Clcn1 (chloride voltage-gated channel 1) - Rat Genome Database

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Gene: Clcn1 (chloride voltage-gated channel 1) Rattus norvegicus
Analyze
Symbol: Clcn1
Name: chloride voltage-gated channel 1
RGD ID: 2360
Description: Enables voltage-gated chloride channel activity. Involved in chloride transport. Predicted to be located in sarcolemma. Predicted to be part of chloride channel complex. Human ortholog(s) of this gene implicated in Thomsen disease and myotonia congenita. Orthologous to human CLCN1 (chloride voltage-gated channel 1); INTERACTS WITH ammonium chloride; atorvastatin calcium; bisphenol A.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: chloride channel 1; chloride channel 1 (skeletal muscle); chloride channel 1, skeletal muscle; chloride channel protein 1; chloride channel protein, skeletal muscle; chloride channel, voltage-sensitive 1; clC-1; SMCC
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Is Marker For: Strains:   WF.BBDR-(Clcn1-D4Rat228)/Wor  
Candidate Gene For: Bp116
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8472,138,739 - 72,168,113 (+)NCBIGRCr8
mRatBN7.2471,171,949 - 71,201,483 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl471,172,547 - 71,199,984 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx476,092,286 - 76,119,750 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0472,005,543 - 72,033,007 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0470,425,008 - 70,452,467 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0471,674,218 - 71,704,318 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl471,675,383 - 71,702,819 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.04136,479,719 - 136,509,472 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4470,052,319 - 70,081,449 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.1470,328,448 - 70,357,579 (+)NCBI
Celera466,103,038 - 66,130,477 (+)NCBICelera
RH 3.4 Map4433.61RGD
Cytogenetic Map4q24NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


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

Biological Process

Cellular Component

Molecular Function

References

References - curated
# Reference Title Reference Citation
1. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
2. Rat ISS GO annotations from GOA human gene data--August 2006 GOA data from the GO Consortium
3. High-density rat radiation hybrid maps containing over 24,000 SSLPs, genes, and ESTs provide a direct link to the rat genome sequence. Kwitek AE, etal., Genome Res. 2004 Apr;14(4):750-7
4. Genomic organization of the human muscle chloride channel CIC-1 and analysis of novel mutations leading to Becker-type myotonia. Lorenz C, etal., Hum Mol Genet 1994 Jun;3(6):941-6.
5. Rat ISS GO annotations from MGI mouse gene data--August 2006 MGD data from the GO Consortium
6. Electronic Transfer of LocusLink and RefSeq Data NCBI rat LocusLink and RefSeq merged data July 26, 2002
7. OMIM Disease Annotation Pipeline OMIM Disease Annotation Pipeline
8. GOA pipeline RGD automated data pipeline
9. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
10. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
11. Primary structure and functional expression of a developmentally regulated skeletal muscle chloride channel. Steinmeyer K, etal., Nature 1991 Nov 28;354(6351):301-4.
Additional References at PubMed
PMID:2453798   PMID:7721815   PMID:15139012   PMID:19220292   PMID:19786584   PMID:22521272   PMID:26007199   PMID:26021757   PMID:26502825  


