Dkc1 dyskerin pseudouridine synthase 1 [Rattus norvegicus (Norway rat)] - Gene

Summary

Official Symbol: Dkc1provided by RGD
Official Full Name: dyskerin pseudouridine synthase 1provided by RGD
Primary source: RGD:621780
See related: AllianceGenome:RGD:621780
Gene type: protein coding
RefSeq status: PROVISIONAL
Organism: Rattus norvegicus
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
Also known as: Nap57
Summary: 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). [provided by Alliance of Genome Resources, Nov 2024]
Annotation information: Annotation category: suggests misassembly; Annotation category: partial on reference assembly
Expression: Biased expression in Thymus (RPKM 99.5), Adrenal (RPKM 85.6) and 9 other tissues See more
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Genomic context

Location:: X;Y

Exon count:: 7

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCr8 (GCF_036323735.1)	X	NC_086039.1 (157751651..157757796)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	Y Unlocalized Scaffold	NW_023637718.1 (22717..38582, complement)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	X	NC_005120.4 (155844914..155862363, complement)

Chromosome X - NC_086039.1 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages
Description: 320 RNA samples isolated from 11 organs (adrenal gland, brain, heart, kidney, liver, lung, muscle, spleen, thymus, and testes or uterus) from both sexes of Fischer 344 rats across four developmental stages (2-, 6-, 21-, and 104-weeks-old)
BioProject: PRJNA238328
Publication: PMID 24510058
Analysis date: Mon Jun 6 17:44:12 2016

Bibliography

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GeneRIFs: Gene References Into Functions

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Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Gene Ontology Provided by RGD

Function	Evidence Code	Pubs
enables RNA binding	IEA Inferred from Electronic Annotation more info
enables RNA binding	ISO Inferred from Sequence Orthology more info
enables box H/ACA snoRNA binding	ISO Inferred from Sequence Orthology more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables pseudouridine synthase activity	IBA Inferred from Biological aspect of Ancestor more info
enables pseudouridine synthase activity	IEA Inferred from Electronic Annotation more info
enables pseudouridine synthase activity	ISO Inferred from Sequence Orthology more info
enables pseudouridine synthase activity	ISS Inferred from Sequence or Structural Similarity more info
enables telomerase RNA binding	ISO Inferred from Sequence Orthology more info
contributes_to telomerase activity	ISO Inferred from Sequence Orthology more info
enables telomerase activity	ISO Inferred from Sequence Orthology more info

Process	Evidence Code	Pubs
involved_in 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 box H/ACA sno(s)RNA metabolic process	ISO Inferred from Sequence Orthology more info
involved_in enzyme-directed rRNA pseudouridine synthesis	ISO Inferred from Sequence Orthology more info
involved_in enzyme-directed rRNA pseudouridine synthesis	ISS Inferred from Sequence or Structural Similarity more info
involved_in mRNA pseudouridine synthesis	IBA Inferred from Biological aspect of Ancestor more info
involved_in positive regulation of cell population proliferation	IDA Inferred from Direct Assay more info	PubMed
involved_in positive regulation of telomerase RNA localization to Cajal body	ISO Inferred from Sequence Orthology more info
acts_upstream_of positive regulation of telomere maintenance via telomerase	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within positive regulation of telomere maintenance via telomerase	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within protein localization to Cajal body	ISO Inferred from Sequence Orthology more info	PubMed
involved_in pseudouridine synthesis	IEA Inferred from Electronic Annotation more info
involved_in rRNA pseudouridine synthesis	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within rRNA pseudouridine synthesis	ISO Inferred from Sequence Orthology more info
involved_in regulation of telomerase RNA localization to Cajal body	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within scaRNA localization to Cajal body	ISO Inferred from Sequence Orthology more info
involved_in snRNA pseudouridine synthesis	IBA Inferred from Biological aspect of Ancestor more info
involved_in snoRNA guided rRNA pseudouridine synthesis	IDA Inferred from Direct Assay more info	PubMed
involved_in telomerase RNA stabilization	ISO Inferred from Sequence Orthology more info
involved_in telomere maintenance via telomerase	ISO Inferred from Sequence Orthology more info
involved_in telomere maintenance via telomerase	ISS Inferred from Sequence or Structural Similarity more info

Component	Evidence Code	Pubs
located_in Cajal body	IDA Inferred from Direct Assay more info	PubMed
located_in Cajal body	IEA Inferred from Electronic Annotation more info
located_in Cajal body	ISO Inferred from Sequence Orthology more info
part_of box H/ACA snoRNP complex	IBA Inferred from Biological aspect of Ancestor more info
part_of box H/ACA snoRNP complex	IDA Inferred from Direct Assay more info	PubMed
part_of box H/ACA snoRNP complex	ISO Inferred from Sequence Orthology more info
part_of box H/ACA telomerase RNP complex	ISO Inferred from Sequence Orthology more info
located_in fibrillar center	ISO Inferred from Sequence Orthology more info
located_in nucleolus	ISO Inferred from Sequence Orthology more info
located_in nucleoplasm	IDA Inferred from Direct Assay more info	PubMed
located_in nucleoplasm	ISO Inferred from Sequence Orthology more info
located_in nucleus	ISO Inferred from Sequence Orthology more info
part_of telomerase holoenzyme complex	ISO Inferred from Sequence Orthology more info
part_of telomerase holoenzyme complex	ISS Inferred from Sequence or Structural Similarity more info

General protein information

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Preferred Names: H/ACA ribonucleoprotein complex subunit DKC1

Names: dyskeratosis congenita 1, dyskerin; h/ACA ribonucleoprotein complex subunit 4; nopp140-associated protein of 57 kDa; nucleolar protein NAP57; nucleolar protein family A member 4; snoRNP protein DKC1

NP_596910.1

EC 5.4.99.-

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)

NM_133419.1 → NP_596910.1 H/ACA ribonucleoprotein complex subunit DKC1

See identical proteins and their annotated locations for NP_596910.1

Status: PROVISIONAL

Source sequence(s)

Z34922

UniProtKB/Swiss-Prot

P40615, Q499M9

UniProtKB/TrEMBL

A0A0G2K700

Conserved Domains (4) summary

cd02572
Location:89 → 271

PseudoU_synth_hDyskerin; Pseudouridine synthase, human dyskerin like

TIGR00425
Location:57 → 382

CBF5; rRNA pseudouridine synthase, putative

pfam01472
Location:298 → 371

PUA; PUA domain

pfam08068
Location:50 → 107

DKCLD; DKCLD (NUC011) domain