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UBE2D3 ubiquitin conjugating enzyme E2 D3 [ Homo sapiens (human) ]

Gene ID: 7323, updated on 1-Jun-2020

Summary

Official Symbol
UBE2D3provided by HGNC
Official Full Name
ubiquitin conjugating enzyme E2 D3provided by HGNC
Primary source
HGNC:HGNC:12476
See related
Ensembl:ENSG00000109332 MIM:602963
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
UBC4/5; UBCH5C; E2(17)KB3
Summary
The modification of proteins with ubiquitin is an important cellular mechanism for targeting abnormal or short-lived proteins for degradation. Ubiquitination involves at least three classes of enzymes: ubiquitin-activating enzymes, or E1s, ubiquitin-conjugating enzymes, or E2s, and ubiquitin-protein ligases, or E3s. This gene encodes a member of the E2 ubiquitin-conjugating enzyme family. This enzyme functions in the ubiquitination of the tumor-suppressor protein p53, which is induced by an E3 ubiquitin-protein ligase. [provided by RefSeq, Jan 2017]
Expression
Ubiquitous expression in bone marrow (RPKM 59.8), thyroid (RPKM 40.1) and 25 other tissues See more
Orthologs

Genomic context

See UBE2D3 in Genome Data Viewer
Location:
4q24
Exon count:
13
Annotation release Status Assembly Chr Location
109.20200522 current GRCh38.p13 (GCF_000001405.39) 4 NC_000004.12 (102794383..102868893, complement)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 4 NC_000004.11 (103715540..103790050, complement)

Chromosome 4 - NC_000004.12Genomic Context describing neighboring genes Neighboring gene mannosidase beta Neighboring gene mannosidase beta like pseudogene Neighboring gene WD repeat domain 12 pseudogene Neighboring gene uncharacterized LOC102723704 Neighboring gene UBE2D3 antisense RNA 1 Neighboring gene RNA, U7 small nuclear 151 pseudogene Neighboring gene CDGSH iron sulfur domain 2 Neighboring gene solute carrier family 9 member B1 Neighboring gene poly(A) binding protein cytoplasmic 1 pseudogene 7

Genomic regions, transcripts, and products

Expression

  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Pathways from PubChem

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Clone Names

  • MGC5416, MGC43926

Gene Ontology Provided by GOA

Function Evidence Code Pubs
ATP binding IEA
Inferred from Electronic Annotation
more info
 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
ubiquitin conjugating enzyme activity IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
ubiquitin conjugating enzyme activity IDA
Inferred from Direct Assay
more info
PubMed 
ubiquitin protein ligase binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
ubiquitin-protein transferase activity IDA
Inferred from Direct Assay
more info
PubMed 
Process Evidence Code Pubs
BMP signaling pathway TAS
Traceable Author Statement
more info
 
DNA repair IEA
Inferred from Electronic Annotation
more info
 
MyD88-independent toll-like receptor signaling pathway TAS
Traceable Author Statement
more info
 
TRIF-dependent toll-like receptor signaling pathway TAS
Traceable Author Statement
more info
 
apoptotic process IEA
Inferred from Electronic Annotation
more info
 
cellular protein modification process TAS
Traceable Author Statement
more info
PubMed 
cellular response to cadmium ion IEA
Inferred from Electronic Annotation
more info
 
cellular response to mercury ion IEA
Inferred from Electronic Annotation
more info
 
negative regulation of transcription by RNA polymerase II TAS
Traceable Author Statement
more info
 
positive regulation of protein targeting to mitochondrion HMP PubMed 
proteasome-mediated ubiquitin-dependent protein catabolic process IDA
Inferred from Direct Assay
more info
PubMed 
protein K11-linked ubiquitination IDA
Inferred from Direct Assay
more info
PubMed 
protein K48-linked ubiquitination IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
protein K48-linked ubiquitination IDA
Inferred from Direct Assay
more info
PubMed 
protein autoubiquitination IDA
Inferred from Direct Assay
more info
PubMed 
protein monoubiquitination IDA
Inferred from Direct Assay
more info
PubMed 
protein polyubiquitination IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
protein polyubiquitination IDA
Inferred from Direct Assay
more info
PubMed 
protein targeting to peroxisome TAS
Traceable Author Statement
more info
 
