Cln6 (CLN6, transmembrane ER protein) - Rat Genome Database

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Gene: Cln6 (CLN6, transmembrane ER protein) Rattus norvegicus
Analyze
Symbol: Cln6
Name: CLN6, transmembrane ER protein
RGD ID: 1309714
Description: 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 6A; and neuronal ceroid lipofuscinosis 6B. Orthologous to human CLN6 (CLN6 transmembrane ER protein); INTERACTS WITH 17alpha-ethynylestradiol; acetamide; bisphenol A.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: ceroid-lipofuscinosis neuronal protein 6; ceroid-lipofuscinosis, neuronal 6; ceroid-lipofuscinosis, neuronal 6, late infantile; ceroid-lipofuscinosis, neuronal 6, late infantile, variant; LOC315746
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
mRatBN7.2863,303,356 - 63,318,360 (+)NCBImRatBN7.2
mRatBN7.2 Ensembl863,303,029 - 63,318,360 (+)Ensembl
Rnor_6.0867,733,215 - 67,748,170 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl867,733,215 - 67,748,172 (+)EnsemblRnor6.0rn6Rnor6.0
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
JBrowse: View Region in Genome Browser (JBrowse)
Model


References

Additional References at PubMed
PMID:9600738   PMID:11722572   PMID:15010453   PMID:15265688   PMID:15647513   PMID:16857350   PMID:17237713   PMID:18317235   PMID:19941651   PMID:19946888   PMID:26681805  


Genomics

Comparative Map Data
Cln6
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2863,303,356 - 63,318,360 (+)NCBImRatBN7.2
mRatBN7.2 Ensembl863,303,029 - 63,318,360 (+)Ensembl
Rnor_6.0867,733,215 - 67,748,170 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl867,733,215 - 67,748,172 (+)EnsemblRnor6.0rn6Rnor6.0
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
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381568,206,992 - 68,257,215 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p13 Ensembl1568,206,992 - 68,257,211 (-)EnsemblGRCh38hg38GRCh38
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
(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
(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
ROS_Cfam_1.0 Ensembl3032,442,021 - 32,459,751 (-)Ensembl
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 (+)NCBIChlSab1.1chlSab2
Vero_WHO_p1.0NW_023666048126,190,316 - 126,209,504 (-)NCBIVero_WHO_p1.0
Cln6
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046247814,866,896 - 4,879,321 (+)NCBIHetGla_female_1.0hetGla2

Position Markers
RH131007  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2863,318,169 - 63,318,360 (+)MAPPERmRatBN7.2
mRatBN7.21745,886,101 - 45,886,303 (+)MAPPERmRatBN7.2
Rnor_6.01748,455,564 - 48,455,765NCBIRnor6.0
Rnor_6.0867,747,980 - 67,748,170NCBIRnor6.0
Rnor_5.01746,508,844 - 46,509,045UniSTSRnor5.0
Rnor_5.0867,476,727 - 67,476,917UniSTSRnor5.0
RGSC_v3.4867,001,823 - 67,002,013UniSTSRGSC3.4
RGSC_v3.41753,705,754 - 53,705,955UniSTSRGSC3.4
Celera1741,984,143 - 41,984,344UniSTS
Celera862,733,083 - 62,733,273UniSTS
Cytogenetic Map17q11UniSTS
Cytogenetic Map8q24UniSTS
RH143855  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2863,318,070 - 63,318,230 (+)MAPPERmRatBN7.2
Rnor_6.0867,747,881 - 67,748,040NCBIRnor6.0
Rnor_5.0867,476,628 - 67,476,787UniSTSRnor5.0
RGSC_v3.4867,001,724 - 67,001,883UniSTSRGSC3.4
Celera862,732,984 - 62,733,143UniSTS
RH 3.4 Map8793.7UniSTS
Cytogenetic Map8q24UniSTS


