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

    Gene ID: 7323, updated on 7-Apr-2024

    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; AllianceGenome:HGNC:12476
    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
    NEW
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    Try the new Transcript table

    Genomic context

    Location:
    4q24
    Exon count:
    13
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 4 NC_000004.12 (102794383..102868895, complement)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 4 NC_060928.1 (106108341..106183222, complement)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 4 NC_000004.11 (103715540..103790052, complement)

    Chromosome 4 - NC_000004.12Genomic Context describing neighboring genes Neighboring gene mannosidase beta Neighboring gene WD repeat domain 12 pseudogene Neighboring gene ReSE screen-validated silencer GRCh37_chr4:103675856-103676033 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21757 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15599 Neighboring gene uncharacterized LOC102723704 Neighboring gene uncharacterized LOC124900743 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr4:103746355-103747554 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:103748137-103748698 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:103748699-103749260 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21760 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21761 Neighboring gene UBE2D3 antisense RNA 1 Neighboring gene RNA, U7 small nuclear 151 pseudogene Neighboring gene small nucleolar RNA U13 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21762 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15602 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15603 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

    Clone Names

    • MGC5416, MGC43926

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables ATP binding IEA
    Inferred from Electronic Annotation
    more info
     
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    enables ubiquitin conjugating enzyme activity IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    enables ubiquitin conjugating enzyme activity IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables ubiquitin protein ligase activity IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables ubiquitin protein ligase binding IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    enables ubiquitin-protein transferase activity IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables ubiquitin-protein transferase activity TAS
    Traceable Author Statement
    more info
     
    Process Evidence Code Pubs
    involved_in DNA repair IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in apoptotic process IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in negative regulation of BMP signaling pathway TAS
    Traceable Author Statement
    more info
     
    involved_in negative regulation of transcription by RNA polymerase II TAS
    Traceable Author Statement
    more info
     
    involved_in positive regulation of protein targeting to mitochondrion HMP PubMed 
    involved_in proteasome-mediated ubiquitin-dependent protein catabolic process IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in protein K11-linked ubiquitination IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in protein K11-linked ubiquitination IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in protein K48-linked ubiquitination IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in protein K48-linked ubiquitination IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in protein K6-linked ubiquitination IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in protein autoubiquitination IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in protein modification process TAS
    Traceable Author Statement
    more info
    PubMed 
    involved_in protein monoubiquitination IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in protein polyubiquitination IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in protein ubiquitination IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in ubiquitin-dependent protein catabolic process IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    Component Evidence Code Pubs
    located_in cytosol TAS
    Traceable Author Statement
    more info
     
    located_in endosome membrane IEA
    Inferred from Electronic Annotation
    more info
     
    located_in extracellular exosome HDA PubMed 
    located_in nucleoplasm TAS
    Traceable Author Statement
    more info
     
    is_active_in nucleus IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    located_in plasma membrane IEA
    Inferred from Electronic Annotation
    more info
     
    part_of ubiquitin ligase complex IBA
    Inferred from Biological aspect of Ancestor
    more info
     

    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_024309970.1
    XP_054206763.1

    NCBI Reference Sequences (RefSeq)

    NEW Try the new Transcript table

    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_001300795.2NP_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)
      AC018797, AI651378, AK127304, BQ719030, BU677139, CD242548, DA550074, DB234695
      Consensus CDS
      CCDS75172.1
      UniProtKB/TrEMBL
      D6RAH7, D6RFM0
      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
      A6NJ93, A6NJB1, A6NM99, P47986, P61077, Q6IB88, Q6NXS4, Q8N924
      UniProtKB/TrEMBL
      A0A087WY85
      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
      A6NJ93, A6NJB1, A6NM99, P47986, P61077, Q6IB88, Q6NXS4, Q8N924
      UniProtKB/TrEMBL
      A0A087WY85
      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_181887.3NP_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
      A6NJ93, A6NJB1, A6NM99, P47986, P61077, Q6IB88, Q6NXS4, Q8N924
      UniProtKB/TrEMBL
      A0A087WY85
      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
      A6NJ93, A6NJB1, A6NM99, P47986, P61077, Q6IB88, Q6NXS4, Q8N924
      UniProtKB/TrEMBL
      A0A087WY85
      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
      A6NJ93, A6NJB1, A6NM99, P47986, P61077, Q6IB88, Q6NXS4, Q8N924
      UniProtKB/TrEMBL
      A0A087WY85
      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_181890.3NP_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
      A6NJ93, A6NJB1, A6NM99, P47986, P61077, Q6IB88, Q6NXS4, Q8N924
      UniProtKB/TrEMBL
      A0A087WY85
      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
      A6NJ93, A6NJB1, A6NM99, P47986, P61077, Q6IB88, Q6NXS4, Q8N924
      UniProtKB/TrEMBL
      A0A087WY85
      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_181892.4NP_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
      Consensus CDS
      CCDS3661.1
      UniProtKB/TrEMBL
      A0A087WY85
      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_181893.3NP_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/TrEMBL
      A0A087WY85
      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: GCF_000001405.40-RS_2023_10

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

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000004.12 Reference GRCh38.p14 Primary Assembly

      Range
      102794383..102868895 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_024454202.2XP_024309970.1  ubiquitin-conjugating enzyme E2 D3 isoform X1

      UniProtKB/Swiss-Prot
      A6NJ93, A6NJB1, A6NM99, P47986, P61077, Q6IB88, Q6NXS4, Q8N924
      UniProtKB/TrEMBL
      A0A087WY85
      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 ...

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060928.1 Alternate T2T-CHM13v2.0

      Range
      106108341..106183222 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054350788.1XP_054206763.1  ubiquitin-conjugating enzyme E2 D3 isoform X1

      UniProtKB/Swiss-Prot
      A6NJ93, A6NJB1, A6NM99, P47986, P61077, Q6IB88, Q6NXS4, Q8N924