Clic6 (chloride intracellular channel 6) - Rat Genome Database

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Gene: Clic6 (chloride intracellular channel 6) Rattus norvegicus
Analyze
Symbol: Clic6
Name: chloride intracellular channel 6
RGD ID: 727938
Description: Enables dopamine receptor binding activity and identical protein binding activity. Predicted to be involved in chloride transmembrane transport and regulation of monoatomic ion transmembrane transport. Located in plasma membrane. Orthologous to human CLIC6 (chloride intracellular channel 6); INTERACTS WITH 17alpha-ethynylestradiol; 2,3,7,8-tetrachlorodibenzodioxine; ammonium chloride.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: chloride intracellular channel protein 6; Clic6b; intracellular chloride channel 6b
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
mRatBN7.21131,737,813 - 31,780,360 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1131,737,813 - 31,780,061 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1140,432,325 - 40,474,994 (+)NCBIRnor_SHR
UTH_Rnor_SHRSP_BbbUtx_1.01133,103,806 - 33,146,473 (+)NCBIRnor_SHRSP
UTH_Rnor_WKY_Bbb_1.01132,262,687 - 32,305,152 (+)NCBIRnor_WKY
Rnor_6.01132,655,653 - 32,698,004 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1132,655,616 - 32,699,382 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01136,259,974 - 36,302,131 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41132,516,492 - 32,559,195 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.11132,572,734 - 32,615,438 (+)NCBI
Celera1131,389,140 - 31,431,254 (+)NCBICelera
Cytogenetic Map11q11NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


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. CLIC6, a member of the intracellular chloride channel family, interacts with dopamine D(2)-like receptors. Griffon N, etal., Brain Res Mol Brain Res 2003 Sep 10;117(1):47-57.
3. Rat ISS GO annotations from MGI mouse gene data--August 2006 MGD data from the GO Consortium
4. NCBI rat LocusLink and RefSeq merged data October 15, 2003 NCBI rat LocusLink and RefSeq merged data October 15, 2003
5. GOA pipeline RGD automated data pipeline
6. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
7. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:19056867  


