Ube3d (ubiquitin protein ligase E3D) - Rat Genome Database

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Gene: Ube3d (ubiquitin protein ligase E3D) Rattus norvegicus
Analyze
Symbol: Ube3d
Name: ubiquitin protein ligase E3D
RGD ID: 1306773
Description: Predicted to enable cyclin binding activity; ubiquitin conjugating enzyme binding activity; and ubiquitin protein ligase activity. Predicted to be involved in proteasome-mediated ubiquitin-dependent protein catabolic process and protein ubiquitination. Predicted to be part of ubiquitin ligase complex. Predicted to be active in cytosol and nucleus. Orthologous to human UBE3D (ubiquitin protein ligase E3D); INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; 2,3,7,8-Tetrachlorodibenzofuran; bisphenol A.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: E3 ubiquitin-protein ligase E3D; HECT-type E3 ubiquitin transferase E3D; hypothetical LOC315863; LOC315863; MGC124836; RGD1306773; UbcH10 binding protein with a hect-like domain; ubcH10-binding protein with a HECT-like domain; Ube2cbp; ubiquitin-conjugating enzyme E2C binding protein; ubiquitin-conjugating enzyme E2C-binding protein
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2887,245,503 - 87,413,104 (-)NCBImRatBN7.2
mRatBN7.2 Ensembl887,245,589 - 87,413,057 (-)Ensembl
Rnor_6.0893,948,689 - 94,120,477 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl893,948,767 - 94,120,458 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0893,463,000 - 93,633,611 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4891,537,389 - 91,704,052 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1891,675,636 - 91,726,778 (-)NCBI
Celera886,850,461 - 87,016,589 (-)NCBICelera
Cytogenetic Map8q31NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component

Molecular Function

References

References - curated
# Reference Title Reference Citation
1. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
2. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
3. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:12477932   PMID:15749827  


Genomics

Comparative Map Data
Ube3d
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2887,245,503 - 87,413,104 (-)NCBImRatBN7.2
mRatBN7.2 Ensembl887,245,589 - 87,413,057 (-)Ensembl
Rnor_6.0893,948,689 - 94,120,477 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl893,948,767 - 94,120,458 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0893,463,000 - 93,633,611 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4891,537,389 - 91,704,052 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1891,675,636 - 91,726,778 (-)NCBI
Celera886,850,461 - 87,016,589 (-)NCBICelera
Cytogenetic Map8q31NCBI
UBE3D
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38682,880,802 - 83,065,841 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p13 Ensembl682,892,390 - 83,065,841 (-)EnsemblGRCh38hg38GRCh38
GRCh37683,602,109 - 83,775,560 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36683,658,905 - 83,832,264 (-)NCBINCBI36hg18NCBI36
Celera684,035,429 - 84,208,843 (-)NCBI
Cytogenetic Map6q14.1NCBI
HuRef680,830,086 - 81,003,588 (-)NCBIHuRef
CHM1_1683,699,816 - 83,873,224 (-)NCBICHM1_1
T2T-CHM13v2.0684,111,958 - 84,288,846 (-)NCBI
Ube2cbp
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39986,189,287 - 86,347,027 (-)NCBIGRCm39mm39
GRCm39 Ensembl986,189,359 - 86,347,003 (-)Ensembl
GRCm38986,307,234 - 86,464,976 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl986,307,306 - 86,464,950 (-)EnsemblGRCm38mm10GRCm38
MGSCv37986,200,841 - 86,358,523 (-)NCBIGRCm37mm9NCBIm37
MGSCv36986,103,952 - 86,261,668 (-)NCBImm8
Celera983,374,429 - 83,536,852 (-)NCBICelera
Cytogenetic Map9E3.1NCBI
Ube3d
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495541110,642,047 - 10,797,612 (-)EnsemblChiLan1.0
ChiLan1.0NW_00495541110,642,102 - 10,797,612 (-)NCBIChiLan1.0ChiLan1.0
UBE3D
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.1684,062,079 - 84,236,826 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl684,062,079 - 84,236,860 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v0680,729,751 - 80,962,322 (-)NCBIMhudiblu_PPA_v0panPan3
UBE3D
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.11243,264,956 - 43,475,583 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl1243,282,372 - 43,476,086 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha1243,078,353 - 43,288,980 (-)NCBI
ROS_Cfam_1.01244,032,015 - 44,241,623 (-)NCBI
ROS_Cfam_1.0 Ensembl1243,994,228 - 44,241,887 (-)Ensembl
UMICH_Zoey_3.11243,372,224 - 43,581,804 (-)NCBI
UNSW_CanFamBas_1.01243,320,940 - 43,530,526 (-)NCBI
UU_Cfam_GSD_1.01243,481,894 - 43,691,291 (-)NCBI
Ube3d
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440494678,607,940 - 78,752,364 (-)NCBI
SpeTri2.0NW_0049365107,718,552 - 7,862,946 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
UBE3D
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl183,140,635 - 83,295,785 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1183,140,479 - 83,295,865 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2193,417,743 - 93,474,534 (+)NCBISscrofa10.2Sscrofa10.2susScr3
UBE3D
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1137,558,463 - 7,737,630 (-)NCBIChlSab1.1chlSab2
ChlSab1.1 Ensembl137,558,321 - 7,737,485 (-)EnsemblChlSab1.1chlSab2
Vero_WHO_p1.0NW_023666040183,768,030 - 183,941,569 (-)NCBIVero_WHO_p1.0
Ube3d
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_00462479911,523,473 - 11,703,079 (+)EnsemblHetGla_female_1.0hetGla2
HetGla 1.0NW_00462479911,523,477 - 11,702,781 (+)NCBIHetGla_female_1.0hetGla2

