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    DPH3 diphthamide biosynthesis 3 [ Homo sapiens (human) ]

    Gene ID: 285381, updated on 9-Dec-2024

    Summary

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    Official Symbol
    DPH3provided by HGNC
    Official Full Name
    diphthamide biosynthesis 3provided by HGNC
    Primary source
    HGNC:HGNC:27717
    See related
    Ensembl:ENSG00000154813 MIM:608959; AllianceGenome:HGNC:27717
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    DESR1; DPH3A; KTI11; ZCSL2; DELGIP; DELGIP1
    Summary
    This gene encodes a CSL zinc finger-containing protein that is required for dipthamide biosynthesis. The encoded protein is necessary for the initial step in the modification of a histidine residue in elongation factor-2 to diphthamide. This modified residue is a target for ADP ribosylation by the bacterial toxins diphtheria toxin and Pseudomonas exotoxin A. Alternative splicing results in multiple transcript variants that encode the same isoform. [provided by RefSeq, Feb 2009]
    Expression
    Ubiquitous expression in thyroid (RPKM 7.2), small intestine (RPKM 6.5) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See DPH3 in Genome Data Viewer
    Location:
    3p25.1
    Exon count:
    3
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 3 NC_000003.12 (16257061..16264943, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (16258288..16266169, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (16298568..16306450, complement)

    Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124906216 Neighboring gene uncharacterized LOC124909349 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19539 Neighboring gene polypeptide N-acetylgalactosaminyltransferase 15 Neighboring gene H3K27ac hESC enhancer GRCh37_chr3:16285879-16286378 Neighboring gene Sharpr-MPRA regulatory region 8904 Neighboring gene uncharacterized LOC124906218 Neighboring gene H3K27ac hESC enhancer GRCh37_chr3:16297189-16297690 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19540 Neighboring gene oxidoreductase NAD binding domain containing 1 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14113 Neighboring gene THAP domain containing 5 pseudogene 2 Neighboring gene uncharacterized LOC107986065 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14114 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr3:16343021-16343602

    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. Solution structure of human DESR1, a CSL zinc-binding protein. Wu F, et al. Proteins, 2008 Apr. PMID 18214955
    2. Dph3, a small protein required for diphthamide biosynthesis, is essential in mouse development. Liu S, et al. Mol Cell Biol, 2006 May. PMID 16648478, Free PMC Article
    3. Frequent DPH3 promoter mutations in skin cancers. Denisova E, et al. Oncotarget, 2015 Nov 3. PMID 26416425, Free PMC Article
    4. Retroviral insertional mutagenesis identifies a small protein required for synthesis of diphthamide, the target of bacterial ADP-ribosylating toxins. Liu S, et al. Mol Cell, 2003 Sep. PMID 14527407
    5. Characterisation of an evolutionary conserved protein interacting with the putative guanine nucleotide exchange factor DelGEF and modulating secretion. Sjölinder M, et al. Exp Cell Res, 2004 Mar 10. PMID 14980502

    See all (20) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. The results from this study show occurrence of frequent somatic non-coding mutations adjacent to a pre-existing binding site for Ets transcription factors within the directional promoter of DPH3 and OXNAD1 genes in three major skin cancers.
      Title: Frequent DPH3 promoter mutations in skin cancers.
    2. Solution structure of human DESR1, a CSL zinc-binding protein.
      Title: Solution structure of human DESR1, a CSL zinc-binding protein.
    3. DelGIP1is a binding partner of deafness locus putative guanine nucleotide exchange factor; downregulation of DelGIP1 induced increased extracellular secretion of proteoglycans indicating a possible role for DelGIP1 in the secretion process
      Title: Characterisation of an evolutionary conserved protein interacting with the putative guanine nucleotide exchange factor DelGEF and modulating secretion.
    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

    • MGC20197

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables ferrous iron binding ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    enables iron chaperone activity ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in negative regulation of protein secretion IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in positive regulation of binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in protein histidyl modification to diphthamide IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in protein histidyl modification to diphthamide ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in tRNA wobble base 5-methoxycarbonylmethyl-2-thiouridinylation ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    Component Evidence Code Pubs
    located_in cytoplasm IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in cytosol IDA
    Inferred from Direct Assay
    more info
    		  
    located_in cytosol TAS
    Traceable Author Statement
    more info
    		  
    located_in nucleoplasm IDA
    Inferred from Direct Assay
    more info
    		  
    located_in nucleus IDA
    Inferred from Direct Assay
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    diphthamide biosynthesis protein 3
    Names
    CSL-type zinc finger-containing protein 2
    DPH3 homolog (KTI11, S. cerevisiae)
    DPH3, KTI11 homolog
    DPH3A, KTI11 homolog A
    Del-GEF interacting protein
    deafness locus putative guanine nucleotide exchange factor interacting protein 1
    delGEF-interacting protein 1
    diphtheria toxin and Pseudomonas exotoxin A sensitivity required gene 1
    zinc finger, CSL domain containing 2
    zinc finger, CSL-type containing 2

    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_001047434.3 → NP_001040899.1  diphthamide biosynthesis protein 3 isoform 2

      See identical proteins and their annotated locations for NP_001040899.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) lacks an exon in the coding region but maintains the reading frame compared to variant 1. This variant encodes isoform 2, which is shorter than isoform 1.
      Source sequence(s)
      AC090953, AK022970
      Consensus CDS
      CCDS43058.1
      UniProtKB/Swiss-Prot
      Q96FX2
      Related
      ENSP00000373285.4, ENST00000383775.4
      Conserved Domains (1) summary
      pfam05207
      Location:6 → 45
      zf-CSL; CSL zinc finger

    2. NM_206831.3 → NP_996662.1  diphthamide biosynthesis protein 3 isoform 1

      See identical proteins and their annotated locations for NP_996662.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).
      Source sequence(s)
      AC090953, DA875039
      Consensus CDS
      CCDS2629.1
      UniProtKB/Swiss-Prot
      Q96FX2
      Related
      ENSP00000419599.1, ENST00000488423.2
      Conserved Domains (1) summary
      pfam05207
      Location:6 → 60
      zf-CSL; CSL zinc finger

    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_000003.12 Reference GRCh38.p14 Primary Assembly

      Range
      16257061..16264943 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060927.1 Alternate T2T-CHM13v2.0

      Range
      16258288..16266169 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q96FX2.1 GenPept UniProtKB/Swiss-Prot:Q96FX2

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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