Cln6 (ceroid-lipofuscinosis, neuronal 6) - Rat Genome Database

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Gene: Cln6 (ceroid-lipofuscinosis, neuronal 6) Mus musculus
Analyze
Symbol: Cln6
Name: ceroid-lipofuscinosis, neuronal 6
RGD ID: 1320202
MGI Page MGI
Description: Predicted to enable lysophosphatidic acid binding activity; protein homodimerization activity; and sulfatide binding activity. Acts upstream of or within several processes, including locomotion involved in locomotory behavior; lysosome organization; 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. Is expressed in several structures, including central nervous system and retina. Used to study neuronal ceroid lipofuscinosis 6. 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); INTERACTS WITH 1,2-dimethylhydrazine; 2,3,7,8-tetrachlorodibenzodioxine; choline.
Type: protein-coding
RefSeq Status: VALIDATED
Also known as: 1810065L06Rik; AW743417; ceroid-lipofuscinosis neuronal protein 6; D9Bwg1455e; nclf; neuronal ceroid lipofuscinosis
RGD Orthologs
Human
Rat
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: GRCm38 - Mouse Genome Assembly GRCm38
Position:
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39962,746,067 - 62,759,288 (+)NCBIGRCm39mm39
GRCm39 Ensembl962,746,067 - 62,759,288 (+)Ensembl
GRCm38962,838,785 - 62,852,006 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl962,838,785 - 62,852,006 (+)EnsemblGRCm38mm10GRCm38
MGSCv37962,686,594 - 62,699,809 (+)NCBIGRCm37mm9NCBIm37
MGSCv36962,636,793 - 62,650,008 (+)NCBImm8
Celera960,064,132 - 60,077,378 (+)NCBICelera
Cytogenetic Map9BNCBI
cM Map933.89NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

Molecular Function

References

Additional References at PubMed
PMID:8889548   PMID:9371744   PMID:9600738   PMID:10349636   PMID:10922068   PMID:11042159   PMID:11076861   PMID:11217851   PMID:11727201   PMID:11731229   PMID:11853768   PMID:12466851  
PMID:12477932   PMID:14610273   PMID:15226823   PMID:15647513   PMID:15782199   PMID:16141072   PMID:16141073   PMID:16332269   PMID:16602821   PMID:17868323   PMID:18498441   PMID:19235893  
PMID:19640925   PMID:21677750   PMID:21873635   PMID:22012656   PMID:22536393   PMID:22701626   PMID:23279039   PMID:23789114   PMID:24084090   PMID:24124525   PMID:24223841   PMID:24423645  
PMID:25992714   PMID:26681805   PMID:27626380   PMID:27654426   PMID:28378742   PMID:29091030   PMID:29606505   PMID:30372735   PMID:32290105   PMID:32597833   PMID:33368303  


