Human Gene SMARCA4 (ENST00000646693.2_3) from GENCODE V47lift37
  Description: SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 4, transcript variant 10 (from RefSeq NM_001387283.1)
Gencode Transcript: ENST00000646693.2_3
Gencode Gene: ENSG00000127616.22_21
Transcript (Including UTRs)
   Position: hg19 chr19:11,071,706-11,172,949 Size: 101,244 Total Exon Count: 36 Strand: +
Coding Region
   Position: hg19 chr19:11,094,828-11,172,492 Size: 77,665 Coding Exon Count: 35 

Page IndexSequence and LinksPrimersMalaCardsCTDGene Alleles
Microarray ExpressionRNA StructureProtein StructureOther SpeciesGO AnnotationsmRNA Descriptions
PathwaysOther NamesGeneReviewsModel InformationMethods
Data last updated at UCSC: 2024-08-22 23:36:26

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr19:11,071,706-11,172,949)mRNA (may differ from genome)Protein (1679 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblExonPrimerGeneCardsHGNC
MalacardsMGIPubMedUniProtKBWikipedia

-  Primer design for this transcript
 

Primer3Plus can design qPCR Primers that straddle exon-exon-junctions, which amplify only cDNA, not genomic DNA.
Click here to load the transcript sequence and exon structure into Primer3Plus

Exonprimer can design one pair of Sanger sequencing primers around every exon, located in non-genic sequence.
Click here to open Exonprimer with this transcript

To design primers for a non-coding sequence, zoom to a region of interest and select from the drop-down menu: View > In External Tools > Primer3


-  MalaCards Disease Associations
  MalaCards Gene Search: SMARCA4
Diseases sorted by gene-association score: coffin-siris syndrome 4* (1230), rhabdoid tumor predisposition syndrome 2* (1069), ovarian small cell carcinoma* (374), smarca4-deficient sarcoma of thorax* (350), rhabdoid cancer* (294), familial rhabdoid tumor* (247), coffin-siris syndrome 1* (212), smarca4-related coffin-siris syndrome* (100), atypical teratoid rhabdoid tumor (17), tumor predisposition syndrome (16), central nervous system sarcoma (11), ovarian melanoma (11), schimke immunoosseous dysplasia (10), alpha thalassemia-x-linked intellectual disability syndrome (10), small cell carcinoma (9), bacteremia (8), enamel erosion (8), tooth erosion (7), root caries (7), gingival disease (7), epilepsy, familial temporal lobe, 1 (6), hypertrichosis (6), lymphosarcoma (5), thalassemias, alpha- (4), medulloblastoma (4), borjeson-forssman-lehmann syndrome (4), lung cancer (2)
* = Manually curated disease association

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene

+  Common Gene Haplotype Alleles
  Press "+" in the title bar above to open this section.

+  Microarray Expression Data
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-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -88.10173-0.509 Picture PostScript Text
3' UTR -129.80457-0.284 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  InterPro Domains: Graphical view of domain structure
IPR006576 - BRK_domain
IPR001487 - Bromodomain
IPR018359 - Bromodomain_CS
IPR014978 - Gln-Leu-Gln_QLQ
IPR013999 - HAS_subgr
IPR014012 - Helicase/SANT-assoc_DNA-bd
IPR014001 - Helicase_ATP-bd
IPR001650 - Helicase_C
IPR006562 - HSA
IPR000330 - SNF2_N

Pfam Domains:
PF00176 - SNF2-related domain
PF00271 - Helicase conserved C-terminal domain
PF00439 - Bromodomain
PF04851 - Type III restriction enzyme, res subunit
PF07529 - HSA
PF07533 - BRK domain
PF08880 - QLQ
PF14619 - Snf2-ATP coupling, chromatin remodelling complex

SCOP Domains:
47370 - Bromodomain
52540 - P-loop containing nucleoside triphosphate hydrolases
160481 - BRK domain-like

ModBase Predicted Comparative 3D Structure on Q9HBD4
FrontTopSide
The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
No orthologNo orthologNo orthologNo orthologNo orthologNo ortholog
Gene DetailsGene Details    
Gene SorterGene Sorter    
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-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0005524 ATP binding
GO:0016817 hydrolase activity, acting on acid anhydrides
GO:0016887 ATPase activity
GO:0042393 histone binding

Biological Process:
GO:0006355 regulation of transcription, DNA-templated
GO:0043044 ATP-dependent chromatin remodeling

