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SNAP47 Gene

protein-coding   GIFtS: 47
GCID: GC01P227917

Synaptosomal-Associated Protein, 47kDa

(Previous name: chromosome 1 open reading frame 142)
(Previous symbol: C1orf142)
  Search for SNAP47
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
Synaptosomal-Associated Protein, 47kDa1 2     SNAP-472 3
C1orf1421 2 3     SVAP12 3
Epididymis Luminal Protein 1702 3     Chromosome 1 Open Reading Frame 1421
Synaptosomal-Associated 47 KDa Protein2 3     Synaptosomal-Associated Protein 472
HEL1702 3     

External Ids:    HGNC: 306691   Entrez Gene: 1168412   Ensembl: ENSG000001437407   UniProtKB: Q5SQN13   

Export aliases for SNAP47 gene to outside databases

Previous GC identifers: GC01P225984 GC01P198439


(According to Entrez Gene, GeneCards, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
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GeneCards Summary for SNAP47 Gene:
SNAP47 (synaptosomal-associated protein, 47kDa) is a protein-coding gene.

UniProtKB/Swiss-Prot: SNP47_HUMAN, Q5SQN1
Function: Plays a role in intracellular membrane fusion (By similarity)




(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:
NC_000001.11  NT_167186.2  NC_018912.2  
Regulatory elements:
   Regulatory transcription factor binding sites in the SNAP47 gene promoter:
         LHX3b/Lhx3b   AML1a   AREB6   POU2F1   POU2F1a   FOXO4   Sox9   LHX3a/Lhx3a   ATF6   
         Other transcription factors

Browse SwitchGear Promoter luciferase reporter plasmids
   Search Chromatin IP Primers for SNAP47

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat SNAP47


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

Entrez Gene cytogenetic band: 1q42.13   Ensembl cytogenetic band:  1q42.13   HGNC cytogenetic band: 1q42.13

SNAP47 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
SNAP47 gene location

GeneLoc information about chromosome 1         GeneLoc Exon Structure

GeneLoc location for GC01P227917:  view genomic region     (about GC identifiers)

Start:
227,916,240 bp from pter      End:
227,968,932 bp from pter
Size:
52,693 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, and/or Cloud-Clone Corp.,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, and/or Cloud-Clone Corp., Antibodies by EMD Millipore, R&D Systems, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, LSBio, Abcam, and/or Cloud-Clone Corp.)
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UniProtKB/Swiss-Prot: SNP47_HUMAN, Q5SQN1 (See protein sequence)
Recommended Name: Synaptosomal-associated protein 47  
Size: 464 amino acids; 52562 Da
Subunit: Forms a complex containing SNAP47, VAMP2 and STX1A (By similarity). Associates with the BLOC-1 complex.
Interacts with BLOC1S6
Sequence caution: Sequence=BAB70779.1; Type=Erroneous initiation; Note=Translation N-terminally extended;
Secondary accessions: B6EDE0 Q5HYB5 Q5TBZ3 Q8N558 Q8TB31 Q8TCW8 Q8WV46 Q96CQ3 Q96FE1 Q96I66
Q96NU3 Q9BT10 Q9BVB2
Alternative splicing: 4 isoforms:  Q5SQN1-1   Q5SQN1-2   Q5SQN1-3   Q5SQN1-4   

Explore the universe of human proteins at neXtProt for SNAP47: NX_Q5SQN1

Explore proteomics data for SNAP47 at MOPED

Post-translational modifications: 

  • Modification sites at neXtProt
  • Modification sites at PhosphoSitePlus

  • See SNAP47 Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

    REFSEQ proteins: NP_444280.2  
    ENSEMBL proteins: 
     ENSP00000355722   ENSP00000355721   ENSP00000402730   ENSP00000411128   ENSP00000475207  
     ENSP00000314157  

    SNAP47 Human Recombinant Protein Products:

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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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    1 InterPro protein domain:
     IPR000727 T_SNARE_dom

    Graphical View of Domain Structure for InterPro Entry Q5SQN1

    ProtoNet protein and cluster: Q5SQN1

    UniProtKB/Swiss-Prot: SNP47_HUMAN, Q5SQN1
    Similarity: Belongs to the SVAP1 family
    Similarity: Contains 2 t-SNARE coiled-coil homology domains


    SNAP47 for domains           About GeneDecksing


    (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, and Vector BioLabs, Cell Lines from GenScript, ESI BIO, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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    Molecular Function:

         UniProtKB/Swiss-Prot Summary: SNP47_HUMAN, Q5SQN1
    Function: Plays a role in intracellular membrane fusion (By similarity)

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

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005515protein binding IPI19546860
         
    SNAP47 for ontologies           About GeneDecksing


    Phenotypes:
         2 MGI mutant phenotypes (inferred from 1 allele(MGI details for Snap47):
     hematopoietic system  skeleton 

