P07825 (SYPH_RAT) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
Synaptophysin

Alternative name(s):
Major synaptic vesicle protein p38

Gene names

Name:

Syp

Organism

Rattus norvegicus (Rat)

Taxonomic identifier

10116 [NCBI]

Taxonomic lineage

Eukaryota › Metazoa › Chordata › Craniata › Vertebrata › Euteleostomi › Mammalia › Eutheria › Euarchontoglires › Glires › Rodentia › Sciurognathi › Muroidea › Muridae › Murinae › Rattus

Protein attributes

Sequence length	307 AA.
Sequence status	Complete.
Protein existence	Evidence 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 By similarity. Ref.7
Subcellular location	Cytoplasmic vesicle › secretory vesicle › synaptic vesicle membrane; Multi-pass membrane protein. Cell junction › synapse › synaptosome.
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. Ref.7
Sequence similarities	Belongs to the synaptophysin/synaptobrevin family. Contains 1 MARVEL domain.

Ontologies

Keywords
Cellular component	Cell junction Cytoplasmic vesicle Membrane Synapse Synaptosome
Domain	Repeat Transmembrane Transmembrane helix
Ligand	Calcium
PTM	Glycoprotein Phosphoprotein Ubl conjugation
Technical term	Complete proteome Direct protein sequencing Reference proteome
Gene Ontology (GO)
Cellular component	cell junction Inferred from electronic annotation. Source: UniProtKB-KW excitatory synapse Inferred from direct assay. Source: BHF-UCL integral to synaptic vesicle membrane Traceable author statement. Source: RGD neuron projection terminus Inferred from direct assay Ref.7. Source: RGD protein complex Inferred from direct assay. Source: RGD synaptosome Inferred from direct assay. Source: RGD
Molecular function	syntaxin-1 binding Inferred from direct assay. Source: MGI transporter activity Inferred from electronic annotation. Source: InterPro
Complete GO annotation...

Binary interactions

With	Entry	#Exp.	IntAct	Notes
Rabac1	O35394	2	EBI-976085,EBI-2028510
Srcin1	Q9QWI6-2	2	EBI-976085,EBI-775607	From a different organism.

Sequence annotation (Features)

	Feature key	Position(s)	Length	Description	Graphical view	Feature identifier
Molecule processing
	Chain	1 – 307	307	Synaptophysin		PRO_0000179163
Regions
	Topological domain	1 – 19	19	Cytoplasmic Potential
	Transmembrane	20 – 43	24	Helical; Potential
	Topological domain	44 – 101	58	Vesicular Potential
	Transmembrane	102 – 125	24	Helical; Potential
	Topological domain	126 – 132	7	Cytoplasmic Potential
	Transmembrane	133 – 156	24	Helical; Potential
	Topological domain	157 – 194	38	Vesicular Potential
	Transmembrane	195 – 218	24	Helical; Potential
	Topological domain	219 – 307	89	Cytoplasmic Potential
	Domain	15 – 222	208	MARVEL
	Region	249 – 298	50	Repeats, Gly-rich
Amino acid modifications
	Modified residue	75	1	Phosphotyrosine By similarity
	Modified residue	221	1	Phosphothreonine Potential
	Modified residue	273	1	Phosphotyrosine Potential
	Modified residue	289	1	Phosphotyrosine Potential
	Glycosylation	53	1	N-linked (GlcNAc...) Potential

Sequences

	Sequence		Length	Mass (Da)
	P07825 [UniParc]. Last modified August 1, 1988. Version 1. Checksum: A245E4F70BF0EAF0	FASTA	307	33,311
	10 20 30 40 50 60 MDVVNQLVAG GQFRVVKEPL GFVKVLQWVF AIFAFATCGS YTGELRLSVE CANKTESALN 70 80 90 100 110 120 IEVEFEYPFR LHQVYFDAPS CVKGGTTKIF LVGDYSSSAE FFVTVAVFAF LYSMGALATY 130 140 150 160 170 180 IFLQNKYREN NKGPMMDFLA TAVFAFMWLV SSSAWAKGLS DVKMATDPEN IIKEMPMCRQ 190 200 210 220 230 240 TGNTCKELRD PVTSGLNTSV VFGFLNLVLW VGNLWFVFKE TGWAAPFMRA PPGAPEKQPA 250 260 270 280 290 300 PGDAYGDAGY GQGPGGYGPQ DSYGPQGGYQ PDYGQPASGG GGYGPQGDYG QQGYGQQGAP TSFSNQM

