Clic3 (chloride intracellular channel 3) - Rat Genome Database

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Gene: Clic3 (chloride intracellular channel 3) Rattus norvegicus
Analyze
Symbol: Clic3
Name: chloride intracellular channel 3
RGD ID: 1307249
Description: Predicted to enable chloride channel activity and protein-disulfide reductase (glutathione) activity. Predicted to be involved in chloride transport and positive regulation of sprouting angiogenesis. Predicted to be located in extracellular matrix and nuclear body. Predicted to be part of chloride channel complex. Predicted to be active in cytoplasm and membrane. Orthologous to human CLIC3 (chloride intracellular channel 3); INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; 3,3',4,4',5-pentachlorobiphenyl; acrylamide.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: chloride intracellular channel protein 3; LOC296566; MGC109225
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8328,670,176 - 28,672,166 (+)NCBIGRCr8
mRatBN7.238,271,416 - 8,274,023 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl38,272,097 - 8,274,018 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx311,377,185 - 11,379,096 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0319,963,409 - 19,965,320 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0318,153,257 - 18,155,168 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.032,675,732 - 2,678,248 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl32,676,296 - 2,680,565 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.032,657,743 - 2,659,664 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.433,622,894 - 3,624,805 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.133,623,545 - 3,624,807 (+)NCBI
Celera33,097,212 - 3,099,123 (+)NCBICelera
Cytogenetic Map3p13NCBI
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. Rat ISS GO annotations from MGI mouse gene data--August 2006 MGD data from the GO Consortium
4. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
5. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. Strausberg RL, etal., Proc Natl Acad Sci U S A. 2002 Dec 24;99(26):16899-903. Epub 2002 Dec 11.
Additional References at PubMed
PMID:8889548   PMID:9880541   PMID:12947022   PMID:19056867   PMID:23376485  


