P08247 (SYPH_HUMAN) 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

Homo sapiens (Human) [Reference proteome]

Taxonomic identifier

9606 [NCBI]

Taxonomic lineage

cellular organisms › Eukaryota › Opisthokonta › Metazoa › Eumetazoa › Bilateria › Deuterostomia › Chordata › Craniata › Vertebrata › Gnathostomata › Teleostomi › Euteleostomi › Sarcopterygii › Tetrapoda › Amniota › Mammalia › Theria › Eutheria › Euarchontoglires › Primates › Haplorrhini › Simiiformes › Catarrhini › Hominoidea › Hominidae › Homininae › Homo

Protein attributes

Sequence length	313 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. 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 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 adaptative 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 component	Cell junction Cytoplasmic vesicle Membrane Synapse Synaptosome
Coding sequence diversity	Polymorphism
Disease	Disease mutation Mental retardation
Domain	Repeat Transmembrane Transmembrane helix
Ligand	Calcium
PTM	Glycoprotein Phosphoprotein Ubl conjugation
Technical term	Complete proteome Reference proteome
Gene Ontology (GO)
Biological_process	cellular response to organic substance Inferred from electronic annotation. Source: Compara regulation of long-term neuronal synaptic plasticity Inferred from sequence or structural similarity. Source: UniProtKB 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_component	cell junction Inferred from electronic annotation. Source: UniProtKB-KW excitatory synapse Inferred from electronic annotation. Source: Compara integral to synaptic vesicle membrane Non-traceable author statement Ref.2. Source: UniProtKB neuron projection terminus Inferred from electronic annotation. Source: Compara presynaptic active zone Inferred from electronic annotation. Source: Compara presynaptic membrane Inferred from electronic annotation. Source: Compara protein complex Inferred from electronic annotation. Source: Compara
Molecular_function	calcium ion binding Non-traceable author statement. Source: UniProtKB cholesterol binding Inferred from direct assay PubMed 10620806. Source: UniProtKB transporter activity Inferred from electronic annotation. Source: InterPro
Complete GO annotation...

Sequence annotation (Features)

	Feature key	Position(s)	Length	Description	Graphical view	Feature identifier
Molecule processing
	Chain	1 – 313	313	Synaptophysin		PRO_0000179161
Regions
	Topological domain	1 – 25	25	Cytoplasmic Potential
	Transmembrane	26 – 49	24	Helical; Potential
	Topological domain	50 – 106	57	Vesicular Potential
	Transmembrane	107 – 130	24	Helical; Potential
	Topological domain	131 – 137	7	Cytoplasmic Potential
	Transmembrane	138 – 161	24	Helical; Potential
	Topological domain	162 – 199	38	Vesicular Potential
	Transmembrane	200 – 223	24	Helical; Potential
	Topological domain	224 – 313	90	Cytoplasmic Potential
	Domain	21 – 227	207	MARVEL
	Region	254 – 305	52	Repeats, Gly-rich
Amino acid modifications
	Modified residue	81	1	Phosphotyrosine By similarity
	Glycosylation	59	1	N-linked (GlcNAc...) Potential
Natural variations
	Natural variant	2	1	L → Q. Ref.8		VAR_062983
	Natural variant	158	1	S → L. Ref.8		VAR_062984
	Natural variant	166	1	D → N. Ref.8		VAR_062985
	Natural variant	217	1	G → R in MRXSYP. Ref.8		VAR_062986
	Natural variant	248	1	D → N. Ref.8		VAR_062987
	Natural variant	277	1	D → E in an individual affected by mental retardation; unknown pathological role. Ref.8		VAR_062988
	Natural variant	293	1	G → S in an individual affected by mental retardation; unknown pathological role. Ref.8		VAR_062989
Experimental info
	Sequence conflict	196	1	P → L in AAH64550. Ref.6

Sequences

	Sequence		Length	Mass (Da)
	P08247 [UniParc]. Last modified August 1, 1991. Version 3. Checksum: 592289C43B12EFA7	FASTA	313	33,845
	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

References

	« Hide 'large scale' referencesShow '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. , 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. , 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. , 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.
IPI	IPI00027770.
PIR	A35699.
RefSeq	NP_003170.1. NM_003179.2.
UniGene	Hs.632804.
3D structure databases
ProteinModelPortal	P08247.
ModBase	Search...
Protein-protein interaction databases
STRING	9606.ENSP00000263233.
PTM databases
PhosphoSite	P08247.
Polymorphism databases
DMDM	135162.
Proteomic databases
PaxDb	P08247.
PRIDE	P08247.
Protocols and materials databases
DNASU	6855.
StructuralBiologyKnowledgebase	Search...
Genome annotation databases
Ensembl	ENST00000263233; ENSP00000263233; ENSG00000102003. ENST00000479808; ENSP00000418169; ENSG00000102003. ENST00000594524; ENSP00000470571; ENSG00000268353. ENST00000599440; ENSP00000473186; ENSG00000268353.
GeneID	6855.
KEGG	hsa:6855.
UCSC	uc004dmz.1. human.
Organism-specific databases
CTD	6855.
GeneCards	GC0XM049044.
H-InvDB	HIX0203320.
HGNC	HGNC:11506. SYP.
HPA	CAB000076. HPA002858.
MIM	300802. phenotype. 313475. gene.
neXtProt	NX_P08247.
Orphanet	777. X-linked nonsyndromic intellectual deficit.
PharmGKB	PA36288.
GenAtlas	Search...
Phylogenomic databases
eggNOG	NOG82723.
HOGENOM	HOG000252913.
HOVERGEN	HBG006681.
InParanoid	P08247.
OMA	AYGDAGY.
OrthoDB	EOG4JM7QJ.
PhylomeDB	P08247.
Gene expression databases
ArrayExpress	P08247.
Bgee	P08247.
CleanEx	HS_SYP.
Genevestigator	P08247.
GermOnline	ENSG00000102003. Homo sapiens.
Family and domain databases
InterPro	IPR008253. Marvel. IPR021128. MARVEL-like_dom. IPR001285. Synaptophysin/porin. [Graphical view]
PANTHER	PTHR10306. PTHR10306. 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
ChiTaRS	SYP. human.
GenomeRNAi	6855.
NextBio	26757.
SOURCE	Search...

Entry information

Entry name

SYPH_HUMAN

Accession

Primary (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:	May 1, 2013
This is version 117 of the entry and version 3 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Chordata Protein Annotation Program

Disclaimer

Any 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.