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    DKC1 dyskerin pseudouridine synthase 1 [ Homo sapiens (human) ]

    Gene ID: 1736, updated on 20-Apr-2017
    Official Symbol
    DKC1provided by HGNC
    Official Full Name
    dyskerin pseudouridine synthase 1provided by HGNC
    Primary source
    HGNC:HGNC:2890
    See related
    Ensembl:ENSG00000130826 MIM:300126; Vega:OTTHUMG00000024242
    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
    DKC; CBF5; DKCX; NAP57; NOLA4; XAP101
    Summary
    This gene functions in two distinct complexes. It plays an active role in telomerase stabilization and maintenance, as well as recognition of snoRNAs containing H/ACA sequences which provides stability during biogenesis and assembly into H/ACA small nucleolar RNA ribonucleoproteins (snoRNPs). This gene is highly conserved and widely expressed, and may play additional roles in nucleo-cytoplasmic shuttling, DNA damage response, and cell adhesion. Mutations have been associated with X-linked dyskeratosis congenita. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jan 2014]
    Orthologs
    Location:
    Xq28
    Exon count:
    14
    Annotation release Status Assembly Chr Location
    108 current GRCh38.p7 (GCF_000001405.33) X NC_000023.11 (154762742..154777689)
    105 previous assembly GRCh37.p13 (GCF_000001405.25) X NC_000023.10 (153991031..154005964)

    Chromosome X - NC_000023.11Genomic Context describing neighboring genes Neighboring gene olfactory receptor family 3 subfamily B member 1 pseudogene Neighboring gene GRB2 associated binding protein 3 Neighboring gene small nucleolar RNA, H/ACA box 36A Neighboring gene microRNA 664b Neighboring gene small nucleolar RNA, H/ACA box 56 Neighboring gene membrane palmitoylated protein 1 Neighboring gene high mobility group nucleosome binding domain 1 pseudogene 37

    • 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 Jun 15 11:32:44 2016

    GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

    Associated conditions

    Description Tests
    Dyskeratosis congenita X-linked
    MedGen: C1148551 OMIM: 305000 GeneReviews: Dyskeratosis Congenita
    Compare labs
    Hoyeraal Hreidarsson syndrome
    MedGen: C1846142 GeneReviews: Not available
    Compare labs

    Copy number response

    Description
    Copy number response
    Triplosensitivity

    No evidence available (Last evaluated (2012-04-25)

    ClinGen Genome Curation Page
    Haploinsufficency

    Little evidence for dosage pathogenicity (Last evaluated (2012-04-25)

    ClinGen Genome Curation PagePubMed

    Replication interactions

    Interaction Pubs
    Knockdown of dyskeratosis congenita 1, dyskerin (DKC1) by shRNA library screening inhibits HIV-1 replication in cultured Jurkat T-cells PubMed

    Go to the HIV-1, Human Interaction Database

    • Cell Cycle, organism-specific biosystem (from REACTOME)
      Cell Cycle, organism-specific biosystem
      Cell Cycle
    • Chromosome Maintenance, organism-specific biosystem (from REACTOME)
      Chromosome Maintenance, organism-specific biosystemChromosome maintenance is critical for stable chromosome function in mammalian and other eukaryotic cells. Aspects of telomere maintenance and nucleosome assembly are covered here.
    • Extension of Telomeres, organism-specific biosystem (from REACTOME)
      Extension of Telomeres, organism-specific biosystemTelomerase acts as reverse transcriptase in the elongation of telomeres (Smogorzewska and de Lange 2004).
    • Gene Expression, organism-specific biosystem (from REACTOME)
      Gene Expression, organism-specific biosystemGene Expression covers the pathways by which genomic DNA is transcribed to yield RNA, the regulation of these transcription processes, and the pathways by which newly-made RNA Transcripts are process...
    • H/ACA ribonucleoprotein complex, organism-specific biosystem (from KEGG)
      H/ACA ribonucleoprotein complex, organism-specific biosystemStructural complex; Genetic information processing; RNA processing
    • H/ACA ribonucleoprotein complex, conserved biosystem (from KEGG)
      H/ACA ribonucleoprotein complex, conserved biosystemStructural complex; Genetic information processing; RNA processing
    • Regulation of Telomerase, organism-specific biosystem (from Pathway Interaction Database)
      Regulation of Telomerase, organism-specific biosystem
      Regulation of Telomerase
    • Ribosome biogenesis in eukaryotes, organism-specific biosystem (from KEGG)
      Ribosome biogenesis in eukaryotes, organism-specific biosystemRibosomes are the cellular factories responsible for making proteins. In eukaryotes, ribosome biogenesis involves the production and correct assembly of four rRNAs and about 80 ribosomal proteins. It...
    • Ribosome biogenesis in eukaryotes, conserved biosystem (from KEGG)
      Ribosome biogenesis in eukaryotes, conserved biosystemRibosomes are the cellular factories responsible for making proteins. In eukaryotes, ribosome biogenesis involves the production and correct assembly of four rRNAs and about 80 ribosomal proteins. It...
    • Telomere Extension By Telomerase, organism-specific biosystem (from REACTOME)
      Telomere Extension By Telomerase, organism-specific biosystemHumans, like most eukaryotic organisms, add direct repeats to the telomere using a specialized DNA polymerase called telomerase. Telomerase is a ribonucleoprotein (RNP) complex minimally composed of...
    • Telomere Maintenance, organism-specific biosystem (from REACTOME)
      Telomere Maintenance, organism-specific biosystemTelomeres are protein-DNA complexes at the ends of linear chromosomes that are important for genome stability. Telomeric DNA in humans, as in many eukaryotic organisms, consists of tandem repeats (B...
    • rRNA modification in the nucleus and cytosol, organism-specific biosystem (from REACTOME)
      rRNA modification in the nucleus and cytosol, organism-specific biosystemHuman ribosomal RNAs (rRNAs) contain about 200 residues that are enzymatically modified after transcription in the nucleolus (Maden and Khan 1977, Maden 1988, Maden and Hughes 1997, reviewed in Herna...
    • rRNA processing, organism-specific biosystem (from REACTOME)
      rRNA processing, organism-specific biosystemEach eukaryotic cytosolic ribosome contains 4 molecules of RNA: 28S rRNA (25S rRNA in yeast), 5.8S rRNA, and 5S rRNA in the 60S subunit and 18S rRNA in the 40S subunit. The 18S rRNA, 5.8S rRNA, and 2...
    • rRNA processing in the nucleus and cytosol, organism-specific biosystem (from REACTOME)
      rRNA processing in the nucleus and cytosol, organism-specific biosystemEach eukaryotic cytosolic ribosome contains 4 molecules of RNA: 28S rRNA (25S rRNA in yeast), 5.8S rRNA, and 5S rRNA in the 60S subunit and 18S rRNA in the 40S subunit. The 18S rRNA, 5.8S rRNA, and 2...
    Products Interactant Other Gene Complex Source Pubs Description

