Cln8 (CLN8, transmembrane ER and ERGIC protein) - Rat Genome Database

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Gene: Cln8 (CLN8, transmembrane ER and ERGIC protein) Rattus norvegicus
Analyze
Symbol: Cln8
Name: CLN8, transmembrane ER and ERGIC protein
RGD ID: 1359518
Description: Predicted to enable ceramide binding activity. Predicted to be involved in several processes, including ceramide metabolic process; cholesterol metabolic process; and lipid homeostasis. Predicted to act upstream of or within several processes, including adult walking behavior; glutamate reuptake; and neurofilament cytoskeleton organization. Predicted to be located in endoplasmic reticulum-Golgi intermediate compartment; mitochondrion; and presynapse. Predicted to be active in endoplasmic reticulum. Human ortholog(s) of this gene implicated in neuronal ceroid lipofuscinosis 8 and neuronal ceroid lipofuscinosis 8 northern epilepsy variant. Orthologous to human CLN8 (CLN8 transmembrane ER and ERGIC protein); INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; bisphenol A; endosulfan.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: ceroid-lipofuscinosis, neuronal 8; ceroid-lipofuscinosis, neuronal 8 (epilepsy, progressive with mental retardation); MGC93871
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21674,749,662 - 74,759,553 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1674,749,662 - 74,759,774 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1680,026,976 - 80,036,939 (-)NCBIRnor_SHR
UTH_Rnor_SHRSP_BbbUtx_1.01683,480,545 - 83,490,508 (-)NCBIRnor_SHRSP
UTH_Rnor_WKY_Bbb_1.01678,729,989 - 78,739,875 (-)NCBIRnor_WKY
Rnor_6.01679,828,321 - 79,838,212 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1679,828,324 - 79,838,212 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01679,403,685 - 79,413,576 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41679,569,745 - 79,579,636 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.11679,570,012 - 79,579,901 (-)NCBI
Celera1672,565,615 - 72,575,506 (-)NCBICelera
Cytogenetic Map16q12.5NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
Gene Ontology Annotations     Click to see Annotation Detail View

Molecular Function

References

References - curated
# Reference Title Reference Citation
1. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
2. Localization of wild-type and mutant neuronal ceroid lipofuscinosis CLN8 proteins in non-neuronal and neuronal cells. Lonka L, etal., J Neurosci Res 2004 Jun 15;76(6):862-71.
3. Rat ISS GO annotations from MGI mouse gene data--August 2006 MGD data from the GO Consortium
4. OMIM Disease Annotation Pipeline OMIM Disease Annotation Pipeline
5. GOA pipeline RGD automated data pipeline
6. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
7. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
8. Comprehensive gene review and curation RGD comprehensive gene curation
9. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. Strausberg RL, etal., Proc Natl Acad Sci U S A. 2002 Dec 24;99(26):16899-903. Epub 2002 Dec 11.
Additional References at PubMed
PMID:1658691   PMID:2061715   PMID:3783318   PMID:7613514   PMID:7668363   PMID:7683855   PMID:8095977   PMID:8125718   PMID:8144516   PMID:8160780   PMID:8282051   PMID:8389815  
PMID:8873145   PMID:9059519   PMID:9151333   PMID:9245501   PMID:9600674   PMID:9918704   PMID:10087069   PMID:10215924   PMID:10508524   PMID:10861296   PMID:12020865   PMID:15213005  
PMID:15489334   PMID:15565184   PMID:15647513   PMID:15885820   PMID:16086686   PMID:18317235   PMID:19941651   PMID:21052544  


