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    Cln3 CLN3 lysosomal/endosomal transmembrane protein, battenin [ Mus musculus (house mouse) ]

    Gene ID: 12752, updated on 3-Dec-2024

    Summary

    Official Symbol
    Cln3provided by MGI
    Official Full Name
    CLN3 lysosomal/endosomal transmembrane protein, batteninprovided by MGI
    Primary source
    MGI:MGI:107537
    See related
    Ensembl:ENSMUSG00000030720 AllianceGenome:MGI:107537
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Mus musculus
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
    Summary
    This gene encodes a transmembrane protein called battenin that is involved in lysosomal function. Mutations in this, as well as other neuronal ceroid-lipofuscinosis genes, cause a number of neurodegenerative diseases collectively known as neuronal ceroid lipofuscinoses, the most common of which is juvenile neuronal ceroid-lipofuscinosis (Batten disease). Alternate splicing results in multiple transcript variants. [provided by RefSeq, Aug 2016]
    Expression
    Ubiquitous expression in ovary adult (RPKM 13.8), colon adult (RPKM 12.9) and 28 other tissues See more
    Orthologs
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    See Cln3 in Genome Data Viewer
    Location:
    7 F3; 7 69.16 cM
    Exon count:
    21
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCm39 (GCF_000001635.27) 7 NC_000073.7 (126170571..126184991, complement)
    108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 7 NC_000073.6 (126571207..126585817, complement)

    Chromosome 7 - NC_000073.7Genomic Context describing neighboring genes Neighboring gene eukaryotic translation initiation factor 3, subunit C Neighboring gene predicted gene, 24596 Neighboring gene predicted gene, 25579 Neighboring gene CapStarr-seq enhancer MGSCv37_chr7:133726956-133727139 Neighboring gene microRNA 7059 Neighboring gene apolipoprotein B receptor Neighboring gene interleukin 27 Neighboring gene predicted gene, 39086

    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)

    General gene information

    Markers

    Gene Ontology Provided by MGI

    Function Evidence Code Pubs
    enables calcium-dependent protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    enables glycolipid binding ISO
    Inferred from Sequence Orthology
    more info
     
    enables glycolipid binding ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    enables sulfatide binding ISO
    Inferred from Sequence Orthology
    more info
     
    enables sulfatide binding ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    Process Evidence Code Pubs
    involved_in Golgi to lysosome transport ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in Golgi to lysosome transport ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in L-arginine transmembrane transport ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in L-arginine transmembrane transport ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    acts_upstream_of_or_within actin cytoskeleton organization IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    acts_upstream_of_or_within action potential IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    acts_upstream_of_or_within amino acid transport IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in amyloid precursor protein catabolic process ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in amyloid precursor protein catabolic process ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    acts_upstream_of_or_within associative learning IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    acts_upstream_of_or_within autophagosome maturation IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in autophagosome-lysosome fusion IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    acts_upstream_of_or_within blood vessel endothelial cell migration IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    acts_upstream_of_or_within endocytosis IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    acts_upstream_of_or_within establishment of localization in cell IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in glycerophospholipid biosynthetic process ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in glycerophospholipid biosynthetic process ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in glycolipid transport ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in glycolipid transport ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in intracellular water homeostasis IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    acts_upstream_of_or_within ionotropic glutamate receptor signaling pathway IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in learning or memory IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in lysosomal lumen acidification IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    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
     
    involved_in lysosomal lumen pH elevation ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in lysosomal lumen pH elevation ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in lysosomal protein catabolic process IMP
    Inferred from Mutant Phenotype
    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 macroautophagy IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    acts_upstream_of_or_within membrane organization IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in negative regulation of apoptotic process IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in negative regulation of apoptotic process ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in negative regulation of apoptotic process ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    acts_upstream_of_or_within negative regulation of catalytic activity IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    acts_upstream_of_or_within negative regulation of neuron apoptotic process IDA
    Inferred from Direct Assay
    more info
    PubMed 
    acts_upstream_of_or_within negative regulation of proteolysis IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    acts_upstream_of_or_within neuromuscular process controlling balance IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in phagosome-lysosome docking IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in phagosome-lysosome fusion IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in plasma membrane raft organization IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in positive regulation of Golgi to plasma membrane protein transport IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in positive regulation of caveolin-mediated endocytosis IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in positive regulation of pinocytosis IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    acts_upstream_of_or_within positive regulation of protein phosphorylation IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    acts_upstream_of_or_within protein localization to membrane IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    acts_upstream_of_or_within protein localization to plasma membrane IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    acts_upstream_of protein phosphorylation IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    acts_upstream_of_or_within protein processing IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in receptor-mediated endocytosis ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in receptor-mediated endocytosis ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in regulation of arginine biosynthetic process IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in regulation of autophagosome maturation IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in regulation of autophagosome size IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in regulation of autophagy IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in regulation of cellular response to osmotic stress ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in regulation of cellular response to osmotic stress ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in regulation of cytoskeleton organization ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in regulation of cytoskeleton organization ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    acts_upstream_of_or_within regulation of cytosolic calcium ion concentration IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in regulation of fibroblast migration ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in regulation of fibroblast migration ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    acts_upstream_of_or_within regulation of filopodium assembly IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    acts_upstream_of_or_within regulation of gene expression ISO
    Inferred from Sequence Orthology
    more info
    PubMed 
    involved_in regulation of modification of synaptic structure IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in regulation of phagosome maturation IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in regulation of protein localization to plasma membrane IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in regulation of protein processing ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in regulation of protein processing ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in regulation of short-term neuronal synaptic plasticity IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in regulation of synaptic transmission, GABAergic IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in regulation of synaptic transmission, glutamatergic IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in renal potassium excretion IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in vesicle transport along microtubule ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in vesicle transport along microtubule ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    Component Evidence Code Pubs
    located_in Golgi apparatus ISO
    Inferred from Sequence Orthology
    more info
     
