Iyd (iodotyrosine deiodinase) - Rat Genome Database

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Gene: Iyd (iodotyrosine deiodinase) Rattus norvegicus
Analyze
Symbol: Iyd
Name: iodotyrosine deiodinase
RGD ID: 1309288
Description: Predicted to have FMN binding activity and iodide peroxidase activity. Predicted to be involved in thyroid hormone metabolic process and tyrosine metabolic process. Predicted to localize to cytoplasmic vesicle membrane; integral component of plasma membrane; and nucleoplasm. Human ortholog(s) of this gene implicated in thyroid dyshormonogenesis 4. Orthologous to human IYD (iodotyrosine deiodinase); INTERACTS WITH (+)-schisandrin B; 1-naphthyl isothiocyanate; 2,3,7,8-tetrachlorodibenzodioxine.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: iodotyrosine dehalogenase 1; iodotyrosine deiodinase 1; IYD-1; LOC308129; MGC109018; RGD1309288; similar to RIKEN cDNA 0610009A07
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
mRatBN7.2140,003,999 - 40,019,323 (+)NCBI
Rnor_6.0 Ensembl140,086,470 - 40,101,840 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.0140,086,513 - 40,100,966 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.0141,435,347 - 41,449,800 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4134,244,640 - 34,259,649 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1134,247,584 - 34,262,592 (+)NCBI
Celera135,702,067 - 35,717,263 (+)NCBICelera
Cytogenetic Map1p11NCBI
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
(+)-schisandrin B  (EXP)
1,2-dinitrobenzene  (ISO)
1,4-bis(2-ethylhexyl) sulfosuccinate  (ISO)
1-monolauroylglycerol  (ISO)
1-naphthyl isothiocyanate  (EXP)
2,2',4,5'-Tetrabromodiphenyl ether  (ISO)
2,2'-Methylenebis(4-methyl-6-tert-butylphenol)  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,ISO)
2,4,5-trichlorophenol  (ISO)
2,4-di-tert-butylphenol  (ISO)
2,6-di-tert-butylphenol  (ISO)
3,3',4',5-tetrachlorosalicylanilide  (ISO)
3,3',5,5'-tetrabromobisphenol A  (ISO)
3-nitrotyrosine  (ISO)
4,5-dichloro-2-n-octyl-3(2H)-isothiazolone  (ISO)
4-hydroxyphenyl retinamide  (ISO)
4-nonylphenol  (ISO)
4-octylphenol  (ISO)
4-tert-Octylphenol  (ISO)
acetamide  (EXP)
acrylamide  (EXP)
aflatoxin B1  (ISO)
benzalkonium chloride  (ISO)
benzbromarone  (ISO)
benzo[a]pyrene  (ISO)
bisphenol A  (EXP)
Bisphenol A diglycidyl ether  (ISO)
bithionol  (ISO)
Brilliant Blue  (ISO)
bromophenol blue  (ISO)
calcitriol  (ISO)
captan  (ISO)
cetyltrimethylammonium ion  (ISO)
chlordecone  (ISO)
chlorhexidine  (ISO)
clomiphene  (ISO)
cyclosporin A  (ISO)
DDT  (ISO)
dibutyl phthalate  (ISO)
Dichlorophen  (ISO)
dicofol  (ISO)
dinocap  (ISO)
dioxygen  (ISO)
dodecylbenzenesulfonic acid  (ISO)
dodecyltrimethylammonium ion  (ISO)
endosulfan  (EXP)
eosin YS dye  (ISO)
erythrosin B  (ISO)
Fast green FCF  (ISO)
flusalan  (ISO)
flutamide  (EXP)
folpet  (ISO)
glafenine  (EXP)
hexadecanoic acid  (ISO)
linoleic acid  (ISO)
masoprocol  (ISO)
methyl linoleate  (ISO)
methylene blue  (ISO)
methyltrioctylammonium chloride  (ISO)
monoiodotyrosine  (ISO)
morin  (ISO)
NADP zwitterion  (ISO)
NADP(+)  (ISO)
nefazodone  (EXP)
nimesulide  (EXP)
nitrofurazone  (ISO)
O-methyleugenol  (ISO)
octyl gallate  (ISO)
oleic acid  (ISO)
p-tert-Amylphenol  (ISO)
paracetamol  (ISO)
perfluorodecanoic acid  (ISO)
perfluorooctane-1-sulfonic acid  (ISO)
perfluoroundecanoic acid  (ISO)
phthalaldehyde  (ISO)
rac-1-monolauroylglycerol  (ISO)
riboflavin  (ISO)
rose bengal  (ISO)
rotenone  (EXP)
Sirius red 4B  (ISO)
sodium arsenite  (ISO)
sodium dodecyl sulfate  (ISO)
sodium myristyl sulfate  (ISO)
tamoxifen  (ISO)
testosterone  (ISO)
Tetrachlorobisphenol A  (ISO)
tetrachloromethane  (EXP,ISO)
tetradecanoic acid  (ISO)
tribromosalicylanilide  (ISO)
triclosan  (ISO)
triflumizole  (ISO)
troglitazone  (ISO)
valproic acid  (ISO)
zoledronic acid  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component

