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P08247

- SYPH_HUMAN

UniProt

P08247 - SYPH_HUMAN

Protein

Synaptophysin

Gene

SYP

Organism
Homo sapiens (Human)
Status
Reviewed - Annotation score: 5 out of 5- Experimental evidence at protein leveli
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    • History
      Entry version 132 (01 Oct 2014)
      Sequence version 3 (01 Aug 1991)
      Previous versions | rss
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    Functioni

    Possibly involved in structural functions as organizing other membrane components or in targeting the vesicles to the plasma membrane. Involved in the regulation of short-term and long-term synaptic plasticity By similarity.By similarity

    GO - Molecular functioni

    1. cholesterol binding Source: UniProtKB
    2. transporter activity Source: InterPro

    GO - Biological processi

    1. cellular response to organic substance Source: Ensembl
    2. endocytosis Source: UniProtKB
    3. regulation of long-term neuronal synaptic plasticity Source: UniProtKB
    4. regulation of neuronal synaptic plasticity Source: RefGenome
    5. regulation of opioid receptor signaling pathway Source: UniProtKB
    6. regulation of short-term neuronal synaptic plasticity Source: UniProtKB
    7. synaptic vesicle maturation Source: UniProtKB
    8. synaptic vesicle membrane organization Source: UniProtKB

    Keywords - Ligandi

    Calcium

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Synaptophysin
    Alternative name(s):
    Major synaptic vesicle protein p38
    Gene namesi
    Name:SYP
    OrganismiHomo sapiens (Human)
    Taxonomic identifieri9606 [NCBI]
    Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
    ProteomesiUP000005640: Chromosome X

    Organism-specific databases

    HGNCiHGNC:11506. SYP.

    Subcellular locationi

    GO - Cellular componenti

    1. cell junction Source: UniProtKB-KW
    2. excitatory synapse Source: Ensembl
    3. integral component of synaptic vesicle membrane Source: UniProtKB
    4. neuron projection Source: ParkinsonsUK-UCL
    5. neuron projection terminus Source: Ensembl
    6. presynaptic active zone Source: Ensembl
    7. presynaptic membrane Source: Ensembl
    8. protein complex Source: Ensembl

    Keywords - Cellular componenti

    Cell junction, Cytoplasmic vesicle, Membrane, Synapse, Synaptosome

    Pathology & Biotechi

    Involvement in diseasei

    Mental retardation, X-linked, SYP-related (MRXSYP) [MIM:300802]: A disorder characterized by significantly below average general intellectual functioning associated with impairments in adaptive behavior and manifested during the developmental period.1 Publication
    Note: The disease is caused by mutations affecting the gene represented in this entry.
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Natural varianti217 – 2171G → R in MRXSYP. 1 Publication
    VAR_062986

    Keywords - Diseasei

    Disease mutation, Mental retardation

    Organism-specific databases

    MIMi300802. phenotype.
    Orphaneti777. X-linked non-syndromic intellectual disability.
    PharmGKBiPA36288.

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 313313SynaptophysinPRO_0000179161Add
    BLAST

    Amino acid modifications

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Glycosylationi59 – 591N-linked (GlcNAc...)Sequence Analysis
    Modified residuei81 – 811PhosphotyrosineBy similarity

    Post-translational modificationi

    Ubiquitinated; mediated by SIAH1 or SIAH2 and leading to its subsequent proteasomal degradation.By similarity

    Keywords - PTMi

    Glycoprotein, Phosphoprotein, Ubl conjugation

    Proteomic databases

    MaxQBiP08247.
    PaxDbiP08247.
    PRIDEiP08247.

    PTM databases

    PhosphoSiteiP08247.

    Expressioni

    Tissue specificityi

    Characteristic of a type of small (30-80 nm) neurosecretory vesicles, including presynaptic vesicles, but also vesicles of various neuroendocrine cells of both neuronal and epithelial phenotype.

    Gene expression databases

    ArrayExpressiP08247.
    BgeeiP08247.
    CleanExiHS_SYP.
    GenevestigatoriP08247.