Genomics

Comparative Map Data
Cln6
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39962,746,067 - 62,759,288 (+)NCBIGRCm39mm39
GRCm39 Ensembl962,746,067 - 62,759,288 (+)Ensembl
GRCm38962,838,785 - 62,852,006 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl962,838,785 - 62,852,006 (+)EnsemblGRCm38mm10GRCm38
MGSCv37962,686,594 - 62,699,809 (+)NCBIGRCm37mm9NCBIm37
MGSCv36962,636,793 - 62,650,008 (+)NCBImm8
Celera960,064,132 - 60,077,378 (+)NCBICelera
Cytogenetic Map9BNCBI
cM Map933.89NCBI
CLN6
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl1568,206,992 - 68,257,211 (-)EnsemblGRCh38hg38GRCh38
GRCh381568,206,992 - 68,229,728 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh371568,499,330 - 68,522,066 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361566,286,384 - 66,309,079 (-)NCBINCBI36hg18NCBI36
Build 341566,286,385 - 66,309,079NCBI
Celera1545,384,244 - 45,406,985 (-)NCBI
Cytogenetic Map15q23NCBI
HuRef1545,330,044 - 45,352,792 (-)NCBIHuRef
CHM1_11568,617,284 - 68,640,038 (-)NCBICHM1_1
Cln6
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2863,303,356 - 63,318,360 (+)NCBImRatBN7.2
Rnor_6.0 Ensembl867,733,215 - 67,748,172 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.0867,733,215 - 67,748,170 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.0867,461,962 - 67,476,917 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4866,987,057 - 67,002,013 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1866,996,226 - 67,037,937 (+)NCBI
Celera862,718,317 - 62,733,273 (+)NCBICelera
Cytogenetic Map8q24NCBI
Cln6
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554507,876,522 - 7,886,581 (+)EnsemblChiLan1.0
ChiLan1.0NW_0049554507,876,572 - 7,885,305 (+)NCBIChiLan1.0ChiLan1.0
CLN6
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.11565,425,472 - 65,436,699 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1565,425,472 - 65,985,242 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v01547,156,583 - 47,215,805 (-)NCBIMhudiblu_PPA_v0panPan3
CLN6
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.13032,246,394 - 32,264,251 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl3032,246,411 - 32,264,240 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha3032,180,849 - 32,198,636 (-)NCBI
ROS_Cfam_1.03032,442,020 - 32,459,741 (-)NCBI
UMICH_Zoey_3.13032,370,298 - 32,388,114 (-)NCBI
UNSW_CanFamBas_1.03032,432,245 - 32,450,063 (-)NCBI
UU_Cfam_GSD_1.03032,678,083 - 32,695,922 (-)NCBI
Cln6
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024408640110,222,378 - 110,236,565 (-)NCBI
SpeTri2.0NW_00493647128,069,058 - 28,084,607 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
CLN6
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1166,107,228 - 166,126,584 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11166,107,895 - 166,126,054 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21183,878,601 - 183,893,266 (-)NCBISscrofa10.2Sscrofa10.2susScr3
CLN6
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.12615,259,186 - 15,278,249 (+)NCBI
Vero_WHO_p1.0NW_023666048126,190,316 - 126,209,504 (-)NCBI
Cln6
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046247814,866,896 - 4,879,321 (+)NCBI

Position Markers
AW743417  
Mouse AssemblyChrPosition (strand)SourceJBrowse
GRCm38962,850,725 - 62,850,971UniSTSGRCm38
MGSCv37962,698,532 - 62,698,778UniSTSGRCm37
Celera960,076,101 - 60,076,347UniSTS
Cytogenetic Map9BUniSTS
cM Map935.0UniSTS
Whitehead/MRC_RH9615.96UniSTS
AW822070  
Mouse AssemblyChrPosition (strand)SourceJBrowse
GRCm38962,851,692 - 62,851,944UniSTSGRCm38
MGSCv37962,699,499 - 62,699,751UniSTSGRCm37
Celera960,077,068 - 60,077,320UniSTS
Cytogenetic Map9BUniSTS
cM Map935.0UniSTS
Whitehead/MRC_RH9616.6UniSTS
RH125063  
Mouse AssemblyChrPosition (strand)SourceJBrowse
GRCm38962,851,769 - 62,851,858UniSTSGRCm38
MGSCv37962,699,576 - 62,699,665UniSTSGRCm37
Celera960,077,145 - 60,077,234UniSTS
Cytogenetic Map9BUniSTS
cM Map935.0UniSTS
D9Bwg1455e  
Mouse AssemblyChrPosition (strand)SourceJBrowse
GRCm38962,851,830 - 62,851,985UniSTSGRCm38
MGSCv37962,699,637 - 62,699,792UniSTSGRCm37
Celera960,077,206 - 60,077,361UniSTS
Cytogenetic Map9BUniSTS
cM Map936.0UniSTS
cM Map935.0UniSTS