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
70197BpQTLcluster8Blood pressure QTL cluster 83.482arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)846531639119088624Rat
70197BpQTLcluster8Blood pressure QTL cluster 83.482arterial blood pressure trait (VT:2000000)pulse pressure (CMO:0000292)846531639119088624Rat
70197BpQTLcluster8Blood pressure QTL cluster 83.482arterial blood pressure trait (VT:2000000)absolute change in systolic blood pressure (CMO:0000607)846531639119088624Rat
70197BpQTLcluster8Blood pressure QTL cluster 83.482arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)846531639119088624Rat
631216Stl9Serum triglyceride level QTL 94.710.0001blood triglyceride amount (VT:0002644)serum triglyceride level (CMO:0000360)84186701070386132Rat
2303171Bp331Blood pressure QTL 3315.570.005arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)861290298119084929Rat
2303564Gluco43Glucose level QTL 433blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)82613018771130187Rat
2303570Gluco48Glucose level QTL 482blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)84980583194805831Rat
2303572Insul13Insulin level QTL 132blood insulin amount (VT:0001560)blood insulin level (CMO:0000349)82613018771130187Rat
61464Niddm11Non-insulin dependent diabetes mellitus QTL 113.10.001blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)83558203280582032Rat
70161Bp62Blood pressure QTL 622.90.001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)84269268490165460Rat
724514Uae15Urinary albumin excretion QTL 152.9urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)82950266570386295Rat
1331769Rf39Renal function QTL 393.871urine output (VT:0003620)timed urine volume (CMO:0000260)84186687675097878Rat
737824Hcar10Hepatocarcinoma resistance QTL 102.9liver integrity trait (VT:0010547)liver tumorous lesion number (CMO:0001068)84071306682925667Rat
1298065Scl16Serum cholesterol level QTL 163.8blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)83085640475856404Rat
1298079Activ2Activity QTL 29.50.000001voluntary movement trait (VT:0003491)rearing measurement (CMO:0001515)84186687686866876Rat
631650Stl6Serum triglyceride level QTL 640.0019blood triglyceride amount (VT:0002644)plasma triglyceride level (CMO:0000548)810378157112202585Rat
631664Hcar3Hepatocarcinoma resistance QTL 32.90.0005liver integrity trait (VT:0010547)volume of individual liver tumorous lesion (CMO:0001078)85423764499103503Rat
1331837Bw23Body weight QTL 234.190.00007body mass (VT:0001259)body weight (CMO:0000012)84653172299083736Rat
1331838Niddm61Non-insulin dependent diabetes mellitus QTL 613.530.0004blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)83646953599083736Rat
1582222Epfw2Epididymal fat weight QTL 23.20.0005epididymal fat pad mass (VT:0010421)epididymal fat pad weight to body weight ratio (CMO:0000658)83173772976737729Rat
1582243Bw66Body weight QTL 663.40.0048body mass (VT:0001259)body weight (CMO:0000012)85423764485365202Rat
1582254Kidm31Kidney mass QTL 313kidney mass (VT:0002707)both kidneys wet weight (CMO:0000085)85423764485365202Rat
731182Uae24Urinary albumin excretion QTL 246.4urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)81933115293965294Rat
631271Lecl1Lens clarity QTL 10.001lens clarity trait (VT:0001304)age of onset/diagnosis of cataract (CMO:0001584)81898416884531599Rat
1300177Cm2Cardiac mass QTL 23.65heart mass (VT:0007028)heart weight (CMO:0000017)854259986100382532Rat
1581557Eae16Experimental allergic encephalomyelitis QTL 163.8nervous system integrity trait (VT:0010566)experimental autoimmune encephalomyelitis incidence/prevalence measurement (CMO:0001046)88462195110921472Rat
2301402Bp316Blood pressure QTL 3160.005arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)85396876598968765Rat
2293697Bmd39Bone mineral density QTL 39femur strength trait (VT:0010010)femur total energy absorbed before break (CMO:0001677)85404374498968765Rat
631842Inf1Infertility severity QTL 14.10.001seminal gland mass (VT:0010524)seminal vesicle wet weight (CMO:0001603)82266233067662330Rat
1578755Pur5Proteinuria QTL 53.30.0001total urine protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)830848154101699754Rat
1578765Klgr1Kidney lesion grade QTL 13.30.0001kidney morphology trait (VT:0002135)organ lesion measurement (CMO:0000677)830848154101699754Rat
1578769Uae31Urinary albumin excretion QTL 313.30.001urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)830848154101699754Rat
1300146Rf17Renal function QTL 172.9renal blood flow trait (VT:2000006)absolute change in renal blood flow rate (CMO:0001168)82824291273242912Rat
1549908Neudeg1Neurodegradation QTL 15.50nervous system integrity trait (VT:0010566)logarithm of the ratio of the lesioned side motor neuron count to contralateral side motor neuron count (CMO:0001986)83018886794457446Rat
2316950Scl66Serum cholesterol level QTL 664.1blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)830848259105647037Rat
1554321Bmd3Bone mineral density QTL 37.90.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)840952565123900184Rat
2313046Bss78Bone structure and strength QTL 783.50.0001tibia strength trait (VT:1000284)tibia total energy absorbed before break (CMO:0001736)83084815482460899Rat
2313057Bss76Bone structure and strength QTL 7630.0001tibia size trait (VT:0100001)tibia midshaft cross-sectional area (CMO:0001717)83084815482460899Rat
2313067Bss77Bone structure and strength QTL 773.10.0001tibia size trait (VT:0100001)tibia midshaft endosteal cross-sectional area (CMO:0001716)83084815482460899Rat
2313086Bss60Bone structure and strength QTL 604.10.0001tibia length (VT:0004357)tibia length (CMO:0000450)85009524982460899Rat
2313088Bss75Bone structure and strength QTL 753.10.0001body length (VT:0001256)body length, nose to rump (CMO:0000079)83084815482460899Rat
1358892Kidm26Kidney mass QTL 263.69kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)82720571599103503Rat
1358896Bp262Blood pressure QTL 2622.89arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)82720571599103503Rat
1358906Bp253Blood pressure QTL 25340.0004arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)84071306693965294Rat
1358907Cm40Cardiac mass QTL 401.89heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)82720571599103503Rat
1358912Bw51Body weight QTL 512.95body mass (VT:0001259)body weight (CMO:0000012)851351728107062046Rat
61358Bp39Blood pressure QTL 392arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)83555193880551938Rat
4889938Bss89Bone structure and strength QTL 893.8tibia size trait (VT:0100001)tibia cortical bone volume (CMO:0001725)85009524982460899Rat
5684973Bss100Bone structure and strength QTL 1004.7tibia area (VT:1000281)tibia area measurement (CMO:0001382)85009524982460899Rat
8662823Vetf5Vascular elastic tissue fragility QTL 51.9artery integrity trait (VT:0010639)patent ductus arteriosus score (CMO:0002566)82824291299525068Rat
10402857Bp380Blood pressure QTL 3800.95arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)85396876598968765Rat
12879878Bw183Body weight QTL 1830.001body mass (VT:0001259)body weight (CMO:0000012)84329616998968765Rat
12879879Cm99Cardiac mass QTL 990.001heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)84329616998968765Rat
12879882Am8Aortic mass QTL 80.001aorta mass (VT:0002845)aorta weight to aorta length to body weight ratio (CMO:0002722)84329616998968765Rat
12879880Cm100Cardiac mass QTL 1000.001heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)84329616998968765Rat
12879881Cm101Cardiac mass QTL 1010.001heart right ventricle mass (VT:0007033)heart right ventricle weight to body weight ratio (CMO:0000914)84329616998968765Rat
12879883Kidm65Kidney mass QTL 650.001kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)84329616998968765Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:110
Count of miRNA genes:92
Interacting mature miRNAs:101
Transcripts:ENSRNOT00000034926
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


