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    Nptn neuroplastin [ Rattus norvegicus (Norway rat) ]

    Gene ID: 56064, updated on 27-Nov-2024

    Summary

    Official Symbol
    Nptnprovided by RGD
    Official Full Name
    neuroplastinprovided by RGD
    Primary source
    RGD:620296
    See related
    EnsemblRapid:ENSRNOG00000009029 AllianceGenome:RGD:620296
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Rattus norvegicus
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
    Also known as
    SDR-1; Sdfr1
    Summary
    Enables cell adhesion molecule binding activity; transmembrane transporter binding activity; and type 1 fibroblast growth factor receptor binding activity. Involved in several processes, including homophilic cell adhesion via plasma membrane adhesion molecules; modulation of chemical synaptic transmission; and positive regulation of signal transduction. Located in several cellular components, including cell surface; inhibitory synapse; and presynaptic membrane. Is active in several cellular components, including GABA-ergic synapse; Schaffer collateral - CA1 synapse; and synaptic membrane. Orthologous to human NPTN (neuroplastin). [provided by Alliance of Genome Resources, Nov 2024]
    Expression
    Biased expression in Brain (RPKM 771.0), Heart (RPKM 500.1) and 9 other tissues See more
    Orthologs
    NEW
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    Genomic context

    See Nptn in Genome Data Viewer
    Location:
    8q24
    Exon count:
    11
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCr8 (GCF_036323735.1) 8 NC_086026.1 (67892678..67959231)
    RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 8 NC_051343.1 (58996873..59063402)
    106 previous assembly Rnor_6.0 (GCF_000001895.5) 8 NC_005107.4 (63379062..63445694)

    Chromosome 8 - NC_086026.1Genomic Context describing neighboring genes Neighboring gene inhibitory synaptic factor 1 Neighboring gene Cd276 molecule Neighboring gene nucleophosmin-like Neighboring gene REC114 meiotic recombination protein Neighboring gene hyperpolarization activated cyclic nucleotide-gated potassium channel 4

    Genomic regions, transcripts, and products

    Expression

    • Project title: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages
    • Description: 320 RNA samples isolated from 11 organs (adrenal gland, brain, heart, kidney, liver, lung, muscle, spleen, thymus, and testes or uterus) from both sexes of Fischer 344 rats across four developmental stages (2-, 6-, 21-, and 104-weeks-old)
    • BioProject: PRJNA238328
    • Publication: PMID 24510058
    • Analysis date: Mon Jun 6 17:44:12 2016

    Bibliography

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Gene Ontology Provided by RGD

    Function Evidence Code Pubs
    enables cell adhesion molecule binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables cell-cell adhesion mediator activity IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    enables transmembrane transporter binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    enables type 1 fibroblast growth factor receptor binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    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
     
    acts_upstream_of_or_within excitatory synapse assembly ISO
    Inferred from Sequence Orthology
    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 IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in intracellular calcium ion homeostasis IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in intracellular calcium ion homeostasis ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in long-term synaptic potentiation IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in modulation of chemical synaptic transmission IEA
    Inferred from Electronic Annotation
    more info
     
    acts_upstream_of_or_within modulation of chemical synaptic transmission ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in negative regulation of cytokine production IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in negative regulation of cytokine production ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in negative regulation of cytokine production ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in positive regulation of ERK1 and ERK2 cascade IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in positive regulation of cytosolic calcium ion concentration IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in positive regulation of fibroblast growth factor receptor signaling pathway IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in positive regulation of long-term neuronal synaptic plasticity IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in positive regulation of long-term synaptic potentiation IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in positive regulation of neuron projection development IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in positive regulation of protein localization IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in positive regulation of protein phosphorylation IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in regulation of cell adhesion TAS
    Traceable Author Statement
    more info
    PubMed 
    involved_in regulation of receptor localization to synapse IEA
    Inferred from Electronic Annotation
    more info
     
    acts_upstream_of_or_within regulation of receptor localization to synapse ISO
    Inferred from Sequence Orthology
    more info
     
