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    DPH5 diphthamide biosynthesis 5 [ Homo sapiens (human) ]

    Gene ID: 51611, updated on 10-Dec-2024

    Summary

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    Official Symbol
    DPH5provided by HGNC
    Official Full Name
    diphthamide biosynthesis 5provided by HGNC
    Primary source
    HGNC:HGNC:24270
    See related
    Ensembl:ENSG00000117543 MIM:611075; AllianceGenome:HGNC:24270
    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
    AD-018; CGI-30; NEDSFF; NPD015; HSPC143
    Summary
    This gene encodes a component of the diphthamide synthesis pathway. Diphthamide is a post-translationally modified histidine residue found only on translation elongation factor 2. It is conserved from archaebacteria to humans, and is targeted by diphtheria toxin and Pseudomonas exotoxin A to halt cellular protein synthesis. The yeast and Chinese hamster homologs of this protein catalyze the trimethylation of the histidine residue on elongation factor 2, resulting in a diphthine moiety that is subsequently amidated to yield diphthamide. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2008]
    Expression
    Ubiquitous expression in ovary (RPKM 15.2), thyroid (RPKM 9.2) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See DPH5 in Genome Data Viewer
    Location:
    1p21.2
    Exon count:
    8
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (100989623..101025784, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (100838455..100874670, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (101455179..101491340, complement)

    Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene Sharpr-MPRA regulatory region 5467 Neighboring gene MPRA-validated peak338 silencer Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:101359730-101360453 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:101360454-101361176 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1388 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1389 Neighboring gene exostosin like glycosyltransferase 2 Neighboring gene solute carrier family 30 member 7 Neighboring gene heterogeneous nuclear ribonucleoprotein A1 pseudogene 68 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1390 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr1:101490870-101492069 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1122 Neighboring gene DPH5 divergent transcript Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:101519189-101519689 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1123 Neighboring gene Sharpr-MPRA regulatory region 5182 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1124 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1392 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1393 Neighboring gene small Cajal body-specific RNA 16

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • 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

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    Related articles in PubMed

    1. A modified form of diphthamide causes immunotoxin resistance in a lymphoma cell line with a deletion of the WDR85 gene. Wei H, et al. J Biol Chem, 2013 Apr 26. PMID 23486472, Free PMC Article
    2. The post-translational trimethylation of diphthamide studied in vitro. Moehring JM, et al. J Biol Chem, 1988 Mar 15. PMID 3346227
    3. Identification of the proteins required for biosynthesis of diphthamide, the target of bacterial ADP-ribosylating toxins on translation elongation factor 2. Liu S, et al. Mol Cell Biol, 2004 Nov. PMID 15485916, Free PMC Article
    4. Drug-gene interactions and the search for missing heritability: a cross-sectional pharmacogenomics study of the QT interval. Avery CL, et al. Pharmacogenomics J, 2014 Feb. PMID 23459443, Free PMC Article
    5. Gene expression profiling in the human hypothalamus-pituitary-adrenal axis and full-length cDNA cloning. Hu RM, et al. Proc Natl Acad Sci U S A, 2000 Aug 15. PMID 10931946, Free PMC Article

    See all (24) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. The yeast and Chinese hamster homologs of human DPH5 catalyze the trimethylation step in the biosynthesis of diphthamide
      Title: Identification of the proteins required for biosynthesis of diphthamide, the target of bacterial ADP-ribosylating toxins on translation elongation factor 2.
    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

    Associated conditions

    Description Tests
    Neurodevelopmental disorder with short stature, prominent forehead, and feeding difficulties
    MedGen: C5774228 OMIM: 620070 GeneReviews: Not available
    		not available

    EBI GWAS Catalog

    Description
    Drug-gene interactions and the search for missing heritability: a cross-sectional pharmacogenomics study of the QT interval.
    EBI GWAS Catalog

    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

    • MGC61450

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables diphthine methyl ester synthase activity EXP
    Inferred from Experiment
    more info
    		 PubMed 
    enables diphthine methyl ester synthase activity NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in methylation IEA
    Inferred from Electronic Annotation
    more info
    		  
    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 protein histidyl modification to diphthamide NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    involved_in protein histidyl modification to diphthamide TAS
    Traceable Author Statement
    more info
    		  
    Component Evidence Code Pubs
    located_in cytosol TAS
    Traceable Author Statement
    more info
    		  

    General protein information

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    Preferred Names
    diphthine methyl ester synthase
    Names
    DPH5 homolog
    diphthamide biosynthesis methyltransferase
    diphthine synthase
    protein x 0011
    NP_001070862.1
    NP_001070863.1
    NP_057042.2
    XP_005270995.1
    XP_011539872.1
    XP_024303368.1
    XP_047278469.1
    XP_047278470.1
    XP_047278471.1
    XP_054192957.1
    XP_054192958.1
    XP_054192959.1
    XP_054192960.1
    XP_054192961.1
    XP_054192962.1

