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Aliases for NPTN Gene

Aliases for NPTN Gene

  • Neuroplastin 2 3 3 5
  • Stromal Cell Derived Factor Receptor 1 2 3
  • Stromal Cell-Derived Receptor 1 3 4
  • SDFR1 3 4
  • SDR-1 3 4
  • SDR1 3 4
  • GP55 3
  • GP65 3
  • Np55 3
  • Np65 3

External Ids for NPTN Gene

Previous HGNC Symbols for NPTN Gene

  • SDFR1

Previous GeneCards Identifiers for NPTN Gene

  • GC15M071640
  • GC15M073852
  • GC15M050683

Summaries for NPTN Gene

Entrez Gene Summary for NPTN Gene

  • This gene encodes a type I transmembrane protein belonging to the Ig superfamily. The protein is believed to be involved in cell-cell interactions or cell-substrate interactions. Alternative splicing results in multiple transcript variants. [provided by RefSeq, May 2009]

GeneCards Summary for NPTN Gene

NPTN (Neuroplastin) is a Protein Coding gene. Diseases associated with NPTN include Allergic Bronchopulmonary Aspergillosis and Acute Erythroid Leukemia. Among its related pathways are Transmission across Chemical Synapses and Akt Signaling. GO annotations related to this gene include cell adhesion molecule binding and type 1 fibroblast growth factor receptor binding. An important paralog of this gene is BSG.

UniProtKB/Swiss-Prot for NPTN Gene

  • Probable homophilic and heterophilic cell adhesion molecule involved in long term potentiation at hippocampal excitatory synapses through activation of p38MAPK. May also regulate neurite outgrowth by activating the FGFR1 signaling pathway. May play a role in synaptic plasticity (By similarity).

Gene Wiki entry for NPTN Gene

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

Genomics for NPTN Gene

Regulatory Elements for NPTN Gene

Enhancers for NPTN 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
GH15F073564 0.2 ENCODE 12 +69.6 69640 0.2 SOX13 CTCF ZNF792 TAL1 JUN MAX ZIC2 RAD21 NCOR1 POLR2A NPTN NPTN-IT1 MRPS15P1
GH15F073606 1.1 Ensembl ENCODE 11.9 +26.0 26034 3.0 CTCF JUNB REST ZIC2 GATA3 JUND GLIS1 EED IKZF1 ZNF524 NPTN C15orf59 GC15M073574
GH15F073605 0.5 Ensembl ENCODE 11.9 +28.1 28109 0.4 PKNOX1 JUND ZFHX2 NFE2L2 NPTN GC15M073574
GH15F073596 1.3 Ensembl ENCODE 11.9 +34.1 34134 8.0 PKNOX1 ZNF133 INSM2 FEZF1 NFXL1 ZNF2 ZEB1 ZNF335 ZNF366 SCRT2 NPTN BBS4 ISLR ADPGK GC15M073574 NPTN-IT1
GH15F073704 0.4 ENCODE 11.9 -71.1 -71055 0.9 CTCF PKNOX1 IRF2 KLF17 ZNF2 RAD21 YY1 ZNF664 ZBTB48 POLR2A NPTN HCN4 GC15P073700 ENSG00000276807
- Elite enhancer/Elite enhancer-gene association Download Table
Download GeneHancer data dump

Enhancers around NPTN on UCSC Golden Path with GeneCards custom track

Promoters for NPTN Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00000411107 1934 3201 HDGF PKNOX1 CREB3L1 ARID4B SIN3A YBX1 DMAP1 ZNF2 ZNF302 ZNF143

Genomic Location for NPTN Gene

Chromosome:
15
Start:
73,560,003 bp from pter
End:
73,634,134 bp from pter
Size:
74,132 bases
Orientation:
Minus strand

Genomic View for NPTN Gene

Genes around NPTN on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
NPTN Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for NPTN Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for NPTN Gene

Proteins for NPTN Gene

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

    Protein Symbol:
    Q9Y639-NPTN_HUMAN
    Recommended name:
    Neuroplastin
    Protein Accession:
    Q9Y639
    Secondary Accessions:
    • B2RAL7
    • B7Z4D3
    • B7ZLL2
    • Q17R52
    • Q59EJ9
    • Q6NVX7
    • Q9Y640

    Protein attributes for NPTN Gene

    Size:
    398 amino acids
    Molecular mass:
    44387 Da
    Quaternary structure:
    No Data Available
    SequenceCaution:
    • Sequence=BAD93049.1; Type=Erroneous initiation; Note=Translation N-terminally shortened.; Evidence={ECO:0000305};

    Alternative splice isoforms for NPTN Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for NPTN Gene

Post-translational modifications for NPTN Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