Genomics

Comparative Map Data
Cln8
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21674,749,662 - 74,759,553 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1674,749,662 - 74,759,774 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1680,026,976 - 80,036,939 (-)NCBIRnor_SHR
UTH_Rnor_SHRSP_BbbUtx_1.01683,480,545 - 83,490,508 (-)NCBIRnor_SHRSP
UTH_Rnor_WKY_Bbb_1.01678,729,989 - 78,739,875 (-)NCBIRnor_WKY
Rnor_6.01679,828,321 - 79,838,212 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1679,828,324 - 79,838,212 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01679,403,685 - 79,413,576 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41679,569,745 - 79,579,636 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.11679,570,012 - 79,579,901 (-)NCBI
Celera1672,565,615 - 72,575,506 (-)NCBICelera
Cytogenetic Map16q12.5NCBI
CLN8
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh3881,753,059 - 1,786,570 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p13 Ensembl81,755,778 - 1,801,711 (+)EnsemblGRCh38hg38GRCh38
GRCh3781,711,955 - 1,734,736 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 3681,699,277 - 1,722,143 (+)NCBINCBI36Build 36hg18NCBI36
Build 3481,699,347 - 1,719,857NCBI
Celera81,654,899 - 1,677,784 (+)NCBICelera
Cytogenetic Map8p23.3NCBI
HuRef81,526,501 - 1,549,279 (+)NCBIHuRef
CHM1_181,711,562 - 1,734,347 (+)NCBICHM1_1
T2T-CHM13v2.081,542,478 - 1,565,133 (+)NCBIT2T-CHM13v2.0
Cln8
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39814,931,335 - 14,951,720 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl814,931,335 - 14,951,720 (+)EnsemblGRCm39 Ensembl
GRCm38814,881,335 - 14,901,720 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl814,881,335 - 14,901,720 (+)EnsemblGRCm38mm10GRCm38
MGSCv37814,888,536 - 14,901,720 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv36814,888,866 - 14,900,339 (+)NCBIMGSCv36mm8
Celera815,052,911 - 15,066,094 (+)NCBICelera
Cytogenetic Map8A1.1NCBI
cM Map87.59NCBI
Cln8
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495540357,924,873 - 57,938,690 (-)EnsemblChiLan1.0
ChiLan1.0NW_00495540357,926,711 - 57,938,698 (-)NCBIChiLan1.0ChiLan1.0
CLN8
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.181,658,644 - 1,677,624 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl81,658,694 - 1,700,754 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v085,587,875 - 5,606,883 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
CLN8
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.13730,863,098 - 30,885,831 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl3730,867,479 - 30,884,895 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha3731,632,530 - 31,649,934 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.03730,888,770 - 30,912,784 (+)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl3730,894,473 - 30,912,781 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.13730,804,432 - 30,821,842 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.03730,743,370 - 30,760,756 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.03730,752,705 - 30,770,116 (+)NCBIUU_Cfam_GSD_1.0
Cln8
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024404943980,126 - 1,002,741 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_004936615985,634 - 1,003,172 (+)EnsemblSpeTri2.0
SpeTri2.0NW_004936615993,092 - 999,976 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
CLN8
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1533,288,301 - 33,304,631 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11533,282,524 - 33,325,598 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21537,752,783 - 37,782,093 (+)NCBISscrofa10.2Sscrofa10.2susScr3
CLN8
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.181,424,402 - 1,445,505 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl81,433,953 - 1,445,021 (+)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366605443,311,682 - 43,332,398 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Cln8
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_004624861968,219 - 977,467 (+)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_004624861960,643 - 977,292 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Cln8
101 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:568
Count of miRNA genes:265
Interacting mature miRNAs:319
Transcripts:ENSRNOT00000016756
Prediction methods:Microtar, Miranda, Rnahybrid, Targetscan
Result types:miRGate_prediction

The detailed report is available here: Full Report CSV TAB Printer

miRNA Target Status data imported from miRGate (http://mirgate.bioinfo.cnio.es/).
For more information about miRGate, see PMID:25858286 or access the full paper here.


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1600378Arunc4Aerobic running capacity QTL 40.03exercise endurance trait (VT:0002332)maximum distance run on treadmill (CMO:0001406)1638024580345693Rat
70205Gcr3Gastric cancer resistance QTL 32.3stomach morphology trait (VT:0000470)stomach tumor depth of invasion (CMO:0001888)161769679182635055Rat
70205Gcr3Gastric cancer resistance QTL 32.3stomach morphology trait (VT:0000470)stomach tumor depth of invasion (CMO:0001888)161769679182635055Rat
70205Gcr3Gastric cancer resistance QTL 32.3stomach morphology trait (VT:0000470)stomach tumor diameter (CMO:0001889)161769679182635055Rat
70205Gcr3Gastric cancer resistance QTL 32.3stomach morphology trait (VT:0000470)stomach tumor diameter (CMO:0001889)161769679182635055Rat
70215Niddm29Non-insulin dependent diabetes mellitus QTL 293.54blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)161900443575226532Rat
1578768Stresp22Stress response QTL 222.8thymus mass (VT:0004954)thymus wet weight (CMO:0000855)163528887080288870Rat
2293690Bss45Bone structure and strength QTL 455.130.0001lumbar vertebra morphology trait (VT:0010494)lumbar vertebra cortical cross-sectional area (CMO:0001690)163775215682752156Rat
2300163Bmd64Bone mineral density QTL 645.30.0001lumbar vertebra mineral mass (VT:0010511)volumetric bone mineral density (CMO:0001553)163775215682752156Rat
7205510Activ5Activity QTL 53.780.00028locomotor behavior trait (VT:0001392)number of entries into a discrete space in an experimental apparatus (CMO:0000960)164239634584729064Rat
8694429Bw164Body weight QTL 16450.001body lean mass (VT:0010483)lean tissue morphological measurement (CMO:0002184)165272646484729064Rat
8694364Abfw7Abdominal fat weight QTL 712.220.001visceral adipose mass (VT:0010063)abdominal fat pad weight to body weight ratio (CMO:0000095)165272646484729064Rat
7411648Foco22Food consumption QTL 22150.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)165272646484729064Rat
631525Pia14Pristane induced arthritis QTL 144.4joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)165571108783402471Rat
1298527Arunc2Aerobic running capacity QTL 22.9exercise endurance trait (VT:0002332)maximum distance run on treadmill (CMO:0001406)166853271675029966Rat

