Clca2 (chloride channel accessory 2) - Rat Genome Database

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Gene: Clca2 (chloride channel accessory 2) Mus musculus
Analyze
Symbol: Clca2
Name: chloride channel accessory 2
RGD ID: 1552051
MGI Page MGI
Description: Enables chloride channel activity and ligand-gated monoatomic ion channel activity. Acts upstream of or within chloride transport. Located in plasma membrane. Is expressed in several structures, including alimentary system; genitourinary system; immune system; skin; and telencephalon. Orthologous to human CLCA2 (chloride channel accessory 2).
Type: protein-coding
RefSeq Status: REVIEWED
Previously known as: 4732440A06; AI586120; calcium-activated chloride channel family member 5; calcium-activated chloride channel regulator 2; chloride channel calcium activated 2; chloride channel calcium activated 5; Clc; Clca5; mCLCA5
RGD Orthologs
Human
Rat
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: GRCm39 - Mouse Genome Assembly GRCm39
Position:
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm393144,776,021 - 144,805,204 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl3144,776,024 - 144,805,204 (-)EnsemblGRCm39 Ensembl
GRCm383145,070,260 - 145,099,443 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl3145,070,263 - 145,099,443 (-)EnsemblGRCm38mm10GRCm38
MGSCv373144,733,229 - 144,762,005 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv363145,007,651 - 145,036,427 (-)NCBIMGSCv36mm8
Celera3151,513,121 - 151,541,898 (-)NCBICelera
Cytogenetic Map3H2NCBI
cM Map369.31NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component

Phenotype Annotations     Click to see Annotation Detail View
References

References - curated
# Reference Title Reference Citation
1. MGDs mouse GO annotations MGD data from the GO Consortium
2. MGD IEA MGD IEA
3. Analysis of the mouse transcriptome based on functional annotation of 60,770 full-length cDNAs. Okazaki Y, etal., Nature. 2002 Dec 5;420(6915):563-73.
4. Mouse MP Annotation Import Pipeline RGD automated import pipeline
5. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
6. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
7. Database resources of the National Center for Biotechnology Information. Wheeler DL, etal., Nucleic Acids Res 2001 Jan 1;29(1):11-6.
Additional References at PubMed
PMID:10349636   PMID:11042159   PMID:11076861   PMID:11217851   PMID:12477932   PMID:15284223   PMID:15292178   PMID:16141072   PMID:16141073   PMID:16569774   PMID:19210762   PMID:20012443  
PMID:21267068   PMID:21862448   PMID:21873635   PMID:22647633   PMID:25828855   PMID:26075897   PMID:27711075   PMID:29743348  


