Ubd (ubiquitin D) - Rat Genome Database
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Gene: Ubd (ubiquitin D) Rattus norvegicus
Analyze
Symbol: Ubd
Name: ubiquitin D
RGD ID: 69418
Description: Predicted to have proteasome binding activity. Involved in response to organonitrogen compound. Predicted to localize to aggresome; cytoplasm; and nuclear lumen. Orthologous to human UBD (ubiquitin D); INTERACTS WITH (+)-schisandrin B; 1,3-dinitrobenzene; 1-chloro-2,4-dinitrobenzene.
Type: protein-coding
RefSeq Status: VALIDATED
Also known as: diubiquitin; ubiquitin-like protein FAT10
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Alliance Genes
More Info more info ...
Latest Assembly: Rnor_6.0 - RGSC Genome Assembly v6.0
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2201,385,487 - 1,387,438 (-)NCBI
Rnor_6.0 Ensembl201,876,173 - 1,897,814 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.0201,876,175 - 1,878,126 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.0203,917,777 - 3,919,728 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4201,475,944 - 1,477,895 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1201,475,953 - 1,477,895 (-)NCBI
Celera202,096,127 - 2,098,078 (-)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)
1,2-dimethylhydrazine  (ISO)
1,3-dinitrobenzene  (EXP)
1-chloro-2,4-dinitrobenzene  (EXP)
1-naphthyl isothiocyanate  (EXP)
17beta-estradiol  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (ISO)
2,4,6-trinitrobenzenesulfonic acid  (ISO)
3,4-dichloroaniline  (EXP)
3,4-methylenedioxymethamphetamine  (ISO)
3,5-diethoxycarbonyl-1,4-dihydrocollidine  (ISO)
3,7-dihydropurine-6-thione  (EXP)
4,4'-diaminodiphenylmethane  (EXP)
4-(ethoxymethylene)-2-phenyloxazol-5-one  (EXP)
4-hydroxyphenyl retinamide  (ISO)
7,12-dimethyltetraphene  (EXP)
acrylamide  (EXP)
aflatoxin B1  (EXP,ISO)
all-trans-retinoic acid  (ISO)
ammonium chloride  (EXP)
amphetamine  (EXP)
antirheumatic drug  (ISO)
arsane  (ISO)
arsenic atom  (ISO)
azathioprine  (ISO)
benzo[a]pyrene  (ISO)
benzo[a]pyrene diol epoxide I  (ISO)
beta-naphthoflavone  (EXP)
bisphenol A  (EXP,ISO)
bromobenzene  (EXP)
Butylparaben  (ISO)
cadmium dichloride  (EXP)
carbon nanotube  (ISO)
cefaloridine  (EXP)
chlorohydrocarbon  (EXP)
cholesterol  (ISO)
choline  (ISO)
cisplatin  (ISO)
clofibrate  (EXP)
copper(II) sulfate  (ISO)
cyclophosphamide  (ISO)
cyclosporin A  (ISO)
dibenz[a,h]anthracene  (ISO)
dibenzo[a,l]pyrene  (ISO)
dicrotophos  (ISO)
diethyl maleate  (EXP)
diethylstilbestrol  (EXP)
dimethylarsinic acid  (EXP)
endosulfan  (EXP)
ethanol  (ISO)
flutamide  (EXP)
folic acid  (ISO)
gadodiamide hydrate  (ISO)
Genipin  (ISO)
glycidol  (EXP)
GW 4064  (ISO)
indole-3-methanol  (EXP)
irinotecan  (EXP)
iron(III) nitrilotriacetate  (EXP)
L-methionine  (ISO)
leflunomide  (EXP)
lipopolysaccharide  (ISO)
manganese(II) chloride  (EXP)
mercaptopurine  (EXP)
methotrexate  (ISO)
methylmercury chloride  (EXP)
methylparaben  (ISO)
N-methyl-4-phenylpyridinium  (EXP)
N-nitrosodiethylamine  (EXP,ISO)
N-nitrosodimethylamine  (ISO)
naphthalene  (EXP)
nickel sulfate  (ISO)
O-methyleugenol  (EXP)
ochratoxin A  (EXP)
oxaliplatin  (EXP)
paracetamol  (EXP,ISO)
perfluorooctanoic acid  (EXP)
phenobarbital  (ISO)
phenylmercury acetate  (ISO)
pirinixic acid  (ISO)
potassium bromate  (EXP)
progesterone  (ISO)
promethazine  (EXP)
propiconazole  (ISO)
purine-6-thiol  (EXP)
quercetin  (ISO)
quinolin-8-ol  (ISO)
S-adenosyl-L-methioninate  (ISO)
S-adenosyl-L-methionine  (ISO)
silicon dioxide  (EXP,ISO)
silver atom  (ISO)
silver(0)  (ISO)
sodium arsenite  (ISO)
sodium dichromate  (EXP)
tacrolimus hydrate  (ISO)
tetrachloroethene  (ISO)
tetrachloromethane  (EXP)
thioacetamide  (EXP)
titanium dioxide  (EXP,ISO)
topotecan  (EXP)
trichloroethene  (ISO)
trimellitic anhydride  (EXP)
tris(2-butoxyethyl) phosphate  (ISO)
urethane  (ISO)
ursodeoxycholic acid  (EXP)
valproic acid  (ISO)
zoledronic acid  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component
aggresome  (IEA,ISO,ISS)
cellular_component  (ND)
cytoplasm  (IEA,ISO,ISS)
fibrillar center  (IEA,ISO)
nucleoplasm  (IEA,ISO)
nucleus  (IBA,ISO,ISS)

