Ddx21 DExD-box helicase 21 [Rattus norvegicus (Norway rat)] - Gene

Summary

Official Symbol: Ddx21provided by RGD
Official Full Name: DExD-box helicase 21provided by RGD
Primary source: RGD:1307306
See related: Ensembl:ENSRNOG00000043099 AllianceGenome:RGD:1307306
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: Ddx21a; Ddx21b
Summary: Predicted to enable RNA binding activity; RNA helicase activity; and identical protein binding activity. Predicted to be involved in cellular macromolecule biosynthetic process; positive regulation of I-kappaB kinase/NF-kappaB signaling; and positive regulation of myeloid dendritic cell cytokine production. Predicted to act upstream of or within response to exogenous dsRNA and response to virus. Predicted to be located in chromosome; cytosol; and nucleoplasm. Predicted to be active in nucleolus. Orthologous to human DDX21 (DExD-box helicase 21). [provided by Alliance of Genome Resources, Apr 2022]
Expression: Biased expression in Thymus (RPKM 377.8), Spleen (RPKM 339.5) and 9 other tissues See more
Orthologs: human mouse all
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Genomic context

Location:: 20q11

Exon count:: 15

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCr8 (GCF_036323735.1)	20	NC_086038.1 (31077044..31097238, complement)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	20	NC_051355.1 (30534319..30554513, complement)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	20	NC_005119.4 (32213147..32232632, complement)

Chromosome 20 - NC_086038.1 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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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
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

What's a GeneRIF?

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Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

RH129516 (e-PCR)
- UniSTS:212819

D10Ertd645e (e-PCR), detects polymorphism
- UniSTS:167026

RH133206 (e-PCR)
- UniSTS:216489

RH144150 (e-PCR)
- UniSTS:233396

BI302095 (e-PCR)
- UniSTS:247535

Gene Ontology Provided by RGD

Function	Evidence Code	Pubs
enables 7SK snRNA binding	ISO Inferred from Sequence Orthology more info
enables 7SK snRNA binding	ISS Inferred from Sequence or Structural Similarity more info
enables ATP binding	IEA Inferred from Electronic Annotation more info
enables ATP hydrolysis activity	IEA Inferred from Electronic Annotation more info
enables RNA helicase activity	IBA Inferred from Biological aspect of Ancestor more info
enables RNA helicase activity	ISO Inferred from Sequence Orthology more info
enables RNA helicase activity	ISS Inferred from Sequence or Structural Similarity more info
enables double-stranded RNA binding	ISO Inferred from Sequence Orthology more info
enables identical protein binding	ISO Inferred from Sequence Orthology more info
enables mRNA binding	IBA Inferred from Biological aspect of Ancestor more info
enables miRNA binding	ISO Inferred from Sequence Orthology more info
enables miRNA binding	ISS Inferred from Sequence or Structural Similarity more info
enables rRNA binding	ISO Inferred from Sequence Orthology more info
enables rRNA binding	ISS Inferred from Sequence or Structural Similarity more info
enables snoRNA binding	ISO Inferred from Sequence Orthology more info
enables snoRNA binding	ISS Inferred from Sequence or Structural Similarity more info

Process	Evidence Code	Pubs
involved_in R-loop processing	ISO Inferred from Sequence Orthology more info
involved_in R-loop processing	ISS Inferred from Sequence or Structural Similarity more info
involved_in defense response to virus	IEA Inferred from Electronic Annotation more info
involved_in innate immune response	IEA Inferred from Electronic Annotation more info
involved_in positive regulation of canonical NF-kappaB signal transduction	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of canonical NF-kappaB signal transduction	ISS Inferred from Sequence or Structural Similarity more info
involved_in positive regulation of myeloid dendritic cell cytokine production	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of transcription by RNA polymerase III	ISO Inferred from Sequence Orthology more info
involved_in rRNA processing	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within response to exogenous dsRNA	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within response to virus	ISO Inferred from Sequence Orthology more info
involved_in transcription by RNA polymerase II	ISO Inferred from Sequence Orthology more info
involved_in transcription by RNA polymerase II	ISS Inferred from Sequence or Structural Similarity more info

Component	Evidence Code	Pubs
part_of B-WICH complex	ISO Inferred from Sequence Orthology more info
located_in chromosome	ISO Inferred from Sequence Orthology more info
located_in cytosol	ISO Inferred from Sequence Orthology more info
located_in cytosol	ISS Inferred from Sequence or Structural Similarity more info
located_in mitochondrion	IEA Inferred from Electronic Annotation more info
is_active_in nucleolus	IBA Inferred from Biological aspect of Ancestor more info
located_in nucleolus	ISO Inferred from Sequence Orthology more info
located_in nucleolus	ISS Inferred from Sequence or Structural Similarity more info
located_in nucleoplasm	ISO Inferred from Sequence Orthology more info
located_in nucleoplasm	ISS Inferred from Sequence or Structural Similarity more info

General protein information

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Preferred Names: nucleolar RNA helicase 2

Names: DEAD (Asp-Glu-Ala-Asp) box helicase 21; DEAD (Asp-Glu-Ala-Asp) box polypeptide 21; DEAD (Asp-Glu-Ala-Asp) box polypeptide 21a; DEAD (Asp-Glu-Ala-Asp) box polypeptide 21b; DEAD box protein 21; DEAD-box helicase 21; RH II/Gu; gu-alpha; nucleolar RNA helicase Gu; nucleolar RNA helicase II

NP_001032278.1

EC 3.6.4.13

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_001037201.1 → NP_001032278.1 nucleolar RNA helicase 2

See identical proteins and their annotated locations for NP_001032278.1

Status: PROVISIONAL

Source sequence(s)

BC105878

UniProtKB/Swiss-Prot

Q3B8Q1

UniProtKB/TrEMBL

A6K457

Related

ENSRNOP00000063494.1, ENSRNOT00000068184.2

Conserved Domains (7) summary

PRK01297
Location:112 → 557

PRK01297; ATP-dependent RNA helicase RhlB; Provisional

cd00079
Location:425 → 534

HELICc; Helicase superfamily c-terminal domain; associated with DEXDc-, DEAD-, and DEAH-box proteins, yeast initiation factor 4A, Ski2p, and Hepatitis C virus NS3 helicases; this domain is found in a wide variety of helicases and helicase related proteins; may ...

cd00268
Location:184 → 391

DEADc; DEAD-box helicases. A diverse family of proteins involved in ATP-dependent RNA unwinding, needed in a variety of cellular processes including splicing, ribosome biogenesis and RNA degradation. The name derives from the sequence of the Walker B motif ...

cd12936
Location:613 → 705

GUCT_RHII_Gualpha_beta; RNA-binding GUCT domain found in vertebrate RNA helicase II/Gualpha (RH-II/Gualpha), RNA helicase II/Gubeta (RH-II/Gubeta) and similar proteins

pfam05466
Location:7 → 165

BASP1; Brain acid soluble protein 1 (BASP1 protein)

pfam15502
Location:707 → 780

MPLKIP; M-phase-specific PLK1-interacting protein

cl17173
Location:716 → 765

AdoMet_MTases; S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy). ...