Ncald (neurocalcin delta) - Rat Genome Database
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Gene: Ncald (neurocalcin delta) Rattus norvegicus
Analyze
Symbol: Ncald
Name: neurocalcin delta
RGD ID: 1560287
Description: Exhibits actin binding activity and alpha-tubulin binding activity. Predicted to be involved in calcium-mediated signaling and regulation of systemic arterial blood pressure. Localizes to cytosol. Orthologous to human NCALD (neurocalcin delta); INTERACTS WITH 17alpha-ethynylestradiol; 17beta-estradiol; 2,3,7,8-tetrachlorodibenzodioxine.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: neurocalcin-delta
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
mRatBN7.2768,532,671 - 68,964,740 (-)NCBI
Rnor_6.0 Ensembl776,199,306 - 76,488,216 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.0776,199,305 - 76,632,847 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.0776,320,073 - 76,747,866 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4772,875,314 - 72,976,373 (-)NCBIRGSC3.4rn4RGSC3.4
Celera765,599,587 - 65,694,343 (-)NCBICelera
Cytogenetic Map7q22NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View
COVID-19  (ISO)

Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
1,2-dichloroethane  (ISO)
17alpha-ethynylestradiol  (EXP,ISO)
17beta-estradiol  (EXP)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,ISO)
2,3,7,8-Tetrachlorodibenzofuran  (EXP)
2,4-dinitrotoluene  (EXP)
2-methoxyethanol  (EXP)
2-methylcholine  (ISO)
4-hydroxyphenyl retinamide  (ISO)
7,12-dimethyltetraphene  (ISO)
aflatoxin B1  (ISO)
aflatoxin B2  (ISO)
all-trans-retinoic acid  (EXP,ISO)
antirheumatic drug  (ISO)
asbestos  (ISO)
atrazine  (ISO)
belinostat  (ISO)
benzo[a]pyrene  (ISO)
benzo[e]pyrene  (ISO)
bis(2-ethylhexyl) phthalate  (ISO)
bisphenol A  (EXP,ISO)
bromobenzene  (EXP)
cadmium sulfate  (ISO)
carbon nanotube  (ISO)
chloroprene  (ISO)
cocaine  (ISO)
cyclosporin A  (ISO)
cytarabine  (ISO)
dibutyl phthalate  (ISO)
diethylstilbestrol  (EXP)
diuron  (EXP)
dorsomorphin  (ISO)
endosulfan  (EXP)
entinostat  (ISO)
ethanol  (EXP,ISO)
flutamide  (EXP)
folic acid  (ISO)
genistein  (ISO)
gentamycin  (EXP)
hydroquinone O-beta-D-glucopyranoside  (ISO)
kojic acid  (ISO)
L-ascorbic acid  (ISO)
mercury dibromide  (ISO)
methamphetamine  (EXP)
methapyrilene  (ISO)
methyl methanesulfonate  (ISO)
methylmercury chloride  (ISO)
N-nitrosodiethylamine  (EXP)
nickel atom  (ISO)
p-chloromercuribenzoic acid  (ISO)
panobinostat  (ISO)
paracetamol  (EXP,ISO)
phenobarbital  (ISO)
phenylephrine  (EXP)
phenylmercury acetate  (ISO)
pirinixic acid  (ISO)
SB 431542  (ISO)
silicon dioxide  (ISO)
Soman  (EXP)
sunitinib  (ISO)
tetrachloromethane  (EXP)
thapsigargin  (ISO)
titanium dioxide  (ISO)
trichloroethene  (EXP)
trichostatin A  (ISO)
tunicamycin  (ISO)
valdecoxib  (EXP)
valproic acid  (ISO)
vinclozolin  (EXP)
vorinostat  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component
cytosol  (IDA)

Molecular Function

References

Additional References at PubMed
PMID:15489334   PMID:22871113   PMID:23088492   PMID:23376485  


