Clca2 (chloride channel accessory 2) - Rat Genome Database

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Gene: Clca2 (chloride channel accessory 2) Rattus norvegicus
Analyze
Symbol: Clca2
Name: chloride channel accessory 2
RGD ID: 1304894
Description: Predicted to have intracellular calcium activated chloride channel activity and ligand-gated ion channel activity. Predicted to be involved in chloride transport. Predicted to localize to several cellular components, including cytosol; integral component of plasma membrane; and nucleus. Orthologous to human CLCA2 (chloride channel accessory 2); INTERACTS WITH 17beta-estradiol; 17beta-estradiol 3-benzoate; 2,5-hexanedione.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: calcium-activated chloride channel regulator 2; chloride channel calcium activated 5; chloride channel, calcium activated, family member 2; Clca5; LOC308016
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: Rnor_6.0 - RGSC Genome Assembly v6.0
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.22233,993,619 - 234,022,691 (-)NCBI
Rnor_6.0 Ensembl2250,954,397 - 250,981,623 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.02250,954,423 - 250,981,544 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.02269,482,241 - 269,509,237 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.42243,114,775 - 243,142,349 (-)NCBIRGSC3.4rn4RGSC3.4
Celera2225,983,314 - 226,010,397 (-)NCBICelera
Cytogenetic Map2q44NCBI
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

References

Additional References at PubMed
PMID:15284223   PMID:25212661  


Genomics

Comparative Map Data
Clca2
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.22233,993,619 - 234,022,691 (-)NCBI
Rnor_6.0 Ensembl2250,954,397 - 250,981,623 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.02250,954,423 - 250,981,544 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.02269,482,241 - 269,509,237 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.42243,114,775 - 243,142,349 (-)NCBIRGSC3.4rn4RGSC3.4
Celera2225,983,314 - 226,010,397 (-)NCBICelera
Cytogenetic Map2q44NCBI
CLCA2
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl186,424,171 - 86,456,553 (+)EnsemblGRCh38hg38GRCh38
GRCh38186,424,144 - 86,456,553 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh37186,889,854 - 86,922,236 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36186,662,413 - 86,694,829 (+)NCBINCBI36hg18NCBI36
Build 34186,601,845 - 86,634,259NCBI
Celera185,133,768 - 85,166,240 (+)NCBI
Cytogenetic Map1p22.3NCBI
HuRef185,000,753 - 85,032,874 (+)NCBIHuRef
CHM1_1187,004,629 - 87,037,098 (+)NCBICHM1_1
Clca2
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm393144,776,021 - 144,805,204 (-)NCBIGRCm39mm39
GRCm39 Ensembl3144,776,024 - 144,805,204 (-)Ensembl
GRCm383145,070,260 - 145,099,443 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl3145,070,263 - 145,099,443 (-)EnsemblGRCm38mm10GRCm38
MGSCv373144,733,229 - 144,762,005 (-)NCBIGRCm37mm9NCBIm37
MGSCv363145,007,651 - 145,036,427 (-)NCBImm8
Celera3151,513,121 - 151,541,898 (-)NCBICelera
Cytogenetic Map3H2NCBI
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
PanPan1.1187,808,002 - 87,840,605 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl187,808,205 - 87,840,605 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v01118,954,863 - 118,987,264 (+)NCBIMhudiblu_PPA_v0panPan3
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 (-)NCBI
ROS_Cfam_1.0662,205,308 - 62,244,815 (-)NCBI
UMICH_Zoey_3.1661,738,026 - 61,777,512 (-)NCBI
UNSW_CanFamBas_1.0661,701,435 - 61,740,933 (-)NCBI
UU_Cfam_GSD_1.0662,207,245 - 62,246,736 (-)NCBI
Clca2
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440505896,893,563 - 96,928,155 (+)NCBI
SpeTri2.0NW_004936865202,970 - 237,072 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
CLCA2
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl4129,670,637 - 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 (-)NCBI
ChlSab1.1 Ensembl2046,975,337 - 47,006,646 (-)Ensembl
Vero_WHO_p1.0NW_02366603370,803,176 - 70,835,376 (+)NCBI
Clca2
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462474211,182,852 - 11,217,222 (-)NCBI

