Tpo (thyroid peroxidase) - Rat Genome Database
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Gene: Tpo (thyroid peroxidase) Rattus norvegicus
Analyze
Symbol: Tpo
Name: thyroid peroxidase
RGD ID: 3900
Description: Predicted to have iodide peroxidase activity. Involved in cellular response to nitric oxide and response to lipid. Localizes to cell surface and plasma membrane. Human ortholog(s) of this gene implicated in congenital hypothyroidism; glomerulonephritis; and thyroid dyshormonogenesis 2A. Orthologous to human TPO (thyroid peroxidase); PARTICIPATES IN thyroid hormone biosynthetic pathway; autoimmune thyroiditis pathway; cytokine mediated signaling pathway; INTERACTS WITH (S)-naringenin; 1,3-benzothiazole-2-thiol; 2,2',4,4'-Tetrabromodiphenyl ether.
Type: protein-coding
RefSeq Status: VALIDATED
Also known as: truncated thyroid peroxidase
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
mRatBN7.2646,698,402 - 46,768,199 (-)NCBI
Rnor_6.0 Ensembl649,021,044 - 49,089,855 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.0649,020,918 - 49,089,855 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.0657,702,091 - 57,770,914 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4647,954,848 - 48,025,740 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1647,957,973 - 48,028,866 (-)NCBI
Celera645,906,515 - 45,971,940 (-)NCBICelera
RH 3.4 Map6299.2RGD
Cytogenetic Map6q16NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
(S)-naringenin  (EXP)
1,3-benzothiazole-2-thiol  (EXP,ISO)
17beta-hydroxy-5alpha-androstan-3-one  (ISO)
2,2',4,4'-Tetrabromodiphenyl ether  (EXP)
2,4-Dihydroxybenzophenone  (EXP)
4,4'-diaminodiphenylmethane  (EXP)
4-Aminophenyl ether  (EXP)
5-azacytidine  (ISO)
6-propyl-2-thiouracil  (EXP,ISO)
acrylamide  (EXP)
all-trans-retinoic acid  (ISO)
amiodarone  (ISO)
amitrole  (EXP,ISO)
ammonium chloride  (EXP)
arsenous acid  (ISO)
asbestos  (ISO)
bathocuproine disulfonic acid  (EXP)
benzo[a]pyrene  (EXP,ISO)
benzo[e]pyrene  (ISO)
benzophenone  (ISO)
bis(2-chloroethyl) sulfide  (ISO)
bisphenol A  (EXP)
C60 fullerene  (EXP)
carbaryl  (ISO)
copper atom  (EXP)
copper(0)  (EXP)
cyclosporin A  (ISO)
daidzein  (EXP,ISO)
decabromodiphenyl ether  (EXP)
diarsenic trioxide  (ISO)
dibenz[a,h]anthracene  (ISO)
dibutyl phthalate  (ISO)
doxorubicin  (ISO)
efavirenz  (ISO)
Ethylenethiourea  (ISO)
genistein  (EXP,ISO)
glutathione  (ISO)
iodide salt  (ISO)
isoniazide  (EXP)
isoprenaline  (EXP)
mancozeb  (EXP)
methapyrilene  (ISO)
methimazole  (EXP,ISO)
minocycline  (EXP)
N-acetyl-L-cysteine  (EXP)
N-Vinyl-2-pyrrolidone  (EXP)
nevirapine  (ISO)
nitrogen dioxide  (ISO)
o-anisidine  (EXP)
oxymetholone  (ISO)
ozone  (ISO)
perfluorooctane-1-sulfonic acid  (ISO)
phenobarbital  (EXP)
pregnenolone 16alpha-carbonitrile  (EXP)
propanal  (ISO)
pyridine-2,3-diol  (EXP)
pyrrolidine dithiocarbamate  (EXP)
quercetin  (EXP)
resorcinol  (EXP,ISO)
resveratrol  (EXP)
salicylhydroxamic acid  (EXP)
silver atom  (ISO)
silver(0)  (ISO)
silver(1+) nitrate  (ISO)
sodium azide  (EXP)
sodium iodide  (ISO)
sodium perchlorate  (EXP)
Tesaglitazar  (EXP)
thyroxine  (EXP)
triclocarban  (EXP)
triclosan  (EXP,ISO)
triphenyl phosphate  (EXP)
troglitazone  (EXP)
valproic acid  (ISO)
vemurafenib  (ISO)
vinclozolin  (ISO)
vorinostat  (ISO)
zineb  (ISO)
ziram  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

Molecular Function

References

Additional References at PubMed
PMID:2233737   PMID:12387814   PMID:14651853   PMID:17379648   PMID:17709379   PMID:20629314   PMID:21149635   PMID:21619833   PMID:22664934   PMID:23064013   PMID:24625548   PMID:26610751  
PMID:31439949  


