Clca5 (chloride channel accessory 5) - Rat Genome Database

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Gene: Clca5 (chloride channel accessory 5) Rattus norvegicus
Analyze
No known orthologs.
Symbol: Clca5
Name: chloride channel accessory 5
RGD ID: 621100
Description: Predicted to enable intracellularly calcium-gated chloride channel activity. Predicted to be involved in chloride transmembrane transport. Predicted to be active in plasma membrane. Orthologous to human CLCA3P (chloride channel accessory 3, pseudogene); INTERACTS WITH 17beta-estradiol; 17beta-estradiol 3-benzoate; paraquat.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: Ca(2+)-activated chloride channel splicing; calcium activated chloride channel; chloride channel calcium activated 2; chloride channel calcium activated 4; CLCA; Clca2; Clca4; LOC362052; rbCLCA
RGD Orthologs
Alliance Orthologs
More Info homologs ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr82236,456,923 - 236,479,220 (-)NCBIGRCr8
mRatBN7.22233,796,569 - 233,818,867 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl2233,796,575 - 233,818,949 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx2241,581,795 - 241,604,085 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.02239,475,816 - 239,498,142 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.02234,339,405 - 234,361,689 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.02250,755,976 - 250,778,269 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl2250,755,869 - 250,778,323 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.02269,282,797 - 269,305,090 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.42242,915,248 - 242,937,541 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera2225,786,217 - 225,808,433 (-)NCBICelera
Cytogenetic Map2q44NCBI
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. Electronic Transfer of LocusLink and RefSeq Data NCBI rat LocusLink and RefSeq merged data July 26, 2002
3. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:16023076   PMID:16137643   PMID:23297403  


Genomics

Variants

.
Variants in Clca5
108 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:69
Count of miRNA genes:50
Interacting mature miRNAs:59
Transcripts:ENSRNOT00000017824
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
631563Hcuc3Hepatic copper content QTL 33.87liver copper amount (VT:0003065)liver copper weight to liver dry weight ratio (CMO:0001512)2229059610249053267Rat
1331767Hrtrt12Heart rate QTL 123.373heart pumping trait (VT:2000009)heart rate (CMO:0000002)2218414747240841241Rat
1598813Memor9Memory QTL 92.7exploratory behavior trait (VT:0010471)average horizontal distance between subject and target during voluntary locomotion in an experimental apparatus (CMO:0002674)2199341726234244620Rat
8693697Alc36Alcohol consumption QTL 3620.592drinking behavior trait (VT:0001422)calculated ethanol drink intake rate (CMO:0001615)2217139753236660713Rat
1298075Scl17Serum cholesterol level QTL 173.4blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)2211744537249053267Rat
2293833Kiddil8Kidney dilation QTL 82.9kidney pelvis morphology trait (VT:0004194)hydronephrosis severity score (CMO:0001208)2219753301247136170Rat
1598835Anxrr18Anxiety related response QTL 182.98body movement coordination trait (VT:0005424)number of rearing movements in an experimental apparatus (CMO:0001752)2200990457245990457Rat
2298479Eau5Experimental allergic uveoretinitis QTL 50.0021uvea integrity trait (VT:0010551)experimental autoimmune uveitis score (CMO:0001504)2202446871237938339Rat
1300126Bp175Blood pressure QTL 1753.46arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)2214226044247136170Rat
7207490Bss111Bone structure and strength QTL 1116.4femur morphology trait (VT:0000559)femur midshaft cortical cross-sectional area (CMO:0001663)2211744537249053267Rat
7207484Bss108Bone structure and strength QTL 1085.3femur strength trait (VT:0010010)femur total energy absorbed before break (CMO:0001677)2211744537249053267Rat
2313073Bmd75Bone mineral density QTL 754.10.0001tibia mineral mass (VT:1000283)total volumetric bone mineral density (CMO:0001728)2215377404237938339Rat
8693622Alc26Alcohol consumption QTL 262.40.667drinking behavior trait (VT:0001422)calculated ethanol drink intake rate (CMO:0001615)2221136523241305619Rat
7411555Bw132Body weight QTL 1320.001body mass (VT:0001259)body weight gain (CMO:0000420)2223389739249053267Rat
61366Iddm3Insulin dependent diabetes mellitus QTL 34.7blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)2189599258234599258Rat
61398Bp50Blood pressure QTL 504.4arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)2189599258234599258Rat
9587428Epfw6Epididymal fat weight QTL 67.470.001epididymal fat pad mass (VT:0010421)epididymal fat pad weight to body weight ratio (CMO:0000658)2223389739249053267Rat
7207482Bss107Bone structure and strength QTL 1077femur strength trait (VT:0010010)femur ultimate force (CMO:0001675)2211744537249053267Rat
2293844Kiddil7Kidney dilation QTL 73.5kidney pelvis morphology trait (VT:0004194)hydronephrosis severity score (CMO:0001208)2219753301247136170Rat
1641891Alcrsp17Alcohol response QTL 17response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)2149559561249053267Rat
2317752Glom23Glomerulus QTL 233.6urine protein amount (VT:0005160)urine protein level (CMO:0000591)2193452645245889826Rat
1549836Bss2Bone structure and strength QTL 27.5femur strength trait (VT:0010010)femur midshaft polar moment of inertia (CMO:0001669)2211744537249053267Rat
724534Uae6Urinary albumin excretion QTL 610urine albumin amount (VT:0002871)urine albumin level (CMO:0000130)278665619249053267Rat
2317885Alcrsp28Alcohol response QTL 282.10.63response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)2212828222249053267Rat