    SNAP47 for phenotypes           About GeneDecksing

    Animal Models:
       inGenious Targeting Laboratory: Let us create your new Knockout/Knockin mouse model for SNAP47
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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
    SNP47_HUMAN, Q5SQN1: Endomembrane system (By similarity). Cytoplasm, perinuclear region (By similarity).
    Note=Appears to be exclusively membrane-bound (By similarity)
    Subcellular locations from COMPARTMENTS: 

    CompartmentConfidence
    nucleus3
    cytosol1

    Gene Ontology (GO): 4 cellular component terms:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0012505endomembrane system IEA--
    GO:0016020membrane IEA--
    GO:0031083colocalizes with BLOC-1 complex IDA19546860
    GO:0048471perinuclear region of cytoplasm IEA--

    SNAP47 for ontologies           About GeneDecksing


    (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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    SuperPaths for SNAP47 About    
    See pathways by source

    SuperPathContained pathways About
    1Nicotine Pathway (Dopaminergic Neuron), Pharmacodynamics
    SNARE interactions in vesicular transport0.40

    Pathways by source                                                                                                                                                                 See SuperPaths
    Show all pathways




    1 Kegg Pathway  (Kegg details for SNAP47):
        SNARE interactions in vesicular transport


    SNAP47 for pathways           About GeneDecksing

        Custom Pathway & Disease-focused RT2 Profiler PCR Arrays for SNAP47
    Interactions:

        Search GeneGlobe Interaction Network for SNAP47

    STRING Interaction Network Preview (showing 5 interactants - click image to see 25)

    Selected Interacting proteins for SNAP47 (Q5SQN13 ENSP000003557214) via UniProtKB, MINT, STRING, and/or I2D (see all 37)
    InteractantInteraction Details
    GeneCardExternal ID(s)
    NSFP464593I2D: score=1 
    SNAP29ENSP000002157304STRING: ENSP00000215730
    EXOC4ENSP000002538614STRING: ENSP00000253861
    YKT6ENSP000002233694STRING: ENSP00000223369
    EXOC2ENSP000002304494STRING: ENSP00000230449
    About this table

    (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 SNAP47 (SNP47)



    (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,
    Conferences by KenesGroup, 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, Primers from OriGene, and/or QIAGEN )
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    REFSEQ mRNAs for SNAP47 gene: 
    NM_053052.3  

    Unigene Cluster for SNAP47:

    Synaptosomal-associated protein, 47kDa
    Hs.325081  [show with all ESTs]
    Unigene Representative Sequence: AK054633
    12 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000480897(uc001hqx.4 uc001hqy.4) ENST00000480265 ENST00000475930
    ENST00000366760(uc001hra.2) ENST00000491439 ENST00000366759(uc001hrf.2)
    ENST00000418653(uc001hre.3) ENST00000426344(uc001hrd.3) ENST00000470038
    ENST00000606873 ENST00000478768 ENST00000315781
    miRNA
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      QuantiFast Probe-based Assays in human, mouse, rat SNAP47

    Additional mRNA sequence: 

    AK054633.1 AY090635.2 AY358188.1 BC001332.1 BC004418.1 BC007786.2 BC011145.1 BC014059.2 
    BC018760.1 BC025231.1 BX648570.1 FJ236305.1 

    18 DOTS entries:

    DT.95160338  DT.100834422  DT.100834433  DT.100834424  DT.100834442  DT.100834432  DT.100834441  DT.40298067 
    DT.100834444  DT.101965331  DT.100763515  DT.100834434  DT.91760117  DT.100834447  DT.91760118  DT.95160324 
    DT.425850  DT.95160318 

    Selected AceView cDNA sequences (see all 262):

    BQ671794 AW961059 Z42931 BQ719824 BC018760 T67723 AI611823 Z39049 
    BU849669 BM825317 T31965 BC025231 BU542842 BM560147 NM_053052 BM465127 
    CK904303 BM693158 AA393361 AY090635 BQ014791 AW013951 BC067081 AI553839 

    GeneLoc Exon Structure

    4 Alternative Splicing Database (ASD) splice patterns (SP) for SNAP47    About this scheme

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


    ECgene alternative splicing isoforms for SNAP47

    (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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    SNAP47 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: ACTGCATCTT
    SNAP47 Expression
    About this image


    SNAP47 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
     
     Neurons
             Mature Horizontal Cells Inner Nuclear Layer
     
     Eye (Sensory Organs)
             Mature Horizontal Cells Inner Nuclear Layer
    SNAP47 Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

    SNAP47 Protein Expression

    SOURCE GeneReport for Unigene cluster: Hs.325081
        Custom PCR Arrays for SNAP47
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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 chordates.