Position Markers
RH94569  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2887,337,051 - 87,337,208 (+)MAPPERmRatBN7.2
mRatBN7.25146,686,949 - 146,687,106 (+)MAPPERmRatBN7.2
Rnor_6.0894,041,606 - 94,041,762NCBIRnor6.0
Rnor_6.05152,686,605 - 152,686,761NCBIRnor6.0
Rnor_5.0893,555,446 - 93,555,602UniSTSRnor5.0
Rnor_5.05156,472,203 - 156,472,359UniSTSRnor5.0
Cytogenetic Map8q31UniSTS
Cytogenetic Map5q36UniSTS


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1581557Eae16Experimental allergic encephalomyelitis QTL 163.8nervous system integrity trait (VT:0010566)experimental autoimmune encephalomyelitis incidence/prevalence measurement (CMO:0001046)88462195110921472Rat
631650Stl6Serum triglyceride level QTL 640.0019blood triglyceride amount (VT:0002644)plasma triglyceride level (CMO:0000548)810378157112202585Rat
731182Uae24Urinary albumin excretion QTL 246.4urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)81933115293965294Rat
1358892Kidm26Kidney mass QTL 263.69kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)82720571599103503Rat
1358896Bp262Blood pressure QTL 2622.89arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)82720571599103503Rat
1358907Cm40Cardiac mass QTL 401.89heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)82720571599103503Rat
8662823Vetf5Vascular elastic tissue fragility QTL 51.9artery integrity trait (VT:0010639)patent ductus arteriosus score (CMO:0002566)82824291299525068Rat
1549908Neudeg1Neurodegradation QTL 15.50nervous system integrity trait (VT:0010566)logarithm of the ratio of the lesioned side motor neuron count to contralateral side motor neuron count (CMO:0001986)83018886794457446Rat
1578755Pur5Proteinuria QTL 53.30.0001total urine protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)830848154101699754Rat
1578765Klgr1Kidney lesion grade QTL 13.30.0001kidney morphology trait (VT:0002135)organ lesion measurement (CMO:0000677)830848154101699754Rat
1578769Uae31Urinary albumin excretion QTL 313.30.001urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)830848154101699754Rat
2316950Scl66Serum cholesterol level QTL 664.1blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)830848259105647037Rat
1331838Niddm61Non-insulin dependent diabetes mellitus QTL 613.530.0004blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)83646953599083736Rat
1358906Bp253Blood pressure QTL 25340.0004arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)84071306693965294Rat
1554321Bmd3Bone mineral density QTL 37.90.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)840952565123900184Rat
70161Bp62Blood pressure QTL 622.90.001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)84269268490165460Rat
12879882Am8Aortic mass QTL 80.001aorta mass (VT:0002845)aorta weight to aorta length to body weight ratio (CMO:0002722)84329616998968765Rat
12879878Bw183Body weight QTL 1830.001body mass (VT:0001259)body weight (CMO:0000012)84329616998968765Rat
12879879Cm99Cardiac mass QTL 990.001heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)84329616998968765Rat
12879880Cm100Cardiac mass QTL 1000.001heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)84329616998968765Rat
12879881Cm101Cardiac mass QTL 1010.001heart right ventricle mass (VT:0007033)heart right ventricle weight to body weight ratio (CMO:0000914)84329616998968765Rat
