Dkc1 (dyskerin pseudouridine synthase 1) - Rat Genome Database

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Gene: Dkc1 (dyskerin pseudouridine synthase 1) Rattus norvegicus
Analyze
Symbol: Dkc1
Name: dyskerin pseudouridine synthase 1
RGD ID: 621780
Description: Predicted to enable box H/ACA snoRNA binding activity; pseudouridine synthase activity; and telomerase RNA binding activity. Predicted to contribute to telomerase activity. Involved in positive regulation of cell population proliferation and snoRNA guided rRNA pseudouridine synthesis. Located in Cajal body and nucleolus. Part of box H/ACA snoRNP complex. 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); PARTICIPATES IN ribosome biogenesis pathway; INTERACTS WITH (+)-schisandrin B; 2,3,7,8-tetrachlorodibenzodioxine; 2,3,7,8-Tetrachlorodibenzofuran.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: dyskeratosis congenita 1, dyskerin; dyskerin; h/ACA ribonucleoprotein complex subunit 4; H/ACA ribonucleoprotein complex subunit DKC1; Nap57; nopp140-associated protein of 57 kDa; nucleolar protein family A member 4; nucleolar protein NAP57; snoRNP protein DKC1
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rnor_6.0X155,844,914 - 155,862,363 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 EnsemblX155,844,857 - 155,862,475 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01151,564,354 - 151,578,635 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
Celera1135,295,501 - 135,310,658 (-)ENTREZGENECelera
Cytogenetic MapXq37NCBI


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
(+)-schisandrin B  (EXP)
(-)-alpha-phellandrene  (ISO)
1-chloro-2,4-dinitrobenzene  (ISO)
17beta-estradiol  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,ISO)
2,3,7,8-Tetrachlorodibenzofuran  (EXP)
2,4,6-tribromophenol  (ISO)
2,4-dinitrotoluene  (EXP)
2-butoxyethanol  (ISO)
2-nitrofluorene  (EXP)
3,3',5,5'-tetrabromobisphenol A  (ISO)
3-chloropropane-1,2-diol  (EXP)
4-(ethoxymethylene)-2-phenyloxazol-5-one  (ISO)
4-(N-nitrosomethylamino)-1-(3-pyridyl)butan-1-one  (EXP)
4-amino-2,6-dinitrotoluene  (EXP)
afimoxifene  (ISO)
aflatoxin B1  (EXP,ISO)
alpha-phellandrene  (ISO)
arsane  (ISO)
arsenic atom  (ISO)
benzo[a]pyrene  (ISO)
benzo[a]pyrene diol epoxide I  (ISO)
bicalutamide  (ISO)
bis(2-chloroethyl) sulfide  (ISO)
bisphenol A  (EXP,ISO)
C60 fullerene  (EXP)
carbon nanotube  (ISO)
CGP 52608  (ISO)
chloropicrin  (ISO)
choline  (ISO)
cisplatin  (ISO)
cobalt dichloride  (ISO)
coumestrol  (ISO)
cyclosporin A  (ISO)
decabromodiphenyl ether  (ISO)
deoxynivalenol  (ISO)
diethylstilbestrol  (EXP)
disodium selenite  (ISO)
Enterolactone  (ISO)
ethanol  (ISO)
ethyl methanesulfonate  (ISO)
eugenol  (ISO)
finasteride  (EXP)
flutamide  (EXP)
folic acid  (ISO)
folpet  (ISO)
hexadecanoic acid  (ISO)
hydrogen peroxide  (ISO)
ivermectin  (ISO)
L-methionine  (ISO)
lead(0)  (ISO)
lead(2+)  (ISO)
menadione  (ISO)
methapyrilene  (EXP)
methyl methanesulfonate  (ISO)
methylmercury chloride  (ISO)
methylparaben  (ISO)
methylseleninic acid  (ISO)
N,N-diethyl-m-toluamide  (EXP)
N-nitrosodimethylamine  (EXP)
nickel sulfate  (ISO)
oxaliplatin  (EXP)
paraquat  (EXP)
pentachlorophenol  (ISO)
perfluorononanoic acid  (ISO)
perfluorooctanoic acid  (EXP)
permethrin  (EXP)
phenobarbital  (ISO)
piperonyl butoxide  (EXP)
pirinixic acid  (EXP)
resveratrol  (ISO)
silicon dioxide  (ISO)
Soman  (EXP)
succimer  (ISO)
temozolomide  (ISO)
tetrachloromethane  (EXP,ISO)
topotecan  (EXP)
Tributyltin oxide  (ISO)
triptonide  (ISO)
tungsten  (ISO)
urethane  (ISO)
valproic acid  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