QTLs in Region (GRCm38)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
13208563Bmiq8_mbody mass index QTL 8 (mouse)92500000069000000Mouse
10043847Hdlq89_mHDL QTL 89 (mouse)Not determined92938163163381774Mouse
1301782Chol11_mcholesterol 11 (mouse)Not determined92938163163381774Mouse
1301365Ap5q_malcohol preference 5 QTL (mouse)Not determined93014186664141979Mouse
1357746Vtbt7_mvertebral trabecular bone trait 7 (mouse)Not determined93082861764828723Mouse
1302180Actd4_mactivity-distance traveled 4 (mouse)Not determined93252326366523557Mouse
4141148Cq5_mcholesterol QTL 5 (mouse)Not determined93254112166541246Mouse
1301692Hts_mhypothermia sensitivity (mouse)Not determined93259987266600121Mouse
4141323Ptnu3_mproteinuria 3 (mouse)Not determined93297840266978536Mouse
1357709Si5lq3_mserum IGFBP-5 level QTL 3 (mouse)Not determined93319972567199840Mouse
1558872Ibdq1_minflammatory bowel disease QTL 1 (mouse)Not determined93406754473531973Mouse
1301252Etohc3_methanol consumption 3 (mouse)Not determined93512317869123299Mouse
1301972Cocrb8_mcocaine related behavior 8 (mouse)Not determined93512317869123299Mouse
1558968Tbdr1_mbody temperature response to dietary restriction, QTL 1 (mouse)Not determined93512317869123299Mouse
4142042Alpq3_malcohol preference QTL 3 (mouse)Not determined93739490198819654Mouse
10043971Obq32_mobesity QTL 32 (mouse)Not determined93791224471912244Mouse
12791002Arlsq2_maortic root lesion size QTL 2 (mouse)93819229172192291Mouse
12790986Pcho9_mplasma cholesterol 9 (mouse)93819229172192291Mouse
12790992Arlsq1_maortic root lesion size QTL 1 (mouse)93819229172192291Mouse
12738449Spcq2_msperm count QTL 2 (mouse)93949260173492601Mouse
4141071Ath29_matherosclerosis 29 (mouse)Not determined94050829874700643Mouse
1301702Brm1_mbrachyury modifier 1 (mouse)Not determined94089776474897921Mouse
1301558Stheal8_msoft tissue heal 8 (mouse)Not determined94357343177573577Mouse
10045639Heal28_mwound healing/regeneration 28 (mouse)Not determined94357343177573577Mouse
1301435Trigq1_mtriglyceride QTL 1 (mouse)Not determined94452089278520980Mouse
4141572Ntta3_mneurotensin transcript abundance 3 (mouse)Not determined4668637365923895Mouse
1300716Cd4ts4_mCD4 T cell subset 4 (mouse)Not determined94892377482923895Mouse
1300563Pgia5_mproteoglycan induced arthritis 5 (mouse)Not determined94892377482923895Mouse
1301051Eae9_msusceptibility to experimental allergic encephalomyelitis 9 (mouse)Not determined94950899863332570Mouse
1301049El4_mepilepsy 4 (mouse)Not determined94950899867244166Mouse
4141224Dxmod_mdoxorubicin nephropathy modifier (mouse)Not determined49541121101528921Mouse
14746993Manh66_mmandible shape 66 (mouse)94990676683906766Mouse
1301184Bdln4_mbody length 4 (mouse)Not determined95024403884244166Mouse
1301241Renf1_mrenal failure 1 (mouse)Not determined95212317899910428Mouse
13525008Hrtiq1_mheart rate time index, QTL 1 (mouse)95251479868648726Mouse
12790990Tgl7_mtriglyceride 7 (mouse)95465267888652678Mouse
10043877Adip21_madiposity 21 (mouse)Not determined95653182690531973Mouse
1301287Feml2_mfemur length in high growth mice 2 (mouse)Not determined95760000063300000Mouse
1301965Vmbic5_mventral midbrain iron content 5 (mouse)Not determined95768420965923895Mouse
1301549Bbaa9_mB.burgdorferi-associated arthritis 9 (mouse)Not determined95789776471574472Mouse
4141676Neogq1_mneonatal growth QTL 1 (mouse)Not determined95789776486239920Mouse
13525007Lfhrvq1_mlow frequency time index heart rate varaiblity, QTL 1 (mouse)95887703568648726Mouse
1301172Fembrs6_mfemur breaking strength 6 (mouse)Not determined95911710593117252Mouse
1301803Stheal9_msoft tissue heal 9 (mouse)Not determined95911710593117252Mouse
5491195Mobq8_mmultigenic obesity QTL 8 (mouse)Not determined95946266493462846Mouse
1300848Skull13_mskull morphology 13 (mouse)Not determined95946266493462846Mouse
1301456Adip5_madiposity 5 (mouse)Not determined95946266493462846Mouse
13207569Tcq13_mtotal cholesterol QTL 13 (mouse)959990000109260000Mouse
1301611Lrnx3_mlearning contextual 3 (mouse)Not determined96224248596242599Mouse

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:1053
Count of miRNA genes:512
Interacting mature miRNAs:607
Transcripts:ENSMUST00000034776, ENSMUST00000124984, ENSMUST00000138276, ENSMUST00000141821
Prediction methods: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.


