Ube3c (ubiquitin protein ligase E3C) - Rat Genome Database

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Pathways
Gene: Ube3c (ubiquitin protein ligase E3C) Rattus norvegicus
Analyze
Symbol: Ube3c
Name: ubiquitin protein ligase E3C
RGD ID: 1559986
Description: Predicted to enable ubiquitin protein ligase activity. Predicted to be involved in protein K29-linked ubiquitination; protein K48-linked ubiquitination; and ubiquitin-dependent protein catabolic process. Predicted to act upstream of or within autophagosome assembly and phosphatidylinositol phosphate biosynthetic process. Orthologous to human UBE3C (ubiquitin protein ligase E3C); PARTICIPATES IN ubiquitin/proteasome degradation pathway; INTERACTS WITH (+)-schisandrin B; 17alpha-ethynylestradiol; 2,3,7,8-tetrachlorodibenzodioxine.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: LOC362294; RGD1559986; similar to ubiquitin protein ligase E3C; ubiquitin-protein ligase E3C
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Black Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: GRCr8 - GRCr8 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr846,323,831 - 6,425,085 (-)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl46,323,831 - 6,424,845 (-)EnsemblGRCr8
mRatBN7.245,648,932 - 5,749,922 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl45,648,690 - 5,750,011 (-)EnsemblmRatBN7.2
Rnor_6.042,505,912 - 2,606,710 (+)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl42,505,909 - 2,606,655 (+)Ensemblrn6Rnor6.0
Rnor_5.042,558,670 - 2,659,587 (+)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.44889,640 - 991,900 (-)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera44,569,408 - 4,670,465 (+)NCBICelera
Cytogenetic Map4q11NCBI
JBrowse:




Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Molecular Function

Molecular Pathway Annotations     Click to see Annotation Detail View
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. KEGG Annotation Import Pipeline Pipeline to import KEGG annotations from KEGG into RGD
3. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:11278995   PMID:31505169  


Genomics

Comparative Map Data
Ube3c
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr846,323,831 - 6,425,085 (-)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl46,323,831 - 6,424,845 (-)EnsemblGRCr8
mRatBN7.245,648,932 - 5,749,922 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl45,648,690 - 5,750,011 (-)EnsemblmRatBN7.2
Rnor_6.042,505,912 - 2,606,710 (+)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl42,505,909 - 2,606,655 (+)Ensemblrn6Rnor6.0
Rnor_5.042,558,670 - 2,659,587 (+)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.44889,640 - 991,900 (-)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera44,569,408 - 4,670,465 (+)NCBICelera
Cytogenetic Map4q11NCBI
UBE3C
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh387157,138,926 - 157,269,370 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl7157,138,922 - 157,269,372 (+)Ensemblhg38GRCh38
GRCh377156,931,620 - 157,062,064 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 367156,624,425 - 156,754,823 (+)NCBIBuild 36Build 36hg18NCBI36
Build 347156,431,139 - 156,561,538NCBI
Celera7151,358,691 - 151,489,117 (+)NCBICelera
Cytogenetic Map7q36.3NCBI
HuRef7150,661,434 - 150,792,261 (+)NCBIHuRef
CHM1_17156,940,195 - 157,070,555 (+)NCBICHM1_1
T2T-CHM13v2.07158,326,736 - 158,457,202 (+)NCBIT2T-CHM13v2.0
CRA_TCAGchr7v27156,160,941 - 156,291,386 (+)NCBI
Ube3c
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39529,774,240 - 29,881,075 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl529,774,240 - 29,881,090 (+)EnsemblGRCm39 EnsemblGRCm39
GRCm38529,569,242 - 29,676,077 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl529,569,242 - 29,676,092 (+)Ensemblmm10GRCm38
MGSCv37529,895,782 - 30,002,617 (+)NCBIMGSCv37MGSCv37mm9NCBIm37
MGSCv36529,900,029 - 30,006,864 (+)NCBIMGSCv36mm8
Celera527,085,025 - 27,191,855 (+)NCBICelera
Cytogenetic Map5B1NCBI
cM Map515.12NCBI
Ube3c
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_004955579127,533 - 207,522 (+)Ensembl
ChiLan1.0NW_004955579127,535 - 207,522 (+)NCBIChiLan1.0ChiLan1.0
UBE3C
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v26193,582,714 - 193,714,341 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan1745,592,983 - 45,724,609 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v07148,756,024 - 148,886,688 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.17160,474,770 - 160,580,046 (+)NCBIPanPan1.1PanPan1.1panPan2
PanPan1.1 Ensembl7160,474,767 - 160,580,046 (+)EnsemblpanPan2panpan1.1
UBE3C
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.11619,590,115 - 19,716,664 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl1619,589,172 - 19,777,260 (+)EnsemblcanFam3CanFam3.1
Dog10K_Boxer_Tasha1620,165,614 - 20,284,646 (+)NCBIDog10K_Boxer_TashaDog10K_Boxer_Tasha
ROS_Cfam_1.01621,320,824 - 21,447,476 (+)NCBIROS_Cfam_1.0ROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl1621,320,338 - 21,447,456 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.11619,689,672 - 19,816,144 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.01620,271,842 - 20,398,679 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.01620,324,371 - 20,451,051 (+)NCBIUU_Cfam_GSD_1.0UU_Cfam_GSD_1.0
Ube3c
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_0244051181,724,225 - 1,817,737 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_004936797451,356 - 529,731 (-)EnsemblSpeTri2.0 Ensembl
SpeTri2.0NW_004936797452,597 - 529,631 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
UBE3C
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl181,542,163 - 1,653,982 (-)EnsemblsusScr11Sscrofa11.1
Sscrofa11.1181,542,454 - 1,654,274 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2181,571,168 - 1,621,715 (-)NCBISscrofa10.2Sscrofa10.2susScr3
UBE3C
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.121125,262,772 - 125,397,639 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl21125,262,906 - 125,397,898 (+)EnsemblChlSab1.1 EnsemblchlSab2Vervet-AGM
Vero_WHO_p1.0NW_02366607221,496,329 - 21,632,911 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Ube3c
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046248001,274,825 - 1,366,553 (-)EnsemblHetGla_female_1.0 EnsemblhetGla2HetGla_female_1.0 Ensembl
HetGla 1.0NW_0046248001,276,697 - 1,366,547 (-)NCBIHetGla 1.0HetGla 1.0hetGla2
Ube3c
(Rattus rattus - black rat)
Black Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rrattus_CSIRO_v16158,840,443 - 158,940,469 (-)NCBIRrattus_CSIRO_v1