Genomics

Comparative Map Data
Clcn1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8472,138,739 - 72,168,113 (+)NCBIGRCr8
mRatBN7.2471,171,949 - 71,201,483 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl471,172,547 - 71,199,984 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx476,092,286 - 76,119,750 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0472,005,543 - 72,033,007 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0470,425,008 - 70,452,467 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0471,674,218 - 71,704,318 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl471,675,383 - 71,702,819 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.04136,479,719 - 136,509,472 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4470,052,319 - 70,081,449 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.1470,328,448 - 70,357,579 (+)NCBI
Celera466,103,038 - 66,130,477 (+)NCBICelera
RH 3.4 Map4433.61RGD
Cytogenetic Map4q24NCBI
CLCN1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh387143,316,111 - 143,352,083 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl7143,316,111 - 143,352,083 (+)EnsemblGRCh38hg38GRCh38
GRCh377143,013,204 - 143,049,176 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 367142,723,341 - 142,759,219 (+)NCBINCBI36Build 36hg18NCBI36
Build 347142,530,055 - 142,565,934NCBI
Celera7137,850,084 - 137,885,958 (+)NCBICelera
Cytogenetic Map7q34NCBI
HuRef7137,350,584 - 137,386,478 (+)NCBIHuRef
CHM1_17142,950,106 - 142,986,018 (+)NCBICHM1_1
T2T-CHM13v2.07144,671,527 - 144,707,513 (+)NCBIT2T-CHM13v2.0
CRA_TCAGchr7v27142,415,337 - 142,451,223 (+)NCBI
Clcn1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39642,263,552 - 42,292,693 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl642,263,619 - 42,292,690 (+)EnsemblGRCm39 Ensembl
GRCm38642,284,851 - 42,315,764 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl642,286,685 - 42,315,756 (+)EnsemblGRCm38mm10GRCm38
MGSCv37642,236,684 - 42,264,655 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv36642,216,292 - 42,244,263 (+)NCBIMGSCv36mm8
Celera642,231,004 - 42,259,063 (+)NCBICelera
Cytogenetic Map6B2.1NCBI
cM Map620.57NCBI
Clcn1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_004955494319,738 - 348,511 (-)EnsemblChiLan1.0
ChiLan1.0NW_004955494318,137 - 349,568 (-)NCBIChiLan1.0ChiLan1.0
CLCN1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v26180,166,368 - 180,207,234 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan1732,176,625 - 32,217,491 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v07135,308,966 - 135,346,734 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.17147,801,440 - 147,837,654 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl7147,801,440 - 147,836,701 (+)Ensemblpanpan1.1panPan2
CLCN1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1166,342,772 - 6,373,580 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl166,342,772 - 6,373,580 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha167,331,919 - 7,362,475 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0166,196,701 - 6,227,304 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl166,196,701 - 6,227,304 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1166,144,363 - 6,174,910 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0165,996,056 - 6,026,611 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0166,071,349 - 6,101,933 (-)NCBIUU_Cfam_GSD_1.0
Clcn1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440511812,112,783 - 12,144,385 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_004936527759,047 - 790,670 (+)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_004936527759,012 - 791,302 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
CLCN1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl186,902,542 - 6,940,449 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1186,902,540 - 6,941,530 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2187,143,450 - 7,181,431 (-)NCBISscrofa10.2Sscrofa10.2susScr3
CLCN1
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.121112,196,136 - 112,237,836 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl21112,197,518 - 112,236,115 (+)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_0236660728,923,045 - 8,982,440 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Clcn1
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_00462480011,418,225 - 11,446,666 (-)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_00462480011,417,040 - 11,446,732 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Clcn1
123 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:55
Count of miRNA genes:49
Interacting mature miRNAs:54
Transcripts:ENSRNOT00000051265
