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

Gene ID: 306128, updated on 4-Jan-2025

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 several functions, including 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 visual perception. Predicted to be located in several cellular components, including Golgi apparatus; perinuclear region of cytoplasm; and vacuole. Predicted to be active in lysosomal membrane. 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, Jan 2025]
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

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