Cellular Component:
GO:0005634 nucleus
GO:0016514 SWI/SNF complex


-  Descriptions from all associated GenBank mRNAs
  LP955720 - Sequence 2 from Patent WO2017214373.
BC150298 - Homo sapiens SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 4, mRNA (cDNA clone MGC:167032 IMAGE:8860365), complete cds.
AK290033 - Homo sapiens cDNA FLJ77531 complete cds, highly similar to Homo sapiens SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 4 (SMARCA4), mRNA.
U29175 - Human transcriptional activator (BRG1) mRNA, complete cds.
D26156 - Homo sapiens mRNA for transcriptional activator hSNF2b, complete cds.
BC136644 - Homo sapiens SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 4, mRNA (cDNA clone MGC:168257 IMAGE:9020634), complete cds.
AB590582 - Synthetic construct DNA, clone: pFN21AE0798, Homo sapiens SMARCA4 gene for SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 4, without stop codon, in Flexi system.
BC151849 - Synthetic construct Homo sapiens clone IMAGE:100013606, MGC:167207 SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 4 (SMARCA4) mRNA, encodes complete protein.
EU430756 - Homo sapiens SMARCA4 isoform 3 mRNA, complete cds, alternatively spliced.
EU430757 - Homo sapiens SMARCA4 isoform 2 mRNA, complete cds, alternatively spliced.
EU430758 - Homo sapiens SMARCA4 isoform 4 mRNA, complete cds, alternatively spliced.
EU430759 - Homo sapiens SMARCA4 isoform 1 mRNA, complete cds, alternatively spliced.
AB209313 - Homo sapiens mRNA for SWI/SNF-related matrix-associated actin-dependent regulator of chromatin a4 variant protein.
AK299761 - Homo sapiens cDNA FLJ60344 complete cds, highly similar to Probable global transcription activator SNF2L4 (EC 3.6.1.-).
AK308763 - Homo sapiens cDNA, FLJ98804.
AK303352 - Homo sapiens cDNA FLJ60382 complete cds, highly similar to Probable global transcription activator SNF2L4(EC 3.6.1.-).
AK055168 - Homo sapiens cDNA FLJ30606 fis, clone CTONG2000330, highly similar to Probable global transcription activator SNF2L4 (EC 3.6.1.-).
AK097105 - Homo sapiens cDNA FLJ39786 fis, clone SPLEN2002695, highly similar to POSSIBLE GLOBAL TRANSCRIPTION ACTIVATOR SNF2L2.
AK026573 - Homo sapiens cDNA: FLJ22920 fis, clone KAT06686, highly similar to HSU29175 Human transcriptional activator (BRG1) mRNA.
MB474734 - JP 2019527037-A/2: DIAGNOSTIC AND THERAPEUTIC METHODS FOR CANCER.
BC139917 - Homo sapiens SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 4, mRNA (cDNA clone IMAGE:40148118), partial cds.
BC139924 - Homo sapiens SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 4, mRNA (cDNA clone IMAGE:40148973), partial cds.
BC007302 - Homo sapiens cDNA clone IMAGE:3351917, containing frame-shift errors.
BC035916 - Homo sapiens SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 4, mRNA (cDNA clone IMAGE:5520352).
JD406865 - Sequence 387889 from Patent EP1572962.
JD191179 - Sequence 172203 from Patent EP1572962.
JD518746 - Sequence 499770 from Patent EP1572962.
JD138569 - Sequence 119593 from Patent EP1572962.
JD428717 - Sequence 409741 from Patent EP1572962.
JD234331 - Sequence 215355 from Patent EP1572962.
JD236070 - Sequence 217094 from Patent EP1572962.

-  Biochemical and Signaling Pathways
  BioCarta from NCI Cancer Genome Anatomy Project
h_vdrPathway - Control of Gene Expression by Vitamin D Receptor
h_hSWI-SNFpathway - Chromatin Remodeling by hSWI/SNF ATP-dependent Complexes

-  Other Names for This Gene
  Alternate Gene Symbols: ENST00000646693.1, hCG_29955 , NM_001387283, Q9HBD4, Q9HBD4_HUMAN, SMARCA4 , uc328mtr.1
UCSC ID: ENST00000646693.2_3
RefSeq Accession: NM_001387283.1
Protein: Q9HBD4

-  GeneReviews for This Gene
  GeneReviews article(s) related to gene SMARCA4:
cdh-ov (Congenital Diaphragmatic Hernia Overview)
coffin-siris (Coffin-Siris Syndrome)
rtps (Rhabdoid Tumor Predisposition Syndrome)

-  Gene Model Information
  Click here for a detailed description of the fields of the table above.

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.