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    DPH6 diphthamine biosynthesis 6 [ Homo sapiens (human) ]

    Gene ID: 89978, updated on 5-Mar-2024

    Summary

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    Official Symbol
    DPH6provided by HGNC
    Official Full Name
    diphthamine biosynthesis 6provided by HGNC
    Primary source
    HGNC:HGNC:30543
    See related
    Ensembl:ENSG00000134146 MIM:618391; AllianceGenome:HGNC:30543
    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
    ATPBD4
    Summary
    Enables diphthine-ammonia ligase activity. Predicted to be involved in peptidyl-diphthamide biosynthetic process from peptidyl-histidine. Located in nucleolus and nucleoplasm. [provided by Alliance of Genome Resources, Apr 2022]
    Expression
    Ubiquitous expression in thyroid (RPKM 1.3), ovary (RPKM 0.9) and 25 other tissues See more
    Orthologs
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    Genomic context

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    Location:
    15q14
    Exon count:
    16
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 15 NC_000015.10 (35144977..35546165, complement)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 15 NC_060939.1 (32950308..33351518, complement)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 15 NC_000015.9 (35663081..35838366, complement)

    Chromosome 15 - NC_000015.10Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105370765 Neighboring gene U2 small nuclear RNA auxiliary factor 1-like 4 pseudogene Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9190 Neighboring gene PRELID1 pseudogene 4 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr15:35475024-35476004 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:35537116-35537669 Neighboring gene H3K27ac hESC enhancer GRCh37_chr15:35544243-35544742 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr15:35545952-35546470 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr15:35546471-35546990 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr15:35548334-35549533 Neighboring gene H3K27ac hESC enhancer GRCh37_chr15:35555863-35556362 Neighboring gene acidic nuclear phosphoprotein 32 family member A pseudogene 1 Neighboring gene Sharpr-MPRA regulatory region 14069 Neighboring gene nuclear transport factor 2 pseudogene 6 Neighboring gene RNA binding motif protein 17 pseudogene 4 Neighboring gene uncharacterized LOC124903464 Neighboring gene heterogeneous nuclear ribonucleoprotein A1 pseudogene 45 Neighboring gene microRNA 3942 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:35837367-35838301 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6292 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6293 Neighboring gene Sharpr-MPRA regulatory region 8232 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9191 Neighboring gene DPH6 divergent transcript Neighboring gene MED14-independent group 3 enhancer GRCh37_chr15:36165880-36167079 Neighboring gene uncharacterized LOC105370766 Neighboring gene microRNA 4510

    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. The amidation step of diphthamide biosynthesis in yeast requires DPH6, a gene identified through mining the DPH1-DPH5 interaction network. Uthman S, et al. PLoS Genet, 2013. PMID 23468660, Free PMC Article
    2. Chemogenomic approach identified yeast YLR143W as diphthamide synthetase. Su X, et al. Proc Natl Acad Sci U S A, 2012 Dec 4. PMID 23169644, Free PMC Article
    3. High-content genome-wide RNAi screens identify regulators of parkin upstream of mitophagy. Hasson SA, et al. Nature, 2013 Dec 12. PMID 24270810, Free PMC Article
    4. ΔNp63α Suppresses TGFB2 Expression and RHOA Activity to Drive Cell Proliferation in Squamous Cell Carcinomas. Abraham CG, et al. Cell Rep, 2018 Sep 18. PMID 30232004, Free PMC Article
    5. Systematic interactome mapping of acute lymphoblastic leukemia cancer gene products reveals EXT-1 tumor suppressor as a Notch1 and FBWX7 common interactor. Daakour S, et al. BMC Cancer, 2016 May 26. PMID 27229929, Free PMC Article

    See all (20) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. The previously uncharacterized human gene ATPBD4 is the ortholog of yeast YLR143W, a diphthamide synthetase, and fully rescues the deletion of YLR143W in yeast.
      Title: Chemogenomic approach identified yeast YLR143W as diphthamide synthetase.
    2. Observational study of gene-disease association, gene-environment interaction, and pharmacogenomic / toxicogenomic. (HuGE Navigator)
      Title: Variation at the NFATC2 locus increases the risk of thiazolidinedione-induced edema in the Diabetes REduction Assessment with ramipril and rosiglitazone Medication (DREAM) study.
    3. Observational study of gene-disease association. (HuGE Navigator)
      Title: Gene-centric association signals for lipids and apolipoproteins identified via the HumanCVD BeadChip.
    4. Clinical trial of gene-disease association and gene-environment interaction. (HuGE Navigator)
      Title: Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score.
    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