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 (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
619616Bp79Blood pressure QTL 790.0292arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)4521460278882945Rat
2303168Bp330Blood pressure QTL 3304.250.017arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)45214602146446691Rat
631261Tcas3Tongue tumor susceptibility QTL 36.88tongue integrity trait (VT:0010553)number of squamous cell tumors of the tongue with diameter greater than 3 mm (CMO:0001950)41081417091360527Rat
2316958Gluco58Glucose level QTL 5810blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)411320076180699135Rat
6909122Insul22Insulin level QTL 224.63blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)42690728575585128Rat
6909128Pancm4Pancreatic morphology QTL 411.35pancreas mass (VT:0010144)pancreas wet weight (CMO:0000626)42690728575585128Rat
8655906Rf60Renal function QTL 603.8blood creatinine amount (VT:0005328)creatinine clearance (CMO:0000765)42949419581006281Rat
12798520Anxrr55Anxiety related response QTL 554.450.01locomotor behavior trait (VT:0001392)number of rearing movements with lid-pushing in an experimental apparatus (CMO:0002715)432583980114627242Rat
8552782Vie1Viral induced encephalitis QTL 126.4brain integrity trait (VT:0010579)encephalitis incidence/prevalence measurement (CMO:0002361)43443048482490359Rat
8552801Bw143Body weight QTL 1437.3body mass (VT:0001259)change in body weight to body weight ratio (CMO:0002216)43443048482490359Rat
8552809Vie5Viral induced encephalitis QTL 525.3brain integrity trait (VT:0010579)encephalitis incidence/prevalence measurement (CMO:0002361)43443048482490359Rat
8655961Kidm43Kidney mass QTL 4318kidney mass (VT:0002707)both kidneys wet weight (CMO:0000085)436303261103194984Rat
1358352Srcrt3Stress Responsive Cort QTL 32.29blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)438465774146803430Rat
61475Aia2Adjuvant induced arthritis QTL 25.8joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)43950527573892441Rat
1331807Rf31Renal function QTL 312.988urine potassium amount (VT:0010539)urine potassium level (CMO:0000128)43952426474726312Rat
1300139Hrtrt6Heart rate QTL 62.85heart pumping trait (VT:2000009)heart rate (CMO:0000002)439524264116179656Rat
61445Strs3Sensitivity to stroke QTL 33cerebrum integrity trait (VT:0010549)post-insult time to onset of cerebrovascular lesion (CMO:0002343)44043338885433388Rat
8694439Bw168Body weight QTL 1689.570.001retroperitoneal fat pad mass (VT:0010430)retroperitoneal fat pad weight to body weight ratio (CMO:0000635)44043341485433414Rat
6893678Bw108Body weight QTL 1082.60.006body mass (VT:0001259)body weight (CMO:0000012)44345797688457976Rat
1576305Emca6Estrogen-induced mammary cancer QTL 65.8mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)444463720155883716Rat
1354612Foco1Food consumption QTL 18.87eating behavior trait (VT:0001431)food intake rate (CMO:0000427)444463908148090542Rat
1354660Salc1Saline consumption QTL 111.26drinking behavior trait (VT:0001422)saline drink intake rate (CMO:0001627)444463908148090542Rat
2312567Glom19Glomerulus QTL 191.90.006kidney glomerulus morphology trait (VT:0005325)index of glomerular damage (CMO:0001135)445456990146803430Rat
1298082Stresp4Stress response QTL 4blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)450119848146803430Rat
4889969Bss96Bone structure and strength QTL 964.9tibia size trait (VT:0100001)tibia cortical bone volume (CMO:0001725)45664777678882945Rat
4889972Bss97Bone structure and strength QTL 975.6tibia size trait (VT:0100001)tibia total bone volume (CMO:0001724)45664777678882945Rat
5685009Bmd86Bone mineral density QTL 863.7tibia mineral mass (VT:1000283)bone mineral density (CMO:0001226)45664777678882945Rat
5685012Bmd87Bone mineral density QTL 875.1tibia mineral mass (VT:1000283)bone mineral content (CMO:0001554)45664777678882945Rat
70200Alc18Alcohol consumption QTL 189.2drinking behavior trait (VT:0001422)ethanol intake volume to total fluid intake volume ratio (CMO:0001591)456647873149491524Rat
1641833Alc21Alcohol consumption QTL 218.60.0001drinking behavior trait (VT:0001422)ethanol drink intake rate (CMO:0001407)456698790126192555Rat
634311Sach7Saccharin preference QTL 7taste sensitivity trait (VT:0001986)saccharin intake volume to total fluid intake volume ratio (CMO:0001601)45711443281266970Rat
631546Bp86Blood pressure QTL 863.2arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)45711443291360801Rat
61336Bp21Blood pressure QTL 214.6arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)45711470578881294Rat
1358363Sradr3Stress Responsive Adrenal Weight QTL 36.19adrenal gland mass (VT:0010420)both adrenal glands wet weight (CMO:0000164)457486946102486946Rat