Markers in Region
RH131751  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.22233,826,314 - 233,826,525 (+)MAPPERmRatBN7.2
Rnor_6.02250,785,716 - 250,785,926NCBIRnor6.0
Rnor_5.02269,312,537 - 269,312,747UniSTSRnor5.0
RGSC_v3.42242,944,988 - 242,945,198UniSTSRGSC3.4
Celera2225,815,879 - 225,816,089UniSTS
Cytogenetic Map2q44UniSTS
BE199161  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.22233,996,311 - 233,996,411 (+)MAPPERmRatBN7.2
Rnor_6.02250,955,657 - 250,955,756NCBIRnor6.0
Rnor_5.02269,483,497 - 269,483,596UniSTSRnor5.0
RGSC_v3.42243,116,009 - 243,116,108UniSTSRGSC3.4
Celera2225,984,548 - 225,984,647UniSTS
Cytogenetic Map2q44UniSTS
RH143389  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.22233,999,648 - 233,999,768 (+)MAPPERmRatBN7.2
Rnor_6.02250,958,994 - 250,959,113NCBIRnor6.0
Rnor_5.02269,486,834 - 269,486,953UniSTSRnor5.0
RGSC_v3.42243,119,346 - 243,119,465UniSTSRGSC3.4
Celera2225,987,885 - 225,988,004UniSTS
Cytogenetic Map2q44UniSTS
AI008454  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.22233,995,619 - 233,995,774 (+)MAPPERmRatBN7.2
Rnor_6.02250,954,965 - 250,955,119NCBIRnor6.0
Rnor_5.02269,482,805 - 269,482,959UniSTSRnor5.0
RGSC_v3.42243,115,317 - 243,115,471UniSTSRGSC3.4
Celera2225,983,856 - 225,984,010UniSTS
RH 3.4 Map21662.41UniSTS
Cytogenetic Map2q44UniSTS


Expression

RNA-SEQ Expression

alimentary part of gastrointestinal system
appendage
circulatory system
ectoderm
endocrine system
endoderm
exocrine system
hemolymphoid system
hepatobiliary system
integumental system
mesenchyme
mesoderm
nervous system
renal system
reproductive system
respiratory system
9 10 21 47 77 76 45 25 45 6 165 68 27 35 49 31