    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

    • MGC14798

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables ATP binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables diphthine-ammonia ligase activity EXP
    Inferred from Experiment
    more info
    		 PubMed 
    enables diphthine-ammonia ligase activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables diphthine-ammonia ligase activity TAS
    Traceable Author Statement
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in protein histidyl modification to diphthamide IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in protein histidyl modification to diphthamide IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in protein histidyl modification to diphthamide TAS
    Traceable Author Statement
    more info
    		 PubMed 
    Component Evidence Code Pubs
    located_in cytosol TAS
    Traceable Author Statement
    more info
    		  

    General protein information

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    Preferred Names
    diphthine--ammonia ligase
    Names
    ATP binding domain 4
    ATP-binding domain-containing protein 4
    DPH6 homolog
    diphthamide synthase
    diphthamide synthetase
    protein DPH6 homolog
    NP_001135444.1
    NP_542381.1
    XP_011520462.1
    XP_016878197.1
    XP_016878198.1
    XP_047289219.1
    XP_047289220.1
    XP_047289221.1
    XP_054235083.1
    XP_054235084.1
    XP_054235085.1

    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_001141972.2 → NP_001135444.1  diphthine--ammonia ligase isoform 2

      See identical proteins and their annotated locations for NP_001135444.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) differs in the 3' UTR and coding sequence compared to variant 1. The resulting isoform (2) has a shorter and distinct C-terminus compared to isoform 1.
      Source sequence(s)
      AC015994, AK125017
      Consensus CDS
      CCDS45213.1
      UniProtKB/Swiss-Prot
      Q7L8W6
      Related
      ENSP00000406976.2, ENST00000440392.3
      Conserved Domains (1) summary
      cl00292
      Location:2 → 104
      AANH_like; Adenine nucleotide alpha hydrolases superfamily including N type ATP PPases, ATP sulphurylases Universal Stress Response protein and electron transfer flavoprotein (ETF). The domain forms a apha/beta/apha fold which binds to Adenosine nucleotide.

    2. NM_080650.4 → NP_542381.1  diphthine--ammonia ligase isoform 1

      See identical proteins and their annotated locations for NP_542381.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) encodes the longer isoform (1).
      Source sequence(s)
      AC019288, AK094007, BC008485, DB250468
      Consensus CDS
      CCDS10043.1
      UniProtKB/Swiss-Prot
      B3KWG1, Q7L8W6, Q96HJ6
      Related
      ENSP00000256538.4, ENST00000256538.9
      Conserved Domains (1) summary
      cd01994
      Location:2 → 215
      Alpha_ANH_like_IV; This is a subfamily of Adenine nucleotide alpha hydrolases superfamily.Adeninosine nucleotide alpha hydrolases superfamily includes N type ATP PPases and ATP sulphurylases. It forms a apha/beta/apha fold which binds to Adenosine group. This subfamily ...

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000015.10 Reference GRCh38.p14 Primary Assembly

      Range
      35144977..35546165 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047433263.1 → XP_047289219.1  diphthine--ammonia ligase isoform X2

    2. XM_017022708.3 → XP_016878197.1  diphthine--ammonia ligase isoform X1

    3. XM_047433264.1 → XP_047289220.1  diphthine--ammonia ligase isoform X2

    4. XM_047433265.1 → XP_047289221.1  diphthine--ammonia ligase isoform X2

    5. XM_011522160.3 → XP_011520462.1  diphthine--ammonia ligase isoform X2

      Conserved Domains (1) summary
      cd01994
      Location:2 → 215
      Alpha_ANH_like_IV; This is a subfamily of Adenine nucleotide alpha hydrolases superfamily.Adeninosine nucleotide alpha hydrolases superfamily includes N type ATP PPases and ATP sulphurylases. It forms a apha/beta/apha fold which binds to Adenosine group. This subfamily ...

    6. XM_017022709.3 → XP_016878198.1  diphthine--ammonia ligase isoform X3

    RNA

    1. XR_001751412.3 RNA Sequence

    2. XR_007064493.1 RNA Sequence

    3. XR_001751413.3 RNA Sequence

    4. XR_001751411.3 RNA Sequence

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060939.1 Alternate T2T-CHM13v2.0

      Range
      32950308..33351518 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054379109.1 → XP_054235084.1  diphthine--ammonia ligase isoform X2

    2. XM_054379108.1 → XP_054235083.1  diphthine--ammonia ligase isoform X1

    3. XM_054379110.1 → XP_054235085.1  diphthine--ammonia ligase isoform X3

    RNA

    1. XR_008489029.1 RNA Sequence

    2. XR_008489028.1 RNA Sequence

    3. XR_008489027.1 RNA Sequence

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q7L8W6.3 GenPept UniProtKB/Swiss-Prot:Q7L8W6

    Gene LinkOut

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

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