Molecular Function

References

Additional References at PubMed
PMID:11445583   PMID:12730673   PMID:15060004   PMID:15831455   PMID:16495226   PMID:16495380   PMID:16707496   PMID:16782901   PMID:17889673   PMID:19028597   PMID:19033385   PMID:19959714  
PMID:21601015   PMID:23416168   PMID:24452267  


Genomics

Candidate Gene Status
Ubd is a candidate Gene for QTL Iddm37
Ubd is a candidate Gene for QTL Pur27
Ubd is a candidate Gene for QTL Pur30
Comparative Map Data
Ubd
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2201,385,487 - 1,387,438 (-)NCBI
Rnor_6.0 Ensembl201,876,173 - 1,897,814 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.0201,876,175 - 1,878,126 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.0203,917,777 - 3,919,728 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4201,475,944 - 1,477,895 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1201,475,953 - 1,477,895 (-)NCBI
Celera202,096,127 - 2,098,078 (-)NCBICelera
Cytogenetic Map20p12NCBI
UBD
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl629,555,515 - 29,559,732 (-)EnsemblGRCh38hg38GRCh38
GRCh38629,555,515 - 29,559,732 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh37629,523,292 - 29,527,509 (-)NCBIGRCh37GRCh37hg19GRCh37
GRCh37629,523,389 - 29,527,702 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36629,631,387 - 29,635,681 (-)NCBINCBI36hg18NCBI36
Build 34629,631,386 - 29,635,681NCBI
Celera631,129,472 - 31,133,785 (-)NCBI
Cytogenetic Map6p22.1NCBI
HuRef629,330,776 - 29,334,782 (-)NCBIHuRef
CHM1_1629,525,538 - 29,529,852 (-)NCBICHM1_1
Ubd
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391737,504,783 - 37,506,992 (+)NCBIGRCm39mm39
GRCm381737,193,892 - 37,196,101 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1737,193,892 - 37,196,095 (+)EnsemblGRCm38mm10GRCm38
MGSCv371737,330,837 - 37,333,046 (+)NCBIGRCm37mm9NCBIm37
MGSCv361736,801,615 - 36,803,894 (+)NCBImm8
Celera1740,616,710 - 40,618,919 (+)NCBICelera
Cytogenetic Map17B1NCBI
Ubd
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495558329,438 - 31,555 (-)EnsemblChiLan1.0
ChiLan1.0NW_00495558329,438 - 29,873 (-)NCBIChiLan1.0ChiLan1.0
UBD
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.1630,018,444 - 30,022,814 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl630,018,444 - 30,022,814 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v0629,359,680 - 29,364,014 (-)NCBIMhudiblu_PPA_v0panPan3
UBD
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.13526,426,919 - 26,436,189 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
Ubd
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
SpeTri2.0NW_0049367231,218,621 - 1,221,070 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
UBD
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl722,501,130 - 22,503,094 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1722,501,130 - 22,502,883 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2725,330,502 - 25,332,256 (+)NCBISscrofa10.2Sscrofa10.2susScr3
UBD
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11743,061,243 - 43,065,135 (+)NCBI
ChlSab1.1 Ensembl1743,061,826 - 43,064,869 (+)Ensembl

