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    Dph6 diphthamine biosynthesis 6 [ Rattus norvegicus (Norway rat) ]

    Gene ID: 362191, updated on 9-Dec-2024

    Summary

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    Official Symbol
    Dph6provided by RGD
    Official Full Name
    diphthamine biosynthesis 6provided by RGD
    Primary source
    RGD:1310006
    See related
    EnsemblRapid:ENSRNOG00000037356 AllianceGenome:RGD:1310006
    Gene type
    protein coding
    RefSeq status
    PROVISIONAL
    Organism
    Rattus norvegicus
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
    Also known as
    Atpbd4; RGD1310006
    Summary
    Predicted to enable diphthine-ammonia ligase activity. Predicted to be involved in protein histidyl modification to diphthamide. Orthologous to human DPH6 (diphthamine biosynthesis 6). [provided by Alliance of Genome Resources, Dec 2024]
    Expression
    Biased expression in Kidney (RPKM 38.1), Thymus (RPKM 32.5) and 9 other tissues See more
    Orthologs
    human mouse all
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    Genomic context

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    See Dph6 in Genome Data Viewer
    Location:
    3q35
    Exon count:
    11
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCr8 (GCF_036323735.1) 3 NC_086021.1 (121761495..121891727, complement)
    RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 3 NC_051338.1 (101307229..101437463, complement)
    106 previous assembly Rnor_6.0 (GCF_000001895.5) 3 NC_005102.4 (106007721..106136662, complement)

    Chromosome 3 - NC_086021.1Genomic Context describing neighboring genes Neighboring gene zinc finger protein 770 Neighboring gene uncharacterized LOC120101629 Neighboring gene uncharacterized LOC102552721 Neighboring gene uncharacterized LOC134486424 Neighboring gene small nucleolar RNA SNORA17

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages
    • Description: 320 RNA samples isolated from 11 organs (adrenal gland, brain, heart, kidney, liver, lung, muscle, spleen, thymus, and testes or uterus) from both sexes of Fischer 344 rats across four developmental stages (2-, 6-, 21-, and 104-weeks-old)
    • BioProject: PRJNA238328
    • Publication: PMID 24510058
    • Analysis date: Mon Jun 6 17:44:12 2016

    Bibliography

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    Related articles in PubMed

    1. 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
    2. 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
    3. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). Gerhard DS, et al. Genome Res, 2004 Oct. PMID 15489334, Free PMC Article
    4. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. Strausberg RL, et al. Proc Natl Acad Sci U S A, 2002 Dec 24. PMID 12477932, Free PMC Article
    5. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Gaudet P, et al. Brief Bioinform, 2011 Sep. PMID 21873635, Free PMC Article

    GeneRIFs: Gene References Into Functions

    Pathways from PubChem

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    General gene information

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    Markers

    Homology

    Gene Ontology Provided by RGD

    Function Evidence Code Pubs
    enables ATP binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables diphthine-ammonia ligase activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables diphthine-ammonia ligase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables diphthine-ammonia ligase activity ISO
    Inferred from Sequence Orthology
    more info
    		  
    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
    		  

    General protein information

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    Preferred Names
    diphthine--ammonia ligase
    Names
    ATP binding domain 4
    ATP-binding domain-containing protein 4
    diphthamide synthase
    diphthamide synthetase
    protein DPH6 homolog
    NP_001014203.1
    XP_038961384.1
    XP_063140227.1
    XP_063140228.1
    XP_063140229.1

    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_001014181.1 → NP_001014203.1  diphthine--ammonia ligase

      See identical proteins and their annotated locations for NP_001014203.1

      Status: PROVISIONAL

      Source sequence(s)
      BC087148
      UniProtKB/Swiss-Prot
      Q5M9F5
      UniProtKB/TrEMBL
      A0A8I5ZRV2
      Related
      ENSRNOP00000076614.1, ENSRNOT00000107739.3
      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_036323735.1-RS_2024_02

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

    Reference GRCr8

    Genomic

    1. NC_086021.1 Reference GRCr8

      Range
      121761495..121891727 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_063284157.1 → XP_063140227.1  diphthine--ammonia ligase isoform X1

      UniProtKB/TrEMBL
      A0A8I5ZRV2
      Related
      ENSRNOP00000098515.2, ENSRNOT00000120931.2

    2. XM_039105456.2 → XP_038961384.1  diphthine--ammonia ligase isoform X2

      UniProtKB/TrEMBL
      A0A8I5ZRV2, F1LP07
      Related
      ENSRNOP00000102453.1, ENSRNOT00000124225.1
      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 ...

    3. XM_063284159.1 → XP_063140229.1  diphthine--ammonia ligase isoform X4

    4. XM_063284158.1 → XP_063140228.1  diphthine--ammonia ligase isoform X3

    RNA

    1. XR_010064662.1 RNA Sequence

    2. XR_010064661.1 RNA Sequence

    Nucleotide Protein Strain
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q5M9F5.1 GenPept UniProtKB/Swiss-Prot:Q5M9F5

    Gene LinkOut

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

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