Dkc1 (dyskerin pseudouridine synthase 1)

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. 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

Alliance Genes

More Info

more info ...

More Info

Species	Gene symbol and name	Data Source	Assertion derived from	less info ...
Orthologs ¹				less info ...
Homo sapiens (human):	DKC1 (dyskerin pseudouridine synthase 1)	HGNC	Ensembl, HomoloGene, Inparanoid, NCBI, Panther
Mus musculus (house mouse):	Dkc1 (dyskeratosis congenita 1, dyskerin)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Chinchilla lanigera (long-tailed chinchilla):	Dkc1 (dyskerin pseudouridine synthase 1)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Pan paniscus (bonobo/pygmy chimpanzee):	DKC1 (dyskerin pseudouridine synthase 1)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Canis lupus familiaris (dog):	DKC1 (dyskerin pseudouridine synthase 1)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Ictidomys tridecemlineatus (thirteen-lined ground squirrel):	Dkc1 (dyskerin pseudouridine synthase 1)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Sus scrofa (pig):	DKC1 (dyskerin pseudouridine synthase 1)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Chlorocebus sabaeus (green monkey):	DKC1 (dyskerin pseudouridine synthase 1)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Heterocephalus glaber (naked mole-rat):	Dkc1 (dyskerin pseudouridine synthase 1)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Alliance orthologs ³
Homo sapiens (human):	DKC1 (dyskerin pseudouridine synthase 1)	Alliance	DIOPT (Ensembl Compara\|HGNC\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Mus musculus (house mouse):	Dkc1 (dyskeratosis congenita 1, dyskerin)	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Danio rerio (zebrafish):	dkc1 (dyskeratosis congenita 1, dyskerin)	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Saccharomyces cerevisiae (baker's yeast):	CBF5	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Caenorhabditis elegans (roundworm):	K01G5.5	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Drosophila melanogaster (fruit fly):	Nop60B	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)

Latest Assembly:

mRatBN7.2 - mRatBN7.2 Assembly

NCBI Annotation Information:

Annotation category: partial on reference assembly

Position:

Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCr8	X	157,751,651 - 157,757,796 (+)	NCBI		GRCr8
UTH_Rnor_SHR_Utx	Y	2,037,843 - 2,053,706 (-)	NCBI	Rnor_SHR	UTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0	X	158,304,360 - 158,320,224 (+)	NCBI	Rnor_SHRSP	UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0	X	155,976,554 - 155,992,422 (+)	NCBI	Rnor_WKY	UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0	X	155,844,914 - 155,862,363 (-)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_6.0 Ensembl	X	155,844,857 - 155,862,475 (-)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_5.0	1	151,564,354 - 151,578,635 (-)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
Celera	1	135,295,501 - 135,310,658 (-)	ENTREZGENE		Celera
Cytogenetic Map	X	;Y	NCBI

Annotation Click to see Annotation Detail View

Disease Annotations Click to see Annotation Detail View

adrenoleukodystrophy (ISO)

anemia (ISO)

aplastic anemia (ISO)

autistic disorder (ISO)

B-Cell Chronic Lymphocytic Leukemia (ISO)

Barth syndrome (ISO)

Cataracts, Hearing Impairment, Nephrotic Syndrome, and Enterocolitis 1 (ISO)

cerebellar hypoplasia (ISO)

cerebral creatine deficiency syndrome 1 (ISO)

disease of cellular proliferation (ISO)

dyskeratosis congenita (ISO,ISS)

Emery-Dreifuss muscular dystrophy (ISO)

favism (ISO)

genetic disease (ISO)

Hoyeraal Hreidarsson Syndrome (ISO)

immunodeficiency 33 (ISO)

lymphopenia (ISO)

paraplegia (ISO)

periventricular nodular heterotopia (ISO)

primary immunodeficiency disease (ISO)

pulmonary fibrosis (ISO)

Splenomegaly (ISO)

X-linked dyskeratosis congenita (ISO)

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)

4,4'-sulfonyldiphenol (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)

Bisphenol B (ISO)

bisphenol F (EXP)

C60 fullerene (EXP)

caffeine (ISO)

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)

epoxiconazole (ISO)

ethanol (ISO)

ethyl methanesulfonate (ISO)

eugenol (ISO)

finasteride (EXP)

flutamide (EXP)

folic acid (ISO)

folpet (ISO)