Position Markers
RH130544  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.0201,876,371 - 1,876,575NCBIRnor6.0
Rnor_5.0203,917,973 - 3,918,177UniSTSRnor5.0
RGSC_v3.4201,476,140 - 1,476,344UniSTSRGSC3.4
Celera202,096,323 - 2,096,527UniSTS
RH 3.4 Map203.2UniSTS
Cytogenetic Map20p12UniSTS
D9S1880  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.0201,876,079 - 1,876,951NCBIRnor6.0
Rnor_5.0203,917,681 - 3,918,553UniSTSRnor5.0
RGSC_v3.4201,475,848 - 1,476,720UniSTSRGSC3.4
Celera202,096,031 - 2,096,903UniSTS
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
724519Bp144Blood pressure QTL 1440.001arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)2015192000Rat
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

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:13
Count of miRNA genes:13
Interacting mature miRNAs:13
Transcripts:ENSRNOT00000000995
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 2 1 19 10 17 10 5 2 2
Low 1 12 17 10 2 10 7 9 1 17 19 9 7
Below cutoff 6 1 1 1 1 1 19 4 11 1

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000000995   ⟹   ENSRNOP00000000995
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl201,876,173 - 1,878,126 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000079061
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl201,876,552 - 1,897,814 (-)Ensembl
RefSeq Acc Id: NM_053299   ⟹   NP_445751
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2201,385,487 - 1,387,438 (-)NCBI
Rnor_6.0201,876,175 - 1,878,126 (-)NCBI
Rnor_5.0203,917,777 - 3,919,728 (-)NCBI
RGSC_v3.4201,475,944 - 1,477,895 (-)RGD
Celera202,096,127 - 2,098,078 (-)RGD
Sequence:
Protein Sequences
Protein RefSeqs NP_445751 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein CAC42833 (Get FASTA)   NCBI Sequence Viewer  
  CAE84074 (Get FASTA)   NCBI Sequence Viewer  
  EDL84635 (Get FASTA)   NCBI Sequence Viewer  
  Q921A3 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: NP_445751   ⟸   NM_053299
- UniProtKB: Q921A3 (UniProtKB/Swiss-Prot),   A0A0G2JSG8 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000000995   ⟸   ENSRNOT00000000995
Protein Domains
Ubiquitin-like

Transcriptome

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

Promoters
RGD ID:13701266
Promoter ID:EPDNEW_R11790
Type:single initiation site
Name:Ubd_1
Description:ubiquitin D
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_6.0201,878,087 - 1,878,147EPDNEW

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)
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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
20 3917956 3917957 T G snv SBH/Ygl (MCW), SBN/Ygl (MCW), MHS/Gib (KNAW), WAG/Rij (KNAW), HWY/Slc (KyushuU), SBN/Ygl (KNAW), MNS/Gib (KNAW), HTX/Kyo (KyushuU), RCS/Kyo (KyushuU), SBH/Ygl (KNAW)


Assembly: Rnor_6.0

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
20 1876354 1876355 T G snv SBH/Ygl (MCW), SBN/Ygl (MCW), MHS/Gib (RGD), WAG/Rij (RGD), SBH/Ygl (RGD), SBN/Ygl (RGD), MNS/Gib (RGD)


Assembly: RGSC_v3.4

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
20 1476123 1476124 T G snv MHS/Gib (ICL), MNS/Gib (ICL), WAG/Rij (ICL), SBN/Ygl (ICL), SBH/Ygl (ICL)


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:69418 AgrOrtholog
Ensembl Genes ENSRNOG00000000768 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000000995 ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000000995 ENTREZGENE, UniProtKB/TrEMBL
InterPro Ubiquitin UniProtKB/Swiss-Prot
  Ubiquitin-like_dom UniProtKB/TrEMBL
  Ubiquitin-like_domsf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Ubiquitin_D UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Ubiquitin_dom UniProtKB/Swiss-Prot
  Ubiquitin_dom UniProtKB/TrEMBL
KEGG Report rno:29168 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
NCBI Gene 29168 ENTREZGENE
PANTHER PTHR47731 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam ubiquitin UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Ubd PhenoGen
PRINTS UBIQUITIN UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PROSITE UBIQUITIN_2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
SMART UBQ UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP SSF54236 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
TIGR TC235459
UniProt A0A0G2JSG8 ENTREZGENE, UniProtKB/TrEMBL
  Q921A3 ENTREZGENE, UniProtKB/Swiss-Prot
UniProt Secondary Q6MFX3 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2002-06-10 Ubd  ubiquitin D       Name updated 70584 APPROVED

RGD Curation Notes
Note Type Note Reference
gene_mapping found in the major histocompatibility RT1 complex 1300431