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NPTN neuroplastin [ Homo sapiens (human) ]

Gene ID: 27020, updated on 12-Aug-2018

Summary

Official Symbol
NPTNprovided by HGNC
Official Full Name
neuroplastinprovided by HGNC
Primary source
HGNC:HGNC:17867
See related
Ensembl:ENSG00000156642 MIM:612820; Vega:OTTHUMG00000137586
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
GP55; GP65; SDR1; np55; np65; SDFR1
Summary
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]
Expression
Ubiquitous expression in brain (RPKM 67.5), endometrium (RPKM 61.9) and 25 other tissues See more
Orthologs

Genomic context

See NPTN in Genome Data Viewer
Location:
15q24.1
Exon count:
13
Annotation release Status Assembly Chr Location
109 current GRCh38.p12 (GCF_000001405.38) 15 NC_000015.10 (73560003..73633412, complement)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 15 NC_000015.9 (73852344..73925753, complement)

Chromosome 15 - NC_000015.10Genomic Context describing neighboring genes Neighboring gene VISTA enhancer hs2161 Neighboring gene serine-aspartate repeat-containing protein I-like Neighboring gene REC114 meiotic recombination protein Neighboring gene mitochondrial ribosomal protein S15 pseudogene 1 Neighboring gene NPTN intronic transcript 1 Neighboring gene uncharacterized LOC105370891 Neighboring gene CD276 molecule

Genomic regions, transcripts, and products

Expression

  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Jun 15 11:32:44 2016

Bibliography

GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

Pathways from BioSystems

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Clone Names

  • MGC102805, DKFZp686L2477

Gene Ontology Provided by GOA

Function Evidence Code Pubs
cell adhesion molecule binding ISS
Inferred from Sequence or Structural Similarity
more info
 
cell-cell adhesion mediator activity IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
ion channel binding IEA
Inferred from Electronic Annotation
more info
 
type 1 fibroblast growth factor receptor binding ISS
Inferred from Sequence or Structural Similarity
more info
 
Process Evidence Code Pubs
axon guidance IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
dendrite self-avoidance IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
excitatory synapse assembly IEA
Inferred from Electronic Annotation
more info
 
homophilic cell adhesion via plasma membrane adhesion molecules IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
homophilic cell adhesion via plasma membrane adhesion molecules ISS
Inferred from Sequence or Structural Similarity
more info
 
long-term synaptic potentiation ISS
Inferred from Sequence or Structural Similarity
more info
 
positive regulation of ERK1 and ERK2 cascade IEA
Inferred from Electronic Annotation
more info
 
positive regulation of cellular protein localization IEA
Inferred from Electronic Annotation
more info
 
positive regulation of cytosolic calcium ion concentration ISS
Inferred from Sequence or Structural Similarity
more info
 
positive regulation of fibroblast growth factor receptor signaling pathway ISS
Inferred from Sequence or Structural Similarity
more info
 
positive regulation of long-term neuronal synaptic plasticity ISS
Inferred from Sequence or Structural Similarity
more info
 
positive regulation of long-term synaptic potentiation IEA
Inferred from Electronic Annotation
more info
 
positive regulation of neuron projection development ISS
Inferred from Sequence or Structural Similarity
more info
 
positive regulation of protein phosphorylation ISS
Inferred from Sequence or Structural Similarity
more info
 
regulation of receptor localization to synapse IEA
Inferred from Electronic Annotation
more info
 
trans-synaptic signaling by trans-synaptic complex, modulating synaptic transmission IEA
Inferred from Electronic Annotation
more info
 
visual learning IEA
Inferred from Electronic Annotation
more info
 
Component Evidence Code Pubs
GABA-ergic synapse IEA
Inferred from Electronic Annotation
more info
 
Schaffer collateral - CA1 synapse IEA
Inferred from Electronic Annotation
more info
 
axon IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
cell surface HDA PubMed 
dendrite IEA
Inferred from Electronic Annotation
more info
 
glutamatergic synapse IEA
Inferred from Electronic Annotation
more info
 
inhibitory synapse IEA
Inferred from Electronic Annotation
more info
 
integral component of postsynaptic density membrane IEA
Inferred from Electronic Annotation
more info
 
integral component of presynaptic active zone membrane IEA
Inferred from Electronic Annotation
more info
 
plasma membrane IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
presynaptic membrane ISS
Inferred from Sequence or Structural Similarity
more info
 

General protein information

Preferred Names
neuroplastin
Names
SDR-1
stromal cell derived factor receptor 1
stromal cell-derived receptor 1

NCBI Reference Sequences (RefSeq)

RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

mRNA and Protein(s)

