SMARCB1 Gene
protein-coding GIFtS: 64
GCID: GC22P024129
|
|
SWI/SNF related, matrix associated, actin dependent regulator...
(Previous symbol: SNF5L1)
| |
Aliases
for SMARCB1 gene
(According to
1HGNC,
2Entrez Gene,
3UniProtKB/Swiss-Prot,
4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc,
7Ensembl,
8DME,
9miRBase,
and/or 10fRNAdb)
About This Section
|
| Aliases |
|---|
| SWI/SNF Related, Matrix Associated, Actin Dependent Regulator Of Chromatin,Subfamily B, Member 11 2 | | HSNF51 | | BAF471 2 3 | | SNF5 Homolog2 3 | | SNF5L11 2 3 | | RTPS12 5 | | RDT1 2 5 | | SNF52 5 | | INI12 3 5 | | Ini11 | | Sfh1p1 2 | | MRD152 | | Snr11 2 | | Malignant Rhabdoid Tumor Suppressor2 | | HSNFS1 | | Sucrose Nonfermenting, Yeast, Homolog-Like 12 | | Integrase Interactor 1 Protein2 3 | | SWI/SNF-Related Matrix-Associated Actin-Dependent Regulator Of ChromatinSubfamily B Member 12 | | BRG1-Associated Factor 472 3 | | |
Export aliases for SMARCB1 gene to outside databasesPrevious 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:
The protein encoded by this gene is part of a complex that relieves repressive chromatin structures, allowing thetranscriptional machinery to access its targets more effectively. The encoded nuclear protein may also bind to andenhance the DNA joining activity of HIV-1 integrase. This gene has been found to be a tumor suppressor, and mutationsin it have been associated with malignant rhabdoid tumors. Two transcript variants encoding different isoforms havebeen found for this gene. (provided by RefSeq, Jul 2008)
UniProtKB/Swiss-Prot: SNF5_HUMAN, Q12824Function: Core component of the BAF (hSWI/SNF) complex. This ATP-dependent chromatin-remodeling complex plays importantroles 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 thannormal. This change in supercoiling would be due to the conversion of up to one-half of the nucleosomes onpolynucleosomal arrays into asymmetric structures, termed altosomes, each composed of 2 histones octamers. Stimulatesin vitro the remodeling activity of SMARCA4/BRG1/BAF190A. Involved in activation of CSF1 promoter. Belongs to theneural progenitors-specific chromatin remodeling complex (npBAF complex) and the neuron-specific chromatin remodelingcomplex (nBAF complex). During neural development a switch from a stem/progenitor to a post-mitotic chromatinremodeling mechanism occurs as neurons exit the cell cycle and become committed to their adult state. The transitionfrom proliferating neural stem/progenitor cells to post-mitotic neurons requires a switch in subunit composition ofthe npBAF and nBAF complexes. As neural progenitors exit mitosis and differentiate into neurons, npBAF complexes whichcontain ACTL6A/BAF53A and PHF10/BAF45A, are exchanged for homologous alternative ACTL6B/BAF53B and DPF1/BAF45B orDPF3/BAF45C subunits in neuron-specific complexes (nBAF). The npBAF complex is essential for theself-renewal/proliferative capacity of the multipotent neural stem cells. The nBAF complex along with CREST plays arole regulating the activity of genes essential for dendrite growth (By similarity). Plays a key role in cell-cyclecontrol and causes cell cycle arrest in G0/G1. Also involved in vitamin D-coupled transcription regulation via itsassociation with the WINAC complex, a chromatin-remodeling complex recruited by vitamin D receptor (VDR), which isrequired for the ligand-bound VDR-mediated transrepression of the CYP27B1 gene
