Clcn3 (chloride voltage-gated channel 3) - Rat Genome Database

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Gene: Clcn3 (chloride voltage-gated channel 3) Rattus norvegicus
Analyze
Symbol: Clcn3
Name: chloride voltage-gated channel 3
RGD ID: 621219
Description: Enables voltage-gated chloride channel activity. Involved in chloride transport. Located in apical plasma membrane; inhibitory synapse; and synaptic vesicle. Is active in glutamatergic synapse and postsynaptic membrane. Orthologous to human CLCN3 (chloride voltage-gated channel 3); INTERACTS WITH 17alpha-ethynylestradiol; 2,4-dinitrotoluene; ammonium chloride.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: chloride channel 3; chloride channel protein 3; chloride channel, voltage-sensitive 3; chloride transporter ClC-3; ClC-3; h(+)/Cl(-) exchange transporter 3; protein kinase C-regulated chloride channel
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
mRatBN7.21629,127,419 - 29,200,133 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1629,127,419 - 29,200,119 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1632,722,030 - 32,795,004 (+)NCBIRnor_SHR
UTH_Rnor_SHRSP_BbbUtx_1.01636,155,756 - 36,228,732 (+)NCBIRnor_SHRSP
UTH_Rnor_WKY_Bbb_1.01632,357,272 - 32,430,251 (+)NCBIRnor_WKY
Rnor_6.01632,448,821 - 32,520,649 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1632,449,116 - 32,519,148 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01632,283,743 - 32,355,489 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41632,447,259 - 32,518,533 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.11632,447,333 - 32,517,457 (+)NCBI
Celera1629,122,247 - 29,193,279 (+)NCBICelera
Cytogenetic Map16p12NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
(R,R,R)-alpha-tocopherol  (ISO)
(S)-nicotine  (ISO)
1,2-dimethylhydrazine  (ISO)
17alpha-ethynylestradiol  (EXP,ISO)
2,3,7,8-tetrachlorodibenzodioxine  (ISO)
2,4-dinitrotoluene  (EXP)
2-hydroxypropanoic acid  (ISO)
4,4'-diisothiocyano-trans-stilbene-2,2'-disulfonic acid  (ISO)
4-hydroxyphenyl retinamide  (ISO)
5-fluorouracil  (ISO)
5-Nitro-2-(3-phenylpropylamino)benzoic acid  (ISO)
acetazolamide  (ISO)
acrolein  (ISO)
aflatoxin B1  (ISO)
alpha-pinene  (ISO)
ammonium chloride  (EXP)
Aroclor 1254  (ISO)
benzo[a]pyrene  (ISO)
beta-carotene  (ISO)
bisphenol A  (EXP,ISO)
cadmium dichloride  (ISO)
carbon nanotube  (ISO)
chlorpyrifos  (EXP)
cisplatin  (ISO)
cycloheximide  (ISO)
cyclosporin A  (ISO)
D-gluconic acid  (ISO)
D-mannitol  (ISO)
dextran sulfate  (ISO)
dibutyl phthalate  (ISO)
dorsomorphin  (ISO)
elemental selenium  (ISO)
ethanol  (ISO)
flutamide  (EXP)
genistein  (EXP)
gentamycin  (EXP)
hydrogen peroxide  (ISO)
indinavir  (ISO)
isoprenaline  (ISO)
isotretinoin  (ISO)
ivermectin  (ISO)
lamivudine  (ISO)
lead diacetate  (EXP)
leflunomide  (ISO)
methapyrilene  (EXP)
nefazodone  (EXP)
nicotine  (ISO)
nitrofen  (EXP)
ozone  (ISO)
paracetamol  (EXP,ISO)
perfluorooctanoic acid  (EXP)
pirinixic acid  (ISO)
piroxicam  (ISO)
propiconazole  (ISO)
quercetin  (ISO)
rac-lactic acid  (ISO)
saquinavir  (ISO)
sarin  (ISO)
SB 431542  (ISO)
selenium atom  (ISO)
simvastatin  (EXP)
sodium arsenate  (ISO)
sodium arsenite  (ISO)
sunitinib  (ISO)
temozolomide  (ISO)
tert-butyl hydroperoxide  (ISO)
testosterone enanthate  (ISO)
tetrachloromethane  (EXP,ISO)
thioacetamide  (EXP)
titanium dioxide  (ISO)
topotecan  (ISO)
trichloroethene  (ISO)
trichostatin A  (ISO)
triphenyl phosphate  (EXP)
urethane  (ISO)
valproic acid  (ISO)
vitamin E  (ISO)
vorinostat  (ISO)
zidovudine  (ISO)
zinc atom  (ISO)
zinc(0)  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

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. Rat ISS GO annotations from GOA human gene data--August 2006 GOA data from the GO Consortium
3. Detection of ClC-3 and ClC-5 in epididymal epithelium: immunofluorescence and RT-PCR after LCM. Isnard-Bagnis C, etal., Am J Physiol Cell Physiol 2003 Jan;284(1):C220-32.
