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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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See DPH6 in Genome Data Viewer
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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