Gene Wiki entry for SMARCB1
|
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 69),
Regulatory elements and Epigenetics data according to
QIAGEN,
SABiosciences, and/or
SwitchGear Genomics)
About This Section
| RefSeq DNA sequence:- NC_000022.10 NC_018933.1 NT_011520.12
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
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: 22q11.23SMARCB1 Gene in genomic location: bands according to Ensembl, locations according to
 (and/or Entrez Gene and/or Ensembl if different)
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,
neXtProt,
Ensembl,
and/or Reactome,
Modification sites according to 2PhosphoSitePlus,
Specific Peptides from DME,
Protein expression images according to data from SPIRE MOPED and PaxDb,
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
Uscn,
Biochemical Assays by
EMD Millipore,
R&D Systems,
OriGene,
GenScript,
Cell Signaling Technology,
Enzo Life Sciences, and/or
Uscn,
Ontologies according to Gene
Ontology Consortium 01 Mar 2013 and
Entrez Gene,
Antibodies by
EMD Millipore,
R&D Systems,
GenScript,
Cell Signaling Technology,
OriGene,
Novus Biologicals,
Thermo Fisher Scientific,
Abcam, and/or
Uscn)
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 containsDPF3. 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 andMAEL. Interacts with PPP1R15A. Binds tightly to the human immunodeficiency virus-type 1 (HIV-1) integrase in vitro andstimulates its DNA-joining activity. Interacts with human papillomavirus 18 E1 protein to stimulate its viralreplication. Interacts with Epstein-Barr virus protein EBNA-2. Component of neural progenitors-specific chromatinremodeling 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 (nBAFcomplex) 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 Q9UBH2Alternative splicing: 2 isoforms: Q12824-1 Q12824-2 Explore the universe of human proteins at neXtProt for SMARCB1: NX_Q12824
Post-translational modifications:
View modification sites using PhosphoSitePlus2View neXtProt modification sites for NX_Q12824
SMARCB1 Protein expression data from MOPED and PaxDb: About this image 
REFSEQ proteins (2 alternative transcripts):
NP_001007469.1 NP_003064.2
ENSEMBL proteins: ENSP00000388489 ENSP00000340883 ENSP00000263121 ENSP00000383984 ENSP00000385226
Human Recombinant Protein Products:
Gene Ontology (GO): 5/10 cellular component terms (GO ID links to tree view) (see all 10): About this table
SMARCB1 for ontologies About GeneDecksing
SMARCB1 Antibody Products:
Assay Products for SMARCB1: |
Protein
Domains /
Families
for SMARCB1 gene(According to InterPro, ProtoNet,
UniProtKB, and/or BLOCKS,
Sets of similar genes according to GeneDecks)
About This Section
|
SMARCB1 for domains About GeneDecksing
2 InterPro domains/families:Graphical View of Domain Structure for InterPro Entry Q12824ProtoNet protein and cluster: Q12824 1 Blocks protein family: IPB006939 SNF5/SMARCB1/INI1
UniProtKB/Swiss-Prot: SNF5_HUMAN, Q12824Similarity: Belongs to the SNF5 family |
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,
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,
Clones from EMD Millipore,
OriGene,
SwitchGear Genomics,
GenScript,
Sino Biological,
DNA2.0,
and Vector BioLabs,
Cell Lines from GenScript,
LifeMap BioReagents,
In Situ Hybridization Assays from Advanced Cell Diagnostics,
Ontologies according to Gene Ontology Consortium 01 Mar 2013 via
Entrez Gene.)
