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SYNGR4 Gene

protein-coding   GIFtS: 45
GCID: GC19P048867

Synaptogyrin 4

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(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
Synaptogyrin 41 2
synaptogyrin-42

External Ids:    HGNC: 115021   Entrez Gene: 235462   Ensembl: ENSG000001054677   OMIM: 6083735   UniProtKB: O954733   

Export aliases for SYNGR4 gene to outside databases

Previous GC identifers: GC19P049513 GC19P049235 GC19P053543 GC19P053559 GC19P045248


(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 SYNGR4 Gene:
This gene encodes an integral membrane protein. The gene belongs to the synaptogyrin gene family. Like other
members of the family the protein contains four transmembrane regions. The exact function of this protein is
unclear. (provided by RefSeq, Jul 2008)

GeneCards Summary for SYNGR4 Gene:
SYNGR4 (synaptogyrin 4) is a protein-coding gene. An important paralog of this gene is SYNGR1.




(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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RefSeq DNA sequence at NCBI GenBank:
NC_000019.9  NT_011109.17  NC_018930.2  
Regulatory elements:
   Regulatory transcription factor binding sites in the SYNGR4 gene promoter:
         SRF   NF-1   p53   SRF (504 AA)   YY1   Meis-1b   Arnt   Meis-1a   ZID   Meis-1   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidSYNGR4 promoter sequence
   Search Chromatin IP Primers for SYNGR4

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat SYNGR4


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

Entrez Gene cytogenetic band: 19q13.3   Ensembl cytogenetic band:  19q13.33   HGNC cytogenetic band: 19q13.3

SYNGR4 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
SYNGR4 gene location

GeneLoc information about chromosome 19         GeneLoc Exon Structure

GeneLoc location for GC19P048867:  view genomic region     (about GC identifiers)

Start:
48,867,651 bp from pter      End:
48,879,634 bp from pter
Size:
11,984 bases      Orientation:
plus 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: SNG4_HUMAN, O95473 (See protein sequence)
Recommended Name: Synaptogyrin-4  
Size: 234 amino acids; 25820 Da
Secondary accessions: Q3KP58

Explore the universe of human proteins at neXtProt for SYNGR4: NX_O95473

Explore proteomics data for SYNGR4 at MOPED

Post-translational modifications: 

  • Modification sites at neXtProt
  • Modification sites at PhosphoSitePlus

  • See SYNGR4 Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

    REFSEQ proteins: NP_036583.2  
    ENSEMBL proteins: 
     ENSP00000344041   ENSP00000469900   ENSP00000472198   ENSP00000469430  

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    (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:
     IPR016579 Synaptogyrin
     IPR008253 Marvel

    Graphical View of Domain Structure for InterPro Entry O95473

    ProtoNet protein and cluster: O95473

    1 Blocks protein domain: IPB008253 Marvel

    UniProtKB/Swiss-Prot: SNG4_HUMAN, O95473
    Similarity: Belongs to the synaptogyrin family
    Similarity: Contains 1 MARVEL domain


    Find genes that share domains with SYNGR4           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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    Animal Models:
       inGenious Targeting Laboratory: Let us create your new Knockout/Knockin mouse model for SYNGR4
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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
    SNG4_HUMAN, O95473: Membrane; Multi-pass membrane protein
    Subcellular locations from COMPARTMENTS: 

    CompartmentConfidence
    plasma membrane3
    cytosol1
    nucleus1

    Gene Ontology (GO): 2 cellular component terms:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0016020membrane ----
    GO:0016021integral component of membrane IEA--

    Find genes that share ontologies with SYNGR4           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 SYNGR4
    Interactions:

        Search GeneGlobe Interaction Network for SYNGR4

    (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
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    Browse Tocris compounds for SYNGR4 (SNG4)



    (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 SYNGR4 gene: 
    NM_012451.3  

    Unigene Cluster for SYNGR4:

    Synaptogyrin 4
    Hs.408333  [show with all ESTs]
    Unigene Representative Sequence: NM_012451
    4 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000344846(uc002piz.3) ENST00000600863 ENST00000601610 ENST00000595322

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    Additional mRNA sequence: 

    AJ011733.1 BC106891.2 

    1 DOTS entry:

    DT.206820 

    23 AceView cDNA sequences:

    NM_012451 AA953389 AI081072 AI222412 AJ011733 BM792897 AI582272 BM854750 
    BM797584 BV176232 BF508220 AI032366 AI214923 AA835071 BG219279 AA551879 
    BG720827 AA719355 AI214645 AA442893 AA442228 AA971366 AW662802 

    GeneLoc Exon Structure

    5 Alternative Splicing Database (ASD) splice patterns (SP) for SYNGR4    About this scheme

    ExUns: 1 ^ 2 ^ 3 ^ 4 ^ 5 ^ 6a · 6b · 6c ^ 7 ^ 8a · 8b
    SP1:                                                                  
    SP2:              -     -                                             
    SP3:              -     -                             -               
    SP4:                    -                                             
    SP5:                                -     -     -     -               


    ECgene alternative splicing isoforms for SYNGR4

    (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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    SYNGR4 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: --
    SYNGR4 Expression
    About this image


    SYNGR4 expression in embryonic tissues and stem cells    About this table
    Data from LifeMap, the Embryonic Development and Stem Cells Database
     selected tissues (see all 2) fully expand
     
