Cln3 (CLN3 lysosomal/endosomal transmembrane protein, battenin) - Rat Genome Database

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Gene: Cln3 (CLN3 lysosomal/endosomal transmembrane protein, battenin) Rattus norvegicus
Analyze
Symbol: Cln3
Name: CLN3 lysosomal/endosomal transmembrane protein, battenin
RGD ID: 1359537
Description: 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); INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; 3-chloropropane-1,2-diol; bisphenol A.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: battenin; ceroid lipofuscinosis, neuronal 3, juvenile (Batten, Spielmeyer-Vogt disease); ceroid-lipofuscinosis, neuronal 3; CLN3, battenin; Cln3p; MGC94583
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Black Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: GRCr8 - GRCr8 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81190,586,649 - 190,600,034 (-)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl1190,586,650 - 190,597,929 (-)EnsemblGRCr8
mRatBN7.21181,156,071 - 181,169,458 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1181,156,073 - 181,167,434 (-)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx1189,507,073 - 189,518,479 (-)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01196,693,161 - 196,704,568 (-)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01189,360,633 - 189,371,909 (-)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.01197,986,384 - 197,999,726 (-)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1197,986,385 - 197,997,664 (-)Ensemblrn6Rnor6.0
Rnor_5.01204,965,144 - 204,978,485 (-)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.41185,713,096 - 185,724,375 (-)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera1178,814,090 - 178,825,369 (-)NCBICelera
RGSC_v3.11185,862,977 - 185,874,256 (-)NCBI
Cytogenetic Map1q36NCBI
JBrowse:




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

Biological Process
actin cytoskeleton organization  (ISO)
action potential  (ISO)
amino acid transport  (IEA,ISO)
amyloid precursor protein catabolic process  (ISO)
associative learning  (ISO)
autophagosome maturation  (ISO)
autophagosome-lysosome fusion  (IEA,ISO)
biological_process  (ND)
cell migration  (ISO)
endocytosis  (IEA,ISO)
establishment of localization in cell  (IEA)
glycerophospholipid biosynthetic process  (ISO)
glycolipid transport  (ISO)
Golgi to lysosome transport  (ISO)
intracellular monoatomic cation homeostasis  (IEA)
intracellular water homeostasis  (IEA,ISO)
ionotropic glutamate receptor signaling pathway  (ISO)
L-arginine transmembrane transport  (ISO)
learning or memory  (IEA,ISO)
lysosomal lumen acidification  (IBA,ISO)
lysosomal lumen pH elevation  (ISO)
lysosomal protein catabolic process  (IEA,ISO)
lysosome organization  (IBA,IEA,ISO)
macroautophagy  (ISO)
membrane organization  (IEA,ISO)
negative regulation of apoptotic process  (IEA,ISO)
negative regulation of catalytic activity  (ISO)
negative regulation of neuron apoptotic process  (ISO)
negative regulation of proteolysis  (ISO)
neuromuscular process controlling balance  (ISO)
phagosome-lysosome docking  (IEA,ISO)
phagosome-lysosome fusion  (IEA,ISO)
plasma membrane raft organization  (IEA,ISO)
positive regulation of caveolin-mediated endocytosis  (IEA,ISO)
positive regulation of Golgi to plasma membrane protein transport  (IEA,ISO)
positive regulation of pinocytosis  (IEA,ISO)
positive regulation of protein phosphorylation  (ISO)
protein localization to membrane  (ISO)
protein localization to plasma membrane  (ISO)
protein processing  (ISO)
receptor-mediated endocytosis  (ISO)
regulation of arginine biosynthetic process  (IEA,ISO)
regulation of autophagosome maturation  (IEA,ISO)
regulation of autophagosome size  (IEA,ISO)
regulation of autophagy  (IEA,ISO)
regulation of cellular response to osmotic stress  (ISO)
regulation of cytoskeleton organization  (ISO)
regulation of cytosolic calcium ion concentration  (ISO)
regulation of fibroblast migration  (ISO)
regulation of filopodium assembly  (ISO)
regulation of gene expression  (ISO)
regulation of modification of synaptic structure  (IEA,ISO)
regulation of phagosome maturation  (IEA,ISO)
regulation of protein localization to plasma membrane  (IEA,ISO)
regulation of protein processing  (ISO)
regulation of proteolysis  (IEA)
regulation of short-term neuronal synaptic plasticity  (IEA,ISO)
regulation of synaptic transmission, GABAergic  (IEA,ISO)
regulation of synaptic transmission, glutamatergic  (IEA,ISO)
renal potassium excretion  (IEA,ISO)
vesicle transport along microtubule  (ISO)

