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 and proteolysis. 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: GRCr8 - GRCr8 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr82236,456,923 - 236,479,220 (-)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl2236,456,929 - 236,479,220 (-)EnsemblGRCr8
mRatBN7.22233,796,569 - 233,818,867 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl2233,796,575 - 233,818,949 (-)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx2241,581,795 - 241,604,085 (-)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.02239,475,816 - 239,498,142 (-)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.02234,339,405 - 234,361,689 (-)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.02250,755,976 - 250,778,269 (-)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl2250,755,869 - 250,778,323 (-)Ensemblrn6Rnor6.0
Rnor_5.02269,282,797 - 269,305,090 (-)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.42242,915,248 - 242,937,541 (-)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera2225,786,217 - 225,808,433 (-)NCBICelera
Cytogenetic Map2q44NCBI
JBrowse:




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

Biological Process

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
223 total Variants
miRNA Target Status (No longer updated)

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 (GRCr8)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1331734Bp204Blood pressure QTL 2043.61192arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)2170656145239614549Rat
631501Bp101Blood pressure QTL 1012.4arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)2205135267250135267Rat
2307174Activ3Activity QTL 34.830.000058locomotor behavior trait (VT:0001392)number of entries into a discrete space in an experimental apparatus (CMO:0000960)2210956252251712708Rat
1598813Memor9Memory QTL 92.7exploratory behavior trait (VT:0010471)average horizontal distance between subject and target during voluntary locomotion in an experimental apparatus (CMO:0002674)2202029709236904960Rat
8693697Alc36Alcohol consumption QTL 3620.592drinking behavior trait (VT:0001422)calculated ethanol drink intake rate (CMO:0001615)2219814164239320906Rat
1331794Bp202Blood pressure QTL 2023.66819arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)2143344967251712708Rat
1298075Scl17Serum cholesterol level QTL 173.4blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)2214404877251712708Rat
1331805Cm29Cardiac mass QTL 293.50746heart mass (VT:0007028)heart wet weight (CMO:0000069)2143344967251712708Rat
1300126Bp175Blood pressure QTL 1753.46arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)2204795005249795005Rat
7207484Bss108Bone structure and strength QTL 1085.3femur strength trait (VT:0010010)femur total energy absorbed before break (CMO:0001677)2214404877251712708Rat
2313073Bmd75Bone mineral density QTL 754.10.0001tibia mineral mass (VT:1000283)total volumetric bone mineral density (CMO:0001728)2218051934251712708Rat
61398Bp50Blood pressure QTL 504.4arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)2192287802237287802Rat
7207482Bss107Bone structure and strength QTL 1077femur strength trait (VT:0010010)femur ultimate force (CMO:0001675)2214404877251712708Rat
61467Bp14Blood pressure QTL 142.2arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)2205135267250135267Rat
1549836Bss2Bone structure and strength QTL 27.5femur strength trait (VT:0010010)femur midshaft polar moment of inertia (CMO:0001669)2214404877251712708Rat
2317752Glom23Glomerulus QTL 233.6urine protein amount (VT:0005160)urine protein level (CMO:0000591)2196140964251540988Rat
70175BpQTLCluster3Blood pressure QTL cluster 34.128arterial blood pressure trait (VT:2000000)absolute change in systolic blood pressure (CMO:0000607)2205135267250135267Rat
1331767Hrtrt12Heart rate QTL 123.373heart pumping trait (VT:2000009)heart rate (CMO:0000002)2221088977243501206Rat
2293833Kiddil8Kidney dilation QTL 82.9kidney pelvis morphology trait (VT:0004194)hydronephrosis severity score (CMO:0001208)2220274283249795005Rat
1598835Anxrr18Anxiety related response QTL 182.98body movement coordination trait (VT:0005424)number of rearing movements in an experimental apparatus (CMO:0001752)2203664411248664411Rat
7207490Bss111Bone structure and strength QTL 1116.4femur morphology trait (VT:0000559)femur midshaft cortical cross-sectional area (CMO:0001663)2214404877251712708Rat
8693622Alc26Alcohol consumption QTL 262.40.667drinking behavior trait (VT:0001422)calculated ethanol drink intake rate (CMO:0001615)2223810546243965570Rat
61366Iddm3Insulin dependent diabetes mellitus QTL 34.7blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)2192287802237287802Rat
2293844Kiddil7Kidney dilation QTL 73.5kidney pelvis morphology trait (VT:0004194)hydronephrosis severity score (CMO:0001208)2220274283249795005Rat
1641891Alcrsp17Alcohol response QTL 17response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)2151869660251712708Rat

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
musculoskeletal system
nervous system
renal system
reproductive system
respiratory system
16 11 29 60 77 76 45 41 45 6 229 102 11 35 58 80 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
GRCr8 Ensembl2236,463,961 - 236,479,220 (-)Ensembl
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
GRCr8 Ensembl2236,456,929 - 236,479,220 (-)Ensembl
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, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000083535.3 UniProtKB/TrEMBL
  ENSRNOT00000085670 ENTREZGENE
  ENSRNOT00000085670.3 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 A0A0G2K072_RAT UniProtKB/TrEMBL
  A5LIC0_RAT UniProtKB/TrEMBL
  Q4H2C5 ENTREZGENE, UniProtKB/TrEMBL
  Q75ZI5 ENTREZGENE, UniProtKB/TrEMBL
UniProt Secondary A0A0G2K941 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