Clca1 (chloride channel accessory 1) - Rat Genome Database

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Gene: Clca1 (chloride channel accessory 1) Rattus norvegicus
Analyze
Symbol: Clca1
Name: chloride channel accessory 1
RGD ID: 1306258
Description: Predicted to enable intracellular calcium activated chloride channel activity. Involved in cellular response to hypoxia. Located in zymogen granule membrane. Human ortholog(s) of this gene implicated in asthma and chronic obstructive pulmonary disease. Orthologous to human CLCA1 (chloride channel accessory 1); INTERACTS WITH 17alpha-ethynylestradiol; 17beta-estradiol; 17beta-estradiol 3-benzoate.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: calcium-activated chloride channel regulator 1; chloride channel calcium activated 3; Clca3; LOC308015
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
mRatBN7.22233,938,677 - 233,964,369 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl2233,938,677 - 233,964,369 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx2241,727,691 - 241,753,301 (-)NCBIRnor_SHR
UTH_Rnor_SHRSP_BbbUtx_1.02239,617,800 - 239,643,385 (-)NCBIRnor_SHRSP
UTH_Rnor_WKY_Bbb_1.02234,485,318 - 234,510,926 (-)NCBIRnor_WKY
Rnor_6.02250,897,980 - 250,923,711 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl2250,897,969 - 250,923,744 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.02269,425,672 - 269,451,524 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.42243,057,135 - 243,084,146 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.12243,043,871 - 243,070,886 (-)NCBI
Celera2225,927,785 - 225,953,924 (-)NCBICelera
Cytogenetic Map2q44NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

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. Expression of HCLCA1 in cystic fibrosis lungs is associated with mucus overproduction. Hauber HP, etal., Eur Respir J. 2004 Jun;23(6):846-50.
4. CLCA1 gene polymorphisms in chronic obstructive pulmonary disease. Hegab AE, etal., J Med Genet 2004 Mar;41(3):e27.
5. Association of the hCLCA1 gene with childhood and adult asthma. Kamada F, etal., Genes Immun. 2004 Nov;5(7):540-7.
6. Rat ISS GO annotations from MGI mouse gene data--August 2006 MGD data from the GO Consortium
7. Role of gob-5 in mucus overproduction and airway hyperresponsiveness in asthma. Nakanishi A, etal., Proc Natl Acad Sci U S A. 2001 Apr 24;98(9):5175-80. Epub 2001 Apr 10.
8. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
9. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
10. Comprehensive gene review and curation RGD comprehensive gene curation
11. Hypoxic/ischemic conditions induce expression of the putative pro-death gene Clca1 via activation of extrasynaptic N-methyl-D-aspartate receptors. Wahl AS, etal., Neuroscience. 2009 Jan 12;158(1):344-52. Epub 2008 Jun 14.
12. Increased expression of human calcium-activated chloride channel 1 is correlated with mucus overproduction in the airways of Chinese patients with chronic obstructive pulmonary disease. Wang K, etal., Chin Med J (Engl). 2007 Jun 20;120(12):1051-7.
13. Genome-wide profiling identifies epithelial cell genes associated with asthma and with treatment response to corticosteroids. Woodruff PG, etal., Proc Natl Acad Sci U S A. 2007 Oct 2;104(40):15858-63. Epub 2007 Sep 26.
Additional References at PubMed
PMID:12019299   PMID:19558866   PMID:23266329   PMID:26510883  