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 3 28 32 22 18 22 1 52 35 40 10
Low 15 25 19 1 19 8 10 22 1 1 8
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000034926   ⟹   ENSRNOP00000035915
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl863,303,378 - 63,318,354 (+)Ensembl
Rnor_6.0 Ensembl867,733,215 - 67,748,170 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000078091   ⟹   ENSRNOP00000073335
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl863,303,029 - 63,318,360 (+)Ensembl
Rnor_6.0 Ensembl867,739,800 - 67,748,172 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000096355   ⟹   ENSRNOP00000076671
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl863,308,929 - 63,318,360 (+)Ensembl
RefSeq Acc Id: NM_001191794   ⟹   NP_001178723
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2863,303,406 - 63,318,360 (+)NCBI
Rnor_6.0867,733,215 - 67,748,170 (+)NCBI
Rnor_5.0867,461,962 - 67,476,917 (+)NCBI
Celera862,718,317 - 62,733,273 (+)NCBI
Sequence:
RefSeq Acc Id: XM_006243238   ⟹   XP_006243300
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2863,303,356 - 63,318,360 (+)NCBI
Rnor_6.0867,733,219 - 67,748,170 (+)NCBI
Rnor_5.0867,461,962 - 67,476,917 (+)NCBI
Sequence:
Protein Sequences
Protein RefSeqs NP_001178723 (Get FASTA)   NCBI Sequence Viewer  
  XP_006243300 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: NP_001178723   ⟸   NM_001191794
- UniProtKB: D3ZZ46 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006243300   ⟸   XM_006243238
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: ENSRNOP00000073335   ⟸   ENSRNOT00000078091
RefSeq Acc Id: ENSRNOP00000035915   ⟸   ENSRNOT00000034926
RefSeq Acc Id: ENSRNOP00000076671   ⟸   ENSRNOT00000096355