1558651Swd3Spike wave discharge measurement QTL 34.620.000024brain electrophysiology trait (VT:0010557)brain spike-and-wave discharge frequency (CMO:0001742)45843213392991462Rat
631671Iddm11Insulin dependent diabetes mellitus QTL 113.60.0012blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)45863587778886137Rat
738009Sach4Saccharine consumption QTL 44.90.000016consumption behavior trait (VT:0002069)saccharin intake volume to total fluid intake volume ratio (CMO:0001601)459948935154902892Rat
738016Alc16Alcohol consumption QTL 163.60.00015consumption behavior trait (VT:0002069)ethanol drink intake rate to body weight ratio (CMO:0001616)459948935154902892Rat
738031Alc14Alcohol consumption QTL 147.60.00003consumption behavior trait (VT:0002069)ethanol drink intake rate to body weight ratio (CMO:0001616)459948935154902892Rat
1578657Bss12Bone structure and strength QTL 128.9femur morphology trait (VT:0000559)femoral neck cross-sectional area (CMO:0001697)460220938105220938Rat
1578658Bss13Bone structure and strength QTL 138femur strength trait (VT:0010010)femoral neck polar moment of inertia (CMO:0001670)460220938105220938Rat
2300179Bmd50Bone mineral density QTL 505.90.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)460928534105928534Rat
1549843Bw53Body weight QTL 530.0001body mass (VT:0001259)body weight gain (CMO:0000420)461697658103194791Rat
1549839Bw52Body weight QTL 520.0001body mass (VT:0001259)body weight gain (CMO:0000420)461697658115089733Rat
61418Pia5Pristane induced arthritis QTL 54.5joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)462277855128289560Rat
6478743Anxrr40Anxiety related response QTL 400.83076defecation behavior trait (VT:0010462)defecation rate (CMO:0000998)462753847107753847Rat
6478772Anxrr49Anxiety related response QTL 490.15488defecation behavior trait (VT:0010462)defecation rate (CMO:0000998)462753847107753847Rat
6478684Anxrr30Anxiety related response QTL 300.00087defecation behavior trait (VT:0010462)defecation rate (CMO:0000998)462753847107753847Rat
631651Bp124Blood pressure QTL 1243arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)462879517107879517Rat
7394826Bw126Body weight QTL 1260.002body mass (VT:0001259)body weight gain (CMO:0000420)46293326987483707Rat
8552807Vie4Viral induced encephalitis QTL 47.3brain integrity trait (VT:0010579)encephalitis incidence/prevalence measurement (CMO:0002361)46293350882490359Rat
70192BpQTLcluster5Blood pressure QTL cluster 54.183arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)462933508114921294Rat
70192BpQTLcluster5Blood pressure QTL cluster 54.183arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)462933508114921294Rat
70192BpQTLcluster5Blood pressure QTL cluster 54.183arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)462933508114921294Rat
70192BpQTLcluster5Blood pressure QTL cluster 54.183arterial blood pressure trait (VT:2000000)percent change in mean arterial blood pressure (CMO:0002035)462933508114921294Rat
70192BpQTLcluster5Blood pressure QTL cluster 54.183arterial blood pressure trait (VT:2000000)percent change in systolic blood pressure (CMO:0000747)462933508114921294Rat
70192BpQTLcluster5Blood pressure QTL cluster 54.183arterial blood pressure trait (VT:2000000)absolute change in pulse pressure (CMO:0001882)462933508114921294Rat
70192BpQTLcluster5Blood pressure QTL cluster 54.183arterial blood pressure trait (VT:2000000)absolute change in mean arterial blood pressure (CMO:0000533)462933508114921294Rat
631674Iddm14Insulin dependent diabetes mellitus QTL 14blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)464528739157573521Rat
2312569Pur19Proteinuria QTL 193.40.001urine total protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)46588210796130297Rat
2317577Eae24Experimental allergic encephalomyelitis QTL 24nervous system integrity trait (VT:0010566)post-insult time to onset of experimental autoimmune encephalomyelitis (CMO:0001422)46699318572752834Rat
2317577Eae24Experimental allergic encephalomyelitis QTL 24nervous system integrity trait (VT:0010566)percentage of study population developing experimental autoimmune encephalomyelitis during a period of time (CMO:0001047)46699318572752834Rat
2317577Eae24Experimental allergic encephalomyelitis QTL 24nervous system integrity trait (VT:0010566)experimental autoimmune encephalomyelitis severity score (CMO:0001419)46699318572752834Rat
61330Eau1Experimental allergic uveoretinitis QTL 10.0003uvea integrity trait (VT:0010551)experimental autoimmune uveitis score (CMO:0001504)470362013132642728Rat
634344Hcar7Hepatocarcinoma resistance QTL 77.8liver integrity trait (VT:0010547)liver tumorous lesion area to total liver area ratio (CMO:0001075)470808386115808386Rat
634344Hcar7Hepatocarcinoma resistance QTL 77.8liver integrity trait (VT:0010547)liver tumorous lesion number (CMO:0001068)470808386115808386Rat