Cellular Component

Molecular Function

References

References - curated
# Reference Title Reference Citation
1. Characterization of Cln3p, the gene product responsible for juvenile neuronal ceroid lipofuscinosis, as a lysosomal integral membrane glycoprotein. Ezaki J, etal., J Neurochem 2003 Dec;87(5):1296-308.
2. 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.
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. A galactosylceramide binding domain is involved in trafficking of CLN3 from Golgi to rafts via recycling endosomes. Persaud-Sawin DA, etal., Pediatr Res. 2004 Sep;56(3):449-63. Epub 2004 Jul 7.
6. GOA pipeline RGD automated data pipeline
7. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
8. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
9. Comprehensive gene review and curation RGD comprehensive gene curation
10. 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:9384607   PMID:9949212   PMID:10191111   PMID:10191112   PMID:10191116   PMID:10191118   PMID:10191119   PMID:10332042   PMID:10440905   PMID:10527801   PMID:10924275   PMID:11590129  
PMID:11722572   PMID:12706816   PMID:12763292   PMID:14644441   PMID:14699076   PMID:15471887   PMID:15588329   PMID:15598649   PMID:15885820   PMID:16239221   PMID:16251196   PMID:16412658  
PMID:16483786   PMID:16714284   PMID:17189291   PMID:17482562   PMID:17855597   PMID:17868323   PMID:17897319   PMID:18317235   PMID:18621045   PMID:18817525   PMID:19284480   PMID:19941651  
PMID:20219947   PMID:20850431   PMID:22261744   PMID:23769828   PMID:23840424   PMID:24227717   PMID:24792215   PMID:25878248   PMID:26450516   PMID:27101989   PMID:29135436   PMID:29780879  