Genomics

Comparative Map Data
Clic3
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8328,670,176 - 28,672,166 (+)NCBIGRCr8
mRatBN7.238,271,416 - 8,274,023 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl38,272,097 - 8,274,018 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx311,377,185 - 11,379,096 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0319,963,409 - 19,965,320 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0318,153,257 - 18,155,168 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.032,675,732 - 2,678,248 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl32,676,296 - 2,680,565 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.032,657,743 - 2,659,664 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.433,622,894 - 3,624,805 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.133,623,545 - 3,624,807 (+)NCBI
Celera33,097,212 - 3,099,123 (+)NCBICelera
Cytogenetic Map3p13NCBI
CLIC3
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh389136,994,608 - 136,996,568 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl9136,994,608 - 136,996,568 (-)EnsemblGRCh38hg38GRCh38
GRCh379139,889,060 - 139,891,020 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 369139,008,881 - 139,010,845 (-)NCBINCBI36Build 36hg18NCBI36
Build 349137,164,896 - 137,166,861NCBI
Celera9110,401,370 - 110,403,334 (-)NCBICelera
Cytogenetic Map9q34.3NCBI
HuRef9109,348,166 - 109,350,130 (-)NCBIHuRef
CHM1_19140,037,817 - 140,039,781 (-)NCBICHM1_1
T2T-CHM13v2.09149,229,019 - 149,230,979 (-)NCBIT2T-CHM13v2.0
Clic3
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39225,346,855 - 25,348,789 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl225,346,850 - 25,348,788 (+)EnsemblGRCm39 Ensembl
GRCm38225,456,843 - 25,458,777 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl225,456,838 - 25,458,776 (+)EnsemblGRCm38mm10GRCm38
MGSCv37225,312,363 - 25,314,292 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv36225,278,852 - 25,280,781 (+)NCBIMGSCv36mm8
Celera225,184,332 - 25,186,261 (+)NCBICelera
Cytogenetic Map2A3NCBI
cM Map217.27NCBI
Clic3
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049555135,020,144 - 5,021,936 (-)EnsemblChiLan1.0
ChiLan1.0NW_0049555135,020,105 - 5,022,000 (-)NCBIChiLan1.0ChiLan1.0
CLIC3
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v2112,401,954 - 2,404,212 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan192,404,606 - 2,406,683 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v09108,054,934 - 108,057,100 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.19137,023,465 - 137,025,522 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl9137,023,505 - 137,025,361 (-)Ensemblpanpan1.1panPan2
CLIC3
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1948,634,061 - 48,637,083 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl948,634,878 - 48,637,015 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha947,848,449 - 47,850,740 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0949,512,882 - 49,515,171 (+)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl949,512,968 - 49,515,955 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1948,289,095 - 48,291,384 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0948,587,812 - 48,590,101 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0948,635,170 - 48,637,460 (+)NCBIUU_Cfam_GSD_1.0
Clic3
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024404947202,424,519 - 202,427,338 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_004936669948,667 - 950,539 (+)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_004936669947,743 - 950,539 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
CLIC3
(Sus scrofa - pig)		 No map positions available.
CLIC3
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1121,198,192 - 1,200,296 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl121,198,387 - 1,200,246 (+)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_0236660584,101,042 - 4,103,201 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Clic3
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_004624760911,145 - 912,951 (+)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_004624760911,124 - 912,922 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Clic3
9 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:47
Count of miRNA genes:46
Interacting mature miRNAs:47
Transcripts:ENSRNOT00000020497
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
70202Alc19Alcohol consumption QTL 192.5drinking behavior trait (VT:0001422)ethanol intake volume to total fluid intake volume ratio (CMO:0001591)3127494778Rat
631679Cm10Cardiac mass QTL 107.340.0001heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)3131158234Rat
631831Alc8Alcohol consumption QTL 82.7consumption behavior trait (VT:0002069)calculated ethanol drink intake rate (CMO:0001615)3133230976Rat
61468Bp15Blood pressure QTL 154.4blood pressure trait (VT:0000183)diastolic blood pressure (CMO:0000005)3133278763Rat
61468Bp15Blood pressure QTL 154.4blood pressure trait (VT:0000183)systolic blood pressure (CMO:0000004)3133278763Rat
61468Bp15Blood pressure QTL 154.4blood pressure trait (VT:0000183)pulse pressure (CMO:0000292)3133278763Rat
631545Bp85Blood pressure QTL 853.1arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)3133278763Rat
4889966Bss95Bone structure and strength QTL 954.4tibia area (VT:1000281)tibia-fibula cross-sectional area (CMO:0001718)3136847613Rat
2312664Scl62Serum cholesterol level QTL 620.05blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)3138710544Rat
631568Bp92Blood pressure QTL 922.20.005arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)3139874793Rat
2290452Scl56Serum cholesterol level QTL 562.26blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)3191609953Rat
1358185Ept6Estrogen-induced pituitary tumorigenesis QTL 66.7pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)3653764510778823Rat
2292615Ept17Estrogen-induced pituitary tumorigenesis QTL 176.7pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)3653764510778823Rat
1298526Arunc3Aerobic running capacity QTL 32.2exercise endurance trait (VT:0002332)maximum distance run on treadmill (CMO:0001406)3822719433703538Rat
10401810Kidm53Kidney mass QTL 53kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)3822719447233430Rat

Markers in Region
RH139551  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.238,270,243 - 8,270,452 (+)MAPPERmRatBN7.2
Rnor_6.032,674,469 - 2,674,677NCBIRnor6.0
Rnor_5.032,655,882 - 2,656,090UniSTSRnor5.0
RGSC_v3.433,621,027 - 3,621,235UniSTSRGSC3.4
Celera33,095,345 - 3,095,553UniSTS
Cytogenetic Map3p13UniSTS
RH140389  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.238,270,239 - 8,270,359 (+)MAPPERmRatBN7.2
Rnor_6.032,674,465 - 2,674,584NCBIRnor6.0
Rnor_5.032,655,878 - 2,655,997UniSTSRnor5.0
RGSC_v3.433,621,023 - 3,621,142UniSTSRGSC3.4
Celera33,095,341 - 3,095,460UniSTS
Cytogenetic Map3p13UniSTS


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 16 5 11
Low 3 29 31 15 19 15 8 11 20 15 23 8
Below cutoff 14 26 26 26 31 4 12