protein ubiquitination IDA
Inferred from Direct Assay
more info
PubMed 
protein ubiquitination TAS
Traceable Author Statement
more info
 
ubiquitin-dependent protein catabolic process IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
Component Evidence Code Pubs
cytosol TAS
Traceable Author Statement
more info
 
endosome membrane IEA
Inferred from Electronic Annotation
more info
 
extracellular exosome HDA PubMed 
nucleoplasm TAS
Traceable Author Statement
more info
 
nucleus IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
plasma membrane IEA
Inferred from Electronic Annotation
more info
 
ubiquitin ligase complex IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 

General protein information

Preferred Names
ubiquitin-conjugating enzyme E2 D3
Names
(E3-independent) E2 ubiquitin-conjugating enzyme D3
E2 ubiquitin-conjugating enzyme D3
ubiquitin carrier protein D3
ubiquitin conjugating enzyme E2D 3
ubiquitin-conjugating enzyme E2(17)KB 3
ubiquitin-conjugating enzyme E2-17 kDa 3
ubiquitin-conjugating enzyme E2D 3 (UBC4/5 homolog, yeast)
ubiquitin-conjugating enzyme E2D 3 (homologous to yeast UBC4/5)
ubiquitin-protein ligase D3
NP_001287724.1
NP_003331.1
NP_871615.1
NP_871616.1
NP_871617.1
NP_871618.1
NP_871619.1
NP_871620.1
NP_871621.1
NP_871622.1
XP_016864073.1
XP_024309970.1

NCBI Reference Sequences (RefSeq)

RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

mRNA and Protein(s)

  1. NM_001300795.1NP_001287724.1  ubiquitin-conjugating enzyme E2 D3 isoform 4

    See identical proteins and their annotated locations for NP_001287724.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (10) differs in its 5' UTR and uses a downstream start codon, compared to variant 1. The encoded isoform (4) has a shorter N-terminus, compared to isoform 1.
    Source sequence(s)
    AI651378, AK127304, BQ719030, BU677139, CD242548, DA550074, DB234695
    Consensus CDS
    CCDS75172.1
    UniProtKB/TrEMBL
    D6RAH7
    Related
    ENSP00000424359.1, ENST00000507845.5
    Conserved Domains (1) summary
    cl00154
    Location:1117
    UBCc; Ubiquitin-conjugating enzyme E2, catalytic (UBCc) domain. This is part of the ubiquitin-mediated protein degradation pathway in which a thiol-ester linkage forms between a conserved cysteine and the C-terminus of ubiquitin and complexes with ubiquitin ...
  2. NM_003340.6NP_003331.1  ubiquitin-conjugating enzyme E2 D3 isoform 1

    See identical proteins and their annotated locations for NP_003331.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) encodes the predominant isoform (1).
    Source sequence(s)
    AC018797, BC003395, BM750658, BM967209, DA557036
    Consensus CDS
    CCDS3660.1
    UniProtKB/Swiss-Prot
    P61077
    UniProtKB/TrEMBL
    A0A024RDH2
    Related
    ENSP00000378280.4, ENST00000394801.8
    Conserved Domains (1) summary
    cl00154
    Location:1146
    UBCc; Ubiquitin-conjugating enzyme E2, catalytic (UBCc) domain. This is part of the ubiquitin-mediated protein degradation pathway in which a thiol-ester linkage forms between a conserved cysteine and the C-terminus of ubiquitin and complexes with ubiquitin ...
  3. NM_181886.3NP_871615.1  ubiquitin-conjugating enzyme E2 D3 isoform 1

