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    UBE3D ubiquitin protein ligase E3D [ Homo sapiens (human) ]

    Gene ID: 90025, updated on 27-Dec-2024

    Summary

    Official Symbol
    UBE3Dprovided by HGNC
    Official Full Name
    ubiquitin protein ligase E3Dprovided by HGNC
    Primary source
    HGNC:HGNC:21381
    See related
    Ensembl:ENSG00000118420 MIM:612495; AllianceGenome:HGNC:21381
    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
    H10BH; UBE2CBP; YJR141W; C6orf157
    Summary
    Enables cyclin binding activity; ubiquitin protein ligase activity; and ubiquitin-like protein conjugating enzyme binding activity. Involved in protein autoubiquitination; protein monoubiquitination; and protein polyubiquitination. Part of ubiquitin ligase complex. Is active in cytosol. [provided by Alliance of Genome Resources, Dec 2024]
    Expression
    Low expression observed in reference dataset See more
    Orthologs
    NEW
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    Genomic context

    See UBE3D in Genome Data Viewer
    Location:
    6q14.1
    Exon count:
    21
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 6 NC_000006.12 (82880802..83065841, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (84098732..84288846, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (83602109..83775560, complement)

    Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105377876 Neighboring gene MPRA-validated peak5925 silencer Neighboring gene uncharacterized LOC105377877 Neighboring gene MPRA-validated peak5926 silencer Neighboring gene leucine aminopeptidase 3 pseudogene 1 Neighboring gene ReSE screen-validated silencer GRCh37_chr6:83710771-83710962 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr6:83747652-83748851 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24780 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24781 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17355 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24782 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24783 Neighboring gene NANOG hESC enhancer GRCh37_chr6:83821047-83821571 Neighboring gene DOP1 leucine zipper like protein A Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17356 Neighboring gene H3K27ac hESC enhancer GRCh37_chr6:83902947-83903446 Neighboring gene phosphoglucomutase 3 Neighboring gene RWD domain containing 2A

    Genomic regions, transcripts, and products

    Expression

    • Project title: Tissue-specific circular RNA induction during human fetal development
    • Description: 35 human fetal samples from 6 tissues (3 - 7 replicates per tissue) collected between 10 and 20 weeks gestational time were sequenced using Illumina TruSeq Stranded Total RNA
    • BioProject: PRJNA270632
    • Publication: PMID 26076956
    • Analysis date: Mon Apr 2 22:54:59 2018

    Bibliography

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Clone Names

    • MGC126561, MGC126587, DKFZp434A1520

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables cyclin binding IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    enables cyclin binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    enables ubiquitin conjugating enzyme binding IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    enables ubiquitin protein ligase activity IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    enables ubiquitin protein ligase activity IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables ubiquitin-like protein conjugating enzyme binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    Process Evidence Code Pubs
    involved_in proteasome-mediated ubiquitin-dependent protein catabolic process IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in protein autoubiquitination IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in protein autoubiquitination IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in protein monoubiquitination IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in protein monoubiquitination IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in protein polyubiquitination IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in protein polyubiquitination IDA
    Inferred from Direct Assay
    more info
    PubMed 
    Component Evidence Code Pubs
    is_active_in cytosol IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    is_active_in cytosol IDA
    Inferred from Direct Assay
    more info
    PubMed 
    is_active_in nucleus IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    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
    E3 ubiquitin-protein ligase E3D
    Names
    HECT-type E3 ubiquitin transferase E3D
    UBCH10 binding protein with a hect-like domain
    ubcH10-binding protein with a HECT-like domain
    ubiquitin-conjugating enzyme E2C-binding protein
    NP_001291366.1
    NP_001337531.1
    NP_001337532.1
    NP_001337533.1
    NP_001397862.1
    NP_944602.1
    XP_011534540.1
    XP_011534542.1
    XP_011534543.1
    XP_016866947.1
    XP_016866948.1
    XP_047275461.1
    XP_047275462.1
    XP_054212690.1
    XP_054212691.1
    XP_054212692.1
    XP_054212693.1
    XP_054212694.1
    XP_054212695.1
    XP_054212696.1

    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_001304437.2NP_001291366.1  E3 ubiquitin-protein ligase E3D isoform 2

      See identical proteins and their annotated locations for NP_001291366.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) has an alternate splice site in the 5' region, which results in translation initiation at a downstream AUG start codon, compared to variant 1. The resulting isoform (2) is shorter at the N-terminus, compared to isoform 1. Variants 2 and 3 both encode the same isoform (2).
      Source sequence(s)
      AL034377, BC036049, BC057845, BC071763
      UniProtKB/Swiss-Prot
      Q7Z6J8
      UniProtKB/TrEMBL
      Q4G0J6, Q4G0X5
      Conserved Domains (1) summary
      pfam09814
      Location:75345
      HECT_2; HECT-like Ubiquitin-conjugating enzyme (E2)-binding
    2. NM_001350602.2NP_001337531.1  E3 ubiquitin-protein ligase E3D isoform 2