Genomics

Comparative Map Data
Cln3
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81190,586,649 - 190,600,034 (-)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl1190,586,650 - 190,597,929 (-)EnsemblGRCr8
mRatBN7.21181,156,071 - 181,169,458 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1181,156,073 - 181,167,434 (-)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx1189,507,073 - 189,518,479 (-)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01196,693,161 - 196,704,568 (-)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01189,360,633 - 189,371,909 (-)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.01197,986,384 - 197,999,726 (-)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1197,986,385 - 197,997,664 (-)Ensemblrn6Rnor6.0
Rnor_5.01204,965,144 - 204,978,485 (-)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.41185,713,096 - 185,724,375 (-)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera1178,814,090 - 178,825,369 (-)NCBICelera
RGSC_v3.11185,862,977 - 185,874,256 (-)NCBI
Cytogenetic Map1q36NCBI
CLN3
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381628,466,653 - 28,492,082 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1628,474,111 - 28,495,575 (-)Ensemblhg38GRCh38
GRCh371628,477,974 - 28,503,403 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361628,396,101 - 28,411,124 (-)NCBIBuild 36Build 36hg18NCBI36
Build 341628,396,101 - 28,410,717NCBI
Celera1627,700,143 - 27,715,170 (+)NCBICelera
Cytogenetic Map16p12.1NCBI
HuRef1626,514,259 - 26,529,549 (-)NCBIHuRef
CHM1_11629,500,208 - 29,515,233 (-)NCBICHM1_1
T2T-CHM13v2.01628,903,667 - 28,920,379 (+)NCBIT2T-CHM13v2.0
T2T-CHM13v2.01628,747,320 - 28,747,572 (-)NCBIT2T-CHM13v2.0
Cln3
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm397126,170,571 - 126,184,991 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl7126,170,379 - 126,184,989 (-)EnsemblGRCm39 EnsemblGRCm39
GRCm387126,571,207 - 126,585,817 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl7126,571,207 - 126,585,817 (-)Ensemblmm10GRCm38
MGSCv377133,714,914 - 133,727,794 (-)NCBIMGSCv37MGSCv37mm9NCBIm37
MGSCv367126,362,548 - 126,374,368 (-)NCBIMGSCv36mm8
Celera7126,395,665 - 126,433,408 (-)NCBICelera
Cytogenetic Map7F3NCBI
cM Map769.16NCBI
Cln3
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554936,696,241 - 6,707,849 (-)Ensembl
ChiLan1.0NW_0049554936,696,520 - 6,707,849 (-)NCBIChiLan1.0ChiLan1.0
LOC117978823
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v21831,065,290 - 31,097,172 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan11634,996,679 - 35,011,769 (+)NCBINHGRI_mPanPan1
CLN3
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1618,252,543 - 18,266,033 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl618,254,139 - 18,266,033 (+)EnsemblcanFam3CanFam3.1
Dog10K_Boxer_Tasha619,832,816 - 19,844,709 (+)NCBIDog10K_Boxer_TashaDog10K_Boxer_Tasha
ROS_Cfam_1.0618,390,161 - 18,402,054 (+)NCBIROS_Cfam_1.0ROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl618,390,161 - 18,402,054 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1618,189,180 - 18,201,073 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0618,104,266 - 18,116,159 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0618,420,341 - 18,432,234 (+)NCBIUU_Cfam_GSD_1.0UU_Cfam_GSD_1.0
Cln3
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024409344123,857,474 - 123,870,439 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_00493650111,955,184 - 11,967,436 (-)EnsemblSpeTri2.0 Ensembl
SpeTri2.0NW_00493650111,955,334 - 11,967,338 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
CLN3
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl318,433,836 - 18,450,290 (+)EnsemblsusScr11Sscrofa11.1
Sscrofa11.1318,433,564 - 18,450,296 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
CLN3
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1526,320,132 - 26,343,009 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl526,320,061 - 26,337,402 (-)EnsemblChlSab1.1 EnsemblchlSab2Vervet-AGM
Vero_WHO_p1.0NW_0236660683,236,192 - 3,251,867 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Cln3
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_00462478212,995,277 - 13,005,087 (-)EnsemblHetGla_female_1.0 EnsemblhetGla2HetGla_female_1.0 Ensembl
HetGla 1.0NW_00462478212,995,277 - 13,004,980 (-)NCBIHetGla 1.0HetGla 1.0hetGla2
Cln3
(Rattus rattus - black rat)
Black Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rrattus_CSIRO_v1275,340,955 - 75,352,557 (+)NCBIRrattus_CSIRO_v1

Variants

.
Variants in Cln3
91 total Variants
miRNA Target Status (No longer updated)

Predicted Target Of
Summary Value
Count of predictions:50
Count of miRNA genes:44
Interacting mature miRNAs:46
Transcripts:ENSRNOT00000025898
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.


