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    Cln6 ceroid-lipofuscinosis, neuronal 6 [ Mus musculus (house mouse) ]

    Gene ID: 76524, updated on 9-Dec-2024

    Summary

    Official Symbol
    Cln6provided by MGI
    Official Full Name
    ceroid-lipofuscinosis, neuronal 6provided by MGI
    Primary source
    MGI:MGI:2159324
    See related
    Ensembl:ENSMUSG00000032245 AllianceGenome:MGI:2159324
    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
    nclf; D9Bwg1455e; 1810065L06Rik
    Summary
    Predicted to enable lysophosphatidic acid binding activity; protein homodimerization activity; and sulfatide binding activity. Acts upstream of or within several processes, including locomotion involved in locomotory behavior; lysosome organization; and visual perception. Predicted to be located in several cellular components, including early endosome; endoplasmic reticulum lumen; and membrane raft. Predicted to be active in endoplasmic reticulum and membrane. Is expressed in several structures, including central nervous system and retina. Used to study neuronal ceroid lipofuscinosis 6A. Human ortholog(s) of this gene implicated in neuronal ceroid lipofuscinosis; neuronal ceroid lipofuscinosis 6A; and neuronal ceroid lipofuscinosis 6B. Orthologous to human CLN6 (CLN6 transmembrane ER protein). [provided by Alliance of Genome Resources, Dec 2024]
    Expression
    Ubiquitous expression in testis adult (RPKM 42.3), placenta adult (RPKM 37.5) and 26 other tissues See more
    Orthologs
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    Genomic context

    See Cln6 in Genome Data Viewer
    Location:
    9 B; 9 33.89 cM
    Exon count:
    7
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCm39 (GCF_000001635.27) 9 NC_000075.7 (62746067..62759288)
    108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 9 NC_000075.6 (62838785..62852006)

    Chromosome 9 - NC_000075.7Genomic Context describing neighboring genes Neighboring gene dCTP pyrophosphatase 1 pseudogene Neighboring gene CapStarr-seq enhancer MGSCv37_chr9:62659735-62659918 Neighboring gene fem 1 homolog b Neighboring gene STARR-positive B cell enhancer ABC_E6750 Neighboring gene STARR-seq mESC enhancer starr_24388 Neighboring gene STARR-seq mESC enhancer starr_24389 Neighboring gene ribsomal protein S2 pseudogene Neighboring gene calmodulin-like 4 Neighboring gene protein inhibitor of activated STAT 1 Neighboring gene STARR-positive B cell enhancer ABC_E10555 Neighboring gene STARR-positive B cell enhancer ABC_E6752 Neighboring gene STARR-positive B cell enhancer ABC_E9029 Neighboring gene STARR-positive B cell enhancer ABC_E9765 Neighboring gene STARR-positive B cell enhancer ABC_E9766 Neighboring gene predicted gene, 35574

    Genomic regions, transcripts, and products

    Expression

    • 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

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?

    Variation

    Alleles

    Alleles of this type are documented at Mouse Genome Informatics  (MGI)
    • Endonuclease-mediated (3) 
    • Spontaneous (1)  1 citation
    • Targeted (3) 

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Gene Ontology Provided by MGI

    Function Evidence Code Pubs
    enables lysophosphatidic acid binding ISO
    Inferred from Sequence Orthology
    more info
     
    enables protein homodimerization activity ISO
    Inferred from Sequence Orthology
    more info
     
    enables sulfatide binding ISO
    Inferred from Sequence Orthology
    more info
     
    Component Evidence Code Pubs
    located_in early endosome ISO
    Inferred from Sequence Orthology
    more info
     
    is_active_in endoplasmic reticulum IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    located_in endoplasmic reticulum ISO
    Inferred from Sequence Orthology
    more info
     
    located_in endoplasmic reticulum lumen ISO
    Inferred from Sequence Orthology
    more info
     
    located_in intracellular membrane-bounded organelle ISO
    Inferred from Sequence Orthology
    more info
     
    is_active_in membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    located_in membrane raft ISO
    Inferred from Sequence Orthology
    more info
     
    located_in nucleolus ISO
    Inferred from Sequence Orthology
    more info
     

    General protein information

    Preferred Names
    ceroid-lipofuscinosis neuronal protein 6

    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_001033175.3NP_001028347.1  ceroid-lipofuscinosis neuronal protein 6

      See identical proteins and their annotated locations for NP_001028347.1

      Status: VALIDATED

      Source sequence(s)
      AC164614
      Consensus CDS
      CCDS23267.1
      UniProtKB/TrEMBL
      A0PJN2, Q3U466
      Related
      ENSMUSP00000034776.7, ENSMUST00000034776.13
      Conserved Domains (1) summary
      pfam15156
      Location:27306
      CLN6; Ceroid-lipofuscinosis neuronal protein 6

    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
      62746067..62759288
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)