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

Gene ID: 76524, updated on 8-Feb-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 6. Human ortholog(s) of this gene implicated in neuronal ceroid lipofuscinosis; neuronal ceroid lipofuscinosis 4A; and neuronal ceroid lipofuscinosis 6. Orthologous to human CLN6 (CLN6 transmembrane ER protein). [provided by Alliance of Genome Resources, Apr 2022]
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)
  • Spontaneous (1)  1 citation
  • Targeted (3) 
  • Endonuclease-mediated (1) 

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 protein homodimerization activity ISS
Inferred from Sequence or Structural Similarity
more info
PubMed 
enables sulfatide binding ISO
Inferred from Sequence Orthology
more info
 
Process Evidence Code Pubs
involved_in cholesterol metabolic process ISO
Inferred from Sequence Orthology
more info
 
involved_in cholesterol metabolic process ISS
Inferred from Sequence or Structural Similarity
more info
PubMed 
involved_in ganglioside metabolic process ISO
Inferred from Sequence Orthology
more info
 
involved_in ganglioside metabolic process ISS
Inferred from Sequence or Structural Similarity
more info
PubMed 
involved_in glycosaminoglycan metabolic process ISO
Inferred from Sequence Orthology
more info
 
involved_in glycosaminoglycan metabolic process ISS
Inferred from Sequence or Structural Similarity
more info
PubMed 
acts_upstream_of_or_within locomotion involved in locomotory behavior IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in lysosomal lumen acidification ISO
Inferred from Sequence Orthology
more info
 
involved_in lysosomal lumen acidification ISS
Inferred from Sequence or Structural Similarity
more info
PubMed 
involved_in lysosome organization IBA
Inferred from Biological aspect of Ancestor
more info
 
acts_upstream_of_or_within lysosome organization IMP
Inferred from Mutant Phenotype
more info
PubMed 
acts_upstream_of_or_within macromolecule catabolic process IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in positive regulation of proteolysis ISO
Inferred from Sequence Orthology
more info
 
involved_in positive regulation of proteolysis ISS
Inferred from Sequence or Structural Similarity
more info
PubMed 
acts_upstream_of_or_within visual perception IMP
Inferred from Mutant Phenotype
more info
PubMed 
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 ISS
Inferred from Sequence or Structural Similarity
more info
PubMed 
located_in endoplasmic reticulum lumen ISO
Inferred from Sequence Orthology
more info
 
located_in endoplasmic reticulum lumen ISS
Inferred from Sequence or Structural Similarity
more info
PubMed 
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)

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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_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)