Molecular Function

Molecular Pathway Annotations     Click to see Annotation Detail View
References

References - curated
# Reference Title Reference Citation
1. Telomere phenotypes in females with heterozygous mutations in the dyskeratosis congenita 1 (DKC1) gene. Alder JK, etal., Hum Mutat. 2013 Nov;34(11):1481-5. doi: 10.1002/humu.22397. Epub 2013 Sep 11.
2. Stepwise RNP assembly at the site of H/ACA RNA transcription in human cells. Darzacq X, etal., J Cell Biol. 2006 Apr 24;173(2):207-18. Epub 2006 Apr 17.
3. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
4. X-linked dyskeratosis congenita is caused by mutations in a highly conserved gene with putative nucleolar functions. Heiss NS, etal., Nat Genet 1998 May;19(1):32-8.
5. X-linked dyskeratosis congenita is predominantly caused by missense mutations in the DKC1 gene. Knight SW, etal., Am J Hum Genet. 1999 Jul;65(1):50-8.
6. Unexplained aplastic anaemia, immunodeficiency, and cerebellar hypoplasia (Hoyeraal-Hreidarsson syndrome) due to mutations in the dyskeratosis congenita gene, DKC1. Knight SW, etal., Br J Haematol. 1999 Nov;107(2):335-9.
7. NAP57, a mammalian nucleolar protein with a putative homolog in yeast and bacteria. Meier UT and Blobel G, J Cell Biol 1994 Dec;127(6 Pt 1):1505-14.
8. Electronic Transfer of LocusLink and RefSeq Data NCBI rat LocusLink and RefSeq merged data July 26, 2002
9. OMIM Disease Annotation Pipeline OMIM Disease Annotation Pipeline
10. KEGG Annotation Import Pipeline Pipeline to import KEGG annotations from KEGG into RGD
11. Changes in the expression of telomere maintenance genes suggest global telomere dysfunction in B-chronic lymphocytic leukemia. Poncet D, etal., Blood. 2008 Feb 15;111(4):2388-91. Epub 2007 Dec 12.
12. GOA pipeline RGD automated data pipeline
13. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
14. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
15. Dyskeratosis congenita and cancer in mice deficient in ribosomal RNA modification. Ruggero D, etal., Science. 2003 Jan 10;299(5604):259-62.
16. Mutational analysis of telomere complex genes in Indian population with acquired aplastic anemia. Singh I, etal., Leuk Res. 2015 Sep 7. pii: S0145-2126(15)30370-2. doi: 10.1016/j.leukres.2015.08.018.
17. Architecture and assembly of mammalian H/ACA small nucleolar and telomerase ribonucleoproteins. Wang C and Meier UT, EMBO J. 2004 Apr 21;23(8):1857-67. Epub 2004 Mar 25.
18. Immunopurified small nucleolar ribonucleoprotein particles pseudouridylate rRNA independently of their association with phosphorylated Nopp140. Wang C, etal., Mol Cell Biol 2002 Dec;22(24):8457-66.
19. The box C/D and H/ACA snoRNPs: key players in the modification, processing and the dynamic folding of ribosomal RNA. Watkins NJ and Bohnsack MT, Wiley Interdiscip Rev RNA. 2012 May-Jun;3(3):397-414. doi: 10.1002/wrna.117. Epub 2011 Nov 7.
20. Conserved composition of mammalian box H/ACA and box C/D small nucleolar ribonucleoprotein particles and their interaction with the common factor Nopp140. Yang Y, etal., Mol Biol Cell 2000 Feb;11(2):567-77.
Additional References at PubMed
PMID:12135483   PMID:12477932   PMID:15240872   PMID:18082603   PMID:20351177   PMID:22206666   PMID:22527283   PMID:22658674   PMID:23685356   PMID:23726835   PMID:25219674   PMID:25467444  
PMID:26950371   PMID:29695869  


