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

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: human all
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Genomic context

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_000073.7 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: Mouse ENCODE transcriptome data 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

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

A mouse mutant deficient in both neuronal ceroid lipofuscinosis-associated proteins CLN3 and TPP1.
Title: A mouse mutant deficient in both neuronal ceroid lipofuscinosis-associated proteins CLN3 and TPP1.
CLN3 is required for the clearance of glycerophosphodiesters from lysosomes.
Title: CLN3 is required for the clearance of glycerophosphodiesters from lysosomes.
Loss of CLN3, the gene mutated in juvenile neuronal ceroid lipofuscinosis, leads to metabolic impairment and autophagy induction in retinal pigment epithelium.
Title: Loss of CLN3, the gene mutated in juvenile neuronal ceroid lipofuscinosis, leads to metabolic impairment and autophagy induction in retinal pigment epithelium.
Therapeutic efficacy of antisense oligonucleotides in mouse models of CLN3 Batten disease.
Title: Therapeutic efficacy of antisense oligonucleotides in mouse models of CLN3 Batten disease.
Cln3-mutations underlying juvenile neuronal ceroid lipofuscinosis cause significantly reduced levels of Palmitoyl-protein thioesterases-1 (Ppt1)-protein and Ppt1-enzyme activity in the lysosome.
Title: Cln3-mutations underlying juvenile neuronal ceroid lipofuscinosis cause significantly reduced levels of Palmitoyl-protein thioesterases-1 (Ppt1)-protein and Ppt1-enzyme activity in the lysosome.
These results show that CLN3 deficiency alters antigen presenting cells, which can be a major contributor to the autoimmune response in juvenile neuronal ceroid lipofuscinosis.
Title: Antigen presenting cell abnormalities in the Cln3(-/-) mouse model of juvenile neuronal ceroid lipofuscinosis.
Loss of CLN3 protein leads to early presynaptic changes and altered short-term plasticity in a mouse model of juvenile Batten disease.
Title: Altered Cerebellar Short-Term Plasticity but No Change in Postsynaptic AMPA-Type Glutamate Receptors in a Mouse Model of Juvenile Batten Disease.
Our subcellular localization study in neurons refines the localization and subcellular targeting of CLN3 to late endosomal-lysosomal compartments
Title: Revisiting the neuronal localization and trafficking of CLN3 in juvenile neuronal ceroid lipofuscinosis.
findings in two distinct lysosome-related degradative pathways constitute the first description of a deficit in the retinal pigment epithelium caused by loss of CLN3
Title: Photoreceptor phagosome processing defects and disturbed autophagy in retinal pigment epithelium of Cln3Δex1-6 mice modelling juvenile neuronal ceroid lipofuscinosis (Batten disease).
The small GTPase Cdc42 is misregulated in the absence of CLN3, and thus may be a common link to multiple cellular defects.
Title: CLN3 deficient cells display defects in the ARF1-Cdc42 pathway and actin-dependent events.

Submit: New GeneRIF Correction See all GeneRIFs (33)

Variation

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Alleles

Alleles of this type are documented at Mouse Genome Informatics (MGI)

Endonuclease-mediated (3) 1 citation
Targeted (7) 1 citation

General gene information

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Markers

U47106 (e-PCR)
- UniSTS:125756

AI323623 (e-PCR)
- UniSTS:179650

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

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Preferred Names: battenin

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

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)

NM_001146311.3 → NP_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:40 → 437

CLN3; CLN3 protein
NM_001329789.2 → NP_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:40 → 413

CLN3; CLN3 protein
NM_001402715.1 → NP_001389644.1 battenin isoform 1

Status: REVIEWED

Source sequence(s)

AC125169

UniProtKB/Swiss-Prot

O35934, P70400, Q61124
NM_001402716.1 → NP_001389645.1 battenin isoform 1

Status: REVIEWED

Source sequence(s)

AC125169

UniProtKB/Swiss-Prot

O35934, P70400, Q61124
NM_001402717.1 → NP_001389646.1 battenin isoform 1

Status: REVIEWED

Source sequence(s)

AC125169

UniProtKB/Swiss-Prot

O35934, P70400, Q61124
NM_001402718.1 → NP_001389647.1 battenin isoform 1

Status: REVIEWED

Source sequence(s)

AC125169

UniProtKB/Swiss-Prot

O35934, P70400, Q61124
NM_001402719.1 → NP_001389648.1 battenin isoform 1

Status: REVIEWED

Source sequence(s)

AC125169

UniProtKB/Swiss-Prot

O35934, P70400, Q61124

Related

ENSMUSP00000111973.3, ENSMUST00000116269.9
NM_001402720.1 → NP_001389649.1 battenin isoform 1

Status: REVIEWED

Source sequence(s)

AC125169

UniProtKB/Swiss-Prot

O35934, P70400, Q61124
NM_001402721.1 → NP_001389650.1 battenin isoform 2

Status: REVIEWED

Source sequence(s)

AC125169

UniProtKB/TrEMBL

Q6PAH4
NM_001402722.1 → NP_001389651.1 battenin isoform 2

Status: REVIEWED

Source sequence(s)

AC125169

UniProtKB/TrEMBL

Q6PAH4
NM_009907.5 → NP_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:40 → 437

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

NC_000073.7 Reference GRCm39 C57BL/6J

Range

126170571..126184991 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_036152622.1 → XP_036008515.1 battenin isoform X1

UniProtKB/Swiss-Prot

O35934, P70400, Q61124

UniProtKB/TrEMBL

Q8C5B1

Conserved Domains (1) summary

pfam02487
Location:40 → 437

CLN3; CLN3 protein
XM_036152621.1 → XP_036008514.1 battenin isoform X1

UniProtKB/Swiss-Prot

O35934, P70400, Q61124

UniProtKB/TrEMBL

Q8C5B1

Conserved Domains (1) summary

pfam02487
Location:40 → 437

CLN3; CLN3 protein
XM_036152625.1 → XP_036008518.1 battenin isoform X3

Conserved Domains (1) summary

cl15430
Location:1 → 222

Nucleoside_tran; Nucleoside transporter
XM_036152620.1 → XP_036008513.1 battenin isoform X1

UniProtKB/Swiss-Prot

O35934, P70400, Q61124

UniProtKB/TrEMBL

Q8C5B1

Conserved Domains (1) summary

pfam02487
Location:40 → 437

CLN3; CLN3 protein
XM_036152624.1 → XP_036008517.1 battenin isoform X2

UniProtKB/TrEMBL

Q8C5B1

Conserved Domains (1) summary

cl15430
Location:1 → 383

Nucleoside_tran; Nucleoside transporter
XM_036152623.1 → XP_036008516.1 battenin isoform X1

UniProtKB/Swiss-Prot

O35934, P70400, Q61124

UniProtKB/TrEMBL

Q8C5B1

Conserved Domains (1) summary

pfam02487
Location:40 → 437

CLN3; CLN3 protein
XM_030242058.2 → XP_030097918.1 battenin isoform X3

Conserved Domains (1) summary

cl15430
Location:1 → 222

Nucleoside_tran; Nucleoside transporter