Cln3 CLN3 lysosomal/endosomal transmembrane protein, battenin [Rattus norvegicus (Norway rat)] - Gene

Summary

Official Symbol: Cln3provided by RGD
Official Full Name: CLN3 lysosomal/endosomal transmembrane protein, batteninprovided by RGD
Primary source: RGD:1359537
See related: EnsemblRapid:ENSRNOG00000019103 AllianceGenome:RGD:1359537
Gene type: protein coding
RefSeq status: PROVISIONAL
Organism: Rattus norvegicus
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
Summary: Predicted to enable calcium-dependent protein binding activity and sulfatide binding activity. Predicted to be involved in several processes, including modulation of chemical synaptic transmission; regulation of vesicle-mediated transport; and vacuole organization. Predicted to act upstream of or within several processes, including autophagosome maturation; regulation of filopodium assembly; and regulation of macromolecule metabolic process. Located in endosome. Human ortholog(s) of this gene implicated in neuronal ceroid lipofuscinosis 3. Orthologous to human CLN3 (CLN3 lysosomal/endosomal transmembrane protein, battenin). [provided by Alliance of Genome Resources, Dec 2024]
Expression: Biased expression in Spleen (RPKM 65.1), Lung (RPKM 52.9) and 9 other tissues See more
Orthologs: human mouse all
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Genomic context

Location:: 1q36

Exon count:: 22

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCr8 (GCF_036323735.1)	1	NC_086019.1 (190586649..190600034, complement)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	1	NC_051336.1 (181156071..181169458, complement)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	1	NC_005100.4 (197986384..197999726, complement)

Chromosome 1 - NC_086019.1 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: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages
Description: 320 RNA samples isolated from 11 organs (adrenal gland, brain, heart, kidney, liver, lung, muscle, spleen, thymus, and testes or uterus) from both sexes of Fischer 344 rats across four developmental stages (2-, 6-, 21-, and 104-weeks-old)
BioProject: PRJNA238328
Publication: PMID 24510058
Analysis date: Mon Jun 6 17:44:12 2016

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

developed a CLN3 siRNA-inhibited primary rat neuron model to further study etoposide-induced calcium changes and apoptosis in CLN3 disease followed by recovery experiments with amlodipine
Title: Amlodipine prevents apoptotic cell death by correction of elevated intracellular calcium in a primary neuronal model of Batten disease (CLN3 disease).
AP-1 and AP-3 facilitate lysosomal targeting of Batten disease protein CLN3 via its dileucine motif
Title: AP-1 and AP-3 facilitate lysosomal targeting of Batten disease protein CLN3 via its dileucine motif.

Submit: New GeneRIF Correction

General gene information

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Gene Ontology Provided by RGD

Function	Evidence Code	Pubs
enables calcium-dependent protein binding	ISO Inferred from Sequence Orthology more info
enables glycolipid binding	ISO Inferred from Sequence Orthology more info
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	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within action potential	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within amino acid transport	ISO Inferred from Sequence Orthology more info
involved_in amyloid precursor protein catabolic process	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within associative learning	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within autophagosome maturation	ISO Inferred from Sequence Orthology more info
involved_in autophagosome-lysosome fusion	ISO Inferred from Sequence Orthology more info
involved_in biological_process	ND No biological Data available more info
acts_upstream_of_or_within blood vessel endothelial cell migration	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within endocytosis	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within establishment of localization in cell	ISO Inferred from Sequence Orthology more info
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	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within ionotropic glutamate receptor signaling pathway	ISO Inferred from Sequence Orthology more info
involved_in learning or memory	ISO Inferred from Sequence Orthology more info
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	ISO Inferred from Sequence Orthology more info
involved_in lysosome organization	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within lysosome organization	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within macroautophagy	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within membrane organization	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of apoptotic process	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within negative regulation of catalytic activity	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within negative regulation of neuron apoptotic process	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within negative regulation of proteolysis	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within neuromuscular process controlling balance	ISO Inferred from Sequence Orthology more info
involved_in phagosome-lysosome docking	ISO Inferred from Sequence Orthology more info
involved_in phagosome-lysosome fusion	ISO Inferred from Sequence Orthology more info
involved_in plasma membrane raft organization	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of Golgi to plasma membrane protein transport	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of caveolin-mediated endocytosis	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of pinocytosis	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within positive regulation of protein phosphorylation	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within protein localization to membrane	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within protein localization to plasma membrane	ISO Inferred from Sequence Orthology more info
acts_upstream_of protein phosphorylation	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within protein processing	ISO Inferred from Sequence Orthology more info
involved_in receptor-mediated endocytosis	ISO Inferred from Sequence Orthology more info
involved_in regulation of arginine biosynthetic process	ISO Inferred from Sequence Orthology more info
involved_in regulation of autophagosome maturation	ISO Inferred from Sequence Orthology more info
involved_in regulation of autophagosome size	ISO Inferred from Sequence Orthology more info
involved_in regulation of autophagy	ISO Inferred from Sequence Orthology more info
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	ISO Inferred from Sequence Orthology more info
involved_in regulation of fibroblast migration	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within regulation of filopodium assembly	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within regulation of gene expression	ISO Inferred from Sequence Orthology more info
involved_in regulation of modification of synaptic structure	ISO Inferred from Sequence Orthology more info
involved_in regulation of phagosome maturation	ISO Inferred from Sequence Orthology more info
involved_in regulation of protein localization to plasma membrane	ISO Inferred from Sequence Orthology more info
involved_in regulation of protein processing	ISO Inferred from Sequence Orthology more info
involved_in regulation of short-term neuronal synaptic plasticity	ISO Inferred from Sequence Orthology more info
involved_in regulation of synaptic transmission, GABAergic	ISO Inferred from Sequence Orthology more info
involved_in regulation of synaptic transmission, glutamatergic	ISO Inferred from Sequence Orthology more info
involved_in renal potassium excretion	ISO Inferred from Sequence Orthology more info
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	ISO Inferred from Sequence Orthology more info
located_in autophagosome	ISO Inferred from Sequence Orthology more info
located_in caveola	ISO Inferred from Sequence Orthology more info
located_in cytoplasm	ISO Inferred from Sequence Orthology more info
located_in cytoplasmic vesicle	ISO Inferred from Sequence Orthology more info
located_in cytosol	IEA Inferred from Electronic Annotation more info
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
located_in 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	ISO Inferred from Sequence Orthology more info
located_in membrane	ISO Inferred from Sequence Orthology more info
located_in membrane raft	ISO Inferred from Sequence Orthology more info
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 synaptic vesicle	ISO Inferred from Sequence Orthology more info
located_in trans-Golgi network	ISO Inferred from Sequence Orthology more info

