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P08247 (SYPH_HUMAN) Reviewed, UniProtKB/Swiss-Prot

Last modified April 16, 2014. Version 127. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (5) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Web links·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended name:
Synaptophysin
Alternative name(s):
Major synaptic vesicle protein p38
Gene names
Name:SYP
OrganismHomo sapiens (Human) [Reference proteome]
Taxonomic identifier9606 [NCBI]
Taxonomic lineageEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo

Protein attributes

Sequence length313 AA.
Sequence statusComplete.
Protein existenceEvidence at protein level

General annotation (Comments)

Function

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.

Subunit structure

Homohexamer or homotetramer. Interacts with SRCIN1. Ref.7

Subcellular location

Cytoplasmic vesiclesecretory vesiclesynaptic vesicle membrane; Multi-pass membrane protein. Cell junctionsynapsesynaptosome.

Tissue specificity

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.

Domain

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

Post-translational modification

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

Involvement in disease

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.
Note: The disease is caused by mutations affecting the gene represented in this entry. Ref.8

Sequence similarities

Belongs to the synaptophysin/synaptobrevin family.

Contains 1 MARVEL domain.

Ontologies

Keywords
   Cellular componentCell junction
Cytoplasmic vesicle
Membrane
Synapse
Synaptosome
   Coding sequence diversityPolymorphism
   DiseaseDisease mutation
Mental retardation
   DomainRepeat
Transmembrane
Transmembrane helix
   LigandCalcium
   PTMGlycoprotein
Phosphoprotein
Ubl conjugation
   Technical termComplete proteome
Reference proteome
Gene Ontology (GO)
   Biological_processcellular response to organic substance

Inferred from electronic annotation. Source: Ensembl

endocytosis

Inferred from sequence or structural similarity. Source: UniProtKB

regulation of long-term neuronal synaptic plasticity

Inferred from sequence or structural similarity. Source: UniProtKB

regulation of neuronal synaptic plasticity

Inferred from Biological aspect of Ancestor. Source: RefGenome

regulation of opioid receptor signaling pathway

Inferred from sequence or structural similarity. Source: UniProtKB

regulation of short-term neuronal synaptic plasticity

Inferred from sequence or structural similarity. Source: UniProtKB

synaptic vesicle maturation

Non-traceable author statement PubMed 10620806. Source: UniProtKB

synaptic vesicle membrane organization

Non-traceable author statement PubMed 10620806. Source: UniProtKB

   Cellular_componentcell junction

Inferred from electronic annotation. Source: UniProtKB-KW

excitatory synapse

Inferred from electronic annotation. Source: Ensembl

integral component of synaptic vesicle membrane

Non-traceable author statement Ref.2. Source: UniProtKB

neuron projection terminus

Inferred from electronic annotation. Source: Ensembl

presynaptic active zone

Inferred from electronic annotation. Source: Ensembl

presynaptic membrane

Inferred from electronic annotation. Source: Ensembl

protein complex

Inferred from electronic annotation. Source: Ensembl

   Molecular_functioncholesterol binding

Inferred from direct assay PubMed 10620806. Source: UniProtKB

transporter activity

Inferred from electronic annotation. Source: InterPro

Complete GO annotation...

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 313313Synaptophysin
PRO_0000179161

Regions

Topological domain1 – 2525Cytoplasmic Potential
Transmembrane26 – 4924Helical; Potential
Topological domain50 – 10657Vesicular Potential
Transmembrane107 – 13024Helical; Potential
Topological domain131 – 1377Cytoplasmic Potential
Transmembrane138 – 16124Helical; Potential
Topological domain162 – 19938Vesicular Potential
Transmembrane200 – 22324Helical; Potential
Topological domain224 – 31390Cytoplasmic Potential
Domain21 – 227207MARVEL
Region254 – 30552Repeats, Gly-rich

Amino acid modifications

Modified residue811Phosphotyrosine By similarity
Glycosylation591N-linked (GlcNAc...) Potential

Natural variations

Natural variant21L → Q. Ref.8
VAR_062983
Natural variant1581S → L. Ref.8
VAR_062984
Natural variant1661D → N. Ref.8
VAR_062985
Natural variant2171G → R in MRXSYP. Ref.8
VAR_062986
Natural variant2481D → N. Ref.8
VAR_062987
Natural variant2771D → E in an individual affected by mental retardation; unknown pathological role. Ref.8
VAR_062988
Natural variant2931G → S in an individual affected by mental retardation; unknown pathological role. Ref.8
Corresponds to variant rs139475570 [ dbSNP | Ensembl ].
VAR_062989

Experimental info

Sequence conflict1961P → L in AAH64550. Ref.6

Sequences

Sequence LengthMass (Da)Tools
P08247 [UniParc].