Genomics

Comparative Map Data
Clca1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.22233,938,677 - 233,964,369 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl2233,938,677 - 233,964,369 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx2241,727,691 - 241,753,301 (-)NCBIRnor_SHR
UTH_Rnor_SHRSP_BbbUtx_1.02239,617,800 - 239,643,385 (-)NCBIRnor_SHRSP
UTH_Rnor_WKY_Bbb_1.02234,485,318 - 234,510,926 (-)NCBIRnor_WKY
Rnor_6.02250,897,980 - 250,923,711 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl2250,897,969 - 250,923,744 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.02269,425,672 - 269,451,524 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.42243,057,135 - 243,084,146 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.12243,043,871 - 243,070,886 (-)NCBI
Celera2225,927,785 - 225,953,924 (-)NCBICelera
Cytogenetic Map2q44NCBI
CLCA1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38186,468,927 - 86,500,259 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p13 Ensembl186,468,368 - 86,500,259 (+)EnsemblGRCh38hg38GRCh38
GRCh37186,934,610 - 86,965,942 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36186,707,114 - 86,738,565 (+)NCBINCBI36Build 36hg18NCBI36
Build 34186,646,071 - 86,677,963NCBI
Celera185,178,525 - 85,209,980 (+)NCBICelera
Cytogenetic Map1p22.3NCBI
HuRef185,045,156 - 85,076,624 (+)NCBIHuRef
CHM1_1187,049,378 - 87,080,831 (+)NCBICHM1_1
T2T-CHM13v2.0186,308,943 - 86,340,288 (+)NCBIT2T-CHM13v2.0
Clca1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm393144,710,298 - 144,738,537 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl3144,709,578 - 144,738,537 (-)EnsemblGRCm39 Ensembl
GRCm383145,004,537 - 145,032,776 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl3145,003,817 - 145,032,776 (-)EnsemblGRCm38mm10GRCm38
MGSCv373144,667,501 - 144,695,740 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv363144,941,924 - 144,970,145 (-)NCBIMGSCv36mm8
Celera3151,445,713 - 151,476,303 (-)NCBICelera
Cytogenetic Map3H2NCBI
cM Map369.26NCBI
Clca1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554237,684,709 - 7,714,449 (-)EnsemblChiLan1.0
ChiLan1.0NW_0049554237,684,741 - 7,714,438 (-)NCBIChiLan1.0ChiLan1.0
CLCA1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.1187,852,383 - 87,884,267 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl187,852,599 - 87,884,751 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v01118,999,099 - 119,030,839 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
CLCA1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1661,620,755 - 61,650,111 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl661,620,995 - 61,650,083 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha664,334,464 - 64,364,165 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0662,160,281 - 62,189,982 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl662,160,878 - 62,189,975 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1661,693,037 - 61,722,731 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0661,656,245 - 61,686,130 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0662,162,204 - 62,191,927 (-)NCBIUU_Cfam_GSD_1.0
Clca1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440505896,941,723 - 96,975,427 (+)NCBIHiC_Itri_2
SpeTri2.0NW_004936865155,284 - 188,988 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
CLCA1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl4129,620,874 - 129,655,385 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.14129,621,259 - 129,655,385 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.24142,139,255 - 142,173,314 (-)NCBISscrofa10.2Sscrofa10.2susScr3
CLCA1
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.12046,930,713 - 46,964,301 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl2046,927,412 - 46,963,737 (-)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366603370,846,708 - 70,880,438 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Clca1
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_00462474211,145,413 - 11,172,369 (-)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_00462474211,145,406 - 11,172,369 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Clca1
263 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:411
Count of miRNA genes:236
Interacting mature miRNAs:278
Transcripts:ENSRNOT00000018373
Prediction methods:Microtar, 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
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 1
Medium 2 9
Low 2 23 9 10 2
Below cutoff 2 13 4 9 4 3 4 5 11 23 3

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000084996   ⟹   ENSRNOP00000070057
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl2233,938,677 - 233,964,369 (-)Ensembl
Rnor_6.0 Ensembl2250,897,969 - 250,923,744 (-)Ensembl
RefSeq Acc Id: NM_001107449   ⟹   NP_001100919
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.22233,938,677 - 233,964,369 (-)NCBI
Rnor_6.02250,897,980 - 250,923,711 (-)NCBI
Rnor_5.02269,425,672 - 269,451,524 (-)NCBI
RGSC_v3.42243,057,135 - 243,084,146 (-)RGD
Celera2225,927,785 - 225,953,924 (-)RGD
Sequence:
Protein Sequences
Protein RefSeqs NP_001100919 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein EDL82389 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: NP_001100919   ⟸   NM_001107449
- Peptide Label: precursor
- UniProtKB: A0A0G2JWX9 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000070057   ⟸   ENSRNOT00000084996
Protein Domains
VWFA

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-A0A0G2JWX9-F1-model_v2 AlphaFold A0A0G2JWX9 1-910 view protein structure

Transcriptome

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

Promoters
RGD ID:13691805
Promoter ID:EPDNEW_R2330
Type:multiple initiation site
Name:Clca1_1
Description:chloride channel accessory 1
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_6.02250,923,723 - 250,923,783EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1306258 AgrOrtholog
BioCyc Gene G2FUF-50932 BioCyc
Ensembl Genes ENSRNOG00000060831 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000070057 ENTREZGENE
  ENSRNOP00000070057.1 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000084996 ENTREZGENE
  ENSRNOT00000084996.2 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
  Ig-like_fold UniProtKB/TrEMBL
  VWF_A UniProtKB/TrEMBL
  vWFA_dom_sf UniProtKB/TrEMBL
KEGG Report rno:308015 UniProtKB/TrEMBL
NCBI Gene 308015 ENTREZGENE
PANTHER CALCIUM-ACTIVATED CHLORIDE CHANNEL REGULATOR UniProtKB/TrEMBL
  CALCIUM-ACTIVATED CHLORIDE CHANNEL REGULATOR 1 UniProtKB/TrEMBL
Pfam CLCA_N UniProtKB/TrEMBL
  VWA_2 UniProtKB/TrEMBL
PhenoGen Clca1 PhenoGen
PROSITE VWFA UniProtKB/TrEMBL
SMART VWA UniProtKB/TrEMBL
Superfamily-SCOP SSF53300 UniProtKB/TrEMBL
TIGRFAMs hCaCC UniProtKB/TrEMBL
UniProt A0A0G2JWX9 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2010-11-11 Clca1  chloride channel accessory 1  Clca3  chloride channel calcium activated 3  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-04-30 Clca3  chloride channel calcium activated 3   Clca3_predicted  chloride channel calcium activated 3 (predicted)  'predicted' is removed 2292626 APPROVED
2005-01-12 Clca3_predicted  chloride channel calcium activated 3 (predicted)      Symbol and Name status set to approved 70820 APPROVED