Sequence


Ensembl Acc Id: ENSRNOT00000017824   ⟹   ENSRNOP00000017824
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl2233,796,575 - 233,818,949 (-)Ensembl
Rnor_6.0 Ensembl2250,755,869 - 250,778,323 (-)Ensembl
Ensembl Acc Id: ENSRNOT00000083535   ⟹   ENSRNOP00000074850
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl2233,796,786 - 233,818,867 (-)Ensembl
Rnor_6.0 Ensembl2250,756,434 - 250,778,269 (-)Ensembl
Ensembl Acc Id: ENSRNOT00000085670   ⟹   ENSRNOP00000071331
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl2233,796,575 - 233,818,867 (-)Ensembl
Rnor_6.0 Ensembl2250,755,982 - 250,778,269 (-)Ensembl
RefSeq Acc Id: NM_001013202   ⟹   NP_001013220
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr82236,456,923 - 236,479,220 (-)NCBI
mRatBN7.22233,796,569 - 233,818,867 (-)NCBI
Rnor_6.02250,755,976 - 250,778,269 (-)NCBI
Rnor_5.02269,282,797 - 269,305,090 (-)NCBI
RGSC_v3.42242,915,248 - 242,937,541 (-)RGD
Celera2225,786,217 - 225,808,433 (-)RGD
Sequence:
RefSeq Acc Id: XM_063282229   ⟹   XP_063138299
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr82236,456,923 - 236,468,051 (-)NCBI
RefSeq Acc Id: NP_001013220   ⟸   NM_001013202
- Peptide Label: precursor
- UniProtKB: Q4H2C5 (UniProtKB/TrEMBL),   Q75ZI5 (UniProtKB/TrEMBL)
- Sequence:
Ensembl Acc Id: ENSRNOP00000071331   ⟸   ENSRNOT00000085670
Ensembl Acc Id: ENSRNOP00000074850   ⟸   ENSRNOT00000083535
Ensembl Acc Id: ENSRNOP00000017824   ⟸   ENSRNOT00000017824
RefSeq Acc Id: XP_063138299   ⟸   XM_063282229
- Peptide Label: isoform X1
Protein Domains
VWFA

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-F1M7N4-F1-model_v2 AlphaFold F1M7N4 1-903 view protein structure

Transcriptome

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


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:621100 AgrOrtholog
BioCyc Gene G2FUF-50939 BioCyc
Ensembl Genes ENSRNOG00000013334 Ensembl, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000017824.6 UniProtKB/TrEMBL
  ENSRNOT00000083535.2 UniProtKB/TrEMBL
  ENSRNOT00000085670.2 UniProtKB/TrEMBL
Gene3D-CATH 2.60.40.10 UniProtKB/TrEMBL
  3.40.50.410 UniProtKB/TrEMBL
InterPro CaCC_prot UniProtKB/TrEMBL
  Cl_channel_Ca UniProtKB/TrEMBL
  CLCR UniProtKB/TrEMBL
  Ig-like_fold UniProtKB/TrEMBL
  VWF_A UniProtKB/TrEMBL
  vWFA_dom_sf UniProtKB/TrEMBL
KEGG Report rno:362052 UniProtKB/TrEMBL
NCBI Gene Clca5 ENTREZGENE
PANTHER CALCIUM-ACTIVATED CHLORIDE CHANNEL REGULATOR UniProtKB/TrEMBL
  CALCIUM-ACTIVATED CHLORIDE CHANNEL REGULATOR 3A-1-RELATED UniProtKB/TrEMBL
Pfam CLCA_N UniProtKB/TrEMBL
  VWA UniProtKB/TrEMBL
  VWA_2 UniProtKB/TrEMBL
PhenoGen Clca5 PhenoGen
PROSITE VWFA UniProtKB/TrEMBL
RatGTEx ENSRNOG00000013334 RatGTEx
SMART VWA UniProtKB/TrEMBL
Superfamily-SCOP SSF53300 UniProtKB/TrEMBL
UniProt A0A0G2K941_RAT UniProtKB/TrEMBL
  A5LIC0_RAT UniProtKB/TrEMBL
  F1M7N4_RAT UniProtKB/TrEMBL
  Q4H2C5 ENTREZGENE, UniProtKB/TrEMBL
  Q75ZI5 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2010-11-11 Clca5  chloride channel accessory 5  Clca5l  chloride channel calcium activated 5l  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2010-11-11 Clca5l  chloride channel calcium activated 5l  Clca2  chloride channel calcium activated 2  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2006-11-29 Clca2  chloride channel calcium activated 2  Clca4  chloride channel calcium activated 4  Data merged from RGD:1307141 737654 APPROVED
2005-12-06 Clca4  chloride channel calcium activated 4  Clca4_predicted  chloride channel calcium activated 4 (predicted)  Symbol and Name updated 1559027 APPROVED
2005-01-12 Clca4_predicted  chloride channel calcium activated 4 (predicted)      Symbol and Name status set to approved 70820 APPROVED
2002-08-07 Clca2  chloride channel calcium activated 2      Symbol and Name status set to provisional 70820 PROVISIONAL

RGD Curation Notes
Note Type Note Reference
gene_disease adhesion of the human homolog with beta(4)integrin may contribute to lung metastasis by breast cancer cells 634641