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Aliases for SYP Gene

Aliases for SYP Gene

  • Synaptophysin 2 3
  • Major Synaptic Vesicle Protein P38 3 4
  • MRXSYP 3
  • MRX96 3
  • MRX 6

External Ids for SYP Gene

Previous GeneCards Identifiers for SYP Gene

  • GC0XM047830
  • GC0XM047286
  • GC0XM047850
  • GC0XM048070
  • GC0XM048800
  • GC0XM048931
  • GC0XM049044
  • GC0XM046701

Summaries for SYP Gene

Entrez Gene Summary for SYP Gene

  • This gene encodes an integral membrane protein of small synaptic vesicles in brain and endocrine cells. The protein also binds cholesterol and is thought to direct targeting of vesicle-associated membrane protein 2 (synaptobrevin) to intracellular compartments. Mutations in this gene are associated with X-linked mental retardation (XLMR). [provided by RefSeq, Aug 2011]

GeneCards Summary for SYP Gene

SYP (Synaptophysin) is a Protein Coding gene. Diseases associated with SYP include mental retardation, x-linked 96 and syp-related x-linked mental retardation. Among its related pathways are Neuroscience and Synaptic vesicle cycle. GO annotations related to this gene include calcium ion binding and transporter activity. An important paralog of this gene is SYNPR.

UniProtKB/Swiss-Prot for SYP Gene

  • 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).

Gene Wiki entry for SYP Gene

No data available for Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for SYP Gene

Genomics for SYP Gene

Regulatory Elements for SYP Gene

Epigenetics Products

  • DNA Methylation CpG Assay Predesigned for Pyrosequencing in human,mouse,rat

Genomic Location for SYP Gene

49,187,804 bp from pter
49,200,259 bp from pter
12,456 bases
Minus strand

Genomic View for SYP Gene

UCSC Golden Path with GeneCards custom track
Cytogenetic band:
Genomic Location for SYP Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for SYP Gene

Proteins for SYP Gene

  • Protein details for SYP Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    Protein Accession:
    Secondary Accessions:
    • B2R7L6
    • B7Z359
    • Q6P2F7

    Protein attributes for SYP Gene

    313 amino acids
    Molecular mass:
    33845 Da
    Quaternary structure:
    • Homohexamer or homotetramer. Interacts with SRCIN1.

    Alternative splice isoforms for SYP Gene


neXtProt entry for SYP Gene

Proteomics data for SYP Gene at MOPED

Post-translational modifications for SYP Gene

  • Ubiquitinated; mediated by SIAH1 or SIAH2 and leading to its subsequent proteasomal degradation.
  • Glycosylation at Asn59
  • Modification sites at PhosphoSitePlus

Other Protein References for SYP Gene

Antibody Products

  • Cell Signaling Technology (CST) Antibodies for SYP (SYP)

No data available for DME Specific Peptides for SYP Gene

Domains for SYP Gene

Protein Domains for SYP Gene

Suggested Antigen Peptide Sequences for SYP Gene

Graphical View of Domain Structure for InterPro Entry



  • P08247
  • The calcium-binding activity is thought to be localized in the cytoplasmic tail of the protein
  • Contains 1 MARVEL domain.
  • Belongs to the synaptophysin/synaptobrevin family.
genes like me logo Genes that share domains with SYP: view

No data available for Gene Families for SYP Gene

Function for SYP Gene

Molecular function for SYP Gene

GENATLAS Biochemistry: synaptophysin (integral protein of small presynaptic vesicles of neurons)
UniProtKB/Swiss-Prot 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).

Gene Ontology (GO) - Molecular Function for SYP Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005215 transporter activity IEA --
GO:0005515 protein binding --
GO:0015485 cholesterol binding IDA 10620806
GO:0017075 syntaxin-1 binding IEA --
GO:0019904 protein domain specific binding --
genes like me logo Genes that share ontologies with SYP: view

Phenotypes for SYP Gene

genes like me logo Genes that share phenotypes with SYP: view

Animal Models for SYP Gene

MGI Knock Outs for SYP:

Animal Model Products

CRISPR Products

miRNA for SYP Gene

miRTarBase miRNAs that target SYP

Inhibitory RNA Products

  • Predesigned siRNA for gene silencing in human,mouse,rat for SYP

In Situ Assay Products

Flow Cytometry Products

No data available for Enzyme Numbers (IUBMB) , Transcription Factor Targeting and HOMER Transcription for SYP Gene

Localization for SYP Gene

Subcellular locations from UniProtKB/Swiss-Prot for SYP Gene

Cytoplasmic vesicle, secretory vesicle, synaptic vesicle membrane; Multi-pass membrane protein. Cell junction, synapse, synaptosome.