Genomics

Comparative Map Data
Ncald
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2768,532,671 - 68,964,740 (-)NCBI
Rnor_6.0 Ensembl776,199,306 - 76,488,216 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.0776,199,305 - 76,632,847 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.0776,320,073 - 76,747,866 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4772,875,314 - 72,976,373 (-)NCBIRGSC3.4rn4RGSC3.4
Celera765,599,587 - 65,694,343 (-)NCBICelera
Cytogenetic Map7q22NCBI
NCALD
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl8101,686,542 - 102,124,907 (-)EnsemblGRCh38hg38GRCh38
GRCh388101,686,542 - 102,124,907 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh378102,698,770 - 103,137,135 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 368102,767,946 - 103,206,311 (-)NCBINCBI36hg18NCBI36
Build 348102,768,135 - 102,872,363NCBI
Celera898,883,681 - 99,322,037 (-)NCBI
Cytogenetic Map8q22.3NCBI
HuRef897,897,521 - 98,335,560 (-)NCBIHuRef
CHM1_18102,739,049 - 103,177,412 (-)NCBICHM1_1
Ncald
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391537,366,419 - 37,792,816 (-)NCBIGRCm39mm39
GRCm39 Ensembl1537,366,419 - 37,792,814 (-)Ensembl
GRCm381537,366,175 - 37,792,519 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1537,366,175 - 37,792,570 (-)EnsemblGRCm38mm10GRCm38
MGSCv371537,295,930 - 37,722,183 (-)NCBIGRCm37mm9NCBIm37
MGSCv361537,310,764 - 37,736,996 (-)NCBImm8
Celera1537,985,866 - 38,409,233 (-)NCBICelera
Cytogenetic Map15B3.1NCBI
cM Map1514.94NCBI
Ncald
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495541726,535,859 - 26,563,301 (-)EnsemblChiLan1.0
ChiLan1.0NW_00495541726,535,859 - 26,885,944 (-)NCBIChiLan1.0ChiLan1.0
NCALD
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.18100,488,400 - 100,931,079 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl8100,488,400 - 100,520,842 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v0898,324,885 - 98,767,804 (-)NCBIMhudiblu_PPA_v0panPan3
NCALD
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1 Ensembl133,369,570 - 3,512,566 (-)EnsemblCanFam3.1canFam3CanFam3.1
CanFam3.1133,367,036 - 3,678,505 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
Ncald
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
SpeTri2.0NW_00493647041,573,238 - 41,852,349 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
NCALD
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl434,924,383 - 35,367,430 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1434,924,261 - 35,369,393 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2437,798,498 - 38,264,852 (+)NCBISscrofa10.2Sscrofa10.2susScr3
NCALD
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1896,530,414 - 96,735,422 (-)NCBI
ChlSab1.1 Ensembl896,530,302 - 96,644,281 (-)Ensembl
Ncald
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462476318,918,781 - 19,191,221 (-)NCBI