Genomics

Comparative Map Data
Clic6
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21131,737,813 - 31,780,360 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1131,737,813 - 31,780,061 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1140,432,325 - 40,474,994 (+)NCBIRnor_SHR
UTH_Rnor_SHRSP_BbbUtx_1.01133,103,806 - 33,146,473 (+)NCBIRnor_SHRSP
UTH_Rnor_WKY_Bbb_1.01132,262,687 - 32,305,152 (+)NCBIRnor_WKY
Rnor_6.01132,655,653 - 32,698,004 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1132,655,616 - 32,699,382 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01136,259,974 - 36,302,131 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41132,516,492 - 32,559,195 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.11132,572,734 - 32,615,438 (+)NCBI
Celera1131,389,140 - 31,431,254 (+)NCBICelera
Cytogenetic Map11q11NCBI
CLIC6
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh382134,668,994 - 34,718,223 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p13 Ensembl2134,668,994 - 34,718,227 (+)EnsemblGRCh38hg38GRCh38
GRCh372136,041,293 - 36,090,521 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 362134,963,558 - 35,012,389 (+)NCBINCBI36Build 36hg18NCBI36
Build 342134,963,557 - 35,012,389NCBI
Celera2121,241,258 - 21,290,092 (+)NCBICelera
Cytogenetic Map21q22.12NCBI
HuRef2121,520,561 - 21,569,502 (+)NCBIHuRef
CHM1_12135,603,984 - 35,652,808 (+)NCBICHM1_1
T2T-CHM13v2.02133,051,578 - 33,100,790 (+)NCBIT2T-CHM13v2.0
Clic6
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391692,295,035 - 92,338,129 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1692,282,624 - 92,338,131 (+)EnsemblGRCm39 Ensembl
GRCm381692,498,147 - 92,541,241 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1692,485,736 - 92,541,243 (+)EnsemblGRCm38mm10GRCm38
MGSCv371692,498,392 - 92,541,486 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv361692,387,006 - 92,430,100 (+)NCBIMGSCv36mm8
Celera1693,581,042 - 93,624,278 (+)NCBICelera
Cytogenetic Map16C4NCBI
Clic6
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0NW_00495540734,002,656 - 34,042,524 (+)NCBIChiLan1.0ChiLan1.0
CLIC6
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.12134,409,056 - 34,457,307 (+)NCBIpanpan1.1PanPan1.1panPan2
Mhudiblu_PPA_v02121,041,763 - 21,089,958 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
CLIC6
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.13130,003,448 - 30,102,939 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl3130,091,335 - 30,100,842 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha3129,156,624 - 29,202,157 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.03129,303,623 - 29,403,853 (+)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl3129,358,233 - 29,403,507 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.13129,224,227 - 29,269,813 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.03129,238,956 - 29,284,553 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.03129,675,108 - 29,775,259 (+)NCBIUU_Cfam_GSD_1.0
Clic6
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440497129,651,093 - 29,693,204 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049365007,774,597 - 7,816,702 (-)EnsemblSpeTri2.0
SpeTri2.0NW_0049365007,774,962 - 7,816,658 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
CLIC6
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl13198,251,119 - 198,303,857 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.113198,250,702 - 198,303,830 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.213208,079,952 - 208,131,097 (+)NCBISscrofa10.2Sscrofa10.2susScr3
CLIC6
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1278,703,815 - 78,752,183 (+)NCBIChlSab1.1ChlSab1.1chlSab2
Vero_WHO_p1.0NW_0236660546,522,713 - 6,569,852 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Clic6
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_00462474522,816,292 - 22,861,613 (+)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_00462474522,807,618 - 22,861,521 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Clic6
324 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:29
Count of miRNA genes:28
Interacting mature miRNAs:29
Transcripts:ENSRNOT00000034383
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
1598842Glom10Glomerulus QTL 103.4kidney glomerulus morphology trait (VT:0005325)index of glomerular damage (CMO:0001135)11135331169Rat
1300147Bp187Blood pressure QTL 1873.67arterial blood pressure trait (VT:2000000)blood pressure time series experimental set point of the baroreceptor response (CMO:0002593)11169446234Rat
1558659Tescar1Testicular tumor resistance QTL 13.9testis integrity trait (VT:0010572)percentage of study population developing testis tumors during a period of time (CMO:0001261)11104193166113562Rat
1641927Alcrsp10Alcohol response QTL 10alcohol metabolism trait (VT:0015089)blood ethanol level (CMO:0000535)11843667453436674Rat
724517Uae18Urinary albumin excretion QTL 183.7urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)111647204744285911Rat
724554Iddm17Insulin dependent diabetes mellitus QTL 170.001blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)111897620886241447Rat
10058952Gmadr6Adrenal mass QTL 62.290.0072adrenal gland mass (VT:0010420)both adrenal glands wet weight to body weight ratio (CMO:0002411)112295940367959403Rat
8694376Bw156Body weight QTL 1562.250.001body lean mass (VT:0010483)lean tissue morphological measurement (CMO:0002184)112328045668280456Rat
9590313Scort20Serum corticosterone level QTL 206.510.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)112328045668280456Rat
9589032Epfw10Epididymal fat weight QTL 109.290.001epididymal fat pad mass (VT:0010421)epididymal fat pad weight to body weight ratio (CMO:0000658)112328045668280456Rat
8694424Bw162Body weight QTL 1623.80.001body lean mass (VT:0010483)lean tissue morphological measurement (CMO:0002184)112328045668280456Rat
724563Uae10Urinary albumin excretion QTL 106urine albumin amount (VT:0002871)urine albumin level (CMO:0000130)112767241082846715Rat
1300130Rf20Renal function QTL 204.44kidney glomerulus integrity trait (VT:0010546)kidney glomerulus diameter (CMO:0001166)112952841860324829Rat
1300110Stl7Serum triglyceride level QTL 74.64blood triglyceride amount (VT:0002644)plasma triglyceride level (CMO:0000548)112952841882566702Rat
2298551Neuinf10Neuroinflammation QTL 103.7nervous system integrity trait (VT:0010566)spinal cord beta-2 microglobulin mRNA level (CMO:0002125)113123913478851519Rat