Subcellular locations from

Jensen Localization Image for SYP Gene COMPARTMENTS Subcellular localization image for SYP gene
Compartment Confidence
cytoskeleton 3
plasma membrane 3
extracellular 2
golgi apparatus 2
mitochondrion 2
nucleus 2
cytosol 1
endoplasmic reticulum 1
endosome 1
lysosome 1

Gene Ontology (GO) - Cellular Components for SYP Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0008021 synaptic vesicle ISS --
GO:0016020 membrane --
GO:0030054 cell junction IEA --
GO:0030285 integral component of synaptic vesicle membrane NAS 1975480
GO:0030672 synaptic vesicle membrane IEA --
genes like me logo Genes that share ontologies with SYP: view

Pathways for SYP Gene

SuperPathways for SYP Gene

genes like me logo Genes that share pathways with SYP: view

Pathways by source for SYP Gene

1 Cell Signaling Technology pathway for SYP Gene
1 BioSystems pathway for SYP Gene

Gene Ontology (GO) - Biological Process for SYP Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006810 transport --
GO:0006897 endocytosis ISS --
GO:0016188 synaptic vesicle maturation NAS 10620806
GO:0048168 regulation of neuronal synaptic plasticity IBA --
GO:0048169 regulation of long-term neuronal synaptic plasticity ISS --
genes like me logo Genes that share ontologies with SYP: view

Compounds for SYP Gene

(1) HMDB Compounds for SYP Gene

Compound Synonyms Cas Number PubMed IDs
  • Ca

(79) Novoseek inferred chemical compound relationships for SYP Gene

Compound -log(P) Hits PubMed IDs
smcc 69.5 2
paraffin 55.8 18
reticulin 55.6 1
s 100 54.8 4
mucicarmine 54.5 1
genes like me logo Genes that share compounds with SYP: view

Transcripts for SYP Gene

Unigene Clusters for SYP Gene

Representative Sequences:

CRISPR Products

Inhibitory RNA Products

  • Predesigned siRNA for gene silencing in human,mouse,rat for SYP

Primer Products

Flow Cytometry Products

Alternative Splicing Database (ASD) splice patterns (SP) for SYP Gene

ExUns: 1a · 1b ^ 2a · 2b ^ 3 ^ 4a · 4b · 4c ^ 5a · 5b · 5c ^ 6a · 6b ^ 7a · 7b ^ 8a · 8b
SP1: - - - -
SP2: - - - - - -
SP3: - -
SP4: - - - - -
SP5: - - - - - - - -
SP6: -
SP7: - -

Relevant External Links for SYP Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for SYP Gene

mRNA expression in normal human tissues for SYP Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for SYP Gene

This gene is overexpressed in Brain - Frontal Cortex (BA9) (7.5), Brain - Anterior cingulate cortex (BA24) (6.7), Brain - Cortex (6.3), Brain - Hippocampus (4.6), and Brain - Hypothalamus (4.1).

Integrated Proteomics: protein expression from ProteomicsDB, PaxDb, MOPED, and MaxQB for SYP Gene

SOURCE GeneReport for Unigene cluster for SYP Gene Hs.632804

mRNA Expression by UniProt/SwissProt for SYP Gene

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
genes like me logo Genes that share expressions with SYP: view

In Situ Assay Products

Orthologs for SYP Gene

This gene was present in the common ancestor of animals.