    Markers

    Homology

    Clone Names

    • FLJ97620

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    RNA binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    box H/ACA snoRNA binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    pseudouridine synthase activity IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    telomerase RNA binding IC
    Inferred by Curator
    more info
    PubMed 
    telomerase RNA binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    telomerase activity IDA
    Inferred from Direct Assay
    more info
    PubMed 
    contributes_to telomerase activity IDA
    Inferred from Direct Assay
    more info
    PubMed 
    Process Evidence Code Pubs
    RNA processing TAS
    Traceable Author Statement
    more info
    PubMed 
    box H/ACA snoRNA 3'-end processing IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    cell proliferation TAS
    Traceable Author Statement
    more info
    PubMed 
    mRNA pseudouridine synthesis IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    positive regulation of establishment of protein localization to telomere IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    positive regulation of telomerase RNA localization to Cajal body IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    positive regulation of telomerase activity IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    positive regulation of telomere maintenance via telomerase IEA
    Inferred from Electronic Annotation
    more info
     
    rRNA processing TAS
    Traceable Author Statement
    more info
    PubMed 
    rRNA pseudouridine synthesis IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    rRNA pseudouridine synthesis TAS
    Traceable Author Statement
    more info
     
    regulation of telomerase RNA localization to Cajal body IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    snRNA pseudouridine synthesis IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    telomerase RNA stabilization IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    telomere maintenance via telomerase IDA
    Inferred from Direct Assay
    more info
    PubMed 
    telomere maintenance via telomerase IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    telomere maintenance via telomerase TAS
    Traceable Author Statement
    more info
     
    Component Evidence Code Pubs
    box H/ACA scaRNP complex TAS
    Traceable Author Statement
    more info
    PubMed 
    box H/ACA snoRNP complex IDA
    Inferred from Direct Assay
    more info
    PubMed 
    box H/ACA snoRNP complex TAS
    Traceable Author Statement
    more info
    PubMed 
    box H/ACA telomerase RNP complex IDA
    Inferred from Direct Assay
    more info
    PubMed 
    box H/ACA telomerase RNP complex TAS
    Traceable Author Statement
    more info
    PubMed 
    cytoplasm IEA
    Inferred from Electronic Annotation
    more info
     
    fibrillar center IDA
    Inferred from Direct Assay
    more info
     
    nucleolus TAS
    Traceable Author Statement
    more info
    PubMed 
    nucleoplasm TAS
    Traceable Author Statement
    more info
     
    nucleus IDA
    Inferred from Direct Assay
    more info
     
    telomerase holoenzyme complex IDA
    Inferred from Direct Assay
    more info
    PubMed 
    telomerase holoenzyme complex TAS
    Traceable Author Statement
    more info
    PubMed 
    Preferred Names
    H/ACA ribonucleoprotein complex subunit 4
    Names
    CBF5 homolog
    dyskeratosis congenita 1, dyskerin
    nopp140-associated protein of 57 kDa
    nucleolar protein NAP57
    nucleolar protein family A member 4
    snoRNP protein DKC1

    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.