12879883Kidm65Kidney mass QTL 650.001kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)84329616998968765Rat
70197BpQTLcluster8Blood pressure QTL cluster 83.482arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)846531639119088624Rat
70197BpQTLcluster8Blood pressure QTL cluster 83.482arterial blood pressure trait (VT:2000000)pulse pressure (CMO:0000292)846531639119088624Rat
70197BpQTLcluster8Blood pressure QTL cluster 83.482arterial blood pressure trait (VT:2000000)absolute change in systolic blood pressure (CMO:0000607)846531639119088624Rat
70197BpQTLcluster8Blood pressure QTL cluster 83.482arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)846531639119088624Rat
1331837Bw23Body weight QTL 234.190.00007body mass (VT:0001259)body weight (CMO:0000012)84653172299083736Rat
2303570Gluco48Glucose level QTL 482blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)84980583194805831Rat
1358912Bw51Body weight QTL 512.95body mass (VT:0001259)body weight (CMO:0000012)851351728107062046Rat
10402857Bp380Blood pressure QTL 3800.95arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)85396876598968765Rat
2301402Bp316Blood pressure QTL 3160.005arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)85396876598968765Rat
2293697Bmd39Bone mineral density QTL 39femur strength trait (VT:0010010)femur total energy absorbed before break (CMO:0001677)85404374498968765Rat
631664Hcar3Hepatocarcinoma resistance QTL 32.90.0005liver integrity trait (VT:0010547)volume of individual liver tumorous lesion (CMO:0001078)85423764499103503Rat
1300177Cm2Cardiac mass QTL 23.65heart mass (VT:0007028)heart weight (CMO:0000017)854259986100382532Rat
2303171Bp331Blood pressure QTL 3315.570.005arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)861290298119084929Rat
631653Bp125Blood pressure QTL 1253.3arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)866142385111142385Rat
631210Bw3Body weight QTL35.9mesenteric fat pad mass (VT:0010427)mesenteric fat pad weight to body weight ratio (CMO:0000654)869349194112783834Rat
1300171Bp184Blood pressure QTL 1843.66arterial blood pressure trait (VT:2000000)blood pressure time series experimental set point of the baroreceptor response (CMO:0002593)870513503118219066Rat
8694446Bw170Body weight QTL 17012.070.001retroperitoneal fat pad mass (VT:0010430)retroperitoneal fat pad weight to body weight ratio (CMO:0000635)871888757116888757Rat
9590292Uminl3Urine mineral level QTL 33.620.001urine mineral amount (VT:0015086)urine electrolyte level (CMO:0000593)871888757116888757Rat
8694200Abfw4Abdominal fat weight QTL 49.070.001visceral adipose mass (VT:0010063)abdominal fat pad weight to body weight ratio (CMO:0000095)871888757116888757Rat
8694392Bw161Body weight QTL 1618.060.001body lean mass (VT:0010483)lean tissue morphological measurement (CMO:0002184)871888757116888757Rat
1549909Stresp11Stress response QTL 116.830.0019stress-related behavior trait (VT:0010451)number of approaches toward negative stimulus before onset of defensive burying response (CMO:0001960)873473045118473045Rat
2300181Bmd55Bone mineral density QTL 555.70.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)876468691121468691Rat
