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SGCZ Gene

protein-coding   GIFtS: 42
GCID: GC08M013991

Sarcoglycan, Zeta

  See SGCZ-related disease
at  

(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, 10fRNAdb, 12H-InvDB, 13NCBI, 14NONCODE, and/or 15RNAdb)
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Aliases
Sarcoglycan, Zeta1 2
ZSG12 3
zeta-SG2
zeta-sarcoglycan2
Zeta-SG3

External Ids:    HGNC: 140751   Entrez Gene: 1378682   Ensembl: ENSG000001850537   OMIM: 6081135   UniProtKB: Q96LD13   

Export aliases for SGCZ gene to outside databases

Previous GC identifers: GC08M013721 GC08M013908 GC08M013957 GC08M012489


(According to Entrez Gene, GeneCards, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
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Entrez Gene summary for SGCZ Gene:
The zeta-sarcoglycan gene measures over 465 kb and localizes to 8p22. This protein is part of the sarcoglycan
complex, a group of 6 proteins. The sarcoglycans are all N-glycosylated transmembrane proteins with a short
intra-cellular domain, a single transmembrane region and a large extra-cellular domain containing a
carboxyl-terminal cluster with several conserved cysteine residues. The sarcoglycan complex is part of the
dystrophin-associated glycoprotein complex (DGC), which bridges the inner cytoskeleton and the extra-cellular
matrix. (provided by RefSeq, Jul 2008)

GeneCards Summary for SGCZ Gene:
SGCZ (sarcoglycan, zeta) is a protein-coding gene. Diseases associated with SGCZ include generalized epilepsy with febrile seizures plus. An important paralog of this gene is SGCG.

UniProtKB/Swiss-Prot: SGCZ_HUMAN, Q96LD1
Function: Component of the sarcoglycan complex, a subcomplex of the dystrophin-glycoprotein complex which forms a
link between the F-actin cytoskeleton and the extracellular matrix. May play a role in the maintenance of
striated muscle membrane stability (By similarity)

Gene Wiki entry for SGCZ 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 75), Regulatory elements and Epigenetics data according to QIAGEN, and/or SwitchGear Genomics)
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Regulatory elements:
   Regulatory transcription factor binding sites in the SGCZ gene promoter:
         GCNF   CUTL1   NF-AT   Nkx3-1 v2   IRF-2   Pax-3   NF-AT2   GCNF-1   GCNF-2   NF-AT1   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidSGCZ promoter sequence
   Search Chromatin IP Primers for SGCZ

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat SGCZ


Genomic Location:
Genomic View: UCSC Golden Path with GeneCards custom track

Entrez Gene cytogenetic band: 8p22   Ensembl cytogenetic band:  8p22   HGNC cytogenetic band: 8p22

SGCZ Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
SGCZ gene location

GeneLoc information about chromosome 8         GeneLoc Exon Structure

GeneLoc location for GC08M013991:  view genomic region     (about GC identifiers)

Start:
13,947,373 bp from pter      End:
15,095,848 bp from pter
Size:
1,148,476 bases      Orientation:
minus strand

(According to 1UniProtKB, HORDE, 2neXtProt, Ensembl, and/or Reactome, Modification sites according to PhosphoSitePlus, Specific Peptides from DME, 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, Cloud-Clone Corp., and/or eBioscience,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, Cloud-Clone Corp., and/or eBioscience, Antibodies by EMD Millipore, R&D Systems, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, LSBio, Abcam, Cloud-Clone Corp, and/or others.)
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UniProtKB/Swiss-Prot: SGCZ_HUMAN, Q96LD1 (See protein sequence)
Recommended Name: Zeta-sarcoglycan  
Size: 299 amino acids; 32949 Da
Secondary accessions: Q6REU0
Alternative splicing: 2 isoforms:  Q96LD1-1   Q96LD1-2   (No experimental confirmation available)

Explore the universe of human proteins at neXtProt for SGCZ: NX_Q96LD1

Explore proteomics data for SGCZ at MOPED

Post-translational modifications: 

  • Glycosylation2 at Asn62, Asn110

  • See SGCZ Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

    REFSEQ proteins: NP_631906.2  
    ENSEMBL proteins: 
     ENSP00000371512   ENSP00000405224  

    SGCZ Human Recombinant Protein Products:

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    Search eBioscience for ELISAs for SGCZ 


    (According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
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    2 InterPro protein domains:
     IPR006875 Sarcoglycan
     IPR027662 Sgcz

    Graphical View of Domain Structure for InterPro Entry Q96LD1

    ProtoNet protein and cluster: Q96LD1

    1 Blocks protein domain: IPB006875 Sarcoglycan complex subunit protein

    UniProtKB/Swiss-Prot: SGCZ_HUMAN, Q96LD1
    Similarity: Belongs to the sarcoglycan beta/delta/gamma/zeta family