Genomics

Comparative Map Data
Clca2
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm393144,776,021 - 144,805,204 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl3144,776,024 - 144,805,204 (-)EnsemblGRCm39 Ensembl
GRCm383145,070,260 - 145,099,443 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl3145,070,263 - 145,099,443 (-)EnsemblGRCm38mm10GRCm38
MGSCv373144,733,229 - 144,762,005 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv363145,007,651 - 145,036,427 (-)NCBIMGSCv36mm8
Celera3151,513,121 - 151,541,898 (-)NCBICelera
Cytogenetic Map3H2NCBI
cM Map369.31NCBI
CLCA2
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38186,424,171 - 86,456,553 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl186,424,171 - 86,456,553 (+)EnsemblGRCh38hg38GRCh38
GRCh37186,889,854 - 86,922,236 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36186,662,413 - 86,694,829 (+)NCBINCBI36Build 36hg18NCBI36
Build 34186,601,845 - 86,634,259NCBI
Celera185,133,768 - 85,166,240 (+)NCBICelera
Cytogenetic Map1p22.3NCBI
HuRef185,000,753 - 85,032,874 (+)NCBIHuRef
CHM1_1187,004,629 - 87,037,098 (+)NCBICHM1_1
T2T-CHM13v2.0186,264,193 - 86,296,574 (+)NCBIT2T-CHM13v2.0
Clca2
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr82236,655,419 - 236,682,669 (-)NCBIGRCr8
mRatBN7.22233,993,619 - 234,022,691 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl2233,995,078 - 234,022,199 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx2241,783,941 - 241,811,118 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.02239,672,060 - 239,699,210 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.02234,541,565 - 234,568,742 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.02250,954,423 - 250,981,544 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl2250,954,397 - 250,981,623 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.02269,482,241 - 269,509,237 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.42243,114,775 - 243,142,349 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera2225,983,314 - 226,010,397 (-)NCBICelera
Cytogenetic Map2q44NCBI
Clca2
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554237,728,652 - 7,760,697 (-)EnsemblChiLan1.0
ChiLan1.0NW_0049554237,729,032 - 7,760,340 (-)NCBIChiLan1.0ChiLan1.0
CLCA2
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v21140,503,490 - 140,536,078 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan11139,655,368 - 139,691,488 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v01118,954,863 - 118,987,264 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.1187,808,002 - 87,840,605 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl187,808,205 - 87,840,605 (+)Ensemblpanpan1.1panPan2
CLCA2
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1661,665,120 - 61,705,760 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl661,666,105 - 61,704,746 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha664,379,479 - 64,415,767 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0662,205,308 - 62,244,815 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl662,205,904 - 62,244,664 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1661,738,026 - 61,777,512 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0661,701,435 - 61,740,933 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0662,207,245 - 62,246,736 (-)NCBIUU_Cfam_GSD_1.0
Clca2
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440505896,893,563 - 96,928,155 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_004936865202,555 - 237,099 (-)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_004936865202,970 - 237,072 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
CLCA2
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl4129,670,638 - 129,704,846 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.14129,670,634 - 129,704,765 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.24142,188,545 - 142,223,419 (-)NCBISscrofa10.2Sscrofa10.2susScr3
CLCA2
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.12046,974,030 - 47,007,723 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl2046,975,337 - 47,006,646 (-)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366603370,803,176 - 70,835,376 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Clca2
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_00462474211,183,711 - 11,212,388 (-)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_00462474211,182,852 - 11,217,222 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Clca2
779 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:489
Count of miRNA genes:340
Interacting mature miRNAs:401
Transcripts:ENSMUST00000029929, ENSMUST00000040465, ENSMUST00000159643
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 (GRCm39)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1302056Orgwq4_morgan weight QTL 4 (mouse)Not determined330067588147304689Mouse
27226732Tibmd3_mtibia midshaft diameter 3, 10 week (mouse)396607316147805636Mouse
1300752Ap6q_malcohol preference 6 QTL (mouse)Not determined3100372912147045722Mouse
27226733Tibmd6_mtibia midshaft diameter 6, 16 week (mouse)3101307316149805637Mouse
1302093Orgwq5_morgan weight QTL 5 (mouse)Not determined3107376936147304689Mouse
1301381Bomb1_mbone marrow pre-B 1 (mouse)Not determined3111133243145133417Mouse
1301100Bdt2_mbone density traits 2 (mouse)Not determined3114736617148736784Mouse
10043919Afpq8_mabdominal fat percent QTL 8 (mouse)Not determined3119057332153057456Mouse
1558868Ses9_msalmonella enteritidis susceptibility 9 (mouse)Not determined3119057332153057456Mouse
4141935Tgq15_mtriglyceride QTL 15 (mouse)Not determined119318586153318586Mouse
4142449Tgq14_mtriglyceride QTL 14 (mouse)Not determined119318586153318586Mouse
1302151Lprm2_mlymphoproliferation modifier 2 (mouse)Not determined3119778857153779044Mouse
10412240Alpq6_malcohol preference QTL 6 (mouse)Not determined3120772078154772078Mouse
4142245Pstc1_mperiosteal circumference 1 (mouse)Not determined3126270248159745316Mouse
1301218Letohc1_mlow ethanol consumption 1 (mouse)Not determined3126352986159745316Mouse
1301347Fpli_mfasting plasma insulin (mouse)Not determined3126460514159745316Mouse
1301563Alcp3_malcohol preference locus 3 (mouse)Not determined3130736935159745316Mouse
11039523Tbbr1_mTrypanosoma brucei brucei response 1 (mouse)3130849375159745316Mouse
1300753Eae10_msusceptibility to experimental allergic encephalomyelitis 10 (mouse)Not determined3131736617148451178Mouse
10412120Ccs3_mcolon cancer susceptibility 3 (mouse)Not determined3131754536146017669Mouse
1301528Loco1_mlocomotor activity 1 (mouse)Not determined3133461893159745316Mouse
1301221Hrtfm2_mheart failure modifier 2 (mouse)Not determined3143270248147045722Mouse
1301222Scc7_mcolon tumor susceptibility 7 (mouse)Not determined3143352986156364108Mouse

Markers in Region
BE199161  
Mouse AssemblyChrPosition (strand)SourceJBrowse
GRCm383145,071,487 - 145,071,586UniSTSGRCm38
MGSCv373144,734,451 - 144,734,550UniSTSGRCm37
Celera3151,514,343 - 151,514,442UniSTS
Cytogenetic Map3H2UniSTS
Whitehead/MRC_RH31594.43UniSTS
Clca5  
Mouse AssemblyChrPosition (strand)SourceJBrowse
Cytogenetic Map3H2UniSTS
cM Map3 UniSTS
AI586120  
Mouse AssemblyChrPosition (strand)SourceJBrowse
GRCm383145,070,434 - 145,070,578UniSTSGRCm38
MGSCv373144,733,398 - 144,733,542UniSTSGRCm37
Celera3151,513,290 - 151,513,434UniSTS
Cytogenetic Map3H2UniSTS
Whitehead/MRC_RH31593.09UniSTS


