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    DTX3 deltex E3 ubiquitin ligase 3 [ Homo sapiens (human) ]

    Gene ID: 196403, updated on 27-Nov-2024

    Summary

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    Official Symbol
    DTX3provided by HGNC
    Official Full Name
    deltex E3 ubiquitin ligase 3provided by HGNC
    Primary source
    HGNC:HGNC:24457
    See related
    Ensembl:ENSG00000178498 MIM:613142; AllianceGenome:HGNC:24457
    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
    RNF154; deltex3
    Summary
    DTX3 functions as an E3 ubiquitin ligase (Takeyama et al., 2003 [PubMed 12670957]).[supplied by OMIM, Nov 2009]
    Expression
    Ubiquitous expression in brain (RPKM 21.6), endometrium (RPKM 16.7) and 24 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See DTX3 in Genome Data Viewer
    Location:
    12q13.3
    Exon count:
    6
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 12 NC_000012.12 (57604824..57609802)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 12 NC_060936.1 (57572308..57578021)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 12 NC_000012.11 (57998607..58003585)

    Chromosome 12 - NC_000012.12Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4584 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:57944162-57944754 Neighboring gene kinesin family member 5A Neighboring gene ReSE screen-validated silencer GRCh37_chr12:57955995-57956161 Neighboring gene ReSE screen-validated silencer GRCh37_chr12:57956855-57957072 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6549 Neighboring gene H3K27ac hESC enhancer GRCh37_chr12:57984713-57985214 Neighboring gene phosphatidylinositol-5-phosphate 4-kinase type 2 gamma Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:57997977-57998488 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:57998489-57999001 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4586 Neighboring gene Rho guanine nucleotide exchange factor 25 Neighboring gene uncharacterized LOC101927583 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:58013541-58014107 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:58014245-58015064 Neighboring gene solute carrier family 26 member 10, pseudogene

    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. Silencing DTX3L Inhibits the Progression of Cervical Carcinoma by Regulating PI3K/AKT/mTOR Signaling Pathway. Hu W, et al. Int J Mol Sci, 2023 Jan 3. PMID 36614304, Free PMC Article
    2. DTX3 copy number increase in breast cancer: a study of associations to molecular subtype, proliferation and prognosis. Valla M, et al. Breast Cancer Res Treat, 2021 May. PMID 33616774, Free PMC Article
    3. Ubiquitin ligase DTX3 empowers mutant p53 to promote ovarian cancer development. Wang S, et al. Genes Dis, 2022 May. PMID 35782979, Free PMC Article
    4. Ubiquitination of NOTCH2 by DTX3 suppresses the proliferation and migration of human esophageal carcinoma. Ding XY, et al. Cancer Sci, 2020 Feb. PMID 31854042, Free PMC Article
    5. Novel Isoform DTX3c Associates with UBE2N-UBA1 and Cdc48/p97 as Part of the EphB4 Degradation Complex Regulated by the Autocrine IGF-II/IR(A) Signal in Malignant Mesothelioma. Scalia P, et al. Int J Mol Sci, 2023 Apr 17. PMID 37108544, Free PMC Article

    See all (28) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Silencing DTX3L Inhibits the Progression of Cervical Carcinoma by Regulating PI3K/AKT/mTOR Signaling Pathway.
      Title: Silencing DTX3L Inhibits the Progression of Cervical Carcinoma by Regulating PI3K/AKT/mTOR Signaling Pathway.
    2. DTX3 copy number increase in breast cancer: a study of associations to molecular subtype, proliferation and prognosis.
      Title: DTX3 copy number increase in breast cancer: a study of associations to molecular subtype, proliferation and prognosis.
    3. DTX3, a novel E3 ligase for NOTCH2 was identified, and promoted its ubiquitination and degradation. DTX3 overexpression suppressed the proliferation and tumorigenicity of human oesophageal carcinoma cells. The analysis of tissue samples from patients revealed that the expression of DTX3 was low in esophageal cancer cells.
      Title: Ubiquitination of NOTCH2 by DTX3 suppresses the proliferation and migration of human esophageal carcinoma.
    4. We show here that both molecules (Deltex (DTX) and AIP4) interact and partially colocalize to endocytic vesicles, and that AIP4 targets DTX for lysosomal degradation.
      Title: Itch/AIP4 mediates Deltex degradation through the formation of K29-linked polyubiquitin chains.
    5. It is reported that BBAP and the human family of DTX proteins (DTX1, DTX2, and DTX3) function as E3 ligases based on their capacity for self-ubiquitination.
      Title: The BAL-binding protein BBAP and related Deltex family members exhibit ubiquitin-protein isopeptide ligase activity.
    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)

    Pathways from PubChem

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    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • FLJ34766, MGC138863, MGC138864

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables metal ion binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables transferase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables ubiquitin protein ligase activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Process Evidence Code Pubs
    involved_in Notch signaling pathway IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in Notch signaling pathway IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in protein ubiquitination IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in protein ubiquitination IEA
    Inferred from Electronic Annotation
    more info
    		  