    Organism-specific databases

    HPAiCAB000076.
    CAB055505.
    HPA002858.

    Interactioni

    Subunit structurei

    Homohexamer or homotetramer. Interacts with SRCIN1.1 Publication

    Protein-protein interaction databases

    BioGridi112721. 9 interactions.
    IntActiP08247. 1 interaction.
    STRINGi9606.ENSP00000263233.

    Structurei

    3D structure databases

    ProteinModelPortaliP08247.
    ModBaseiSearch...
    MobiDBiSearch...

    Topological domain

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Topological domaini1 – 2525CytoplasmicSequence AnalysisAdd
    BLAST
    Topological domaini50 – 10657VesicularSequence AnalysisAdd
    BLAST
    Topological domaini131 – 1377CytoplasmicSequence Analysis
    Topological domaini162 – 19938VesicularSequence AnalysisAdd
    BLAST
    Topological domaini224 – 31390CytoplasmicSequence AnalysisAdd
    BLAST

    Transmembrane

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Transmembranei26 – 4924HelicalSequence AnalysisAdd
    BLAST
    Transmembranei107 – 13024HelicalSequence AnalysisAdd
    BLAST
    Transmembranei138 – 16124HelicalSequence AnalysisAdd
    BLAST
    Transmembranei200 – 22324HelicalSequence AnalysisAdd
    BLAST

    Family & Domainsi

    Domains and Repeats

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Domaini21 – 227207MARVELPROSITE-ProRule annotationAdd
    BLAST

    Region

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Regioni254 – 30552Repeats, Gly-richAdd
    BLAST

    Domaini

    The calcium-binding activity is thought to be localized in the cytoplasmic tail of the protein.

    Sequence similaritiesi

    Belongs to the synaptophysin/synaptobrevin family.Curated
    Contains 1 MARVEL domain.PROSITE-ProRule annotation

    Keywords - Domaini

    Repeat, Transmembrane, Transmembrane helix

    Phylogenomic databases

    eggNOGiNOG82723.
    HOGENOMiHOG000252913.
    HOVERGENiHBG006681.
    InParanoidiP08247.
    OMAiAYGDAGY.
    PhylomeDBiP08247.
    TreeFamiTF315804.

    Family and domain databases

    InterProiIPR008253. Marvel.
    IPR001285. Synaptophysin/porin.
    IPR028714. SYP.
    [Graphical view]
    PANTHERiPTHR10306. PTHR10306. 1 hit.
    PTHR10306:SF10. PTHR10306:SF10. 1 hit.
    PfamiPF01284. MARVEL. 1 hit.
    [Graphical view]
    PRINTSiPR00220. SYNAPTOPHYSN.
    PROSITEiPS51225. MARVEL. 1 hit.
    PS00604. SYNAPTOP. 1 hit.
    [Graphical view]

    Sequencei

    Sequence statusi: Complete.

    P08247-1 [UniParc]FASTAAdd to Basket

    « Hide

    MLLLADMDVV NQLVAGGQFR VVKEPLGFVK VLQWVFAIFA FATCGSYSGE    50
    LQLSVDCANK TESDLSIEVE FEYPFRLHQV YFDAPTCRGG TTKVFLVGDY 100
    SSSAEFFVTV AVFAFLYSMG ALATYIFLQN KYRENNKGPM LDFLATAVFA 150
    FMWLVSSSAW AKGLSDVKMA TDPENIIKEM PVCRQTGNTC KELRDPVTSG 200
    LNTSVVFGFL NLVLWVGNLW FVFKETGWAA PFLRAPPGAP EKQPAPGDAY 250
    GDAGYGQGPG GYGPQDSYGP QGGYQPDYGQ PAGSGGSGYG PQGDYGQQGY 300
    GPQGAPTSFS NQM 313
    Length:313
    Mass (Da):33,845
    Last modified:August 1, 1991 - v3
    Checksum:i592289C43B12EFA7
    GO

    Experimental Info

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Sequence conflicti196 – 1961P → L in AAH64550. (PubMed:15489334)Curated