Expression


Sequence


Reference Sequences
RefSeq Acc Id: ENSMUST00000034776   ⟹   ENSMUSP00000034776
RefSeq Status:
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm38.p6 Ensembl962,838,785 - 62,852,006 (+)Ensembl
RefSeq Acc Id: ENSMUST00000124984   ⟹   ENSMUSP00000115675
RefSeq Status:
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm38.p6 Ensembl962,847,033 - 62,851,162 (+)Ensembl
RefSeq Acc Id: ENSMUST00000138276   ⟹   ENSMUSP00000117833
RefSeq Status:
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm38.p6 Ensembl962,846,015 - 62,850,711 (+)Ensembl
RefSeq Acc Id: ENSMUST00000141821   ⟹   ENSMUSP00000114283
RefSeq Status:
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm38.p6 Ensembl962,838,792 - 62,846,018 (+)Ensembl
RefSeq Acc Id: NM_001033175   ⟹   NP_001028347
RefSeq Status: VALIDATED
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39962,746,067 - 62,759,288 (+)NCBI
GRCm38962,838,785 - 62,852,006 (+)NCBI
MGSCv37962,686,594 - 62,699,809 (+)RGD
Celera960,064,132 - 60,077,378 (+)RGD
cM Map9 ENTREZGENE
Sequence:
Protein Sequences
Protein RefSeqs NP_001028347 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAI16795 (Get FASTA)   NCBI Sequence Viewer  
  AAI16799 (Get FASTA)   NCBI Sequence Viewer  
  BAE32568 (Get FASTA)   NCBI Sequence Viewer  
  EDL26029 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: NP_001028347   ⟸   NM_001033175
- UniProtKB: Q3U466 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSMUSP00000115675   ⟸   ENSMUST00000124984
RefSeq Acc Id: ENSMUSP00000117833   ⟸   ENSMUST00000138276
RefSeq Acc Id: ENSMUSP00000034776   ⟸   ENSMUST00000034776
RefSeq Acc Id: ENSMUSP00000114283   ⟸   ENSMUST00000141821

Promoters
RGD ID:6844333
Promoter ID:MM_KWN:57690
Type:CpG-Island
SO ACC ID:SO:0000170
Source:MPROMDB
Tissues & Cell Lines:BoneMarrow_0Hour,   BoneMarrow_2Hour,   BoneMarrow_4Hour,   Kidney
Transcripts:OTTMUST00000083630,   OTTMUST00000083631
Position:
Mouse AssemblyChrPosition (strand)Source
MGSCv36962,686,496 - 62,686,997 (+)MPROMDB
RGD ID:8669908
Promoter ID:EPDNEW_M12984
Type:initiation region
Name:Cln6_1
Description:Mus musculus ceroid-lipofuscinosis, neuronal 6 , mRNA.
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Single-end sequencing.
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm38962,838,785 - 62,838,845EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene MGI:2159324 AgrOrtholog
Ensembl Genes ENSMUSG00000032245 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSMUSP00000034776 ENTREZGENE, UniProtKB/TrEMBL
  ENSMUSP00000114283 UniProtKB/TrEMBL
  ENSMUSP00000115675 UniProtKB/TrEMBL
  ENSMUSP00000117833 UniProtKB/TrEMBL
Ensembl Transcript ENSMUST00000034776 ENTREZGENE, UniProtKB/TrEMBL
  ENSMUST00000124984 UniProtKB/TrEMBL
  ENSMUST00000138276 UniProtKB/TrEMBL
  ENSMUST00000141821 UniProtKB/TrEMBL
InterPro CLN6 UniProtKB/TrEMBL
KEGG Report mmu:76524 UniProtKB/TrEMBL
MGD MGI:2159324 ENTREZGENE
NCBI Gene 76524 ENTREZGENE
PANTHER PTHR16244 UniProtKB/TrEMBL
Pfam CLN6 UniProtKB/TrEMBL
PhenoGen Cln6 PhenoGen
UniProt A0PJN2_MOUSE UniProtKB/TrEMBL
  D6RE34_MOUSE UniProtKB/TrEMBL
  F6SXC2_MOUSE UniProtKB/TrEMBL
  F6YAC1_MOUSE UniProtKB/TrEMBL
  Q3U466 ENTREZGENE, UniProtKB/TrEMBL