FR900359 (ISO)

glyphosate (EXP,ISO)

hexadecanoic acid (ISO)

hydrogen peroxide (ISO)

ivermectin (ISO)

L-methionine (ISO)

lead(0) (ISO)

menadione (ISO)

methapyrilene (EXP)

methoxychlor (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)

rotenone (EXP)

SB 431542 (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

Biological Process

box H/ACA sno(s)RNA 3'-end processing (IBA,IEA)

box H/ACA sno(s)RNA metabolic process (ISO)

enzyme-directed rRNA pseudouridine synthesis (ISO,ISS)

mRNA pseudouridine synthesis (IBA,IEA)

positive regulation of cell population proliferation (IDA)

positive regulation of establishment of protein localization to telomere (ISO)

positive regulation of protein localization to Cajal body (ISO)

positive regulation of telomerase RNA localization to Cajal body (ISO)

positive regulation of telomere maintenance via telomerase (ISO)

pseudouridine synthesis (IEA)

regulation of telomerase RNA localization to Cajal body (ISO)

RNA processing (IEA)

rRNA pseudouridine synthesis (IBA,IEA,ISO)

scaRNA localization to Cajal body (ISO)

snoRNA guided rRNA pseudouridine synthesis (IDA)

snRNA pseudouridine synthesis (IBA,IEA)

telomerase RNA stabilization (ISO)

telomere maintenance via telomerase (ISO,ISS)

Cellular Component

box H/ACA snoRNP complex (IBA,IDA,IEA,ISO)

box H/ACA telomerase RNP complex (ISO)

Cajal body (IDA,IEA,ISO)

fibrillar center (ISO)

nucleolus (ISO)

nucleoplasm (IDA,IEA,ISO)

nucleus (ISO)

telomerase holoenzyme complex (ISO,ISS)

Molecular Function

box H/ACA snoRNA binding (ISO)

protein binding (IPI,ISO)

pseudouridine synthase activity (IBA,IEA,ISO,ISS)

RNA binding (IEA,ISO)

telomerase activity (ISO)

telomerase RNA binding (ISO)

Molecular Pathway Annotations Click to see Annotation Detail View

ribosome biogenesis pathway (IEA,ISO)

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 Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCr8	X	157,751,651 - 157,757,796 (+)	NCBI		GRCr8
UTH_Rnor_SHR_Utx	Y	2,037,843 - 2,053,706 (-)	NCBI	Rnor_SHR	UTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0	X	158,304,360 - 158,320,224 (+)	NCBI	Rnor_SHRSP	UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0	X	155,976,554 - 155,992,422 (+)	NCBI	Rnor_WKY	UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0	X	155,844,914 - 155,862,363 (-)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_6.0 Ensembl	X	155,844,857 - 155,862,475 (-)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_5.0	1	151,564,354 - 151,578,635 (-)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
Celera	1	135,295,501 - 135,310,658 (-)	ENTREZGENE		Celera
Cytogenetic Map	X	;Y	NCBI

DKC1
(Homo sapiens - human)

Human Assembly	Chr	Position (strand)	Source	Genome Browsers
Human Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCh38	X	154,762,864 - 154,777,689 (+)	NCBI	GRCh38	GRCh38	hg38	GRCh38
GRCh38.p14 Ensembl	X	154,762,742 - 154,777,689 (+)	Ensembl	GRCh38		hg38	GRCh38
GRCh37	X	153,991,139 - 154,005,964 (+)	NCBI	GRCh37	GRCh37	hg19	GRCh37
Build 36	X	153,644,344 - 153,659,154 (+)	NCBI	NCBI36	Build 36	hg18	NCBI36
Build 34	X	153,554,853 - 153,569,664	NCBI
Celera	X	154,149,596 - 154,164,527 (+)	NCBI		Celera
Cytogenetic Map	X	q28	NCBI
HuRef	X	142,534,593 - 142,549,324 (+)	NCBI		HuRef
CHM1_1	X	153,902,723 - 153,917,646 (+)	NCBI		CHM1_1
T2T-CHM13v2.0	X	152,999,274 - 153,014,101 (+)	NCBI		T2T-CHM13v2.0

Dkc1
(Mus musculus - house mouse)

