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Protein

Synaptophysin

Gene

SYP

Organism
Homo sapiens (Human)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

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

  • cholesterol binding Source: UniProtKB
  • protein self-association Source: ParkinsonsUK-UCL
  • transporter activity Source: InterPro

GO - Biological processi

Complete GO annotation...

Keywords - Ligandi

Calcium

Enzyme and pathway databases

BioCyciZFISH:ENSG00000102003-MONOMER.

Protein family/group databases

TCDBi9.B.130.1.4. the tetraspan vesicle membrane protein (tvp) family.

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
Proteomesi
  • UP000005640 Componenti: Chromosome X

Organism-specific databases

HGNCiHGNC:11506. SYP.

Subcellular locationi

Topology

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Topological domaini1 – 25CytoplasmicSequence analysisAdd BLAST25
Transmembranei26 – 49HelicalSequence analysisAdd BLAST24
Topological domaini50 – 106VesicularSequence analysisAdd BLAST57
Transmembranei107 – 130HelicalSequence analysisAdd BLAST24
Topological domaini131 – 137CytoplasmicSequence analysis7
Transmembranei138 – 161HelicalSequence analysisAdd BLAST24
Topological domaini162 – 199VesicularSequence analysisAdd BLAST38
Transmembranei200 – 223HelicalSequence analysisAdd BLAST24
Topological domaini224 – 313CytoplasmicSequence analysisAdd BLAST90

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Cell junction, Cytoplasmic vesicle, Membrane, Synapse, Synaptosome

Pathology & Biotechi

Involvement in diseasei

Mental retardation, X-linked, SYP-related (MRXSYP)1 Publication
The disease is caused by mutations affecting the gene represented in this entry.
Disease descriptionA disorder characterized by significantly below average general intellectual functioning associated with impairments in adaptive behavior and manifested during the developmental period.
See also OMIM:300802
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Natural variantiVAR_062986217G → R in MRXSYP. 1 PublicationCorresponds to variant rs137852561dbSNPEnsembl.1

Keywords - Diseasei

Disease mutation, Mental retardation

Organism-specific databases

DisGeNETi6855.
MalaCardsiSYP.
MIMi300802. phenotype.
OpenTargetsiENSG00000102003.
Orphaneti777. X-linked non-syndromic intellectual disability.
PharmGKBiPA36288.

Polymorphism and mutation databases

BioMutaiSYP.
DMDMi135162.

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00001791611 – 313SynaptophysinAdd BLAST313

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Glycosylationi59N-linked (GlcNAc...)Sequence analysis1
Modified residuei81PhosphotyrosineBy similarity1

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

EPDiP08247.
MaxQBiP08247.
PaxDbiP08247.
PeptideAtlasiP08247.
PRIDEiP08247.

PTM databases

iPTMnetiP08247.
PhosphoSitePlusiP08247.

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

BgeeiENSG00000102003.
CleanExiHS_SYP.
ExpressionAtlasiP08247. baseline and differential.
GenevisibleiP08247. HS.

Organism-specific databases

HPAiCAB000076.
CAB055505.
HPA002858.

Interactioni

Subunit structurei

Homohexamer or homotetramer. Interacts with SRCIN1.1 Publication

GO - Molecular functioni

  • protein self-association Source: ParkinsonsUK-UCL

Protein-protein interaction databases

BioGridi112721. 35 interactors.
IntActiP08247. 1 interactor.
STRINGi9606.ENSP00000263233.

Structurei

3D structure databases

ProteinModelPortaliP08247.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini21 – 227MARVELPROSITE-ProRule annotationAdd BLAST207

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni254 – 305Repeats, Gly-richAdd BLAST52

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

eggNOGiENOG410IDYC. Eukaryota.
ENOG4111J4N. LUCA.
GeneTreeiENSGT00390000010039.
HOGENOMiHOG000252913.
HOVERGENiHBG006681.
InParanoidiP08247.
OMAiGWAAPFM.
OrthoDBiEOG091G0ZEI.
PhylomeDBiP08247.
TreeFamiTF315804.