Expression


Sequence


Reference Sequences
RefSeq Acc Id: ENSMUST00000040465   ⟹   ENSMUSP00000036029
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39 Ensembl3144,776,024 - 144,804,865 (-)Ensembl
GRCm38.p6 Ensembl3145,070,263 - 145,099,104 (-)Ensembl
RefSeq Acc Id: ENSMUST00000197121
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39 Ensembl3144,804,605 - 144,805,204 (-)Ensembl
GRCm38.p6 Ensembl3145,098,844 - 145,099,443 (-)Ensembl
RefSeq Acc Id: ENSMUST00000198993   ⟹   ENSMUSP00000143161
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39 Ensembl3144,777,518 - 144,804,867 (-)Ensembl
GRCm38.p6 Ensembl3145,071,757 - 145,099,106 (-)Ensembl
RefSeq Acc Id: NM_001409792   ⟹   NP_001396721
RefSeq Status: REVIEWED
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm393144,776,025 - 144,804,831 (-)NCBI
RefSeq Acc Id: NM_178697   ⟹   NP_848812
RefSeq Status: REVIEWED
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm393144,776,025 - 144,804,831 (-)NCBI
GRCm383145,070,263 - 145,099,106 (-)NCBI
MGSCv373144,733,229 - 144,762,005 (-)RGD
Celera3151,513,121 - 151,541,898 (-)RGD
cM Map3 ENTREZGENE
Sequence:
RefSeq Acc Id: XM_006501432   ⟹   XP_006501495
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm393144,776,021 - 144,805,204 (-)NCBI
GRCm383145,070,260 - 145,099,443 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006501433   ⟹   XP_006501496
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm393144,776,021 - 144,804,904 (-)NCBI
GRCm383145,070,260 - 145,099,143 (-)NCBI
Sequence:
Reference Protein Sequences
RefSeq Acc Id: NP_848812   ⟸   NM_178697
- Peptide Label: isoform 1
- UniProtKB: Q8BZF7 (UniProtKB/Swiss-Prot),   Q8BG22 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: XP_006501495   ⟸   XM_006501432
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: XP_006501496   ⟸   XM_006501433
- Peptide Label: isoform X2
- Sequence:
RefSeq Acc Id: ENSMUSP00000143161   ⟸   ENSMUST00000198993
RefSeq Acc Id: ENSMUSP00000036029   ⟸   ENSMUST00000040465
RefSeq Acc Id: NP_001396721   ⟸   NM_001409792
- Peptide Label: isoform 2
Protein Domains
VWFA

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-Q8BG22-F1-model_v2 AlphaFold Q8BG22 1-942 view protein structure

Promoters
RGD ID:6882566
Promoter ID:EPDNEW_M4734
Type:initiation region
Name:Clca2_1
Description:Mus musculus chloride channel accessory 2 , mRNA.
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Single-end sequencing.
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm383145,099,070 - 145,099,130EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene MGI:2139758 AgrOrtholog
Ensembl Genes ENSMUSG00000036960 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript ENSMUST00000040465 ENTREZGENE
  ENSMUST00000040465.11 UniProtKB/Swiss-Prot
  ENSMUST00000198993 ENTREZGENE
  ENSMUST00000198993.2 UniProtKB/Swiss-Prot
Gene3D-CATH 3.40.50.410 UniProtKB/Swiss-Prot
InterPro CLCA_chordata UniProtKB/Swiss-Prot
  CLCA_N UniProtKB/Swiss-Prot
  VWF_A UniProtKB/Swiss-Prot
  vWFA_dom_sf UniProtKB/Swiss-Prot
KEGG Report mmu:229933 UniProtKB/Swiss-Prot
MGD MGI:2139758 ENTREZGENE
NCBI Gene 229933 ENTREZGENE
PANTHER CALCIUM-ACTIVATED CHLORIDE CHANNEL REGULATOR UniProtKB/Swiss-Prot
  CALCIUM-ACTIVATED CHLORIDE CHANNEL REGULATOR 2 UniProtKB/Swiss-Prot
Pfam CLCA UniProtKB/Swiss-Prot
  VWA_2 UniProtKB/Swiss-Prot
PhenoGen Clca2 PhenoGen
PROSITE VWFA UniProtKB/Swiss-Prot
SMART VWA UniProtKB/Swiss-Prot
Superfamily-SCOP SSF53300 UniProtKB/Swiss-Prot
UniProt CLCA2_MOUSE UniProtKB/Swiss-Prot, ENTREZGENE
  Q8BZF7 ENTREZGENE
UniProt Secondary Q8BZF7 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2015-10-20 Clca2  chloride channel accessory 2    chloride channel calcium activated 2  Symbol and/or name change 5135510 APPROVED
2015-01-20 Clca2  chloride channel calcium activated 2  Clca5  chloride channel calcium activated 5  Symbol and/or name change 5135510 APPROVED