Mouse Assembly	Chr	Position (strand)	Source	Genome Browsers
Mouse Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCm39	X	74,139,460 - 74,153,382 (+)	NCBI	GRCm39	GRCm39	mm39
GRCm39 Ensembl	X	74,139,460 - 74,153,383 (+)	Ensembl		GRCm39 Ensembl
GRCm38	X	75,095,854 - 75,109,776 (+)	NCBI	GRCm38	GRCm38	mm10	GRCm38
GRCm38.p6 Ensembl	X	75,095,854 - 75,109,777 (+)	Ensembl	GRCm38		mm10	GRCm38
MGSCv37	X	72,341,193 - 72,355,115 (+)	NCBI	GRCm37	MGSCv37	mm9	NCBIm37
Celera	X	66,500,704 - 66,514,600 (+)	NCBI		Celera
Cytogenetic Map	X	A7.3	NCBI
cM Map	X	38.15	NCBI

Dkc1
(Chinchilla lanigera - long-tailed chinchilla)

Chinchilla Assembly	Chr	Position (strand)	Source	Genome Browsers
Chinchilla Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
ChiLan1.0 Ensembl	NW_004955594	847,815 - 856,510 (-)	Ensembl	ChiLan1.0
ChiLan1.0	NW_004955594	846,997 - 857,255 (-)	NCBI	ChiLan1.0	ChiLan1.0

DKC1
(Pan paniscus - bonobo/pygmy chimpanzee)

Bonobo Assembly	Chr	Position (strand)	Source	Genome Browsers
Bonobo Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
NHGRI_mPanPan1-v2	X	154,742,073 - 154,756,376 (+)	NCBI		NHGRI_mPanPan1-v2
NHGRI_mPanPan1	X	154,745,681 - 154,759,888 (+)	NCBI		NHGRI_mPanPan1
Mhudiblu_PPA_v0	X	144,243,493 - 144,257,419 (+)	NCBI	Mhudiblu_PPA_v0	Mhudiblu_PPA_v0	panPan3
PanPan1.1	X	154,084,412 - 154,098,475 (+)	NCBI	panpan1.1	PanPan1.1	panPan2
PanPan1.1 Ensembl	X	154,084,412 - 154,098,475 (+)	Ensembl	panpan1.1		panPan2

DKC1
(Canis lupus familiaris - dog)

Dog Assembly	Chr	Position (strand)	Source	Genome Browsers
Dog Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
CanFam3.1	X	122,838,787 - 122,850,870 (+)	NCBI	CanFam3.1	CanFam3.1	canFam3	CanFam3.1
CanFam3.1 Ensembl	X	122,838,645 - 122,850,884 (+)	Ensembl	CanFam3.1		canFam3	CanFam3.1
Dog10K_Boxer_Tasha	X	107,832,003 - 107,844,116 (+)	NCBI		Dog10K_Boxer_Tasha
ROS_Cfam_1.0	X	125,964,983 - 125,977,098 (+)	NCBI		ROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl	X	125,965,006 - 125,977,095 (+)	Ensembl		ROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1	X	121,712,979 - 121,725,092 (+)	NCBI		UMICH_Zoey_3.1
UNSW_CanFamBas_1.0	X	124,236,220 - 124,248,333 (+)	NCBI		UNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0	X	123,929,308 - 123,941,420 (+)	NCBI		UU_Cfam_GSD_1.0

Dkc1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)

Squirrel Assembly	Chr	Position (strand)	Source	Genome Browsers
Squirrel Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
HiC_Itri_2	X	119,776,274 - 119,785,590 (+)	NCBI		HiC_Itri_2
SpeTri2.0	NW_004936927	134,770 - 144,057 (+)	NCBI	SpeTri2.0	SpeTri2.0		SpeTri2.0

DKC1
(Sus scrofa - pig)

Pig Assembly	Chr	Position (strand)	Source	Genome Browsers
Pig Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
Sscrofa11.1 Ensembl	X	125,218,923 - 125,229,525 (+)	Ensembl	Sscrofa11.1		susScr11	Sscrofa11.1
Sscrofa11.1	X	125,218,928 - 125,228,881 (+)	NCBI	Sscrofa11.1	Sscrofa11.1	susScr11	Sscrofa11.1
Sscrofa10.2	X	143,254,306 - 143,264,249 (-)	NCBI	Sscrofa10.2	Sscrofa10.2	susScr3