4. Rat ISS GO annotations from MGI mouse gene data--August 2006 MGD data from the GO Consortium
5. Electronic Transfer of LocusLink and RefSeq Data NCBI rat LocusLink and RefSeq merged data July 26, 2002
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. Presynaptic CLC-3 determines quantal size of inhibitory transmission in the hippocampus. Riazanski V, etal., Nat Neurosci. 2011 Apr;14(4):487-94. doi: 10.1038/nn.2775. Epub 2011 Mar 6.
10. Expression and canalicular localization of two isoforms of the ClC-3 chloride channel from rat hepatocytes. Shimada K, etal., Am J Physiol Gastrointest Liver Physiol 2000 Aug;279(2):G268-76.
11. Disruption of ClC-3, a chloride channel expressed on synaptic vesicles, leads to a loss of the hippocampus. Stobrawa SM, etal., Neuron. 2001 Jan;29(1):185-96.
12. CLC-3 channels modulate excitatory synaptic transmission in hippocampal neurons. Wang XQ, etal., Neuron. 2006 Oct 19;52(2):321-33. doi: 10.1016/j.neuron.2006.08.035.
13. CLC-3 deficiency leads to phenotypes similar to human neuronal ceroid lipofuscinosis. Yoshikawa M, etal., Genes Cells 2002 Jun;7(6):597-605.
Additional References at PubMed
PMID:8155321   PMID:8889548   PMID:11274166   PMID:12183454   PMID:12471024   PMID:15073168   PMID:15723096   PMID:16522634   PMID:18339705   PMID:18823498   PMID:19910686   PMID:19946888  
PMID:20519092   PMID:21373935   PMID:22168445   PMID:23181279   PMID:23536605   PMID:24611720   PMID:26436462   PMID:29158167   PMID:29527534   PMID:30025794   PMID:30468668   PMID:32247607  


Genomics

Comparative Map Data
Clcn3
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21629,127,419 - 29,200,133 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1629,127,419 - 29,200,119 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1632,722,030 - 32,795,004 (+)NCBIRnor_SHR
UTH_Rnor_SHRSP_BbbUtx_1.01636,155,756 - 36,228,732 (+)NCBIRnor_SHRSP
UTH_Rnor_WKY_Bbb_1.01632,357,272 - 32,430,251 (+)NCBIRnor_WKY
Rnor_6.01632,448,821 - 32,520,649 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1632,449,116 - 32,519,148 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01632,283,743 - 32,355,489 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41632,447,259 - 32,518,533 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.11632,447,333 - 32,517,457 (+)NCBI
Celera1629,122,247 - 29,193,279 (+)NCBICelera
Cytogenetic Map16p12NCBI
CLCN3
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh384169,620,578 - 169,723,673 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p13 Ensembl4169,612,633 - 169,723,673 (+)EnsemblGRCh38hg38GRCh38
GRCh374170,541,729 - 170,644,824 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 364170,778,297 - 170,878,732 (+)NCBINCBI36Build 36hg18NCBI36
Build 344170,916,451 - 171,016,886NCBI
Celera4167,874,695 - 167,975,138 (+)NCBICelera
Cytogenetic Map4q33NCBI
HuRef4166,296,448 - 166,399,155 (+)NCBIHuRef
CHM1_14170,518,267 - 170,620,908 (+)NCBICHM1_1
T2T-CHM13v2.04172,980,359 - 173,083,792 (+)NCBIT2T-CHM13v2.0
Clcn3
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39861,363,423 - 61,436,353 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl861,363,423 - 61,436,334 (-)EnsemblGRCm39 Ensembl
GRCm38860,910,389 - 60,983,317 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl860,910,389 - 60,983,300 (-)EnsemblGRCm38mm10GRCm38
MGSCv37863,389,186 - 63,462,108 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv36863,802,531 - 63,875,442 (-)NCBIMGSCv36mm8
Celera863,477,568 - 63,550,480 (-)NCBICelera
Cytogenetic Map8B3.1NCBI
cM Map830.9NCBI
Clcn3
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495540336,625,770 - 36,710,201 (-)EnsemblChiLan1.0
ChiLan1.0NW_00495540336,625,871 - 36,710,201 (-)NCBIChiLan1.0ChiLan1.0
CLCN3
