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Aliases for DKC1 Gene

Aliases for DKC1 Gene

  • Dyskeratosis Congenita 1, Dyskerin 2 3
  • Nopp140-Associated Protein Of 57 KDa 3 4
  • Nucleolar Protein Family A Member 4 3 4
  • Nucleolar Protein NAP57 3 4
  • SnoRNP Protein DKC1 3 4
  • CBF5 Homolog 3 4
  • NOLA4 3 4
  • DKCX 3 6
  • H/ACA Ribonucleoprotein Complex Subunit 4 3
  • EC 5.4.99.- 4
  • EC 5.4.99 63
  • Dyskerin 4
  • XAP101 3
  • NAP57 3
  • CBF5 3
  • DKC 3

External Ids for DKC1 Gene

Previous HGNC Symbols for DKC1 Gene

  • DKC

Previous GeneCards Identifiers for DKC1 Gene

  • GC0XP148054
  • GC0XP150371
  • GC0XP151576
  • GC0XP152458
  • GC0XP153554
  • GC0XP153984

Summaries for DKC1 Gene

Entrez Gene Summary for DKC1 Gene

  • 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]

GeneCards Summary for DKC1 Gene

DKC1 (Dyskeratosis Congenita 1, Dyskerin) is a Protein Coding gene. Diseases associated with DKC1 include dyskeratosis congenita, x-linked and dyskeratosis congenita. Among its related pathways are Apoptotic Pathways in Synovial Fibroblasts and Cell Cycle, Mitotic. GO annotations related to this gene include RNA binding and telomerase activity.

UniProtKB/Swiss-Prot for DKC1 Gene

  • Isoform 1: Required for ribosome biogenesis and telomere maintenance. Probable catalytic subunit of H/ACA small nucleolar ribonucleoprotein (H/ACA snoRNP) complex, which catalyzes pseudouridylation of rRNA. This involves the isomerization of uridine such that the ribose is subsequently attached to C5, instead of the normal N1. Each rRNA can contain up to 100 pseudouridine (psi) residues, which may serve to stabilize the conformation of rRNAs. Also required for correct processing or intranuclear trafficking of TERC, the RNA component of the telomerase reverse transcriptase (TERT) holoenzyme

  • Isoform 3: Promotes cell to cell and cell to substratum adhesion, increases the cell proliferation rate and leads to cytokeratin hyper-expression (when overexpressed in HeLa cells)

Gene Wiki entry for DKC1 Gene

No data available for Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for DKC1 Gene

Genomics for DKC1 Gene

Regulatory Elements for DKC1 Gene

Epigenetics Products

  • DNA Methylation CpG Assay Predesigned for Pyrosequencing in human,mouse,rat

Genomic Location for DKC1 Gene

Start:
154,762,742 bp from pter
End:
154,777,689 bp from pter
Size:
14,948 bases
Orientation:
Plus strand

Genomic View for DKC1 Gene

UCSC Golden Path with GeneCards custom track
Cytogenetic band:
Genomic Location for DKC1 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for DKC1 Gene

Proteins for DKC1 Gene

  • Protein details for DKC1 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    O60832-DKC1_HUMAN
    Recommended name:
    H/ACA ribonucleoprotein complex subunit 4
    Protein Accession:
    O60832
    Secondary Accessions:
    • F5BSB3
    • O43845
    • Q96G67
    • Q9Y505

    Protein attributes for DKC1 Gene

    Size:
    514 amino acids
    Molecular mass:
    57674 Da
    Quaternary structure:
    • Part of the H/ACA small nucleolar ribonucleoprotein (H/ACA snoRNP) complex, which contains NHP2/NOLA2, GAR1/NOLA1, NOP10/NOLA3, and DKC1/NOLA4, which is presumed to be the catalytic subunit. The complex contains a stable core formed by binding of one or two NOP10-DKC1 heterodimers to NHP2; GAR1 subsequently binds to this core via DKC1. The complex binds a box H/ACA small nucleolar RNA (snoRNA), which may target the specific site of modification within the RNA substrate. During assembly, the complex contains NAF1 instead of GAR1/NOLA1. The complex also interacts with TERC, which contains a 3-terminal domain related to the box H/ACA snoRNAs. Specific interactions with snoRNAs or TERC are mediated by GAR1 and NHP2. Associates with NOLC1/NOPP140. H/ACA snoRNPs interact with the SMN complex, consisting of SMN1 or SMN2, GEMIN2/SIP1, DDX20/GEMIN3, and GEMIN4. This is mediated by interaction between GAR1 and SMN1 or SMN2. The SMN complex may be required for correct assembly of the H/ACA snoRNP complex. Component of the telomerase holoenzyme complex at least composed of TERT, DKC1, WRAP53/TCAB1, NOP10, NHP2, GAR1, TEP1, EST1A, POT1 and a telomerase RNA template component (TERC). Interacts with SHQ1; this interaction may lead to the stabilization of DKC1, from the time of its synthesis until its association with NOP10, NHP2, and NAF1 at the nascent H/ACA RNA.