Position Markers
RH132339  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.0776,199,328 - 76,199,516NCBIRnor6.0
Rnor_5.0776,320,096 - 76,320,284UniSTSRnor5.0
RGSC_v3.4772,875,337 - 72,875,525UniSTSRGSC3.4
Celera765,599,610 - 65,599,798UniSTS
RH 3.4 Map7639.8UniSTS
Cytogenetic Map7q22UniSTS
RH134791  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.01252,307,627 - 52,307,821NCBIRnor6.0
Rnor_6.0776,278,848 - 76,279,042NCBIRnor6.0
Rnor_5.01254,042,998 - 54,043,192UniSTSRnor5.0
Rnor_5.0776,398,810 - 76,399,004UniSTSRnor5.0
RGSC_v3.41246,394,273 - 46,394,467UniSTSRGSC3.4
RGSC_v3.4772,960,558 - 72,960,752UniSTSRGSC3.4
Celera1247,805,399 - 47,805,593UniSTS
Celera765,678,528 - 65,678,722UniSTS
Cytogenetic Map7q22UniSTS
Cytogenetic Map12q16UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
634336Anxrr17Anxiety related response QTL 173.66locomotor behavior trait (VT:0001392)number of entries into a discrete space in an experimental apparatus (CMO:0000960)72920071124838025Rat
1643004Pain2Pain QTL 21mechanical nociception trait (VT:0002734)self mutilation severity score (CMO:0002145)712328467106995532Rat
1300132Bp182Blood pressure QTL 1823.49arterial blood pressure trait (VT:2000000)blood pressure time series experimental set point of the baroreceptor response (CMO:0002593)72536563393155402Rat
1641885Alcrsp9Alcohol response QTL 9alcohol metabolism trait (VT:0015089)blood ethanol level (CMO:0000535)73138152976381529Rat
1549840Bss5Bone structure and strength QTL 59.8femur strength trait (VT:0010010)femur midshaft polar moment of inertia (CMO:0001669)73203505377035053Rat
61439Cia8Collagen induced arthritis QTL 85.1joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)73257294277572942Rat
10402855Bp379Blood pressure QTL 3790.21arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)73586772980867729Rat
1300127Srn1Serum renin concentration QTL 13.87blood renin amount (VT:0003349)plasma renin activity level (CMO:0000116)73586772993155402Rat
10755453Coatc12Coat color QTL 120coat/hair pigmentation trait (VT:0010463)pigmented ventral coat/hair area to total ventral coat/hair area ratio (CMO:0001812)73854770683547706Rat
631534Lnnr1Liver neoplastic nodule remodeling QTL 13.850.001liver integrity trait (VT:0010547)liver remodeling tumorous lesion number to liver total tumorous lesion number ratio (CMO:0001705)74087268285872682Rat
7411605Foco14Food consumption QTL 1424.10.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)74087268285872682Rat
631513Scl7Serum cholesterol level QTL 74.1blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)74530157390301573Rat
61357Bp38Blood pressure QTL 381.60.052arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)748118835128611831Rat
634326Hc3Hypercalciuria QTL 32.1urine calcium amount (VT:0002985)urine calcium excretion rate (CMO:0000763)75025210395252103Rat
631504Cm27Cardiac mass QTL 273.45heart left ventricle mass (VT:0007031)heart left ventricle wet weight (CMO:0000071)750704769128085642Rat
10053722Scort27Serum corticosterone level QTL 272.410.0083blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)75079381895793818Rat
1358361Sradr5Stress Responsive Adrenal Weight QTL 55.55adrenal gland mass (VT:0010420)both adrenal glands wet weight (CMO:0000164)751251919118477612Rat
1300179Kidm5Kidney mass QTL 53.51kidney mass (VT:0002707)left kidney wet weight (CMO:0000083)751251919145729302Rat
1300149Cm6Cardiac mass QTL 64.09heart mass (VT:0007028)heart left ventricle weight to body weight ratio (CMO:0000530)751252005111589099Rat
61428Scl3Serum cholesterol level QTL 33.2blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)75320034498200344Rat
738030Anxrr8Anxiety related response QTL 84.1exploratory behavior trait (VT:0010471)number of entries into a discrete space in an experimental apparatus (CMO:0000960)75425951299259512Rat
2316947Rf58Renal function QTL 587.8kidney glomerulus morphology trait (VT:0005325)index of glomerular damage (CMO:0001135)755072862123602998Rat
2316952Pur22Proteinuria QTL 225.2urine protein amount (VT:0005160)urine protein level (CMO:0000591)755072862123602998Rat
2316955Stl24Serum triglyceride level QTL 247.1blood triglyceride amount (VT:0002644)plasma triglyceride level (CMO:0000548)755072862123602998Rat
2300178Bmd54Bone mineral density QTL 545.30.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)755495689100495689Rat
2293644Bmd29Bone mineral density QTL 295.40.0001femur size trait (VT:1000369)femoral neck cross-sectional area (CMO:0001697)755495689100495689Rat
2293667Bss42Bone structure and strength QTL 427.250.0001lumbar vertebra size trait (VT:0010518)lumbar vertebra cross-sectional area (CMO:0001689)755495689100495689Rat
2293678Bss24Bone structure and strength QTL 246.710.0001femur morphology trait (VT:0000559)femur cross-sectional area (CMO:0001661)755495689100495689Rat
2293685Bmd21Bone mineral density QTL 214.20.0003femur mineral mass (VT:0010011)total volumetric bone mineral density (CMO:0001728)755495689100495689Rat
2293696Bmd32Bone mineral density QTL 325.10.0001femur strength trait (VT:0010010)femoral neck polar moment of inertia (CMO:0001670)755495689100495689Rat
2293707Bss32Bone structure and strength QTL 327.640.0001femur strength trait (VT:0010010)femur midshaft polar moment of inertia (CMO:0001669)755495689100495689Rat
1300151Bp181Blood pressure QTL 1813.36arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)761047589113228378Rat
2317035Aia16Adjuvant induced arthritis QTL 162.71joint integrity trait (VT:0010548)right rear ankle joint diameter (CMO:0002150)768518460113518460Rat
1576303Ept7Estrogen-induced pituitary tumorigenesis QTL 73.7pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)769399586111043530Rat
1559283Emca4Estrogen-induced mammary cancer QTL 43.7mammary gland integrity trait (VT:0010552)percentage of study population developing mammary tumors during a period of time (CMO:0000948)769399586111043530Rat
1298528Bp169Blood pressure QTL 1690.0001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)770421228115421228Rat
70173Niddm19Non-insulin dependent diabetes mellitus QTL 194.330.00005blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)771448715145729302Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:678
Count of miRNA genes:297
Interacting mature miRNAs:374
Transcripts:ENSRNOT00000064513
Prediction methods:Microtar, Miranda, 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 10 18 14 14 70 33 24 11
Low 33 39 27 19 27 8 11 4 2 17 8
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000064513   ⟹   ENSRNOP00000062447
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl776,199,306 - 76,294,663 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000080024   ⟹   ENSRNOP00000073597
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl776,199,311 - 76,488,216 (-)Ensembl
RefSeq Acc Id: NM_001024371   ⟹   NP_001019542
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2768,532,671 - 68,628,761 (-)NCBI
Rnor_6.0776,199,305 - 76,294,663 (-)NCBI
Rnor_5.0776,320,073 - 76,747,866 (-)NCBI
RGSC_v3.4772,875,314 - 72,976,373 (-)RGD
Celera765,599,587 - 65,694,343 (-)RGD
Sequence:
RefSeq Acc Id: XM_008765456   ⟹   XP_008763678
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2768,532,671 - 68,964,740 (-)NCBI
Rnor_6.0776,199,305 - 76,632,847 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017595065   ⟹   XP_017450554
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2768,532,671 - 68,964,496 (-)NCBI
Rnor_6.0776,199,305 - 76,632,600 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017595066   ⟹   XP_017450555
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0776,199,305 - 76,632,823 (-)NCBI
Sequence:
RefSeq Acc Id: XM_039079786   ⟹   XP_038935714
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2768,532,671 - 68,938,680 (-)NCBI
RefSeq Acc Id: XM_039079787   ⟹   XP_038935715
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2768,532,671 - 68,938,681 (-)NCBI
Reference Sequences
RefSeq Acc Id: NP_001019542   ⟸   NM_001024371
- UniProtKB: Q5PQN0 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: XP_008763678   ⟸   XM_008765456
- Peptide Label: isoform X1
- UniProtKB: Q5PQN0 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: XP_017450555   ⟸   XM_017595066
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: XP_017450554   ⟸   XM_017595065
- Peptide Label: isoform X1
- UniProtKB: Q5PQN0 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: ENSRNOP00000073597   ⟸   ENSRNOT00000080024
RefSeq Acc Id: ENSRNOP00000062447   ⟸   ENSRNOT00000064513
RefSeq Acc Id: XP_038935715   ⟸   XM_039079787
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038935714   ⟸   XM_039079786
- Peptide Label: isoform X1
Protein Domains
EF-hand