About This Section
|
Function Summary:
UniProtKB/Swiss-Prot: SNF5_HUMAN, Q12824Function: Core component of the BAF (hSWI/SNF) complex. This ATP-dependent chromatin-remodeling complex plays importantroles 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 thannormal. This change in supercoiling would be due to the conversion of up to one-half of the nucleosomes onpolynucleosomal arrays into asymmetric structures, termed altosomes, each composed of 2 histones octamers. Stimulatesin vitro the remodeling activity of SMARCA4/BRG1/BAF190A. Involved in activation of CSF1 promoter. Belongs to theneural progenitors-specific chromatin remodeling complex (npBAF complex) and the neuron-specific chromatin remodelingcomplex (nBAF complex). During neural development a switch from a stem/progenitor to a post-mitotic chromatinremodeling mechanism occurs as neurons exit the cell cycle and become committed to their adult state. The transitionfrom proliferating neural stem/progenitor cells to post-mitotic neurons requires a switch in subunit composition ofthe npBAF and nBAF complexes. As neural progenitors exit mitosis and differentiate into neurons, npBAF complexes whichcontain ACTL6A/BAF53A and PHF10/BAF45A, are exchanged for homologous alternative ACTL6B/BAF53B and DPF1/BAF45B orDPF3/BAF45C subunits in neuron-specific complexes (nBAF). The npBAF complex is essential for theself-renewal/proliferative capacity of the multipotent neural stem cells. The nBAF complex along with CREST plays arole regulating the activity of genes essential for dendrite growth (By similarity). Plays a key role in cell-cyclecontrol and causes cell cycle arrest in G0/G1. Also involved in vitamin D-coupled transcription regulation via itsassociation with the WINAC complex, a chromatin-remodeling complex recruited by vitamin D receptor (VDR), which isrequired 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 ofchromatin,subfamily B,member 1,component of the chromatin remodeling complex,preferentially expressed in muscle andpancreas,mutated in atypical teratoid and rhabdoid tumors,tumor suppressor gene (see TSG22D),frequently deleted inchronic myeloid leukemia
Clone
Products: |  | Browse Clones for the Expression of Recombinant Proteins Available from EMD Millipore | |  | OriGene Myc/DDK tagged cDNA clones in CMV expression vector in human, mouse, rat for SMARCB1 (see all 5)
OriGene untagged cDNA clones in CMV expression vector in human, mouse, rat for SMARCB1 (see all 2)
OriGene custom cloning services – gene synthesis, subcloning, mutagenesis,
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Synthesis Service for SMARCB1 | |  | Vector BioLabs ready-to-use adenovirus/AAV for human, mouse, rat SMARCB1 |
In Situ Assay
Products: |
 | Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for SMARCB1 |
Gene Ontology (GO): 4 molecular function terms (GO ID links to tree view): About this table
SMARCB1 for ontologies About GeneDecksing
2 GenomeRNAi human phenotypes for SMARCB1:
Animal Models:
Mouse knock-outs for SMARCB1: Smarcb1tm1Gvk Smarcb1tm1Sho
14 MGI mutant phenotypes (inferred from 7 alleles ) (MGI details for Smarcb1):
SMARCB1 for phenotypes About GeneDecksing
|
Pathways & Interactions
for SMARCB1 gene
(Pathways according to
EMD Millipore,
R&D Systems,
Cell Signaling Technology,
KEGG,
PharmGKB,
BioSystems,
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 Mar 2013 via
Entrez Gene).
About This Section
|
Unified GeneCards pathways - 5/7 super-pathways (see all 7) About this table
See pathways by source
| Super-pathway | contained gene-specific pathways |
|---|
| 1 | Development_Ligand-dependent activation of the ESR1/AP-1 pathway | | | 2 | BRCA1 Pathway | | | 3 | AMPK Enzyme Complex Pathway | | | 4 | TNF-alpha/NF-kB Signaling Pathway | | | 5 | Regulation of retinoblastoma protein | |
Pathway sources
See GeneCards unified pathways
Show all pathways
2 EMD Millipore Pathways for SMARCB1
4 Downloadable PowerPoint Slides of QIAGEN Pathway Central Maps for SMARCB1
1 
Cell Signaling Technology (CST) Pathway for SMARCB1
2  GeneGo (Thomson Reuters) Pathways for SMARCB1
2  BioSystems Pathways for SMARCB1
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)
5/876 Interacting proteins for SMARCB1 (Q128241, 2, 3 ENSP000002631214) via UniProtKB, MINT, STRING, and/or I2D (see all 876)| Interactant | Interaction Details |
|---|
| GeneCard | External ID(s) |
|---|