General protein information

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Preferred Names: battenin

Names: CLN3, battenin; Cln3p; ceroid lipofuscinosis, neuronal 3, juvenile (Batten, Spielmeyer-Vogt disease); ceroid-lipofuscinosis, neuronal 3

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_001006971.1 → NP_001006972.1 battenin

See identical proteins and their annotated locations for NP_001006972.1

Status: PROVISIONAL

Source sequence(s)

BC083704

UniProtKB/TrEMBL

A0A8I6ALZ9, Q5XIH8

Related

ENSRNOP00000025898.5, ENSRNOT00000025898.6

Conserved Domains (1) summary

pfam02487
Location:40 → 437

CLN3; CLN3 protein

RefSeqs of Annotated Genomes: GCF_036323735.1-RS_2024_02

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCr8

Genomic

NC_086019.1 Reference GRCr8

Range

190586649..190600034 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_039107249.2 → XP_038963177.1 battenin isoform X1

UniProtKB/TrEMBL

A0A8I6ALZ9, Q5XIH8

Conserved Domains (1) summary

pfam02487
Location:40 → 437

CLN3; CLN3 protein
XM_039107253.2 → XP_038963181.1 battenin isoform X1

UniProtKB/TrEMBL

A0A8I6ALZ9, Q5XIH8

Conserved Domains (1) summary

pfam02487
Location:40 → 437

CLN3; CLN3 protein
XM_039107240.2 → XP_038963168.1 battenin isoform X1

UniProtKB/TrEMBL

A0A8I6ALZ9, Q5XIH8

Conserved Domains (1) summary

pfam02487
Location:40 → 437

CLN3; CLN3 protein
XM_039107246.2 → XP_038963174.1 battenin isoform X1

UniProtKB/TrEMBL

A0A8I6ALZ9, Q5XIH8

Conserved Domains (1) summary

pfam02487
Location:40 → 437

CLN3; CLN3 protein
XM_039107268.2 → XP_038963196.1 battenin isoform X2

UniProtKB/TrEMBL

F7F0I2

Conserved Domains (1) summary

pfam02487
Location:45 → 388

CLN3; CLN3 protein
XM_039107273.2 → XP_038963201.1 battenin isoform X3

UniProtKB/TrEMBL

A6I990, F7F0I2

Conserved Domains (1) summary

pfam02487
Location:1 → 383

CLN3; CLN3 protein
XM_039107263.1 → XP_038963191.1 battenin isoform X2

UniProtKB/TrEMBL

F7F0I2

Conserved Domains (1) summary

pfam02487
Location:45 → 388

CLN3; CLN3 protein
XM_008759875.4 → XP_008758097.1 battenin isoform X4

UniProtKB/TrEMBL

F7F0I2

Conserved Domains (1) summary

pfam02487
Location:12 → 356

CLN3; CLN3 protein