Pvalb (parvalbumin) - Rat Genome Database

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Gene: Pvalb (parvalbumin) Rattus norvegicus
Analyze
Symbol: Pvalb
Name: parvalbumin
RGD ID: 3457
Description: Enables calcium ion binding activity and identical protein binding activity. Involved in cochlea development. Located in several cellular components, including cuticular plate; neuronal cell body; and stereocilium. Part of protein-containing complex. Orthologous to human PVALB (parvalbumin); PARTICIPATES IN calcium/calcium-mediated signaling pathway; INTERACTS WITH (+)-pilocarpine; 6-propyl-2-thiouracil; acrylamide.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: PALB1; Parvalbumin (calcium binding protein); parvalbumin alpha; Pva
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Allele / Splice: Pvalbem1(flpo)Berke  
Genetic Models: LE-Pvalbem1(flpo)Berke/Rrrc
Is Marker For: Strains:   LE-Tg(Pvalb-icre)2Ottc  
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.27109,772,939 - 109,787,954 (-)NCBImRatBN7.2
mRatBN7.2 Ensembl7109,772,593 - 109,784,561 (-)Ensembl
Rnor_6.07119,428,657 - 119,443,674 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl7119,429,019 - 119,441,487 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.07119,420,581 - 119,435,235 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.47116,115,034 - 116,127,508 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.17116,148,899 - 116,163,894 (-)NCBI
Celera7106,113,144 - 106,125,613 (-)NCBICelera
RH 3.4 Map7812.5RGD
Cytogenetic Map7q34NCBI
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
(+)-pilocarpine  (EXP)
(S)-nicotine  (ISO)
1,1-dichloroethene  (ISO)
17beta-estradiol  (ISO)
2,2',4,4',5,5'-hexachlorobiphenyl  (ISO)
2,2',4,4'-Tetrabromodiphenyl ether  (ISO)
2,2',5,5'-tetrachlorobiphenyl  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (ISO)
6-propyl-2-thiouracil  (EXP)
acrylamide  (EXP)
ammonium chloride  (EXP)
amphetamine  (EXP)
apocynin  (ISO)
apomorphine  (EXP)
benzo[a]pyrene  (ISO)
bis(2-ethylhexyl) phthalate  (ISO)
bisphenol A  (EXP)
butanal  (ISO)
cannabidiol  (EXP)
carbon nanotube  (ISO)
Citreoviridin  (ISO)
clozapine  (EXP)
cocaine  (EXP,ISO)
copper atom  (EXP)
copper(0)  (EXP)
crocidolite asbestos  (ISO)
Cuprizon  (EXP)
dexamethasone  (ISO)
dichloroacetic acid  (ISO)
diethylstilbestrol  (EXP)
diuron  (EXP)
domoic acid  (ISO)
dorsomorphin  (ISO)
ethanol  (ISO)
genistein  (EXP)
graphite  (ISO)
haloperidol  (EXP)
ketamine  (ISO)
L-ascorbic acid  (EXP)
lead diacetate  (EXP)
lead(0)  (EXP)
lead(2+)  (EXP)
mancozeb  (ISO)
manganese atom  (ISO)
manganese(0)  (ISO)
manganese(II) chloride  (ISO)
mercury atom  (ISO)
mercury(0)  (ISO)
methylmercury chloride  (ISO)
morphine  (ISO)
N-methyl-4-phenylpyridinium  (EXP)
nicotine  (ISO)
PCB138  (ISO)
phencyclidine  (EXP)
phenylmercury acetate  (ISO)
picrotoxin  (EXP)
pioglitazone  (ISO)
poly(I:C)  (EXP)
propiconazole  (ISO)
rotenone  (EXP)
SB 431542  (ISO)
SKF 38393  (EXP)
sodium fluoride  (ISO)
Soman  (EXP)
testosterone enanthate  (ISO)
tetrachloroethene  (ISO)
tetrodotoxin  (EXP)
triptonide  (ISO)
valproic acid  (EXP,ISO)
vancomycin  (ISO)
vinclozolin  (EXP)