| SMARCD1 | Q96GM52, 3, ENSP000003784144 | MINT-7945693 MINT-7947479 I2D:
score=7 STRING: ENSP00000378414 | | HDAC2 | Q927692, 3, ENSP000003813314 | MINT-7945693 MINT-7947479 I2D:
score=2 STRING: ENSP00000381331 | | NCOR1 | O753762, 3, ENSP000002687124 | MINT-7945693 MINT-7947479 I2D:
score=2 STRING: ENSP00000268712 | | SMARCA2 | P515312, 3, ENSP000002657734 | MINT-7945693 MINT-7894924 I2D:
score=2 STRING: ENSP00000265773 | | ARID1A | O144972, 3, ENSP000003204854 | MINT-7945693 MINT-7947479 I2D:
score=1 STRING: ENSP00000320485 |
About this table
Gene Ontology (GO): 5/16 biological process terms (GO ID links to tree view) (see all 16): About this table
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, and Drugs according to
DrugBank,
Enzo Life Sciences, and/or
PharmGKB, with drugs/clinical trials/news
search links to CenterWatch)
About This Section
|
 Browse Tocris compounds for SMARCB1
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 235 Homo sapiens; Mar 10 2013) or GenBank,
RefSeq according to Entrez Gene,
DOTS (version 10), and/or
AceView,
transcript ids from Ensembl
with links to UCSC,
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,
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_0030737 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
Clone
Products: | | OriGene Myc/DDK tagged cDNA clones in CMV expression vector in human, mouse, rat for SMARCB1 (see all 5)
OriGene untagged cDNA clones in CMV expression vector in human, mouse, rat for SMARCB1 (see all 2)
OriGene custom cloning services – gene synthesis, subcloning, mutagenesis,
variant library, vector shuttling
| | | GenScript: all cDNA clones in your preferred vector (see all 2): SMARCB1 (NM_003073) | | | DNA2.0 Custom Codon Optimized Gene
Synthesis Service for SMARCB1 | | | Vector BioLabs ready-to-use adenovirus/AAV for human, mouse, rat SMARCB1 |
Additional cDNA 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): CR590517 BE612477 H04220 AI680381 CD369902 AI271563 CR625181 BG032753 BU501149 BQ015000 AI219922 AU143041 BE267929 BM680044 BQ642732 BM823889 AI537937 CA411818 CR600940 AI075165 BM842594 AI241194 AY562997 BE223100
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)
See probesets specificity/sensitivity at GeneAnnot
About this imageBioGPS
CGAP TAG: --
About this image
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 |
Primer
Products: | | OriGene genome-wide validated SYBR primer pairs in human, mouse, rat for SMARCB1
Browse OriGene validated miRNA SYBR primer pairs
| | | SABiosciences RT2 qPCR Primer Assay in human, mouse, rat SMARCB1 | | | QIAGEN QuantiTect SYBR Green Assays in human, mouse, rat SMARCB1 | | | QIAGEN 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
|
This gene was present in the common ancestor of eukaryotes.
Orthologs for SMARCB1 gene from 9/27 species (see all 27) 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 |
-- |
95(a) |
1 ↔ 1 |
AAWZ02039747(3389-7260) |
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 |
thale cress
(Arabidopsis thaliana) |
eudicotyledons |
BSH6 |
chromatin structure-remodeling complex protein BSH... |
26(a) |
1 ↔ 1 |
3(6017212-6019666) |
rice
(Oryza sativa) |
Liliopsida |
-- |
SWI/SNF-related matrix-associated actin-dependent ... |
24(a) |
1 ↔ 1 |
2(30066068-30069075) |
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,
UniProtKB, 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
|
| Genomic Data | Transcription Related Data | Allele Frequencies | | SNP ID | Valid | Clinical
significance | Chr 22 pos | Sequence | # | AA
Chg | Type | More | # | Allele
freq | Pop | Total
sample | More |
|---|
HapMap Linkage Disequilibrium report for SMARCB1 (24129150 - 24176705 bp)
Structural Variations (Copy Number Variations, Insertions/Deletions, Inversions)
Database of Genomic Variants (DGV) variations for SMARCB1: --
Human Gene Mutation Database (HGMD): SMARCB1
| 5/7 SABiosciences Cancer Mutation PCR Assays for SMARCB1 (see all 7): |
| 3 SABiosciences Cancer Mutation PCR Arrays containing SMARCB1: |
| | QIAGEN SeqTarget long-range PCR primers in human, mouse, rat for resequencing SMARCB1 |
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Disorders
/ Diseases
for SMARCB1 gene
(in which this Gene is Involved, According to MalaCards,
OMIM, UniProtKB,
the University of Copenhagen DISEASES
database, Novoseek,
Genatlas, GeneTests,
GAD,
HuGE Navigator,
and/or TGDB.)