Genomics

Comparative Map Data
Dkc1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rnor_6.0X155,844,914 - 155,862,363 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 EnsemblX155,844,857 - 155,862,475 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01151,564,354 - 151,578,635 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
Celera1135,295,501 - 135,310,658 (-)ENTREZGENECelera
Cytogenetic MapXq37NCBI
DKC1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38X154,762,864 - 154,777,689 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p13 EnsemblX154,762,742 - 154,777,689 (+)EnsemblGRCh38hg38GRCh38
GRCh37X153,991,139 - 154,005,964 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36X153,644,344 - 153,659,154 (+)NCBINCBI36hg18NCBI36
Build 34X153,554,853 - 153,569,664NCBI
CeleraX154,149,596 - 154,164,527 (+)NCBI
Cytogenetic MapXq28NCBI
HuRefX142,534,593 - 142,549,324 (+)NCBIHuRef
CHM1_1X153,902,723 - 153,917,646 (+)NCBICHM1_1
T2T-CHM13v2.0X152,999,274 - 153,014,101 (+)NCBI
Dkc1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39X74,139,460 - 74,153,382 (+)NCBIGRCm39mm39
GRCm39 EnsemblX74,139,460 - 74,153,383 (+)Ensembl
GRCm38X75,095,854 - 75,109,776 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 EnsemblX75,095,854 - 75,109,777 (+)EnsemblGRCm38mm10GRCm38
MGSCv37X72,341,193 - 72,355,115 (+)NCBIGRCm37mm9NCBIm37
CeleraX66,500,704 - 66,514,600 (+)NCBICelera
Cytogenetic MapXA7.3NCBI
Dkc1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_004955594847,815 - 856,510 (-)EnsemblChiLan1.0
ChiLan1.0NW_004955594846,997 - 857,255 (-)NCBIChiLan1.0ChiLan1.0
DKC1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.1X154,084,412 - 154,098,475 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 EnsemblX154,084,412 - 154,098,475 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v0X144,243,493 - 144,257,419 (+)NCBIMhudiblu_PPA_v0panPan3
DKC1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1X122,838,787 - 122,850,870 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 EnsemblX122,838,645 - 122,850,884 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_TashaX107,832,003 - 107,844,116 (+)NCBI
ROS_Cfam_1.0X125,964,983 - 125,977,098 (+)NCBI
ROS_Cfam_1.0 EnsemblX125,965,006 - 125,977,095 (+)Ensembl
UMICH_Zoey_3.1X121,712,979 - 121,725,092 (+)NCBI
UNSW_CanFamBas_1.0X124,236,220 - 124,248,333 (+)NCBI
UU_Cfam_GSD_1.0X123,929,308 - 123,941,420 (+)NCBI
Dkc1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2X119,776,274 - 119,785,590 (+)NCBI
SpeTri2.0NW_004936927134,770 - 144,057 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
DKC1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 EnsemblX125,218,923 - 125,229,525 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1X125,218,928 - 125,228,881 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2X143,254,306 - 143,264,249 (-)NCBISscrofa10.2Sscrofa10.2susScr3
DKC1
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1X129,015,883 - 129,029,741 (+)NCBIChlSab1.1chlSab2
ChlSab1.1 EnsemblX129,016,046 - 129,030,001 (+)EnsemblChlSab1.1chlSab2
Vero_WHO_p1.0NW_02366606566,994,088 - 67,007,910 (+)NCBIVero_WHO_p1.0
Dkc1
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_004624963469,408 - 479,207 (-)EnsemblHetGla_female_1.0hetGla2
HetGla 1.0NW_004624963468,673 - 479,317 (-)NCBIHetGla_female_1.0hetGla2

Position Markers
RH138539  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.0X155,845,378 - 155,845,963NCBIRnor6.0
Rnor_5.01151,564,818 - 151,565,403UniSTSRnor5.0
Celera1135,295,965 - 135,296,550UniSTS
RH 3.4 Map11621.02UniSTS

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:30
Count of miRNA genes:29
Interacting mature miRNAs:29
Transcripts:ENSRNOT00000074205
Prediction methods:Miranda, Rnahybrid
Result types:miRGate_prediction

The detailed report is available here: Full Report CSV TAB Printer

miRNA Target Status data imported from miRGate (http://mirgate.bioinfo.cnio.es/).
For more information about miRGate, see PMID:25858286 or access the full paper here.