QTLs in Region (GRCr8)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1578778Pur4Proteinuria QTL 43.30.003urine total protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)1160111531262090437Rat
1354646Kidm18Kidney mass QTL 185.7kidney mass (VT:0002707)calculated kidney weight (CMO:0000160)1160573753266453731Rat
1354652Kidm20Kidney mass QTL 204.3kidney mass (VT:0002707)calculated kidney weight (CMO:0000160)1186658830266453731Rat
2302378Insul11Insulin level QTL 113.25blood insulin amount (VT:0001560)serum insulin level (CMO:0000358)1153679879198679879Rat
1354653Despr9Despair related QTL 90.00019locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)1177339686222339686Rat
1578770Stresp23Stress response QTL 23kidney sympathetic nerve activity (VT:0004050)stimulated renal sympathetic nerve activity to basal renal sympathetic nerve activity ratio (CMO:0001786)1132760429191848948Rat
2293673Bss27Bone structure and strength QTL 2718.630.0001femur morphology trait (VT:0000559)femur midshaft cortical cross-sectional area (CMO:0001663)1181059071226059071Rat
61326Eae6Experimental allergic encephalomyelitis QTL 65.3body mass (VT:0001259)change in body weight (CMO:0002045)1182383862191260518Rat
2293677Bss41Bone structure and strength QTL 419.380.0001lumbar vertebra size trait (VT:0010518)lumbar vertebra cross-sectional area (CMO:0001689)1181059071226059071Rat
70160Bw18Body weight QTL 185.7body mass (VT:0001259)body weight (CMO:0000012)1153679879205813246Rat
1549830Bss1Bone structure and strength QTL 14.8femur strength trait (VT:0010010)femur ultimate force (CMO:0001675)1182039247227039247Rat
8694166Bw147Body weight QTL 1476.830.001body mass (VT:0001259)body weight gain (CMO:0000420)1153788989198788989Rat
70163Bw20Body weight QTL 205.1body mass (VT:0001259)body weight (CMO:0000012)1183564652228564652Rat
1354624Cm35Cardiac mass QTL355.7heart left ventricle mass (VT:0007031)calculated heart weight (CMO:0000073)1186658830266453731Rat
1600397Edcs4Endometrial carcinoma susceptibility QTL 42.2uterus morphology trait (VT:0001120)percentage of study population developing endometrioid carcinoma during a period of time (CMO:0001759)1176288899270518180Rat
1354636Lmblg1Limb length QTL 16.4tibia length (VT:0004357)tibia length (CMO:0000450)1160573753210707719Rat
1549837Hcar15Hepatocarcinoma resistance QTL 150.05liver integrity trait (VT:0010547)liver tumorous lesion number (CMO:0001068)1162548015270518180Rat
2293689Bss47Bone structure and strength QTL 477.250.0001lumbar vertebra size trait (VT:0010518)lumbar vertebra trabecular cross-sectional area (CMO:0001692)1181059071226059071Rat
152025235Bw194Body weight QTL 1944.86body mass (VT:0001259)1132966869252856240Rat
61341Bp26Blood pressure QTL 26arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)1139442053223964440Rat
1598853Memor3Memory QTL 34.5exploratory behavior trait (VT:0010471)total horizontal distance resulting from voluntary locomotion in an experimental apparatus (CMO:0001443)1152919152268496042Rat
1354634Kidm12Kidney mass QTL 123.9kidney mass (VT:0002707)right kidney wet weight (CMO:0000082)1160573753210707719Rat
4889428Stresp24Stress response QTL 240.05heart pumping trait (VT:2000009)absolute change in electrocardiographic low frequency R-R spectral component to high frequency R-R spectral component ratio (CMO:0002162)1165278545210278545Rat
152025232Bw192Body weight QTL 1923.93body mass (VT:0001259)1127329268206393015Rat
1578759Uae30Urinary albumin excretion QTL 303.30.003urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)1160111531262090437Rat
