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

    Gene ID: 90025, updated on 9-Dec-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, Dec 2024]
    Expression
    Low expression observed in reference dataset See more
    Orthologs
    mouse all
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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
    • 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. Cytoplasmic binding partners of the Integrator endonuclease INTS11 and its paralog CPSF73 are required for their nuclear function. Lin MH, et al. Mol Cell, 2024 Aug 8. PMID 39032490,

    See all (22) 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)

    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 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

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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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    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_001304437.2 → 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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