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

Gene ID: 12752, updated on 3-Apr-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
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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 protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
enables sulfatide binding ISO
Inferred from Sequence Orthology
more info
 
Process Evidence Code Pubs
involved_in Golgi to lysosome transport ISO
Inferred from Sequence Orthology
more info
 
involved_in L-arginine transmembrane transport ISO
Inferred from Sequence Orthology
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
 
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 glycolipid transport ISO
Inferred from Sequence Orthology
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 pH elevation ISO
Inferred from Sequence Orthology
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
 
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 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 cytoskeleton organization ISO
Inferred from Sequence Orthology
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
 
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 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
 
Component Evidence Code Pubs
located_in Golgi apparatus ISO
Inferred from Sequence Orthology
more info
 
located_in Golgi membrane ISO
Inferred from Sequence Orthology
more info
 
located_in Golgi stack ISO
Inferred from Sequence Orthology
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 cytoplasm ISO
Inferred from Sequence Orthology
more info
 
located_in cytoplasmic vesicle IDA
Inferred from Direct Assay
more info
PubMed 
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 membrane ISO
Inferred from Sequence Orthology
more info
 
located_in endoplasmic reticulum ISO
Inferred from Sequence Orthology
more info
 
located_in endoplasmic reticulum membrane ISO
Inferred from Sequence Orthology
more info
 
colocalizes_with 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 lysosomal membrane ISO
Inferred from Sequence Orthology
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 raft IDA
Inferred from Direct Assay
more info
PubMed 
located_in membrane raft ISO
Inferred from Sequence Orthology
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 nucleus ISO
Inferred from Sequence Orthology
more info
 
located_in plasma membrane ISO
Inferred from Sequence Orthology
more info
 
located_in recycling endosome ISO
Inferred from Sequence Orthology
more info
 
located_in synapse IEA
Inferred from Electronic Annotation
more info
 
located_in synaptic vesicle ISO
Inferred from Sequence Orthology
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
 

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
  4. NM_001402716.1NP_001389645.1  battenin isoform 1

    Status: REVIEWED

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

    Status: REVIEWED

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

    Status: REVIEWED

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

    Status: REVIEWED

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

    Status: REVIEWED

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

    Status: REVIEWED

    Source sequence(s)
    AC125169
    UniProtKB/TrEMBL
    Q6PAH4
  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