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000020497   ⟹   ENSRNOP00000020497
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl38,272,111 - 8,274,018 (+)Ensembl
Rnor_6.0 Ensembl32,676,296 - 2,680,565 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000095258   ⟹   ENSRNOP00000081757
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl38,272,097 - 8,274,018 (+)Ensembl
RefSeq Acc Id: NM_001013080   ⟹   NP_001013098
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8328,670,255 - 28,672,166 (+)NCBI
mRatBN7.238,272,111 - 8,274,022 (+)NCBI
Rnor_6.032,676,336 - 2,678,247 (+)NCBI
Rnor_5.032,657,743 - 2,659,664 (+)NCBI
RGSC_v3.433,622,894 - 3,624,805 (+)RGD
Celera33,097,212 - 3,099,123 (+)RGD
Sequence:
RefSeq Acc Id: XM_006233590   ⟹   XP_006233652
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8328,670,176 - 28,672,166 (+)NCBI
mRatBN7.238,271,416 - 8,274,023 (+)NCBI
Rnor_6.032,675,732 - 2,678,248 (+)NCBI
Rnor_5.032,657,743 - 2,659,664 (+)NCBI
Sequence:
Protein Sequences
Protein RefSeqs NP_001013098 (Get FASTA)   NCBI Sequence Viewer  
  XP_006233652 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein EDL93586 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000020497
  ENSRNOP00000020497.5
  ENSRNOP00000081757.1
Reference Protein Sequences
RefSeq Acc Id: NP_001013098   ⟸   NM_001013080
- UniProtKB: D3ZY91 (UniProtKB/TrEMBL),   A6JT62 (UniProtKB/TrEMBL),   A0A8I5ZSV9 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006233652   ⟸   XM_006233590
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: ENSRNOP00000020497   ⟸   ENSRNOT00000020497
RefSeq Acc Id: ENSRNOP00000081757   ⟸   ENSRNOT00000095258
Protein Domains
GST N-terminal

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-D3ZY91-F1-model_v2 AlphaFold D3ZY91 1-237 view protein structure

Transcriptome

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

Promoters
RGD ID:13691879
Promoter ID:EPDNEW_R2403
Type:multiple initiation site
Name:Clic3_1
Description:chloride intracellular channel 3
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_6.032,676,310 - 2,676,370EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1307249 AgrOrtholog
BioCyc Gene G2FUF-50452 BioCyc
Ensembl Genes ENSRNOG00000015184 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000020497 ENTREZGENE
  ENSRNOT00000020497.8 UniProtKB/TrEMBL
  ENSRNOT00000095258.1 UniProtKB/TrEMBL
Gene3D-CATH 1.20.1050.10 UniProtKB/TrEMBL
  Glutaredoxin UniProtKB/TrEMBL
IMAGE_CLONE IMAGE:7308966 IMAGE-MGC_LOAD
InterPro Glutathione-S-Trfase_C_sf UniProtKB/TrEMBL
  Glutathione_S-Trfase UniProtKB/TrEMBL
  Glutathione_S-Trfase_N UniProtKB/TrEMBL
  Int_Cl_channel UniProtKB/TrEMBL
  Thioredoxin-like_sf UniProtKB/TrEMBL
KEGG Report rno:296566 UniProtKB/TrEMBL
MGC_CLONE MGC:109225 IMAGE-MGC_LOAD
NCBI Gene 296566 ENTREZGENE
PANTHER CHLORIDE INTRACELLULAR CHANNEL PROTEIN UniProtKB/TrEMBL
  CHLORIDE INTRACELLULAR CHANNEL PROTEIN 6-RELATED UniProtKB/TrEMBL
Pfam GST_C_2 UniProtKB/TrEMBL
  GST_N_2 UniProtKB/TrEMBL
PhenoGen Clic3 PhenoGen
PRINTS INTCLCHANNEL UniProtKB/TrEMBL
PROSITE GST_NTER UniProtKB/TrEMBL
RatGTEx ENSRNOG00000015184 RatGTEx
Superfamily-SCOP GST_C_like UniProtKB/TrEMBL
  Thiordxn-like_fd UniProtKB/TrEMBL
UniProt A0A8I5ZSV9 ENTREZGENE, UniProtKB/TrEMBL
  A6JT62 ENTREZGENE, UniProtKB/TrEMBL
  D3ZY91 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2005-12-06 Clic3  chloride intracellular channel 3  Clic3_predicted  chloride intracellular channel 3 (predicted)  Symbol and Name updated 1559027 APPROVED
2005-01-12 Clic3_predicted  chloride intracellular channel 3 (predicted)      Symbol and Name status set to approved 70820 APPROVED