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.14173,909,980 - 174,014,786 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl4173,925,474 - 174,011,681 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v04161,838,061 - 161,943,072 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
CLCN3
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.12520,528,708 - 20,616,687 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl2520,528,699 - 20,615,070 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha2521,198,852 - 21,249,735 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.02520,704,517 - 20,792,549 (+)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl2520,704,520 - 20,792,546 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.12520,623,955 - 20,675,230 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.02520,560,112 - 20,611,064 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.02520,659,558 - 20,710,662 (+)NCBIUU_Cfam_GSD_1.0
Clcn3
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440494321,264,313 - 21,345,811 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049365161,678,653 - 1,760,294 (+)EnsemblSpeTri2.0
SpeTri2.0NW_0049365161,678,610 - 1,760,099 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
CLCN3
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1420,026,685 - 20,127,155 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11420,037,628 - 20,127,160 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21421,332,126 - 21,421,643 (-)NCBISscrofa10.2Sscrofa10.2susScr3
CLCN3
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.17115,826,756 - 115,926,842 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl7115,826,778 - 115,928,609 (+)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366603795,772,878 - 95,874,689 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Clcn3
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046247691,156,460 - 1,232,612 (+)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_0046247691,156,522 - 1,246,531 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Clcn3
354 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:134
Count of miRNA genes:111
Interacting mature miRNAs:118
Transcripts:ENSRNOT00000050549
Prediction methods:Miranda, Rnahybrid
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
9590151Scort8Serum corticosterone level QTL 88.450.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)16130836262Rat
2302380Slep6Serum leptin concentration QTL 63.36blood leptin amount (VT:0005667)serum leptin level (CMO:0000780)16132139025Rat
2307172Activ4Activity QTL 43.710.00023locomotor behavior trait (VT:0001392)number of entries into a discrete space in an experimental apparatus (CMO:0000960)16133418960Rat
1354584Despr6Despair related QTL 63.10.0067locomotor behavior trait (VT:0001392)amount of time spent in voluntary immobility (CMO:0001043)16139533930Rat
2303566Bw90Body weight QTL 902body mass (VT:0001259)body weight (CMO:0000012)16139533930Rat
631561Hcuc2Hepatic copper content QTL 22.8liver copper amount (VT:0003065)liver total copper weight (CMO:0001507)16139533949Rat
6903319Bw114Body weight QTL 1142.70.0037body mass (VT:0001259)body weight (CMO:0000012)16143534949Rat
7411664Foco30Food consumption QTL 30110.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)16144588133Rat
1354625Despr7Despair related QTL 73.160.016locomotor behavior trait (VT:0001392)amount of time spent in voluntary immobility (CMO:0001043)16144977551Rat
1600378Arunc4Aerobic running capacity QTL 40.03exercise endurance trait (VT:0002332)maximum distance run on treadmill (CMO:0001406)1638024580345693Rat
2293343Glom16Glomerulus QTL 167.4kidney glomerulus integrity trait (VT:0010546)kidney sclerotic glomeruli count to total glomeruli count ratio (CMO:0001269)1683223646053497Rat
