for drugs/clinical trials and news about 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,
    RNAi Products from EMD Millipore,
    siRNAs from OriGene, QIAGEN, shRNA from OriGene, microRNA from QIAGEN,
    Tagged/untagged cDNA clones from OriGene, SwitchGear Genomics, GenScript, DNA2.0, Vector BioLabs, Sirion Biotech, Primers from OriGene, SABiosciences, and/or QIAGEN )
    About This Section
    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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    8/9 QIAGEN miScript miRNA 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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    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 

    24/25 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 

    24/454 AceView cDNA sequences (see all 454):

    AI537937 BM841815 AJ011738 BE407182 AI610780 BQ015000 CR617530 AI075165 
    BM931937 CR621760 CR620956 AI680381 AI820549 BE281546 BQ683919 AI361160 
    AY207470 BE612477 CD369902 BU194177 BQ018870 BQ069831 AI241194 CR601509 

    GeneLoc Exon Structure

    5/7 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™, plus additional links to Genevestigator, and/or SOURCE, and/or BioGPS, and/or UniProtKB,
    PCR Arrays from SABiosciences, Primers from OriGene, SABiosciences, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
    About This Section

    SMARCB1 expression in normal human tissues (normalized intensities)      SMARCB1 embryonic expression: see
    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 
     5/34 selected tissues (see all 34) fully expand
     
     Epithelium
             vagina ; squamous epithelial cells   
     
     Uterus
             uterus, post-menopause ; glandular cells   
     
     Testis (Reproductive System)    fully expand to see all 4 entries
             Leydig Cells Testis Interstitium
             seminal vesicle ; glandular cells   
     
     Colon (Gastrointestinal Tract)    fully expand to see all 4 entries
             colon ; peripheral nerve/ganglion   
     
     Brain (Nervous System)    fully expand to see all 4 entries
             Cerebral Cortex

    See SMARCB1 Protein Expression from SPIRE MOPED and PaxDB
    Genevestigator expression for SMARCB1

    SOURCE GeneReport for Unigene cluster: Hs.534350
        SABiosciences Expression via Pathway-Focused 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

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

    Orthologs for SMARCB1 gene from 8/19 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 SMARCB11 SWI/SNF related, matrix associated, actin dependent more 84.68(n)
    96.88(a)    		   378892  NM_001039255.1  NP_001034344.1 
    lizard
    (Anolis carolinensis)    		 Reptilia SMARCB16
    		 Uncharacterized protein
    		 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
    Protein SNFC-51    		 49(a)3
    54.87(n)1
    55.06(a)1    		   III(4476586-4477873)3
    1755711  NM_065489.31  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)
    About This Section
    		  --

    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) and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers from QIAGEN, Cancer Mutation PCR Arrays and Assays and Copy Number PCR Arrays from SABiosciences)
    About This Section

    10/1351 SNPs in SMARCB1 are shown (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) 10/11 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
    5/7 SABiosciences Cancer Mutation PCR Assays for SMARCB1 (see all 7):
    Cosmic IdAA Change
    991p.Y47*
    24595p.R53*
    1002p.R40*
    992p.R158*
    29382p.A382fs*5
    3 SABiosciences Cancer Mutation PCR Arrays containing SMARCB1:
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    Soft Tissue Tumors
    Tumor Suppressor Panel 384HT
    QIAGEN SeqTarget long-range PCR primers in human, mouse, rat 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
    		 OMIM gene information: 601607   
    OMIM disorders: 609322  
    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 adaptative 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

    • 20/73 diseases for SMARCB1 (see all 73):    About MalaCards
    rhabdoid tumor    atypical teratoid rhabdoid tumor    meningioma    epithelioid sarcoma
    choroid plexus carcinoma    chromosome 22q deletion    rhabdoid cancer    monosomy 22
    rhabdoid meningioma    rhabdoid predisposition syndrome 1    neurilemmomatosis    smarcb1-related coffin-siris syndrome
    rhabdoid tumor predisposition syndrome 1    tumor predisposition syndrome    pleomorphic xanthoastrocytoma    coffin-siris syndrome
    choroid plexus papilloma    epithelioid malignant peripheral nerve sheath tumor    mesoblastic nephroma    retroperitoneal leiomyosarcoma

    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

    10/27 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

    PubMed articles for SMARCB1 gene, integrated from 9 sources (see all 320):
    (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. (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. (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. (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. (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. (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. (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. (1999)
    8. Clinical and molecular features in patients with atyp ical teratoid rhabdoid tumor or malignant rhabdoid tumor. (PubMed id 19902524)1, 4, 9 Kordes U....Schneppenheim R. (2010)
    9. Spectrum of SMARCB1/INI1 mutations in familial and sp oradic rhabdoid tumors. (PubMed id 21108436)1, 4 Eaton K.W....Biegel J.A. (2011)
    10. SMARCB1 mutations are not a common cause of multiple meningiomas. (PubMed id 20472658)1, 4 Hadfield K.D....Evans D.G. (2010)

    External Searches for SMARCB1 gene

    (in PubMed, OMIM, and NCBI Bookshelf)
    About This Section
     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)
    About This Section
    Entrez Gene: 6598 HGNC: 11103 AceView: SMARCB1 Ensembl:ENSG00000099956 euGenes: HUgn6598
    ECgene: SMARCB1 H-InvDB: SMARCB1

    Other Databases showing SMARCB1 gene

    (According to HUGE)
    About This Section
    		   --

    Specialized Databases showing SMARCB1 gene

    (According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL,
    Wikipedia and/or GeneReviews via UniProtKB/Swiss-Prot)
    About This Section
    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/sites/GeneTests/lab/gene/SMARCB1
    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
    		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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    About This Section

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     Antibodies for SMARCB1
     ELISAs for SMARCB1
     CLIAs for SMARCB1
     Search LifeMap BioReagents cell lines for SMARCB1
     Gene Synthesis
     Protein Engineering
     Variant Library Synthesis
     Codon Optimization
     Protein Production and Purification
     Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for SMARCB1
     SwitchGear 3'UTR luciferase reporter plasmids for SMARCB1
     SwitchGear Promoter luciferase reporter plasmids for SMARCB1
     ThermoFisher Antibodies for SMARCB1
     Vector BioLabs ready-to-use adenovirus/AAV for human, mouse, rat SMARCB1
     inGenious Targeting Laboratory - Custom generated mouse model solutions for SMARCB1
     inGenious Targeting Laboratory - Custom generated inducible mouse model solutions for SMARCB1
    Customized:
     lentivirus for stable overexpression of SMARCB1
     lentivirus expression plasmids for stable overexpression of SMARCB1
     adenovirus for overexpression of SMARCB1
     LSBio Antibodies in human, mouse, rat for SMARCB1
    		Customized transgenic rodents for:
     Humanization
     Biomarker expression
     Off-target effect monitoring
     Translational medicine
     Tissue-specific gene expresssion
     Time-controlled gene expresssion
           
    GeneCards Homepage - Last full update: 23 Oct 2013 - Incrementals: 3 Nov 2013 , 7 Nov 2013 , 23 Jan 2014

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    (GIFtS: 73)
    transforming growth factor, beta 1
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