    Component Evidence Code Pubs
    located_in cytoplasm IEA
    Inferred from Electronic Annotation
    more info
    		  
    is_active_in nucleoplasm IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  

    General protein information

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    Preferred Names
    probable E3 ubiquitin-protein ligase DTX3
    Names
    RING finger protein 154
    RING-type E3 ubiquitin transferase DTX3
    deltex 3, E3 ubiquitin ligase
    deltex homolog 3
    protein deltex-3
    NP_001273174.1
    NP_001273175.1
    NP_848597.1
    XP_005268754.1
    XP_005268755.1
    XP_005268757.1
    XP_005268760.1
    XP_011536324.1
    XP_024304644.1
    XP_047284435.1
    XP_047284436.1
    XP_047284437.1
    XP_047284438.1
    XP_047284439.1
    XP_047284440.1
    XP_054227353.1
    XP_054227354.1
    XP_054227355.1
    XP_054227356.1
    XP_054227357.1
    XP_054227358.1
    XP_054227359.1
    XP_054227360.1
    XP_054227361.1

    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_001286245.2 → NP_001273174.1  probable E3 ubiquitin-protein ligase DTX3 isoform b

      See identical proteins and their annotated locations for NP_001273174.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (3) lacks an alternate exon in the 5' UTR, uses an alternate splice site in the 5' coding region, and initiates translation at an alternate upstream start codon, compared to variant 1. The encoded isoform (b) has a distinct N-terminus and is longer than isoform a.
      Source sequence(s)
      AK094385, DA684401
      Consensus CDS
      CCDS66410.1
      UniProtKB/Swiss-Prot
      Q8N9I9
      Related
      ENSP00000448696.1, ENST00000551632.1
      Conserved Domains (2) summary
      cd16711
      Location:166 → 206
      RING-HC_DTX3; RING finger, HC subclass, found in E3 ubiquitin-protein ligase Deltex3 (DTX3) and similar proteins
      pfam18102
      Location:213 → 347
      DTC; Deltex C-terminal domain

    2. NM_001286246.2 → NP_001273175.1  probable E3 ubiquitin-protein ligase DTX3 isoform a

      See identical proteins and their annotated locations for NP_001273175.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) lacks an alternate exon in the 5' UTR, compared to variant 1. Both variants 1 and 2 encode the same isoform (a).
      Source sequence(s)
      AK094385, DA684401
      Consensus CDS
      CCDS41800.1
      UniProtKB/Swiss-Prot
      Q53ZZ2, Q8N9I9, Q8NAU6, Q8NDS8
      Related
      ENSP00000449294.1, ENST00000548804.5
      Conserved Domains (2) summary
      cd16711
      Location:163 → 203
      RING-HC_DTX3; RING finger, HC subclass, found in E3 ubiquitin-protein ligase Deltex3 (DTX3) and similar proteins
      pfam18102
      Location:210 → 344
      DTC; Deltex C-terminal domain

    3. NM_178502.4 → NP_848597.1  probable E3 ubiquitin-protein ligase DTX3 isoform a

      See identical proteins and their annotated locations for NP_848597.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) represents the longest transcript and encodes the shorter isoform (a). Both variants 1 and 2 encode the same isoform (a).
      Source sequence(s)
      AK092085, AK094385
      Consensus CDS
      CCDS41800.1
      UniProtKB/Swiss-Prot
      Q53ZZ2, Q8N9I9, Q8NAU6, Q8NDS8
      Related
      ENSP00000338050.3, ENST00000337737.8
      Conserved Domains (2) summary
      cd16711
      Location:163 → 203
      RING-HC_DTX3; RING finger, HC subclass, found in E3 ubiquitin-protein ligase Deltex3 (DTX3) and similar proteins
      pfam18102
      Location:210 → 344
      DTC; Deltex C-terminal domain

    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_000012.12 Reference GRCh38.p14 Primary Assembly

      Range
      57604824..57609802
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047428480.1 → XP_047284436.1  probable E3 ubiquitin-protein ligase DTX3 isoform X1

    2. XM_047428484.1 → XP_047284440.1  probable E3 ubiquitin-protein ligase DTX3 isoform X2

      UniProtKB/Swiss-Prot
      Q53ZZ2, Q8N9I9, Q8NAU6, Q8NDS8
      Related
      ENSP00000447873.1, ENST00000548198.5

    3. XM_011538022.3 → XP_011536324.1  probable E3 ubiquitin-protein ligase DTX3 isoform X2

      See identical proteins and their annotated locations for XP_011536324.1

      UniProtKB/Swiss-Prot
      Q53ZZ2, Q8N9I9, Q8NAU6, Q8NDS8
      Conserved Domains (2) summary
      cd16711
      Location:163 → 203
      RING-HC_DTX3; RING finger, HC subclass, found in E3 ubiquitin-protein ligase Deltex3 (DTX3) and similar proteins
      pfam18102
      Location:210 → 344
      DTC; Deltex C-terminal domain