61343Bp28Blood pressure QTL 28arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)1161077990206077990Rat
2293693Bss22Bone structure and strength QTL 2233.520.0001femur morphology trait (VT:0000559)femur cross-sectional area (CMO:0001661)1181059071226059071Rat
1358902Bw47Body weight QTL 471.67body mass (VT:0001259)body weight (CMO:0000012)199645382221502378Rat
2300161Bmd43Bone mineral density QTL 438.40.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)1181059071226059071Rat
61347Bp197Blood pressure QTL 1974.2arterial blood pressure trait (VT:2000000)blood pressure measurement (CMO:0000003)1168063662213063662Rat
61348Bp30Blood pressure QTL 302.4arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)1159894717207261263Rat
8655649Arrd1Age-related retinal degeneration QTL 14.89retinal layer morphology trait (VT:0003727)percentage of study population developing retinopathy during a period of time (CMO:0002453)1109493780193400781Rat
2303622Vencon6Ventilatory control QTL 60.001respiration trait (VT:0001943)respiration rate (CMO:0000289)1163992710208992710Rat
631214Bw61Body weight QTL613.40.0001intramuscular adipose amount (VT:0010044)intramuscular fat area (CMO:0001162)1182535316227535316Rat
7771612Cm80Cardiac mass QTL 808.4heart left ventricle mass (VT:0007031)heart left ventricle weight (CMO:0000776)1146080545243492863Rat
731168Bp154Blood pressure QTL 1543.4arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)1103779152223964440Rat
631205Bp196Blood pressure QTL 19640.0001arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)198879955208479939Rat
1300158Bp173Blood pressure QTL 1733.48arterial blood pressure trait (VT:2000000)blood pressure time series experimental set point of the baroreceptor response (CMO:0002593)1155359438194575574Rat
2300174Bmd42Bone mineral density QTL 428.40.0001lumbar vertebra mineral mass (VT:0010511)bone mineral density (CMO:0001226)1181059071226059071Rat
737828Hcas3Hepatocarcinoma susceptibility QTL 34.9liver integrity trait (VT:0010547)liver tumorous lesion volume to total liver volume ratio (CMO:0001082)1153679879232414077Rat
1354661Bw33Body weight QTL 335.2body mass (VT:0001259)body weight (CMO:0000012)1160573753266453731Rat
1358886Bp260Blood pressure QTL 2603.67arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)1160574007235238518Rat
1331751Bp199Blood pressure QTL 1993.60022arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)1116099376191260518Rat
2293654Bss30Bone structure and strength QTL 3032.650.0001femur strength trait (VT:0010010)femur midshaft polar moment of inertia (CMO:0001669)1181059071226059071Rat
724531Uae5Urinary albumin excretion QTL 54urine albumin amount (VT:0002871)urine albumin level (CMO:0000130)1160111426262090599Rat
2300187Bmd41Bone mineral density QTL 418.90.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)1181059071226059071Rat
1641895Bp298Blood pressure QTL 298arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)1132760429191848948Rat
1354580Scort1Serum corticosterone level QTL 13.4blood corticosterone amount (VT:0005345)blood corticosterone level (CMO:0001172)1154961463266453731Rat
70209Niddm23Non-insulin dependent diabetes mellitus QTL 232.82blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)1162753891207753891Rat
1358294Bw37Body weight QTL 3750.000011body mass (VT:0001259)body weight (CMO:0000012)1180739993225739993Rat
634314Niddm44Non-insulin dependent diabetes mellitus QTL 44blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)151941022208479811Rat
2312420Pur17Proteinuria QTL 177.10.0001urine protein amount (VT:0005160)urine total protein excretion rate (CMO:0000756)1172718770228180370Rat