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"Synaptophysin: molecular organization and mRNA expression as determined from cloned cDNA." Leube R.E., Kaiser P., Seiter A., Zimbelmann R., Franke W.W., Rehm H., Knaus P., Prior P., Betz H., Reinke H., Beyreuther K., Wiedenmann B. EMBO J. 6:3261-3268(1987) [PubMed: 3123215] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [MRNA].
[2]	"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: 3120152] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [MRNA].
[3]	"A synaptic vesicle protein with a novel cytoplasmic domain and four transmembrane regions." Suedhof T.C., Lottspeich F., Greengard P., Mehl E., Jahn R. Science 238:1142-1144(1987) [PubMed: 3120313] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [MRNA], PARTIAL PROTEIN SEQUENCE.
[4]	"The synaptophysin-encoding gene in rat and man is specifically transcribed in neuroendocrine cells." Bargou R.C.E.F., Leube R.E. Gene 99:197-204(1991) [PubMed: 1902431] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
[5]	"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: 15489334] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA]. Tissue: Prostate.
[6]	"Cloning and sequence analysis of cDNA encoding p38, a major synaptic vesicle protein." Buckley K.M., Floor E., Kelly R.B. J. Cell Biol. 105:2447-2456(1987) [PubMed: 3121632] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [MRNA] OF 13-307. Tissue: Brain.
[7]	"Regulation of synaptophysin degradation by mammalian homologues of Seven in Absentia." Wheeler T.C., Chin L.-S., Li Y., Roudabush F.L., Li L. J. Biol. Chem. 277:10273-10282(2002) [PubMed: 11786535] [Abstract] Cited for: INTERACTION WITH SIAH1 AND SIAH2, DEGRADATION. Strain: Sprague-Dawley.
+	Additional computationally mapped references.

Cross-references

Sequence databases
EMBL GenBank DDBJ	X06177 mRNA. Translation: CAA29543.1. X06388 mRNA. Translation: CAA29685.1. M58396 , M58402, M58401, M58399 Genomic DNA. Translation: AAA42196.1. BC099798 mRNA. Translation: AAH99798.1. X06655 mRNA. Translation: CAA29854.1.
IPI	IPI00211360.
PIR	B27287. JU0464.
RefSeq	NP_036796.1. NM_012664.2.
UniGene	Rn.11067.
3D structure databases
ModBase	Search...
Protein-protein interaction databases
IntAct	P07825. 10 interactions.
MINT	MINT-362223.
STRING	P07825.
PTM databases
PhosphoSite	P07825.
Proteomic databases
PRIDE	P07825.
Protocols and materials databases
StructuralBiologyKnowledgebase	Search...
Genome annotation databases
GeneID	24804.
KEGG	rno:24804.
UCSC	NM_012664. rat.
Organism-specific databases
CTD	6855.
RGD	3802. Syp.
Phylogenomic databases
eggNOG	roNOG06112.
GeneTree	ENSGT00390000010039.
HOVERGEN	HBG006681.
InParanoid	P07825.
OrthoDB	EOG4JM7QJ.
Gene expression databases
ArrayExpress	P07825.
Genevestigator	P07825.
GermOnline	ENSRNOG00000010223. Rattus norvegicus.
Family and domain databases
InterPro	IPR008253. Marvel. IPR021128. MARVEL-like_dom. IPR001285. Synaptophysin/porin. [Graphical view]
PANTHER	PTHR10306. Synaptophysin. 1 hit.
Pfam	PF01284. MARVEL. 1 hit. [Graphical view]
PRINTS	PR00220. SYNAPTOPHYSN.
PROSITE	PS51225. MARVEL. 1 hit. PS00604. SYNAPTOP. 1 hit. [Graphical view]
ProtoNet	Search...
Other
NextBio	604472.

Entry information

Entry name

SYPH_RAT

Accession

Primary (citable) accession number: P07825
Secondary accession number(s): Q499R3

Entry history

Integrated into UniProtKB/Swiss-Prot:	August 1, 1988
Last sequence update:	August 1, 1988
Last modified:	December 14, 2011
This is version 104 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Chordata Protein Annotation Program