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-D3ZZ46-F1-model_v2 AlphaFold D3ZZ46 1-308 view protein structure

Transcriptome

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

Promoters
RGD ID:13696055
Promoter ID:EPDNEW_R6580
Type:initiation region
Name:Cln6_1
Description:CLN6, transmembrane ER protein
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Single-end sequencing.
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0867,733,135 - 67,733,195EPDNEW

Strain Variation

Strain Sequence Variants (MRatBN7.2)
ACI/EurMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
ACI/N (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN-Lx/CubMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/NHsdMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/NHsdMcwi (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/SsN (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BUF/N (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BXH2/CubMcwi (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BXH3/CubMcwi (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
DA/OlaHsd (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Envigo
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/DuCrl (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/N (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/NCrl (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/Stm (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FHH/EurMcwi (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FXLE16/Stm (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FXLE18/Stm (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
GK/FarMcwi (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB10/IpcvMcwi (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB2/IpcvMcwi (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB20/IpcvMcwi (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB31/IpcvMcwi (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB4/IpcvMcwi (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LE/Stm (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEW/Crl (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF10A/StmMcwi (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF11/Stm (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF1A/Stm (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF1C/Stm (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF2B/Stm (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF3/Stm (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF4/Stm (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LH/MavRrrcAek (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LL/MavRrrcAek (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LN/MavRrrcAek (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
M520/N (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
M520/NRrrcMcwi (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
MR/N (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
MWF/Hsd (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
PVG/Seac (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SHR/OlalpcvMcwi (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SHRSP/A3NCrl (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SR/JrHsd (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Envigo
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SS/JrHsdMcwi (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WAG/RijCrl (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WKY/N (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WKY/NCrl (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WN/N (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
Damaging Variants


Assembly: Rnor_6.0

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
8 67744790 67744791 T G snv ACI/EurMcwi (MCW)


Assembly: Rnor_5.0

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
8 67473537 67473538 T G snv ACI/EurMcwi (MCW), FHH/EurMcwi (MCW)
8 67473601 67473602 G A snv BUF/MNa (KyushuU)
8 67473610 67473611 T C snv BUF/MNa (KyushuU)


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1309714 AgrOrtholog
BioCyc Gene G2FUF-30150 BioCyc
Ensembl Genes ENSRNOG00000007164 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000035915 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOP00000073335 ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000034926 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOT00000078091 ENTREZGENE, UniProtKB/TrEMBL
InterPro CLN6 UniProtKB/TrEMBL
KEGG Report rno:315746 UniProtKB/TrEMBL
NCBI Gene 315746 ENTREZGENE
PANTHER PTHR16244 UniProtKB/TrEMBL
Pfam CLN6 UniProtKB/TrEMBL
PhenoGen Cln6 PhenoGen
UniProt A0A0G2K587_RAT UniProtKB/TrEMBL
  D3ZZ46 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2017-06-12 Cln6  CLN6, transmembrane ER protein  Cln6  ceroid-lipofuscinosis, neuronal 6, late infantile, variant  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2012-01-10 Cln6  ceroid-lipofuscinosis, neuronal 6, late infantile, variant  Cln6  ceroid-lipofuscinosis, neuronal 6  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-04-30 Cln6  ceroid-lipofuscinosis, neuronal 6   Cln6_predicted  ceroid-lipofuscinosis, neuronal 6 (predicted)  'predicted' is removed 2292626 APPROVED
2005-01-12 Cln6_predicted  ceroid-lipofuscinosis, neuronal 6 (predicted)      Symbol and Name status set to approved 70820 APPROVED