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Aliases for SYP Gene

Aliases for SYP Gene

  • Synaptophysin 2 3 3 5
  • Major Synaptic Vesicle Protein P38 3 4
  • MRXSYP 3
  • MRX96 3

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 identical protein binding and protein domain specific binding. 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 CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for SYP Gene

Genomics for SYP Gene

Regulatory Elements for SYP Gene

Enhancers for SYP Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH0XG048710 1.5 FANTOM5 ENCODE 9.9 +486.7 486726 6.0 HDGF FOXA2 PKNOX1 CREB3L1 ARNT ARID4B SIN3A DMAP1 FEZF1 ZNF2 ENSG00000204620 ZNF182 ZNF630 ZNF81 ENSG00000270012 PRAF2 SYP PQBP1 OTUD5 PIM2
GH0XG048834 1 ENCODE 9.9 +365.1 365079 2.3 ZNF133 ARID4B GLI4 ZNF2 KLF7 SP3 SP5 YY2 MIER2 REST ZNF81 ENSG00000204620 ENSG00000270012 ZNF182 CCDC120 PCSK1N PRAF2 SYP GRIPAP1 ERAS
GH0XG049199 1.1 ENCODE 0.7 -0.1 -60 1.2 CREB3L1 AGO1 ZFP64 ARID4B SIN3A YY1 SLC30A9 ZNF766 CBX5 ZNF207 ENSG00000204620 CACNA1F SYP
GH0XG049229 1 Ensembl ENCODE 0.3 -30.6 -30553 1.7 HDAC1 CTCF KLF1 ATF1 RB1 SIN3A BCL11B EGR1 POLR2A NR2F6 CACNA1F SYP
GH0XG049209 0.7 ENCODE 0.4 -9.8 -9767 0.2 BCOR CTCF ESRRA ZMYM3 ATF2 ZNF664 ZFHX2 JUND EGR1 ZNF341 SYP CACNA1F
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around SYP on UCSC Golden Path with GeneCards custom track

Promoters for SYP Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00000246563 -41 1001 CREB3L1 AGO1 ZFP64 ARID4B SIN3A YY1 SLC30A9 ZNF766 CBX5 ZNF207

Genomic Location for SYP Gene

Chromosome:
X
Start:
49,187,804 bp from pter
End:
49,200,259 bp from pter
Size:
12,456 bases
Orientation:
Minus strand

Genomic View for SYP Gene

Genes around SYP on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
SYP Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
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:
    P08247-SYPH_HUMAN
    Recommended name:
    Synaptophysin
    Protein Accession:
    P08247
    Secondary Accessions:
    • B2R7L6
    • B7Z359
    • Q6P2F7

    Protein attributes for SYP Gene

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

    Alternative splice isoforms for SYP Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for SYP Gene

Post-translational modifications for SYP Gene

  • Ubiquitinated; mediated by SIAH1 or SIAH2 and leading to its subsequent proteasomal degradation.
  • Glycosylation at isoforms=59
  • 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 & Families for SYP Gene

Gene Families for SYP Gene

Protein Domains for SYP Gene

Suggested Antigen Peptide Sequences for SYP Gene

Graphical View of Domain Structure for InterPro Entry

P08247

UniProtKB/Swiss-Prot:

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

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:0015485 cholesterol binding IDA 10620806
GO:0042169 SH2 domain binding IEA --
GO:0042802 identical protein binding IEA --
GO:0043621 protein self-association TAS 15217342
genes like me logo Genes that share ontologies with SYP: view
genes like me logo Genes that share phenotypes with SYP: view

Human Phenotype Ontology for SYP Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Models for SYP Gene

MGI Knock Outs for SYP:

Animal Model Products

CRISPR Products

Inhibitory RNA Products

Clone Products

  • Applied Biological Materials Clones for SYP

No data available for Enzyme Numbers (IUBMB) , Transcription Factor Targets 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