Variants

.
Variants in Ube3c
541 total Variants
miRNA Target Status (No longer updated)

Predicted Target Of
Summary Value
Count of predictions:90
Count of miRNA genes:85
Interacting mature miRNAs:88
Transcripts:ENSRNOT00000015232
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.


QTLs in Region (GRCr8)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
61408Scl23Serum cholesterol level QTL 230.0005blood HDL phospholipid amount (VT:0010504)serum high density lipoprotein phospholipid level (CMO:0001567)4128392287Rat
631209Bw2Body weight QTL24.2retroperitoneal fat pad mass (VT:0010430)retroperitoneal fat pad weight to body weight ratio (CMO:0000635)4145429897Rat
8552803Bw144Body weight QTL 14416body mass (VT:0001259)change in body weight to body weight ratio (CMO:0002216)4135396961Rat
8552801Bw143Body weight QTL 1437.3body mass (VT:0001259)change in body weight to body weight ratio (CMO:0002216)4135396961Rat
2303168Bp330Blood pressure QTL 3304.250.017arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)45889999148002343Rat
9589046Scfw2Subcutaneous fat weight QTL 25.540.001subcutaneous adipose mass (VT:1000472)abdominal subcutaneous fat pad weight (CMO:0002069)4132668025Rat
8552903Pigfal2Plasma insulin-like growth factor 1 level QTL 27.3blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)4132668025Rat
724557Plsm1Polydactyly-luxate syndrome (PLS) morphotypes QTL 10.0003forelimb integrity trait (VT:0010562)front foot phalanges count (CMO:0001947)4128392287Rat
9590100Sffal4Serum free fatty acids level QTL 47.360.05blood free fatty acid amount (VT:0001553)plasma free fatty acids level (CMO:0000546)4132668025Rat
61351Bp33Blood pressure QTL 330.0018arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)4128392287Rat
61415Eae11Experimental allergic encephalomyelitis QTL 112.9nervous system integrity trait (VT:0010566)post-insult time to onset of experimental autoimmune encephalomyelitis (CMO:0001422)4140471598Rat
1357341Gluco5Glucose level QTL 56.4adipocyte free fatty acid secretion trait (VT:0010465)absolute change in adipocyte free fatty acid secretion per unit volume (CMO:0001446)4134142783Rat
619616Bp79Blood pressure QTL 790.0292arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)4588999950889999Rat
1357343Gluco4Glucose level QTL 40.00002adipocyte glucose uptake trait (VT:0004185)adipocyte maximal glucose uptake to basal glucose uptake ratio (CMO:0000874)4134142783Rat
8552809Vie5Viral induced encephalitis QTL 525.3brain integrity trait (VT:0010579)encephalitis incidence/prevalence measurement (CMO:0002361)4135396961Rat
8552782Vie1Viral induced encephalitis QTL 126.4brain integrity trait (VT:0010579)encephalitis incidence/prevalence measurement (CMO:0002361)4135396961Rat
738021Hcar13Hepatocarcinoma resistance QTL 134.3liver integrity trait (VT:0010547)liver nonremodeling tumorous lesion volume to total liver volume ratio (CMO:0001464)4133538816Rat
70192BpQTLcluster5Blood pressure QTL cluster 54.183arterial blood pressure trait (VT:2000000)absolute change in mean arterial blood pressure (CMO:0000533)4163900697Rat
631642Stl2Serum triglyceride level QTL 23.3blood triglyceride amount (VT:0002644)serum triglyceride level (CMO:0000360)4589457557613242Rat
