Human Gene SGCE (uc003unn.2)
  Description: Homo sapiens sarcoglycan, epsilon (SGCE), transcript variant 3, mRNA.
RefSeq Summary (NM_001099400): This gene encodes the epsilon member of the sarcoglycan family. Sarcoglycans are transmembrane proteins that are components of the dystrophin-glycoprotein complex, which link the actin cytoskeleton to the extracellular matrix. Unlike other family members which are predominantly expressed in striated muscle, the epsilon sarcoglycan is more broadly expressed. Mutations in this gene are associated with myoclonus-dystonia syndrome. This gene is imprinted, with preferential expression from the paternal allele. Alternatively spliced transcript variants encoding different isoforms have been found for this gene. A pseudogene associated with this gene is located on chromosome 2. [provided by RefSeq, Oct 2016].
Transcript (Including UTRs)
   Position: hg19 chr7:94,214,536-94,285,521 Size: 70,986 Total Exon Count: 11 Strand: -
Coding Region
   Position: hg19 chr7:94,214,777-94,285,410 Size: 70,634 Coding Exon Count: 11 

Page IndexSequence and LinksUniProtKB CommentsPrimersGenetic AssociationsMalaCards
CTDGene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein Structure
Other SpeciesmRNA DescriptionsOther NamesGeneReviewsModel InformationMethods
Data last updated at UCSC: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr7:94,214,536-94,285,521)mRNA (may differ from genome)Protein (451 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
GeneNetworkH-INVHGNCLynxMalacardsMGI
OMIMPubMedTreefamUniProtKBWikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: E9PF60_HUMAN
DESCRIPTION: SubName: Full=Epsilon-sarcoglycan;
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


-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): SGCE
CDC HuGE Published Literature: SGCE

-  MalaCards Disease Associations
  MalaCards Gene Search: SGCE
Diseases sorted by gene-association score: dystonia-11, myoclonic* (1360), dystonia (31), myoclonus (28), movement disease (21), obsessive-compulsive disorder (11), split-hand/foot malformation 1 with sensorineural hearing loss (9), dystonia-1, torsion (9), focal dystonia (8), spinocerebellar ataxia 14 (7), gilles de la tourette syndrome (6), asperger syndrome (6), dystonia, dopa-responsive, with or without hyperphenylalaninemia (6), hemidystonia (6), dystonia-12 (5)
* = Manually curated disease association

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene           more ... click here to view the complete list

+  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: 48.22 RPKM in Ovary
Total median expression: 846.04 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 -25.50111-0.230 Picture PostScript Text
3' UTR -34.50241-0.143 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
IPR006644 - Cadg
IPR008908 - Sarcoglycan_2

Pfam Domains:
PF05510 - Sarcoglycan alpha/epsilon

SCOP Domains:
49313 - Cadherin-like

ModBase Predicted Comparative 3D Structure on E9PF60
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 orthologGenome BrowserNo orthologNo orthologNo ortholog
Gene Details     
Gene Sorter     
  Ensembl   
  Protein Sequence   
  Alignment   

-  Descriptions from all associated GenBank mRNAs
  AY359042 - Homo sapiens clone DNA53987 SGCE (UNQ433) mRNA, complete cds.
AF036364 - Homo sapiens epsilon-sarcoglycan (ESG) mRNA, complete cds.
BC021709 - Homo sapiens sarcoglycan, epsilon, mRNA (cDNA clone MGC:26495 IMAGE:4822278), complete cds.
AJ000534 - Homo sapiens mRNA for epsilon-sarcoglycan.
AK298220 - Homo sapiens cDNA FLJ52341 complete cds, highly similar to Homo sapiens sarcoglycan, epsilon (SGCE), mRNA.
AB117974 - Homo sapiens ESG mRNA for brain epsilon-sarcoglycan, complete cds.
AF516515 - Homo sapiens mutant epsilon-sarcoglycan mRNA, complete cds.
AK313438 - Homo sapiens cDNA, FLJ93977, Homo sapiens sarcoglycan, epsilon (SGCE), mRNA.
KJ897936 - Synthetic construct Homo sapiens clone ccsbBroadEn_07330 SGCE gene, encodes complete protein.
KR709475 - Synthetic construct Homo sapiens clone CCSBHm_00002563 SGCE (SGCE) mRNA, encodes complete protein.
KR709476 - Synthetic construct Homo sapiens clone CCSBHm_00002564 SGCE (SGCE) mRNA, encodes complete protein.
KR709477 - Synthetic construct Homo sapiens clone CCSBHm_00002575 SGCE (SGCE) mRNA, encodes complete protein.
KR709478 - Synthetic construct Homo sapiens clone CCSBHm_00002578 SGCE (SGCE) mRNA, encodes complete protein.
DQ894063 - Synthetic construct Homo sapiens clone IMAGE:100008523; FLH167043.01L; RZPDo839G0887D sarcoglycan, epsilon (SGCE) gene, encodes complete protein.
EU176189 - Synthetic construct Homo sapiens clone IMAGE:100006577; FLH263898.01X; RZPDo839B01246D sarcoglycan, epsilon (SGCE) gene, encodes complete protein.
KU178449 - Homo sapiens sarcoglycan epsilon isoform 1 (SGCE) mRNA, partial cds.
KU178450 - Homo sapiens sarcoglycan epsilon isoform 2 (SGCE) mRNA, partial cds, alternatively spliced.
AK295021 - Homo sapiens cDNA FLJ50763 complete cds, highly similar to Homo sapiens sarcoglycan, epsilon (SGCE), mRNA.
AF031920 - Homo sapiens epsilon-sarcoglycan mRNA, partial cds.
JD279881 - Sequence 260905 from Patent EP1572962.
CU692388 - Synthetic construct Homo sapiens gateway clone IMAGE:100019393 5' read SGCE mRNA.
LF213015 - JP 2014500723-A/20518: Polycomb-Associated Non-Coding RNAs.
JD062130 - Sequence 43154 from Patent EP1572962.
MA448592 - JP 2018138019-A/20518: Polycomb-Associated Non-Coding RNAs.

-  Other Names for This Gene
  Alternate Gene Symbols: E9PF60, E9PF60_HUMAN, NM_001099400, NP_001092870
UCSC ID: uc003unn.2
RefSeq Accession: NM_001099400
Protein: E9PF60 CCDS: CCDS47642.1

-  GeneReviews for This Gene
  GeneReviews article(s) related to gene SGCE:
dystonia-ov (Hereditary Dystonia Overview)
myo-dystonia (SGCE Myoclonus-Dystonia)

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_001099400.1
exon count: 11CDS single in 3' UTR: no RNA size: 1717
ORF size: 1356CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 2824.00frame shift in genome: no % Coverage: 99.48
has start codon: yes stop codon in genome: no # of Alignments: 1
has end codon: yes retained intron: no # AT/AC introns 0
selenocysteine: no end bleed into intron: 0# strange splices: 0
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.