Clcc1 (chloride channel CLIC-like 1) - Rat Genome Database

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Gene: Clcc1 (chloride channel CLIC-like 1) Rattus norvegicus
Analyze
Symbol: Clcc1
Name: chloride channel CLIC-like 1
RGD ID: 708359
Description: Exhibits chloride channel activity. Involved in chloride transport. Localizes to cytoplasm and nucleus. Colocalizes with Golgi apparatus and endoplasmic reticulum. Human ortholog(s) of this gene implicated in retinitis pigmentosa 32. Orthologous to human CLCC1 (chloride channel CLIC like 1); INTERACTS WITH 2,6-dinitrotoluene; 3,4-methylenedioxymethamphetamine; 6-propyl-2-thiouracil.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: chloride channel CLIC-like protein 1; LOC170927; Mclc; Mid-1-related chloride channel 1; mid-1-related chloride channel protein 1
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: Rnor_6.0 - RGSC Genome Assembly v6.0
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.22196,296,350 - 196,326,914 (+)NCBI
Rnor_6.0 Ensembl2211,450,484 - 211,479,884 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.02211,450,426 - 211,479,885 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.02230,923,372 - 230,952,836 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.42204,245,357 - 204,278,530 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.12204,208,110 - 204,241,283 (+)NCBI
Celera2188,943,040 - 188,970,221 (+)NCBICelera
Cytogenetic Map2q34NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Molecular Function

References

Additional References at PubMed
PMID:12477932   PMID:19946888   PMID:31653868  


Genomics

Comparative Map Data
Clcc1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.22196,296,350 - 196,326,914 (+)NCBI
Rnor_6.0 Ensembl2211,450,484 - 211,479,884 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.02211,450,426 - 211,479,885 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.02230,923,372 - 230,952,836 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.42204,245,357 - 204,278,530 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.12204,208,110 - 204,241,283 (+)NCBI
Celera2188,943,040 - 188,970,221 (+)NCBICelera
Cytogenetic Map2q34NCBI
CLCC1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl1108,929,508 - 108,963,457 (-)EnsemblGRCh38hg38GRCh38
GRCh38.p13 Ensembl1108,927,361 - 108,963,504 (-)EnsemblGRCh38hg38GRCh38
GRCh381108,929,505 - 108,963,484 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh371109,472,127 - 109,506,106 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361109,273,653 - 109,307,634 (-)NCBINCBI36hg18NCBI36
Celera1107,741,688 - 107,775,523 (-)NCBI
Cytogenetic Map1p13.3NCBI
HuRef1107,364,991 - 107,398,998 (-)NCBIHuRef
CHM1_11109,587,075 - 109,621,067 (-)NCBICHM1_1
Clcc1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm393108,561,194 - 108,586,156 (+)NCBIGRCm39mm39
GRCm39 Ensembl3108,561,229 - 108,586,156 (+)Ensembl
GRCm383108,653,878 - 108,678,840 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl3108,653,913 - 108,678,840 (+)EnsemblGRCm38mm10GRCm38
MGSCv373108,456,831 - 108,481,758 (+)NCBIGRCm37mm9NCBIm37
MGSCv363108,782,303 - 108,806,068 (+)NCBImm8
Celera3110,988,607 - 111,013,587 (+)NCBICelera
Cytogenetic Map3F3NCBI
Clcc1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0NW_00495543512,387,575 - 12,408,801 (-)NCBIChiLan1.0ChiLan1.0
CLCC1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.11110,474,158 - 110,505,626 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1110,473,752 - 110,505,613 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v01111,309,680 - 111,340,851 (-)NCBIMhudiblu_PPA_v0panPan3
CLCC1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1642,807,432 - 42,829,317 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl642,807,064 - 42,829,273 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha645,582,407 - 45,604,915 (+)NCBI
ROS_Cfam_1.0643,139,838 - 43,162,167 (+)NCBI
UMICH_Zoey_3.1642,870,406 - 42,892,709 (+)NCBI
UNSW_CanFamBas_1.0642,828,824 - 42,851,132 (+)NCBI
UU_Cfam_GSD_1.0643,270,389 - 43,292,703 (+)NCBI
Clcc1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440505819,574,603 - 19,596,108 (+)NCBI
SpeTri2.0NW_004936704518,040 - 539,526 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
CLCC1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl4111,080,655 - 111,101,329 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.14111,080,648 - 111,101,007 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.24121,572,770 - 121,592,914 (+)NCBISscrofa10.2Sscrofa10.2susScr3
CLCC1
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.12024,627,309 - 24,657,684 (+)NCBI
ChlSab1.1 Ensembl2024,610,854 - 24,655,653 (+)Ensembl
Clcc1
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046247724,705,198 - 4,744,052 (-)NCBI

