Calb2 (calbindin 2) - Rat Genome Database

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Gene: Calb2 (calbindin 2) Rattus norvegicus
Analyze
Symbol: Calb2
Name: calbindin 2
RGD ID: 620981
Description: Enables calcium ion binding activity. Predicted to be involved in regulation of long-term synaptic potentiation and regulation of presynaptic cytosolic calcium ion concentration. Located in several cellular components, including cuticular plate; stereocilium; and synaptic membrane. Orthologous to human CALB2 (calbindin 2); PARTICIPATES IN calcium/calcium-mediated signaling pathway; INTERACTS WITH (R)-lipoic acid; 2,3,7,8-tetrachlorodibenzodioxine; 2,3,7,8-Tetrachlorodibenzofuran.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: calretinin; CR; MGC105356
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
mRatBN7.21938,114,435 - 38,141,438 (-)NCBI
Rnor_6.0 Ensembl1941,482,728 - 41,509,658 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.01941,482,743 - 41,509,617 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.01952,310,641 - 52,337,700 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41940,023,072 - 40,051,150 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11940,027,952 - 40,056,031 (-)NCBI
Celera1937,512,226 - 37,538,062 (-)NCBICelera
Cytogenetic Map19q12NCBI
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
(R)-lipoic acid  (EXP)
1,2-dimethylhydrazine  (ISO)
17beta-estradiol  (ISO)
2,2',4,4',5,5'-hexachlorobiphenyl  (ISO)
2,2',5,5'-tetrachlorobiphenyl  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,ISO)
2,3,7,8-Tetrachlorodibenzofuran  (EXP)
2-hydroxypropanoic acid  (ISO)
3-chloropropane-1,2-diol  (EXP)
3-isobutyl-1-methyl-7H-xanthine  (ISO)
3-methylcholanthrene  (ISO)
5-fluorouracil  (ISO)
6-propyl-2-thiouracil  (EXP)
aflatoxin B1  (ISO)
ammonium chloride  (EXP)
amphetamine  (ISO)
arsane  (ISO)
arsenic atom  (ISO)
arsenous acid  (ISO)
asbestos  (ISO)
benzo[a]pyrene  (ISO)
bis(2-ethylhexyl) phthalate  (ISO)
bisphenol A  (EXP,ISO)
bisphenol F  (ISO)
Brodifacoum  (EXP)
butanal  (ISO)
Butylparaben  (ISO)
C60 fullerene  (EXP)
cadmium atom  (ISO)
carmustine  (ISO)
cefaloridine  (EXP)
copper(II) sulfate  (ISO)
crocidolite asbestos  (ISO)
cyclosporin A  (ISO)
cytarabine  (ISO)
DDE  (EXP)
DDT  (EXP)
dexamethasone  (ISO)
diarsenic trioxide  (ISO)
dorsomorphin  (ISO)
doxorubicin  (ISO)
ethanol  (ISO)
flutamide  (EXP)
hydroquinone  (ISO)
indometacin  (ISO)
ketamine  (EXP)
L-ascorbic acid  (EXP)
lead diacetate  (EXP)
lead(0)  (EXP,ISO)
lead(2+)  (EXP,ISO)
Licochalcone B  (ISO)
lipoic acid  (EXP)
methamphetamine  (EXP)
methylisothiazolinone  (ISO)
methylmercury chloride  (ISO)
methylparaben  (ISO)
N-Nitrosopyrrolidine  (ISO)
nickel atom  (ISO)
O-methyleugenol  (ISO)
oxaliplatin  (ISO)
panobinostat  (ISO)
PCB138  (EXP,ISO)
pentanal  (ISO)
picrotoxin  (EXP)
pirinixic acid  (EXP,ISO)
potassium dichromate  (ISO)
rac-lactic acid  (ISO)
raloxifene  (ISO)
rotenone  (ISO)
SB 431542  (ISO)
simvastatin  (EXP)
sodium arsenate  (ISO)
sodium arsenite  (ISO)
temozolomide  (ISO)
toluene  (EXP)
trichostatin A  (ISO)
triclosan  (ISO)
valproic acid  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