2312660Bw95Body weight QTL 950.05inguinal fat pad mass (VT:0010424)inguinal fat pad weight to body weight ratio (CMO:0001253)1683223659492508Rat
2312663Slep9Serum leptin concentration QTL 90.001blood leptin amount (VT:0005667)serum leptin level (CMO:0000780)1683223659492508Rat
2312666Insul16Insulin level QTL 160.01blood insulin amount (VT:0001560)serum insulin level (CMO:0000358)1683223659492508Rat
2312669Stl23Serum triglyceride level QTL 230.01blood triglyceride amount (VT:0002644)serum triglyceride level (CMO:0000360)1683223659492508Rat
2306902Bp339Blood pressure QTL 3390.01arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)16338015043025077Rat
70183BpQTLcluster13Blood pressure QTL cluster 133.654arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)16422760943025077Rat
70183BpQTLcluster13Blood pressure QTL cluster 133.654arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)16422760943025077Rat
70183BpQTLcluster13Blood pressure QTL cluster 133.654arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)16422760943025077Rat
737819Hcas4Hepatocarcinoma susceptibility QTL 44.43liver integrity trait (VT:0010547)volume of individual liver tumorous lesion (CMO:0001078)16422760946975965Rat
61405Niddm6Non-insulin dependent diabetes mellitus QTL 63.660.001blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)16422760948972724Rat
61338Bp23Blood pressure QTL 234.3arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)16422760949227609Rat
737826Alc11Alcohol consumption QTL 113.2consumption behavior trait (VT:0002069)ethanol drink intake rate (CMO:0001407)16422760960252231Rat
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
2302057Pia29Pristane induced arthritis QTL 293.60.001blood autoantibody amount (VT:0003725)serum immunoglobulin M-type rheumatoid factor level relative to an arbitrary reference serum (CMO:0002111)162173597566735975Rat
8694453Bw172Body weight QTL 1728.330.001retroperitoneal fat pad mass (VT:0010430)retroperitoneal fat pad weight to body weight ratio (CMO:0000635)162432551369325513Rat
6903294Stl30Serum triglyceride level QTL 302.60.0013blood triglyceride amount (VT:0002644)plasma triglyceride level (CMO:0000548)162515279370152793Rat

Markers in Region
UniSTS:238126  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21629,187,987 - 29,188,532 (+)MAPPERmRatBN7.2
mRatBN7.2568,280,773 - 68,281,315 (+)MAPPERmRatBN7.2
Rnor_6.0570,462,975 - 70,463,516NCBIRnor6.0
Rnor_6.01632,509,512 - 32,510,056NCBIRnor6.0
Rnor_5.01632,344,352 - 32,344,896UniSTSRnor5.0
Rnor_5.0574,620,539 - 74,621,080UniSTSRnor5.0
RGSC_v3.4571,095,184 - 71,095,725UniSTSRGSC3.4
RGSC_v3.41632,507,686 - 32,508,230UniSTSRGSC3.4
Celera1629,182,635 - 29,183,179UniSTS
Celera567,175,084 - 67,175,625UniSTS
Cytogenetic Map5q24UniSTS
Cytogenetic Map16p12UniSTS
Cytogenetic Map4q24UniSTS
RH142804  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21629,198,251 - 29,198,411 (+)MAPPERmRatBN7.2
Rnor_6.01632,518,770 - 32,518,929NCBIRnor6.0
Rnor_5.01632,353,610 - 32,353,769UniSTSRnor5.0
RGSC_v3.41632,518,153 - 32,518,312UniSTSRGSC3.4
Celera1629,192,899 - 29,193,058UniSTS
Cytogenetic Map16p12UniSTS
RH139046  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21629,198,391 - 29,198,537 (+)MAPPERmRatBN7.2
Rnor_6.01632,518,910 - 32,519,055NCBIRnor6.0
Rnor_5.01632,353,750 - 32,353,895UniSTSRnor5.0
RGSC_v3.41632,518,293 - 32,518,438UniSTSRGSC3.4
Celera1629,193,039 - 29,193,184UniSTS
Cytogenetic Map16p12UniSTS


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 42 52 36 18 36 8 8 74 35 39 11 8
Low 1 5 5 1 5 3 2
Below cutoff

Sequence

Nucleotide Sequences