Position Markers
RH131755  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.22196,326,624 - 196,326,804 (+)MAPPER
Rnor_6.02211,479,596 - 211,479,775NCBIRnor6.0
Rnor_5.02230,952,547 - 230,952,726UniSTSRnor5.0
RGSC_v3.42204,278,241 - 204,278,420UniSTSRGSC3.4
Celera2188,969,932 - 188,970,111UniSTS
RH 3.4 Map21398.5UniSTS
Cytogenetic Map2q34UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
70175BpQTLCluster3Blood pressure QTL cluster 34.128arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)2140566078217498545Rat
70175BpQTLCluster3Blood pressure QTL cluster 34.128arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)2140566078217498545Rat
70175BpQTLCluster3Blood pressure QTL cluster 34.128arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)2140566078217498545Rat
70175BpQTLCluster3Blood pressure QTL cluster 34.128arterial blood pressure trait (VT:2000000)pulse pressure (CMO:0000292)2140566078217498545Rat
70175BpQTLCluster3Blood pressure QTL cluster 34.128arterial blood pressure trait (VT:2000000)absolute change in systolic blood pressure (CMO:0000607)2140566078217498545Rat
71113Cari2Carrageenan-induced inflammation QTL 22.70.009hypodermis integrity trait (VT:0010550)inflammatory exudate volume (CMO:0001429)2147522550217498710Rat
631266Bp132Blood pressure QTL 1320.0005arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)246537589217498710Rat
61458Bp10Blood pressure QTL 103.42arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)2204003742231132207Rat
61467Bp14Blood pressure QTL 142.2arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)243133606217498545Rat
61467Bp14Blood pressure QTL 142.2arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)243133606217498545Rat
61469Bp16Blood pressure QTL 165.64arterial blood pressure trait (VT:2000000)blood pressure measurement (CMO:0000003)2184730446229730446Rat
70162Bp63Blood pressure QTL 635.64arterial blood pressure trait (VT:2000000)blood pressure measurement (CMO:0000003)2184730446229730446Rat
724568Uae13Urinary albumin excretion QTL 134.4urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)2149114878225501939Rat
1331734Bp204Blood pressure QTL 2043.61192arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)2181990297240020001Rat
1331745Bp203Blood pressure QTL 2034.377arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)2204585642235290110Rat
1331760Bp206Blood pressure QTL 2063.62454arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)256244671217498710Rat
1298074Bp164Blood pressure QTL 1640.003arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)242776916217498710Rat
1298076Bp166Blood pressure QTL 1660.0009arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)2141583337217498710Rat
1298080Bp163Blood pressure QTL 1630.02arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)266828049217498710Rat
1298083Bp158Blood pressure QTL 1582.62arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)2204003742231132207Rat
1298085Bp165Blood pressure QTL 1650.0006arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)242776916217498710Rat
1331794Bp202Blood pressure QTL 2023.66819arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)2147122993240020001Rat
1331805Cm29Cardiac mass QTL 293.50746heart mass (VT:0007028)heart wet weight (CMO:0000069)2147122993240020001Rat
2307174Activ3Activity QTL 34.830.000058locomotor behavior trait (VT:0001392)number of entries into a discrete space in an experimental apparatus (CMO:0000960)2183984665228984665Rat
1581499Esta2Estrogen-induced thymic atrophy QTL 2thymus mass (VT:0004954)thymus wet weight (CMO:0000855)2204585642243689611Rat
738013Alc15Alcohol consumption QTL 154.10.00022consumption behavior trait (VT:0002069)ethanol drink intake rate to body weight ratio (CMO:0001616)2199380312244380312Rat
631501Bp101Blood pressure QTL 1012.4arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)2157914409217498545Rat
631507Bp105Blood pressure QTL 1050.001arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)2116075644228737869Rat
1302793Bw16Body weight QTL 1650.0001body mass (VT:0001259)body weight (CMO:0000012)2169852800217498545Rat
1641891Alcrsp17Alcohol response QTL 17response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)2155965557254121739Rat
1641925Alcrsp2Alcohol response QTL 2response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)2155965557237742948Rat
1598838Bp290Blood pressure QTL 2901.9arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)2181522444226522444Rat
2301408Kidm36Kidney mass QTL 360.002kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)2205583921243562243Rat
2300189Bmd48Bone mineral density QTL 485.80.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)2194378622239378622Rat
634308Sach6Saccharin preference QTL 64.9taste sensitivity trait (VT:0001986)saccharin intake volume to total fluid intake volume ratio (CMO:0001601)2116075644228737869Rat