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component

Molecular Function

Molecular Pathway Annotations     Click to see Annotation Detail View
References

Additional References at PubMed
PMID:3707914   PMID:3856270   PMID:6754379   PMID:8289291   PMID:10036163   PMID:12115678   PMID:12149208   PMID:12477932   PMID:12577320   PMID:12653564   PMID:12716955   PMID:12974622  
PMID:14978725   PMID:15005610   PMID:15287728   PMID:15479642   PMID:16040009   PMID:16459206   PMID:17177263   PMID:17198372   PMID:17545482   PMID:17594127   PMID:17706751   PMID:18218708  
PMID:18637710   PMID:18789377   PMID:18977019   PMID:19004479   PMID:19168302   PMID:19397388   PMID:19885653   PMID:20882544   PMID:20883785   PMID:21411124   PMID:21561603   PMID:21679927  
PMID:21915341   PMID:21930674   PMID:21933624   PMID:22037839   PMID:22221733   PMID:22306612   PMID:23044920   PMID:23047329   PMID:23152631   PMID:23376485   PMID:23628656   PMID:23718120  
PMID:24657285   PMID:25553513   PMID:26650043   PMID:26698582   PMID:27432008   PMID:29107660   PMID:29788232   PMID:30176502   PMID:31804491  


Genomics

Comparative Map Data
Pvalb
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.27109,772,939 - 109,787,954 (-)NCBImRatBN7.2
mRatBN7.2 Ensembl7109,772,593 - 109,784,561 (-)Ensembl
Rnor_6.07119,428,657 - 119,443,674 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl7119,429,019 - 119,441,487 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.07119,420,581 - 119,435,235 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.47116,115,034 - 116,127,508 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.17116,148,899 - 116,163,894 (-)NCBI
Celera7106,113,144 - 106,125,613 (-)NCBICelera
RH 3.4 Map7812.5RGD
Cytogenetic Map7q34NCBI
PVALB
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl2236,800,684 - 36,819,479 (-)EnsemblGRCh38hg38GRCh38
GRCh382236,800,703 - 36,819,499 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh372237,196,747 - 37,215,543 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 362235,526,691 - 35,545,463 (-)NCBINCBI36hg18NCBI36
Build 342235,521,245 - 35,540,017NCBI
Celera2220,994,687 - 21,013,451 (-)NCBI
Cytogenetic Map22q12.3NCBI
HuRef2220,158,898 - 20,177,656 (-)NCBIHuRef
CHM1_12237,150,960 - 37,169,738 (-)NCBICHM1_1
Pvalb
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391578,075,312 - 78,090,600 (-)NCBIGRCm39mm39
GRCm39 Ensembl1578,075,314 - 78,090,600 (-)Ensembl
GRCm381578,191,112 - 78,206,400 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1578,191,114 - 78,206,400 (-)EnsemblGRCm38mm10GRCm38
MGSCv371578,021,547 - 78,036,781 (-)NCBIGRCm37mm9NCBIm37
MGSCv361578,018,372 - 78,033,606 (-)NCBImm8
Celera1579,652,042 - 79,667,286 (-)NCBICelera
Cytogenetic Map15E1NCBI
cM Map1536.93NCBI
Pvalb
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495541323,329,467 - 23,345,487 (-)EnsemblChiLan1.0
ChiLan1.0NW_00495541323,329,467 - 23,345,487 (-)NCBIChiLan1.0ChiLan1.0
PVALB
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.12235,551,448 - 35,568,316 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl2235,551,448 - 35,568,316 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v02217,715,109 - 17,731,587 (-)NCBIMhudiblu_PPA_v0panPan3
PVALB
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.11027,655,896 - 27,674,309 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl1027,655,905 - 27,707,332 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha1027,610,209 - 27,628,586 (+)NCBI
ROS_Cfam_1.01028,447,846 - 28,466,434 (+)NCBI
UMICH_Zoey_3.11028,169,344 - 28,187,929 (+)NCBI
UNSW_CanFamBas_1.01028,477,867 - 28,496,446 (+)NCBI
UU_Cfam_GSD_1.01028,656,677 - 28,675,084 (+)NCBI
Pvalb
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440494511,038,062 - 11,053,610 (+)NCBI
SpeTri2.0NW_0049364924,048,459 - 4,064,024 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
PVALB
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl510,955,491 - 10,973,289 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1510,953,559 - 10,973,300 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.258,553,390 - 8,573,107 (+)NCBISscrofa10.2Sscrofa10.2susScr3
PVALB
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11919,501,100 - 19,520,031 (-)NCBI
ChlSab1.11919,501,100 - 19,520,031 (-)NCBI
ChlSab1.1 Ensembl1919,501,293 - 19,517,340 (-)Ensembl
Vero_WHO_p1.0NW_023666045106,347,684 - 106,364,427 (+)NCBI
Pvalb
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462475210,969,746 - 10,985,437 (+)NCBI