10059600Bp378Blood pressure QTL 3783.080.05arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)1186298393231298393Rat
1354591Cm36Cardiac mass QTL 364.1heart left ventricle mass (VT:0007031)calculated heart weight (CMO:0000073)1111949780210707719Rat
2312558Glom17Glomerulus QTL 173.90.001kidney glomerulus morphology trait (VT:0005325)index of glomerular damage (CMO:0001135)1175967553200707874Rat
10059597Bp377Blood pressure QTL 3773.420.025arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)134565911208798288Rat
631519Pia11Pristane induced arthritis QTL 115.3joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)193903998191260518Rat
619614Bp78Blood pressure QTL 780.001arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)1178547286206690557Rat
634321Hc1Hypercalciuria QTL 12.91urine calcium amount (VT:0002985)urine calcium excretion rate (CMO:0000763)1188241285250779312Rat
724562Rends1Renal damage susceptibility QTL 10.05kidney glomerulus integrity trait (VT:0010546)index of glomerular damage (CMO:0001135)1139442053223964440Rat
2292222Bp307Blood pressure QTL 3073.060.0014arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)1186298393231298393Rat
2292220Bp306Blood pressure QTL 3063.470.00087arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)1186298393231298393Rat
1354615Cm32Cardiac mass QTL 325.2heart left ventricle mass (VT:0007031)heart left ventricle wet weight (CMO:0000071)1111949780210707719Rat
1600380Niddm70Non-insulin dependent diabetes mellitus QTL 703.10.0008blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)1185979875230979875Rat
1354610Bw34Body weight QTL 344.1body mass (VT:0001259)body weight (CMO:0000012)1160573753266453731Rat
1354620Kidm19Kidney mass QTL 194kidney mass (VT:0002707)calculated kidney weight (CMO:0000160)1160573753210707719Rat
1576310Schws2Schwannoma susceptibility QTL 20.029nervous system integrity trait (VT:0010566)percentage of study population developing trigeminal nerve neurilemmomas during a period of time (CMO:0002017)1153788989198788989Rat
1354618Kidm15Kidney mass QTL 155kidney mass (VT:0002707)left kidney wet weight (CMO:0000083)1165707719210707719Rat
6903303Scl34Serum cholesterol QTL 342.50.0033blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)1173363824227535316Rat
631544Bp84Blood pressure QTL 845.6arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)1132760429191190115Rat
152025212Bw190Body weight QTL 1905.7body mass (VT:0001259)1132966869206393015Rat
1358189Cstrr1Cold stress response QTL 10.0001catecholamine amount (VT:0010543)urine norepinephrine level (CMO:0001629)1132760429191848948Rat
1354606Bp246Blood pressure QTL 2463.6arterial blood pressure trait (VT:2000000)pulse pressure (CMO:0000292)1111949780228180370Rat
738032Hcas5Hepatocarcinoma susceptibility QTL 53.12liver integrity trait (VT:0010547)liver tumorous lesion number (CMO:0001068)1185857683270518180Rat
2325727Pia41Pristane induced arthritis QTL 41joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1188241285233241285Rat
7411599Foco11Food consumption QTL 1118.50.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)1153788989198788989Rat
1354602Bw35Body weight QTL 3512.2body mass (VT:0001259)body weight (CMO:0000012)1160573753210707719Rat
2325725Eae31Experimental allergic encephalomyelitis QTL 31nervous system integrity trait (VT:0010566)experimental autoimmune encephalomyelitis severity score (CMO:0001419)1188241285197807511Rat
631670Iddm10Insulin dependent diabetes mellitus QTL 101.9blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)1183564652205813246Rat