1358356Srcrt1Stress Responsive Cort QTL13.66blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)2175403337239166203Rat
1578648Bss11Bone structure and strength QTL 114.7femur morphology trait (VT:0000559)femoral neck cortical cross-sectional area (CMO:0001702)2118446646227707979Rat
1300165Rf9Renal function QTL 93.28kidney glomerulus integrity trait (VT:0010546)index of glomerular damage (CMO:0001135)2138901276217498710Rat
1354605Rf48Renal function QTL 482.9blood creatinine amount (VT:0005328)plasma creatinine level (CMO:0000537)275687495221880419Rat
1354609Niddm62Non-insulin dependent diabetes mellitus QTL 624.720.000006insulin secretion trait (VT:0003564)plasma insulin level (CMO:0000342)2158159186217498710Rat
1354622Kidm16Kidney mass QTL 163kidney mass (VT:0002707)left kidney wet weight (CMO:0000083)283819608239166203Rat
1354648Bp239Blood pressure QTL 2390.001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)266828236243550655Rat
1354649Kidm17Kidney mass QTL 172.9kidney mass (VT:0002707)calculated kidney weight (CMO:0000160)283819608243901375Rat
2301966Bp322Blood pressure QTL 3223.58arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)2158159186217498710Rat
1359022Ppulsi1Prepulse inhibition QTL 13.63prepulse inhibition trait (VT:0003088)acoustic startle response measurement (CMO:0001519)2142053350228984665Rat
1554319Bmd2Bone mineral density QTL 213.40.0001lumbar vertebra area (VT:0010570)lumbar vertebra cross-sectional area (CMO:0001689)2118446793228582621Rat
2306901Bp337Blood pressure QTL 3370.01arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)2177680772243901375Rat
1358913Cm41Cardiac mass QTL 412.73heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)223837491218957222Rat
1358917Cm42Cardiac mass QTL 422.82heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)223837491218957222Rat
1359031Bp275Blood pressure QTL 275arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)2200453324236318668Rat
1359031Bp275Blood pressure QTL 275arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)2200453324236318668Rat
2317752Glom23Glomerulus QTL 233.6urine protein amount (VT:0005160)urine protein level (CMO:0000591)2208594330263179188Rat
2293084Iddm26Insulin dependent diabetes mellitus QTL 262.9blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)2188838511228984665Rat
61366Iddm3Insulin dependent diabetes mellitus QTL 34.7blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)2204585642249585642Rat
61374Edpm2Estrogen-dependent pituitary mass QTL 24.420.86pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)278321410217498710Rat
61398Bp50Blood pressure QTL 504.4arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)2204585642249585642Rat
61417Cia10Collagen induced arthritis QTL 103.4joint integrity trait (VT:0010548)experimental arthritis severity measurement (CMO:0001459)2194998627239998627Rat
4889834Pur24Proteinuria QTL 245.80.014total urine protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)2198704357217498710Rat
8694435Bw166Body weight QTL 16614.080.001retroperitoneal fat pad mass (VT:0010430)retroperitoneal fat pad weight to body weight ratio (CMO:0000635)2197253963242253963Rat
9589044Scfw1Subcutaneous fat weight QTL 15.80.001subcutaneous adipose mass (VT:1000472)abdominal subcutaneous fat pad weight (CMO:0002069)2197253963242253963Rat
8694383Bw158Body weight QTL 1587.690.001body lean mass (VT:0010483)lean tissue morphological measurement (CMO:0002184)2197253963242253963Rat
7488925Bp364Blood pressure QTL 3640.001arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)2174160958219160958Rat
7488927Bp365Blood pressure QTL 3650.008arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)2177339806222339806Rat
8662843Vetf9Vascular elastic tissue fragility QTL 92.05thoracic aorta molecular composition trait (VT:0010568)aorta wall extracellular elastin dry weight to aorta wall extracellular collagen weight ratio (CMO:0002003)2169852670243026643Rat
8662832Vetf7Vascular elastic tissue fragility QTL 73.5aorta elastin amount (VT:0003905)aorta wall extracellular elastin dry weight to aorta wall dry weight ratio (CMO:0002002)283754907237610852Rat
8694194Abfw1Abdominal fat weight QTL 111.70.001visceral adipose mass (VT:0010063)abdominal fat pad weight to body weight ratio (CMO:0000095)2197253963242253963Rat
10755499Bp389Blood pressure QTL 3892.61arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)216679272245624402Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:1011
Count of miRNA genes:310
Interacting mature miRNAs:402
Transcripts:ENSRNOT00000027617, ENSRNOT00000051701, ENSRNOT00000055859
Prediction methods:Microtar, 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 53 37 19 37 1 3 74 35 39 11 1
Low 15 4 4 4 7 8 2 7
Below cutoff