61437Cia6Collagen induced arthritis QTL 6joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)882460758122812818Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:182
Count of miRNA genes:131
Interacting mature miRNAs:146
Transcripts:ENSRNOT00000014600
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
Medium 4 4 4 14 2 9
Low 3 43 53 37 19 37 8 11 60 33 32 11 8
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000014600   ⟹   ENSRNOP00000014600
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl887,245,589 - 87,413,057 (-)Ensembl
Rnor_6.0 Ensembl893,948,767 - 94,120,458 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000080195   ⟹   ENSRNOP00000071165
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl887,293,545 - 87,412,990 (-)Ensembl
Rnor_6.0 Ensembl893,949,125 - 94,120,433 (-)Ensembl
RefSeq Acc Id: NM_001039610   ⟹   NP_001034699
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2887,245,582 - 87,413,057 (-)NCBI
Rnor_6.0893,948,760 - 94,120,458 (-)NCBI
Rnor_5.0893,463,000 - 93,633,611 (-)NCBI
RGSC_v3.4891,537,389 - 91,704,052 (-)RGD
Celera886,850,461 - 87,016,589 (-)RGD
Sequence:
RefSeq Acc Id: XM_006243479   ⟹   XP_006243541
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2887,245,503 - 87,413,099 (-)NCBI
Rnor_6.0893,948,689 - 94,120,477 (-)NCBI
Rnor_5.0893,463,000 - 93,633,611 (-)NCBI
Sequence:
RefSeq Acc Id: XM_039081531   ⟹   XP_038937459
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2887,365,500 - 87,413,103 (-)NCBI
RefSeq Acc Id: XM_039081532   ⟹   XP_038937460
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2887,303,330 - 87,413,103 (-)NCBI
RefSeq Acc Id: XR_001839187
RefSeq Status:
Type: NON-CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2887,245,503 - 87,413,099 (-)NCBI
Rnor_6.0893,948,689 - 94,120,477 (-)NCBI
Sequence:
RefSeq Acc Id: XR_005487831
RefSeq Status:
Type: NON-CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2887,245,503 - 87,413,101 (-)NCBI
RefSeq Acc Id: XR_005487832
RefSeq Status:
Type: NON-CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2887,245,503 - 87,413,101 (-)NCBI
RefSeq Acc Id: XR_005487833
RefSeq Status:
Type: NON-CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2887,245,503 - 87,413,100 (-)NCBI
RefSeq Acc Id: XR_005487834
RefSeq Status:
Type: NON-CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2887,245,503 - 87,413,104 (-)NCBI
RefSeq Acc Id: XR_005487835
RefSeq Status:
Type: NON-CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2887,245,503 - 87,374,286 (-)NCBI
Protein Sequences
Protein RefSeqs NP_001034699 (Get FASTA)   NCBI Sequence Viewer  
  XP_006243541 (Get FASTA)   NCBI Sequence Viewer  
  XP_038937459 (Get FASTA)   NCBI Sequence Viewer  
  XP_038937460 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAI01917 (Get FASTA)   NCBI Sequence Viewer  
  Q3T1H6 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: NP_001034699   ⟸   NM_001039610
- UniProtKB: Q3T1H6 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: XP_006243541   ⟸   XM_006243479
- Peptide Label: isoform X1
- UniProtKB: A0A0G2JZS6 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000071165   ⟸   ENSRNOT00000080195
RefSeq Acc Id: ENSRNOP00000014600   ⟸   ENSRNOT00000014600
RefSeq Acc Id: XP_038937460   ⟸   XM_039081532
- Peptide Label: isoform X2
RefSeq Acc Id: XP_038937459   ⟸   XM_039081531
- Peptide Label: isoform X2