    Alternative splice isoforms for DKC1 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for DKC1 Gene

Proteomics data for DKC1 Gene at MOPED

Post-translational modifications for DKC1 Gene

  • Ubiquitination at Lys39, Lys80, Lys151, Lys191, Lys302, and Lys394
  • Modification sites at PhosphoSitePlus

Other Protein References for DKC1 Gene

Domains for DKC1 Gene

Suggested Antigen Peptide Sequences for DKC1 Gene

Graphical View of Domain Structure for InterPro Entry

O60832

UniProtKB/Swiss-Prot:

DKC1_HUMAN :
  • O60832
Domain:
  • Contains 1 PUA domain.
Family:
  • Belongs to the pseudouridine synthase TruB family.
genes like me logo Genes that share domains with DKC1: view

No data available for Gene Families for DKC1 Gene

Function for DKC1 Gene

Molecular function for DKC1 Gene

GENATLAS Biochemistry: dyskerin,multifunctional protein,mainly expressed in the rapidly dividing cells of the epithelia and the hemopoietic system located in the nucleoli and the coiled bodies,possibly in pseudo-uridylation,involved in rRNA biosynthesis,ribosomal subunit assembly,and/or centromere/microtubule binding,ortholog of the rat NAP57 and yeast CBF5
UniProtKB/Swiss-Prot CatalyticActivity: RNA uridine = RNA pseudouridine
UniProtKB/Swiss-Prot Function: Isoform 1: Required for ribosome biogenesis and telomere maintenance. Probable catalytic subunit of H/ACA small nucleolar ribonucleoprotein (H/ACA snoRNP) complex, which catalyzes pseudouridylation of rRNA. This involves the isomerization of uridine such that the ribose is subsequently attached to C5, instead of the normal N1. Each rRNA can contain up to 100 pseudouridine (psi) residues, which may serve to stabilize the conformation of rRNAs. Also required for correct processing or intranuclear trafficking of TERC, the RNA component of the telomerase reverse transcriptase (TERT) holoenzyme
UniProtKB/Swiss-Prot Function: Isoform 3: Promotes cell to cell and cell to substratum adhesion, increases the cell proliferation rate and leads to cytokeratin hyper-expression (when overexpressed in HeLa cells)

Enzyme Numbers (IUBMB) for DKC1 Gene

Gene Ontology (GO) - Molecular Function for DKC1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003720 telomerase activity IDA 12135483
GO:0003723 RNA binding TAS 10591218
GO:0005515 protein binding IPI 16601202
GO:0009982 pseudouridine synthase activity IBA --
GO:0044822 poly(A) RNA binding IDA 22658674
genes like me logo Genes that share ontologies with DKC1: view
genes like me logo Genes that share phenotypes with DKC1: view

Animal Models for DKC1 Gene

MGI Knock Outs for DKC1:

Animal Model Products

miRNA for DKC1 Gene

miRTarBase miRNAs that target DKC1

Inhibitory RNA Products

  • Predesigned siRNA for gene silencing in human,mouse,rat for DKC1

In Situ Assay Products

Flow Cytometry Products

No data available for Transcription Factor Targeting and HOMER Transcription for DKC1 Gene

Localization for DKC1 Gene

Subcellular locations from UniProtKB/Swiss-Prot for DKC1 Gene

Isoform 1: Nucleus, nucleolus. Nucleus, Cajal body. Note=Also localized to Cajal bodies (coiled bodies).
Isoform 3: Cytoplasm.