Position Markers
RH94476  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.27109,788,050 - 109,788,237 (+)MAPPERmRatBN7.2
Rnor_6.07119,443,767 - 119,443,953NCBIRnor6.0
Rnor_5.07119,435,354 - 119,435,540UniSTSRnor5.0
RGSC_v3.47116,129,788 - 116,129,974UniSTSRGSC3.4
Celera7106,127,893 - 106,128,079UniSTS
RH 3.4 Map7812.5UniSTS
Cytogenetic Map7q34UniSTS
X59382  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.27109,773,294 - 109,773,429 (+)MAPPERmRatBN7.2
Rnor_6.07119,429,011 - 119,429,145NCBIRnor6.0
Rnor_5.07119,420,598 - 119,420,732UniSTSRnor5.0
RGSC_v3.47116,115,027 - 116,115,161UniSTSRGSC3.4
Celera7106,113,137 - 106,113,271UniSTS
Cytogenetic Map7q34UniSTS
RH135405  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.27109,773,134 - 109,773,328 (+)MAPPERmRatBN7.2
Rnor_6.07119,428,851 - 119,429,044NCBIRnor6.0
Rnor_5.07119,420,438 - 119,420,631UniSTSRnor5.0
RGSC_v3.47116,114,867 - 116,115,060UniSTSRGSC3.4
Celera7106,112,977 - 106,113,170UniSTS
RH 3.4 Map7813.1UniSTS
Cytogenetic Map7q34UniSTS


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
2306821Bp335Blood pressure QTL 3350.001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)7106571501135012528Rat
2316947Rf58Renal function QTL 587.8kidney glomerulus morphology trait (VT:0005325)index of glomerular damage (CMO:0001135)768938720113886318Rat
2316952Pur22Proteinuria QTL 225.2urine protein amount (VT:0005160)urine protein level (CMO:0000591)768938720113886318Rat
2316955Stl24Serum triglyceride level QTL 247.1blood triglyceride amount (VT:0002644)plasma triglyceride level (CMO:0000548)768938720113886318Rat
631687Hcas1Hepatocarcinoma susceptibility QTL 13.90.001liver integrity trait (VT:0010547)liver tumorous lesion volume to total liver volume ratio (CMO:0001082)791412594129807172Rat
2317052Aia17Adjuvant induced arthritis QTL 172.13joint integrity trait (VT:0010548)left rear ankle joint diameter (CMO:0002149)781737938126737938Rat
731174Uae23Urinary albumin excretion QTL 232.40.0042urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)7104603555135012528Rat
631504Cm27Cardiac mass QTL 273.45heart left ventricle mass (VT:0007031)heart left ventricle wet weight (CMO:0000071)744421311118198041Rat
634322Bw12Body weight QTL 120body mass (VT:0001259)body weight (CMO:0000012)783153392128153392Rat
634331Pia17Pristane induced arthritis QTL 174.7joint integrity trait (VT:0010548)arthritic paw count (CMO:0001460)773829340130221005Rat
7411654Foco25Food consumption QTL 259.30.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)775918751120918751Rat
7411607Foco15Food consumption QTL 150.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)775918751120918751Rat
1300179Kidm5Kidney mass QTL 53.51kidney mass (VT:0002707)left kidney wet weight (CMO:0000083)743747012135012528Rat
1331728Bp214Blood pressure QTL 2142.825arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)780221299124373579Rat
1331731Bp216Blood pressure QTL 2162.851arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)7102297359133492884Rat
1331746Kidm9Kidney mass QTL 93.934kidney mass (VT:0002707)right kidney wet weight (CMO:0000082)780221299112308525Rat
1331768Kidm10Kidney mass QTL 104.62096kidney mass (VT:0002707)left kidney wet weight (CMO:0000083)780221299125221299Rat
1357336Gluco6Glucose level QTL 63.4blood glucose amount (VT:0000188)serum glucose level (CMO:0000543)794811326116294265Rat
1357338Stl17Serum triglyceride level QTL 173.23blood triglyceride amount (VT:0002644)serum triglyceride level (CMO:0000360)769736356112729554Rat
1549899Stresp8Stress response QTL 84.370.0008stress-related behavior trait (VT:0010451)defensive burying duration (CMO:0001961)790482196135012528Rat
1558655Swd4Spike wave discharge measurement QTL 43.680.0002brain electrophysiology trait (VT:0010557)brain spike-and-wave discharge severity grade (CMO:0001988)786983365131983365Rat
1358891Bp265Blood pressure QTL 2652.21arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)783591953134666232Rat
1358914Bp266Blood pressure QTL 266arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)783591953134666232Rat
61357Bp38Blood pressure QTL 381.60.052arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)741333674119109060Rat
70173Niddm19Non-insulin dependent diabetes mellitus QTL 194.330.00005blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)764002457135012528Rat
71114Niddm14Non-insulin dependent diabetes mellitus QTL 144.5blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)784257275129257275Rat
70159Bp61Blood pressure QTL 610.0001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)7103146217116738842Rat
2298475Eau6Experimental allergic uveoretinitis QTL 60.0029uvea integrity trait (VT:0010551)experimental autoimmune uveitis score (CMO:0001504)784257275129257275Rat
2299163Iddm34Insulin dependent diabetes mellitus QTL 342.71blood glucose amount (VT:0000188)age at onset/diagnosis of type 1 diabetes mellitus (CMO:0001140)791281130135012528Rat
731176Glom5Glomerulus QTL 52.50.0035kidney glomerulus morphology trait (VT:0005325)count of superficial glomeruli not directly contacting the kidney surface (CMO:0001002)796670164135012528Rat
2313102Bmd79Bone mineral density QTL 792.30.0001tibia mineral mass (VT:1000283)total volumetric bone mineral density (CMO:0001728)794811085116738842Rat
631540Bw9Body weight QTL 94.5body mass (VT:0001259)body weight (CMO:0000012)769736226117455174Rat
634336Anxrr17Anxiety related response QTL 173.66locomotor behavior trait (VT:0001392)number of entries into a discrete space in an experimental apparatus (CMO:0000960)7924703115097879Rat