Genomics

Comparative Map Data
Tpo
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2646,698,402 - 46,768,199 (-)NCBI
Rnor_6.0 Ensembl649,021,044 - 49,089,855 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.0649,020,918 - 49,089,855 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.0657,702,091 - 57,770,914 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4647,954,848 - 48,025,740 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1647,957,973 - 48,028,866 (-)NCBI
Celera645,906,515 - 45,971,940 (-)NCBICelera
RH 3.4 Map6299.2RGD
Cytogenetic Map6q16NCBI
TPO
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl21,374,066 - 1,543,711 (+)EnsemblGRCh38hg38GRCh38
GRCh3821,413,288 - 1,543,673 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh3721,417,235 - 1,547,445 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 3621,396,242 - 1,525,502 (+)NCBINCBI36hg18NCBI36
Build 3421,396,241 - 1,525,502NCBI
Celera21,466,953 - 1,592,423 (+)NCBI
Cytogenetic Map2p25.3NCBI
HuRef21,408,795 - 1,531,941 (+)NCBIHuRef
CHM1_121,409,624 - 1,546,343 (+)NCBICHM1_1
Tpo
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391230,104,658 - 30,182,983 (-)NCBIGRCm39mm39
GRCm39 Ensembl1230,104,658 - 30,182,623 (-)Ensembl
GRCm381230,054,659 - 30,132,984 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1230,054,659 - 30,132,624 (-)EnsemblGRCm38mm10GRCm38
MGSCv371230,739,526 - 30,817,474 (-)NCBIGRCm37mm9NCBIm37
MGSCv361230,640,713 - 30,718,661 (-)NCBImm8
Celera1231,518,105 - 31,587,543 (-)NCBICelera
Cytogenetic Map12A2NCBI
cM Map1213.0NCBI
Tpo
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_004955487494,746 - 529,416 (-)EnsemblChiLan1.0
ChiLan1.0NW_004955487485,029 - 530,287 (-)NCBIChiLan1.0ChiLan1.0
TPO
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.12A1,334,608 - 1,493,308 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl2A1,335,556 - 1,493,055 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v02A1,364,083 - 1,491,284 (+)NCBIMhudiblu_PPA_v0panPan3
TPO
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1 Ensembl17773,790 - 810,043 (+)EnsemblCanFam3.1canFam3CanFam3.1
CanFam3.117773,790 - 810,044 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
Tpo
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
SpeTri2.0NW_004936532391,181 - 435,132 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
TPO
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl3132,384,583 - 132,408,943 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.13132,384,677 - 132,409,750 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.23141,795,655 - 141,820,693 (-)NCBISscrofa10.2Sscrofa10.2susScr3
TPO
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.114106,148,214 - 106,255,442 (-)NCBI
ChlSab1.1 Ensembl14106,146,946 - 106,255,298 (-)Ensembl
Tpo
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046248461,934,084 - 1,962,637 (-)NCBI