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for SYP gene
Compartment Confidence
plasma membrane 5
cytoskeleton 3
extracellular 2
mitochondrion 2
nucleus 2
endoplasmic reticulum 2
cytosol 2
lysosome 2
golgi apparatus 2
endosome 1

Gene Ontology (GO) - Cellular Components for SYP Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0008021 synaptic vesicle IEA,ISS --
GO:0016020 membrane IEA --
GO:0016021 integral component of membrane IEA --
GO:0030054 cell junction IEA --
GO:0030285 integral component of synaptic vesicle membrane NAS 1975480
genes like me logo Genes that share ontologies with SYP: view

Pathways & Interactions 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 IEA --
GO:0006897 endocytosis ISS --
GO:0016188 synaptic vesicle maturation NAS 10620806
GO:0048168 regulation of neuronal synaptic plasticity IBA,IEA --
GO:0048169 regulation of long-term neuronal synaptic plasticity ISS --
genes like me logo Genes that share ontologies with SYP: view

No data available for SIGNOR curated interactions for SYP Gene

Drugs & Compounds for SYP Gene

(42) Drugs for SYP Gene - From: HMDB and Novoseek

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
calcium Nutra 0

(37) Additional Compounds for SYP Gene - From: Novoseek

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
genes like me logo Genes that share compounds with SYP: view

Transcripts for SYP Gene

Unigene Clusters for SYP Gene

Synaptophysin:
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

Clone Products

  • Applied Biological Materials Clones for SYP

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: - -
SP8:

Relevant External Links for SYP Gene

GeneLoc Exon Structure for
SYP
ECgene alternative splicing isoforms for
SYP

Expression for SYP Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for SYP Gene

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

This gene is overexpressed in Brain - Frontal Cortex (BA9) (x7.5), Brain - Anterior cingulate cortex (BA24) (x6.7), Brain - Cortex (x6.3), Brain - Hippocampus (x4.6), and Brain - Hypothalamus (x4.1).

Protein differential expression in normal tissues from HIPED for SYP Gene

This gene is overexpressed in Frontal cortex (30.4), Brain (19.0), and Retina (13.5).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MaxQB, and MOPED for SYP Gene



Protein tissue co-expression partners for SYP Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of SYP Gene:

SYP

SOURCE GeneReport for Unigene cluster for SYP Gene:

Hs.632804

mRNA Expression by UniProt/SwissProt for SYP Gene:

P08247-SYPH_HUMAN
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.

Evidence on tissue expression from TISSUES for SYP Gene

  • Nervous system(5)
  • Eye(3.2)
  • Adrenal gland(3)
  • Intestine(3)
  • Pancreas(3)
  • Lung(2.4)
  • Stomach(2.3)
  • Muscle(2.2)
  • Lymph node(2.1)
  • Gall bladder(2)
  • Skin(2)

Phenotype-based relationships between genes and organs from Gene ORGANizer for SYP Gene

Germ Layers:
  • ectoderm
  • endoderm
  • mesoderm
Systems:
  • digestive
  • integumentary
  • nervous
  • reproductive
  • respiratory
  • skeletal muscle
  • skeleton
  • urinary
Organs:
Head and neck:
  • brain
  • cerebellum
  • cheek
  • chin
  • cranial nerve
  • ear
  • eye
  • eyelid
  • face
  • forehead
  • head
  • jaw
  • lip
  • mandible
  • maxilla
  • mouth
  • nose
  • outer ear
  • salivary gland
  • skull
  • tooth
Thorax:
  • lung
  • rib
  • rib cage
Pelvis:
  • pelvis
  • testicle
  • urinary bladder
Limb:
  • ankle
  • digit
  • elbow
  • finger
  • foot
  • hand
  • hip
  • knee
  • lower limb
  • shoulder
  • toe
  • upper limb
  • wrist
General:
  • hair
  • peripheral nerve
  • peripheral nervous system
  • skin
  • spinal column
  • vertebrae
genes like me logo Genes that share expression patterns with SYP: view

