Ddt (D-dopachrome tautomerase) - Rat Genome Database
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Gene: Ddt (D-dopachrome tautomerase) Rattus norvegicus
Analyze
Symbol: Ddt
Name: D-dopachrome tautomerase
RGD ID: 61923
Description: Predicted to have cytokine receptor binding activity; phenylpyruvate tautomerase activity; and protease binding activity. Predicted to be involved in negative regulation of macrophage chemotaxis; positive regulation of inflammatory response; and positive regulation of macromolecule metabolic process. Predicted to localize to extracellular space. Orthologous to human DDT (D-dopachrome tautomerase) and DDTL (D-dopachrome tautomerase like); INTERACTS WITH (+)-schisandrin B; 1,1,1-trichloro-2,2-bis(4-hydroxyphenyl)ethane; 2,2',4,4'-Tetrabromodiphenyl ether.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: D-dopachrome decarboxylase; dopachrome isomerase
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
mRatBN7.22012,884,216 - 12,886,687 (+)NCBI
Rnor_6.0 Ensembl2013,827,132 - 13,831,588 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.02013,827,153 - 13,829,624 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.02016,016,838 - 16,019,309 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.42013,591,785 - 13,594,256 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.12013,592,013 - 13,594,480 (-)NCBI
Celera2014,375,891 - 14,378,362 (+)NCBICelera
Cytogenetic Map20p12NCBI
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)
1,1,1-trichloro-2,2-bis(4-hydroxyphenyl)ethane  (EXP)
1,2-dimethylhydrazine  (ISO)
17beta-estradiol  (ISO)
2,2',4,4',5,5'-hexachlorobiphenyl  (ISO)
2,2',4,4'-Tetrabromodiphenyl ether  (EXP)
2,2',5,5'-tetrachlorobiphenyl  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,ISO)
3',5'-cyclic AMP  (EXP)
3-chloropropane-1,2-diol  (EXP)
3H-1,2-dithiole-3-thione  (EXP)
aflatoxin B1  (ISO)
all-trans-retinoic acid  (ISO)
ammonium chloride  (EXP)
arsenous acid  (ISO)
benzo[a]pyrene  (ISO)
bisphenol A  (EXP)
bromobenzene  (EXP)
cadmium dichloride  (EXP)
carbamazepine  (ISO)
chloropicrin  (ISO)
cisplatin  (ISO)
clobetasol  (ISO)
clofibrate  (ISO)
copper atom  (ISO)
copper(0)  (ISO)
corticosterone  (EXP)
cyclosporin A  (ISO)
diallyl trisulfide  (ISO)
diarsenic trioxide  (ISO)
diazinon  (EXP)
dibutyl phthalate  (EXP)
diclofenac  (ISO)
enzyme inhibitor  (ISO)
flavonoids  (EXP)
flutamide  (EXP)
folic acid  (ISO)
fructose  (EXP)
fumonisin B1  (ISO)
hydralazine  (ISO)
hydrazine  (EXP)
isotretinoin  (ISO)
lipopolysaccharide  (ISO)
lovastatin  (ISO)
methamphetamine  (EXP)
methyl methanesulfonate  (ISO)
N-nitrosomorpholine  (EXP)
O-methyleugenol  (ISO)
ochratoxin A  (EXP)
paracetamol  (ISO)
PCB138  (ISO)
perfluorododecanoic acid  (EXP)
pirinixic acid  (ISO)
progesterone  (EXP)
rotenone  (EXP)
sodium arsenite  (EXP)
sodium fluoride  (ISO)
tetrachloromethane  (EXP,ISO)
trichloroethene  (EXP)
tungsten  (ISO)
valproic acid  (ISO)
vancomycin  (ISO)
vinclozolin  (EXP)
warfarin  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

Molecular Function

References

Additional References at PubMed
PMID:8267597   PMID:19056867   PMID:21817065   PMID:23376485   PMID:23533145  