Position Markers
RH94606  
Rat AssemblyChrPosition (strand)SourceJBrowse
RH 3.4 Map6299.2UniSTS
Cytogenetic Map6q16UniSTS
Tpo  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.0649,061,147 - 49,062,630NCBIRnor6.0
Rnor_5.0657,742,206 - 57,743,689UniSTSRnor5.0
RGSC_v3.4647,997,031 - 47,998,514UniSTSRGSC3.4
Celera645,943,229 - 45,944,712UniSTS
Cytogenetic Map6q16UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
2301972Bp325Blood pressure QTL 3254.8arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)6175623393Rat
1354664Slep2Serum leptin concentration QTL 24.49blood leptin amount (VT:0005667)serum leptin level (CMO:0000780)6112039375023446Rat
1576309Emca7Estrogen-induced mammary cancer QTL 74mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)62537030111715717Rat
1578665Bss16Bone structure and strength QTL 164.4femur morphology trait (VT:0000559)bone trabecular cross-sectional area (CMO:0002311)6616172276002731Rat
1578668Bmd14Bone mineral density QTL 143.8femur mineral mass (VT:0010011)total volumetric bone mineral density (CMO:0001728)6616172276002731Rat
4145119Mcs25Mammary carcinoma susceptibility QTL 250.0001mammary gland integrity trait (VT:0010552)ratio of deaths to total study population during a period of time (CMO:0001023)67009971115379601Rat
634322Bw12Body weight QTL 120body mass (VT:0001259)body weight (CMO:0000012)71017386255173862Rat
1300164Rf15Renal function QTL 153.12renal blood flow trait (VT:2000006)absolute change in renal blood flow rate (CMO:0001168)61312295857516539Rat
10401812Kidm54Kidney mass QTL 54kidney mass (VT:0002707)both kidneys wet weight (CMO:0000085)61681010761810107Rat
10401800Kidm49Kidney mass QTL 49kidney mass (VT:0002707)both kidneys wet weight (CMO:0000085)61681010761810107Rat
8552910Pigfal5Plasma insulin-like growth factor 1 level QTL 54.3blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)61941788764417887Rat
1641898Colcr4Colorectal carcinoma resistance QTL43.710.0007intestine integrity trait (VT:0010554)well differentiated malignant colorectal tumor surface area measurement (CMO:0002077)62151530265784818Rat
2293839Kiddil2Kidney dilation QTL 24.8kidney pelvis morphology trait (VT:0004194)hydronephrosis severity score (CMO:0001208)62204285484763421Rat
2293841Kiddil4Kidney dilation QTL 44.4kidney pelvis morphology trait (VT:0004194)hydronephrosis severity score (CMO:0001208)62204285484763421Rat
8693632Alc27Alcohol consumption QTL 272.20.791drinking behavior trait (VT:0001422)calculated ethanol drink intake rate (CMO:0001615)63425776653855198Rat
1300143Rf14Renal function QTL 142.92renal blood flow trait (VT:2000006)absolute change in renal blood flow rate (CMO:0001168)63436743680490628Rat
1331779Rf38Renal function QTL 382.876kidney blood vessel physiology trait (VT:0100012)absolute change in renal vascular resistance (CMO:0001900)63499565675623393Rat
634318Bw118Body weight QTL 1183.55abdominal fat pad mass (VT:1000711)abdominal fat pad weight (CMO:0000088)63626028860606186Rat
6893340Cm77Cardiac mass QTL 770.260.57heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)63626028884763275Rat
1354632Scl29Serum cholesterol level QTL 293.74blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)63760898075023446Rat
634307Bp141Blood pressure QTL 1414arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)63810630883106308Rat
70199Coreg1Compensatory renal growth QTL 111.8kidney mass (VT:0002707)compensatory renal growth score (CMO:0001894)63819641260606431Rat
9590290Uminl2Urine mineral level QTL 23.960.001urine mineral amount (VT:0015086)urine electrolyte level (CMO:0000593)64167904686679046Rat
9590306Scort18Serum corticosterone level QTL 182.880.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)64167904686679046Rat
9590140Scort4Serum corticosterone level QTL 414.490.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)64167904686679046Rat
634330Pia16Pristane induced arthritis QTL 163.9joint integrity trait (VT:0010548)arthritic paw count (CMO:0001460)648432758108268790Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:43
Count of miRNA genes:38
Interacting mature miRNAs:43
Transcripts:ENSRNOT00000006526
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

circulatory system endocrine system integumental system musculoskeletal system reproductive system respiratory system appendage
High
Medium
Low 5
Below cutoff 2 1 1 1 11 7 1

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000006526   ⟹   ENSRNOP00000006526
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl649,021,044 - 49,089,855 (-)Ensembl
RefSeq Acc Id: NM_019353   ⟹   NP_062226
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2646,698,402 - 46,768,199 (-)NCBI
Rnor_6.0649,021,032 - 49,089,855 (-)NCBI
Rnor_5.0657,702,091 - 57,770,914 (-)NCBI
RGSC_v3.4647,954,848 - 48,025,740 (-)RGD
Celera645,906,515 - 45,971,940 (-)NCBI
Sequence:
RefSeq Acc Id: XM_008764607   ⟹   XP_008762829
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0649,039,247 - 49,089,159 (-)NCBI
Sequence:
RefSeq Acc Id: XM_008764608   ⟹   XP_008762830
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0649,020,918 - 49,089,849 (-)NCBI
Sequence:
Protein Sequences
Protein RefSeqs NP_062226 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAA42250 (Get FASTA)   NCBI Sequence Viewer  
  AAA42265 (Get FASTA)   NCBI Sequence Viewer  
  CAA35257 (Get FASTA)   NCBI Sequence Viewer  
  EDM03234 (Get FASTA)   NCBI Sequence Viewer  
  P14650 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: NP_062226   ⟸   NM_019353
- Peptide Label: precursor
- UniProtKB: F1LN48 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_008762830   ⟸   XM_008764608
- Peptide Label: isoform X2
- Sequence:
RefSeq Acc Id: XP_008762829   ⟸   XM_008764607
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: ENSRNOP00000006526   ⟸   ENSRNOT00000006526
Protein Domains
EGF-like   Sushi