    Find genes that share domains with SGCZ           About GenesLikeMe


    (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,
    transcription factor targeting from QIAGEN and/or HOMER, miRNA Gene Targets from miRTarBase, shRNA from OriGene, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, SwitchGear Genomics, Gene Editing from DNA2.0, Clones from OriGene, GenScript, Sino Biological, DNA2.0, Vector BioLabs and/or Addgene, Cell Lines from GenScript, ESI BIO, In Situ Hybridization Assays from Advanced Cell Diagnostics, Flow cytometry from eBioscience, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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    Molecular Function:

         UniProtKB/Swiss-Prot Summary: SGCZ_HUMAN, Q96LD1
    Function: Component of the sarcoglycan complex, a subcomplex of the dystrophin-glycoprotein complex which forms a
    link between the F-actin cytoskeleton and the extracellular matrix. May play a role in the maintenance of
    striated muscle membrane stability (By similarity)

         Gene Ontology (GO): 1 molecular function term:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005515protein binding ----
         
    Find genes that share ontologies with SGCZ           About GenesLikeMe


    Animal Models:
       inGenious Targeting Laboratory: Let us create your new Knockout/Knockin mouse model for SGCZ
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    SwitchGear 3'UTR luciferase reporter plasmidSGCZ 3' UTR sequence
    Inhib. RNA
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    (According to UniProtKB, COMPARTMENTS Subcellular localization database, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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    Subcellular locations from UniProtKB/Swiss-Prot
    SGCZ_HUMAN, Q96LD1: Cell membrane, sarcolemma; Single-pass type II membrane protein (By similarity). Cytoplasm,
    cytoskeleton (By similarity)
    Subcellular locations from COMPARTMENTS: 

    CompartmentConfidence
    plasma membrane5
    cytoskeleton2
    extracellular2
    cytosol1

    Gene Ontology (GO): Selected cellular component terms (see all 6):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005737cytoplasm IEA--
    GO:0005856cytoskeleton IEA--
    GO:0005886plasma membrane ----
    GO:0016012sarcoglycan complex TAS17438352
    GO:0016021integral component of membrane IEA--

    Find genes that share ontologies with SGCZ           About GenesLikeMe


    (SuperPaths according to PathCards, Pathways according to 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 QIAGEN, 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 Apr 2014 via Entrez Gene).
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        Custom Pathway & Disease-focused RT2 Profiler PCR Arrays for SGCZ
    Interactions:

        Search GeneGlobe Interaction Network for SGCZ

    STRING Interaction Network Preview (showing 5 interactants - click image to see 20)

    Selected Interacting proteins for SGCZ (Q96LD13 ENSP000003715124) via UniProtKB, MINT, STRING, and/or I2D (see all 20)
    InteractantInteraction Details
    GeneCardExternal ID(s)
    SGCDQ926293, ENSP000003383434I2D: score=1 STRING: ENSP00000338343
    SGCGQ133263, ENSP000002188674I2D: score=1 STRING: ENSP00000218867
    DMDP115323, ENSP000003549234I2D: score=1 STRING: ENSP00000354923
    SGCBQ165853, ENSP000003708394I2D: score=1 STRING: ENSP00000370839
    CAV3ENSP000003419404STRING: ENSP00000341940
    About this table

    Gene Ontology (GO): 3 biological process terms:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0046716muscle cell cellular homeostasis TAS17438352
    GO:0055001muscle cell development TAS17438352
    GO:0061024membrane organization TAS17438352

    Find genes that share ontologies with SGCZ           About GenesLikeMe



    (Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience, ApexBio, HMDB, BitterDB, and/or Novoseek, Ligands according to IUPHAR, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB)
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    Browse Small Molecules at EMD Millipore
       Browse drugs & compounds from Enzo Life Sciences
      Browse compounds at ApexBio 

    Browse Tocris compounds for SGCZ



    (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,
    exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
    siRNAs from OriGene, QIAGEN, shRNA from OriGene, microRNA from QIAGEN, SwitchGear Genomics,
    Tagged/untagged cDNA clones from OriGene, GenScript, DNA2.0, Vector BioLabs, and/or Addgene, Primers from OriGene, and/or QIAGEN, Flow cytometry from eBioscience )
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    REFSEQ mRNAs for SGCZ gene: 
    NM_139167.2  

    2 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000382080(uc010lss.3 uc003wwq.3) ENST00000421524
    miRNA
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    Selected qRT-PCR Assays for microRNAs that regulate SGCZ (see all 12):
    hsa-miR-26a-2* hsa-miR-548d-3p hsa-miR-3611 hsa-miR-3647-3p hsa-miR-218 hsa-miR-4287 hsa-miR-513b hsa-miR-124
    SwitchGear 3'UTR luciferase reporter plasmidSGCZ 3' UTR sequence
    Inhib. RNA
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      QuantiTect SYBR Green Assays in human, mouse, rat SGCZ
      QuantiFast Probe-based Assays in human, mouse, rat SGCZ