No data available for DME Specific Peptides for NPTN Gene

Domains & Families for NPTN Gene

Graphical View of Domain Structure for InterPro Entry

Q9Y639

UniProtKB/Swiss-Prot:

NPTN_HUMAN :
  • Some isoforms lack the first Ig-like domain which may confer homophilic adhesion activity. However, they can bind and activate FGFR1 (By similarity).
Domain:
  • Some isoforms lack the first Ig-like domain which may confer homophilic adhesion activity. However, they can bind and activate FGFR1 (By similarity).
  • Contains 3 Ig-like (immunoglobulin-like) domains.
genes like me logo Genes that share domains with NPTN: view

Function for NPTN Gene

Molecular function for NPTN Gene

UniProtKB/Swiss-Prot Function:
Probable homophilic and heterophilic cell adhesion molecule involved in long term potentiation at hippocampal excitatory synapses through activation of p38MAPK. May also regulate neurite outgrowth by activating the FGFR1 signaling pathway. May play a role in synaptic plasticity (By similarity).

Gene Ontology (GO) - Molecular Function for NPTN Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0004714 transmembrane receptor protein tyrosine kinase activity IEA --
GO:0005104 fibroblast growth factor receptor binding IEA --
GO:0005105 type 1 fibroblast growth factor receptor binding ISS --
GO:0044325 ion channel binding IEA --
GO:0050839 cell adhesion molecule binding ISS --
genes like me logo Genes that share ontologies with NPTN: view

Phenotypes for NPTN Gene

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

Animal Model Products

  • Taconic Biosciences Mouse Models for NPTN

Flow Cytometry Products

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for NPTN Gene

Localization for NPTN Gene

Subcellular locations from UniProtKB/Swiss-Prot for NPTN Gene

Cell membrane; Single-pass type I membrane protein. Note=Enriched at postsynaptic density. {ECO:0000250}.

Subcellular locations from

COMPARTMENTS
Jensen Localization Image for NPTN Gene COMPARTMENTS Subcellular localization image for NPTN gene
Compartment Confidence
plasma membrane 5
extracellular 3
cytosol 2
endoplasmic reticulum 2
golgi apparatus 2
mitochondrion 2
nucleus 2
peroxisome 1

Gene Ontology (GO) - Cellular Components for NPTN Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005886 plasma membrane IEA --
GO:0009986 cell surface IDA 19581412
GO:0014069 postsynaptic density IEA --
GO:0016020 membrane IEA --
GO:0016021 integral component of membrane IEA --
genes like me logo Genes that share ontologies with NPTN: view

Pathways & Interactions for NPTN Gene

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

Gene Ontology (GO) - Biological Process for NPTN Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0001934 positive regulation of protein phosphorylation ISS --
GO:0007155 cell adhesion IEA --
GO:0007156 homophilic cell adhesion via plasma membrane adhesion molecules ISS --
GO:0007169 transmembrane receptor protein tyrosine kinase signaling pathway IEA --
GO:0007204 positive regulation of cytosolic calcium ion concentration ISS --
genes like me logo Genes that share ontologies with NPTN: view

No data available for SIGNOR curated interactions for NPTN Gene

Transcripts for NPTN Gene

Unigene Clusters for NPTN Gene

Neuroplastin:
Representative Sequences:

Flow Cytometry Products

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

ExUns: 1a · 1b · 1c · 1d ^ 2 ^ 3 ^ 4a · 4b · 4c ^ 5 ^ 6 ^ 7 ^ 8 ^ 9 ^ 10
SP1: - -
SP2: - - -
SP3: - - - -
SP4:
SP5:
SP6: - -

Relevant External Links for NPTN Gene

GeneLoc Exon Structure for
NPTN
ECgene alternative splicing isoforms for
NPTN

Expression for NPTN Gene

mRNA expression in normal human tissues for NPTN Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Protein differential expression in normal tissues from HIPED for NPTN Gene

This gene is overexpressed in Nasal epithelium (25.1) and Serum (18.5).

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



Protein tissue co-expression partners for NPTN Gene

NURSA nuclear receptor signaling pathways regulating expression of NPTN Gene:

NPTN

SOURCE GeneReport for Unigene cluster for NPTN Gene:

Hs.744867

mRNA Expression by UniProt/SwissProt for NPTN Gene:

Q9Y639-NPTN_HUMAN
Tissue specificity: Isoform 1 is ubiquitously expressed. Isoform 2 is expressed in brain cortex and cerebellum (at protein level).
genes like me logo Genes that share expression patterns with NPTN: view

Primer Products

No data available for mRNA differential expression in normal tissues for NPTN Gene

Orthologs for NPTN Gene

This gene was present in the common ancestor of animals.