RefSeq Transcripts NM_001413712 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  NM_053363 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006253070 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006253071 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006253073 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006253075 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006253076 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006253077 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017600266 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017600267 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039094868 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039094869 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039094870 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039094871 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039094872 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039094873 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039094875 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039094876 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide AF142778 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BF417445 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CB577015 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CH474053 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CV117598 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  JACYVU010000279 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Reference Sequences
RefSeq Acc Id: ENSRNOT00000050549   ⟹   ENSRNOP00000045523
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1629,127,419 - 29,199,253 (+)Ensembl
Rnor_6.0 Ensembl1632,449,116 - 32,519,148 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000083579   ⟹   ENSRNOP00000072280
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1629,154,658 - 29,200,119 (+)Ensembl
Rnor_6.0 Ensembl1632,457,521 - 32,518,268 (+)Ensembl
RefSeq Acc Id: NM_053363   ⟹   NP_445815
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21629,127,419 - 29,198,632 (+)NCBI
Rnor_6.01632,449,116 - 32,519,150 (+)NCBI
Rnor_5.01632,283,743 - 32,355,489 (+)NCBI
RGSC_v3.41632,447,259 - 32,518,533 (+)RGD
Celera1629,122,247 - 29,193,279 (+)RGD
Sequence:
RefSeq Acc Id: XM_039094868   ⟹   XP_038950796
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21629,127,468 - 29,200,133 (+)NCBI
RefSeq Acc Id: XM_039094869   ⟹   XP_038950797
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21629,154,538 - 29,200,133 (+)NCBI
RefSeq Acc Id: XM_039094870   ⟹   XP_038950798
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21629,127,489 - 29,200,133 (+)NCBI
RefSeq Acc Id: XM_039094871   ⟹   XP_038950799
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21629,159,502 - 29,200,133 (+)NCBI
RefSeq Acc Id: XM_039094872   ⟹   XP_038950800
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21629,155,248 - 29,200,133 (+)NCBI
RefSeq Acc Id: XM_039094873   ⟹   XP_038950801
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21629,154,981 - 29,200,133 (+)NCBI
RefSeq Acc Id: XM_039094875   ⟹   XP_038950803
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21629,151,821 - 29,200,133 (+)NCBI
RefSeq Acc Id: XM_039094876   ⟹   XP_038950804
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21629,154,544 - 29,200,133 (+)NCBI
Reference Sequences
RefSeq Acc Id: NP_445815   ⟸   NM_053363
- UniProtKB: Q9R287 (UniProtKB/Swiss-Prot),   P51792 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: ENSRNOP00000072280   ⟸   ENSRNOT00000083579
RefSeq Acc Id: ENSRNOP00000045523   ⟸   ENSRNOT00000050549
RefSeq Acc Id: XP_038950796   ⟸   XM_039094868
- Peptide Label: isoform X1
- UniProtKB: A0A8L2ULZ0 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_038950798   ⟸   XM_039094870
- Peptide Label: isoform X3
RefSeq Acc Id: XP_038950803   ⟸   XM_039094875
- Peptide Label: isoform X3
RefSeq Acc Id: XP_038950797   ⟸   XM_039094869
- Peptide Label: isoform X2
RefSeq Acc Id: XP_038950804   ⟸   XM_039094876
