Ube2d2b (ubiquitin-conjugating enzyme E2D 2B) - Rat Genome Database

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Gene: Ube2d2b (ubiquitin-conjugating enzyme E2D 2B) Rattus norvegicus
Analyze
Symbol: Ube2d2b
Name: ubiquitin-conjugating enzyme E2D 2B
RGD ID: 69425
Description: Predicted to enable ubiquitin conjugating enzyme activity. Involved in cellular response to arsenite(3-) and cellular response to cadmium ion. Predicted to be active in nucleus. Orthologous to human UBE2D4 (ubiquitin conjugating enzyme E2 D4); PARTICIPATES IN altered ubiquitin/proteasome degradation pathway; Alzheimer's disease pathway; ubiquitin/proteasome degradation pathway; INTERACTS WITH 6-propyl-2-thiouracil; acrylamide; amitrole.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: E2 ubiquitin-conjugating enzyme D2B; E2(17)KB 2B; RGD69425; Ube2d2; Ube2d4; ubiquitin carrier protein D2B; ubiquitin-conjugating enzyme; ubiquitin-conjugating enzyme E2 D2B; ubiquitin-conjugating enzyme E2(17)KB 2B; ubiquitin-conjugating enzyme E2-17 kDa 2B; ubiquitin-conjugating enzyme E2D 2; ubiquitin-conjugating enzyme E2D 4; ubiquitin-conjugating enzyme E2D 4 (putative); ubiquitin-protein ligase D2B
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
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
GRCr8142,060,926 - 2,062,400 (-)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl142,048,235 - 2,063,764 (-)EnsemblGRCr8
mRatBN7.2141,915,999 - 1,917,473 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl141,916,845 - 1,917,416 (-)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx141,794,641 - 1,796,115 (-)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0143,096,424 - 3,097,898 (-)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0141,793,104 - 1,794,578 (-)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0142,933,097 - 2,934,571 (-)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl142,933,100 - 2,934,571 (-)Ensemblrn6Rnor6.0
Rnor_5.0142,933,498 - 2,934,972 (-)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.4142,469,772 - 2,471,246 (-)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera141,935,554 - 1,937,028 (-)NCBICelera
RGSC_v3.1142,469,774 - 2,471,246 (-)NCBI
Cytogenetic Map14p22NCBI
JBrowse:




Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component
nucleus  (IBA)

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. Defective ubiquitination of cerebral proteins in Alzheimer's disease. Lopez Salon M, etal., J Neurosci Res 2000 Oct 15;62(2):302-10.
3. Rat ISS GO annotations from MGI mouse gene data--August 2006 MGD data from the GO Consortium
4. Electronic Transfer of LocusLink and RefSeq Data NCBI rat LocusLink and RefSeq merged data July 26, 2002
5. KEGG Annotation Import Pipeline Pipeline to import KEGG annotations from KEGG into RGD
6. GOA pipeline RGD automated data pipeline
7. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
8. Comprehensive gene review and curation RGD comprehensive gene curation
9. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. Strausberg RL, etal., Proc Natl Acad Sci U S A. 2002 Dec 24;99(26):16899-903. Epub 2002 Dec 11.
10. Cadmium toxicity is caused by accumulation of p53 through the down-regulation of Ube2d family genes in vitro and in vivo. Tokumoto M, etal., J Toxicol Sci. 2011 Apr;36(2):191-200.
11. Inorganic arsenic induces apoptosis through downregulation of Ube2d genes and p53 accumulation in rat proximal tubular cells. Tokumoto M, etal., J Toxicol Sci. 2013;38(6):815-20.
12. Molecular cloning, expression and characterization of a ubiquitin conjugation enzyme (E2(17)kB) highly expressed in rat testis. Wing SS and Jain P, Biochem J 1995 Jan 1;305 ( Pt 1):125-32.
13. A novel rat homolog of the Saccharomyces cerevisiae ubiquitin-conjugating enzymes UBC4 and UBC5 with distinct biochemical features is induced during spermatogenesis. Wing SS, etal., Mol Cell Biol 1996 Aug;16(8):4064-72.
Additional References at PubMed
PMID:15489334   PMID:20061386   PMID:21685362  