Genomics

Comparative Map Data
Ddt
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.22012,884,216 - 12,886,687 (+)NCBI
Rnor_6.0 Ensembl2013,827,132 - 13,831,588 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.02013,827,153 - 13,829,624 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.02016,016,838 - 16,019,309 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.42013,591,785 - 13,594,256 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.12013,592,013 - 13,594,480 (-)NCBI
Celera2014,375,891 - 14,378,362 (+)NCBICelera
Cytogenetic Map20p12NCBI
DDT
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl2223,971,378 - 23,980,469 (-)EnsemblGRCh38hg38GRCh38
GRCh38.p13 Ensembl2223,971,365 - 23,979,828 (-)EnsemblGRCh38hg38GRCh38
GRCh382223,971,370 - 23,979,828 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh372224,313,554 - 24,322,019 (-)NCBIGRCh37GRCh37hg19GRCh37
GRCh372224,313,559 - 24,322,019 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 362222,643,554 - 22,652,019 (-)NCBINCBI36hg18NCBI36
Build 342222,638,114 - 22,646,573NCBI
Celera228,114,132 - 8,122,585 (-)NCBI
Cytogenetic Map22q11.23NCBI
HuRef227,261,709 - 7,270,163 (-)NCBIHuRef
CHM1_12224,326,074 - 24,334,537 (-)NCBICHM1_1
Ddt
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391075,607,067 - 75,609,208 (-)NCBIGRCm39mm39
GRCm381075,771,233 - 75,773,374 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1075,771,230 - 75,773,414 (-)EnsemblGRCm38mm10GRCm38
MGSCv371075,233,978 - 75,236,119 (-)NCBIGRCm37mm9NCBIm37
MGSCv361075,214,949 - 75,217,090 (-)NCBImm8
Celera1076,816,014 - 76,818,155 (-)NCBICelera
Cytogenetic Map10C1NCBI
cM Map1038.58NCBI
Ddt
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0NW_00495545510,479,409 - 10,481,080 (-)NCBIChiLan1.0ChiLan1.0
LOC100991346
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.12222,814,869 - 22,815,793 (-)NCBIpanpan1.1PanPan1.1panPan2
DDT
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.12628,520,189 - 28,522,539 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
LOC101963449
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
SpeTri2.0NW_0049366191,043,006 - 1,045,054 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
DDT
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.11449,790,794 - 49,793,196 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21453,233,009 - 53,235,411 (-)NCBISscrofa10.2Sscrofa10.2susScr3
LOC103223037
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1197,077,812 - 7,081,065 (-)NCBI
Ddt
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462474712,473,181 - 12,474,898 (-)NCBI

Position Markers
RH128155  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.02013,825,260 - 13,825,452NCBIRnor6.0
Rnor_5.02016,014,945 - 16,015,137UniSTSRnor5.0
RGSC_v3.42013,595,957 - 13,596,149UniSTSRGSC3.4
Celera2014,373,976 - 14,374,168UniSTS
Cytogenetic Map20p12UniSTS
RH142321  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.02013,829,369 - 13,829,525NCBIRnor6.0
Rnor_5.02016,019,054 - 16,019,210UniSTSRnor5.0
RGSC_v3.42013,591,884 - 13,592,040UniSTSRGSC3.4
Celera2014,378,107 - 14,378,263UniSTS
Cytogenetic Map20p12UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1354642Despr15Despair related QTL 150.0027locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)20124652101Rat
1600382Edcs3Endometrial carcinoma susceptibility QTL33.50.003uterus morphology trait (VT:0001120)percentage of study population developing endometrioid carcinoma during a period of time (CMO:0001759)20125653396Rat
1641893Alcrsp7Alcohol response QTL 7response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)20126305996Rat
2317851Alcrsp22Alcohol response QTL 223.20.05response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)20126305996Rat
7387283Uae44Urinary albumin excretion QTL 440.1712urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)20127357423Rat
9590275Scort15Serum corticosterone level QTL 153.480.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)20128375393Rat
9589155Insul32Insulin level QTL 326.380.001blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)20128375393Rat
9590109Sffal8Serum free fatty acids level QTL 85.320.01blood free fatty acid amount (VT:0001553)plasma free fatty acids level (CMO:0000546)20128375393Rat
7411650Foco23Food consumption QTL 2320.70.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)20128375393Rat
8694189Bw153Body weight QTL 1533.130.001body mass (VT:0001259)body weight gain (CMO:0000420)20128375393Rat
6893685Bw111Body weight QTL 1112.70.004body mass (VT:0001259)body weight (CMO:0000012)20133300419Rat
9590252Scort12Serum corticosterone level QTL 1220.460.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)20137550487Rat
7411668Foco32Food consumption QTL 3280.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)20137550487Rat
2305926Iddm37Insulin dependent diabetes mellitus QTL 376blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)20201865447018654Rat
1641915Colcr9Colorectal carcinoma resistance QTL 92.970.0024intestine integrity trait (VT:0010554)benign colorectal tumor number (CMO:0001795)20299970747999707Rat
2317057Aia27Adjuvant induced arthritis QTL 272.83joint integrity trait (VT:0010548)right rear ankle joint diameter (CMO:0002150)20340211127968216Rat
1558640Prcs2Prostate cancer susceptibility QTL 23.3prostate integrity trait (VT:0010571)percentage of study population developing ventral prostate tumorous lesions during a period of time (CMO:0000943)20403911318872273Rat
4889857Pur27Proteinuria QTL 2712.20.001total urine protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)20403911318872273Rat
1598816Memor12Memory QTL 122.4exploratory behavior trait (VT:0010471)average horizontal distance in proximity to the target during voluntary locomotion in an experimental apparatus (CMO:0002674)20410895649108956Rat
61432Cia1Collagen induced arthritis QTL 1joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)20485547515050565Rat
70154Insul2Insulin level QTL 23.75blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)20587544818739210Rat
1581577Pur15Proteinuria QTL 154.380.0002total urine protein amount (VT:0000032)urine protein excretion rate (CMO:0000759)20865434118872273Rat
4889870Pur30Proteinuria QTL 30190.005total urine protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)20865434130991290Rat
631265Iresp1Immunoglobin response QTL18.3blood anti-double stranded DNA antibody amount (VT:0004762)serum anti-DNA antibody level (CMO:0001533)20965564214411641Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:113
Count of miRNA genes:95
Interacting mature miRNAs:97
Transcripts:ENSRNOT00000001664
Prediction methods:Microtar, Miranda, Rnahybrid, Targetscan
Result types:miRGate_prediction