61333Gluco16Glucose level QTL 164.30.00001adipocyte glucose uptake trait (VT:0004185)absolute change in adipocyte glucose uptake (CMO:0000873)4131106810Rat
9589097Slep11Serum leptin concentration QTL 115.090.001blood leptin amount (VT:0005667)plasma leptin level (CMO:0000781)4132668025Rat

Markers in Region
RH125662  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_5.042,593,724 - 2,593,981NCBIRnor5.0
RGSC_v3.44956,825 - 957,081UniSTSRGSC3.4
Cytogenetic Map4q11UniSTS
RH137703  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.245,696,517 - 5,696,693 (-)MAPPERmRatBN7.2
Rnor_6.042,558,720 - 2,558,895NCBIRnor6.0
Rnor_5.042,611,529 - 2,611,704UniSTSRnor5.0
RGSC_v3.44938,093 - 938,268UniSTSRGSC3.4
Celera44,622,475 - 4,622,650UniSTS
Cytogenetic Map4q11UniSTS


Expression

RNA-SEQ Expression

alimentary part of gastrointestinal system
appendage
circulatory system
ectoderm
endocrine system
endoderm
exocrine system
hemolymphoid system
hepatobiliary system
integumental system
mesenchyme
mesoderm
musculoskeletal system
nervous system
renal system
reproductive system
respiratory system
sensory system
visual system
16 12 67 164 91 90 59 92 59 6 356 192 11 143 81 92 31 17 17

Sequence


Ensembl Acc Id: ENSRNOT00000015232   ⟹   ENSRNOP00000015232
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl46,323,831 - 6,424,845 (-)Ensembl
mRatBN7.2 Ensembl45,648,690 - 5,749,690 (-)Ensembl
Rnor_6.0 Ensembl42,527,434 - 2,606,655 (+)Ensembl
Ensembl Acc Id: ENSRNOT00000092756   ⟹   ENSRNOP00000076040
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl46,323,831 - 6,424,785 (-)Ensembl
mRatBN7.2 Ensembl45,648,690 - 5,750,011 (-)Ensembl
Rnor_6.0 Ensembl42,505,909 - 2,590,678 (+)Ensembl
Ensembl Acc Id: ENSRNOT00000092992   ⟹   ENSRNOP00000075978
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl42,593,876 - 2,606,474 (+)Ensembl
Ensembl Acc Id: ENSRNOT00000125523   ⟹   ENSRNOP00000107741
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl46,336,536 - 6,424,845 (-)Ensembl
RefSeq Acc Id: NM_001427087   ⟹   NP_001414016
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr846,323,831 - 6,424,845 (-)NCBI
RefSeq Acc Id: XM_039108546   ⟹   XP_038964474
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr846,324,078 - 6,403,471 (-)NCBI
mRatBN7.245,649,946 - 5,728,335 (-)NCBI
RefSeq Acc Id: XR_005503372
Type: NON-CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr846,325,719 - 6,425,085 (-)NCBI
mRatBN7.245,648,932 - 5,749,922 (-)NCBI
Protein Sequences
Protein RefSeqs NP_001414016 (Get FASTA)   NCBI Sequence Viewer  
  XP_038964474 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein EDL86428 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000015232
  ENSRNOP00000015232.8
  ENSRNOP00000076040.2
  ENSRNOP00000107741.1
Ensembl Acc Id: ENSRNOP00000076040   ⟸   ENSRNOT00000092756
Ensembl Acc Id: ENSRNOP00000075978   ⟸   ENSRNOT00000092992
Ensembl Acc Id: ENSRNOP00000015232   ⟸   ENSRNOT00000015232
RefSeq Acc Id: XP_038964474   ⟸   XM_039108546
- Peptide Label: isoform X1
RefSeq Acc Id: NP_001414016   ⟸   NM_001427087
- UniProtKB: D3ZHB7 (UniProtKB/TrEMBL),   A0A1B0GWW0 (UniProtKB/TrEMBL)
Ensembl Acc Id: ENSRNOP00000107741   ⟸   ENSRNOT00000125523
Protein Domains
HECT