    See identical proteins and their annotated locations for NP_871615.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) has an additional segment in the 5' UTR, and encodes the same isoform (1), as compared to variant 1.
    Source sequence(s)
    AC018797, BC003395, BM750658, BM788287, BM967209
    Consensus CDS
    CCDS3660.1
    UniProtKB/Swiss-Prot
    P61077
    UniProtKB/TrEMBL
    A0A024RDH2
    Related
    ENSP00000378283.2, ENST00000394804.6
    Conserved Domains (1) summary
    cl00154
    Location:1146
    UBCc; Ubiquitin-conjugating enzyme E2, catalytic (UBCc) domain. This is part of the ubiquitin-mediated protein degradation pathway in which a thiol-ester linkage forms between a conserved cysteine and the C-terminus of ubiquitin and complexes with ubiquitin ...
  4. NM_181887.2NP_871616.1  ubiquitin-conjugating enzyme E2 D3 isoform 1

    See identical proteins and their annotated locations for NP_871616.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) differs in the 5' UTR, and encodes the same isoform (1), as compared to variant 1.
    Source sequence(s)
    AC018797, BM967209, DA588940, U39318
    Consensus CDS
    CCDS3660.1
    UniProtKB/Swiss-Prot
    P61077
    UniProtKB/TrEMBL
    A0A024RDH2
    Related
    ENSP00000318494.7, ENST00000321805.11
    Conserved Domains (1) summary
    cl00154
    Location:1146
    UBCc; Ubiquitin-conjugating enzyme E2, catalytic (UBCc) domain. This is part of the ubiquitin-mediated protein degradation pathway in which a thiol-ester linkage forms between a conserved cysteine and the C-terminus of ubiquitin and complexes with ubiquitin ...
  5. NM_181888.3NP_871617.1  ubiquitin-conjugating enzyme E2 D3 isoform 1

    See identical proteins and their annotated locations for NP_871617.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (4) lacks a segment in the 5' UTR, and encodes the same isoform (1), as compared to variant 1.
    Source sequence(s)
    AC018797, BC003395, BM750658, BM967209, DA335600
    Consensus CDS
    CCDS3660.1
    UniProtKB/Swiss-Prot
    P61077
    UniProtKB/TrEMBL
    A0A024RDH2
    Related
    ENSP00000344069.8, ENST00000349311.12
    Conserved Domains (1) summary
    cl00154
    Location:1146
    UBCc; Ubiquitin-conjugating enzyme E2, catalytic (UBCc) domain. This is part of the ubiquitin-mediated protein degradation pathway in which a thiol-ester linkage forms between a conserved cysteine and the C-terminus of ubiquitin and complexes with ubiquitin ...
  6. NM_181889.2NP_871618.1  ubiquitin-conjugating enzyme E2 D3 isoform 1

    See identical proteins and their annotated locations for NP_871618.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (5) has an alternate 5' UTR exon, and encodes the same isoform (1), as compared to variant 1.
    Source sequence(s)
    AC018797, AK315775, BC003395, BM967209, HY035067
    Consensus CDS
    CCDS3660.1
    UniProtKB/Swiss-Prot
    P61077
    UniProtKB/TrEMBL
    A0A024RDH2
    Related
    ENSP00000378282.5, ENST00000394803.9
    Conserved Domains (1) summary
    cl00154
    Location:1146
    UBCc; Ubiquitin-conjugating enzyme E2, catalytic (UBCc) domain. This is part of the ubiquitin-mediated protein degradation pathway in which a thiol-ester linkage forms between a conserved cysteine and the C-terminus of ubiquitin and complexes with ubiquitin ...
  7. NM_181890.2NP_871619.1  ubiquitin-conjugating enzyme E2 D3 isoform 1

    See identical proteins and their annotated locations for NP_871619.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (6) has an alternate 5' UTR exon, and encodes the same isoform (1), as compared to variant 1.
    Source sequence(s)
    AC018797, BC003395, BM967209, HY109217
    Consensus CDS
    CCDS3660.1
    UniProtKB/Swiss-Prot
    P61077
    UniProtKB/TrEMBL
    A0A024RDH2
    Related
    ENSP00000337208.3, ENST00000338145.7
    Conserved Domains (1) summary
    cl00154
    Location:1146
    UBCc; Ubiquitin-conjugating enzyme E2, catalytic (UBCc) domain. This is part of the ubiquitin-mediated protein degradation pathway in which a thiol-ester linkage forms between a conserved cysteine and the C-terminus of ubiquitin and complexes with ubiquitin ...
  8. NM_181891.3NP_871620.1  ubiquitin-conjugating enzyme E2 D3 isoform 1