    4 AceView cDNA sequences:

    BC069459 AY028700 NM_139167 BE503781 

    GeneLoc Exon Structure


    (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™, Protein expression images according to data from SPIRE 1MOPED, 2PaxDb, and 3MaxQB, plus additional links to SOURCE, and/or BioGPS, and/or UniProtKB,
    PCR Arrays from QIAGEN, Primers from OriGene, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
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    SGCZ expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: GTTTTTAACA
    SGCZ Expression
    About this image

    SGCZ Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

    SGCZ Protein Expression
        Custom PCR Arrays for SGCZ
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    In Situ
    Assay Products:
     

     
    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for SGCZ

    (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)
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    This gene was present in the common ancestor of animals.

    Orthologs for SGCZ gene from Selected species (see all 13)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Sgcz1 , 5 sarcoglycan zeta1, 5 90.03(n)1
    94.86(a)1
      8 (23.31 cM)5
    2444311  NM_145841.21  NP_665840.21 
     375222985 
    chicken
    (Gallus gallus)
    Aves SGCZ1 sarcoglycan, zeta 83.66(n)
    91.12(a)
      422739  XM_429984.4  XP_429984.4 
    lizard
    (Anolis carolinensis)
    Reptilia SGCZ6
    sarcoglycan, zeta
    89(a)
    1 ↔ 1
    5(106264055-106652694)
    tropical clawed frog
    (Xenopus tropicalis)
    Amphibia sgcz1 sarcoglycan, zeta 77.74(n)
    82.21(a)
      100486888  XM_002934665.2  XP_002934711.1 
    zebrafish
    (Danio rerio)
    Actinopterygii LOC1003341261 zeta-sarcoglycan-like 69.01(n)
    73.91(a)
      100334126  XM_002660401.2  XP_002660447.1 
    fruit fly
    (Drosophila melanogaster)
    Insecta Scgdelta6
    Sarcoglycan delta
    26(a)
    1 → many
    X(1639909-1648096)
    worm
    (Caenorhabditis elegans)
    Secernentea sgn-16
    Protein SGN-1 (sgn-1) mRNA, complete cds
    29(a)
    1 → many
    II(8782005-8783639) WBGene00004790


    ENSEMBL Gene Tree for SGCZ (if available)
    TreeFam Gene Tree for SGCZ (if available)

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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    Paralogs for SGCZ gene
    SGCG2  SGCD2  
    2 SIMAP similar genes for SGCZ using alignment to 2 protein entries:     SGCZ_HUMAN (see all proteins):
    SGCD    SGCG

    Find genes that share paralogs with SGCZ           About GenesLikeMe



    (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), the Human Cytochrome P450 Allele Nomenclature Database, and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers, Cancer Mutation PCR Arrays and Assays, and Copy Number PCR Arrays from QIAGEN)
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    Selected SNPs for SGCZ (see all 34659)    About this table                                 

    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 8 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs1402568401,2
    C--12494793(+) GATGG-/TTTTTT 1 -- int10--------
    rs342062201,2
    C--12500361(+) ATATA-/ATTA  
            
    TTATA
    1 -- int10--------
    rs2018679891,2
    C--12500386(+) TTTCA-/AATAATAT 1 -- int10--------
    rs132616281,2
    C--12500392(+) ATAATG/ATATTA 1 -- int14Minor allele frequency- A:0.48NA 126
    rs19731691,2
    C,H--12502078(-) tatatA/Gtatat 1 -- int10--------
    rs2012901171,2
    --12502090(+) TATAT-/ATATAA
            
    TTTTT
    1 -- int10--------
    rs114701631,2
    C--12503279(+) ACACA-/C/CA  
            
    ACACA
    1 -- int11NA 2
    rs2004034121,2
    C--12503279(+) ACACAA/CAACAC 1 -- int10--------
    rs2011908981,2
    C--12503280(+) CACACA/CACACA 1 -- int10--------
    rs58895161,2
    C--12504345(+) TTCTG-/TTTTTT 1 -- int10--------

    HapMap Linkage Disequilibrium report for SGCZ (13947373 - 14197373 bp, first 250kb of SGCZ)

    Structural Variations
         Database of Genomic Variants (DGV) Selected variations for SGCZ (see all 160):    About this table    
    Variant IDTypeSubtypePubMed ID
    esv2736654CNV Deletion23290073
    esv2736646CNV Deletion23290073
    esv2674136CNV Deletion23128226
    esv2421743CNV Deletion20811451
    esv2736650CNV Deletion23290073
    esv2657342CNV Deletion23128226
    esv2661741CNV Deletion23128226
    esv2659369CNV Deletion23128226
    esv1232453CNV Deletion17803354
    esv2736648CNV Deletion23290073