Molecular Function

References

Additional References at PubMed
PMID:12477932   PMID:15289438   PMID:15489334   PMID:16316988   PMID:25395621   PMID:25850545  


Genomics

Comparative Map Data
Iyd
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2140,003,999 - 40,019,323 (+)NCBI
Rnor_6.0 Ensembl140,086,470 - 40,101,840 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.0140,086,513 - 40,100,966 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.0141,435,347 - 41,449,800 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4134,244,640 - 34,259,649 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1134,247,584 - 34,262,592 (+)NCBI
Celera135,702,067 - 35,717,263 (+)NCBICelera
Cytogenetic Map1p11NCBI
IYD
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl6150,368,892 - 150,405,969 (+)EnsemblGRCh38hg38GRCh38
GRCh386150,368,854 - 150,405,969 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh376150,690,148 - 150,727,105 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 366150,731,721 - 150,767,457 (+)NCBINCBI36hg18NCBI36
Build 346150,782,141 - 150,817,878NCBI
Celera6151,424,947 - 151,460,709 (+)NCBI
Cytogenetic Map6q25.1NCBI
HuRef6148,255,114 - 148,290,675 (+)NCBIHuRef
CHM1_16150,954,100 - 150,989,630 (+)NCBICHM1_1
Iyd
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39103,490,274 - 3,504,880 (+)NCBIGRCm39mm39
GRCm39 Ensembl103,490,240 - 3,504,877 (+)Ensembl
GRCm38103,540,274 - 3,554,880 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl103,540,240 - 3,554,877 (+)EnsemblGRCm38mm10GRCm38
MGSCv37106,791,664 - 6,806,262 (-)NCBIGRCm37mm9NCBIm37
MGSCv36106,791,664 - 6,806,262 (-)NCBImm8
Celera103,484,500 - 3,499,071 (+)NCBICelera
Cytogenetic Map10A1NCBI
Iyd
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495543911,033,302 - 11,060,150 (-)EnsemblChiLan1.0
ChiLan1.0NW_00495543910,998,797 - 11,060,078 (-)NCBIChiLan1.0ChiLan1.0
IYD
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.16152,886,367 - 152,922,152 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl6152,886,373 - 152,922,152 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v06148,178,638 - 148,216,122 (+)NCBIMhudiblu_PPA_v0panPan3
IYD
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1140,890,402 - 40,908,437 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl140,890,435 - 40,908,439 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha141,728,455 - 41,748,252 (+)NCBI
ROS_Cfam_1.0141,072,192 - 41,090,715 (+)NCBI
UMICH_Zoey_3.1140,947,672 - 40,967,446 (+)NCBI
UNSW_CanFamBas_1.0140,791,294 - 40,809,809 (+)NCBI
UU_Cfam_GSD_1.0141,295,459 - 41,313,980 (+)NCBI
Iyd
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024404946136,202,719 - 136,221,695 (+)NCBI
SpeTri2.0NW_0049364893,454,757 - 3,472,423 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
IYD
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl115,756,550 - 15,779,164 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1115,756,536 - 15,779,380 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2117,891,407 - 17,908,117 (-)NCBISscrofa10.2Sscrofa10.2susScr3
IYD
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11377,794,539 - 77,828,841 (+)NCBI
ChlSab1.1 Ensembl1377,795,079 - 77,822,379 (+)Ensembl
Vero_WHO_p1.0NW_02366604050,104,222 - 50,134,595 (+)NCBI
Iyd
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046247857,799,975 - 7,824,611 (-)NCBI

