Human Gene SMARCC2 (ENST00000550164.6_10) from GENCODE V47lift37
  Description: SWI/SNF related, matrix associated, actin dependent regulator of chromatin subfamily c member 2, transcript variant 4 (from RefSeq NM_001330288.2)
Gencode Transcript: ENST00000550164.6_10
Gencode Gene: ENSG00000139613.12_16
Transcript (Including UTRs)
   Position: hg19 chr12:56,556,143-56,583,267 Size: 27,125 Total Exon Count: 29 Strand: -
Coding Region
   Position: hg19 chr12:56,557,473-56,583,245 Size: 25,773 Coding Exon Count: 29 

Page IndexSequence and LinksUniProtKB CommentsPrimersMalaCardsCTD
Gene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther Species
GO AnnotationsmRNA DescriptionsPathwaysOther NamesGeneReviewsModel Information
Methods
Data last updated at UCSC: 2024-08-22 23:36:26

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr12:56,556,143-56,583,267)mRNA (may differ from genome)Protein (1245 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
HGNCMalacardsMGIOMIMPubMedUniProtKB
WikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: F8VXC8_HUMAN
DESCRIPTION: SubName: Full=SWI/SNF complex subunit SMARCC2;
CAUTION: The sequence shown here is derived from an Ensembl automatic analysis pipeline and should be considered as preliminary data.

-  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: SMARCC2
Diseases sorted by gene-association score: achalasia-addisonianism-alacrimia syndrome (5), schwannomatosis (5), coffin-siris syndrome 1 (4)

-  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.

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 55.61 RPKM in Brain - Cerebellum
Total median expression: 1595.75 RPKM



View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
  Press "+" in the title bar above to open this section.

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -4.3022-0.195 Picture PostScript Text
3' UTR -406.301330-0.305 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
IPR001357 - BRCT_dom
IPR000953 - Chromo_domain/shadow
IPR009057 - Homeodomain-like
IPR001005 - SANT/Myb
IPR017884 - SANT_dom
IPR007526 - SWIRM
IPR011991 - WHTH_trsnscrt_rep_DNA-bd

Pfam Domains:
PF00249 - Myb-like DNA-binding domain
PF04433 - SWIRM domain
PF13921 - Myb-like DNA-binding domain
PF16495 - SWIRM-associated region 1
PF16496 - SWIRM-associated domain at the N-terminal
PF16498 - SWIRM-associated domain at the C-terminal

SCOP Domains:
46689 - Homeodomain-like
54160 - Chromo domain-like
52113 - BRCT domain
54211 - Ribosomal protein S5 domain 2-like

ModBase Predicted Comparative 3D Structure on F8VXC8
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    
 RGD    
      
      

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0003677 DNA binding
GO:0003682 chromatin binding

Biological Process:
GO:0000122 negative regulation of transcription from RNA polymerase II promoter
GO:0021882 regulation of transcription from RNA polymerase II promoter involved in forebrain neuron fate commitment
GO:0045892 negative regulation of transcription, DNA-templated

Cellular Component:
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0016514 SWI/SNF complex
GO:0071564 npBAF complex
GO:0071565 nBAF complex


-  Descriptions from all associated GenBank mRNAs
  AB209006 - Homo sapiens mRNA for SWI/SNF-related matrix-associated actin-dependent regulator of chromatin c2 isoform b variant protein.
LP955723 - Sequence 5 from Patent WO2017214373.
U66616 - Human SWI/SNF complex 170 KDa subunit (BAF170) mRNA, complete cds.
BC009067 - Homo sapiens SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily c, member 2, mRNA (cDNA clone IMAGE:3854442), partial cds.
BC015697 - Homo sapiens mRNA similar to SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily c, member 2 (cDNA clone IMAGE:4845509).
AK025128 - Homo sapiens cDNA: FLJ21475 fis, clone COL04948, highly similar to HSU66616 Human SWI/SNF complex 170 KDa subunit (BAF170) mRNA.
BC013045 - Homo sapiens SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily c, member 2, mRNA (cDNA clone MGC:17103 IMAGE:4180388), complete cds.
AK293896 - Homo sapiens cDNA FLJ55615 complete cds, highly similar to SWI/SNF-related matrix-associatedactin-dependent regulator of chromatin subfamily C member 2.
AB209293 - Homo sapiens mRNA for SWI/SNF-related matrix-associated actin-dependent regulator of chromatin c2 isoform b variant protein.
JD258112 - Sequence 239136 from Patent EP1572962.
JD548395 - Sequence 529419 from Patent EP1572962.
JD090227 - Sequence 71251 from Patent EP1572962.
JD550841 - Sequence 531865 from Patent EP1572962.
JD163850 - Sequence 144874 from Patent EP1572962.
JD060628 - Sequence 41652 from Patent EP1572962.
JD115508 - Sequence 96532 from Patent EP1572962.
JD489474 - Sequence 470498 from Patent EP1572962.
JD099473 - Sequence 80497 from Patent EP1572962.
JD391169 - Sequence 372193 from Patent EP1572962.
EU176256 - Synthetic construct Homo sapiens clone IMAGE:100006370; FLH169917.01X; RZPDo839F09250D SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily c, member 2 (SMARCC2) gene, encodes complete protein.
AK315153 - Homo sapiens cDNA, FLJ96126.
KJ897581 - Synthetic construct Homo sapiens clone ccsbBroadEn_06975 SMARCC2 gene, encodes complete protein.
BT009924 - Homo sapiens SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily c, member 2 mRNA, complete cds.
AB384911 - Synthetic construct DNA, clone: pF1KB4171, Homo sapiens SMARCC2 gene for SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily C member 2, complete cds, without stop codon, in Flexi system.
BC040645 - Homo sapiens SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily c, member 2, mRNA (cDNA clone IMAGE:4792972), with apparent retained intron.
AL833124 - Homo sapiens mRNA; cDNA DKFZp313D0632 (from clone DKFZp313D0632).
BC026222 - Homo sapiens SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily c, member 2, mRNA (cDNA clone MGC:21969 IMAGE:4395012), complete cds.
MB474737 - JP 2019527037-A/5: DIAGNOSTIC AND THERAPEUTIC METHODS FOR CANCER.

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

-  Other Names for This Gene
  Alternate Gene Symbols: ENST00000550164.1, ENST00000550164.2, ENST00000550164.3, ENST00000550164.4, ENST00000550164.5, F8VXC8, F8VXC8_HUMAN, NM_001330288, SMARCC2 , uc325bcn.1, uc325bcn.2
UCSC ID: ENST00000550164.6_10
RefSeq Accession: NM_001330288.2
Protein: F8VXC8

-  GeneReviews for This Gene
  GeneReviews article(s) related to gene SMARCC2:
coffin-siris (Coffin-Siris 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.