Markers in Region
RH94644  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2471,199,855 - 71,199,964 (+)MAPPERmRatBN7.2
Rnor_6.0471,702,691 - 71,702,799NCBIRnor6.0
Rnor_5.04136,507,088 - 136,507,196UniSTSRnor5.0
RGSC_v3.4470,081,321 - 70,081,429UniSTSRGSC3.4
Celera466,130,349 - 66,130,457UniSTS
RH 3.4 Map4433.61UniSTS
Cytogenetic Map4q23UniSTS


Related Rat Strains
The following Strains have been annotated to Clcn1


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 8 11 2 8
Low 2 43 10 2 13 2 74 10 36 9
Below cutoff 1 32 24 6 24 21 3 2

Sequence


RefSeq Acc Id: ENSRNOT00000051265   ⟹   ENSRNOP00000043372
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl471,172,547 - 71,199,984 (+)Ensembl
Rnor_6.0 Ensembl471,675,383 - 71,702,819 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000104906   ⟹   ENSRNOP00000087495
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl471,172,547 - 71,199,984 (+)Ensembl
RefSeq Acc Id: NM_013147   ⟹   NP_037279
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8472,139,178 - 72,166,614 (+)NCBI
mRatBN7.2471,172,547 - 71,199,984 (+)NCBI
Rnor_6.0471,675,383 - 71,702,819 (+)NCBI
Rnor_5.04136,479,719 - 136,509,472 (+)NCBI
RGSC_v3.4470,052,319 - 70,081,449 (+)RGD
Celera466,103,038 - 66,130,477 (+)RGD
Sequence:
RefSeq Acc Id: XM_008762873   ⟹   XP_008761095
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8472,138,739 - 72,168,113 (+)NCBI
mRatBN7.2471,171,972 - 71,201,483 (+)NCBI
Rnor_6.0471,674,218 - 71,704,318 (+)NCBI
Sequence:
RefSeq Acc Id: XM_039107135   ⟹   XP_038963063
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8472,138,741 - 72,168,113 (+)NCBI
mRatBN7.2471,171,975 - 71,201,483 (+)NCBI
RefSeq Acc Id: NP_037279   ⟸   NM_013147
- UniProtKB: P35524 (UniProtKB/Swiss-Prot),   F1LPY4 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_008761095   ⟸   XM_008762873
- Peptide Label: isoform X2
- UniProtKB: F1LPY4 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000043372   ⟸   ENSRNOT00000051265
RefSeq Acc Id: XP_038963063   ⟸   XM_039107135
- Peptide Label: isoform X1
- UniProtKB: F1LPY4 (UniProtKB/TrEMBL)
RefSeq Acc Id: ENSRNOP00000087495   ⟸   ENSRNOT00000104906
Protein Domains
CBS

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-P35524-F1-model_v2 AlphaFold P35524 1-994 view protein structure

Transcriptome

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

Promoters
RGD ID:13693009
Promoter ID:EPDNEW_R3532
Type:single initiation site
Name:Clcn1_1
Description:chloride voltage-gated channel 1
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_6.0471,675,365 - 71,675,425EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:2360 AgrOrtholog
BioCyc Gene G2FUF-45091 BioCyc
Ensembl Genes ENSRNOG00000016917 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOG00055028197 UniProtKB/Swiss-Prot
  ENSRNOG00060008655 UniProtKB/Swiss-Prot
  ENSRNOG00065016057 UniProtKB/Swiss-Prot
Ensembl Transcript ENSRNOT00000051265 ENTREZGENE
  ENSRNOT00000051265.4 UniProtKB/TrEMBL
  ENSRNOT00000104906.1 UniProtKB/TrEMBL
  ENSRNOT00055048785 UniProtKB/Swiss-Prot
  ENSRNOT00060014449 UniProtKB/Swiss-Prot
  ENSRNOT00065026687 UniProtKB/Swiss-Prot
Gene3D-CATH 3.10.580.10 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Clc chloride channel UniProtKB/Swiss-Prot, 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-1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:25688 UniProtKB/Swiss-Prot
NCBI Gene 25688 ENTREZGENE
PANTHER CHLORIDE CHANNEL PROTEIN 1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  CHLORIDE CHANNEL PROTEIN 2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam Voltage_CLC UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Clcn1 PhenoGen
PRINTS CLCHANNEL UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  CLCHANNEL1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PROSITE CBS UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
RatGTEx ENSRNOG00000016917 RatGTEx
  ENSRNOG00055028197 RatGTEx
  ENSRNOG00060008655 RatGTEx
  ENSRNOG00065016057 RatGTEx
Superfamily-SCOP SSF54631 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SSF81340 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt A0A8I6A8S1_RAT UniProtKB/TrEMBL
  A6IF68_RAT UniProtKB/TrEMBL
  A6IF69_RAT UniProtKB/TrEMBL
  A6IF70_RAT UniProtKB/TrEMBL
  CLCN1_RAT UniProtKB/Swiss-Prot
  F1LPY4 ENTREZGENE, UniProtKB/TrEMBL
  P35524 ENTREZGENE


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2016-02-11 Clcn1  chloride voltage-gated channel 1  Clcn1  chloride channel, voltage-sensitive 1  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2012-07-16 Clcn1  chloride channel, voltage-sensitive 1  Clcn1  chloride channel 1, skeletal muscle  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2012-01-09 Clcn1  chloride channel 1, skeletal muscle  Clcn1  chloride channel 1  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2002-11-06 Clcn1  chloride channel 1    Chloride channel 1 (skeletal muscle)  Name updated 625702 APPROVED
2002-06-10 Clcn1  Chloride channel 1 (skeletal muscle)      Symbol and Name status set to approved 70586 APPROVED

RGD Curation Notes
Note Type Note Reference
gene_disease mutation of the human homolog causes both autosomal dominant (Thomsen's disease) and autosomal recessive (Becker's disease) forms of myotonia congenita 704389