Genomics

Comparative Map Data
Ube2d2b
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8142,060,926 - 2,062,400 (-)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl142,048,235 - 2,063,764 (-)EnsemblGRCr8
mRatBN7.2141,915,999 - 1,917,473 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl141,916,845 - 1,917,416 (-)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx141,794,641 - 1,796,115 (-)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0143,096,424 - 3,097,898 (-)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0141,793,104 - 1,794,578 (-)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0142,933,097 - 2,934,571 (-)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl142,933,100 - 2,934,571 (-)Ensemblrn6Rnor6.0
Rnor_5.0142,933,498 - 2,934,972 (-)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.4142,469,772 - 2,471,246 (-)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera141,935,554 - 1,937,028 (-)NCBICelera
RGSC_v3.1142,469,774 - 2,471,246 (-)NCBI
Cytogenetic Map14p22NCBI
UBE2D4
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38743,926,436 - 43,956,136 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl743,926,436 - 43,956,136 (+)Ensemblhg38GRCh38
GRCh37743,966,035 - 43,995,735 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36743,932,572 - 43,959,688 (+)NCBIBuild 36Build 36hg18NCBI36
Build 34743,739,286 - 43,766,403NCBI
Celera743,955,900 - 43,985,602 (+)NCBICelera
Cytogenetic Map7p13NCBI
HuRef743,850,744 - 43,880,447 (+)NCBIHuRef
CHM1_1743,969,950 - 43,999,662 (+)NCBICHM1_1
T2T-CHM13v2.0744,084,736 - 44,114,438 (+)NCBIT2T-CHM13v2.0
CRA_TCAGchr7v2744,005,536 - 44,035,229 (+)NCBI
Ube2d2b
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm395107,978,028 - 107,979,643 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl5107,977,965 - 107,979,642 (+)EnsemblGRCm39 EnsemblGRCm39
GRCm385107,830,162 - 107,831,777 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl5107,830,099 - 107,831,776 (+)Ensemblmm10GRCm38
MGSCv375108,259,272 - 108,260,783 (+)NCBIMGSCv37MGSCv37mm9NCBIm37
MGSCv365108,070,555 - 108,072,069 (+)NCBIMGSCv36mm8
Celera5104,942,969 - 104,944,480 (+)NCBICelera
Cytogenetic Map5FNCBI
cM Map552.23NCBI
Ube2d4
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554567,924,977 - 7,952,155 (-)Ensembl
ChiLan1.0NW_0049554567,928,715 - 7,952,155 (-)NCBIChiLan1.0ChiLan1.0
UBE2D4
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v2644,496,560 - 44,523,657 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan1792,818,701 - 92,848,433 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v0740,295,047 - 40,324,705 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
Ube2d4
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440511899,769,696 - 99,793,110 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_00493647818,985,711 - 19,002,056 (+)EnsemblSpeTri2.0 Ensembl
SpeTri2.0NW_00493647818,981,457 - 19,003,924 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
UBE2D4
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1848,733,395 - 48,756,291 (-)EnsemblsusScr11Sscrofa11.1
Sscrofa11.11848,735,258 - 48,756,314 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21853,448,345 - 53,469,534 (-)NCBISscrofa10.2Sscrofa10.2susScr3
UBE2D4
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.12114,636,512 - 14,665,170 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl2114,634,384 - 14,664,909 (-)EnsemblChlSab1.1 EnsemblchlSab2Vervet-AGM
Vero_WHO_p1.0NW_0236660627,849,493 - 7,879,247 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Ube2d4
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046247407,965,053 - 7,990,601 (-)NCBIHetGla 1.0HetGla 1.0hetGla2
Ube2d4
(Rattus rattus - black rat)
Black Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rrattus_CSIRO_v11174,721,247 - 74,742,412 (+)NCBIRrattus_CSIRO_v1

Variants

.
Variants in Ube2d2b
3 total Variants
miRNA Target Status (No longer updated)

Predicted Target Of
Summary Value
Count of predictions:52
Count of miRNA genes:51
Interacting mature miRNAs:52
Transcripts:ENSRNOT00000049772
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
7411573Bw139Body weight QTL 1394.70.001body mass (VT:0001259)body weight gain (CMO:0000420)14140068101Rat
9589814Gluco67Glucose level QTL 674.540.001blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)14140068101Rat
634352Apr6Acute phase response QTL 63.7blood interleukin-6 amount (VT:0008595)plasma interleukin-6 level (CMO:0001927)14141415516Rat
71115Niddm15Non-insulin dependent diabetes mellitus QTL 154.8blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)14111334906Rat
71117Niddm17Non-insulin dependent diabetes mellitus QTL 172.35blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)14117877928Rat
70204Niddm20Non-insulin dependent diabetes mellitus QTL 205.10.000008blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)14131893212Rat

Markers in Region
PMC166143P1  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21162,820,385 - 62,820,485 (+)MAPPERmRatBN7.2
mRatBN7.2141,916,947 - 1,917,047 (+)MAPPERmRatBN7.2
Rnor_6.01165,717,122 - 65,717,221NCBIRnor6.0
Rnor_6.0142,934,046 - 2,934,145NCBIRnor6.0
Rnor_5.0142,934,447 - 2,934,546UniSTSRnor5.0
Rnor_5.01168,811,340 - 68,811,439UniSTSRnor5.0
Celera1162,318,530 - 62,318,629UniSTS
Celera141,936,503 - 1,936,602UniSTS
Cytogenetic Map18p11UniSTS
Cytogenetic Map14p22UniSTS


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
9 11 17 70 58 56 28 61 28 5 174 97 1 59 32 43 28 14 14