Subcellular locations from

COMPARTMENTS
Jensen Localization Image for DKC1 Gene COMPARTMENTS Subcellular localization image for DKC1 gene
Compartment Confidence
nucleus 5
cytosol 2
mitochondrion 2
golgi apparatus 1
peroxisome 1

Gene Ontology (GO) - Cellular Components for DKC1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IDA --
GO:0005654 nucleoplasm TAS --
GO:0005697 telomerase holoenzyme complex IDA 12135483
GO:0005730 nucleolus IDA --
GO:0005737 cytoplasm IEA --
genes like me logo Genes that share ontologies with DKC1: view

Pathways for DKC1 Gene

genes like me logo Genes that share pathways with DKC1: view

Pathways by source for DKC1 Gene

1 Qiagen pathway for DKC1 Gene
1 BioSystems pathway for DKC1 Gene

PCR Array Products

  • Pathway & Disease-focused RT² Profiler PCR Arrays

Gene Ontology (GO) - Biological Process for DKC1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000495 box H/ACA snoRNA 3-end processing IBA --
GO:0000723 telomere maintenance TAS --
GO:0001522 pseudouridine synthesis --
GO:0006364 rRNA processing TAS 10556300
GO:0006396 RNA processing TAS 9590285
genes like me logo Genes that share ontologies with DKC1: view

Compounds for DKC1 Gene

(2) HMDB Compounds for DKC1 Gene

Compound Synonyms Cas Number PubMed IDs
Pseudouridine
  • 5-(b-D-Ribofuranosyl)uracil
1445-07-4
Uridine
  • 1-b-D-Ribofuranosyl-2,4(1H,3H)-pyrimidinedione
58-96-8

(3) Novoseek inferred chemical compound relationships for DKC1 Gene

Compound -log(P) Hits PubMed IDs
pseudouridine 88.2 7
uridine 50.8 1
rrna 45.2 3
genes like me logo Genes that share compounds with DKC1: view

Transcripts for DKC1 Gene

Unigene Clusters for DKC1 Gene

Dyskeratosis congenita 1, dyskerin:
Representative Sequences:

Inhibitory RNA Products

  • Predesigned siRNA for gene silencing in human,mouse,rat for DKC1

Primer Products

  • QuantiTect SYBR Green Assays in human,mouse,rat
  • Pre-validated RT² qPCR Primer Assay in human,mouse,rat
  • QuantiFast Probe-based Assays in human,mouse,rat

Flow Cytometry Products

Alternative Splicing Database (ASD) splice patterns (SP) for DKC1 Gene

ExUns: 1a · 1b · 1c · 1d ^ 2a · 2b · 2c ^ 3a · 3b ^ 4 ^ 5a · 5b ^ 6 ^ 7 ^ 8a · 8b · 8c ^ 9 ^ 10 ^ 11a · 11b ^ 12 ^ 13a · 13b ^ 14 ^ 15
SP1: - - -
SP2: - -
SP3: - - -
SP4: -
SP5:
SP6:

Relevant External Links for DKC1 Gene

GeneLoc Exon Structure for
DKC1
ECgene alternative splicing isoforms for
DKC1

Expression for DKC1 Gene

mRNA expression in normal human tissues for DKC1 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Integrated Proteomics: protein expression from ProteomicsDB, PaxDb, MOPED, and MaxQB for DKC1 Gene

SOURCE GeneReport for Unigene cluster for DKC1 Gene Hs.4747

mRNA Expression by UniProt/SwissProt for DKC1 Gene

O60832-DKC1_HUMAN
Tissue specificity: Ubiquitously expressed.
genes like me logo Genes that share expressions with DKC1: view

In Situ Assay Products

No data available for mRNA differential expression in normal tissues for DKC1 Gene

Orthologs for DKC1 Gene

This gene was present in the common ancestor of eukaryotes.