    Orthologs for SNAP47 gene from Selected species (see all 10)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Snap471 , 5 synaptosomal-associated protein, 471, 5 74.43(n)1
    68.2(a)1
      11 (37.70 cM)5
    678261  NM_144521.21  NP_653104.11 
     594071345 
    chicken
    (Gallus gallus)
    Aves SNAP471 synaptosomal-associated protein, 47kDa 67.15(n)
    60.91(a)
      420399  XM_004939091.1  XP_004939148.1 
    lizard
    (Anolis carolinensis)
    Reptilia SNAP476
    synaptosomal-associated protein, 47kDa
    58(a)
    1 ↔ 1
    GL343449.1(447546-480791)
    African clawed frog
    (Xenopus laevis)
    Amphibia 480295532   -- 81.91(n)    48029553 
    zebrafish
    (Danio rerio)
    Actinopterygii Dr.204822 Transcribed sequences 73.4(n)    57061762 


    ENSEMBL Gene Tree for SNAP47 (if available)
    TreeFam Gene Tree for SNAP47 (if available)

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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    (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 SNAP47 (see all 999)    About this table    
    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 1 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs1901859181,2
    --227925283(+) ATTTAC/TTCTTA 1 -- int10--------
    rs1385357741,2
    C--227925426(+) GGAGGA/GAGGAC 1 -- int10--------
    rs2017638321,2
    --227925506(+) GAGAG-/TTGTT 
     TTGGGGA
    TTGTT
    1 -- cds10--------
    rs1813370031,2
    --227925522(+) GATTGA/TGTGAT 1 -- int10--------
    rs2000261301,2
    C--227925522(+) ATTGT-/TTTG/TT
    TGGGGATTGT
    GTGAT
    2 -- int1 cds10--------
    rs781697141,2
    C,F--227925540(+) GTGCTA/GTGGTC 1 -- int12Minor allele frequency- G:0.13CSA WA 120
    rs2015122121,2
    C--227925573(-) TCACAA/CAAGCC 1 -- int10--------
    rs1864148791,2
    --227925603(+) ATTGGA/GGTTTT 1 -- int10--------
    rs1908020391,2
    --227925630(+) CAGAAA/TGTCTG 1 -- int10--------
    rs1402143731,2
    C--227925635(+) TGTCTA/GGAGAA 1 -- int10--------

    HapMap Linkage Disequilibrium report for SNAP47 (227916240 - 227968932 bp)

    Structural Variations
         Database of Genomic Variants (DGV) 6 variations for SNAP47:    About this table    
    Variant IDTypeSubtypePubMed ID
    esv2724217CNV Deletion23290073
    nsv873249CNV Loss21882294
    nsv515496CNV Loss19592680
    esv32853CNV Gain17666407
    esv8091CNV Gain19470904
    nsv826908CNV Gain20364138

    Site Specific Mutation Identification with PCR Assays
    SeqTarget long-range PCR primers for resequencing SNAP47
    DNA2.0 Custom Variant and Variant Library Synthesis for SNAP47

    (in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Conferences by KenesGroup, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
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    (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 SNAP47 gene, integrated from 10 sources (see all 12):
    (articles sorted by number of sources associating them with SNAP47)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. The dysbindin-containing complex (BLOC-1) in brain: developmental regulation, interaction with SNARE proteins and role in neurite outgrowth. (PubMed id 19546860)1, 2 Ghiani C.A....Dell'Angelica E.C. (Mol. Psychiatry 2010)
    2. Identification of SNAP-47, a novel Qbc-SNARE with ubiquitous expression. (PubMed id 16621800)1, 3 Holt M....Jahn R. (J. Biol. Chem. 2006)
    3. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PubMed id 14702039)1, 2 Ota T.... Sugano S. (Nat. Genet. 2004)
    4. The proteomic analysis of endogenous FAT10 substrates identifies p62/SQSTM1 as a substrate of FAT10ylation. (PubMed id 22797925)1 Aichem A....Groettrup M. (J. Cell. Sci. 2012)
    5. Systematic and quantitative assessment of the ubiquitin-modified proteome. (PubMed id 21906983)1 Kim W....Gygi S.P. (Mol. Cell 2011)
    6. Mass spectrometric analysis of lysine ubiquitylation reveals promiscuity at site level. (PubMed id 21139048)1 Danielsen J.M....Nielsen M.L. (amp 2011)
    7. Global identification of modular cullin-RING ligase substrates. (PubMed id 21963094)1 Emanuele M.J....Elledge S.J. (Cell 2011)
    8. The full-ORF clone resource of the German cDNA consortium. (PubMed id 17974005)2 Bechtel S.... Schupp I. (BMC Genomics 2007)
    9. The DNA sequence and biological annotation of human chromosome 1. (PubMed id 16710414)2 Gregory S.G.... Bentley D.R. (Nature 2006)
    10. 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)

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

      Query String
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    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: 116841 HGNC: 30669 AceView: IMAGE3451454 Ensembl:ENSG00000143740 euGenes: HUgn116841
    ECgene: SNAP47 Kegg: 116841 H-InvDB: SNAP47

    (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 SNAP47 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 SNAP47 gene:
    Search GeneIP for patents involving SNAP47

    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, Gene Editing from DNA2.0. Clones from OriGene, GenScript, Sino Biological, DNA2.0, SwitchGear Genomics, Vector BioLabs, Cell lines from GenScript, and ESI BIO, PCR Arrays from QIAGEN, Drugs and/or compounds from EMD Millipore, Tocris Bioscience, Enzo Life Sciences, and/or ApexBio, In Situ Hybridization Assays from
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