    Human Gene Mutation Database (HGMD): SGCZ
    Locus Specific Mutation Databases (LSDB): SGCZ

    Site Specific Mutation Identification with PCR Assays
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    (in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
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    OMIM gene information: 608113    OMIM disorders: --

    1 disease for SGCZ:    
    About MalaCards
    generalized epilepsy with febrile seizures plus


    Find genes that share disorders with SGCZ           About GenesLikeMe

    Genetic Association Database (GAD): SGCZ
    Human Genome Epidemiology (HuGE) Navigator: SGCZ (4 documents)

    Export disorders for SGCZ gene to outside databases

    (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)
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    PubMed articles for SGCZ gene, integrated from 10 sources (see all 23):
    (articles sorted by number of sources associating them with SGCZ)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. Genome-wide meta-analyses identifies seven loci associated with platelet aggregation in response to agonists. (PubMed id 20526338)1, 4 Johnson A.D....Becker L.C. (Nat. Genet. 2010)
    2. Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score. (PubMed id 20379614)1, 4 Rose J.E....Uhl G.R. (Mol. Med. 2010)
    3. Candidate-gene testing for orphan limb-girdle muscular dystrophies. (PubMed id 19472918)1, 4 Aurino S....Nigro V. (Acta Myol 2008)
    4. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PubMed id 15489334)1, 2 Gerhard D.S.... Malek J. (Genome Res. 2004)
    5. Zeta-sarcoglycan, a novel component of the sarcoglycan complex, is reduced in muscular dystrophy. (PubMed id 12189167)1, 3 Wheeler M.T....McNally E.M. (Hum. Mol. Genet. 2002)
    6. Loci associated with N-glycosylation of human immunoglobulin G show pleiotropy with autoimmune diseases and haematological cancers. (PubMed id 23382691)1 Lauc G....Rudan I. (PLoS Genet. 2013)
    7. Evidence for shared genetic risk between methamphetamine-induced psychosis and schizophrenia. (PubMed id 23594818)1 Ikeda M....Iwata N. (Neuropsychopharmacology 2013)
    8. Novel genetic loci identified for the pathophysiology of childhood obesity in the Hispanic population. (PubMed id 23251661)1 Comuzzie A.G....Butte N.F. (PLoS ONE 2012)
    9. Copy number variations associated with obesity-related traits in African Americans: a joint analysis between GENOA and HyperGEN. (PubMed id 22836685)1 Zhao W....Sun Y.V. (Obesity (Silver Spring) 2012)
    10. Genome-wide association for smoking cessation success: participants in the Patch in Practice trial of nicotine replacement. (PubMed id 20235792)4 Uhl G.R....MunafA^ M.R. (Pharmacogenomics 2010)

    (in PubMed, OMIM, and NCBI Bookshelf)
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     ANDOR
    Aliases
    Free Text  

      Query String
    PubMed
    OMIM
    NCBI Bookshelf
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    (According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
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    Entrez Gene: 137868 HGNC: 14075 AceView: SGCZ Ensembl:ENSG00000185053 euGenes: HUgn137868
    ECgene: SGCZ H-InvDB: SGCZ

    (According to HUGE)
    About This Section

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      --

    (According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL, and/or others, e.g. Wikipedia and GeneReviews, via UniProtKB/Swiss-Prot)
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    NameDescription
    PharmGKB entry for SGCZ Pharmacogenomics, SNPs, Pathways

    (Patent information from GeneIP,
    Licensable technologies from WIS Yeda, Salk, Tufts,
    IP news from LifeMap Sciences, Inc.)
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    Patent Information for SGCZ gene:
    Search GeneIP for patents involving SGCZ

    GeneCards and IP:
    Japan Patent Office Licenses GeneCards     European Patent Office Licenses GeneCards     Improving the IP Search



    (Antibodies, recombinant proteins, and assays from EMD Millipore, R&D Systems, OriGene, QIAGEN, GenScript, Cell Signaling Technology, Novus Biologicals, Sino Biological, Enzo Life Sciences, Abcam, ProSpec, Cloud-Clone Corp., Thermo Fisher Scientific, LSBio, eBioscience, and/or others, Gene Editing from DNA2.0. Clones from OriGene, GenScript, Sino Biological, DNA2.0, SwitchGear Genomics, Vector BioLabs, Addgene, Cell lines from GenScript, and ESI BIO, Flow cytometery from eBioscience, PCR Arrays from QIAGEN, Drugs and/or compounds from EMD Millipore, Tocris Bioscience, Enzo Life Sciences, and/or ApexBio, In Situ Hybridization Assays from
    Advanced Cell Diagnostics, Animal models from inGenious Targeting Laboratory, genOway)
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