- Peptide Label: isoform X4
- UniProtKB: A0A0G2K2K6 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_038950801   ⟸   XM_039094873
- Peptide Label: isoform X3
RefSeq Acc Id: XP_038950800   ⟸   XM_039094872
- Peptide Label: isoform X3
RefSeq Acc Id: XP_038950799   ⟸   XM_039094871
- Peptide Label: isoform X3
Protein Domains
CBS

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-P51792-F1-model_v2 AlphaFold P51792 1-818 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:621219 AgrOrtholog
BioCyc Gene G2FUF-11577 BioCyc
Ensembl Genes ENSRNOG00000010682 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000045523 ENTREZGENE
  ENSRNOP00000045523.5 UniProtKB/TrEMBL
  ENSRNOP00000072280 ENTREZGENE
  ENSRNOP00000072280.2 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000050549 ENTREZGENE
  ENSRNOT00000050549.6 UniProtKB/TrEMBL
  ENSRNOT00000083579 ENTREZGENE
  ENSRNOT00000083579.2 UniProtKB/TrEMBL
InterPro CBS_dom UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  CBS_dom_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Cl-channel_core UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Cl-channel_volt-gated UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Cl_channel-3 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:84360 UniProtKB/Swiss-Prot
NCBI Gene 84360 ENTREZGENE
Pfam CBS UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Voltage_CLC UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Clcn3 PhenoGen
PRINTS CLCHANNEL UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  CLCHANNEL3 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PROSITE CBS UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
SMART CBS UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP SSF54631 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SSF81340 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt A0A0G2K2K6 ENTREZGENE, UniProtKB/TrEMBL
  A0A8L2ULZ0 ENTREZGENE, UniProtKB/TrEMBL
  CLCN3_RAT UniProtKB/Swiss-Prot, ENTREZGENE
  Q9R287 ENTREZGENE
UniProt Secondary Q9R287 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2016-02-11 Clcn3  chloride voltage-gated channel 3  Clcn3  chloride channel, voltage-sensitive 3  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2012-07-16 Clcn3  chloride channel, voltage-sensitive 3  Clcn3  chloride channel 3  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2004-02-26 Clcn3  chloride channel 3      Symbol and Name status set to approved 625702 APPROVED
2002-08-07 Clcn3  chloride channel 3      Symbol and Name status set to provisional 70820 PROVISIONAL

RGD Curation Notes
Note Type Note Reference
gene_cellular_localization localized to the canalicular membrane 628537
gene_cellular_localization localized to the canalicular membrane 628538
gene_expression long form is present in all the tissues and the short form is more abundant in the liver, kidney and lungs 628537
gene_expression long form is present in all the tissues and the short form is more abundant in the liver, kidney and lungs 628538
gene_expression expressed in the epididymis and the vas deferens 628537
gene_expression expressed in the epididymis and the vas deferens 628538
gene_function voltage-gated ion channel 628537
gene_function voltage-gated ion channel 628538
gene_process responsible for chloride transport 628537
gene_process responsible for chloride transport 628538
gene_product member of the chloride channel family  
gene_protein two isoforms are present; short form is identical to the sequence and the long form has an insertion of 176 bp upstream of the translation initiation site 628537
gene_protein two isoforms are present; short form is identical to the sequence and the long form has an insertion of 176 bp upstream of the translation initiation site 628538