    acts_upstream_of_or_within synapse organization ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in trans-synaptic signaling by trans-synaptic complex, modulating synaptic transmission EXP
    Inferred from Experiment
    more info
    PubMed 
    involved_in trans-synaptic signaling by trans-synaptic complex, modulating synaptic transmission IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in visual learning IDA
    Inferred from Direct Assay
    more info
    PubMed 
    Component Evidence Code Pubs
    is_active_in GABA-ergic synapse EXP
    Inferred from Experiment
    more info
    PubMed 
    is_active_in GABA-ergic synapse IDA
    Inferred from Direct Assay
    more info
    PubMed 
    is_active_in Schaffer collateral - CA1 synapse EXP
    Inferred from Experiment
    more info
    PubMed 
    is_active_in Schaffer collateral - CA1 synapse IDA
    Inferred from Direct Assay
    more info
    PubMed 
    is_active_in axon IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    located_in cell surface IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in dendrite IDA
    Inferred from Direct Assay
    more info
    PubMed 
    is_active_in glutamatergic synapse EXP
    Inferred from Experiment
    more info
    PubMed 
    is_active_in glutamatergic synapse IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in immunological synapse IEA
    Inferred from Electronic Annotation
    more info
     
    located_in immunological synapse ISO
    Inferred from Sequence Orthology
    more info
     
    located_in immunological synapse ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    located_in inhibitory synapse IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in membrane IEA
    Inferred from Electronic Annotation
    more info
     
    located_in membrane TAS
    Traceable Author Statement
    more info
    PubMed 
    is_active_in plasma membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    located_in plasma membrane TAS
    Traceable Author Statement
    more info
     
    is_active_in postsynaptic density membrane IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in postsynaptic membrane TAS
    Traceable Author Statement
    more info
    PubMed 
    is_active_in presynaptic active zone membrane EXP
    Inferred from Experiment
    more info
    PubMed 
    is_active_in presynaptic active zone membrane IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in presynaptic membrane IDA
    Inferred from Direct Assay
    more info
    PubMed 
    is_active_in synaptic membrane IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in synaptic membrane IDA
    Inferred from Direct Assay
    more info
    PubMed 

    General protein information

    Preferred Names
    neuroplastin
    Names
    glycoprotein 55
    glycoprotein 55/65
    glycoprotein 65
    gp55/65
    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_001413347.1NP_001400276.1  neuroplastin isoform 1 precursor

      Status: VALIDATED

      Source sequence(s)
      JAXUCZ010000008
      UniProtKB/TrEMBL
      A0A8L2Q5B1, A6J511
      Related
      ENSRNOP00000012091.7, ENSRNOT00000012091.9
    2. NM_001413348.1NP_001400277.1  neuroplastin isoform 3 precursor

      Status: VALIDATED

      Source sequence(s)
      JAXUCZ010000008
      UniProtKB/TrEMBL
      A6J512
      Related
      ENSRNOP00000012295.5, ENSRNOT00000012295.8
    3. NM_001413349.1NP_001400278.1  neuroplastin isoform 4 precursor

      Status: VALIDATED

      Source sequence(s)
      JAXUCZ010000008
    4. NM_019380.3NP_062253.1  neuroplastin isoform 2 precursor

      See identical proteins and their annotated locations for NP_062253.1

      Status: VALIDATED

      Source sequence(s)
      JAXUCZ010000008
      UniProtKB/Swiss-Prot
      P97546, P97547, Q6IRE8
      UniProtKB/TrEMBL
      A6J510
      Related
      ENSRNOP00000105040.1, ENSRNOT00000140093.1
      Conserved Domains (2) summary
      cd00096
      Location:3236
      Ig; Ig strand A [structural motif]
      cl11960
      Location:31146
      Ig; Immunoglobulin domain

    RefSeqs of Annotated Genomes: GCF_036323735.1-RS_2024_02

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

    Reference GRCr8

    Genomic

    1. NC_086026.1 Reference GRCr8

      Range
      67892678..67959231
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_063266041.1XP_063122111.1  neuroplastin isoform X1

    2. XM_039082020.2XP_038937948.1  neuroplastin isoform X2

      UniProtKB/TrEMBL
      A6J510
      Conserved Domains (2) summary
      cd00096
      Location:3236
      Ig; Ig strand A [structural motif]
      cl11960
      Location:31146
      Ig; Immunoglobulin domain

    RNA

    1. XR_010054023.1 RNA Sequence

      Related
      ENSRNOT00000107680.2
    2. XR_005487909.2 RNA Sequence