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-Q3T1H6-F1-model_v2 AlphaFold Q3T1H6 1-370 view protein structure

Transcriptome

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

Promoters
RGD ID:13696157
Promoter ID:EPDNEW_R6682
Type:initiation region
Name:Ube3d_1
Description:ubiquitin protein ligase E3D
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_6.0894,120,473 - 94,120,533EPDNEW

Strain Variation

Strain Sequence Variants (mRatBN7.2)
ACI/EurMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
ACI/N (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN-Lx/CubMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/NHsdMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/NHsdMcwi (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/SsN (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BUF/N (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BXH2/CubMcwi (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BXH3/CubMcwi (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
DA/OlaHsd (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Envigo
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/DuCrl (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/N (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/NCrl (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/Stm (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FHH/EurMcwi (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FXLE16/Stm (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FXLE18/Stm (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
GK/FarMcwi (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB10/IpcvMcwi (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB2/IpcvMcwi (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB20/IpcvMcwi (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB31/IpcvMcwi (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB4/IpcvMcwi (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LE/Stm (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEW/Crl (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF10A/StmMcwi (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF11/Stm (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF1A/Stm (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF1C/Stm (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF2B/Stm (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF3/Stm (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF4/Stm (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LH/MavRrrcAek (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LL/MavRrrcAek (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LN/MavRrrcAek (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
M520/N (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
M520/NRrrcMcwi (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
MR/N (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
MWF/Hsd (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
PVG/Seac (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SHR/OlalpcvMcwi (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SHRSP/A3NCrl (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SR/JrHsd (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Envigo
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SS/JrHsdMcwi (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WAG/RijCrl (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WKY/N (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WKY/NCrl (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WN/N (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1306773 AgrOrtholog
BioCyc Gene G2FUF-29644 BioCyc
Ensembl Genes ENSRNOG00000010802 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000014600 ENTREZGENE, UniProtKB/Swiss-Prot
  ENSRNOP00000071165 ENTREZGENE
  ENSRNOP00000071165.2 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000014600 ENTREZGENE, UniProtKB/Swiss-Prot
  ENSRNOT00000080195 ENTREZGENE
  ENSRNOT00000080195.2 UniProtKB/TrEMBL
IMAGE_CLONE IMAGE:7935691 IMAGE-MGC_LOAD
InterPro UBQ-conj_enz_E2-bd_prot UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:315863 UniProtKB/Swiss-Prot
MGC_CLONE MGC:124836 IMAGE-MGC_LOAD
NCBI Gene 315863 ENTREZGENE
PANTHER PTHR31531 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam HECT_2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Ube3d PhenoGen
UniProt A0A0G2JZS6 ENTREZGENE, UniProtKB/TrEMBL
  Q3T1H6 ENTREZGENE, UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2013-03-04 Ube3d  ubiquitin protein ligase E3D  Ube2cbp  ubiquitin-conjugating enzyme E2C binding protein  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-03-07 Ube2cbp  ubiquitin-conjugating enzyme E2C binding protein  RGD1306773  hypothetical LOC315863  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2006-03-07 RGD1306773  hypothetical LOC315863  RGD1306773_predicted  hypothetical LOC315863 (predicted)  Symbol and Name status set to approved 1299863 APPROVED
2005-01-20 RGD1306773_predicted  hypothetical LOC315863 (predicted)  LOC315863_predicted    Symbol and Name status set to approved 1331353 APPROVED
2005-01-12 LOC315863_predicted  hypothetical LOC315863 (predicted)      Symbol and Name status set to provisional 70820 PROVISIONAL