The detailed report is available here: Full Report CSV TAB Printer

miRNA Target Status data imported from miRGate (http://mirgate.bioinfo.cnio.es/).
For more information about miRGate, see PMID:25858286 or access the full paper here.


Expression


RNA-SEQ Expression
High: > 1000 TPM value   Medium: Between 11 and 1000 TPM
Low: Between 0.5 and 10 TPM   Below Cutoff: < 0.5 TPM

alimentary part of gastrointestinal system circulatory system endocrine system exocrine system hemolymphoid system hepatobiliary system integumental system musculoskeletal system nervous system renal system reproductive system respiratory system appendage
High 2 2 2
Medium 3 43 55 39 19 39 8 11 74 35 41 11 8
Low
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000001664   ⟹   ENSRNOP00000001664
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl2013,827,132 - 13,829,626 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000093131   ⟹   ENSRNOP00000076125
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl2013,827,660 - 13,831,588 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000093597
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl2013,827,493 - 13,829,624 (+)Ensembl
RefSeq Acc Id: NM_024131   ⟹   NP_077045
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.22012,884,216 - 12,886,687 (+)NCBI
Rnor_6.02013,827,153 - 13,829,624 (+)NCBI
Rnor_5.02016,016,838 - 16,019,309 (+)NCBI
RGSC_v3.42013,591,785 - 13,594,256 (-)RGD
Celera2014,375,891 - 14,378,362 (+)RGD
Sequence:
Protein Sequences
Protein RefSeqs NP_077045 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein CAA85429 (Get FASTA)   NCBI Sequence Viewer  
  CCP38009 (Get FASTA)   NCBI Sequence Viewer  
  EDL97190 (Get FASTA)   NCBI Sequence Viewer  
  EDL97191 (Get FASTA)   NCBI Sequence Viewer  
  P80254 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: NP_077045   ⟸   NM_024131
- UniProtKB: P80254 (UniProtKB/Swiss-Prot),   A0A0F7RQJ6 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000076125   ⟸   ENSRNOT00000093131
RefSeq Acc Id: ENSRNOP00000001664   ⟸   ENSRNOT00000001664

Transcriptome

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

Promoters
RGD ID:13701535
Promoter ID:EPDNEW_R12059
Type:initiation region
Name:Ddt_1
Description:D-dopachrome tautomerase
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_6.02013,827,132 - 13,827,192EPDNEW

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)
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
M520/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
MHS/Gib (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
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:61923 AgrOrtholog
Ensembl Genes ENSRNOG00000001239 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000001664 ENTREZGENE, UniProtKB/Swiss-Prot
  ENSRNOP00000076125 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000001664 ENTREZGENE, UniProtKB/Swiss-Prot
  ENSRNOT00000093131 UniProtKB/TrEMBL
Gene3D-CATH 3.30.429.10 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
InterPro Macrophage_inhib_fac UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Macrophage_inhib_fac_CS UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Tautomerase/MIF_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:29318 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
NCBI Gene 29318 ENTREZGENE
PANTHER PTHR11954 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam MIF UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Ddt PhenoGen
PROSITE MIF UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP SSF55331 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
TIGR TC204729
UniProt A0A0F7RQJ6 ENTREZGENE, UniProtKB/TrEMBL
  A0A1W2Q637_RAT UniProtKB/TrEMBL
  DOPD_RAT UniProtKB/Swiss-Prot, ENTREZGENE


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2002-06-10 Ddt  D-dopachrome tautomerase      Name updated 70584 APPROVED

RGD Curation Notes
Note Type Note Reference
gene_expression expression is decreased 1.3 fold in SHR compared with WKY rats 1357414
gene_protein 118 amino acids 61570