    Natural variant

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Natural varianti2 – 21L → Q.1 Publication
    VAR_062983
    Natural varianti158 – 1581S → L.1 Publication
    VAR_062984
    Natural varianti166 – 1661D → N.1 Publication
    VAR_062985
    Natural varianti217 – 2171G → R in MRXSYP. 1 Publication
    VAR_062986
    Natural varianti248 – 2481D → N.1 Publication
    VAR_062987
    Natural varianti277 – 2771D → E in an individual affected by mental retardation; unknown pathological role. 1 Publication
    VAR_062988
    Natural varianti293 – 2931G → S in an individual affected by mental retardation; unknown pathological role. 1 Publication
    Corresponds to variant rs139475570 [ dbSNP | Ensembl ].
    VAR_062989

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    X06389 mRNA. Translation: CAA29686.1.
    U93305 Genomic DNA. Translation: AAB92358.1.
    AK313030 mRNA. Translation: BAG35863.1.
    CH471224 Genomic DNA. Translation: EAW50685.1.
    BC064550 mRNA. Translation: AAH64550.1.
    CCDSiCCDS14321.1.
    PIRiA35699.
    RefSeqiNP_003170.1. NM_003179.2.
    UniGeneiHs.632804.

    Genome annotation databases

    EnsembliENST00000263233; ENSP00000263233; ENSG00000102003.
    ENST00000479808; ENSP00000418169; ENSG00000102003.
    GeneIDi6855.
    KEGGihsa:6855.
    UCSCiuc004dmz.1. human.

    Polymorphism databases

    DMDMi135162.

    Keywords - Coding sequence diversityi

    Polymorphism

    Cross-referencesi

    Web resourcesi

    Wikipedia

    Synaptophysin entry

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    X06389 mRNA. Translation: CAA29686.1 .
    U93305 Genomic DNA. Translation: AAB92358.1 .
    AK313030 mRNA. Translation: BAG35863.1 .
    CH471224 Genomic DNA. Translation: EAW50685.1 .
    BC064550 mRNA. Translation: AAH64550.1 .
    CCDSi CCDS14321.1.
    PIRi A35699.
    RefSeqi NP_003170.1. NM_003179.2.
    UniGenei Hs.632804.

    3D structure databases

    ProteinModelPortali P08247.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    BioGridi 112721. 9 interactions.
    IntActi P08247. 1 interaction.
    STRINGi 9606.ENSP00000263233.

    PTM databases

    PhosphoSitei P08247.

    Polymorphism databases

    DMDMi 135162.

    Proteomic databases

    MaxQBi P08247.
    PaxDbi P08247.
    PRIDEi P08247.

    Protocols and materials databases

    DNASUi 6855.
    Structural Biology Knowledgebase Search...

    Genome annotation databases

    Ensembli ENST00000263233 ; ENSP00000263233 ; ENSG00000102003 .
    ENST00000479808 ; ENSP00000418169 ; ENSG00000102003 .
    GeneIDi 6855.
    KEGGi hsa:6855.
    UCSCi uc004dmz.1. human.

    Organism-specific databases

    CTDi 6855.
    GeneCardsi GC0XM049044.
    H-InvDB HIX0203320.
    HGNCi HGNC:11506. SYP.
    HPAi CAB000076.
    CAB055505.
    HPA002858.
    MIMi 300802. phenotype.
    313475. gene.
    neXtProti NX_P08247.
    Orphaneti 777. X-linked non-syndromic intellectual disability.
    PharmGKBi PA36288.
    GenAtlasi Search...

    Phylogenomic databases

    eggNOGi NOG82723.
    HOGENOMi HOG000252913.
    HOVERGENi HBG006681.
    InParanoidi P08247.
    OMAi AYGDAGY.
    PhylomeDBi P08247.
    TreeFami TF315804.

    Miscellaneous databases

    ChiTaRSi SYP. human.
    GeneWikii Synaptophysin.
    GenomeRNAii 6855.
    NextBioi 26757.
    PROi P08247.
    SOURCEi Search...