Sequence

Nucleotide Sequences
RefSeq Transcripts NM_133414 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006233127 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006233128 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008761366 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017590597 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039101611 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039101612 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XR_005500232 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XR_005500233 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide AB052919 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AB052920 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AB052921 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AB052922 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AB052923 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AF117330 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BC081736 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CH473952 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ226377 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  JACYVU010000077 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Reference Sequences
RefSeq Acc Id: ENSRNOT00000027617   ⟹   ENSRNOP00000027617
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl2211,460,373 - 211,478,007 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000051701   ⟹   ENSRNOP00000042185
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl2211,450,484 - 211,479,884 (+)Ensembl
RefSeq Acc Id: NM_133414   ⟹   NP_596905
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.22196,296,406 - 196,326,914 (+)NCBI
Rnor_6.02211,450,484 - 211,479,885 (+)NCBI
Rnor_5.02230,923,372 - 230,952,836 (+)NCBI
RGSC_v3.42204,245,357 - 204,278,530 (+)RGD
Celera2188,943,040 - 188,970,221 (+)RGD
Sequence:
RefSeq Acc Id: XM_006233127   ⟹   XP_006233189
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.02211,450,426 - 211,479,885 (+)NCBI
Rnor_5.02230,923,372 - 230,952,836 (+)NCBI
Sequence:
RefSeq Acc Id: XM_006233128   ⟹   XP_006233190
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.22196,296,367 - 196,326,914 (+)NCBI
Rnor_6.02211,450,452 - 211,479,885 (+)NCBI
Rnor_5.02230,923,372 - 230,952,836 (+)NCBI
Sequence:
RefSeq Acc Id: XM_008761366   ⟹   XP_008759588
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.22196,296,350 - 196,326,914 (+)NCBI
Rnor_6.02211,450,426 - 211,479,885 (+)NCBI
Sequence:
RefSeq Acc Id: XM_017590597   ⟹   XP_017446086
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.22196,296,366 - 196,326,914 (+)NCBI
Rnor_6.02211,450,451 - 211,479,885 (+)NCBI
Sequence:
RefSeq Acc Id: XM_039101611   ⟹   XP_038957539
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.22196,296,367 - 196,326,914 (+)NCBI
RefSeq Acc Id: XM_039101612   ⟹   XP_038957540
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.22196,296,366 - 196,326,914 (+)NCBI
RefSeq Acc Id: XR_005500232
RefSeq Status:
Type: NON-CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.22196,296,366 - 196,326,914 (+)NCBI
RefSeq Acc Id: XR_005500233
RefSeq Status:
Type: NON-CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.22196,296,366 - 196,326,914 (+)NCBI
Reference Sequences
RefSeq Acc Id: NP_596905   ⟸   NM_133414
- Peptide Label: precursor
- Sequence:
RefSeq Acc Id: XP_006233189   ⟸   XM_006233127
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: XP_006233190   ⟸   XM_006233128
- Peptide Label: isoform X1
- UniProtKB: Q9WU61 (UniProtKB/Swiss-Prot),   A0A140TAF5 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_008759588   ⟸   XM_008761366
- Peptide Label: isoform X2
- Sequence:
RefSeq Acc Id: XP_017446086   ⟸   XM_017590597
- Peptide Label: isoform X3
- Sequence:
RefSeq Acc Id: ENSRNOP00000042185   ⟸   ENSRNOT00000051701
RefSeq Acc Id: ENSRNOP00000027617   ⟸   ENSRNOT00000027617
RefSeq Acc Id: XP_038957540   ⟸   XM_039101612
- Peptide Label: isoform X2
RefSeq Acc Id: XP_038957539   ⟸   XM_039101611
- Peptide Label: isoform X1