Transcriptome

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

Promoters
RGD ID:13695297
Promoter ID:EPDNEW_R5822
Type:multiple initiation site
Name:Ncald_1
Description:neurocalcin delta
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_6.0776,294,666 - 76,294,726EPDNEW

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)
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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
FHH/EurMcwi (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)
FHH/EurMcwi (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
FHL/EurMcwi (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)
FHL/EurMcwi (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
GH/OmrMcwi (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)
GK/Ox (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
LE/Stm (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
LEW/Crl (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
LEW/NCrlBR (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
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)
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
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)
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
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:1560287 AgrOrtholog
Ensembl Genes ENSRNOG00000042978 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Protein ENSRNOP00000062447 ENTREZGENE, UniProtKB/Swiss-Prot
  ENSRNOP00000073597 ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript ENSRNOT00000064513 ENTREZGENE, UniProtKB/Swiss-Prot
  ENSRNOT00000080024 UniProtKB/Swiss-Prot
IMAGE_CLONE IMAGE:7193019 IMAGE-MGC_LOAD
InterPro EF-hand-dom_pair UniProtKB/Swiss-Prot
  EF_Hand_1_Ca_BS UniProtKB/Swiss-Prot
  EF_hand_dom UniProtKB/Swiss-Prot
  Recoverin UniProtKB/Swiss-Prot
KEGG Report rno:553106 UniProtKB/Swiss-Prot
MGC_CLONE MGC:94703 IMAGE-MGC_LOAD
NCBI Gene 553106 ENTREZGENE
PANTHER PTHR23055 UniProtKB/Swiss-Prot
Pfam EF-hand_7 UniProtKB/Swiss-Prot
  EF-hand_8 UniProtKB/Swiss-Prot
PhenoGen Ncald 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 NCALD_RAT UniProtKB/Swiss-Prot, ENTREZGENE


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2006-02-09 Ncald  neurocalcin delta      Symbol and Name status set to provisional 70820 PROVISIONAL