Markers in Region
RH129744  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21181,156,170 - 181,156,350 (+)MAPPERmRatBN7.2
Rnor_6.01197,986,484 - 197,986,663NCBIRnor6.0
Rnor_5.01204,965,244 - 204,965,423UniSTSRnor5.0
RGSC_v3.41185,713,196 - 185,713,375UniSTSRGSC3.4
Celera1178,814,190 - 178,814,369UniSTS
Cytogenetic Map1q36UniSTS


Expression

RNA-SEQ Expression

alimentary part of gastrointestinal system
appendage
circulatory system
ectoderm
endocrine system
endoderm
exocrine system
hemolymphoid system
hepatobiliary system
integumental system
mesenchyme
mesoderm
musculoskeletal system
nervous system
renal system
reproductive system
respiratory system
sensory system
visual system
16 12 67 163 91 90 59 92 59 6 356 192 11 142 81 92 31 17 17

Sequence

Nucleotide Sequences
RefSeq Transcripts NM_001006971 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  NM_001439717 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  NM_001439718 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  NM_001439719 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008759871 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008759872 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008759873 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008759875 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039107240 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039107246 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039107249 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039107253 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039107263 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039107268 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039107273 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XR_010065644 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide BC083704 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CH473956 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  JAXUCZ010000001 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Ensembl Acc Id: ENSRNOT00000025898   ⟹   ENSRNOP00000025898
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl1190,586,650 - 190,597,929 (-)Ensembl
mRatBN7.2 Ensembl1181,156,073 - 181,167,434 (-)Ensembl
Rnor_6.0 Ensembl1197,986,385 - 197,997,664 (-)Ensembl
Ensembl Acc Id: ENSRNOT00000117379   ⟹   ENSRNOP00000095097
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl1190,586,650 - 190,597,929 (-)Ensembl
mRatBN7.2 Ensembl1181,156,075 - 181,167,417 (-)Ensembl
Ensembl Acc Id: ENSRNOT00000172311   ⟹   ENSRNOP00000109237
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl1190,586,650 - 190,597,929 (-)Ensembl
RefSeq Acc Id: NM_001006971   ⟹   NP_001006972
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81190,586,649 - 190,597,929 (-)NCBI
mRatBN7.21181,156,071 - 181,167,353 (-)NCBI
Rnor_6.01197,986,384 - 197,997,664 (-)NCBI
Rnor_5.01204,965,144 - 204,978,485 (-)NCBI
RGSC_v3.41185,713,096 - 185,724,375 (-)RGD
Celera1178,814,090 - 178,825,369 (-)RGD
Sequence:
RefSeq Acc Id: XM_008759875   ⟹   XP_008758097
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81190,586,649 - 190,596,560 (-)NCBI
mRatBN7.21181,156,071 - 181,168,656 (-)NCBI
Rnor_6.01197,986,384 - 197,999,041 (-)NCBI
Sequence:
RefSeq Acc Id: XM_039107240   ⟹   XP_038963168
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81190,586,649 - 190,599,547 (-)NCBI
mRatBN7.21181,156,076 - 181,168,971 (-)NCBI
RefSeq Acc Id: XM_039107246   ⟹   XP_038963174
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81190,586,649 - 190,599,229 (-)NCBI
mRatBN7.21181,156,076 - 181,168,655 (-)NCBI
RefSeq Acc Id: XM_039107249   ⟹   XP_038963177
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81190,586,649 - 190,600,034 (-)NCBI
mRatBN7.21181,156,076 - 181,169,458 (-)NCBI
RefSeq Acc Id: XM_039107253   ⟹   XP_038963181
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81190,586,649 - 190,599,547 (-)NCBI
mRatBN7.21181,156,071 - 181,168,655 (-)NCBI
RefSeq Acc Id: XM_039107263   ⟹   XP_038963191
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81190,586,649 - 190,597,464 (-)NCBI
mRatBN7.21181,156,071 - 181,166,888 (-)NCBI
RefSeq Acc Id: XM_039107268   ⟹   XP_038963196
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81190,586,649 - 190,597,545 (-)NCBI
mRatBN7.21181,156,071 - 181,166,937 (-)NCBI
RefSeq Acc Id: XM_039107273   ⟹   XP_038963201
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81190,586,649 - 190,597,544 (-)NCBI
mRatBN7.21181,156,071 - 181,166,969 (-)NCBI
RefSeq Acc Id: XR_010065644
Type: NON-CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81190,587,063 - 190,599,543 (-)NCBI
RefSeq Acc Id: NP_001006972   ⟸   NM_001006971
- UniProtKB: Q5XIH8 (UniProtKB/TrEMBL),   A0A8I6ALZ9 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_008758097   ⟸   XM_008759875
- Peptide Label: isoform X4
- UniProtKB: F7F0I2 (UniProtKB/TrEMBL)
- Sequence:
Ensembl Acc Id: ENSRNOP00000025898   ⟸   ENSRNOT00000025898
RefSeq Acc Id: XP_038963181   ⟸   XM_039107253
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038963201   ⟸   XM_039107273
- Peptide Label: isoform X3
- UniProtKB: A6I990 (UniProtKB/TrEMBL),   F7F0I2 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_038963196   ⟸   XM_039107268
- Peptide Label: isoform X2
- UniProtKB: F7F0I2 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_038963191   ⟸   XM_039107263
- Peptide Label: isoform X2
- UniProtKB: F7F0I2 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_038963177   ⟸   XM_039107249
- Peptide Label: isoform X1
- UniProtKB: Q5XIH8 (UniProtKB/TrEMBL),   A0A8I6ALZ9 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_038963168   ⟸   XM_039107240
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038963174   ⟸   XM_039107246
- Peptide Label: isoform X1
- UniProtKB: Q5XIH8 (UniProtKB/TrEMBL),   A0A8I6ALZ9 (UniProtKB/TrEMBL)
Ensembl Acc Id: ENSRNOP00000095097   ⟸   ENSRNOT00000117379
Ensembl Acc Id: ENSRNOP00000109237   ⟸   ENSRNOT00000172311