Family and domain databases

InterProiIPR008253. Marvel.
IPR001285. Synaptophysin/porin.
IPR028714. SYP.
[Graphical view]
PANTHERiPTHR10306. PTHR10306. 2 hits.
PTHR10306:SF10. PTHR10306:SF10. 2 hits.
PfamiPF01284. MARVEL. 1 hit.
[Graphical view]
PRINTSiPR00220. SYNAPTOPHYSN.
PROSITEiPS51225. MARVEL. 1 hit.
PS00604. SYNAPTOP. 1 hit.
[Graphical view]

Sequences (2)i

Sequence statusi: Complete.

This entry describes 2 isoformsi produced by alternative splicing. AlignAdd to basket

Isoform 1 (identifier: P08247-1) [UniParc]FASTAAdd to basket

This isoform has been chosen as the 'canonical' sequence. All positional information in this entry refers to it. This is also the sequence that appears in the downloadable versions of the entry.

« Hide

        10         20         30         40         50
MLLLADMDVV NQLVAGGQFR VVKEPLGFVK VLQWVFAIFA FATCGSYSGE
60 70 80 90 100
LQLSVDCANK TESDLSIEVE FEYPFRLHQV YFDAPTCRGG TTKVFLVGDY
110 120 130 140 150
SSSAEFFVTV AVFAFLYSMG ALATYIFLQN KYRENNKGPM LDFLATAVFA
160 170 180 190 200
FMWLVSSSAW AKGLSDVKMA TDPENIIKEM PVCRQTGNTC KELRDPVTSG
210 220 230 240 250
LNTSVVFGFL NLVLWVGNLW FVFKETGWAA PFLRAPPGAP EKQPAPGDAY
260 270 280 290 300
GDAGYGQGPG GYGPQDSYGP QGGYQPDYGQ PAGSGGSGYG PQGDYGQQGY
310
GPQGAPTSFS NQM
Length:313
Mass (Da):33,845
Last modified:August 1, 1991 - v3
Checksum:i592289C43B12EFA7
GO
Isoform 2 (identifier: P08247-2) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     1-118: Missing.

Note: No experimental confirmation available.
Show »
Length:195
Mass (Da):20,757
Checksum:i0AA753652E402114
GO

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti196P → L in AAH64550 (PubMed:15489334).Curated1

Natural variant

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Natural variantiVAR_0629832L → Q.1 PublicationCorresponds to variant rs200470034dbSNPEnsembl.1
Natural variantiVAR_062984158S → L.1 Publication1
Natural variantiVAR_062985166D → N.1 Publication1
Natural variantiVAR_062986217G → R in MRXSYP. 1 PublicationCorresponds to variant rs137852561dbSNPEnsembl.1
Natural variantiVAR_062987248D → N.1 PublicationCorresponds to variant rs782086106dbSNPEnsembl.1
Natural variantiVAR_062988277D → E in an individual affected by mental retardation; unknown pathological role. 1 Publication1
Natural variantiVAR_062989293G → S in an individual affected by mental retardation; unknown pathological role. 1 PublicationCorresponds to variant rs139475570dbSNPEnsembl.1

Alternative sequence

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Alternative sequenceiVSP_0568971 – 118Missing in isoform 2. 1 PublicationAdd BLAST118

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X06389 mRNA. Translation: CAA29686.1.
U93305 Genomic DNA. Translation: AAB92358.1.
AK295524 mRNA. Translation: BAH12095.1.
AK313030 mRNA. Translation: BAG35863.1.
AK315953 mRNA. Translation: BAH14324.1.
AF196779 Genomic DNA. No translation available.
CH471224 Genomic DNA. Translation: EAW50685.1.
BC064550 mRNA. Translation: AAH64550.1.
CCDSiCCDS14321.1. [P08247-1]
PIRiA35699.
RefSeqiNP_003170.1. NM_003179.2. [P08247-1]
UniGeneiHs.632804.