      Status: VALIDATED

      Description
      Transcript Variant: This variant (3), as well as variant 2, encodes isoform 2.
      Source sequence(s)
      AL034377, AL139333, AL355613, AL357121
      Conserved Domains (1) summary
      pfam09814
      Location:75345
      HECT_2; HECT-like Ubiquitin-conjugating enzyme (E2)-binding
    3. NM_001350603.2NP_001337532.1  E3 ubiquitin-protein ligase E3D isoform 3

      Status: VALIDATED

      Description
      Transcript Variant: This variant (4), as well as variant 5, encodes isoform 3.
      Source sequence(s)
      AL034377, AL139333, AL355613, AL357121
      Conserved Domains (1) summary
      pfam09814
      Location:5190
      HECT_2; HECT-like Ubiquitin-conjugating enzyme (E2)-binding
    4. NM_001350604.2NP_001337533.1  E3 ubiquitin-protein ligase E3D isoform 3

      Status: VALIDATED

      Description
      Transcript Variant: This variant (5), as well as variant 4, encodes isoform 3.
      Source sequence(s)
      AL034377, AL139333, AL355613, AL357121
      Conserved Domains (1) summary
      pfam09814
      Location:5190
      HECT_2; HECT-like Ubiquitin-conjugating enzyme (E2)-binding
    5. NM_001410933.1NP_001397862.1  E3 ubiquitin-protein ligase E3D isoform 4

      Status: VALIDATED

      Source sequence(s)
      AL139333, AL357121
      Consensus CDS
      CCDS93953.1
      UniProtKB/TrEMBL
      D6RD24
      Related
      ENSP00000427101.1, ENST00000509102.5
    6. NM_198920.3NP_944602.1  E3 ubiquitin-protein ligase E3D isoform 1

      See identical proteins and their annotated locations for NP_944602.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) encodes the longest isoform (1).
      Source sequence(s)
      AB126062, AK298205, AL034377, BC057845, BC071763
      Consensus CDS
      CCDS34491.1
      UniProtKB/Swiss-Prot
      B4DP63, Q5T4W2, Q6IPR4, Q75UG0, Q7Z6J8, Q9NT42
      Related
      ENSP00000358762.3, ENST00000369747.8
      Conserved Domains (1) summary
      pfam09814
      Location:107377
      HECT_2; HECT-like Ubiquitin-conjugating enzyme (E2)-binding

    RNA

    1. NR_146807.2 RNA Sequence

      Status: VALIDATED

      Source sequence(s)
      AL034377, AL139333, AL355613, AL357121
    2. NR_146808.2 RNA Sequence

      Status: VALIDATED

      Source sequence(s)
      AL034377, AL139333, AL355613, AL357121
    3. NR_146809.2 RNA Sequence

      Status: VALIDATED

      Source sequence(s)
      AL034377, AL139333, AL355613, BC143617
      Related
      ENST00000237186.10

    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_000006.12 Reference GRCh38.p14 Primary Assembly

      Range
      82880802..83065841 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_017011458.3XP_016866947.1  E3 ubiquitin-protein ligase E3D isoform X7

    2. XM_011536238.4XP_011534540.1  E3 ubiquitin-protein ligase E3D isoform X1

      Conserved Domains (1) summary
      pfam09814
      Location:13378
      HECT_2; HECT-like Ubiquitin-conjugating enzyme (E2)-binding
    3. XM_047419505.1XP_047275461.1  E3 ubiquitin-protein ligase E3D isoform X5

    4. XM_011536240.3XP_011534542.1  E3 ubiquitin-protein ligase E3D isoform X2

      Conserved Domains (1) summary
      pfam09814
      Location:13378
      HECT_2; HECT-like Ubiquitin-conjugating enzyme (E2)-binding
    5. XM_017011459.3XP_016866948.1  E3 ubiquitin-protein ligase E3D isoform X3

    6. XM_011536241.4XP_011534543.1  E3 ubiquitin-protein ligase E3D isoform X4

      Conserved Domains (1) summary
      pfam09814
      Location:13378
      HECT_2; HECT-like Ubiquitin-conjugating enzyme (E2)-binding
    7. XM_047419506.1XP_047275462.1  E3 ubiquitin-protein ligase E3D isoform X6

    RNA

    1. XR_007059385.1 RNA Sequence

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060930.1 Alternate T2T-CHM13v2.0

      Range
      84098732..84288846 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054356716.1XP_054212691.1  E3 ubiquitin-protein ligase E3D isoform X8

    2. XM_054356715.1XP_054212690.1  E3 ubiquitin-protein ligase E3D isoform X1

    3. XM_054356720.1XP_054212695.1  E3 ubiquitin-protein ligase E3D isoform X5

    4. XM_054356717.1XP_054212692.1  E3 ubiquitin-protein ligase E3D isoform X2

    5. XM_054356718.1XP_054212693.1  E3 ubiquitin-protein ligase E3D isoform X3

    6. XM_054356719.1XP_054212694.1  E3 ubiquitin-protein ligase E3D isoform X4

    7. XM_054356721.1XP_054212696.1  E3 ubiquitin-protein ligase E3D isoform X6

    RNA

    1. XR_008487505.1 RNA Sequence