Expression


RNA-SEQ Expression
High: > 1000 TPM value   Medium: Between 11 and 1000 TPM
Low: Between 0.5 and 10 TPM   Below Cutoff: < 0.5 TPM

alimentary part of gastrointestinal system circulatory system endocrine system exocrine system hemolymphoid system hepatobiliary system integumental system musculoskeletal system nervous system renal system reproductive system respiratory system appendage
High
Medium 3 36 51 35 19 35 5 8 72 35 39 11 5
Low 7 6 6 6 3 3 2 2 3
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000079862
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 EnsemblX155,844,857 - 155,862,475 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000089847   ⟹   ENSRNOP00000074005
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 EnsemblX155,844,914 - 155,862,363 (-)Ensembl
RefSeq Acc Id: NM_133419   ⟹   NP_596910
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0X155,844,914 - 155,862,363 (-)NCBI
Rnor_5.01151,564,354 - 151,578,635 (-)NCBI
Celera1135,295,501 - 135,310,658 (-)ENTREZGENE
Sequence:
Protein Sequences
Protein RefSeqs NP_596910 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAH99832 (Get FASTA)   NCBI Sequence Viewer  
  CAA84402 (Get FASTA)   NCBI Sequence Viewer  
  EDL84960 (Get FASTA)   NCBI Sequence Viewer  
  EDL84961 (Get FASTA)   NCBI Sequence Viewer  
  P40615 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: NP_596910   ⟸   NM_133419
- UniProtKB: P40615 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: ENSRNOP00000074005   ⟸   ENSRNOT00000089847
Protein Domains
PUA

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-P40615-F1-model_v2 AlphaFold P40615 1-509 view protein structure

Transcriptome

eQTL   View at Phenogen
WGCNA   View at Phenogen
Tissue/Strain Expression   View at Phenogen

Promoters
RGD ID:13702036
Promoter ID:EPDNEW_R12560
Type:initiation region
Name:Dkc1_1
Description:dyskerin pseudouridine synthase 1
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Single-end sequencing.
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0X155,862,365 - 155,862,425EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:621780 AgrOrtholog
BioCyc Gene G2FUF-433 BioCyc
Ensembl Genes ENSRNOG00000055562 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000074005 ENTREZGENE
  ENSRNOP00000074005.2 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000089847 ENTREZGENE
  ENSRNOT00000089847.2 UniProtKB/TrEMBL
Gene3D-CATH 2.30.130.10 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
IMAGE_CLONE IMAGE:7314767 IMAGE-MGC_LOAD
  IMAGE:7934021 IMAGE-MGC_LOAD
InterPro Dyskerin-like UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PsdUridine_synth_cat_dom_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PsdUridine_synth_N UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PUA UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PUA-like_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PUA_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  tRNA_PsdUridine_synth_B_fam UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  TruB_C UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Uncharacterised_CHP00451 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:170944 UniProtKB/Swiss-Prot
MGC_CLONE MGC:105335 IMAGE-MGC_LOAD
  MGC:124569 IMAGE-MGC_LOAD
NCBI Gene 170944 ENTREZGENE
PANTHER PTHR23127 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam DKCLD UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PUA UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  TruB_C_2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  TruB_N UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Dkc1 PhenoGen
PROSITE PUA UniProtKB/Swiss-Prot
SMART DKCLD UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PUA UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP SSF55120 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SSF88697 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
TIGRFAMs CBF5 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  unchar_dom_2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt A0A0G2K700_RAT UniProtKB/TrEMBL
  DKC1_RAT UniProtKB/Swiss-Prot, ENTREZGENE
UniProt Secondary Q499M9 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2016-02-24 Dkc1  dyskerin pseudouridine synthase 1  Dkc1  dyskeratosis congenita 1, dyskerin  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2005-01-20 Dkc1  dyskeratosis congenita 1, dyskerin      Symbol and Name status set to approved 1299863 APPROVED
2002-08-07 Dkc1  dyskeratosis congenita 1, dyskerin      Symbol and Name status set to provisional 70820 PROVISIONAL

RGD Curation Notes
Note Type Note Reference
gene_cellular_localization protein localized to fibrillar component of the nucleolus, to coiled bodies, and to the nucleoplasm 728589
gene_expression protein expressed in liver 728589
gene_homology 71% identical to putative yeast (S. cerevisiae) homolog, 50% identical to prokaryotic (E. coli) homolog 728589
gene_physical_interaction protein colocalized with Nopp140 in nuclei of liver cells 728589
gene_protein calculated mass of 52 kDa 728589