DKC1
(Chlorocebus sabaeus - green monkey)

Green Monkey Assembly	Chr	Position (strand)	Source	Genome Browsers
Green Monkey Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
ChlSab1.1	X	129,015,883 - 129,029,741 (+)	NCBI	ChlSab1.1	ChlSab1.1	chlSab2
ChlSab1.1 Ensembl	X	129,016,046 - 129,030,001 (+)	Ensembl	ChlSab1.1	ChlSab1.1 Ensembl	chlSab2
Vero_WHO_p1.0	NW_023666065	66,994,088 - 67,007,910 (+)	NCBI	Vero_WHO_p1.0	Vero_WHO_p1.0

Dkc1
(Heterocephalus glaber - naked mole-rat)

Naked Mole-Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Naked Mole-Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
HetGla_female_1.0 Ensembl	NW_004624963	469,408 - 479,207 (-)	Ensembl	HetGla_female_1.0	HetGla_female_1.0 Ensembl	hetGla2
HetGla 1.0	NW_004624963	468,673 - 479,317 (-)	NCBI	HetGla_female_1.0	HetGla 1.0	hetGla2

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.

Markers in Region

RH138539

Rat Assembly	Chr	Position (strand)	Source	JBrowse
Rnor_6.0	X	155,845,378 - 155,845,963	NCBI	Rnor6.0
Rnor_5.0	1	151,564,818 - 151,565,403	UniSTS	Rnor5.0
Celera	1	135,295,965 - 135,296,550	UniSTS
RH 3.4 Map	1	1621.02	UniSTS

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

View RNA-SEQ Expression Data

Sequence

Nucleotide Sequences


RefSeq Transcripts	NM_133419	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
GenBank Nucleotide	BC087600	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	BC099832	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	CH474099	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	JAXUCZ010000021	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	Z34922	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles

RefSeq Acc Id:

ENSRNOT00000079862

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
Rnor_6.0 Ensembl	X	155,844,857 - 155,862,475 (-)	Ensembl

RefSeq Acc Id:

ENSRNOT00000089847 ⟹ ENSRNOP00000074005

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
Rnor_6.0 Ensembl	X	155,844,914 - 155,862,363 (-)	Ensembl

RefSeq Acc Id:

NM_133419 ⟹ NP_596910

RefSeq Status:

PROVISIONAL

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
GRCr8	X	157,751,651 - 157,757,796 (+)	NCBI
Rnor_6.0	X	155,844,914 - 155,862,363 (-)	NCBI
Rnor_5.0	1	151,564,354 - 151,578,635 (-)	NCBI
Celera	1	135,295,501 - 135,310,658 (-)	ENTREZGENE

Sequence:

show sequence

GTCCCGGCGGCGCGTGGTGACCGTTGGCGTGCGCGGTTCTCGGCTCGCGGCGGCGGTTAGCGGC
GGTTGGCCGGGTTGTCTGCCTGCGACATGGCGGACGCGGAAGCCGCCATGACGTTCCCGAAGAA
GCACAAGAAGAAGAAAGAGCGGAAGCCGCTGCCGGAAGCTGACGTGGCTGAGATCCAGCACGCG
GAAGATTTCCTGATCAAACCGGAGTCCAAGGCGGCTCAGTTGGACACCTCCCAGTGGCCCCTGC
TGCTCAAGAACTTTGACAGACTGAACGTGCGGACGACCCACTACACGCCCATCCCGTGCGGCTC
CAACCCGCTGAAGAGGGAGATCGGGGAGTACGTCAGGACCGGCTTCATCAACCTGGACAAGCCA
TCCAACCCCTCTTCGCACGAGGTCGTGGCCTGGATCCGCCGCATCCTGCGCGTGGAGAAGACGG
GGCACAGCGGGACACTTGACCCCAAGGTCACCGGGTGCCTCATCGTCTGCATCGAGCGCGCCAC
GCGCCTGGTCAAGTCACAGCAGAGCGCGGGCAAAGAGTATGTCGGGGTCGTGCGGCTGCACAAT
GCTATCGAGGGGACCGCCCAGCTCTCCAGGGCCCTGGAGACCCTGACAGGCGCCCTGTTCCAGC
GTCCCCCGCTCATCGCAGCAGTGAAGCGGCAGCTGCGCGTGCGCACAATCTATGAGAGCCGTGT
TGTCGAGTATGACCCTGAGCGCAGGCTGGGTGTGTTCTGGGTGAGCTGCGAGGCTGGCACCTAC
ATCCGGACGCTGTGCGTGCACCTGGGGCTGCTGCTGGGCGTCGGGGGGCAGATGCAGGAGCTGC
GGCGCGTGCGCTCGGGGGTCGTGGGCGAGCGGGACCACATGGTGACCATGCACGACGTCCTGGA
CGCGCAGTATCTATACGACCACCACCGGGACGAGAGCTACCTGCGCCGCGTGGTTTTCCCACTG
GAGAAGCTGCTGACGTCGCACAAGCGCCTGGTGATGAAGGACAGTGCGGTCAACGCCATCTGCT
ACGGCGCGAAGATCATGCTCCCCGGCCTCCTGCGCTACGAGGACGGCATCGAGGTCAACCAGGA
GGTCGTGGTCATCACCACCAAGGGCGAGGCCGTCTGCGTGGCCATCGCACTGATGACGACGGCT
GTGATCTCCACGTGCGACCACGGGGTAGTAGCGAAGATCAAGCGCGTCATCATGGAGCGGGACA
CCTACCCCCGCAAGTGGGGCCTGGGGCCGAAGGCAAGCCAGAAGAAGCAGCTGATCAAGCAGGG
CCTCCTGGACAAACATGGCCGACCCACGGACGGCACCCCCGCCTCCTGGACGCGCGACTACGTG
GACTACAGTGACTCCAGCAAGAAAGCGACGGCCGCCGAAGCCACGCCGGGCCCTGGGGTCACCG
CGGACGCCGCCAGCATCGTGAAAAGGAAACGCGATAGCGACAGCGACGCCGACGAGGCGACGCC
CACTACCACGCCCCGGGTGAAGAAGGAGAAGAAGAAGAAAAAGGAGAAGGCGGACGGCGGGGAG
GAGGCTGCGGAGGACGGGGACGGCGACGCCACAAGGAAGAAAAAGAAGAAGAAGGCAAGGGCGG
CAGAGGAGCTCAGTGGTTAGCGACTACCCCCGACCCCCACGCGGCGACCATCCCGTCCTGTTTT
AAGGACGCGAGGCGTAGGAACGGGGTCTCCACCACTGACCCCTCCACTCACTTGAGCCCCCGAC
GACCGCCCGCGGCGATTCGCCGGAGGCCATGTTGAGCGACACCGCAGACGGCCCTGGCCTGCCC
TCCATTTTTTT

hide 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
Ensembl Protein	ENSRNOP00000074005
	ENSRNOP00000074005.2
	ENSRNOP00055001004
	ENSRNOP00055033814
	ENSRNOP00060011292
	ENSRNOP00060011347
	ENSRNOP00065000307
	ENSRNOP00065018484
GenBank Protein	P40615	(Get FASTA)	NCBI Sequence Viewer

RefSeq Acc Id:

NP_596910 ⟸ NM_133419

- UniProtKB:

Q499M9 (UniProtKB/Swiss-Prot), P40615 (UniProtKB/Swiss-Prot), A0A0G2K700 (UniProtKB/TrEMBL)

- Sequence:

show sequence

MADAEAAMTFPKKHKKKKERKPLPEADVAEIQHAEDFLIKPESKAAQLDTSQWPLLLKNFDRLN
VRTTHYTPIPCGSNPLKREIGEYVRTGFINLDKPSNPSSHEVVAWIRRILRVEKTGHSGTLDPK
VTGCLIVCIERATRLVKSQQSAGKEYVGVVRLHNAIEGTAQLSRALETLTGALFQRPPLIAAVK
RQLRVRTIYESRVVEYDPERRLGVFWVSCEAGTYIRTLCVHLGLLLGVGGQMQELRRVRSGVVG
ERDHMVTMHDVLDAQYLYDHHRDESYLRRVVFPLEKLLTSHKRLVMKDSAVNAICYGAKIMLPG
LLRYEDGIEVNQEVVVITTKGEAVCVAIALMTTAVISTCDHGVVAKIKRVIMERDTYPRKWGLG
PKASQKKQLIKQGLLDKHGRPTDGTPASWTRDYVDYSDSSKKATAAEATPGPGVTADAASIVKR
KRDSDSDADEATPTTTPRVKKEKKKKKEKADGGEEAAEDGDGDATRKKKKKKARAAEELSG

hide sequence

RefSeq Acc Id:

ENSRNOP00000074005 ⟸ ENSRNOT00000089847

Protein Domains

Dyskerin-like 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 Assembly	Chr	Position (strand)	Source
Rnor_6.0	X	155,862,365 - 155,862,425	EPDNEW

Additional Information

External Database Links

Database	Acc Id	Source(s)
AGR Gene	RGD:621780	AgrOrtholog
BioCyc Gene	G2FUF-433	BioCyc
Ensembl Genes	ENSRNOG00000055562	Ensembl, ENTREZGENE, UniProtKB/TrEMBL
	ENSRNOG00055000727	UniProtKB/Swiss-Prot
	ENSRNOG00055024200	UniProtKB/Swiss-Prot
	ENSRNOG00060008746	UniProtKB/Swiss-Prot
	ENSRNOG00060008779	UniProtKB/Swiss-Prot
	ENSRNOG00065000181	UniProtKB/Swiss-Prot
	ENSRNOG00065014381	UniProtKB/Swiss-Prot
Ensembl Transcript	ENSRNOT00000089847	ENTREZGENE
	ENSRNOT00000089847.2	UniProtKB/TrEMBL
	ENSRNOT00055001251	UniProtKB/Swiss-Prot
	ENSRNOT00055041561	UniProtKB/Swiss-Prot
	ENSRNOT00060014638	UniProtKB/Swiss-Prot
	ENSRNOT00060014691	UniProtKB/Swiss-Prot
	ENSRNOT00065000312	UniProtKB/Swiss-Prot
	ENSRNOT00065023745	UniProtKB/Swiss-Prot
Gene3D-CATH	2.30.130.10	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	Pseudouridine synthase	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	H/ACA RIBONUCLEOPROTEIN COMPLEX SUBUNIT DKC1	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	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, UniProtKB/TrEMBL
RatGTEx	ENSRNOG00000055562	RatGTEx
	ENSRNOG00055000727	RatGTEx
	ENSRNOG00055024200	RatGTEx
	ENSRNOG00060008746	RatGTEx
	ENSRNOG00060008779	RatGTEx
	ENSRNOG00065000181	RatGTEx
	ENSRNOG00065014381	RatGTEx
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
UniProt	A0A0G2K700	ENTREZGENE, UniProtKB/TrEMBL
	A6KRP4_RAT	UniProtKB/TrEMBL
	A6KRP5_RAT	UniProtKB/TrEMBL
	DKC1_RAT	UniProtKB/Swiss-Prot, ENTREZGENE
	Q499M9	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

Gene Annotator (Functional Annotation) unavailable	Gene Annotator (Annotation Distribution) unavailable	Variant Visualizer (Genomic Variants) unavailble Variant Visualizer (Genomic Variants) unavailable
Gene Annotator (Functional Annotation)	Gene Annotator (Annotation Distribution)	Variant Visualizer (Genomic Variants)

InterViewer (Protein-Protein Interactions) unavailable	Gviewer (Genome Viewer) unavailable	Variant Visualizer (Damaging Variants) unavailble Variant Visualizer (Damaging Variants) unavailable
InterViewer (Protein-Protein Interactions)	GViewer (Genome Viewer)	Variant Visualizer (Damaging Variants)

Gene Annotator (Annotation Comparison) unavailable	OLGA (Gene List Generator) unavailable
Gene Annotator (Annotation Comparison)	OLGA (Gene List Generator)	Excel (Download)

MOET (Multi-Ontology Enrichement) unavailable	GOLF (Gene-Ortholog Location Finder) unavailable
MOET (Multi-Ontology Enrichement)	GOLF (Gene-Ortholog Location Finder)

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Imported Disease Annotations - CTD

Imported Disease Annotations - MGI

Imported Disease Annotations - OMIM

RGD Manual Annotations

Imported Annotations - KEGG (archival)

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Imported Annotations - KEGG (archival)