    Gene expression databases

    ArrayExpressi P08247.
    Bgeei P08247.
    CleanExi HS_SYP.
    Genevestigatori P08247.

    Family and domain databases

    InterProi IPR008253. Marvel.
    IPR001285. Synaptophysin/porin.
    IPR028714. SYP.
    [Graphical view ]
    PANTHERi PTHR10306. PTHR10306. 1 hit.
    PTHR10306:SF10. PTHR10306:SF10. 1 hit.
    Pfami PF01284. MARVEL. 1 hit.
    [Graphical view ]
    PRINTSi PR00220. SYNAPTOPHYSN.
    PROSITEi PS51225. MARVEL. 1 hit.
    PS00604. SYNAPTOP. 1 hit.
    [Graphical view ]
    ProtoNeti Search...

    Publicationsi

    1. "The cDNA and derived amino acid sequences for rat and human synaptophysin."
      Suedhof T.C., Lottspeich F., Greengard P., Mehl E., Jahn R.
      Nucleic Acids Res. 15:9607-9607(1987) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [MRNA].
    2. "Synaptophysin: structure of the human gene and assignment to the X chromosome in man and mouse."
      Oezcelik T., Lafreniere R.G., Archer B.T. III, Johnston P.A., Willard H.F., Francke U., Suedhof T.C.
      Am. J. Hum. Genet. 47:551-561(1990) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
    3. "Sequence-based exon prediction around the synaptophysin locus reveals a gene-rich area containing novel genes in human proximal Xp."
      Fisher S.E., Ciccodicola A., Tanaka K., Curci A., Desicato S., D'Urso M., Craig I.W.
      Genomics 45:340-347(1997) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
    4. "Complete sequencing and characterization of 21,243 full-length human cDNAs."
      Ota T., Suzuki Y., Nishikawa T., Otsuki T., Sugiyama T., Irie R., Wakamatsu A., Hayashi K., Sato H., Nagai K., Kimura K., Makita H., Sekine M., Obayashi M., Nishi T., Shibahara T., Tanaka T., Ishii S.
      , Yamamoto J., Saito K., Kawai Y., Isono Y., Nakamura Y., Nagahari K., Murakami K., Yasuda T., Iwayanagi T., Wagatsuma M., Shiratori A., Sudo H., Hosoiri T., Kaku Y., Kodaira H., Kondo H., Sugawara M., Takahashi M., Kanda K., Yokoi T., Furuya T., Kikkawa E., Omura Y., Abe K., Kamihara K., Katsuta N., Sato K., Tanikawa M., Yamazaki M., Ninomiya K., Ishibashi T., Yamashita H., Murakawa K., Fujimori K., Tanai H., Kimata M., Watanabe M., Hiraoka S., Chiba Y., Ishida S., Ono Y., Takiguchi S., Watanabe S., Yosida M., Hotuta T., Kusano J., Kanehori K., Takahashi-Fujii A., Hara H., Tanase T.-O., Nomura Y., Togiya S., Komai F., Hara R., Takeuchi K., Arita M., Imose N., Musashino K., Yuuki H., Oshima A., Sasaki N., Aotsuka S., Yoshikawa Y., Matsunawa H., Ichihara T., Shiohata N., Sano S., Moriya S., Momiyama H., Satoh N., Takami S., Terashima Y., Suzuki O., Nakagawa S., Senoh A., Mizoguchi H., Goto Y., Shimizu F., Wakebe H., Hishigaki H., Watanabe T., Sugiyama A., Takemoto M., Kawakami B., Yamazaki M., Watanabe K., Kumagai A., Itakura S., Fukuzumi Y., Fujimori Y., Komiyama M., Tashiro H., Tanigami A., Fujiwara T., Ono T., Yamada K., Fujii Y., Ozaki K., Hirao M., Ohmori Y., Kawabata A., Hikiji T., Kobatake N., Inagaki H., Ikema Y., Okamoto S., Okitani R., Kawakami T., Noguchi S., Itoh T., Shigeta K., Senba T., Matsumura K., Nakajima Y., Mizuno T., Morinaga M., Sasaki M., Togashi T., Oyama M., Hata H., Watanabe M., Komatsu T., Mizushima-Sugano J., Satoh T., Shirai Y., Takahashi Y., Nakagawa K., Okumura K., Nagase T., Nomura N., Kikuchi H., Masuho Y., Yamashita R., Nakai K., Yada T., Nakamura Y., Ohara O., Isogai T., Sugano S.