Position Markers
RH132943  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2140,018,919 - 40,019,124 (+)MAPPER
Rnor_6.0140,100,563 - 40,100,767NCBIRnor6.0
Rnor_5.0141,449,397 - 41,449,601UniSTSRnor5.0
RGSC_v3.4134,259,246 - 34,259,450UniSTSRGSC3.4
Celera135,716,860 - 35,717,064UniSTS
Cytogenetic Map1p11UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
738020Pia8Pristane induced arthritis QTL 84.7joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1164407321Rat
1578650Bmd6Bone mineral density QTL 612.2femur mineral mass (VT:0010011)total volumetric bone mineral density (CMO:0001728)125439343579402Rat
1578651Bmd7Bone mineral density QTL 714.2femur mineral mass (VT:0010011)cortical volumetric bone mineral density (CMO:0001730)125439343579402Rat
1578669Bss9Bone structure and strength QTL 96.3femur morphology trait (VT:0000559)bone trabecular cross-sectional area (CMO:0002311)125439343579402Rat
1554320Bmd1Bone mineral density QTL 112.20.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)125439386904217Rat
1600360Mcs16Mammary carcinoma susceptibility QTL 162.4mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)1186804543724576Rat
7421626Bp360Blood pressure QTL 3600.001arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)1457869349578693Rat
631688Hcas2Hepatocarcinoma susceptibility QTL 230.0001liver integrity trait (VT:0010547)liver tumorous lesion number (CMO:0001068)15655769122614963Rat
4889451Eae29Experimental allergic encephalomyelitis QTL 295.51nervous system integrity trait (VT:0010566)experimental autoimmune encephalomyelitis severity score (CMO:0001419)1565577285706974Rat
1300167Hrtrt2Heart rate QTL 24.35heart pumping trait (VT:2000009)heart rate (CMO:0000002)11131448975844121Rat
2313062Bmd73Bone mineral density QTL 733.90.0001tibia mineral mass (VT:1000283)cortical volumetric bone mineral density (CMO:0001730)11131448983657083Rat
2313065Bss67Bone structure and strength QTL 673.10.0001tibia area (VT:1000281)tibia total energy absorbed before break (CMO:0001736)11131448983657083Rat
2313069Bss68Bone structure and strength QTL 682.90.0001tibia size trait (VT:0100001)tibia total energy absorbed before break (CMO:0001736)11131448983657083Rat
2313075Bss66Bone structure and strength QTL 663.40.0001tibia length (VT:0004357)tibia length (CMO:0000450)11131448983657083Rat
2313077Bss69Bone structure and strength QTL 693.50.0001tibia strength trait (VT:1000284)bone polar moment of inertia (CMO:0001558)11131448983657083Rat
2313092Bmd72Bone mineral density QTL 722.50.0001tibia mineral mass (VT:1000283)total volumetric bone mineral density (CMO:0001728)11131448983657083Rat
2313097Bss70Bone structure and strength QTL 703.50.0001tibia strength trait (VT:1000284)tibia total energy absorbed before break (CMO:0001736)11131448983657083Rat
631508Sald1Serum aldosterone level QTL 13.7blood aldosterone amount (VT:0005346)serum aldosterone level (CMO:0000487)11249343957493439Rat
2302038Pia31Pristane induced arthritis QTL 315.50.001blood autoantibody amount (VT:0003725)serum immunoglobulin M-type rheumatoid factor level relative to an arbitrary reference serum (CMO:0002111)11362925158629251Rat
5684998Bss101Bone structure and strength QTL 1013.6tibia strength trait (VT:1000284)tibia ultimate force (CMO:0001734)11614314349547474Rat
5684999Bss102Bone structure and strength QTL 1025.50.00000072tibia strength trait (VT:1000284)tibia stiffness (CMO:0001735)11614314349547474Rat
634353Rends2Renal damage susceptibility QTL 20.05kidney blood vessel morphology trait (VT:0000530)organ lesion measurement (CMO:0000677)12034156058000154Rat
724520Bp145Blood pressure QTL 1452.10.0024arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)12107930566079305Rat
631494Bp95Blood pressure QTL 95400.0001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)12130082249454378Rat
1558642Prcr2Prostate cancer resistance QTL 24.3prostate integrity trait (VT:0010571)area of ventral prostate occupied by tumorous lesions to total ventral prostate area ratio (CMO:0000899)12181262344409802Rat
1357397Bw41Body weight QTL 414.190.0001body mass (VT:0001259)body weight (CMO:0000012)12340642849547474Rat
1357401Bw43Body weight QTL 433.75body mass (VT:0001259)body weight (CMO:0000012)12340642849547474Rat
1357400Bw62Body weight QTL624.05inguinal fat pad mass (VT:0010424)inguinal fat pad weight to body weight ratio (CMO:0001253)12340642868406428Rat
631495Bp96Blood pressure QTL 964.52arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)123406428108057505Rat
1358192Ept13Estrogen-induced pituitary tumorigenesis QTL 133.4pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)12429779978748000Rat
1358359Sradr1Stress Responsive Adrenal Weight QTL 14.74adrenal gland mass (VT:0010420)both adrenal glands wet weight (CMO:0000164)125951907130917265Rat
1331785Rf27Renal function QTL 274.643urine sodium amount (VT:0006274)urine sodium level (CMO:0000129)13148945479689689Rat
1354643Foco2Food consumption QTL 27.170.0001eating behavior trait (VT:0001431)food intake rate (CMO:0000427)13444911279449112Rat
1354599Bw29Body weight QTL 293.460.001body mass (VT:0001259)body weight (CMO:0000012)13444911279449112Rat
70225Bp58Blood pressure QTL 583.3arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)134993530173445086Rat
1300172Bp172Blood pressure QTL 1723.56arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)13537750894364229Rat
10059597Bp377Blood pressure QTL 3773.420.025arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)135377692217372257Rat
9589820Insglur3Insulin/glucose ratio QTL 310.750.001blood insulin amount (VT:0001560)calculated plasma insulin level (CMO:0002170)13585416780854167Rat
8552900Pigfal1Plasma insulin-like growth factor 1 level QTL 17.4blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)13585416780854167Rat
8552948Pigfal11Plasma insulin-like growth factor 1 level QTL 114.7blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)13585416780854167Rat
1331732Srn4Serum renin concentration QTL 44.467renin activity (VT:0005581)plasma renin activity level (CMO:0000116)13603316579689689Rat
1331792Rf29Renal function QTL 294.589urine potassium amount (VT:0010539)urine potassium level (CMO:0000128)13603316579689689Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:44
Count of miRNA genes:40
Interacting mature miRNAs:42
Transcripts:ENSRNOT00000021895
Prediction methods: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
Medium 21 21 21 21
Low 17 16 16 3 10 3 1
Below cutoff 2 26 15 4 8 4 4 4 51 15 9 4

