DDX23 DEAD-box helicase 23 [Homo sapiens (human)] - Gene

Summary

Official Symbol: DDX23provided by HGNC
Official Full Name: DEAD-box helicase 23provided by HGNC
Primary source: HGNC:HGNC:17347
See related: Ensembl:ENSG00000174243 MIM:612172; AllianceGenome:HGNC:17347
Gene type: protein coding
RefSeq status: REVIEWED
Organism: Homo sapiens
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as: prp28; PRPF28; U5-100K; SNRNP100; U5-100KD
Summary: This gene encodes a member of the DEAD box protein family. DEAD box proteins, characterized by the conserved motif Asp-Glu-Ala-Asp (DEAD), are putative RNA helicases. They are implicated in a number of cellular processes involving alteration of RNA secondary structure, such as translation initiation, nuclear and mitochondrial splicing, and ribosome and spliceosome assembly. Based on their distribution patterns, some members of this family are believed to be involved in embryogenesis, spermatogenesis, and cellular growth and division. The protein encoded by this gene is a component of the U5 snRNP complex; it may facilitate conformational changes in the spliceosome during nuclear pre-mRNA splicing. An alternatively spliced transcript variant has been found for this gene, but its biological validity has not been determined. [provided by RefSeq, Jul 2008]
Expression: Ubiquitous expression in lymph node (RPKM 26.9), appendix (RPKM 25.8) and 25 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 12q13.12

Exon count:: 17

Annotation release	Status	Assembly	Chr	Location
RS_2023_10	current	GRCh38.p14 (GCF_000001405.40)	12	NC_000012.12 (48829756..48852163, complement)
RS_2023_10	current	T2T-CHM13v2.0 (GCF_009914755.1)	12	NC_060936.1 (48791783..48814355, complement)
105.20220307	previous assembly	GRCh37.p13 (GCF_000001405.25)	12	NC_000012.11 (49223539..49245946, complement)

Chromosome 12 - NC_000012.12 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: HPA RNA-seq normal tissues
Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
BioProject: PRJEB4337
Publication: PMID 24309898
Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

METTL3 enhances pancreatic ductal adenocarcinoma progression and gemcitabine resistance through modifying DDX23 mRNA N6 adenosine methylation.
Title: METTL3 enhances pancreatic ductal adenocarcinoma progression and gemcitabine resistance through modifying DDX23 mRNA N6 adenosine methylation.
Syndromic neurodevelopmental disorder associated with de novo variants in DDX23.
Title: Syndromic neurodevelopmental disorder associated with de novo variants in DDX23.
RNA Splicing by the Spliceosome.
Title: RNA Splicing by the Spliceosome.
These data provide new insights into the function of Prp28 in higher eukaryotes, and the requirements for stable tri-small nuclear ribonucleoproteins binding during B complex formation.
Title: A spliceosome intermediate with loosely associated tri-snRNP accumulates in the absence of Prp28 ATPase activity.
new basis of DDX23-Linc00630-HDAC1 signal axis for understanding its pathogenicity, which could be further developed as a valuable therapeutic strategy
Title: DDX23-Linc00630-HDAC1 axis activates the Notch pathway to promote metastasis.
pausing of RNA polymerase II (RNA Pol II) initiates a signaling cascade whereby the serine/arginine protein kinase 2 (SRPK2) phosphorylates the DDX23 helicase, culminating in the suppression of R-loops.
Title: Transcription Dynamics Prevent RNA-Mediated Genomic Instability through SRPK2-Dependent DDX23 Phosphorylation.
SRPK2 knock down results in hypophosphorylation of the arginine-serine (RS) domain-containing human PRP28 protein (PRP28, also known as DDX23), and destabilizes PRP28 association with the tri-snRNP.
Title: Phosphorylation of human PRP28 by SRPK2 is required for integration of the U4/U6-U5 tri-snRNP into the spliceosome.

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Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

EBI GWAS Catalog

Description
Large-scale genome-wide association analysis of bipolar disorder identifies a new susceptibility locus near ODZ4. EBI GWAS Catalog EBI GWAS CatalogPubMed

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

HIV-1 interactions

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Replication interactions

Interaction	Pubs
Knockdown of DEAD (Asp-Glu-Ala-Asp) box polypeptide 23 (DDX23) by siRNA inhibits the early stages of HIV-1 replication in 293T cells infected with VSV-G pseudotyped HIV-1	PubMed

