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    Cln5 CLN5, intracellular trafficking protein [ Rattus norvegicus (Norway rat) ]

    Gene ID: 306128, updated on 9-Dec-2024

    Summary

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    Official Symbol
    Cln5provided by RGD
    Official Full Name
    CLN5, intracellular trafficking proteinprovided by RGD
    Primary source
    RGD:1306965
    See related
    EnsemblRapid:ENSRNOG00000062279 AllianceGenome:RGD:1306965
    Gene type
    protein coding
    RefSeq status
    PROVISIONAL
    Organism
    Rattus norvegicus
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
    Summary
    Predicted to enable D-mannose binding activity; bis(monoacylglycero)phosphate synthase activity; and long-chain fatty acyl-CoA hydrolase activity. Predicted to be involved in several processes, including lysosomal lumen acidification; nervous system development; and signal peptide processing. Predicted to act upstream of or within lysosome organization and visual perception. Predicted to be located in several cellular components, including Golgi apparatus; perinuclear region of cytoplasm; and vacuole. Human ortholog(s) of this gene implicated in neuronal ceroid lipofuscinosis 5. Orthologous to human CLN5 (CLN5 intracellular trafficking protein). [provided by Alliance of Genome Resources, Dec 2024]
    Expression
    Biased expression in Lung (RPKM 98.6), Heart (RPKM 80.0) and 9 other tissues See more
    Orthologs
    human mouse all
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    Genomic context

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    See Cln5 in Genome Data Viewer
    Location:
    15q21
    Exon count:
    4
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCr8 (GCF_036323735.1) 15 NC_086033.1 (86308286..86321679)
    RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 15 NC_051350.1 (79893573..79903438)
    106 previous assembly Rnor_6.0 (GCF_000001895.5) 15 NC_005114.4 (93634815..93644146)

    Chromosome 15 - NC_086033.1Genomic Context describing neighboring genes Neighboring gene U6 spliceosomal RNA Neighboring gene uncharacterized LOC108352966 Neighboring gene F-box and leucine-rich repeat protein 3 Neighboring gene MYC binding protein 2 Neighboring gene cytochrome c, somatic pseudogene Neighboring gene uncharacterized LOC108352959

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • 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

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    Related articles in PubMed

    1. The neuronal ceroid lipofuscinosis protein CLN5: new insights into cellular maturation, transport, and consequences of mutations. Schmiedt ML, et al. Hum Mutat, 2010 Mar. PMID 20052765
    2. Identification of sites of mannose 6-phosphorylation on lysosomal proteins. Sleat DE, et al. Mol Cell Proteomics, 2006 Apr. PMID 16399764
    3. A mouse model for Finnish variant late infantile neuronal ceroid lipofuscinosis, CLN5, reveals neuropathology associated with early aging. Kopra O, et al. Hum Mol Genet, 2004 Dec 1. PMID 15459177
    4. Lysosomal localization of the neuronal ceroid lipofuscinosis CLN5 protein. Isosomppi J, et al. Hum Mol Genet, 2002 Apr 15. PMID 11971870
    5. The mouse ortholog of the neuronal ceroid lipofuscinosis CLN5 gene encodes a soluble lysosomal glycoprotein expressed in the developing brain. Holmberg V, et al. Neurobiol Dis, 2004 Jun. PMID 15207259

    See all (13) citations in PubMed

    GeneRIFs: Gene References Into Functions

    General gene information

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    Markers

    Homology

    Gene Ontology Provided by RGD

    Function Evidence Code Pubs
    enables D-mannose binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables bis(monoacylglycero)phosphate synthase activity ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables hydrolase activity, acting on glycosyl bonds IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables long-chain fatty acyl-CoA hydrolase activity ISO
    Inferred from Sequence Orthology
    more info
    		  
    Process Evidence Code Pubs
    involved_in biological_process ND
    No biological Data available
    more info
    		  
    involved_in brain development ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in glycosylation ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in lysosomal lumen acidification ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in lysosome organization IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    acts_upstream_of_or_within lysosome organization ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in neurogenesis ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in retrograde transport, endosome to Golgi ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in signal peptide processing ISO
    Inferred from Sequence Orthology
    more info
    		  
    acts_upstream_of_or_within visual perception ISO
    Inferred from Sequence Orthology
    more info
    		  
    Component Evidence Code Pubs
    located_in Golgi apparatus ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in cytosol IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in endoplasmic reticulum ISO
    Inferred from Sequence Orthology
    more info
    		  
    is_active_in lysosomal membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in lysosomal membrane ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in lysosome ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in membrane ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in perinuclear region of cytoplasm ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in vacuolar lumen ISO
    Inferred from Sequence Orthology
    more info
    		  

    General protein information

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    Preferred Names
    ceroid-lipofuscinosis neuronal protein 5
    Names
    ceroid-lipofuscinosis, neuronal 5

    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_001191689.1 → NP_001178618.1  ceroid-lipofuscinosis neuronal protein 5 precursor

      Status: PROVISIONAL

      Source sequence(s)
      JAXUCZ010000015
      UniProtKB/TrEMBL
      A0A0G2K6S0
      Conserved Domains (1) summary
      pfam15014
      Location:35 → 332
      CLN5; Ceroid-lipofuscinosis neuronal protein 5

    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_086033.1 Reference GRCr8

      Range
      86308286..86321679
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_039093400.2 → XP_038949328.1  ceroid-lipofuscinosis neuronal protein 5 isoform X1

      UniProtKB/TrEMBL
      A0A0G2K6S0, A0A1W2Q672
      Related
      ENSRNOP00000076164.2, ENSRNOT00000093318.3
      Conserved Domains (1) summary
      pfam15014
      Location:36 → 339
      CLN5; Ceroid-lipofuscinosis neuronal protein 5
    Nucleotide Protein Strain
    Heading Accession and Version

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.