    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_001077394.2 → NP_001070862.1  diphthine methyl ester synthase isoform a

      See identical proteins and their annotated locations for NP_001070862.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) represents the longest transcript. Variants 1 and 2 encode the longer isoform (a).
      Source sequence(s)
      AK125485, BI907367, BM808505, CK002046
      Consensus CDS
      CCDS41358.1
      UniProtKB/Swiss-Prot
      A8JZY6, D3DT62, Q9H2P9, Q9P017, Q9P0I4, Q9Y319
      Related
      ENSP00000418282.1, ENST00000488176.1
      Conserved Domains (1) summary
      PTZ00175
      Location:1 → 272
      PTZ00175; diphthine synthase; Provisional

    2. NM_001077395.2 → NP_001070863.1  diphthine methyl ester synthase isoform b

      See identical proteins and their annotated locations for NP_001070863.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) differs in the 5' UTR and uses an alternate in-frame splice site in the 3' coding region, compared to variant 1. The resulting protein (isoform b) is one amino acid shorter than isoform a.
      Source sequence(s)
      AC093157, AK125485, AK225469, BM808505
      Consensus CDS
      CCDS41359.1
      UniProtKB/Swiss-Prot
      Q9H2P9
      UniProtKB/TrEMBL
      B3KWP1
      Related
      ENSP00000339630.7, ENST00000342173.11
      Conserved Domains (1) summary
      PTZ00175
      Location:1 → 271
      PTZ00175; diphthine synthase; Provisional

    3. NM_015958.3 → NP_057042.2  diphthine methyl ester synthase isoform a

      See identical proteins and their annotated locations for NP_057042.2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) differs in the 5' UTR compared to variant 1. Variants 1 and 2 encode the same isoform (a).
      Source sequence(s)
      AK125485, BC053857, BM808505, DA133565
      Consensus CDS
      CCDS41358.1
      UniProtKB/Swiss-Prot
      A8JZY6, D3DT62, Q9H2P9, Q9P017, Q9P0I4, Q9Y319
      Related
      ENSP00000359127.3, ENST00000370109.8
      Conserved Domains (1) summary
      PTZ00175
      Location:1 → 272
      PTZ00175; diphthine synthase; Provisional

    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_000001.11 Reference GRCh38.p14 Primary Assembly

      Range
      100989623..101025784 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047422514.1 → XP_047278470.1  diphthine methyl ester synthase isoform X3

    2. XM_005270938.3 → XP_005270995.1  diphthine methyl ester synthase isoform X2

      Conserved Domains (1) summary
      cl00304
      Location:1 → 177
      TP_methylase; S-AdoMet dependent tetrapyrrole methylases

    3. XM_024447600.2 → XP_024303368.1  diphthine methyl ester synthase isoform X2

      Conserved Domains (1) summary
      cl00304
      Location:1 → 177
      TP_methylase; S-AdoMet dependent tetrapyrrole methylases

    4. XM_047422513.1 → XP_047278469.1  diphthine methyl ester synthase isoform X1

    5. XM_047422515.1 → XP_047278471.1  diphthine methyl ester synthase isoform X5

    6. XM_011541570.4 → XP_011539872.1  diphthine methyl ester synthase isoform X4

      See identical proteins and their annotated locations for XP_011539872.1

      UniProtKB/TrEMBL
      B3KWP1, D3DT65
      Conserved Domains (1) summary
      cl00304
      Location:1 → 159
      TP_methylase; S-AdoMet dependent tetrapyrrole methylases

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060925.1 Alternate T2T-CHM13v2.0

      Range
      100838455..100874670 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054336987.1 → XP_054192962.1  diphthine methyl ester synthase isoform X5

    2. XM_054336986.1 → XP_054192961.1  diphthine methyl ester synthase isoform X4

      UniProtKB/TrEMBL
      B3KWP1, D3DT65

    3. XM_054336985.1 → XP_054192960.1  diphthine methyl ester synthase isoform X3

    4. XM_054336983.1 → XP_054192958.1  diphthine methyl ester synthase isoform X2

    5. XM_054336984.1 → XP_054192959.1  diphthine methyl ester synthase isoform X2

    6. XM_054336982.1 → XP_054192957.1  diphthine methyl ester synthase isoform X1

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9H2P9.2 GenPept UniProtKB/Swiss-Prot:Q9H2P9

    Gene LinkOut

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

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