    located_in Golgi apparatus ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    located_in Golgi membrane ISO
    Inferred from Sequence Orthology
    more info
     
    located_in Golgi membrane ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    located_in Golgi stack ISO
    Inferred from Sequence Orthology
    more info
     
    located_in Golgi stack ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    located_in autolysosome IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in autophagosome IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in caveola ISO
    Inferred from Sequence Orthology
    more info
     
    located_in caveola ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    located_in cytoplasm ISO
    Inferred from Sequence Orthology
    more info
     
    located_in cytoplasm ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    located_in cytoplasmic vesicle IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in cytosol IEA
    Inferred from Electronic Annotation
    more info
     
    located_in early endosome IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in early endosome ISO
    Inferred from Sequence Orthology
    more info
     
    located_in early endosome ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    located_in early endosome membrane ISO
    Inferred from Sequence Orthology
    more info
     
    located_in early endosome membrane ISS
    Inferred from Sequence or Structural Similarity
    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
     
    located_in endoplasmic reticulum membrane ISO
    Inferred from Sequence Orthology
    more info
     
    located_in endoplasmic reticulum membrane ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    located_in endosome ISO
    Inferred from Sequence Orthology
    more info
     
    located_in late endosome IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in late endosome ISO
    Inferred from Sequence Orthology
    more info
     
    located_in late endosome ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    located_in late endosome membrane IEA
    Inferred from Electronic Annotation
    more info
     
    located_in lysosomal membrane ISO
    Inferred from Sequence Orthology
    more info
     
    located_in lysosomal membrane ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    is_active_in lysosome IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    located_in lysosome IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in lysosome ISO
    Inferred from Sequence Orthology
    more info
     
    located_in membrane ISO
    Inferred from Sequence Orthology
    more info
     
    located_in membrane ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    located_in membrane raft IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in membrane raft ISO
    Inferred from Sequence Orthology
    more info
     
    located_in membrane raft ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    located_in neuron projection IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in neuron projection ISO
    Inferred from Sequence Orthology
    more info
     
    located_in neuron projection ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    located_in nucleus ISO
    Inferred from Sequence Orthology
    more info
     
    located_in nucleus ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    located_in plasma membrane ISO
    Inferred from Sequence Orthology
    more info
     
    located_in plasma membrane ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    located_in recycling endosome ISO
    Inferred from Sequence Orthology
    more info
     
    located_in recycling endosome ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    located_in synaptic vesicle ISO
    Inferred from Sequence Orthology
    more info
     
    located_in synaptic vesicle ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    located_in trans-Golgi network IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in trans-Golgi network ISO
    Inferred from Sequence Orthology
    more info
     
    located_in trans-Golgi network ISS
    Inferred from Sequence or Structural Similarity
    more info
     

    General protein information

    Preferred Names
    battenin
    Names
    ceroid lipofuscinosis, neuronal 3, juvenile (Batten, Spielmeyer-Vogt disease)

    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_001146311.3NP_001139783.1  battenin isoform 1

      See identical proteins and their annotated locations for NP_001139783.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (1). Both variants 1 and 2 encode the same protein.
      Source sequence(s)
      AC125169
      Consensus CDS
      CCDS21833.1
      UniProtKB/Swiss-Prot
      O35934, P70400, Q61124
      UniProtKB/TrEMBL
      Q8C5B1
      Related
      ENSMUSP00000081636.5, ENSMUST00000084589.11
      Conserved Domains (1) summary
      pfam02487
      Location:40437
      CLN3; CLN3 protein
    2. NM_001329789.2NP_001316718.1  battenin isoform 2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) lacks an exon in the coding region compared to variant 1. The resulting isoform (2) has a shorter N-terminus, compared to isoform 1.
      Source sequence(s)
      AC125169
      Consensus CDS
      CCDS90329.1
      UniProtKB/TrEMBL
      Q6PAH4, Q8C5B1
      Related
      ENSMUSP00000095644.3, ENSMUST00000098036.9
      Conserved Domains (1) summary
      pfam02487
      Location:40413
      CLN3; CLN3 protein
    3. NM_001402715.1NP_001389644.1  battenin isoform 1