Position Markers
RH131751  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.22233,826,314 - 233,826,525 (+)MAPPER
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 (+)MAPPER
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 (+)MAPPER
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 (+)MAPPER
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


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
2293833Kiddil8Kidney dilation QTL 82.9kidney pelvis morphology trait (VT:0004194)hydronephrosis severity score (CMO:0001208)2236318496264899009Rat
2293844Kiddil7Kidney dilation QTL 73.5kidney pelvis morphology trait (VT:0004194)hydronephrosis severity score (CMO:0001208)2236318496264899009Rat
1331767Hrtrt12Heart rate QTL 123.373heart pumping trait (VT:2000009)heart rate (CMO:0000002)2235289967257110527Rat
1298075Scl17Serum cholesterol level QTL 173.4blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)2228712271266435125Rat
631563Hcuc3Hepatic copper content QTL 33.87hepatic copper amount (VT:0003065)liver copper weight to liver dry weight ratio (CMO:0001512)2245893572266435125Rat
2317885Alcrsp28Alcohol response QTL 282.10.63response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)2229793522266435125Rat
631514Scl8Serum cholesterol level QTL84.4blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)2231621666266435125Rat
1300126Bp175Blood pressure QTL 1753.46arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)2229606682264899009Rat
1641891Alcrsp17Alcohol response QTL 17response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)2155965557254121739Rat
1598813Memor9Memory QTL 92.7exploratory behavior trait (VT:0010471)average horizontal distance in proximity to the target during voluntary locomotion in an experimental apparatus (CMO:0002674)2214870793251212353Rat
1598835Anxrr18Anxiety related response QTL 182.98body movement coordination trait (VT:0005424)number of rearing movements in an experimental apparatus (CMO:0001752)2217743855262743855Rat
2298479Eau5Experimental allergic uveoretinitis QTL 50.0021uvea integrity trait (VT:0010551)experimental autoimmune uveitis score (CMO:0001504)2217498545254132424Rat
2299161Iddm33Insulin dependent diabetes mellitus QTL 332.98blood glucose amount (VT:0000188)age at onset/diagnosis of type 1 diabetes mellitus (CMO:0001140)2221488355254121739Rat
1549836Bss2Bone structure and strength QTL 27.5femur strength trait (VT:0010010)femur midshaft polar moment of inertia (CMO:0001669)2228712271266435125Rat
2313073Bmd75Bone mineral density QTL 754.10.0001tibia mineral mass (VT:1000283)total volumetric bone mineral density (CMO:0001728)2231224020254132424Rat
2317752Glom23Glomerulus QTL 233.6urine protein amount (VT:0005160)urine protein level (CMO:0000591)2208594330263179188Rat
8693622Alc26Alcohol consumption QTL 262.40.667drinking behavior trait (VT:0001422)calculated ethanol drink intake rate (CMO:0001615)2237712398257579826Rat
9587428Epfw6Epididymal fat weight QTL 67.470.001epididymal fat pad mass (VT:0010421)epididymal fat pad weight to body weight ratio (CMO:0000658)2240679103266435125Rat
7207490Bss111Bone structure and strength QTL 1116.4femur morphology trait (VT:0000559)femur midshaft cortical cross-sectional area (CMO:0001663)2228712271266435125Rat
7411555Bw132Body weight QTL 1320.001body mass (VT:0001259)body weight gain (CMO:0000420)2240679103266435125Rat
7207482Bss107Bone structure and strength QTL 1077femur strength trait (VT:0010010)femur ultimate force (CMO:0001675)2228712271266435125Rat
7207484Bss108Bone structure and strength QTL 1085.3femur strength trait (VT:0010010)femur total energy absorbed before break (CMO:0001677)2228712271266435125Rat
8693697Alc36Alcohol consumption QTL 3620.592drinking behavior trait (VT:0001422)calculated ethanol drink intake rate (CMO:0001615)2233013605253626471Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:298
Count of miRNA genes:197
Interacting mature miRNAs:231
Transcripts:ENSRNOT00000018435
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.