Orthologs for SYP Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia SYP 35
  • 99.72 (n)
  • 99.58 (a)
SYP 36
  • 100 (a)
(Bos Taurus)
Mammalia SYP 35
  • 91.97 (n)
  • 94.46 (a)
SYP 36
  • 94 (a)
(Canis familiaris)
Mammalia SYP 35
  • 90.29 (n)
  • 93.05 (a)
SYP 36
  • 92 (a)
(Mus musculus)
Mammalia Syp 35
  • 90.52 (n)
  • 95.21 (a)
Syp 16
Syp 36
  • 95 (a)
(Monodelphis domestica)
Mammalia SYP 36
  • 83 (a)
(Ornithorhynchus anatinus)
Mammalia -- 36
  • 64 (a)
(Rattus norvegicus)
Mammalia Syp 35
  • 90.41 (n)
  • 95.75 (a)
(Anolis carolinensis)
Reptilia SYP 36
  • 69 (a)
African clawed frog
(Xenopus laevis)
Amphibia syp-B 35
tropical clawed frog
(Silurana tropicalis)
Amphibia syp 35
  • 70.45 (n)
  • 76.98 (a)
(Danio rerio)
Actinopterygii Dr.11716 35
sypa 35
  • 68.49 (n)
  • 72.6 (a)
sypa 36
  • 71 (a)
sypb 36
  • 67 (a)
(Caenorhabditis elegans)
Secernentea sph-1 36
  • 26 (a)
Species with no ortholog for SYP:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • chicken (Gallus gallus)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • fruit fly (Drosophila melanogaster)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea squirt (Ciona intestinalis)
  • sea squirt (Ciona savignyi)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)

Evolution for SYP Gene

Gene Tree for SYP (if available)
Gene Tree for SYP (if available)

Paralogs for SYP Gene

Paralogs for SYP Gene

Selected SIMAP similar genes for SYP Gene using alignment to 5 proteins:

genes like me logo Genes that share paralogs with SYP: view

Variants for SYP Gene

Sequence variations from dbSNP and Humsavar for SYP Gene

SNP ID Clin Chr 0X pos Sequence Context AA Info Type MAF
rs2293945 -- 49,191,162(+) CCCCC(C/T)GCCTT intron-variant
rs2737731 -- 49,189,294(+) AGACA(A/C)AAGAC intron-variant
rs2737732 -- 49,189,495(+) CAACC(A/C)AAAAA intron-variant
rs2856747 -- 49,189,347(+) AGGGG(G/T)TGGGC intron-variant
rs3817677 -- 49,190,221(+) gttgc(C/G)caggc intron-variant

Structural Variations from Database of Genomic Variants (DGV) for SYP Gene

Variant ID Type Subtype PubMed ID
esv32909 CNV Gain+Loss 17666407
nsv528292 CNV Gain 19592680
nsv7442 OTHER Inversion 18451855
nsv205 OTHER Inversion 15895083

Relevant External Links for SYP Gene

HapMap Linkage Disequilibrium report
Human Gene Mutation Database (HGMD)
Locus Specific Mutation Databases (LSDB)

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for SYP Gene

Disorders for SYP Gene

(1) OMIM Diseases for SYP Gene (313475)


  • 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. {ECO:0000269 PubMed:19377476}. Note=The disease is caused by mutations affecting the gene represented in this entry.

(96) Novoseek inferred disease relationships for SYP Gene

Disease -log(P) Hits PubMed IDs
carcinoma neuroendocrine 92.4 22
neurocytoma 88.2 9
neurocytoma central 87.6 11
carcinoid 84.6 43
small cell lung cancer 80.1 30

Relevant External Links for SYP

Genetic Association Database (GAD)
Human Genome Epidemiology (HuGE) Navigator
genes like me logo Genes that share disorders with SYP: view

Publications for SYP Gene

  1. Synaptophysin: structure of the human gene and assignment to the X chromosome in man and mouse. (PMID: 1975480) Oezcelik T. … Suedhof T.C. (Am. J. Hum. Genet. 1990) 3 4 23
  2. Sequence-based exon prediction around the synaptophysin locus reveals a gene-rich area containing novel genes in human proximal Xp. (PMID: 9344658) Fisher S.E. … Craig I.W. (Genomics 1997) 3 4 23
  3. The cDNA and derived amino acid sequences for rat and human synaptophysin. (PMID: 3120152) Suedhof T.C. … Jahn R. (Nucleic Acids Res. 1987) 2 3 4
  4. A systematic, large-scale resequencing screen of X-chromosome coding exons in mental retardation. (PMID: 19377476) Tarpey P.S. … Stratton M.R. (Nat. Genet. 2009) 2 3 4
  5. The analysis of 51 genes in DSM-IV combined type attention deficit hyperactivity disorder: association signals in DRD4, DAT1 and 16 other genes. (PMID: 16894395) Brookes K. … Asherson P. (Mol. Psychiatry 2006) 3 48

Products for SYP Gene

Sources for SYP Gene

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