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    UBE2D1 ubiquitin conjugating enzyme E2 D1 [ Homo sapiens (human) ]

    Gene ID: 7321, updated on 7-Jul-2024

    Summary

    Official Symbol
    UBE2D1provided by HGNC
    Official Full Name
    ubiquitin conjugating enzyme E2 D1provided by HGNC
    Primary source
    HGNC:HGNC:12474
    See related
    Ensembl:ENSG00000072401 MIM:602961; AllianceGenome:HGNC:12474
    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
    SFT; UBCH5; UBC4/5; UBCH5A; E2(17)KB1
    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 is closely related to a stimulator of iron transport (SFT), and is up-regulated in hereditary hemochromatosis. It also functions in the ubiquitination of the tumor-suppressor protein p53 and the hypoxia-inducible transcription factor HIF1alpha by interacting with the E1 ubiquitin-activating enzyme and the E3 ubiquitin-protein ligases. Two transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Mar 2011]
    Expression
    Ubiquitous expression in bone marrow (RPKM 16.4), appendix (RPKM 13.7) and 25 other tissues See more
    Orthologs
    NEW
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    Genomic context

    See UBE2D1 in Genome Data Viewer
    Location:
    10q21.1
    Exon count:
    7
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 10 NC_000010.11 (58335006..58370748)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 10 NC_060934.1 (59189115..59224853)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 10 NC_000010.10 (60094766..60130508)

    Chromosome 10 - NC_000010.11Genomic Context describing neighboring genes Neighboring gene H3K27ac hESC enhancer GRCh37_chr10:60028628-60029184 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2377 Neighboring gene CDGSH iron sulfur domain 1 Neighboring gene uncharacterized LOC112268068 Neighboring gene H3K27ac hESC enhancer GRCh37_chr10:60094430-60094930 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3385 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:60144914-60145570 Neighboring gene transcription factor A, mitochondrial Neighboring gene uncharacterized LOC105378316 Neighboring gene ReSE screen-validated silencer GRCh37_chr10:60207389-60207551

    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?

    Phenotypes

    EBI GWAS Catalog

    Description
    Genome-wide meta-analysis increases to 71 the number of confirmed Crohn's disease susceptibility loci.
    EBI GWAS Catalog

    HIV-1 interactions

    Protein interactions

    Protein Gene Interaction Pubs
    Tat tat Ubiquitination of HIV-1 Tat by Hdm2 requires ubiquitin-conjugating enzyme E2D 1 (UbcH5) PubMed

    Go to the HIV-1, Human Interaction Database

    Pathways from PubChem

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    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
     
    Component Evidence Code Pubs
    located_in cytoplasm IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in cytosol TAS
    Traceable Author Statement
    more info
     
    located_in nucleoplasm TAS
    Traceable Author Statement
    more info
     
    is_active_in nucleus IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    part_of protein-containing complex IDA
    Inferred from Direct Assay
    more info
    PubMed 
    part_of ubiquitin ligase complex IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    part_of ubiquitin ligase complex IDA
    Inferred from Direct Assay
    more info
    PubMed 

    General protein information

    Preferred Names
    ubiquitin-conjugating enzyme E2 D1
    Names
    (E3-independent) E2 ubiquitin-conjugating enzyme D1
    E2 ubiquitin-conjugating enzyme D1
    UBC4/5 homolog
    stimulator of Fe transport
    ubiquitin carrier protein D1
    ubiquitin conjugating enzyme E2D 1
    ubiquitin-conjugating enzyme E2(17)KB 1
    ubiquitin-conjugating enzyme E2-17 kDa 1
    ubiquitin-conjugating enzyme E2D 1 (UBC4/5 homolog, yeast)
    ubiquitin-protein ligase D1
    NP_001191809.1
    NP_003329.1

    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_001204880.2NP_001191809.1  ubiquitin-conjugating enzyme E2 D1 isoform 2

      See identical proteins and their annotated locations for NP_001191809.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) lacks an alternate coding exon compared to variant 1. The resulting isoform (2) uses a downstream start site and has a shorter and distinct N-terminus compared to isoform 1.
      Source sequence(s)
      AC023170, DA618122
      Consensus CDS
      CCDS73139.1
      UniProtKB/TrEMBL
      A0A087WW00
      Related
      ENSP00000479814.1, ENST00000615793.1
      Conserved Domains (1) summary
      COG5078
      Location:3109
      COG5078; Ubiquitin-protein ligase [Posttranslational modification, protein turnover, chaperones]
    2. NM_003338.5NP_003329.1  ubiquitin-conjugating enzyme E2 D1 isoform 1

      See identical proteins and their annotated locations for NP_003329.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).
      Source sequence(s)
      AC023170, BC005980, DA677507
      Consensus CDS
      CCDS7252.1
      UniProtKB/Swiss-Prot
      A6NLF6, A8K786, P51668
      Related
      ENSP00000363019.3, ENST00000373910.9
      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 ...

    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_000010.11 Reference GRCh38.p14 Primary Assembly

      Range
      58335006..58370748
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060934.1 Alternate T2T-CHM13v2.0

      Range
      59189115..59224853
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)