Last modified August 1, 1991. Version 3.
Checksum: 592289C43B12EFA7

FASTA31333,845
        10         20         30         40         50         60 
MLLLADMDVV NQLVAGGQFR VVKEPLGFVK VLQWVFAIFA FATCGSYSGE LQLSVDCANK 

        70         80         90        100        110        120 
TESDLSIEVE FEYPFRLHQV YFDAPTCRGG TTKVFLVGDY SSSAEFFVTV AVFAFLYSMG 

       130        140        150        160        170        180 
ALATYIFLQN KYRENNKGPM LDFLATAVFA FMWLVSSSAW AKGLSDVKMA TDPENIIKEM 

       190        200        210        220        230        240 
PVCRQTGNTC KELRDPVTSG LNTSVVFGFL NLVLWVGNLW FVFKETGWAA PFLRAPPGAP 

       250        260        270        280        290        300 
EKQPAPGDAY GDAGYGQGPG GYGPQDSYGP QGGYQPDYGQ PAGSGGSGYG PQGDYGQQGY 

       310 
GPQGAPTSFS NQM 

« Hide

References

« Hide 'large scale' references
[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. expand/collapse author list , 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]Mural R.J., Istrail S., Sutton G.G., Florea L., Halpern A.L., Mobarry C.M., Lippert R., Walenz B., Shatkay H., Dew I., Miller J.R., Flanigan M.J., Edwards N.J., Bolanos R., Fasulo D., Halldorsson B.V., Hannenhalli S., Turner R. expand/collapse author list , Yooseph S., Lu F., Nusskern D.R., Shue B.C., Zheng X.H., Zhong F., Delcher A.L., Huson D.H., Kravitz S.A., Mouchard L., Reinert K., Remington K.A., Clark A.G., Waterman M.S., Eichler E.E., Adams M.D., Hunkapiller M.W., Myers E.W., Venter J.C.
Submitted (JUL-2005) to the EMBL/GenBank/DDBJ databases
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. expand/collapse author list , 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.
+Additional computationally mapped references.

Web resources

Wikipedia

Synaptophysin entry

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
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.
PIRA35699.
RefSeqNP_003170.1. NM_003179.2.
UniGeneHs.632804.

3D structure databases

ProteinModelPortalP08247.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

BioGrid112721. 10 interactions.
IntActP08247. 1 interaction.
STRING9606.ENSP00000263233.

PTM databases

PhosphoSiteP08247.

Polymorphism databases

DMDM135162.

Proteomic databases

PaxDbP08247.
PRIDEP08247.

Protocols and materials databases

DNASU6855.
StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblENST00000263233; ENSP00000263233; ENSG00000102003.
ENST00000479808; ENSP00000418169; ENSG00000102003.
ENST00000594524; ENSP00000470571; ENSG00000268353.
ENST00000599440; ENSP00000473186; ENSG00000268353.
GeneID6855.
KEGGhsa:6855.
UCSCuc004dmz.1. human.

Organism-specific databases

CTD6855.
GeneCardsGC0XM049044.
H-InvDBHIX0203320.
HGNCHGNC:11506. SYP.
HPACAB000076.
CAB055505.
HPA002858.
MIM300802. phenotype.
313475. gene.
neXtProtNX_P08247.
Orphanet777. X-linked non-syndromic intellectual deficit.
PharmGKBPA36288.
GenAtlasSearch...

Phylogenomic databases

eggNOGNOG82723.
HOGENOMHOG000252913.
HOVERGENHBG006681.
InParanoidP08247.
OMAAYGDAGY.
PhylomeDBP08247.
TreeFamTF315804.

Gene expression databases

ArrayExpressP08247.
BgeeP08247.
CleanExHS_SYP.
GenevestigatorP08247.

Family and domain databases

InterProIPR008253. Marvel.
IPR001285. Synaptophysin/porin.
IPR028714. SYP.
[Graphical view]
PANTHERPTHR10306. PTHR10306. 1 hit.
PTHR10306:SF10. PTHR10306:SF10. 1 hit.
PfamPF01284. MARVEL. 1 hit.
[Graphical view]
PRINTSPR00220. SYNAPTOPHYSN.
PROSITEPS51225. MARVEL. 1 hit.
PS00604. SYNAPTOP. 1 hit.
[Graphical view]
ProtoNetSearch...

Other

ChiTaRSSYP. human.
GeneWikiSynaptophysin.
GenomeRNAi6855.
NextBio26757.
PROP08247.
SOURCESearch...

Entry information

Entry nameSYPH_HUMAN
AccessionPrimary (citable) accession number: P08247
Secondary accession number(s): B2R7L6, Q6P2F7
Entry history
Integrated into UniProtKB/Swiss-Prot: August 1, 1988
Last sequence update: August 1, 1991
Last modified: April 16, 2014
This is version 127 of the entry and version 3 of the sequence. [Complete history]
Entry statusReviewed (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.

Relevant documents

SIMILARITY comments

Index of protein domains and families

MIM cross-references

Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot

Human polymorphisms and disease mutations

Index of human polymorphisms and disease mutations

Human entries with polymorphisms or disease mutations

List of human entries with polymorphisms or disease mutations

Human chromosome X

Human chromosome X: entries, gene names and cross-references to MIM