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    UBE2D4 ubiquitin conjugating enzyme E2 D4 [ Homo sapiens (human) ]

    Gene ID: 51619, updated on 27-Nov-2024

    Summary

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    Official Symbol
    UBE2D4provided by HGNC
    Official Full Name
    ubiquitin conjugating enzyme E2 D4provided by HGNC
    Primary source
    HGNC:HGNC:21647
    See related
    Ensembl:ENSG00000078967 AllianceGenome:HGNC:21647
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    HBUCE1
    Summary
    Enables ubiquitin conjugating enzyme activity. Involved in protein polyubiquitination. Acts upstream of or within protein ubiquitination. Predicted to be part of ubiquitin ligase complex. Predicted to be active in nucleus. [provided by Alliance of Genome Resources, Nov 2024]
    Expression
    Ubiquitous expression in brain (RPKM 6.5), heart (RPKM 5.7) and 25 other tissues See more
    Orthologs
    all
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    Genomic context

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    See UBE2D4 in Genome Data Viewer
    Location:
    7p13
    Exon count:
    10
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 7 NC_000007.14 (43926436..43956136)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 7 NC_060931.1 (44084736..44114438)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 7 NC_000007.13 (43966035..43995735)

    Chromosome 7 - NC_000007.14Genomic Context describing neighboring genes Neighboring gene URGCP-MRPS24 readthrough Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18130 Neighboring gene uncharacterized LOC124901620 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25921 Neighboring gene ReSE screen-validated silencer GRCh37_chr7:43911515-43911690 Neighboring gene upregulator of cell proliferation Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18131 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18132 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18133 Neighboring gene tubulin gamma 1 pseudogene Neighboring gene RNA polymerase II subunit J4 (pseudogene) Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18134 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18135 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:44010479-44010996 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18136 Neighboring gene speedy/RINGO cell cycle regulator family member E1 Neighboring gene Sharpr-MPRA regulatory region 7454 Neighboring gene ReSE screen-validated silencer GRCh37_chr7:44070666-44070855 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:44075983-44076482 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18137 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18138 Neighboring gene RAS p21 protein activator 4C, pseudogene Neighboring gene long intergenic non-protein coding RNA 957

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • 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

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    Related articles in PubMed

    1. Accumulation of p53 via down-regulation of UBE2D family genes is a critical pathway for cadmium-induced renal toxicity. Lee JY, et al. Sci Rep, 2016 Feb 25. PMID 26912277, Free PMC Article
    2. Analysis of the Zn-Binding Domains of TRIM32, the E3 Ubiquitin Ligase Mutated in Limb Girdle Muscular Dystrophy 2H. Lazzari E, et al. Cells, 2019 Mar 16. PMID 30884854, Free PMC Article
    3. Structure and catalytic activation of the TRIM23 RING E3 ubiquitin ligase. Dawidziak DM, et al. Proteins, 2017 Oct. PMID 28681414, Free PMC Article
    4. Inhibition of UVSSA ubiquitination suppresses transcription-coupled nucleotide excision repair deficiency caused by dissociation from USP7. Higa M, et al. FEBS J, 2018 Mar. PMID 29323787
    5. Ube2W conjugates ubiquitin to α-amino groups of protein N-termini. Tatham MH, et al. Biochem J, 2013 Jul 1. PMID 23560854, Free PMC Article

    See all (45) citations in PubMed

    GeneRIFs: Gene References Into Functions

    Phenotypes

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    Find tests for this gene in the NIH Genetic Testing Registry (GTR)

    Review eQTL and phenotype association data in this region using PheGenI

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • FLJ32004

    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 transferase activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    Process Evidence Code Pubs
    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 K27-linked ubiquitination IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in protein K29-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 K63-linked ubiquitination IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in protein K63-linked ubiquitination IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    acts_upstream_of_or_within 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
    is_active_in nucleus IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  

    General protein information

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    Preferred Names
    ubiquitin-conjugating enzyme E2 D4
    Names
    E2 ubiquitin-conjugating enzyme D4
    ubiquitin carrier protein D4
    ubiquitin conjugating enzyme E2 D4 (putative)
    ubiquitin conjugating enzyme E2D 4 (putative)
    ubiquitin-conjugating enzyme HBUCE1
    ubiquitin-protein ligase D4
    NP_057067.1
    XP_006715797.1
    XP_024302563.1
    XP_047276417.1
    XP_047276418.1
    XP_047276419.1
    XP_047276420.1
    XP_054214351.1
    XP_054214352.1
    XP_054214353.1
    XP_054214354.1
    XP_054214355.1
    XP_054214356.1

    NCBI Reference Sequences (RefSeq)

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    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_015983.4 → NP_057067.1  ubiquitin-conjugating enzyme E2 D4

      See identical proteins and their annotated locations for NP_057067.1

      Status: VALIDATED

      Source sequence(s)
      AC004985, AW014299, BC004104, BG499454
      Consensus CDS
      CCDS5474.1
      UniProtKB/Swiss-Prot
      A4D1V0, Q9Y2X8
      Related
      ENSP00000222402.2, ENST00000222402.8
      Conserved Domains (1) summary
      cl00154
      Location:1 → 146
      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_2024_08

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

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000007.14 Reference GRCh38.p14 Primary Assembly

      Range
      43926436..43956136
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_006715734.4 → XP_006715797.1  ubiquitin-conjugating enzyme E2 D4 isoform X2

      Conserved Domains (1) summary
      cl00154
      Location:1 → 146
      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_047420461.1 → XP_047276417.1  ubiquitin-conjugating enzyme E2 D4 isoform X3

    3. XM_047420462.1 → XP_047276418.1  ubiquitin-conjugating enzyme E2 D4 isoform X4

    4. XM_047420463.1 → XP_047276419.1  ubiquitin-conjugating enzyme E2 D4 isoform X5

    5. XM_024446795.2 → XP_024302563.1  ubiquitin-conjugating enzyme E2 D4 isoform X1

      Conserved Domains (1) summary
      cl00154
      Location:54 → 191
      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. XM_047420464.1 → XP_047276420.1  ubiquitin-conjugating enzyme E2 D4 isoform X6

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060931.1 Alternate T2T-CHM13v2.0

      Range
      44084736..44114438
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054358378.1 → XP_054214353.1  ubiquitin-conjugating enzyme E2 D4 isoform X3

    2. XM_054358379.1 → XP_054214354.1  ubiquitin-conjugating enzyme E2 D4 isoform X4

    3. XM_054358377.1 → XP_054214352.1  ubiquitin-conjugating enzyme E2 D4 isoform X2

    4. XM_054358380.1 → XP_054214355.1  ubiquitin-conjugating enzyme E2 D4 isoform X5

    5. XM_054358376.1 → XP_054214351.1  ubiquitin-conjugating enzyme E2 D4 isoform X1

    6. XM_054358381.1 → XP_054214356.1  ubiquitin-conjugating enzyme E2 D4 isoform X6

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9Y2X8.1 GenPept UniProtKB/Swiss-Prot:Q9Y2X8

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