Transcriptome

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

Promoters
RGD ID:13691687
Promoter ID:EPDNEW_R2212
Type:initiation region
Name:Clcc1_1
Description:chloride channel CLIC-like 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_6.02211,450,475 - 211,450,535EPDNEW

Strain Variation

Strain Sequence Variants (Rnor 6.0)
ACI/EurMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
ACI/EurMcwi (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
ACI/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
BBDP/Wor (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
BN/SsN (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
Buf/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
COP/CrCrl (MCW & UW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
University of Wisconsin (Dr. James Shull)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Charles River Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob) and UW Madison (Dr. James Shull)
F344/NCrl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
F344/NRrrc (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
FHH/EurMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHH/EurMcwi (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
FHL/EurMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHL/EurMcwi (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
GH/OmrMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
GK/Ox (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LE/Stm (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/Crl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/NCrlBR (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LH/MavRrrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LL/MavRrrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LN/MavRrrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
M520/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
MHS/Gib (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MNS/Gib (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MR/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
SBH/Ygl (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBH/Ygl sequenced by MCW
SBH/Ygl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SBN/Ygl (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBN/Ygl sequenced by MCW
SBN/Ygl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHR/NHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHRSP/Gcrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SR/JrHsd (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Harlan Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SR/JrHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/Jr (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/JrHsdMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SS/JrHsdMcwi (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WAG/Rij (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/Gcrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
WKY/NCrl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/NHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WN/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
Damaging Variants


Assembly: Rnor_5.0

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
2 230950880 230950881 C T snv DOB/Oda (KyushuU)


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:708359 AgrOrtholog
Ensembl Genes ENSRNOG00000020360 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000027617 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOP00000042185 ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000027617 UniProtKB/TrEMBL
  ENSRNOT00000051701 ENTREZGENE, UniProtKB/TrEMBL
IMAGE_CLONE IMAGE:7128078 IMAGE-MGC_LOAD
InterPro Chloride_chnl_CLIC-like UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:170927 UniProtKB/Swiss-Prot
MGC_CLONE MGC:93226 IMAGE-MGC_LOAD
NCBI Gene 170927 ENTREZGENE
PANTHER PTHR34093 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam MCLC UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Clcc1 PhenoGen
UniProt A0A140TAF5 ENTREZGENE, UniProtKB/TrEMBL
  CLCC1_RAT UniProtKB/Swiss-Prot
  D3ZKI2_RAT UniProtKB/TrEMBL
  Q9WU61 ENTREZGENE
UniProt Secondary Q66HQ5 UniProtKB/Swiss-Prot
  Q8VIE8 UniProtKB/Swiss-Prot
  Q8VIE9 UniProtKB/Swiss-Prot
  Q8VIF0 UniProtKB/Swiss-Prot
  Q8VIF1 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2006-03-30 Clcc1  chloride channel CLIC-like 1  Mclc  Mid-1-related chloride channel 1  Symbol and Name updated 1299863 APPROVED
2005-07-08 Mclc  Mid-1-related chloride channel 1  LOC170927    Symbol updated 1299863 APPROVED