Clca4 (chloride channel accessory 4) - Rat Genome Database

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Gene: Clca4 (chloride channel accessory 4) Rattus norvegicus
Analyze
Symbol: Clca4
Name: chloride channel accessory 4
RGD ID: 1303234
Description: Predicted to enable intracellular calcium activated chloride channel activity and ligand-gated ion channel activity. Predicted to be involved in proteolysis. Predicted to act upstream of or within chloride transmembrane transport. Predicted to be active in plasma membrane. Orthologous to human CLCA4 (chloride channel accessory 4); INTERACTS WITH 17alpha-ethynylestradiol; 17beta-estradiol; 3,3',5,5'-tetrabromobisphenol A.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: calcium-activated chloride channel regulator 4; chloride channel calcium activated 4; chloride channel calcium activated 6; chloride channel regulator 4; chloride channel, calcium activated, family member 4; Clca6; parturition-related protein PRP3; Prp3
RGD Orthologs
Human
Mouse
Bonobo
Dog
Pig
Green Monkey
Alliance Genes
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.22233,883,625 - 233,904,993 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl2233,883,851 - 233,903,089 (-)EnsemblmRatBN7.2 Ensembl
Rnor_6.02250,842,939 - 250,864,060 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl2250,843,165 - 250,862,419 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.02269,371,177 - 269,392,072 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.42243,002,320 - 243,023,215 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.12242,989,059 - 243,009,955 (-)NCBI
Celera2225,872,978 - 225,893,873 (-)NCBICelera
Cytogenetic Map2q44NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component
plasma membrane  (IBA,ISO)

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. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
4. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:19144963   PMID:23376485  


Genomics

Comparative Map Data
Clca4
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.22233,883,625 - 233,904,993 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl2233,883,851 - 233,903,089 (-)EnsemblmRatBN7.2 Ensembl
Rnor_6.02250,842,939 - 250,864,060 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl2250,843,165 - 250,862,419 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.02269,371,177 - 269,392,072 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.42243,002,320 - 243,023,215 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.12242,989,059 - 243,009,955 (-)NCBI
Celera2225,872,978 - 225,893,873 (-)NCBICelera
Cytogenetic Map2q44NCBI
CLCA4
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38186,547,078 - 86,580,754 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p13 Ensembl186,547,078 - 86,580,754 (+)EnsemblGRCh38hg38GRCh38
GRCh37187,012,761 - 87,046,437 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36186,785,347 - 86,819,025 (+)NCBINCBI36Build 36hg18NCBI36
Build 34186,724,781 - 86,758,451NCBI
Celera185,256,746 - 85,290,417 (+)NCBICelera
Cytogenetic Map1p22.3NCBI
HuRef185,123,236 - 85,156,884 (+)NCBIHuRef
CHM1_1187,127,607 - 87,161,285 (+)NCBICHM1_1
T2T-CHM13v2.0186,387,119 - 86,420,795 (+)NCBIT2T-CHM13v2.0
Clca4a
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm393144,658,247 - 144,680,806 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl3144,658,241 - 144,680,806 (-)EnsemblGRCm39 Ensembl
GRCm383144,952,486 - 144,975,045 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl3144,952,480 - 144,975,045 (-)EnsemblGRCm38mm10GRCm38
MGSCv373144,615,450 - 144,638,009 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv363144,890,061 - 144,912,397 (-)NCBIMGSCv36mm8
Celera3151,393,608 - 151,416,192 (-)NCBICelera
Cytogenetic Map3H2NCBI
CLCA4
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.1187,930,549 - 87,964,225 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl187,930,549 - 87,964,218 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v01119,077,318 - 119,111,027 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
CLCA4
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1661,559,472 - 61,584,601 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl661,559,738 - 61,584,177 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha664,273,532 - 64,298,313 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0662,099,324 - 62,124,119 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl662,099,597 - 62,124,493 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1661,632,408 - 61,657,193 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0661,595,579 - 61,620,375 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0662,096,317 - 62,126,025 (-)NCBIUU_Cfam_GSD_1.0
CLCA4
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl4129,491,594 - 129,599,410 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.14129,562,573 - 129,593,123 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.24142,080,452 - 142,110,275 (-)NCBISscrofa10.2Sscrofa10.2susScr3
CLCA4
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.12046,856,330 - 46,890,832 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl2046,856,232 - 46,890,515 (-)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366603370,921,065 - 70,954,895 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0

