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    dkc1 dyskeratosis congenita 1, dyskerin [ Danio rerio (zebrafish) ]

    Gene ID: 613144, updated on 28-Oct-2024

    Summary

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    Official Symbol
    dkc1provided by ZNC
    Official Full Name
    dyskeratosis congenita 1, dyskerinprovided by ZNC
    Primary source
    ZFIN:ZDB-GENE-031118-120
    See related
    Ensembl:ENSDARG00000016484 AllianceGenome:ZFIN:ZDB-GENE-031118-120
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Danio rerio
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Actinopterygii; Neopterygii; Teleostei; Ostariophysi; Cypriniformes; Danionidae; Danioninae; Danio
    Also known as
    fc87a02; fi24a05; fv62a07; wu:fa28f10; wu:fc87a02; wu:fi24a05; wu:fv62a07; zgc:110395
    Summary
    Predicted to enable pseudouridine synthase activity. Acts upstream of or within definitive hemopoiesis and rRNA processing. Predicted to be located in Cajal body. Predicted to be part of box H/ACA snoRNP complex. Is expressed in central nervous system; optic tectum; and proliferative region. Used to study dyskeratosis congenita. Human ortholog(s) of this gene implicated in X-linked dyskeratosis congenita; aplastic anemia; and dyskeratosis congenita. Orthologous to human DKC1 (dyskerin pseudouridine synthase 1). [provided by Alliance of Genome Resources, Oct 2024]
    Orthologs
    human mouse all
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    Genomic context

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    See dkc1 in Genome Data Viewer
    Location:
    chromosome: 21
    Exon count:
    15
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCz11 (GCF_000002035.6) 21 NC_007132.7 (43702016..43716689)
    105 previous assembly GRCz10 (GCF_000002035.5) 21 NC_007132.6 (43706840..43721513)

    Chromosome 21 - NC_007132.7Genomic Context describing neighboring genes Neighboring gene wu:fi34e01 Neighboring gene trimethyllysine hydroxylase, epsilon Neighboring gene small nucleolar RNA SNORD83 Neighboring gene small nucleolar RNA SNORD83 Neighboring gene small nucleolar RNA SNORA36 family Neighboring gene small nucleolar RNA SNORD83 Neighboring gene small nucleolar RNA SNORD83 Neighboring gene PDZ and LIM domain 4 Neighboring gene colony stimulating factor 1 receptor, b

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: Sequencing the Zebrafish transcriptome from a range of tissues and developmental stages Sequencing the Zebrafish transcriptome from a range of tissues and developmental stages
    • Description: Sequencing the Zebrafish transcriptome from a range of tissues and developmental stages
    • BioProject: PRJEB1986
    • Analysis date: Fri Dec 8 19:48:10 2017

    Bibliography

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    Related articles in PubMed

    1. Dual-initiation promoters with intertwined canonical and TCT/TOP transcription start sites diversify transcript processing. Nepal C, et al. Nat Commun, 2020 Jan 10. PMID 31924754, Free PMC Article
    2. Zebrafish models for dyskeratosis congenita reveal critical roles of p53 activation contributing to hematopoietic defects through RNA processing. Zhang Y, et al. PLoS One, 2012. PMID 22299032, Free PMC Article
    3. Pseudouridylation defect due to DKC1 and NOP10 mutations causes nephrotic syndrome with cataracts, hearing impairment, and enterocolitis. Balogh E, et al. Proc Natl Acad Sci U S A, 2020 Jun 30. PMID 32554502, Free PMC Article
    4. FACS-assisted microarray profiling implicates novel genes and pathways in zebrafish gastrointestinal tract development. Stuckenholz C, et al. Gastroenterology, 2009 Oct. PMID 19563808, Free PMC Article
    5. SpG and SpRY variants expand the CRISPR toolbox for genome editing in zebrafish. Liang F, et al. Nat Commun, 2022 Jun 14. PMID 35701400, Free PMC Article

    See all (12) citations in PubMed

    GeneRIFs: Gene References Into Functions

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • MGC110395

    Gene Ontology Provided by ZFIN

    Function Evidence Code Pubs
    enables RNA binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables isomerase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables pseudouridine synthase activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables pseudouridine synthase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    Process Evidence Code Pubs
    acts_upstream_of_or_within RNA modification IEA
    Inferred from Electronic Annotation
    more info
    		  
    acts_upstream_of_or_within RNA processing IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in box H/ACA sno(s)RNA 3'-end processing IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    acts_upstream_of_or_within definitive hemopoiesis IGI
    Inferred from Genetic Interaction
    more info
    		 PubMed 
    acts_upstream_of_or_within definitive hemopoiesis IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in mRNA pseudouridine synthesis IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    acts_upstream_of_or_within pseudouridine synthesis IEA
    Inferred from Electronic Annotation
    more info
    		  
    acts_upstream_of_or_within rRNA processing IEA
    Inferred from Electronic Annotation
    more info
    		  
    acts_upstream_of_or_within rRNA processing IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in rRNA pseudouridine synthesis IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    acts_upstream_of_or_within ribosome biogenesis IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in snRNA pseudouridine synthesis IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Component Evidence Code Pubs
    located_in Cajal body IEA
    Inferred from Electronic Annotation
    more info
    		  
    part_of box H/ACA snoRNP complex IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in nucleus IEA
    Inferred from Electronic Annotation
    more info
    		  
    part_of ribonucleoprotein complex IEA
    Inferred from Electronic Annotation
    more info
    		  

    General protein information

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    Preferred Names
    H/ACA ribonucleoprotein complex subunit DKC1
    Names
    dyskerin
    NP_001028279.2

    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_001033107.2 → NP_001028279.2  H/ACA ribonucleoprotein complex subunit DKC1

      Status: VALIDATED

      Source sequence(s)
      AI477080, AI477818, BC047840, CR792441, CV103822, EB834134
      UniProtKB/Swiss-Prot
      A0A8M1N7N6, F1Q749
      UniProtKB/TrEMBL
      Q7ZUT3
      Related
      ENSDARP00000007628.9, ENSDART00000017176.10
      Conserved Domains (4) summary
      cd02572
      Location:83 → 265
      PseudoU_synth_hDyskerin; Pseudouridine synthase, human dyskerin like
      TIGR00425
      Location:51 → 376
      CBF5; rRNA pseudouridine synthase, putative
      pfam01472
      Location:292 → 365
      PUA; PUA domain
      pfam08068
      Location:44 → 101
      DKCLD; DKCLD (NUC011) domain

    RefSeqs of Annotated Genomes: GCF_000002035.6-RS_2024_08

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

    Reference GRCz11 Primary Assembly

    Genomic

    1. NC_007132.7 Reference GRCz11 Primary Assembly

      Range
      43702016..43716689
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein Strain
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    F1Q749.1 GenPept UniProtKB/Swiss-Prot:F1Q749

    Gene LinkOut

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