Genome annotation databases

EnsembliENST00000263233; ENSP00000263233; ENSG00000102003. [P08247-1]
ENST00000479808; ENSP00000418169; ENSG00000102003. [P08247-1]
GeneIDi6855.
KEGGihsa:6855.
UCSCiuc004dmz.2. human. [P08247-1]

Keywords - Coding sequence diversityi

Alternative splicing, Polymorphism

Cross-referencesi

Web resourcesi

Wikipedia

Synaptophysin entry

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X06389 mRNA. Translation: CAA29686.1.
U93305 Genomic DNA. Translation: AAB92358.1.
AK295524 mRNA. Translation: BAH12095.1.
AK313030 mRNA. Translation: BAG35863.1.
AK315953 mRNA. Translation: BAH14324.1.
AF196779 Genomic DNA. No translation available.
CH471224 Genomic DNA. Translation: EAW50685.1.
BC064550 mRNA. Translation: AAH64550.1.
CCDSiCCDS14321.1. [P08247-1]
PIRiA35699.
RefSeqiNP_003170.1. NM_003179.2. [P08247-1]
UniGeneiHs.632804.

3D structure databases

ProteinModelPortaliP08247.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi112721. 35 interactors.
IntActiP08247. 1 interactor.
STRINGi9606.ENSP00000263233.

Protein family/group databases

TCDBi9.B.130.1.4. the tetraspan vesicle membrane protein (tvp) family.

PTM databases

iPTMnetiP08247.
PhosphoSitePlusiP08247.

Polymorphism and mutation databases

BioMutaiSYP.
DMDMi135162.

Proteomic databases

EPDiP08247.
MaxQBiP08247.
PaxDbiP08247.
PeptideAtlasiP08247.
PRIDEiP08247.

Protocols and materials databases

DNASUi6855.
Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENST00000263233; ENSP00000263233; ENSG00000102003. [P08247-1]
ENST00000479808; ENSP00000418169; ENSG00000102003. [P08247-1]
GeneIDi6855.
KEGGihsa:6855.
UCSCiuc004dmz.2. human. [P08247-1]

Organism-specific databases

CTDi6855.
DisGeNETi6855.
GeneCardsiSYP.
H-InvDBHIX0203320.
HGNCiHGNC:11506. SYP.
HPAiCAB000076.
CAB055505.
HPA002858.
MalaCardsiSYP.
MIMi300802. phenotype.
313475. gene.
neXtProtiNX_P08247.
OpenTargetsiENSG00000102003.
Orphaneti777. X-linked non-syndromic intellectual disability.
PharmGKBiPA36288.
GenAtlasiSearch...

Phylogenomic databases

eggNOGiENOG410IDYC. Eukaryota.
ENOG4111J4N. LUCA.
GeneTreeiENSGT00390000010039.
HOGENOMiHOG000252913.
HOVERGENiHBG006681.
InParanoidiP08247.
OMAiGWAAPFM.
OrthoDBiEOG091G0ZEI.
PhylomeDBiP08247.
TreeFamiTF315804.

Enzyme and pathway databases

BioCyciZFISH:ENSG00000102003-MONOMER.

Miscellaneous databases

ChiTaRSiSYP. human.
GeneWikiiSynaptophysin.
GenomeRNAii6855.
PROiP08247.
SOURCEiSearch...

Gene expression databases

BgeeiENSG00000102003.
CleanExiHS_SYP.
ExpressionAtlasiP08247. baseline and differential.
GenevisibleiP08247. HS.

Family and domain databases

InterProiIPR008253. Marvel.
IPR001285. Synaptophysin/porin.
IPR028714. SYP.
[Graphical view]
PANTHERiPTHR10306. PTHR10306. 2 hits.
PTHR10306:SF10. PTHR10306:SF10. 2 hits.
PfamiPF01284. MARVEL. 1 hit.
[Graphical view]
PRINTSiPR00220. SYNAPTOPHYSN.
PROSITEiPS51225. MARVEL. 1 hit.
PS00604. SYNAPTOP. 1 hit.
[Graphical view]
ProtoNetiSearch...

Entry informationi

Entry nameiSYPH_HUMAN
AccessioniPrimary (citable) accession number: P08247
Secondary accession number(s): B2R7L6, B7Z359, Q6P2F7
Entry historyi
Integrated into UniProtKB/Swiss-Prot: August 1, 1988
Last sequence update: August 1, 1991
Last modified: November 2, 2016
This is version 153 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

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.