Variants

.
Variants in Clca4
1281 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:31
Count of miRNA genes:30
Interacting mature miRNAs:30
Transcripts:ENSRNOT00000017943
Prediction methods:Miranda, Rnahybrid
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
724534Uae6Urinary albumin excretion QTL 610urine albumin amount (VT:0002871)urine albumin level (CMO:0000130)278665619249053267Rat
1641891Alcrsp17Alcohol response QTL 17response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)2149559561249053267Rat
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
2317752Glom23Glomerulus QTL 233.6urine protein amount (VT:0005160)urine protein level (CMO:0000591)2193452645245889826Rat
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
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
7207490Bss111Bone structure and strength QTL 1116.4femur morphology trait (VT:0000559)femur midshaft cortical cross-sectional area (CMO:0001663)2211744537249053267Rat
7207482Bss107Bone structure and strength QTL 1077femur strength trait (VT:0010010)femur ultimate force (CMO:0001675)2211744537249053267Rat
7207484Bss108Bone structure and strength QTL 1085.3femur strength trait (VT:0010010)femur total energy absorbed before break (CMO:0001677)2211744537249053267Rat
1298075Scl17Serum cholesterol level QTL 173.4blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)2211744537249053267Rat
1549836Bss2Bone structure and strength QTL 27.5femur strength trait (VT:0010010)femur midshaft polar moment of inertia (CMO:0001669)2211744537249053267Rat
2317885Alcrsp28Alcohol response QTL 282.10.63response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)2212828222249053267Rat
1300126Bp175Blood pressure QTL 1753.46arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)2214226044247136170Rat
2313073Bmd75Bone mineral density QTL 754.10.0001tibia mineral mass (VT:1000283)total volumetric bone mineral density (CMO:0001728)2215377404237938339Rat
1331767Hrtrt12Heart rate QTL 123.373heart pumping trait (VT:2000009)heart rate (CMO:0000002)2218414747240841241Rat
2293833Kiddil8Kidney dilation QTL 82.9kidney pelvis morphology trait (VT:0004194)hydronephrosis severity score (CMO:0001208)2219753301247136170Rat
2293844Kiddil7Kidney dilation QTL 73.5kidney pelvis morphology trait (VT:0004194)hydronephrosis severity score (CMO:0001208)2219753301247136170Rat
9587428Epfw6Epididymal fat weight QTL 67.470.001epididymal fat pad mass (VT:0010421)epididymal fat pad weight to body weight ratio (CMO:0000658)2223389739249053267Rat
7411555Bw132Body weight QTL 1320.001body mass (VT:0001259)body weight gain (CMO:0000420)2223389739249053267Rat
631563Hcuc3Hepatic copper content QTL 33.87liver copper amount (VT:0003065)liver copper weight to liver dry weight ratio (CMO:0001512)2229059610249053267Rat


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 2 3
Low 1 6 8 29 10
Below cutoff 1 21 12 10 12 2 2 15 6 15 6 2

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000017943   ⟹   ENSRNOP00000017943
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl2233,883,851 - 233,903,089 (-)Ensembl
Rnor_6.0 Ensembl2250,843,165 - 250,862,419 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000103694   ⟹   ENSRNOP00000076720
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl2233,883,851 - 233,902,216 (-)Ensembl
RefSeq Acc Id: NM_201419   ⟹   NP_958822
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.22233,883,851 - 233,904,750 (-)NCBI
Rnor_6.02250,843,165 - 250,864,060 (-)NCBI
Rnor_5.02269,371,177 - 269,392,072 (-)NCBI
RGSC_v3.42243,002,320 - 243,023,215 (-)RGD
Celera2225,872,978 - 225,893,873 (-)RGD
Sequence:
RefSeq Acc Id: XM_017590984   ⟹   XP_017446473
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.22233,883,625 - 233,904,993 (-)NCBI
Rnor_6.02250,842,939 - 250,863,565 (-)NCBI
Sequence:
Protein Sequences
Protein RefSeqs NP_958822 (Get FASTA)   NCBI Sequence Viewer  
  XP_017446473 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAR01113 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: NP_958822   ⟸   NM_201419
- Peptide Label: precursor
- UniProtKB: Q6VPP3 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_017446473   ⟸   XM_017590984
- Peptide Label: isoform X1
- UniProtKB: Q6VPP3 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000017943   ⟸   ENSRNOT00000017943
RefSeq Acc Id: ENSRNOP00000076720   ⟸   ENSRNOT00000103694
Protein Domains
VWFA

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-Q6VPP3-F1-model_v2 AlphaFold Q6VPP3 1-923 view protein structure

Transcriptome

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

Promoters
RGD ID:13691804
Promoter ID:EPDNEW_R2329
Type:multiple initiation site
Name:Clca4_1
Description:chloride channel accessory 4
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_6.02250,862,348 - 250,862,408EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1303234 AgrOrtholog
BioCyc Gene G2FUF-50933 BioCyc
Ensembl Genes ENSRNOG00000029889 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000017943 ENTREZGENE
  ENSRNOP00000017943.4 UniProtKB/TrEMBL
  ENSRNOP00000076720 ENTREZGENE
  ENSRNOP00000076720.1 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000017943 ENTREZGENE
  ENSRNOT00000017943.5 UniProtKB/TrEMBL
  ENSRNOT00000103694 ENTREZGENE
  ENSRNOT00000103694.1 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
  Ig-like_fold UniProtKB/TrEMBL
  VWF_A UniProtKB/TrEMBL
  vWFA_dom_sf UniProtKB/TrEMBL
KEGG Report rno:362053 UniProtKB/TrEMBL
NCBI Gene 362053 ENTREZGENE
Pfam CLCA_N UniProtKB/TrEMBL
  VWA UniProtKB/TrEMBL
PhenoGen Clca4 PhenoGen
PROSITE VWFA UniProtKB/TrEMBL
SMART VWA UniProtKB/TrEMBL
Superfamily-SCOP SSF53300 UniProtKB/TrEMBL
TIGRFAMs hCaCC UniProtKB/TrEMBL
UniProt A0A8I5ZJ95_RAT UniProtKB/TrEMBL
  Q6VPP3 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2009-05-18 Clca4  chloride channel accessory 4  Clca4  chloride channel calcium activated 4  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2009-02-25 Clca4  chloride channel calcium activated 4  Clca4  chloride channel regulator 4  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2009-01-06 Clca4  chloride channel regulator 4  Clca4  chloride channel, calcium activated, family member 4  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-03-03 Clca4  chloride channel, calcium activated, family member 4  Clca6  chloride channel calcium activated 6  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2005-07-08 Clca6  chloride channel calcium activated 6  Prp3  parturition-related protein PRP3  Symbol and Name updated 1299863 APPROVED