    See identical proteins and their annotated locations for NP_871620.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (7) has an additional segment in the 5' UTR, and encodes the same isoform (1), as compared to variant 1.
    Source sequence(s)
    AC018797, BC003395, BM967209, DA494746
    Consensus CDS
    CCDS3660.1
    UniProtKB/Swiss-Prot
    P61077
    UniProtKB/TrEMBL
    A0A024RDH2
    Related
    ENSP00000396901.2, ENST00000453744.7
    Conserved Domains (1) summary
    cl00154
    Location:1146
    UBCc; Ubiquitin-conjugating enzyme E2, catalytic (UBCc) domain. This is part of the ubiquitin-mediated protein degradation pathway in which a thiol-ester linkage forms between a conserved cysteine and the C-terminus of ubiquitin and complexes with ubiquitin ...
  9. NM_181892.3NP_871621.1  ubiquitin-conjugating enzyme E2 D3 isoform 2

    See identical proteins and their annotated locations for NP_871621.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (8) differs in the 5' UTR and has an additional exon in the 3' region, as compared to variant 1. It encodes isoform 2, which has a distinct and one aa longer C-terminus, as compared to isoform 1.
    Source sequence(s)
    AC018797, AK095822, BM967209, DB501483
    Consensus CDS
    CCDS3661.1
    UniProtKB/Swiss-Prot
    P61077
    Related
    ENSP00000345285.5, ENST00000343106.9
    Conserved Domains (1) summary
    cl00154
    Location:1146
    UBCc; Ubiquitin-conjugating enzyme E2, catalytic (UBCc) domain. This is part of the ubiquitin-mediated protein degradation pathway in which a thiol-ester linkage forms between a conserved cysteine and the C-terminus of ubiquitin and complexes with ubiquitin ...
  10. NM_181893.2NP_871622.1  ubiquitin-conjugating enzyme E2 D3 isoform 3

    See identical proteins and their annotated locations for NP_871622.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (9) lacks two consecutive 5' exons, but has an alternate 5' exon, which contains an upstream in-frame start codon, as compared to variant 1. It encodes isoform 3, which has a distinct and two aa longer N-terminus, as compared to isoform 1.
    Source sequence(s)
    AC018797, BM967209, DA965437, HY109217
    Consensus CDS
    CCDS3659.1
    UniProtKB/Swiss-Prot
    P61077
    Related
    ENSP00000349722.6, ENST00000357194.10
    Conserved Domains (1) summary
    cl00154
    Location:6148
    UBCc; Ubiquitin-conjugating enzyme E2, catalytic (UBCc) domain. This is part of the ubiquitin-mediated protein degradation pathway in which a thiol-ester linkage forms between a conserved cysteine and the C-terminus of ubiquitin and complexes with ubiquitin ...

RefSeqs of Annotated Genomes: Homo sapiens Updated Annotation Release 109.

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000004.12 Reference GRCh38.p13 Primary Assembly

    Range
    102794383..102868893 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_017008584.2XP_016864073.1  ubiquitin-conjugating enzyme E2 D3 isoform X2

    UniProtKB/TrEMBL
    D6RAH7
    Related
    ENSP00000426620.1, ENST00000504211.5
    Conserved Domains (1) summary
    cl00154
    Location:1117
    UBCc; Ubiquitin-conjugating enzyme E2, catalytic (UBCc) domain. This is part of the ubiquitin-mediated protein degradation pathway in which a thiol-ester linkage forms between a conserved cysteine and the C-terminus of ubiquitin and complexes with ubiquitin ...
  2. XM_024454202.1XP_024309970.1  ubiquitin-conjugating enzyme E2 D3 isoform X1

    Conserved Domains (1) summary
    cl00154
    Location:1146
    UBCc; Ubiquitin-conjugating enzyme E2, catalytic (UBCc) domain. This is part of the ubiquitin-mediated protein degradation pathway in which a thiol-ester linkage forms between a conserved cysteine and the C-terminus of ubiquitin and complexes with ubiquitin ...
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