Primer 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
chimpanzee
(Pan troglodytes)
Mammalia SYP 34 35
  • 99.72 (n)
cow
(Bos Taurus)
Mammalia SYP 34 35
  • 91.97 (n)
mouse
(Mus musculus)
Mammalia Syp 34 16 35
  • 90.52 (n)
rat
(Rattus norvegicus)
Mammalia Syp 34
  • 90.41 (n)
dog
(Canis familiaris)
Mammalia SYP 34 35
  • 90.29 (n)
oppossum
(Monodelphis domestica)
Mammalia SYP 35
  • 83 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia -- 35
  • 64 (a)
ManyToMany
lizard
(Anolis carolinensis)
Reptilia SYP 35
  • 69 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia syp 34
  • 70.45 (n)
African clawed frog
(Xenopus laevis)
Amphibia syp-B 34
zebrafish
(Danio rerio)
Actinopterygii sypa 34 35
  • 68.49 (n)
sypb 35
  • 67 (a)
OneToMany
Dr.11716 34
worm
(Caenorhabditis elegans)
Secernentea sph-1 35
  • 26 (a)
OneToMany
Species where no ortholog for SYP was found in the sources mined by GeneCards:
  • 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

ENSEMBL:
Gene Tree for SYP (if available)
TreeFam:
Gene Tree for SYP (if available)

Paralogs for SYP Gene

Paralogs for SYP Gene

(4) 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
rs137852561 Pathogenic, Mental retardation, X-linked 96 (MRX96) [MIM:300802] 49,191,730(-) GGGTC(A/C/G)GCAAC reference, missense
rs139475570 Likely benign, Mental retardation, X-linked 96 (MRX96) [MIM:300802] 49,191,502(+) GTCGC(C/T)CTGAG reference, missense
VAR_062988 Mental retardation, X-linked 96 (MRX96) [MIM:300802]
rs181070015 Likely benign 49,188,048(+) CAGGA(C/T)GGGTG upstream-variant-2KB, utr-variant-3-prime
rs185819998 Likely benign 49,194,277(+) AATTC(A/G)GCTGA reference, synonymous-codon

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

Variant ID Type Subtype PubMed ID
esv32909 CNV gain+loss 17666407
nsv205 OTHER inversion 15895083
nsv528292 CNV gain 19592680
nsv7442 OTHER inversion 18451855

Variation tolerance for SYP Gene

Residual Variation Intolerance Score: 61.1% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 0.27; 6.00% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for SYP Gene

Human Gene Mutation Database (HGMD)
SYP
SNPedia medical, phenotypic, and genealogical associations of SNPs for
SYP

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

Disorders for SYP Gene

MalaCards: The human disease database

(225) MalaCards diseases for SYP Gene - From: OMIM, ClinVar, GeneTests, Orphanet, Swiss-Prot, DISEASES, Novoseek, and GeneCards

Disorder Aliases PubMed IDs
mental retardation, x-linked 96
  • mrx96
syp-related x-linked mental retardation
non-syndromic x-linked intellectual disability
  • non-specific x-linked mental retardation
central neurocytoma
  • neurolipocytoma
large cell carcinoma
  • carcinoma large cell
- elite association - COSMIC cancer census association via MalaCards
Search SYP in MalaCards View complete list of genes associated with diseases

UniProtKB/Swiss-Prot

SYPH_HUMAN
  • 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.

Relevant External Links for SYP

Genetic Association Database (GAD)
SYP
Human Genome Epidemiology (HuGE) Navigator
SYP
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
SYP
genes like me logo Genes that share disorders with SYP: view

No data available for Genatlas for SYP Gene

Publications for SYP Gene

  1. 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 64
  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 22 64
  3. 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 22 64
  4. 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 64
  5. Characterization of a multidomain adaptor protein, p140Cap, as part of a pre-synaptic complex. (PMID: 18662323) Ito H. … Nagata K. (J. Neurochem. 2008) 3 4 64

Products for SYP Gene

Sources for SYP Gene

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