     Skeletal Muscle (Muscoskeletal System)    fully expand to see all 2 entries
             Myoblasts Mandibular Arch Muscles
     
     Testis (Reproductive System)
    SYNGR4 Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

    SYNGR4 Protein Expression

    SOURCE GeneReport for Unigene cluster: Hs.408333
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    In Situ
    Assay Products:
     

     
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    (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 SYNGR4 gene from Selected species (see all 10)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Syngr41 , 5 synaptogyrin 41, 5 79.97(n)1
    73.39(a)1
      7 (29.58 cM)5
    588671  NM_021482.21  NP_067457.21 
     458852225 
    lizard
    (Anolis carolinensis)
    Reptilia SYNGR46
    synaptogyrin 4
    46(a)
    1 ↔ 1
    GL343329.1(145517-157230)
    fruit fly
    (Drosophila melanogaster)
    Insecta synaptogyrin6
    synaptogyrin
    19(a)
    1 → many
    2R(9729255-9733757)
    worm
    (Caenorhabditis elegans)
    Secernentea sng-16
    Protein SNG-1 (sng-1) mRNA, complete cds
    19(a)
    1 → many
    X(7327605-7329677) WBGene00004912


    ENSEMBL Gene Tree for SYNGR4 (if available)
    TreeFam Gene Tree for SYNGR4 (if available)

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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    Paralogs for SYNGR4 gene
    SYNGR12  SYNGR32  SYNGR22  
    3 SIMAP similar genes for SYNGR4 using alignment to 4 protein entries:     SNG4_HUMAN (see all proteins):
    SYNGR3    SYNGR2    SYNGR1

    Find genes that share paralogs with SYNGR4           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 SYNGR4 (see all 293)    About this table                                 

    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 19 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs762422621,2
    C,F--48869244(+) AGGAGC/TTCTCA 1 -- int12Minor allele frequency- T:0.04CSA WA 120
    rs751094261,2
    C,F--48869356(+) ACTATA/GGGCCC 1 -- int12Minor allele frequency- G:0.18CSA WA 120
    rs798401051,2
    C,F--48869440(+) TGAGAT/CAACAA 1 -- int11Minor allele frequency- C:0.12EA 120
    rs1893781431,2
    --48869601(+) GAGATA/CATACC 1 -- int10--------
    rs2012933471,2
    --48869654(+) AAAAA-/AA    
       AAAAG
    AAAAA
    1 -- int10--------
    rs1462197061,2
    --48869725(+) GTGGCA/GTGATC 1 -- int10--------
    rs1813921471,2
    --48869734(+) TCTCCA/GCTCAC 1 -- int10--------
    rs118818841,2
    C,F,H--48869812(+) tgtgcA/Gccact 1 -- int11Minor allele frequency- G:0.00NA 2
    rs1120053531,2
    F--48869851(+) AGAGAC/TGGGGT 1 -- int11Minor allele frequency- T:0.00CSA 1
    rs284750451,2
    F--48869905(+) TGTTCC/TGCCCA 1 -- int11Minor allele frequency- T:0.00CSA 1

    HapMap Linkage Disequilibrium report for SYNGR4 (48867651 - 48879634 bp)

    Structural Variations
         Database of Genomic Variants (DGV) 5 variations for SYNGR4:    About this table    
    Variant IDTypeSubtypePubMed ID
    esv2718675CNV Deletion23290073
    nsv912219CNV Loss21882294
    nsv833854CNV Loss17160897
    esv34181CNV Loss18971310
    nsv9739CNV Gain+Loss18304495

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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: 608373    OMIM disorders: --


    Find genes that share disorders with SYNGR4           About GenesLikeMe


    Export disorders for SYNGR4 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 SYNGR4 gene integrated from 10 sources:
    (articles sorted by number of sources associating them with SYNGR4)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. Pathway Analysis of ChIP-Seq-Based NRF1 Target Genes Suggests a Logical Hypothesis of their Involvement in the Pathogenesis of Neurodegenerative Diseases. (PubMed id 24250222)1 Satoh J....Yamamoto Y. (Gene Regul Syst Bio 2013)
    2. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PubMed id 15489334)2 Gerhard D.S.... Malek J. (Genome Res. 2004)
    3. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. (PubMed id 12477932)1 Strausberg R.L....Marra M.A. (Proc. Natl. Acad. Sci. U.S.A. 2002)
    4. A transcript map of the chromosome 19q-Arm glioma tumor suppressor region. (PubMed id 10708517)1 Smith J.S.... Jenkins R.B. (Genomics 2000)
    5. Characterization of the human synaptogyrin gene family. (PubMed id 9760194)1 Kedra D....Dumanski J.P. (Hum. Genet. 1998)
    6. (PubMed id )2 

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

      Query String
    PubMed
    OMIM
    NCBI Bookshelf
      (Note: In FireFox, select the above section and copy using Ctrl-C)

    (According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
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    Entrez Gene: 23546 HGNC: 11502 AceView: SYNGR4 Ensembl:ENSG00000105467 euGenes: HUgn23546
    ECgene: SYNGR4 H-InvDB: SYNGR4

    (According to HUGE)
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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 SYNGR4 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 SYNGR4 gene:
    Search GeneIP for patents involving SYNGR4

    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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