Molecular Function

Molecular Pathway Annotations     Click to see Annotation Detail View
References

Additional References at PubMed
PMID:1988053   PMID:7918640   PMID:12477932   PMID:12577320   PMID:12868005   PMID:14730585   PMID:15093134   PMID:15355314   PMID:15489334   PMID:17177263   PMID:17965879   PMID:18720478  
PMID:18769561   PMID:21080000   PMID:21394464   PMID:21835217   PMID:22037839   PMID:22221733   PMID:23273895   PMID:24134921   PMID:25730969   PMID:25813826  


Genomics

Candidate Gene Status
Calb2 is a candidate Gene for QTL Eau8
Comparative Map Data
Calb2
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21938,114,435 - 38,141,438 (-)NCBI
Rnor_6.0 Ensembl1941,482,728 - 41,509,658 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.01941,482,743 - 41,509,617 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.01952,310,641 - 52,337,700 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41940,023,072 - 40,051,150 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11940,027,952 - 40,056,031 (-)NCBI
Celera1937,512,226 - 37,538,062 (-)NCBICelera
Cytogenetic Map19q12NCBI
CALB2
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl1671,358,713 - 71,390,436 (+)EnsemblGRCh38hg38GRCh38
GRCh381671,358,723 - 71,390,438 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh371671,392,626 - 71,424,336 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 361669,950,127 - 69,981,842 (+)NCBINCBI36hg18NCBI36
Build 341669,950,126 - 69,981,836NCBI
Celera1655,708,128 - 55,740,202 (+)NCBI
Cytogenetic Map16q22.2NCBI
HuRef1657,160,840 - 57,186,546 (+)NCBIHuRef
HuRef1657,186,719 - 57,192,385 (+)NCBIHuRef
CHM1_11672,805,453 - 72,837,193 (+)NCBICHM1_1
Calb2
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm398110,869,158 - 110,894,844 (-)NCBIGRCm39mm39
GRCm39 Ensembl8110,864,134 - 110,894,842 (-)Ensembl
GRCm388110,142,526 - 110,168,212 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl8110,137,502 - 110,168,210 (-)EnsemblGRCm38mm10GRCm38
MGSCv378112,666,438 - 112,692,106 (-)NCBIGRCm37mm9NCBIm37
MGSCv368113,031,667 - 113,057,335 (-)NCBImm8
Celera8114,365,078 - 114,391,219 (-)NCBICelera
Cytogenetic Map8D3NCBI
Calb2
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554844,075,067 - 4,103,559 (+)EnsemblChiLan1.0
ChiLan1.0NW_0049554844,075,103 - 4,103,509 (+)NCBIChiLan1.0ChiLan1.0
CALB2
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.11671,195,770 - 71,227,937 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1671,195,770 - 71,227,937 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v01653,620,317 - 53,653,372 (-)NCBIMhudiblu_PPA_v0panPan3
CALB2
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1577,178,158 - 77,205,663 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl577,177,951 - 77,205,671 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha577,139,985 - 77,167,208 (+)NCBI
ROS_Cfam_1.0577,616,925 - 77,644,159 (+)NCBI
UMICH_Zoey_3.1577,437,354 - 77,464,585 (+)NCBI
UNSW_CanFamBas_1.0577,260,506 - 77,287,715 (+)NCBI
UU_Cfam_GSD_1.0577,759,356 - 77,786,581 (+)NCBI
Calb2
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440934937,217,095 - 37,244,688 (+)NCBI
SpeTri2.0NW_00493647522,344,416 - 22,372,015 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
CALB2
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl614,391,146 - 14,420,663 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1614,392,220 - 14,420,663 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2613,904,114 - 13,933,267 (+)NCBISscrofa10.2Sscrofa10.2susScr3
CALB2
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1554,503,635 - 54,538,304 (+)NCBI
ChlSab1.1 Ensembl554,504,082 - 54,538,441 (+)Ensembl
Vero_WHO_p1.0NW_02366604717,312,991 - 17,345,343 (+)NCBI
Calb2
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462474613,549,339 - 13,577,929 (+)NCBI