Orthologs for NPTN Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia NPTN 34 35
  • 99.66 (n)
dog
(Canis familiaris)
Mammalia NPTN 34 35
  • 95.37 (n)
rat
(Rattus norvegicus)
Mammalia Nptn 34
  • 93.51 (n)
oppossum
(Monodelphis domestica)
Mammalia NPTN 35
  • 90 (a)
OneToOne
mouse
(Mus musculus)
Mammalia Nptn 35
  • 80 (a)
OneToOne
cow
(Bos Taurus)
Mammalia NPTN 35
  • 79 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia NPTN 35
  • 78 (a)
OneToOne
chicken
(Gallus gallus)
Aves NPTN 34 35
  • 77.72 (n)
lizard
(Anolis carolinensis)
Reptilia NPTN 35
  • 74 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia Str.6352 34
African clawed frog
(Xenopus laevis)
Amphibia LOC398501 34
zebrafish
(Danio rerio)
Actinopterygii nptnb 34 35
  • 69.62 (n)
NPTN (3 of 3) 35
  • 64 (a)
OneToMany
NPTN (1 of 3) 35
  • 38 (a)
OneToMany
wufj19g07 34
fruit fly
(Drosophila melanogaster)
Insecta Bsg 35
  • 14 (a)
OneToMany
Species where no ortholog for NPTN 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)
  • 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)
  • 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)
  • worm (Caenorhabditis elegans)

Evolution for NPTN Gene

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

Paralogs for NPTN Gene

Paralogs for NPTN Gene

(3) SIMAP similar genes for NPTN Gene using alignment to 6 proteins:

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

Variants for NPTN Gene

Sequence variations from dbSNP and Humsavar for NPTN Gene

SNP ID Clin Chr 15 pos Sequence Context AA Info Type
rs10162782 -- 73,592,470(+) TCAAT(C/T)AGACA intron-variant
rs1043555 -- 73,560,267(-) TTTTT(C/T)TTTTG intron-variant, nc-transcript-variant, downstream-variant-500B, utr-variant-3-prime
rs1043574 -- 73,560,190(-) TTGAC(A/C)CTGTA intron-variant, nc-transcript-variant, downstream-variant-500B, utr-variant-3-prime
rs1043586 -- 73,560,112(-) TTGTA(A/G)ATGCA intron-variant, nc-transcript-variant, downstream-variant-500B, utr-variant-3-prime
rs1043589 -- 73,560,133(-) CGGTT(C/T)TCATG intron-variant, nc-transcript-variant, downstream-variant-500B, utr-variant-3-prime

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

Variant ID Type Subtype PubMed ID
esv1006009 CNV loss 20482838
esv26087 CNV loss 19812545
esv2749873 CNV deletion 23290073
nsv1121512 CNV deletion 24896259
nsv951989 CNV duplication 24416366
nsv951990 CNV duplication 24416366

Variation tolerance for NPTN Gene

Residual Variation Intolerance Score: 24.9% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 0.66; 14.06% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for NPTN Gene

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

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

Disorders for NPTN Gene

MalaCards: The human disease database

(2) MalaCards diseases for NPTN Gene - From: DISEASES, Novoseek, and GeneCards

Disorder Aliases PubMed IDs
allergic bronchopulmonary aspergillosis
  • pulmonary aspergillus disease
acute erythroid leukemia
  • acute erythroleukemia
- elite association - COSMIC cancer census association via MalaCards
Search NPTN in MalaCards View complete list of genes associated with diseases

Relevant External Links for NPTN

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

No data available for UniProtKB/Swiss-Prot and Genatlas for NPTN Gene

Publications for NPTN Gene

  1. Association study of putative promoter polymorphisms in the neuroplastin gene and schizophrenia. (PMID: 17123723) Saito A. … Ito C. (Neurosci. Lett. 2007) 3 22 46 64
  2. The immunolocalization of the synaptic glycoprotein neuroplastin differs substantially between the human and the rodent brain. (PMID: 17196182) Bernstein H.G. … Kreutz M.R. (Brain Res. 2007) 3 4 22 64
  3. Signal peptide prediction based on analysis of experimentally verified cleavage sites. (PMID: 15340161) Zhang Z. … Henzel W.J. (Protein Sci. 2004) 3 4 64
  4. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PMID: 15489334) Gerhard D.S. … Malek J. (Genome Res. 2004) 3 4 64
  5. Large-scale concatenation cDNA sequencing. (PMID: 9110174) Yu W. … Gibbs R.A. (Genome Res. 1997) 2 3 64

Products for NPTN Gene

Sources for NPTN Gene

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