Related Rat Strains
The following Strains have been annotated to Pvalb


Genetic Models
This gene Pvalb is modified in the following models/strains
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:260
Count of miRNA genes:163
Interacting mature miRNAs:186
Transcripts:ENSRNOT00000067635
Prediction methods:Microtar, Miranda, Rnahybrid
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 8 11 4 8
Medium 2 1 1 22 2 6
Low 2 7 23 8 15 8 22 8 15 5
Below cutoff 17 6 6 2 6 10 3 15

Sequence

Nucleotide Sequences
RefSeq Transcripts NM_022499 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006241929 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039078454 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide AH002223 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AH002224 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BC126090 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CH473950 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ212120 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ214597 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ214667 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ214901 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ214909 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ215072 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ215101 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ215172 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ215177 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ215250 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ215353 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ215367 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ215388 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ215455 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ215472 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ215487 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ215608 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ215681 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ215732 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ215806 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ215845 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ216147 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ216186 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ216201 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ216260 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ216338 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ216339 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ216448 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ216459 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ216533 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ216659 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ216751 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ216789 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ216830 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ216843 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ216867 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ216872 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ216903 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ216906 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ216960 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ216981 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ217053 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ217064 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ217099 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ217132 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ217209 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ217210 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ217263 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ217278 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ217298 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ217358 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ217373 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ217384 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ217418 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ217424 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ217446 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ217489 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ217527 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ217562 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ217576 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ217645 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ217652 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ217677 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ217690 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ217743 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ217749 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ217760 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ217770 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ217787 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ217845 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ217858 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ217860 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ217861 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ217880 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ217886 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ217934 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ217966 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ217976 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ217991 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ218022 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ218035 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ218057 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ223582 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ223596 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ223603 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ223630 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ223664 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ223669 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ223695 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ223712 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ223723 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ223798 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ223803 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ223861 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ223863 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ223909 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ223941 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ223961 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ223988 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ223989 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ223990 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ224014 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ224025 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ224028 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ224037 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ224053 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ224059 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ224083 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ224113 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ224136 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ224173 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ224181 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ224187 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ224242 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ224248 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
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  FQ224417 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ224430 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ224435 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ224463 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ224483 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ224485 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ224488 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ224492 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ224510 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