Protein interactions

Protein	Gene	Interaction	Pubs
Envelope surface glycoprotein gp120	env	Tandem affinity purification and mass spectrometry analysis identify DEAD (Asp-Glu-Ala-Asp) box polypeptide 23 (DDX23), HIV-1 Gag, Gag/Pol, gp120, and Nef incorporated into staufen1 RNP complexes isolated from HIV-1-expressing cells	PubMed
Gag-Pol	gag-pol	Tandem affinity purification and mass spectrometry analysis identify DEAD (Asp-Glu-Ala-Asp) box polypeptide 23 (DDX23), HIV-1 Gag, Gag/Pol, gp120, and Nef incorporated into staufen1 RNP complexes isolated from HIV-1-expressing cells	PubMed
Nef	nef	Tandem affinity purification and mass spectrometry analysis identify DEAD (Asp-Glu-Ala-Asp) box polypeptide 23 (DDX23), HIV-1 Gag, Gag/Pol, gp120, and Nef incorporated into staufen1 RNP complexes isolated from HIV-1-expressing cells	PubMed
Pr55(Gag)	gag	Tandem affinity purification and mass spectrometry analysis identify DEAD (Asp-Glu-Ala-Asp) box polypeptide 23 (DDX23), HIV-1 Gag, Gag/Pol, gp120, and Nef incorporated into staufen1 RNP complexes isolated from HIV-1-expressing cells	PubMed

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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

RH68064 (e-PCR)
- UniSTS:47000

D12S1952 (e-PCR)
- UniSTS:53941

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables ATP binding	IEA Inferred from Electronic Annotation more info
enables ATP hydrolysis activity	IEA Inferred from Electronic Annotation more info
enables RNA binding	HDA more info	PubMed
enables RNA helicase activity	TAS Traceable Author Statement more info
NOT enables helicase activity	IDA Inferred from Direct Assay more info	PubMed
enables mRNA binding	IBA Inferred from Biological aspect of Ancestor more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed

Process	Evidence Code	Pubs
involved_in R-loop processing	IDA Inferred from Direct Assay more info	PubMed
involved_in RNA splicing	TAS Traceable Author Statement more info	PubMed
involved_in RNA splicing, via transesterification reactions	TAS Traceable Author Statement more info	PubMed
involved_in cis assembly of pre-catalytic spliceosome	IC Inferred by Curator more info	PubMed
involved_in mRNA splicing, via spliceosome	IBA Inferred from Biological aspect of Ancestor more info
involved_in mRNA splicing, via spliceosome	IC Inferred by Curator more info	PubMed
involved_in mRNA splicing, via spliceosome	NAS Non-traceable Author Statement more info	PubMed
involved_in mRNA splicing, via spliceosome	TAS Traceable Author Statement more info

Component	Evidence Code	Pubs
part_of U4/U6 x U5 tri-snRNP complex	IDA Inferred from Direct Assay more info	PubMed
part_of U4/U6 x U5 tri-snRNP complex	IPI Inferred from Physical Interaction more info	PubMed
part_of U5 snRNP	IDA Inferred from Direct Assay more info	PubMed
part_of catalytic step 2 spliceosome	IBA Inferred from Biological aspect of Ancestor more info
part_of catalytic step 2 spliceosome	IDA Inferred from Direct Assay more info	PubMed
part_of chromatin	IDA Inferred from Direct Assay more info	PubMed
located_in extracellular exosome	HDA more info	PubMed
located_in nucleolus	IDA Inferred from Direct Assay more info
located_in nucleoplasm	IDA Inferred from Direct Assay more info
located_in nucleoplasm	TAS Traceable Author Statement more info
located_in nucleus	IDA Inferred from Direct Assay more info	PubMed
located_in nucleus	NAS Non-traceable Author Statement more info	PubMed

General protein information

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Preferred Names: probable ATP-dependent RNA helicase DDX23

Names: 100 kDa U5 snRNP-specific protein; DEAD (Asp-Glu-Ala-Asp) box polypeptide 23; DEAD box protein 23; PRP28 homolog, yeast; PRP28p homolog; U5 snRNP 100 kD protein; U5 snRNP-specific 100-kD protein

NP_004809.2

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_004818.3 → NP_004809.2 probable ATP-dependent RNA helicase DDX23

See identical proteins and their annotated locations for NP_004809.2

Status: REVIEWED

Source sequence(s)

AF026402, AK128428, BC002366

Consensus CDS

CCDS8770.1

UniProtKB/Swiss-Prot

B2R600, B4DH15, O43188, Q9BUQ8

UniProtKB/TrEMBL

A0A8V8TR86

Related

ENSP00000310723.2, ENST00000308025.8

Conserved Domains (4) summary

PTZ00121
Location:4 → 351

PTZ00121; MAEBL; Provisional

TIGR01622
Location:80 → 210

SF-CC1; splicing factor, CC1-like family

cd18787
Location:639 → 768

SF2_C_DEAD; C-terminal helicase domain of the DEAD box helicases

cd17945
Location:402 → 628

DEADc_DDX23; DEAD-box helicase domain of DEAD box protein 23