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    Npcd neuronal pentraxin chromo domain [ Mus musculus (house mouse) ]

    Gene ID: 504193, updated on 8-Feb-2024

    Summary

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    Official Symbol
    Npcdprovided by MGI
    Official Full Name
    neuronal pentraxin chromo domainprovided by MGI
    Primary source
    MGI:MGI:3845555
    See related
    Ensembl:ENSMUSG00000089837 AllianceGenome:MGI:3845555
    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
    Cbx6-Nptxr
    Summary
    This gene encodes multiple cytoplasmic proteins composed of a neuronal pentraxin domain linked to a chromo domain. These isoforms are expressed in numerous regions of the central nervous system, where they are present in distinct subcellular arrangements in different brain regions. This gene may play a role in neuronal differentiation. [provided by RefSeq, Jul 2008]
    Expression
    Biased expression in cortex adult (RPKM 148.6), frontal lobe adult (RPKM 84.5) and 7 other tissues See more
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    Genomic context

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    See Npcd in Genome Data Viewer
    Location:
    15 E1; 15 37.85 cM
    Exon count:
    9
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCm39 (GCF_000001635.27) 15 NC_000081.7 (79670552..79718534, complement)
    108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 15 NC_000081.6 (79786351..79834333, complement)

    Chromosome 15 - NC_000081.7Genomic Context describing neighboring genes Neighboring gene STARR-positive B cell enhancer ABC_E390 Neighboring gene dynein, axonemal, light chain 4 Neighboring gene predicted gene, 30977 Neighboring gene predicted gene, 57816 Neighboring gene neuronal pentraxin receptor Neighboring gene chromobox 6 Neighboring gene predicted gene 10856 Neighboring gene STARR-seq mESC enhancer starr_39199 Neighboring gene RIKEN cDNA D730005E14 gene Neighboring gene STARR-positive B cell enhancer ABC_E7391 Neighboring gene apolipoprotein B mRNA editing enzyme, catalytic polypeptide 3

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: 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

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    Related articles in PubMed

    1. A novel substrate of receptor tyrosine phosphatase PTPRO is required for nerve growth factor-induced process outgrowth. Chen B, et al. J Neurosci, 2005 Jan 26. PMID 15673668, Free PMC Article
    2. Interaction of an intracellular pentraxin with a BTB-Kelch protein is associated with ubiquitylation, aggregation and neuronal apoptosis. Tseng LA, et al. Mol Cell Neurosci, 2011 Aug. PMID 21549840, Free PMC Article
    3. Neuronal pentraxin with chromo domain (NPCD) is a novel class of protein expressed in multiple neuronal domains. Chen B, et al. J Comp Neurol, 2005 Jan 24. PMID 15593341
    4. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. Strausberg RL, et al. Proc Natl Acad Sci U S A, 2002 Dec 24. PMID 12477932, Free PMC Article
    5. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Gaudet P, et al. Brief Bioinform, 2011 Sep. PMID 21873635, Free PMC Article

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. We confirm that NPCD isoforms interact with the catalytic phosphatase domain of PTPRO and also that NPCD is likely to be relevant to axon growth and/or guidance.
      Title: A novel substrate of receptor tyrosine phosphatase PTPRO is required for nerve growth factor-induced process outgrowth.
    Submit: New GeneRIF Correction

    Variation

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    Alleles

    Alleles of this type are documented at Mouse Genome Informatics  (MGI)
    • Endonuclease-mediated (1) 

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Readthrough Npcd

    Included genes: Nptxr, Cbx6

    Gene Ontology Provided by MGI

    Function Evidence Code Pubs
    enables protein domain specific binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Component Evidence Code Pubs
    located_in cytoplasm IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in cytoplasmic side of plasma membrane IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in cytosol IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in dendrite IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in filopodium IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in growth cone IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in neuronal cell body IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in nucleus IDA
    Inferred from Direct Assay
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    neuronal pentraxin with chromo domain
    Names
    Cbx6-Nptxr readthrough transcripts

    NCBI Reference Sequences (RefSeq)

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    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_001013360.2 → NP_001013378.2  neuronal pentraxin with chromo domain isoform 1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) lacks an in-frame exon in the central coding region, compared to variant 2. The encoded isoform (1) is shorter, compared to isoform 2.
      Source sequence(s)
      AC113595, AC118227, AY394488, BC060093, CD578976
      UniProtKB/TrEMBL
      H3BLN6, Q6TLW1
      Related
      ENSMUSP00000023060.7, ENSMUST00000023060.13
      Conserved Domains (2) summary
      smart00159
      Location:160 → 366
      PTX; Pentraxin / C-reactive protein / pentaxin family
      smart00298
      Location:10 → 62
      CHROMO; Chromatin organization modifier domain

    2. NM_001013362.2 → NP_001013380.2  neuronal pentraxin with chromo domain isoform 2

      See identical proteins and their annotated locations for NP_001013380.2

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) represents the longer transcript and encodes the longer isoform (2).
      Source sequence(s)
      AC113595, AC118227, AY394489, BC060093, CD578976
      UniProtKB/TrEMBL
      F8VQB8, Q6TLW0
      Related
      ENSMUSP00000086714.6, ENSMUST00000089299.6
      Conserved Domains (2) summary
      smart00159
      Location:257 → 463
      PTX; Pentraxin / C-reactive protein / pentaxin family
      smart00298
      Location:10 → 62
      CHROMO; Chromatin organization modifier domain

    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_000081.7 Reference GRCm39 C57BL/6J

      Range
      79670552..79718534 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Suppressed Reference Sequence(s)

    The following Reference Sequences have been suppressed. Explain

    1. NM_029079.2: Suppressed sequence

      Description
      NM_029079.2: This RefSeq was permanently suppressed because currently there is insufficient support for the transcript and the protein.
    Nucleotide Protein Strain
    Heading Accession and Version

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