Cln6 CLN6, transmembrane ER protein [Rattus norvegicus (Norway rat)] - Gene

Summary

Official Symbol: Cln6provided by RGD
Official Full Name: CLN6, transmembrane ER proteinprovided by RGD
Primary source: RGD:1309714
See related: Ensembl:ENSRNOG00000007164 AllianceGenome:RGD:1309714
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 lysophosphatidic acid binding activity; protein homodimerization activity; and sulfatide binding activity. Predicted to be involved in several processes, including cholesterol metabolic process; ganglioside metabolic process; and lysosomal lumen acidification. Predicted to act upstream of or within cellular macromolecule catabolic process; locomotion involved in locomotory behavior; 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. 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: Biased expression in Spleen (RPKM 92.7), Kidney (RPKM 91.5) and 9 other tissues See more
Orthologs: human mouse all
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Genomic context

Location:: 8q24

Exon count:: 8

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCr8 (GCF_036323735.1)	8	NC_086026.1 (72198773..72213777)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	8	NC_051343.1 (63303356..63318360)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	8	NC_005107.4 (67733215..67748170)

Chromosome 8 - NC_086026.1 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?

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General gene information

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Markers

RH131007 (e-PCR)
- UniSTS:214290

RH143855 (e-PCR)
- UniSTS:233101

Gene Ontology Provided by RGD

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 sulfatide binding	ISO Inferred from Sequence Orthology more info

Process	Evidence Code	Pubs
involved_in biological_process	ND No biological Data available more info
involved_in cholesterol metabolic process	ISO Inferred from Sequence Orthology more info
involved_in ganglioside metabolic process	ISO Inferred from Sequence Orthology more info
involved_in glycosaminoglycan metabolic process	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within locomotion involved in locomotory behavior	ISO Inferred from Sequence Orthology more info
involved_in lysosomal lumen acidification	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 macromolecule catabolic process	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of proteolysis	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within visual perception	ISO Inferred from Sequence Orthology more info

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 lumen	ISO Inferred from Sequence Orthology more info
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	IEA Inferred from Electronic Annotation more info
located_in nucleolus	ISO Inferred from Sequence Orthology more info

General protein information

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Preferred Names: ceroid-lipofuscinosis neuronal protein 6

Names: ceroid-lipofuscinosis, neuronal 6, late infantile

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_001191794.1 → NP_001178723.1 ceroid-lipofuscinosis neuronal protein 6

Status: PROVISIONAL

Source sequence(s)

JAXUCZ010000008

UniProtKB/TrEMBL

A0A8I5YBU0, D3ZZ46

Related

ENSRNOP00000035915.4, ENSRNOT00000034926.7

Conserved Domains (1) summary

pfam15156
Location:27 → 306

CLN6; Ceroid-lipofuscinosis neuronal protein 6

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_086026.1 Reference GRCr8

Range

72198773..72213777

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_006243238.4 → XP_006243300.1 ceroid-lipofuscinosis neuronal protein 6 isoform X1

UniProtKB/TrEMBL

A0A0G2K587, A0A8I5YBU0

Related

ENSRNOP00000073335.2, ENSRNOT00000078091.2

Conserved Domains (1) summary

pfam15156
Location:15 → 294

CLN6; Ceroid-lipofuscinosis neuronal protein 6