Position Markers
D19Rat71  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21938,130,095 - 38,130,307 (-)MAPPER
Rnor_6.01941,493,877 - 41,494,088NCBIRnor6.0
Rnor_5.01952,321,960 - 52,322,171UniSTSRnor5.0
RH 3.4 Map19437.4RGD
RH 3.4 Map19437.4UniSTS
RH 2.0 Map19481.8RGD
SHRSP x BN Map1927.8698RGD
Cytogenetic Map19q12UniSTS
X73985  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21938,114,703 - 38,114,871 (-)MAPPER
Rnor_6.01941,509,181 - 41,509,348NCBIRnor6.0
Rnor_5.01952,337,264 - 52,337,431UniSTSRnor5.0
RGSC_v3.41940,023,341 - 40,023,508UniSTSRGSC3.4
Celera1937,512,495 - 37,512,662UniSTS
Cytogenetic Map19q12UniSTS
RH138609  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21938,114,524 - 38,114,704 (-)MAPPER
Rnor_6.01941,509,348 - 41,509,527NCBIRnor6.0
Rnor_5.01952,337,431 - 52,337,610UniSTSRnor5.0
RGSC_v3.41940,023,162 - 40,023,341UniSTSRGSC3.4
Celera1937,512,316 - 37,512,495UniSTS
RH 3.4 Map19437.3UniSTS
Cytogenetic Map19q12UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
2317848Alcrsp21Alcohol response QTL 211.8999999761581420.05response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)19104464846044648Rat
61447Tcas1Tongue tumor susceptibility QTL 16.08tongue integrity trait (VT:0010553)squamous cell carcinoma of the tongue maximum tumor diameter (CMO:0001875)19195770746957707Rat
7247442Uae39Urinary albumin excretion QTL 39urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)19243296347217667Rat
724566Uae12Urinary albumin excretion QTL 125urine albumin amount (VT:0002871)urine albumin level (CMO:0000130)19243296362275575Rat
9589102Slep13Serum leptin concentration QTL 134.630.001blood leptin amount (VT:0005667)plasma leptin level (CMO:0000781)19370183548701835Rat
8694186Bw152Body weight QTL 1523.340.001body mass (VT:0001259)body weight gain (CMO:0000420)19370183548701835Rat
724565Tcas5Tongue tumor susceptibility QTL 510.04tongue integrity trait (VT:0010553)number of squamous cell tumors of the tongue with diameter greater than 3 mm (CMO:0001950)19500757143907843Rat
1331737Uae29Urinary albumin excretion QTL 295.5urine albumin amount (VT:0002871)urine albumin level (CMO:0000130)19650676160220581Rat
724518Uae19Urinary albumin excretion QTL 195.5urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)19807254547318201Rat
61423Cia14Collagen induced arthritis QTL 143joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)191130392747879277Rat
1331788Rf45Renal function QTL 452.818kidney blood vessel physiology trait (VT:0100012)absolute change in renal blood flow rate (CMO:0001168)191702800352538299Rat
1578764Stresp19Stress response QTL 193.60.001blood renin amount (VT:0003349)plasma renin activity level (CMO:0000116)191899398262275575Rat
7411549Bw130Body weight QTL 13050.001body mass (VT:0001259)body weight gain (CMO:0000420)191917749562275575Rat
2298478Eau8Experimental allergic uveoretinitis QTL 80.0163uvea integrity trait (VT:0010551)experimental autoimmune uveitis score (CMO:0001504)192140778762275575Rat
1549835Tcas7Tongue tumor susceptibility QTL 70.001tongue integrity trait (VT:0010553)squamous cell carcinoma of the head and neck tumor number (CMO:0001876)192445572643907843Rat
61350Bp32Blood pressure QTL 320.012arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)192481825762275575Rat
1354633Bw28Body weight QTL 286.04body mass (VT:0001259)body weight (CMO:0000012)193119430141686140Rat
1354600Salc2Saline consumption QTL 29.910.001drinking behavior trait (VT:0001422)saline drink intake rate (CMO:0001627)193119430141686140Rat
1354607Gmadr1Adrenal mass QTL 15.83adrenal gland mass (VT:0010420)both adrenal glands wet weight (CMO:0000164)193119430141686140Rat
724546Kidm3Kidney mass QTL 33.1kidney mass (VT:0002707)calculated kidney weight (CMO:0000160)193299439262275575Rat
1358200Insglur2Insulin/glucose ratio QTL 24.1blood glucose amount (VT:0000188)serum insulin level (CMO:0000358)193791679960220451Rat
1358200Insglur2Insulin/glucose ratio QTL 24.1blood glucose amount (VT:0000188)serum glucose level (CMO:0000543)193791679960220451Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:88
Count of miRNA genes:73
Interacting mature miRNAs:83
Transcripts:ENSRNOT00000022943
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.