Sequence


Ensembl Acc Id: ENSRNOT00000049772   ⟹   ENSRNOP00000039621
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl142,933,100 - 2,934,571 (-)Ensembl
Ensembl Acc Id: ENSRNOT00000098826   ⟹   ENSRNOP00000082180
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl141,916,845 - 1,917,416 (-)Ensembl
Ensembl Acc Id: ENSRNOT00000162982   ⟹   ENSRNOP00000101492
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl142,048,235 - 2,063,764 (-)Ensembl
RefSeq Acc Id: NM_031001   ⟹   NP_112263
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8142,060,926 - 2,062,400 (-)NCBI
mRatBN7.2141,915,999 - 1,917,473 (-)NCBI
Rnor_6.0142,933,097 - 2,934,571 (-)NCBI
Rnor_5.0142,933,498 - 2,934,972 (-)NCBI
RGSC_v3.4142,469,772 - 2,471,246 (-)RGD
Celera141,935,554 - 1,937,028 (-)RGD
Sequence:
Protein Sequences
Protein RefSeqs NP_112263 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAC52942 (Get FASTA)   NCBI Sequence Viewer  
  AAH78808 (Get FASTA)   NCBI Sequence Viewer  
  EDL83991 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000101492
GenBank Protein P70711 (Get FASTA)   NCBI Sequence Viewer  
RefSeq Acc Id: NP_112263   ⟸   NM_031001
- UniProtKB: P70711 (UniProtKB/Swiss-Prot),   A6KPH8 (UniProtKB/TrEMBL),   A0A8I5ZTI3 (UniProtKB/TrEMBL)
- Sequence:
Ensembl Acc Id: ENSRNOP00000039621   ⟸   ENSRNOT00000049772
Ensembl Acc Id: ENSRNOP00000082180   ⟸   ENSRNOT00000098826
Ensembl Acc Id: ENSRNOP00000101492   ⟸   ENSRNOT00000162982
Protein Domains
UBC core

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-P70711-F1-model_v2 AlphaFold P70711 1-147 view protein structure

Transcriptome

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

Promoters
RGD ID:13699155
Promoter ID:EPDNEW_R9680
Type:initiation region
Name:Ube2d4_1
Description:ubiquitin-conjugating enzyme E2D 4
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_6.0142,934,599 - 2,934,659EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:69425 AgrOrtholog
BioCyc Gene G2FUF-16628 BioCyc
Ensembl Genes ENSRNOG00000034016 Ensembl
  ENSRNOG00000063388 Ensembl
  ENSRNOG00000082439 Ensembl, ENTREZGENE
Ensembl Transcript ENSRNOT00000162982 ENTREZGENE
Gene3D-CATH 3.10.110.10 UniProtKB/Swiss-Prot
IMAGE_CLONE IMAGE:7113229 IMAGE-MGC_LOAD
InterPro UBQ-conjugat_E2 UniProtKB/Swiss-Prot
  UBQ-conjugating_AS UniProtKB/Swiss-Prot
  UBQ-conjugating_enzyme/RWD UniProtKB/Swiss-Prot
KEGG Report rno:79435 UniProtKB/Swiss-Prot
MGC_CLONE MGC:93393 IMAGE-MGC_LOAD
NCBI Gene 79435 ENTREZGENE
PANTHER UBIQUITIN-CONJUGATING ENZYME E2 UniProtKB/Swiss-Prot
Pfam UQ_con UniProtKB/Swiss-Prot
PhenoGen Ube2d2b PhenoGen
PROSITE UBIQUITIN_CONJUGAT_1 UniProtKB/Swiss-Prot
  UBIQUITIN_CONJUGAT_2 UniProtKB/Swiss-Prot
RatGTEx ENSRNOG00000034016 RatGTEx
  ENSRNOG00000063388 RatGTEx
  ENSRNOG00000082439 RatGTEx
SMART UBCc UniProtKB/Swiss-Prot
Superfamily-SCOP SSF54495 UniProtKB/Swiss-Prot
UniProt A0A8I5ZTI3 ENTREZGENE
  A6KPH8 ENTREZGENE, UniProtKB/TrEMBL
  P70711 ENTREZGENE, UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2022-03-07 Ube2d2b  ubiquitin-conjugating enzyme E2D 2B  Ube2d4  ubiquitin-conjugating enzyme E2D 4 (putative)  Name and Symbol changed 629549 APPROVED
2012-02-02 Ube2d4  ubiquitin-conjugating enzyme E2D 4 (putative)  Ube2d4  ubiquitin-conjugating enzyme E2D 4  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2010-05-25 Ube2d4  ubiquitin-conjugating enzyme E2D 4  RGD69425  ubiquitin-conjugating enzyme  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2007-02-20 RGD69425  ubiquitin-conjugating enzyme  Ube2d2  ubiquitin-conjugating enzyme E2D 2   Symbol and Name updated 1299863 APPROVED
2002-06-10 Ube2d2  ubiquitin-conjugating enzyme E2D 2       Name updated 70584 APPROVED

RGD Curation Notes
Note Type Note Reference
gene_expression mRNA expression restricted to round spermatids and induced during puberty, protein found in mature spermatids as well 69394