      Nat. Genet. 36:40-45(2004) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
      Tissue: Amygdala.
    5. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    6. "The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC)."
      The MGC Project Team
      Genome Res. 14:2121-2127(2004) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
      Tissue: Brain.
    7. "Characterization of a multidomain adaptor protein, p140Cap, as part of a pre-synaptic complex."
      Ito H., Atsuzawa K., Sudo K., Di Stefano P., Iwamoto I., Morishita R., Takei S., Semba R., Defilippi P., Asano T., Usuda N., Nagata K.
      J. Neurochem. 107:61-72(2008) [PubMed] [Europe PMC] [Abstract]
      Cited for: INTERACTION WITH SRCIN1.
    8. "A systematic, large-scale resequencing screen of X-chromosome coding exons in mental retardation."
      Tarpey P.S., Smith R., Pleasance E., Whibley A., Edkins S., Hardy C., O'Meara S., Latimer C., Dicks E., Menzies A., Stephens P., Blow M., Greenman C., Xue Y., Tyler-Smith C., Thompson D., Gray K., Andrews J.
      , Barthorpe S., Buck G., Cole J., Dunmore R., Jones D., Maddison M., Mironenko T., Turner R., Turrell K., Varian J., West S., Widaa S., Wray P., Teague J., Butler A., Jenkinson A., Jia M., Richardson D., Shepherd R., Wooster R., Tejada M.I., Martinez F., Carvill G., Goliath R., de Brouwer A.P., van Bokhoven H., Van Esch H., Chelly J., Raynaud M., Ropers H.H., Abidi F.E., Srivastava A.K., Cox J., Luo Y., Mallya U., Moon J., Parnau J., Mohammed S., Tolmie J.L., Shoubridge C., Corbett M., Gardner A., Haan E., Rujirabanjerd S., Shaw M., Vandeleur L., Fullston T., Easton D.F., Boyle J., Partington M., Hackett A., Field M., Skinner C., Stevenson R.E., Bobrow M., Turner G., Schwartz C.E., Gecz J., Raymond F.L., Futreal P.A., Stratton M.R.
      Nat. Genet. 41:535-543(2009) [PubMed] [Europe PMC] [Abstract]
      Cited for: VARIANT MRXSYP ARG-217, VARIANTS [LARGE SCALE ANALYSIS] GLN-2; LEU-158; ASN-166; ASN-248; GLU-277 AND SER-293.

    Entry informationi

    Entry nameiSYPH_HUMAN
    AccessioniPrimary (citable) accession number: P08247
    Secondary accession number(s): B2R7L6, Q6P2F7
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: August 1, 1988
    Last sequence update: August 1, 1991
    Last modified: October 1, 2014
    This is version 132 of the entry and version 3 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programChordata Protein Annotation Program
    DisclaimerAny medical or genetic information present in this entry is provided for research, educational and informational purposes only. It is not in any way intended to be used as a substitute for professional medical advice, diagnosis, treatment or care.

    Miscellaneousi

    Keywords - Technical termi

    Complete proteome, Reference proteome

    Documents

    1. Human chromosome X
      Human chromosome X: entries, gene names and cross-references to MIM
    2. Human entries with polymorphisms or disease mutations
      List of human entries with polymorphisms or disease mutations
    3. Human polymorphisms and disease mutations
      Index of human polymorphisms and disease mutations
    4. MIM cross-references
      Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot
    5. SIMILARITY comments
      Index of protein domains and families

    External Data

    Dasty 3