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|
SMARCB1 for disorders About GeneDecksing
OMIM gene information: 601607
OMIM disorders: 609322
UniProtKB/Swiss-Prot: SNF5_HUMAN, Q12824
Defects in SMARCB1 are a cause of rhabdoid tumor predisposition syndrome type 1 (RTPS1) [MIM:609322]; alsoknown as malignant rhabdoid tumor (MRT). RDT are a highly malignant group of neoplasms that usually occur in earlychildhood. SMARCB1/INI1 is also frequently inactivated in epithelioid sarcomas Defects in SMARCB1 are a cause of schwannomatosis (SCHWA) [MIM:162091]; also called congenital cutaneousneurilemmomatosis. Schwannomas are benign tumors of the peripheral nerve sheath that usually occur singly in otherwisenormal 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-nerveschwannomas; but two-thirds or more of all NF2-affected individuals develop schwannomas in other locations, and dermalschwannomas may precede vestibular tumors in NF2-affected children. There have been several reports of individualswith multiple schwannomas who do not show evidence of vestibular schwannoma. Clinical report suggests thatschwannomatosis is a clinical entity distinct from other forms of neurofibromatosis Defects in SMARCB1 are the cause of mental retardation autosomal dominant type 15 (MRD15) [MIM:614608]. Adisease characterized by multiple congenital anomalies and mental retardation. Mental retardation is defined bysignificantly below average general intellectual functioning associated with impairments in adaptative behavior andmanifested during the developmental period. MRD15 patients manifest developmental delay, hypotonia, absent orhypoplastic fifth finger or toenails, a coarse facial appearance, sparse scalp hair, thick eyebrows, and longeyelashes. Additional variable features include microcephaly, small cerebellum, seizures, hearing loss, abnormaldelayed dentition, hirsutism
20/70  diseases for SMARCB1 (see all 70): About MalaCardsrhabdoid tumors malignant peripheral nerve sheath tumor epithelioid malignant peripheral nerve sheath tumor rhabdoid predisposition syndrome
atypical teratoid rhabdoid tumor rhabdoid predisposition syndrome 1 congenital mesoblastic nephroma extraskeletal myxoid chondrosarcoma
beckwith-wiedemann syndrome mesoblastic nephroma choroid plexus papilloma myxoid chondrosarcoma
collecting duct carcinoma pleomorphic xanthoastrocytoma retroperitoneal leiomyosarcoma primitive neuroectodermal tumor
prolymphocytic leukemia soft tissue sarcoma choroid plexus carcinoma mesenchymal chondrosarcoma
7 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 10/27 Novoseek 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 305):
(articles sorted by number of sources associating them with SMARCB1) | |  | Utopia: connect your pdf to the dynamic
world of online information |
- Interaction of E1 and hSNF5 proteins stimulates replication of human papillomavirus DNA. (PubMed id 10365963)1, 2, 3, 9 Lee D....Choe J. (1999)
- 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)
- 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)
- 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)
- 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)
- 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)
- The mouse ortholog of the human SMARCB1 gene encodes two splice forms. (PubMed id 10208879)1, 2, 9 Bruder C.E.... Kedra D. (1999)
- Germline mutation of INI1/SMARCB1 in familial schwannomatosis. (PubMed id 17357086)1, 2 Hulsebos T.J....Wesseling P. (2007)