    Genomic

    1. NG_009780.1 RefSeqGene

      Range
      4987..19934
      Download
      GenBank, FASTA, Sequence Viewer (Graphics), LRG_55

    mRNA and Protein(s)

    1. NM_001142463.2NP_001135935.1  H/ACA ribonucleoprotein complex subunit 4 isoform 2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) uses an alternate in-frame splice site in the 3' coding region, compared to variant 1. The resulting isoform (2) is shorter than isoform 1.
      Source sequence(s)
      AK307672, BC009928, CD367400, HY050100
      UniProtKB/Swiss-Prot
      O60832
      Conserved Domains (4) summary
      cd02572
      Location:88270
      PseudoU_synth_hDyskerin; Pseudouridine synthase, human dyskerin like
      TIGR00425
      Location:56381
      CBF5; rRNA pseudouridine synthase, putative
      pfam01472
      Location:297370
      PUA; PUA domain
      pfam08068
      Location:49106
      DKCLD; DKCLD (NUC011) domain
    2. NM_001288747.1NP_001275676.1  H/ACA ribonucleoprotein complex subunit 4 isoform 3

      See identical proteins and their annotated locations for NP_001275676.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) uses an alternate 3' exon structure, which results in an early stop codon, compared to variant 1. The resulting protein (isoform 3) has a distinct C-terminus, compared to isoform 1 (PMID: 21820037).
      Source sequence(s)
      BC009928, CD367400, HY050100, JF279874
      Consensus CDS
      CCDS76062.1
      UniProtKB/Swiss-Prot
      O60832
      Related
      ENSP00000478387.1, ENST00000620277.4
      Conserved Domains (4) summary
      cd02572
      Location:88270
      PseudoU_synth_hDyskerin; Pseudouridine synthase, human dyskerin like
      TIGR00425
      Location:56381
      CBF5; rRNA pseudouridine synthase, putative
      pfam01472
      Location:297370
      PUA; PUA domain
      pfam08068
      Location:49106
      DKCLD; DKCLD (NUC011) domain
    3. NM_001363.4NP_001354.1  H/ACA ribonucleoprotein complex subunit 4 isoform 1

      See identical proteins and their annotated locations for NP_001354.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) encodes the longest isoform (1).
      Source sequence(s)
      AK225077, BC009928, CD367400, HY050100
      Consensus CDS
      CCDS14761.1
      UniProtKB/Swiss-Prot
      O60832
      Related
      ENSP00000358563.5, OTTHUMP00000026046, ENST00000369550.9, OTTHUMT00000061180
      Conserved Domains (4) summary
      cd02572
      Location:88270
      PseudoU_synth_hDyskerin; Pseudouridine synthase, human dyskerin like
      TIGR00425
      Location:56381
      CBF5; rRNA pseudouridine synthase, putative
      pfam01472
      Location:297370
      PUA; PUA domain
      pfam08068
      Location:49106
      DKCLD; DKCLD (NUC011) domain

    RNA

    1. NR_110021.1 RNA Sequence

      Status: REVIEWED

      Description
      Transcript Variant: This variant (4) uses an alternate 5' exon structure, compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon, as used in variant 1, may render the transcript a candidate for nonsense-mediated mRNA decay (NMD). PMID: 24219293 indicates that this transcript may not be down-regulated by NMD; however, the potential to encode a truncated, but stable and functional protein has not been demonstrated.
      Source sequence(s)
      BC009928, CD367400, HY050100, KC954523
    2. NR_110022.1 RNA Sequence

      Status: REVIEWED

      Description
      Transcript Variant: This variant (5) uses an alternate 5' exon structure, compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon, as used in variant 1, may render the transcript a candidate for nonsense-mediated mRNA decay (NMD). PMID: 24219293 indicates that this transcript may not be down-regulated by NMD; however, the potential to encode a truncated, but stable and functional protein has not been demonstrated.
      Source sequence(s)
      BC009928, CD367400, HY050100, KC954524
    3. NR_110023.1 RNA Sequence

      Status: REVIEWED

      Description
      Transcript Variant: This variant (6) uses an alternate 5' exon structure, compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon, as used in variant 1, may render the transcript a candidate for nonsense-mediated mRNA decay (NMD). PMID: 24219293 indicates that this transcript may not be down-regulated by NMD; however, the potential to encode a truncated, but stable and functional protein has not been demonstrated.
      Source sequence(s)
      BC009928, CD367400, HY050100, KC954525

    RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 108 details...Open this link in a new tab

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

    Reference GRCh38.p7 Primary Assembly

    Genomic

    1. NC_000023.11 Reference GRCh38.p7 Primary Assembly

      Range
      154762742..154777689
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate CHM1_1.1

    Genomic

    1. NC_018934.2 Alternate CHM1_1.1

      Range
      153902709..153917646
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
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