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000021895   ⟹   ENSRNOP00000021893
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl140,086,470 - 40,101,840 (+)Ensembl
RefSeq Acc Id: NM_001025000   ⟹   NP_001020171
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2140,004,041 - 40,019,323 (+)NCBI
Rnor_6.0140,086,513 - 40,100,966 (+)NCBI
Rnor_5.0141,435,347 - 41,449,800 (+)NCBI
RGSC_v3.4134,244,640 - 34,259,649 (+)RGD
Celera135,702,067 - 35,717,263 (+)RGD
Sequence:
RefSeq Acc Id: XM_039110644   ⟹   XP_038966572
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2140,003,999 - 40,018,788 (+)NCBI
Protein Sequences
Protein RefSeqs NP_001020171 (Get FASTA)   NCBI Sequence Viewer  
  XP_038966572 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAH91241 (Get FASTA)   NCBI Sequence Viewer  
  EDL92877 (Get FASTA)   NCBI Sequence Viewer  
  Q5BK17 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: NP_001020171   ⟸   NM_001025000
- Peptide Label: precursor
- UniProtKB: Q5BK17 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: ENSRNOP00000021893   ⟸   ENSRNOT00000021895
RefSeq Acc Id: XP_038966572   ⟸   XM_039110644
- Peptide Label: isoform X1

Transcriptome

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

Promoters
RGD ID:13689582
Promoter ID:EPDNEW_R107
Type:multiple initiation site
Name:Iyd_1
Description:iodotyrosine deiodinase
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_6.0140,086,503 - 40,086,563EPDNEW

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)
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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
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)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SBN/Ygl (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBN/Ygl sequenced by MCW
SBN/Ygl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHR/NHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHRSP/Gcrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SR/JrHsd (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Harlan Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SR/JrHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/Jr (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/JrHsdMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SS/JrHsdMcwi (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WAG/Rij (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/Gcrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
WKY/NCrl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/NHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WN/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1309288 AgrOrtholog
Ensembl Genes ENSRNOG00000016286 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Protein ENSRNOP00000021893 ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript ENSRNOT00000021895 ENTREZGENE, UniProtKB/Swiss-Prot
Gene3D-CATH 3.40.109.10 UniProtKB/Swiss-Prot
IMAGE_CLONE IMAGE:7326298 IMAGE-MGC_LOAD
InterPro Nitroreductase UniProtKB/Swiss-Prot
  Nitroreductase-like UniProtKB/Swiss-Prot
KEGG Report rno:308129 UniProtKB/Swiss-Prot
MGC_CLONE MGC:109018 IMAGE-MGC_LOAD
NCBI Gene 308129 ENTREZGENE
Pfam Nitroreductase UniProtKB/Swiss-Prot
PhenoGen Iyd PhenoGen
Superfamily-SCOP SSF55469 UniProtKB/Swiss-Prot
UniProt IYD1_RAT UniProtKB/Swiss-Prot, ENTREZGENE


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2008-02-26 Iyd  iodotyrosine deiodinase  RGD1309288  similar to RIKEN cDNA 0610009A07  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2005-12-06 RGD1309288  similar to RIKEN cDNA 0610009A07  RGD1309288_predicted  similar to RIKEN cDNA 0610009A07 (predicted)  Symbol and Name updated 1559027 APPROVED
2005-01-20 RGD1309288_predicted  similar to RIKEN cDNA 0610009A07 (predicted)  LOC308129_predicted    Symbol and Name status set to approved 1331353 APPROVED
2005-01-12 LOC308129_predicted  similar to RIKEN cDNA 0610009A07 (predicted)      Symbol and Name status set to provisional 70820 PROVISIONAL