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-D3ZHB7-F1-model_v2 AlphaFold D3ZHB7 1-936 view protein structure

Transcriptome

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

Promoters
RGD ID:13692773
Promoter ID:EPDNEW_R3297
Type:multiple initiation site
Name:Ube3c_1
Description:ubiquitin protein ligase E3C
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Alternative Promoters:null; see alsoEPDNEW_R3298  
Experiment Methods:Single-end sequencing.
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.042,505,894 - 2,505,954EPDNEW
RGD ID:13692780
Promoter ID:EPDNEW_R3298
Type:initiation region
Name:Ube3c_2
Description:ubiquitin protein ligase E3C
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Alternative Promoters:null; see alsoEPDNEW_R3297  
Experiment Methods:Single-end sequencing.
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.042,506,140 - 2,506,200EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1559986 AgrOrtholog
BioCyc Gene G2FUF-46171 BioCyc
Ensembl Genes ENSRNOG00000010702 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000015232 ENTREZGENE
  ENSRNOT00000015232.9 UniProtKB/TrEMBL
  ENSRNOT00000092756.3 UniProtKB/TrEMBL
  ENSRNOT00000125523.1 UniProtKB/TrEMBL
Gene3D-CATH Hect, E3 ligase catalytic domain UniProtKB/TrEMBL
  Hect, E3 ligase catalytic domain UniProtKB/TrEMBL
  Hect, E3 ligase catalytic domains UniProtKB/TrEMBL
InterPro E3B/C UniProtKB/TrEMBL
  HECT UniProtKB/TrEMBL
  Hect_E3_ubiquitin_ligase UniProtKB/TrEMBL
  IQ_motif_EF-hand-BS UniProtKB/TrEMBL
NCBI Gene 362294 ENTREZGENE
PANTHER PTHR45700 UniProtKB/TrEMBL
  UBIQUITIN-PROTEIN LIGASE E3C UniProtKB/TrEMBL
Pfam HECT UniProtKB/TrEMBL
PhenoGen Ube3c PhenoGen
PROSITE HECT UniProtKB/TrEMBL
  PS50096 UniProtKB/TrEMBL
RatGTEx ENSRNOG00000010702 RatGTEx
SMART HECTc UniProtKB/TrEMBL
  SM00015 UniProtKB/TrEMBL
Superfamily-SCOP HECT UniProtKB/TrEMBL
UniProt A0A1B0GWW0 ENTREZGENE, UniProtKB/TrEMBL
  A0ABK0LU78_RAT UniProtKB/TrEMBL
  D3ZHB7 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2008-02-28 Ube3c  ubiquitin protein ligase E3C  RGD1559986_predicted  similar to ubiquitin protein ligase E3C (predicted)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2006-03-07 RGD1559986_predicted  similar to ubiquitin protein ligase E3C (predicted)  LOC362294  similar to ubiquitin protein ligase E3C  Symbol and Name status set to approved 1299863 APPROVED
2006-02-09 LOC362294  similar to ubiquitin protein ligase E3C      Symbol and Name status set to provisional 70820 PROVISIONAL