    4. XM_047428479.1 → XP_047284435.1  probable E3 ubiquitin-protein ligase DTX3 isoform X1

    5. XM_047428483.1 → XP_047284439.1  probable E3 ubiquitin-protein ligase DTX3 isoform X2

      UniProtKB/Swiss-Prot
      Q53ZZ2, Q8N9I9, Q8NAU6, Q8NDS8

    6. XM_024448876.2 → XP_024304644.1  probable E3 ubiquitin-protein ligase DTX3 isoform X2

      UniProtKB/Swiss-Prot
      Q53ZZ2, Q8N9I9, Q8NAU6, Q8NDS8
      Conserved Domains (2) summary
      cd16711
      Location:163 → 203
      RING-HC_DTX3; RING finger, HC subclass, found in E3 ubiquitin-protein ligase Deltex3 (DTX3) and similar proteins
      pfam18102
      Location:210 → 344
      DTC; Deltex C-terminal domain

    7. XM_005268697.2 → XP_005268754.1  probable E3 ubiquitin-protein ligase DTX3 isoform X1

      See identical proteins and their annotated locations for XP_005268754.1

      UniProtKB/Swiss-Prot
      Q8N9I9
      Conserved Domains (2) summary
      cd16711
      Location:166 → 206
      RING-HC_DTX3; RING finger, HC subclass, found in E3 ubiquitin-protein ligase Deltex3 (DTX3) and similar proteins
      pfam18102
      Location:213 → 347
      DTC; Deltex C-terminal domain

    8. XM_005268698.2 → XP_005268755.1  probable E3 ubiquitin-protein ligase DTX3 isoform X1

      See identical proteins and their annotated locations for XP_005268755.1

      UniProtKB/Swiss-Prot
      Q8N9I9
      Conserved Domains (2) summary
      cd16711
      Location:166 → 206
      RING-HC_DTX3; RING finger, HC subclass, found in E3 ubiquitin-protein ligase Deltex3 (DTX3) and similar proteins
      pfam18102
      Location:213 → 347
      DTC; Deltex C-terminal domain

    9. XM_047428481.1 → XP_047284437.1  probable E3 ubiquitin-protein ligase DTX3 isoform X1

    10. XM_005268703.2 → XP_005268760.1  probable E3 ubiquitin-protein ligase DTX3 isoform X2

      See identical proteins and their annotated locations for XP_005268760.1

      UniProtKB/Swiss-Prot
      Q53ZZ2, Q8N9I9, Q8NAU6, Q8NDS8
      Conserved Domains (2) summary
      cd16711
      Location:163 → 203
      RING-HC_DTX3; RING finger, HC subclass, found in E3 ubiquitin-protein ligase Deltex3 (DTX3) and similar proteins
      pfam18102
      Location:210 → 344
      DTC; Deltex C-terminal domain

    11. XM_005268700.2 → XP_005268757.1  probable E3 ubiquitin-protein ligase DTX3 isoform X1

      See identical proteins and their annotated locations for XP_005268757.1

      UniProtKB/Swiss-Prot
      Q8N9I9
      Conserved Domains (2) summary
      cd16711
      Location:166 → 206
      RING-HC_DTX3; RING finger, HC subclass, found in E3 ubiquitin-protein ligase Deltex3 (DTX3) and similar proteins
      pfam18102
      Location:213 → 347
      DTC; Deltex C-terminal domain

    12. XM_047428482.1 → XP_047284438.1  probable E3 ubiquitin-protein ligase DTX3 isoform X1

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060936.1 Alternate T2T-CHM13v2.0

      Range
      57572308..57578021
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054371378.1 → XP_054227353.1  probable E3 ubiquitin-protein ligase DTX3 isoform X1

    2. XM_054371385.1 → XP_054227360.1  probable E3 ubiquitin-protein ligase DTX3 isoform X2

      UniProtKB/Swiss-Prot
      Q53ZZ2, Q8N9I9, Q8NAU6, Q8NDS8

    3. XM_054371384.1 → XP_054227359.1  probable E3 ubiquitin-protein ligase DTX3 isoform X2

      UniProtKB/Swiss-Prot
      Q53ZZ2, Q8N9I9, Q8NAU6, Q8NDS8

    4. XM_054371379.1 → XP_054227354.1  probable E3 ubiquitin-protein ligase DTX3 isoform X1

    5. XM_054371380.1 → XP_054227355.1  probable E3 ubiquitin-protein ligase DTX3 isoform X1

    6. XM_054371381.1 → XP_054227356.1  probable E3 ubiquitin-protein ligase DTX3 isoform X1

    7. XM_054371386.1 → XP_054227361.1  probable E3 ubiquitin-protein ligase DTX3 isoform X2

      UniProtKB/Swiss-Prot
      Q53ZZ2, Q8N9I9, Q8NAU6, Q8NDS8

    8. XM_054371383.1 → XP_054227358.1  probable E3 ubiquitin-protein ligase DTX3 isoform X1

    9. XM_054371382.1 → XP_054227357.1  probable E3 ubiquitin-protein ligase DTX3 isoform X1

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q8N9I9.2 GenPept UniProtKB/Swiss-Prot:Q8N9I9

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