- SMARCB1/INI1 tumor suppressor gene is frequently inactivated in epithelioid sarcomas. (PubMed id 15899790)1, 2 Modena P.... Sozzi G. (2005)
- Human SWI/SNF generates abundant, structurally altered dinucleosomes on polynucleosomal templates. (PubMed id 16314535)1, 2 Ulyanova N.P. and Schnitzler G.R. (2005)
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External Searches for SMARCB1 gene
(in PubMed,
OMIM, and NCBI Bookshelf)
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|
|
Genome Databases showing SMARCB1 gene
(According to
Entrez Gene,
HGNC,
AceView,
euGenes,
Ensembl,
miRBase,
ECgene,
Kegg,
and/or
H-InvDB)
About This Section
|
|
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
|
| Name | Description |
| PharmGKB entry for SMARCB1 | Pharmacogenomics, SNPs, Pathways | | ATLAS Chromosomes in Cancer entry for SMARCB1 | Genetics and Cytogenetics in Oncology and Haematology | | GeneReviews | http://www.ncbi.nlm.nih.gov/sites/GeneTests/lab/gene/SMARCB1 | | NIEHS-SNPs | http://egp.gs.washington.edu/data/smarcb1/ |
|
| | |
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| 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
|
Products
for SMARCB1 gene(Antibodies, recombinant proteins, and assays from EMD Millipore, R&D Systems, OriGene, QIAGEN, GenScript, Cell Signaling Technology, SABiosciences, Novus Biologicals, Sino Biological, Enzo Life Sciences, Abcam, ProSpec, Uscn, Thermo Fisher Scientific, Gene Editing from DNA2.0, Clones from EMD Millipore, OriGene, GenScript, Sino Biological, DNA2.0, SwitchGear Genomics, Vector BioLabs, Cell lines from GenScript and LifeMap BioReagents, PCR Arrays from SABiosciences, Drugs and/or compounds from EMD Millipore, Tocris Bioscience, and/or
Enzo Life Sciences),
In Situ Hybridization Assays from
Advanced Cell Diagnostics
About This Section
|
 | |
 | |
 |
| | |  | OriGene Antibodies for SMARCB1 | | Browse OriGene shRNA RFPs | | | OriGene 29mer shRNA kits in GFP-retroviral vector in human, mouse, rat for SMARCB1 | | OriGene genome-wide validated SYBR primer pairs in human, mouse, rat for SMARCB1 | | | OriGene Protein Over-expression Lysate for SMARCB1 | | Browse OriGene Fluorogenic Cell Assay Kits | | | OriGene siRNA for SMARCB1 | | OriGene 3'-UTR Clone for SMARCB1 | | | OriGene untagged cDNA clones in CMV expression vector in human, mouse, rat for SMARCB1 | | OriGene Myc/DDK tagged cDNA clones in CMV expression vector in human, mouse, rat for SMARCB1 | | | Browse OriGene GFP tagged cDNA clones in CMV expression vector | | Browse OriGene MicroRNA Expression Plasmids | | | Browse OriGene basic RS shRNAs | | Browse OriGene validated miRNA SYBR primer pairs | | | OriGene Purified Protein for SMARCB1 | | OriGene custom cloning services - gene synthesis, subcloning, mutagenesis,
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| | | QIAGEN Custom miScript Target Protector blocks miRNA-binding site of in human, mouse, rat SMARCB1 | | | QIAGEN SeqTarget long-range PCR primers in human, mouse, rat for resequencing SMARCB1 | | | QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays in human, mouse, rat SMARCB1 | | | QIAGEN FlexiTube/FlexiPlate siRNA for gene silencing in human, mouse, rat SMARCB1 | | | QIAGEN QuantiFast Probe-based Assays in human, mouse, rat SMARCB1 | | | QIAGEN QuantiTect SYBR Green Assays in human, mouse, rat SMARCB1 |
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