Transcriptome

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


Strain Variation

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


Assembly: Rnor_5.0

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
6 57724179 57724180 C T snv ACI/EurMcwi (MCW), ZFDM (KyushuU), FHH/EurMcwi (MCW), FHL/EurMcwi (MCW), SBN/Ygl (MCW), ACI/N (KNAW), ACI/EurMcwi (KNAW), BBDP/WorN (KNAW), SBN/Ygl (KNAW), F344/NRrrc (Illumina) (KNAW), DA/BklArbNsi (KNAW), F344/NRrrc (SOLiD) (KNAW), F344/NCrl (KNAW), F344/NHsd (KNAW), FHH/EurMcwi (KNAW), FHL/EurMcwi (KNAW), LE/Stm (Illumina) (KNAW), LE/Stm (SOLiD) (KNAW), LEW/Crl (KNAW), LEW/NCrl (KNAW), M520/N (KNAW), MNS/Gib (KNAW), WN/N (KNAW), LE/OrlBarth (UDEL), Crl:SD (UDEL), NIG-III/Hok (KyushuU), F344/DuCrlCrlj (KyushuU), LE/Stm (KyushuU), F344/NSlc (KyushuU), RCS/Kyo (KyushuU), F344/Stm (KyushuU), LEC/Tj (KyushuU), F344/Jcl (KyushuU), BDIX/NemOda (KyushuU), BDIX.Cg-Tal/NemOda (KyushuU), KFRS3B/Kyo (KyushuU), COP/CrCrl (MCW & UW)


Assembly: Rnor_6.0

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
6 49039505 49039506 G A snv LEW/NCrlBR (RGD), WN/N (MCW), F344/NRrrc (MCW), LEW/Crl (RGD), SBN/Ygl (RGD), LE/Stm (RGD), MNS/Gib (RGD), FHH/EurMcwi (RGD), F344/NCrl (RGD), FHH/EurMcwi (MCW), ACI/N (MCW), BBDP/Wor (RGD), ACI/EurMcwi (RGD), ACI/EurMcwi (MCW), SBN/Ygl (MCW), FHL/EurMcwi (RGD), FHL/EurMcwi (MCW), COP/CrCrl (MCW & UW), M520/N (MCW)
6 49043120 49043121 C T snv LEW/NCrlBR (RGD), LEW/Crl (RGD), LE/Stm (RGD), FHH/EurMcwi (RGD), F344/NCrl (RGD), BBDP/Wor (RGD), ACI/EurMcwi (RGD), FHL/EurMcwi (RGD), WN/N (MCW), M520/N (MCW), F344/NRrrc (MCW), ACI/N (MCW), SBN/Ygl (MCW), FHL/EurMcwi (MCW), FHH/EurMcwi (MCW), COP/CrCrl (MCW & UW), ACI/EurMcwi (MCW), MNS/Gib (RGD), SBN/Ygl (RGD)
6 49074225 49074226 G A snv Buf/N (MCW)


Assembly: RGSC_v3.4

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
6 47978928 47978929 C T snv FHH/EurMcwi (MDC), DA/BklArbNsi (ICAHN), F344/NRrrc (KNAW), LE/Stm (KNAW), M520/N (KNAW), WN/N (KNAW), ACI/EurMcwi (MCW), FHH/EurMcwi (MCW), FHL/EurMcwi (MCW), COP/CrCrl (MCW & UW), ACI/EurMcwi (ICL), BBDP/WorN (ICL), F344/NCrl (ICL), LE/Stm (ICL), FHH/EurMcwi (ICL), FHL/EurMcwi (ICL), LEW/Crl (ICL), LEW/NCrl (ICL), MNS/Gib (ICL), SBN/Ygl (ICL), LCR/1Mco (UMich), LCR/2Mco (UMich), F344/NHsd (ICAHN), ACI/N (KNAW)


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:3900 AgrOrtholog
Ensembl Genes ENSRNOG00000004646 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000006526 ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000006526 ENTREZGENE, UniProtKB/TrEMBL
Gene3D-CATH 1.10.640.10 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
InterPro EGF-like_Ca-bd_dom UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  EGF-like_dom UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  EGF-type_Asp/Asn_hydroxyl_site UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  EGF_Ca-bd_CS UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Haem_peroxidase_animal UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Haem_peroxidase_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Haem_peroxidase_sf_animal UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Sushi/SCR/CCP_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Sushi_SCR_CCP_dom UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  TPO UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:54314 UniProtKB/TrEMBL
NCBI Gene 54314 ENTREZGENE
PANTHER PTHR11475:SF60 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam An_peroxidase UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  EGF_CA UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Sushi UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Tpo PhenoGen
PRINTS ANPEROXIDASE UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PROSITE ASX_HYDROXYL UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  EGF_2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  EGF_3 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  EGF_CA UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PEROXIDASE_1 UniProtKB/Swiss-Prot
  PEROXIDASE_3 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SUSHI UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
SMART CCP UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  EGF UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  EGF_CA UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP SSF48113 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SSF57535 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt F1LN48 ENTREZGENE, UniProtKB/TrEMBL
  P14650 ENTREZGENE, UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2002-06-10 Tpo  Thyroid peroxidase      Symbol and Name status set to approved 70586 APPROVED