Markers in Region
RH127710  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21674,749,772 - 74,749,991 (+)MAPPERmRatBN7.2
Rnor_6.01679,828,432 - 79,828,650NCBIRnor6.0
Rnor_5.01679,403,796 - 79,404,014UniSTSRnor5.0
RGSC_v3.41679,569,856 - 79,570,074UniSTSRGSC3.4
Celera1672,565,726 - 72,565,944UniSTS
RH 3.4 Map16727.6UniSTS
Cytogenetic Map16q12.5UniSTS


Expression


RNA-SEQ Expression
High: > 1000 TPM value   Medium: Between 11 and 1000 TPM
Low: Between 0.5 and 10 TPM   Below Cutoff: < 0.5 TPM

alimentary part of gastrointestinal system circulatory system endocrine system exocrine system hemolymphoid system hepatobiliary system integumental system musculoskeletal system nervous system renal system reproductive system respiratory system appendage
High
Medium 32 29 29 11 29 66 26 29 3
Low 3 11 28 12 8 12 8 11 8 9 12 8 8
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000016756   ⟹   ENSRNOP00000016756
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1674,749,662 - 74,759,774 (-)Ensembl
Rnor_6.0 Ensembl1679,828,324 - 79,838,212 (-)Ensembl
RefSeq Acc Id: NM_001007686   ⟹   NP_001007687
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21674,749,662 - 74,759,553 (-)NCBI
Rnor_6.01679,828,321 - 79,838,212 (-)NCBI
Rnor_5.01679,403,685 - 79,413,576 (-)NCBI
RGSC_v3.41679,569,745 - 79,579,636 (-)RGD
Celera1672,565,615 - 72,575,506 (-)RGD
Sequence:
RefSeq Acc Id: XM_006253394   ⟹   XP_006253456
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21674,749,662 - 74,759,479 (-)NCBI
Rnor_6.01679,828,321 - 79,838,152 (-)NCBI
Rnor_5.01679,403,685 - 79,413,576 (-)NCBI
Sequence:
Reference Sequences
RefSeq Acc Id: NP_001007687   ⟸   NM_001007686
- UniProtKB: Q6AYM9 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: XP_006253456   ⟸   XM_006253394
- Peptide Label: isoform X1
- UniProtKB: Q6AYM9 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: ENSRNOP00000016756   ⟸   ENSRNOT00000016756
Protein Domains
TLC

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-Q6AYM9-F1-model_v2 AlphaFold Q6AYM9 1-288 view protein structure

Transcriptome

eQTL   View at Phenogen
WGCNA   View at Phenogen
Tissue/Strain Expression   View at Phenogen


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1359518 AgrOrtholog
BioCyc Gene G2FUF-10746 BioCyc
Ensembl Genes ENSRNOG00000012565 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Protein ENSRNOP00000016756 ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript ENSRNOT00000016756 ENTREZGENE, UniProtKB/Swiss-Prot
IMAGE_CLONE IMAGE:7112147 IMAGE-MGC_LOAD
InterPro TLC-dom UniProtKB/Swiss-Prot
KEGG Report rno:306619 UniProtKB/Swiss-Prot
MGC_CLONE MGC:93871 IMAGE-MGC_LOAD
NCBI Gene 306619 ENTREZGENE
Pfam TRAM_LAG1_CLN8 UniProtKB/Swiss-Prot
PhenoGen Cln8 PhenoGen
PROSITE TLC UniProtKB/Swiss-Prot
SMART TLC UniProtKB/Swiss-Prot
UniProt CLN8_RAT UniProtKB/Swiss-Prot, ENTREZGENE


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2017-03-27 Cln8  CLN8, transmembrane ER and ERGIC protein  Cln8  ceroid-lipofuscinosis, neuronal 8  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2015-06-10 Cln8  ceroid-lipofuscinosis, neuronal 8  Cln8  ceroid-lipofuscinosis, neuronal 8 (epilepsy, progressive with mental retardation)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2012-01-10 Cln8  ceroid-lipofuscinosis, neuronal 8 (epilepsy, progressive with mental retardation)  Cln8  ceroid-lipofuscinosis, neuronal 8  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2006-03-30 Cln8  ceroid-lipofuscinosis, neuronal 8      Symbol and Name status set to approved 1299863 APPROVED
2005-07-29 Cln8  ceroid-lipofuscinosis, neuronal 8      Symbol and Name status set to provisional 70820 PROVISIONAL