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Protein

Synaptophysin

Gene

SYP

Organism
Homo sapiens (Human)
Status
Reviewed-Annotation score: -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
  • identical protein binding Source: Ensembl
  • protein self-association Source: ParkinsonsUK-UCL
  • SH2 domain binding Source: Ensembl

GO - Biological processi

Keywordsi

LigandCalcium

Enzyme and pathway databases

SIGNORiP08247

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

EuPathDBiHostDB:ENSG00000102003.10
HGNCiHGNC:11506 SYP
MIMi313475 gene
neXtProtiNX_P08247

Subcellular locationi

Extracellular region or secreted Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi apparatus Nucleus Mitochondrion Manual annotation Automatic computational assertionGraphics by Christian Stolte; Source: COMPARTMENTS

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

Keywords - Cellular componenti

Cell junction, Cytoplasmic vesicle, Membrane, Synapse, Synaptosome

Pathology & Biotechi

Involvement in diseasei

Mental retardation, X-linked 96 (MRX96)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 MRX96. 1 PublicationCorresponds to variant dbSNP:rs137852561EnsemblClinVar.1
Natural variantiVAR_062988277D → E in MRX96; unknown pathological significance. 1 Publication1
Natural variantiVAR_062989293G → S in MRX96; unknown pathological significance. 1 PublicationCorresponds to variant dbSNP:rs139475570EnsemblClinVar.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...) asparagineSequence 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

Binary interactionsi

Show more details

GO - Molecular functioni

  • identical protein binding Source: Ensembl
  • protein self-association Source: ParkinsonsUK-UCL
  • SH2 domain binding Source: Ensembl

Protein-protein interaction databases

BioGridi112721, 39 interactors
IntActiP08247, 9 interactors
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

Keywords - Domaini

Repeat, Transmembrane, Transmembrane helix

Phylogenomic databases

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

Family and domain databases

InterProiView protein in InterPro
IPR008253 Marvel
IPR001285 Synaptophysin/porin
IPR028714 SYP
PANTHERiPTHR10306 PTHR10306, 1 hit
PTHR10306:SF10 PTHR10306:SF10, 1 hit
PfamiView protein in Pfam
PF01284 MARVEL, 1 hit
PRINTSiPR00220 SYNAPTOPHYSN
PROSITEiView protein in PROSITE
PS51225 MARVEL, 1 hit
PS00604 SYNAPTOP, 1 hit

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 → Q1 PublicationCorresponds to variant dbSNP:rs200470034EnsemblClinVar.1
Natural variantiVAR_07922372E → Q1 Publication1
Natural variantiVAR_062984158S → L1 Publication1
Natural variantiVAR_062985166D → N1 Publication1
Natural variantiVAR_062986217G → R in MRX96. 1 PublicationCorresponds to variant dbSNP:rs137852561EnsemblClinVar.1
Natural variantiVAR_062987248D → N1 PublicationCorresponds to variant dbSNP:rs782086106Ensembl.1
Natural variantiVAR_062988277D → E in MRX96; unknown pathological significance. 1 Publication1
Natural variantiVAR_062989293G → S in MRX96; unknown pathological significance. 1 PublicationCorresponds to variant dbSNP:rs139475570EnsemblClinVar.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

Similar proteinsi

Entry informationi

Entry nameiSYPH_HUMAN
AccessioniPrimary (citable) accession number: P08247
Secondary accession number(s): B2R7L6, B7Z359, Q6P2F7
Entry historyiIntegrated into UniProtKB/Swiss-Prot: August 1, 1988
Last sequence update: August 1, 1991
Last modified: May 23, 2018
This is version 163 of the entry and version 3 of the sequence. See 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

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