Markers in Region
5730466J16Rik  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21131,771,139 - 31,772,058 (+)MAPPERmRatBN7.2
Rnor_6.01132,689,090 - 32,690,008NCBIRnor6.0
Rnor_5.01136,293,217 - 36,294,135UniSTSRnor5.0
RGSC_v3.41132,550,281 - 32,551,199UniSTSRGSC3.4
Celera1131,422,344 - 31,423,262UniSTS
Cytogenetic Map11q11UniSTS
G45351  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21131,757,540 - 31,757,829 (+)MAPPERmRatBN7.2
Rnor_6.01132,675,379 - 32,675,667NCBIRnor6.0
Rnor_5.01136,279,506 - 36,279,794UniSTSRnor5.0
RGSC_v3.41132,536,680 - 32,536,968UniSTSRGSC3.4
Celera1131,408,743 - 31,409,031UniSTS
Cytogenetic Map11q11UniSTS


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 31 5
Low 1 4 6 4 2 4 39 16 35 11
Below cutoff 2 28 17 11 3 11 4 5 4 6 1 4

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000034383   ⟹   ENSRNOP00000033206
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1131,737,813 - 31,780,061 (+)Ensembl
Rnor_6.0 Ensembl1132,655,653 - 32,698,004 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000084412   ⟹   ENSRNOP00000068644
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1132,655,616 - 32,699,382 (+)Ensembl
RefSeq Acc Id: NM_176078   ⟹   NP_788267
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21131,737,813 - 31,780,360 (+)NCBI
Rnor_6.01132,655,653 - 32,698,004 (+)NCBI
Rnor_5.01136,259,974 - 36,302,131 (+)NCBI
RGSC_v3.41132,516,492 - 32,559,195 (+)RGD
Celera1131,389,140 - 31,431,254 (+)RGD
Sequence:
Protein Sequences
Protein RefSeqs NP_788267 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAO38057 (Get FASTA)   NCBI Sequence Viewer  
  EDM10768 (Get FASTA)   NCBI Sequence Viewer  
  EDM10769 (Get FASTA)   NCBI Sequence Viewer  
  Q811Q2 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: NP_788267   ⟸   NM_176078
- UniProtKB: A0A0G2JTB6 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000068644   ⟸   ENSRNOT00000084412
RefSeq Acc Id: ENSRNOP00000033206   ⟸   ENSRNOT00000034383
Protein Domains
GST C-terminal

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-Q811Q2-F1-model_v2 AlphaFold Q811Q2 1-612 view protein structure

Transcriptome

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

Promoters
RGD ID:13698068
Promoter ID:EPDNEW_R8593
Type:multiple initiation site
Name:Clic6_1
Description:chloride intracellular channel 6
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_6.01132,655,621 - 32,655,681EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:727938 AgrOrtholog
BioCyc Gene G2FUF-21833 BioCyc
Ensembl Genes ENSRNOG00000026870 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000033206 ENTREZGENE
  ENSRNOP00000033206.5 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000034383 ENTREZGENE
  ENSRNOT00000034383.5 UniProtKB/TrEMBL
InterPro CLIC UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  CLIC-4/6 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Glutathione-S-Trfase_C-like UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Glutathione-S-Trfase_C_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Glutathione_S-Trfase UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Thioredoxin-like_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:304081 UniProtKB/Swiss-Prot
NCBI Gene 304081 ENTREZGENE
PANTHER PTHR45476:SF1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Clic6 PhenoGen
PRINTS INTCLCHANNEL UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PROSITE GST_CTER UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP SSF47616 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SSF52833 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
TIGRFAMs O-ClC UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt A0A0G2JTB6 ENTREZGENE
  CLIC6_RAT UniProtKB/Swiss-Prot
  F1M9X4_RAT UniProtKB/TrEMBL
  Q811Q2 ENTREZGENE
UniProt Secondary A0A0G2JTB6 UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2006-10-03 Clic6    CLIC6  chloride intracellular channel 6  Symbol updated 1299863 APPROVED
2004-09-10 CLIC6  chloride intracellular channel 6  Clic6b  intracellular chloride channel 6b  Symbol and Name updated 1299863 APPROVED

RGD Curation Notes
Note Type Note Reference
gene_domains member of the intracellular chloride channel family 1302428
gene_expression expressed in choroid plexus, striatal proliferative subventricular zone, cerebellum and posterior lobe of pituitary in the adult brain 1302428