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 72 19
Low 1 9 1 13 1 2 2 2 16 18 3 2
Below cutoff 26 25 21 6 21 6 6 12 4 3 6

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000022943   ⟹   ENSRNOP00000022943
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1941,482,728 - 41,509,658 (+)Ensembl
RefSeq Acc Id: NM_053988   ⟹   NP_446440
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21938,114,435 - 38,141,438 (-)NCBI
Rnor_6.01941,482,743 - 41,509,617 (+)NCBI
Rnor_5.01952,310,641 - 52,337,700 (+)NCBI
RGSC_v3.41940,023,072 - 40,051,150 (-)RGD
Celera1937,512,226 - 37,538,062 (-)RGD
Sequence:
Reference Sequences
RefSeq Acc Id: NP_446440   ⟸   NM_053988
- UniProtKB: P47728 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: ENSRNOP00000022943   ⟸   ENSRNOT00000022943
Protein Domains
EF-hand

Transcriptome

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

Promoters
RGD ID:13701129
Promoter ID:EPDNEW_R11653
Type:single initiation site
Name:Calb2_1
Description:calbindin 2
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_6.01941,482,726 - 41,482,786EPDNEW

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)
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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
LL/MavRrrc (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
LN/MavRrrc (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
M520/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
MHS/Gib (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
MNS/Gib (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
MR/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
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)
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
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)
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
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:620981 AgrOrtholog
Ensembl Genes ENSRNOG00000016977 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Protein ENSRNOP00000022943 ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript ENSRNOT00000022943 ENTREZGENE, UniProtKB/Swiss-Prot
IMAGE_CLONE IMAGE:7312595 IMAGE-MGC_LOAD
InterPro CALB2 UniProtKB/Swiss-Prot
  EF-hand-dom_pair UniProtKB/Swiss-Prot
  EF_Hand_1_Ca_BS UniProtKB/Swiss-Prot
  EF_hand_dom UniProtKB/Swiss-Prot
KEGG Report rno:117059 UniProtKB/Swiss-Prot
MGC_CLONE MGC:105356 IMAGE-MGC_LOAD
NCBI Gene 117059 ENTREZGENE
PANTHER PTHR19972:SF4 UniProtKB/Swiss-Prot
Pfam EF-hand_1 UniProtKB/Swiss-Prot
  EF-hand_7 UniProtKB/Swiss-Prot
PhenoGen Calb2 PhenoGen
PROSITE EF_HAND_1 UniProtKB/Swiss-Prot
  EF_HAND_2 UniProtKB/Swiss-Prot
SMART EFh UniProtKB/Swiss-Prot
Superfamily-SCOP SSF47473 UniProtKB/Swiss-Prot
UniProt CALB2_RAT UniProtKB/Swiss-Prot, ENTREZGENE


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2002-08-06 Calb2  calbindin 2      Symbol and Name status set to provisional 70820 PROVISIONAL