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    Nptn neuroplastin [ Mus musculus (house mouse) ]

    Gene ID: 20320, updated on 2-Nov-2024

    Summary

    Official Symbol
    Nptnprovided by MGI
    Official Full Name
    neuroplastinprovided by MGI
    Primary source
    MGI:MGI:108077
    See related
    Ensembl:ENSMUSG00000032336 AllianceGenome:MGI:108077
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Mus musculus
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
    Also known as
    NP65; SDR-1; Sdfr1
    Summary
    Predicted to enable cell adhesion molecule binding activity; transmembrane transporter binding activity; and type 1 fibroblast growth factor receptor binding activity. Involved in intracellular calcium ion homeostasis and negative regulation of cytokine production. Acts upstream of or within excitatory synapse assembly; modulation of chemical synaptic transmission; and regulation of receptor localization to synapse. Located in immunological synapse. Is expressed in several structures, including cardiovascular system; genitourinary system; gut; nervous system; and respiratory system. Orthologous to human NPTN (neuroplastin). [provided by Alliance of Genome Resources, Nov 2024]
    Expression
    Ubiquitous expression in cortex adult (RPKM 131.7), cerebellum adult (RPKM 131.6) and 28 other tissues See more
    Orthologs
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    Genomic context

    See Nptn in Genome Data Viewer
    Location:
    9 B; 9 31.79 cM
    Exon count:
    11
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCm39 (GCF_000001635.27) 9 NC_000075.7 (58489504..58560162)
    108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 9 NC_000075.6 (58582240..58652879)

    Chromosome 9 - NC_000075.7Genomic Context describing neighboring genes Neighboring gene inhibitory synaptic factor 1 Neighboring gene STARR-positive B cell enhancer ABC_E6742 Neighboring gene predicted gene, 53528 Neighboring gene CD276 antigen Neighboring gene STARR-positive B cell enhancer ABC_E1387 Neighboring gene REC114 meiotic recombination protein Neighboring gene predicted gene 20620 Neighboring gene predicted gene, 21183

    Genomic regions, transcripts, and products

    Expression

    • Project title: Mouse ENCODE transcriptome data Mouse ENCODE transcriptome data
    • Description: RNA profiling data sets generated by the Mouse ENCODE project.
    • BioProject: PRJNA66167
    • Publication: PMID 25409824
    • Analysis date: n/a

    Bibliography

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?

    Variation

    Alleles

    Alleles of this type are documented at Mouse Genome Informatics  (MGI)

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Gene Ontology Provided by MGI

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

    General protein information

    Preferred Names
    neuroplastin
    Names
    stromal cell derived factor 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_001293673.2NP_001280602.1  neuroplastin isoform 2 precursor

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) lacks an alternate in-frame exon compared to variant 3. The resulting isoform (2) has the same N- and C-termini but is shorter compared to isoform 3.
      Source sequence(s)
      CT030640
      Consensus CDS
      CCDS81009.1
      Related
      ENSMUSP00000135541.2, ENSMUST00000176557.8
      Conserved Domains (1) summary
      cl11960
      Location:133216
      Ig; Immunoglobulin domain
    2. NM_001357751.2NP_001344680.1  neuroplastin isoform 3 precursor

      Status: VALIDATED

      Description
      Transcript Variant: This variant (3) represents the longest transcript and encodes the longest isoform (3).
      Source sequence(s)
      CT030640
      Conserved Domains (2) summary
      cd00096
      Location:48121
      Ig; Immunoglobulin domain
      cl11960
      Location:249332
      Ig; Immunoglobulin domain
    3. NM_001406062.1NP_001392991.1  neuroplastin isoform 4 precursor

      Status: VALIDATED

      Source sequence(s)
      CT030640
      UniProtKB/Swiss-Prot
      P97300, Q3U519, Q8C637, Q8C6H8
    4. NM_009145.3NP_033171.2  neuroplastin isoform 1 precursor

      See identical proteins and their annotated locations for NP_033171.2

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) lacks an alternate in-frame exon and uses an alternate in-frame splice junction compared to variant 3. The resulting isoform (1) has the same N- and C-termini but is shorter compared to isoform 3.
      Source sequence(s)
      CT030640
      Consensus CDS
      CCDS23245.1
      Related
      ENSMUSP00000082793.6, ENSMUST00000085651.12
      Conserved Domains (1) summary
      cl11960
      Location:133216
      Ig; Immunoglobulin domain

    RNA

    1. NR_151824.2 RNA Sequence

      Status: VALIDATED

      Description
      Transcript Variant: This variant (4) lacks an alternate exon and uses two alternate splice junctions compared to variant 3. This variant is represented as non-coding because the use of the 5'-most expected translational start codon renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
      Source sequence(s)
      CT030640

    RefSeqs of Annotated Genomes: GCF_000001635.27-RS_2024_02

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

    Reference GRCm39 C57BL/6J

    Genomic

    1. NC_000075.7 Reference GRCm39 C57BL/6J

      Range
      58489504..58560162
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_006510883.3XP_006510946.1  neuroplastin isoform X1

      See identical proteins and their annotated locations for XP_006510946.1

      UniProtKB/Swiss-Prot
      P97300, Q3U519, Q8C637, Q8C6H8
      Related
      ENSMUSP00000135199.2, ENSMUST00000177292.8
      Conserved Domains (2) summary
      cd00096
      Location:48121
      Ig; Immunoglobulin domain
      cl11960
      Location:249332
      Ig; Immunoglobulin domain
    2. XM_036154741.1XP_036010634.1  neuroplastin isoform X4

      Conserved Domains (2) summary
      cd00096
      Location:3236
      Ig; Ig strand A [structural motif]
      cl11960
      Location:31146
      Ig; Immunoglobulin domain
    3. XM_036154739.1XP_036010632.1  neuroplastin isoform X2

      Conserved Domains (2) summary
      cd00096
      Location:3236
      Ig; Ig strand A [structural motif]
      cl11960
      Location:31146
      Ig; Immunoglobulin domain
    4. XM_036154740.1XP_036010633.1  neuroplastin isoform X3

      Conserved Domains (2) summary
      cd00096
      Location:3236
      Ig; Ig strand A [structural motif]
      cl11960
      Location:31146
      Ig; Immunoglobulin domain
    5. XM_030244148.2XP_030100008.1  neuroplastin isoform X5

      Conserved Domains (1) summary
      cl11960
      Location:133216
      Ig; Immunoglobulin domain

    RNA

    1. XR_003947819.2 RNA Sequence

    2. XR_004935351.1 RNA Sequence

    3. XR_004935353.1 RNA Sequence

    4. XR_004935352.1 RNA Sequence

    5. XR_004935354.1 RNA Sequence

    6. XR_003947820.2 RNA Sequence