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 3
Low 3 2 17 10 12 10 14 5 8
Below cutoff 2 20 17 5 17 4 4 14 15 24 4

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000018435   ⟹   ENSRNOP00000018435
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl2250,954,397 - 250,981,623 (-)Ensembl
RefSeq Acc Id: NM_001107450   ⟹   NP_001100920
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.22233,995,078 - 234,022,199 (-)NCBI
Rnor_6.02250,954,423 - 250,981,544 (-)NCBI
Rnor_5.02269,482,241 - 269,509,237 (-)NCBI
RGSC_v3.42243,114,775 - 243,142,349 (-)RGD
Celera2225,983,314 - 226,010,397 (-)RGD
Sequence:
RefSeq Acc Id: XM_039102133   ⟹   XP_038958061
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.22233,993,619 - 234,022,691 (-)NCBI
RefSeq Acc Id: XM_039102134   ⟹   XP_038958062
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.22233,997,156 - 234,022,199 (-)NCBI
Protein Sequences
Protein RefSeqs NP_001100920 (Get FASTA)   NCBI Sequence Viewer  
  XP_038958061 (Get FASTA)   NCBI Sequence Viewer  
  XP_038958062 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein EDL82390 (Get FASTA)   NCBI Sequence Viewer  
  EDL82391 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: NP_001100920   ⟸   NM_001107450
- UniProtKB: D3ZVT7 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000018435   ⟸   ENSRNOT00000018435
RefSeq Acc Id: XP_038958061   ⟸   XM_039102133
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038958062   ⟸   XM_039102134
- Peptide Label: isoform X2
Protein Domains
VWFA

Transcriptome

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


Strain Variation

Strain Sequence Variants (Rnor 6.0)
ACI/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
ACI/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
ACI/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
BBDP/Wor (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
BN/SsN (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
Buf/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
COP/CrCrl (MCW & UW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
University of Wisconsin (Dr. James Shull)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Charles River Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob) and UW Madison (Dr. James Shull)
F344/NCrl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
F344/NRrrc (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
FHH/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHH/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
FHL/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHL/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
GH/OmrMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
GK/Ox (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LE/Stm (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/Crl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/NCrlBR (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LH/MavRrrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LL/MavRrrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LN/MavRrrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
M520/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
MHS/Gib (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MNS/Gib (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MR/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
SBH/Ygl (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBH/Ygl sequenced by MCW
SBH/Ygl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SBN/Ygl (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBN/Ygl sequenced by MCW
SBN/Ygl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHR/NHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHRSP/Gcrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SR/JrHsd (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Harlan Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SR/JrHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/Jr (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/JrHsdMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SS/JrHsdMcwi (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WAG/Rij (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/Gcrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
WKY/NCrl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/NHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WN/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1304894 AgrOrtholog
Ensembl Genes ENSRNOG00000013771 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000018435 ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000018435 ENTREZGENE, UniProtKB/TrEMBL
Gene3D-CATH 3.40.50.410 UniProtKB/TrEMBL
InterPro CaCC_prot UniProtKB/TrEMBL
  Cl_channel_Ca UniProtKB/TrEMBL
  VWF_A UniProtKB/TrEMBL
  vWFA_dom_sf UniProtKB/TrEMBL
KEGG Report rno:308016 UniProtKB/TrEMBL
NCBI Gene 308016 ENTREZGENE
Pfam CLCA_N UniProtKB/TrEMBL
  VWA_2 UniProtKB/TrEMBL
PhenoGen Clca2 PhenoGen
PROSITE VWFA UniProtKB/TrEMBL
SMART VWA UniProtKB/TrEMBL
Superfamily-SCOP SSF53300 UniProtKB/TrEMBL
TIGRFAMs hCaCC UniProtKB/TrEMBL
UniProt D3ZVT7 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2010-11-11 Clca2  chloride channel accessory 2  Clca5  chloride channel calcium activated 5  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-03-03 Clca5  chloride channel calcium activated 5  Clca2_predicted  chloride channel, calcium activated, family member 2 (predicted)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2005-01-12 Clca2_predicted  chloride channel, calcium activated, family member 2 (predicted)      Symbol and Name status set to approved 70820 APPROVED