Orthologs for DKC1 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia DKC1 35
  • 98.38 (n)
  • 98.23 (a)
DKC1 36
  • 97 (a)
OneToOne
cow
(Bos Taurus)
Mammalia DKC1 35
  • 88.27 (n)
  • 92.89 (a)
DKC1 36
  • 93 (a)
OneToOne
dog
(Canis familiaris)
Mammalia -- 36
  • 81 (a)
OneToMany
-- 36
  • 91 (a)
OneToMany
DKC1 35
  • 89.3 (n)
  • 93.29 (a)
mouse
(Mus musculus)
Mammalia Dkc1 35
  • 88.91 (n)
  • 91.89 (a)
Dkc1 16
Dkc1 36
  • 91 (a)
OneToOne
oppossum
(Monodelphis domestica)
Mammalia DKC1 36
  • 72 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia -- 36
  • 64 (a)
OneToMany
-- 36
  • 86 (a)
OneToMany
rat
(Rattus norvegicus)
Mammalia Dkc1 35
  • 74.08 (n)
  • 84.29 (a)
chicken
(Gallus gallus)
Aves DKC1 35
  • 76.77 (n)
  • 86.33 (a)
DKC1 36
  • 80 (a)
OneToOne
lizard
(Anolis carolinensis)
Reptilia DKC1 36
  • 70 (a)
OneToOne
African clawed frog
(Xenopus laevis)
Amphibia Xl.21410 35
tropical clawed frog
(Silurana tropicalis)
Amphibia dkc1 35
  • 72.13 (n)
  • 85.25 (a)
rainbow trout
(Oncorhynchus mykiss)
Actinopterygii Omy.12154 35
zebrafish
(Danio rerio)
Actinopterygii dkc1 35
  • 73.13 (n)
  • 82.48 (a)
dkc1 36
  • 76 (a)
OneToOne
wufa28f10 35
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP004739 35
  • 64.84 (n)
  • 72.82 (a)
fruit fly
(Drosophila melanogaster)
Insecta Nop60B 35
  • 64.71 (n)
  • 69.53 (a)
Nop60B 36
  • 65 (a)
OneToOne
Nop60B 37
  • 73 (a)
worm
(Caenorhabditis elegans)
Secernentea K01G5.5 35
  • 61.79 (n)
  • 66.13 (a)
K01G5.5 36
  • 66 (a)
OneToOne
K01G5.5 37
  • 67 (a)
A. gosspyii yeast
(Ashbya gossypii)
Saccharomycetes AGOS_AAL007C 35
  • 63.16 (n)
  • 68.22 (a)
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes CBF5 35
  • 61.48 (n)
  • 66.51 (a)
CBF5 36
  • 62 (a)
OneToOne
CBF5 38
K. lactis yeast
(Kluyveromyces lactis)
Saccharomycetes KLLA0D04796g 35
  • 60.89 (n)
  • 64.64 (a)
Alicante grape
(Vitis vinifera)
eudicotyledons Vvi.9629 35
thale cress
(Arabidopsis thaliana)
eudicotyledons NAP57 35
  • 63.05 (n)
  • 66.98 (a)
barley
(Hordeum vulgare)
Liliopsida Hv.3884 35
corn
(Zea mays)
Liliopsida Zm.10393 35
rice
(Oryza sativa)
Liliopsida Os.13464 35
Os07g0636000 35
  • 61.89 (n)
  • 67.78 (a)
wheat
(Triticum aestivum)
Liliopsida Ta.9549 35
bread mold
(Neurospora crassa)
Ascomycetes NCU01290 35
  • 60.99 (n)
  • 66.91 (a)
fission yeast
(Schizosaccharomyces pombe)
Schizosaccharomycetes cbf5 35
  • 63.74 (n)
  • 70.62 (a)
sea squirt
(Ciona savignyi)
Ascidiacea CSA.2418 36
  • 66 (a)
OneToOne
Species with no ortholog for DKC1:
  • Actinobacteria (Mycobacterium tuberculosis)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • beta proteobacteria (Neisseria meningitidis)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)

Evolution for DKC1 Gene

ENSEMBL:
Gene Tree for DKC1 (if available)
TreeFam:
Gene Tree for DKC1 (if available)

Paralogs for DKC1 Gene

No data available for Paralogs for DKC1 Gene

Variants for DKC1 Gene

Sequence variations from dbSNP and Humsavar for DKC1 Gene

SNP ID Clin Chr 0X pos Sequence Context AA Info Type MAF
rs1127051 Likely benign 154,776,309(+) GGGGC(C/T)GAGCC reference, synonymous-codon, utr-variant-3-prime, nc-transcript-variant
rs1800533 -- 154,776,873(+) TGAAG(A/C/G)CCACT utr-variant-3-prime, nc-transcript-variant
rs2664160 -- 154,770,222(-) CAAAG(C/T)GCTGG intron-variant
rs2728530 -- 154,763,183(+) GGTGA(C/T)TTGGC intron-variant
rs2728531 -- 154,764,279(+) ACCCG(A/T)AGAGG intron-variant