  1. NM_001161363.1NP_001154835.1  neuroplastin isoform c precursor

    See identical proteins and their annotated locations for NP_001154835.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (c) uses an alternate in-frame splice site in the 3' coding region compared to variant b. This results in a shorter protein (isoform c), compared to isoform b.
    Source sequence(s)
    AI357728, AK297184, AK313441, BC105979, CN357076
    Consensus CDS
    CCDS58380.1
    UniProtKB/Swiss-Prot
    Q9Y639
    Related
    ENSP00000457028.1, OTTHUMP00000249169, ENST00000563691.5, OTTHUMT00000420124
    Conserved Domains (3) summary
    pfam13927
    Location:33120
    Ig_3; Immunoglobulin domain
    cl11960
    Location:168219
    Ig; Immunoglobulin domain
    cl28434
    Location:250333
    I-set; Immunoglobulin I-set domain
  2. NM_001161364.1NP_001154836.1  neuroplastin isoform d precursor

    See identical proteins and their annotated locations for NP_001154836.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (d) lacks an alternate in-frame exon in the 5' coding region and uses an alternate in-frame splice site in the 3' coding region, compared to variant b. This results in a shorter protein (isoform d), compared to isoform b.
    Source sequence(s)
    AI357728, BC105979, BC143880, CN357076
    Consensus CDS
    CCDS58379.1
    UniProtKB/Swiss-Prot
    Q9Y639
    Related
    ENSP00000456349.1, OTTHUMP00000249180, ENST00000562924.5, OTTHUMT00000420152
    Conserved Domains (2) summary
    cl11960
    Location:52103
    Ig; Immunoglobulin domain
    cl28434
    Location:134217
    I-set; Immunoglobulin I-set domain
  3. NM_012428.3NP_036560.1  neuroplastin isoform b precursor

    See identical proteins and their annotated locations for NP_036560.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (b), alternatively known as beta, represents the longest transcript and encodes the longest isoform (b).
    Source sequence(s)
    AF109126, AI357728, BC067828, CN357076
    Consensus CDS
    CCDS10249.1
    UniProtKB/Swiss-Prot
    Q9Y639
    Related
    ENSP00000290401.4, OTTHUMP00000174915, ENST00000345330.8, OTTHUMT00000268980
    Conserved Domains (3) summary
    pfam13927
    Location:33120
    Ig_3; Immunoglobulin domain
    cl11960
    Location:168219
    Ig; Immunoglobulin domain
    cl28434
    Location:250333
    I-set; Immunoglobulin I-set domain
  4. NM_017455.3NP_059429.1  neuroplastin isoform a precursor

    See identical proteins and their annotated locations for NP_059429.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (a), alternatively known as alpha, lacks an alternate in-frame exon, compared to variant b. The resulting isoform (a) is shorter, compared to isoform b.
    Source sequence(s)
    AI357728, BC067828, CN357076
    Consensus CDS
    CCDS10250.1
    UniProtKB/Swiss-Prot
    Q9Y639
    Related
    ENSP00000342958.6, OTTHUMP00000174916, ENST00000351217.10, OTTHUMT00000268981
    Conserved Domains (2) summary
    smart00410
    Location:129217
    IG_like; Immunoglobulin like
    cl11960
    Location:52103
    Ig; Immunoglobulin domain

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109 details...Open this link in a new tab

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p12 Primary Assembly

Genomic

  1. NC_000015.10 Reference GRCh38.p12 Primary Assembly

    Range
    73560003..73633412 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_024449900.1XP_024305668.1  neuroplastin isoform X3

    Conserved Domains (3) summary
    cd00096
    Location:1184
    Ig; Immunoglobulin domain
    cl11960
    Location:131182
    Ig; Immunoglobulin domain
    cl28434
    Location:213296
    I-set; Immunoglobulin I-set domain
  2. XM_024449899.1XP_024305667.1  neuroplastin isoform X2

    Conserved Domains (3) summary
    cd00096
    Location:1184
    Ig; Immunoglobulin domain
    cl11960
    Location:131182
    Ig; Immunoglobulin domain
    cl28434
    Location:213296
    I-set; Immunoglobulin I-set domain
  3. XM_011521452.3XP_011519754.1  neuroplastin isoform X1

    Related
    ENSP00000456033.1, OTTHUMP00000249170, ENST00000565282.5
    Conserved Domains (3) summary
    cd00096
    Location:49122
    Ig; Immunoglobulin domain
    smart00410
    Location:245333
    IG_like; Immunoglobulin like
    cl11960
    Location:251333
    Ig; Immunoglobulin domain

RNA

  1. XR_001751220.1 RNA Sequence

  2. XR_001751219.1 RNA Sequence

  3. XR_001751217.1 RNA Sequence

  4. XR_001751216.1 RNA Sequence

  5. XR_001751223.2 RNA Sequence

  6. XR_001751222.2 RNA Sequence

  7. XR_001751221.2 RNA Sequence

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