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

Gene ID: 90025, updated on 2-Nov-2024

Summary

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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. [provided by Alliance of Genome Resources, Nov 2024]
Expression
Low expression observed in reference dataset See more
Orthologs
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Genomic context

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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

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: HPA RNA-seq normal tissues 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. Whole-exome sequencing implicates UBE3D in age-related macular degeneration in East Asian populations. Huang LZ, et al. Nat Commun, 2015 Apr 15. PMID 25872646
  2. Genome-wide association study of biologically informed periodontal complex traits offers novel insights into the genetic basis of periodontal disease. Offenbacher S, et al. Hum Mol Genet, 2016 May 15. PMID 26962152, Free PMC Article
  3. UBE3D Is Involved in Blue Light-Induced Retinal Damage by Regulating Double-Strand Break Repair. Xu N, et al. Invest Ophthalmol Vis Sci, 2022 Sep 1. PMID 36094642, Free PMC Article
  4. A novel UbcH10-binding protein facilitates the ubiquitinylation of cyclin B in vitro. Kobirumaki F, et al. J Biochem, 2005 Feb. PMID 15749827
  5. Viral protein engagement of GBF1 induces host cell vulnerability through synthetic lethality. Navare AT, et al. J Cell Biol, 2022 Nov 7. PMID 36305789, Free PMC Article

See all (21) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. With the exception of associations of BEGAIN with severe and UBE3D with moderate chronic periodontitis (CP) , no other loci were associated with CP in ARIC or aggressive periodontitis in the German sample.
    Title: Genome-wide association study of biologically informed periodontal complex traits offers novel insights into the genetic basis of periodontal disease.
  2. A novel missense SNV, rs7739323, is strongly associated with age-related macular degeneration in an East Asian population.
    Title: Whole-exome sequencing implicates UBE3D in age-related macular degeneration in East Asian populations.
  3. The carboxyl terminal half of H10BH was able to bind cyclin B and ubiquitinylate cyclin B in vitro.
    Title: A novel UbcH10-binding protein facilitates the ubiquitinylation of cyclin B in vitro.
Submit: New GeneRIF Correction

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)

Genotypes

Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

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 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

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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)

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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_001304437.2 → NP_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:75 → 345
    HECT_2; HECT-like Ubiquitin-conjugating enzyme (E2)-binding

  2. NM_001350602.2 → NP_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:75 → 345
    HECT_2; HECT-like Ubiquitin-conjugating enzyme (E2)-binding

  3. NM_001350603.2 → NP_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:5 → 190
    HECT_2; HECT-like Ubiquitin-conjugating enzyme (E2)-binding

  4. NM_001350604.2 → NP_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:5 → 190
    HECT_2; HECT-like Ubiquitin-conjugating enzyme (E2)-binding

  5. NM_001410933.1 → NP_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_198920.3 → NP_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:107 → 377
    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_017011458.3 → XP_016866947.1  E3 ubiquitin-protein ligase E3D isoform X7

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

    Conserved Domains (1) summary
    pfam09814
    Location:13 → 378
    HECT_2; HECT-like Ubiquitin-conjugating enzyme (E2)-binding

  3. XM_047419505.1 → XP_047275461.1  E3 ubiquitin-protein ligase E3D isoform X5

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

    Conserved Domains (1) summary
    pfam09814
    Location:13 → 378
    HECT_2; HECT-like Ubiquitin-conjugating enzyme (E2)-binding

  5. XM_017011459.3 → XP_016866948.1  E3 ubiquitin-protein ligase E3D isoform X3

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

    Conserved Domains (1) summary
    pfam09814
    Location:13 → 378
    HECT_2; HECT-like Ubiquitin-conjugating enzyme (E2)-binding

  7. XM_047419506.1 → XP_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_054356716.1 → XP_054212691.1  E3 ubiquitin-protein ligase E3D isoform X8

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

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

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

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

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

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

RNA

  1. XR_008487505.1 RNA Sequence

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q7Z6J8.2 GenPept UniProtKB/Swiss-Prot:Q7Z6J8

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