Structural Variations from Database of Genomic Variants (DGV) for DKC1 Gene

Variant ID Type Subtype PubMed ID
esv33784 CNV Gain+Loss 17666407

Relevant External Links for DKC1 Gene

HapMap Linkage Disequilibrium report
DKC1
Human Gene Mutation Database (HGMD)
DKC1
Locus Specific Mutation Databases (LSDB)
DKC1

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for DKC1 Gene

Disorders for DKC1 Gene

(1) OMIM Diseases for DKC1 Gene (300126)

UniProtKB/Swiss-Prot

DKC1_HUMAN
  • Dyskeratosis congenita, X-linked (DKCX) [MIM:305000]: A rare, progressive bone marrow failure syndrome characterized by the triad of reticulated skin hyperpigmentation, nail dystrophy, and mucosal leukoplakia. Early mortality is often associated with bone marrow failure, infections, fatal pulmonary complications, or malignancy. {ECO:0000269 PubMed:10364516, ECO:0000269 PubMed:15304085, ECO:0000269 PubMed:17417794, ECO:0000269 PubMed:18802941, ECO:0000269 PubMed:19734544, ECO:0000269 PubMed:19879169, ECO:0000269 PubMed:9590285}. Note=The disease is caused by mutations affecting the gene represented in this entry.
  • Hoyeraal-Hreidarsson syndrome (HHS) [MIM:305000]: A clinically severe variant of dyskeratosis congenita that is characterized by multisystem involvement, early onset in utero, and often results in death in childhood. Affected individuals show intrauterine growth retardation, microcephaly, cerebellar hypoplasia, delayed development, and bone marrow failure resulting in immunodeficiency. {ECO:0000269 PubMed:10583221, ECO:0000269 PubMed:12437656, ECO:0000269 PubMed:19734544, ECO:0000269 PubMed:24914498}. Note=The disease is caused by mutations affecting the gene represented in this entry.

(2) University of Copenhagen DISEASES for DKC1 Gene

(13) Novoseek inferred disease relationships for DKC1 Gene

Disease -log(P) Hits PubMed IDs
dyskeratosis congenita 98.7 46
hoyeraal-hreidarsson syndrome 95.6 5
nail dystrophy 89.6 1
dyskeratosis congenita, autosomal dominant 81.8 1
leukoplakia 79.9 1

Genatlas disease for DKC1 Gene

dyskeratosis congenita,X-linked recessive,characterized by early reticulate skin pigmentation,nail dystrophy,mucosal leukoplakia and progressive bone-marrow failure,including any form of Bloch Sulzberger incontinentia pigmenti and an increased susceptibility to a range of malignancies,including Hoyeraal-Hreidarsson syndrome,X-linked recessive,aplastic anemia,immunodeficiency,microcephaly,cerebellar hypoplasia and growth retardation

Relevant External Links for DKC1

Genetic Association Database (GAD)
DKC1
Human Genome Epidemiology (HuGE) Navigator
DKC1
genes like me logo Genes that share disorders with DKC1: view

Publications for DKC1 Gene

  1. X-linked dyskeratosis congenita is caused by mutations in a highly conserved gene with putative nucleolar functions. (PMID: 9590285) Heiss N.S. … Dokal I. (Nat. Genet. 1998) 2 3 4 23
  2. Mapping and characterization of the X-linked dyskeratosis congenita (DKC) gene. (PMID: 9888995) Hassock S. … Giannelli F. (Genomics 1999) 2 3 4 23
  3. X-linked dyskeratosis congenita is predominantly caused by missense mutations in the DKC1 gene. (PMID: 10364516) Knight S.W. … Poustka A. (Am. J. Hum. Genet. 1999) 3 4 23
  4. Dyskerin localizes to the nucleolus and its mislocalization is unlikely to play a role in the pathogenesis of dyskeratosis congenita. (PMID: 10556300) Heiss N.S. … Poustka A. (Hum. Mol. Genet. 1999) 3 4 23
  5. Unexplained aplastic anaemia, immunodeficiency, and cerebellar hypoplasia (Hoyeraal-Hreidarsson syndrome) due to mutations in the dyskeratosis congenita gene, DKC1. (PMID: 10583221) Knight S.W. … Dokal I. (Br. J. Haematol. 1999) 3 4 23

Products for DKC1 Gene

  • Addgene plasmids for DKC1

Sources for DKC1 Gene

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