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-Q5XIH8-F1-model_v2 AlphaFold Q5XIH8 1-438 view protein structure

Transcriptome

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

Promoters
RGD ID:13690401
Promoter ID:EPDNEW_R926
Type:initiation region
Name:Cln3_1
Description:CLN3, battenin
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_6.01197,997,682 - 197,997,742EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1359537 AgrOrtholog
BioCyc Gene G2FUF-57442 BioCyc
Ensembl Genes ENSRNOG00000019103 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000025898 ENTREZGENE
  ENSRNOT00000025898.6 UniProtKB/TrEMBL
  ENSRNOT00000117379.2 UniProtKB/TrEMBL
  ENSRNOT00000172311.1 UniProtKB/TrEMBL
Gene3D-CATH MFS general substrate transporter like domains UniProtKB/TrEMBL
IMAGE_CLONE IMAGE:7190222 IMAGE-MGC_LOAD
InterPro Battenin_disease_Cln3 UniProtKB/TrEMBL
  Battenin_disease_Cln3_sungr UniProtKB/TrEMBL
  MFS_trans_sf UniProtKB/TrEMBL
KEGG Report rno:293485 UniProtKB/TrEMBL
MGC_CLONE MGC:94583 IMAGE-MGC_LOAD
NCBI Gene 293485 ENTREZGENE
PANTHER Battenin UniProtKB/TrEMBL
  BATTENIN UniProtKB/TrEMBL
Pfam CLN3 UniProtKB/TrEMBL
PhenoGen Cln3 PhenoGen
PIRSF CLN3_BTN1 UniProtKB/TrEMBL
PRINTS BATTENIN UniProtKB/TrEMBL
RatGTEx ENSRNOG00000019103 RatGTEx
Superfamily-SCOP MFS_gen_substrate_transporter UniProtKB/TrEMBL
UniProt A0A8I6ALZ9 ENTREZGENE, UniProtKB/TrEMBL
  A0ABK0LEL9_RAT UniProtKB/TrEMBL
  A6I990 ENTREZGENE, UniProtKB/TrEMBL
  A6I991_RAT UniProtKB/TrEMBL
  A6I992_RAT UniProtKB/TrEMBL
  A6I993_RAT UniProtKB/TrEMBL
  F7F0I2 ENTREZGENE, UniProtKB/TrEMBL
  Q5XIH8 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2019-04-10 Cln3  CLN3 lysosomal/endosomal transmembrane protein, battenin  Cln3  CLN3, battenin  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2017-07-05 Cln3  CLN3, battenin  Cln3  ceroid-lipofuscinosis, neuronal 3  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-09-24 Cln3  ceroid-lipofuscinosis, neuronal 3  Cln3  ceroid lipofuscinosis, neuronal 3, juvenile (Batten, Spielmeyer-Vogt disease)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2006-03-30 Cln3  ceroid lipofuscinosis, neuronal 3, juvenile (Batten, Spielmeyer-Vogt disease)    Cln3p  Name updated 1299863 APPROVED
2005-07-29 Cln3  Cln3p      Symbol and Name status set to provisional 70820 PROVISIONAL