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  FQ224600 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ224613 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ224634 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
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  FQ224673 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ224675 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ224722 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
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  FQ224767 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ224773 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ224778 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ224913 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  JACYVU010000186 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  M12725 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Reference Sequences
RefSeq Acc Id: ENSRNOT00000067635   ⟹   ENSRNOP00000058825
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl7109,772,593 - 109,784,561 (-)Ensembl
Rnor_6.0 Ensembl7119,429,019 - 119,441,487 (-)Ensembl
RefSeq Acc Id: NM_022499   ⟹   NP_071944
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.27109,773,302 - 109,785,771 (-)NCBI
Rnor_6.07119,429,018 - 119,441,487 (-)NCBI
Rnor_5.07119,420,581 - 119,435,235 (-)NCBI
RGSC_v3.47116,115,034 - 116,127,508 (-)RGD
Celera7106,113,144 - 106,125,613 (-)RGD
Sequence:
RefSeq Acc Id: XM_006241929   ⟹   XP_006241991
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.27109,772,939 - 109,787,954 (-)NCBI
Rnor_6.07119,428,657 - 119,443,674 (-)NCBI
Rnor_5.07119,420,581 - 119,435,235 (-)NCBI
Sequence:
RefSeq Acc Id: XM_039078454   ⟹   XP_038934382
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.27109,776,887 - 109,787,954 (-)NCBI
Reference Sequences
RefSeq Acc Id: NP_071944   ⟸   NM_022499
- UniProtKB: P02625 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: XP_006241991   ⟸   XM_006241929
- Peptide Label: isoform X2
- UniProtKB: P02625 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: ENSRNOP00000058825   ⟸   ENSRNOT00000067635
RefSeq Acc Id: XP_038934382   ⟸   XM_039078454
- 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:13695457
Promoter ID:EPDNEW_R5982
Type:multiple initiation site
Name:Pvalb_1
Description:parvalbumin
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_6.07119,441,505 - 119,441,565EPDNEW

Strain Variation

Strain Sequence Variants (Rnor 6.0)
ACI/EurMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
ACI/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)
ACI/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
ACI/N (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
ACI/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
BBDP/Wor (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
BN-Lx/CubMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/NHsdMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/NHsdMcwi (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/SsN (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/SsN (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
BUF/N (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BXH2/CubMcwi (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BXH3/CubMcwi (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
Buf/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
COP/CrCrl (MCW & UW)
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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)
DA/OlaHsd (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Envigo
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/DuCrl (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/N (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/NCrl (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/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
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
F344/Stm (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FHH/EurMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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
FXLE16/Stm (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FXLE18/Stm (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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/FarMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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
HXB10/IpcvMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB2/IpcvMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB20/IpcvMcwi (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB31/IpcvMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB4/IpcvMcwi (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LE/Stm (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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 (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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
LEXF10A/StmMcwi (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF11/Stm (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF1A/Stm (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF1C/Stm (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF2B/Stm (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF3/Stm (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF4/Stm (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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
LH/MavRrrcAek (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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
LL/MavRrrcAek (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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
LN/MavRrrcAek (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
M520/N (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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
M520/NRrrcMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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 (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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
MWF/Hsd (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
PVG/Seac (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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
SHR/OlalpcvMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SHRSP/A3NCrl (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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 (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Envigo
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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 (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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
WAG/RijCrl (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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 (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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 (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WKY/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
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 (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WN/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

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:3457 AgrOrtholog
Ensembl Genes ENSRNOG00000006471 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Protein ENSRNOP00000058825 ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript ENSRNOT00000067635 ENTREZGENE, UniProtKB/Swiss-Prot
IMAGE_CLONE IMAGE:7321065 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
  Parvalbumin UniProtKB/Swiss-Prot
KEGG Report rno:25269 UniProtKB/Swiss-Prot
MGC_CLONE MGC:156648 IMAGE-MGC_LOAD
NCBI Gene 25269 ENTREZGENE
PANTHER PTHR11653 UniProtKB/Swiss-Prot
Pfam EF-hand_7 UniProtKB/Swiss-Prot
PhenoGen Pvalb 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 P02625 ENTREZGENE, UniProtKB/Swiss-Prot
UniProt Secondary A0JN21 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2004-09-10 Pvalb  parvalbumin  Pva    Symbol updated 1299863 APPROVED
2003-04-09 Pva  parvalbumin  Pvalb  Parvalbumin (calcium binding protein)  Symbol and Name updated 629477 APPROVED
2002-06-10 Pvalb  Parvalbumin (calcium binding protein)      Symbol and Name status set to approved 70586 APPROVED