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    NPTN neuroplastin [ Homo sapiens (human) ]

    Gene ID: 27020, updated on 27-Nov-2024

    Summary

    Official Symbol
    NPTNprovided by HGNC
    Official Full Name
    neuroplastinprovided by HGNC
    Primary source
    HGNC:HGNC:17867
    See related
    Ensembl:ENSG00000156642 MIM:612820; AllianceGenome:HGNC:17867
    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
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    See NPTN in Genome Data Viewer
    Location:
    15q24.1
    Exon count:
    11
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 15 NC_000015.10 (73560014..73633389, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 15 NC_060939.1 (71377168..71450559, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 15 NC_000015.9 (73852355..73925730, 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 ReSE screen-validated silencer GRCh37_chr15:73879798-73879963 Neighboring gene NANOG hESC enhancer GRCh37_chr15:73909554-73910143 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr15:73910157-73910718 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6633 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6634 Neighboring gene uncharacterized LOC105370891 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:73975613-73976121 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6635 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6636 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6637 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6638 Neighboring gene H3K27ac hESC enhancer GRCh37_chr15:73977139-73977645 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:73988434-73988945 Neighboring gene H3K27ac-H3K4me1 hESC enhancers GRCh37_chr15:73988946-73989458 and GRCh37_chr15:73989459-73989969 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6639 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:73994347-73995068 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 Apr 4 07:08:55 2018

    Bibliography

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?

    Pathways from PubChem

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Clone Names

    • MGC102805, DKFZp686L2477

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables cell adhesion molecule binding ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    enables cell-cell adhesion mediator activity IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    enables type 1 fibroblast growth factor receptor binding ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    Process Evidence Code Pubs
    involved_in axon guidance IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in dendrite self-avoidance IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in excitatory synapse assembly IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in homophilic cell adhesion via plasma membrane adhesion molecules IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in homophilic cell adhesion via plasma membrane adhesion molecules ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in intracellular calcium ion homeostasis ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in long-term synaptic potentiation ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in negative regulation of cytokine production ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in positive regulation of cytosolic calcium ion concentration ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in positive regulation of fibroblast growth factor receptor signaling pathway ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in positive regulation of long-term neuronal synaptic plasticity ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in positive regulation of neuron projection development ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in positive regulation of protein phosphorylation ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in regulation of receptor localization to synapse IEA
    Inferred from Electronic Annotation
    more info
     
    Component Evidence Code Pubs
    is_active_in axon IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    located_in cell surface HDA PubMed 
    located_in immunological synapse ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    is_active_in plasma membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    located_in postsynaptic density IEA
    Inferred from Electronic Annotation
    more info
     
    located_in 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)

    NEW Try the new Transcript table

    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_001161363.2NP_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)
      AK297184, AK313441, BC105979, CN357076
      Consensus CDS
      CCDS58380.1
      UniProtKB/Swiss-Prot
      Q9Y639
      Related
      ENSP00000457028.1, ENST00000563691.5
      Conserved Domains (3) summary
      pfam13927
      Location:238320
      Ig_3; Immunoglobulin domain
      cd00096
      Location:3236
      Ig; Ig strand A [structural motif]
      cl11960
      Location:31146
      Ig; Immunoglobulin domain
    2. NM_001161364.2NP_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)
      BC105979, BC143880, CN357076
      Consensus CDS
      CCDS58379.1
      UniProtKB/Swiss-Prot
      Q9Y639
      Related
      ENSP00000456349.1, ENST00000562924.5
      Conserved Domains (3) summary
      pfam13927
      Location:122204
      Ig_3; Immunoglobulin domain
      cd00096
      Location:139146
      Ig; Ig strand B [structural motif]
      cl11960
      Location:52103
      Ig; Immunoglobulin domain
    3. NM_012428.4NP_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
      B2RAL7, B7Z4D3, B7ZLL2, Q17R52, Q59EJ9, Q6NVX7, Q9Y639, Q9Y640
      Related
      ENSP00000290401.4, ENST00000345330.9
      Conserved Domains (3) summary
      pfam13927
      Location:238320
      Ig_3; Immunoglobulin domain
      cd00096
      Location:3236
      Ig; Ig strand A [structural motif]
      cl11960
      Location:31146
      Ig; Immunoglobulin domain
    4. NM_017455.4NP_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, ENST00000351217.10
      Conserved Domains (3) summary
      pfam13927
      Location:122204
      Ig_3; Immunoglobulin domain
      cd00096
      Location:139146
      Ig; Ig strand B [structural motif]
      cl11960
      Location:52103
      Ig; Immunoglobulin domain

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

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

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000015.10 Reference GRCh38.p14 Primary Assembly

      Range
      73560014..73633389 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047432389.1XP_047288345.1  neuroplastin isoform X1

    RNA

    1. XR_007064440.1 RNA Sequence

    2. XR_007064439.1 RNA Sequence

    3. XR_007064438.1 RNA Sequence

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060939.1 Alternate T2T-CHM13v2.0

      Range
      71377168..71450559 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054377730.1XP_054233705.1  neuroplastin isoform X1

    RNA

    1. XR_008488940.1 RNA Sequence

    2. XR_008488939.1 RNA Sequence

    3. XR_008488938.1 RNA Sequence