      Status: REVIEWED

      Source sequence(s)
      AC125169
      UniProtKB/Swiss-Prot
      O35934, P70400, Q61124
      UniProtKB/TrEMBL
      Q8C5B1
    4. NM_001402716.1NP_001389645.1  battenin isoform 1

      Status: REVIEWED

      Source sequence(s)
      AC125169
      UniProtKB/Swiss-Prot
      O35934, P70400, Q61124
      UniProtKB/TrEMBL
      Q8C5B1
    5. NM_001402717.1NP_001389646.1  battenin isoform 1

      Status: REVIEWED

      Source sequence(s)
      AC125169
      UniProtKB/Swiss-Prot
      O35934, P70400, Q61124
      UniProtKB/TrEMBL
      Q8C5B1
    6. NM_001402718.1NP_001389647.1  battenin isoform 1

      Status: REVIEWED

      Source sequence(s)
      AC125169
      UniProtKB/Swiss-Prot
      O35934, P70400, Q61124
      UniProtKB/TrEMBL
      Q8C5B1
    7. NM_001402719.1NP_001389648.1  battenin isoform 1

      Status: REVIEWED

      Source sequence(s)
      AC125169
      UniProtKB/Swiss-Prot
      O35934, P70400, Q61124
      UniProtKB/TrEMBL
      Q8C5B1
      Related
      ENSMUSP00000111973.3, ENSMUST00000116269.9
    8. NM_001402720.1NP_001389649.1  battenin isoform 1

      Status: REVIEWED

      Source sequence(s)
      AC125169
      UniProtKB/Swiss-Prot
      O35934, P70400, Q61124
      UniProtKB/TrEMBL
      Q8C5B1
    9. NM_001402721.1NP_001389650.1  battenin isoform 2

      Status: REVIEWED

      Source sequence(s)
      AC125169
      UniProtKB/TrEMBL
      Q6PAH4, Q8C5B1
    10. NM_001402722.1NP_001389651.1  battenin isoform 2

      Status: REVIEWED

      Source sequence(s)
      AC125169
      UniProtKB/TrEMBL
      Q6PAH4, Q8C5B1
    11. NM_009907.5NP_034037.3  battenin isoform 1

      See identical proteins and their annotated locations for NP_034037.3

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) differs in the 5' UTR compared to variant 1. Both variants 1 and 2 encode the same protein.
      Source sequence(s)
      AC125169
      Consensus CDS
      CCDS21833.1
      UniProtKB/Swiss-Prot
      O35934, P70400, Q61124
      UniProtKB/TrEMBL
      Q8C5B1
      Related
      ENSMUSP00000032962.5, ENSMUST00000032962.11
      Conserved Domains (1) summary
      pfam02487
      Location:40437
      CLN3; CLN3 protein

    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_000073.7 Reference GRCm39 C57BL/6J

      Range
      126170571..126184991 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_036152622.1XP_036008515.1  battenin isoform X1

      UniProtKB/Swiss-Prot
      O35934, P70400, Q61124
      UniProtKB/TrEMBL
      Q8C5B1
      Conserved Domains (1) summary
      pfam02487
      Location:40437
      CLN3; CLN3 protein
    2. XM_036152621.1XP_036008514.1  battenin isoform X1

      UniProtKB/Swiss-Prot
      O35934, P70400, Q61124
      UniProtKB/TrEMBL
      Q8C5B1
      Conserved Domains (1) summary
      pfam02487
      Location:40437
      CLN3; CLN3 protein
    3. XM_036152625.1XP_036008518.1  battenin isoform X3

      Conserved Domains (1) summary
      cl15430
      Location:1222
      Nucleoside_tran; Nucleoside transporter
    4. XM_036152620.1XP_036008513.1  battenin isoform X1

      UniProtKB/Swiss-Prot
      O35934, P70400, Q61124
      UniProtKB/TrEMBL
      Q8C5B1
      Conserved Domains (1) summary
      pfam02487
      Location:40437
      CLN3; CLN3 protein
    5. XM_036152624.1XP_036008517.1  battenin isoform X2

      UniProtKB/TrEMBL
      Q8C5B1
      Conserved Domains (1) summary
      cl15430
      Location:1383
      Nucleoside_tran; Nucleoside transporter
    6. XM_036152623.1XP_036008516.1  battenin isoform X1

      UniProtKB/Swiss-Prot
      O35934, P70400, Q61124
      UniProtKB/TrEMBL
      Q8C5B1
      Conserved Domains (1) summary
      pfam02487
      Location:40437
      CLN3; CLN3 protein
    7. XM_030242058.2XP_030097918.1  battenin isoform X3

      Conserved Domains (1) summary
      cl15430
      Location:1222
      Nucleoside_tran; Nucleoside transporter

    RNA

    1. XR_004934004.1 RNA Sequence