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

Gene ID: 9416, updated on 7-Apr-2024

Summary

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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
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Genomic context

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See DDX23 in Genome Data Viewer
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_000012.12Genomic Context describing neighboring genes Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:49194958-49195556 Neighboring gene chromosome 20 open reading frame 27 pseudogene Neighboring gene uncharacterized LOC101927241 Neighboring gene H3K27ac hESC enhancer GRCh37_chr12:49208339-49208840 Neighboring gene H3K27ac hESC enhancer GRCh37_chr12:49208841-49209340 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4413 Neighboring gene calcium voltage-gated channel auxiliary subunit beta 3 Neighboring gene uncharacterized LOC105369755 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6289 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6290 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6291 Neighboring gene Sharpr-MPRA regulatory region 11040 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6292 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6293 Neighboring gene Rho family GTPase 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6294 Neighboring gene RNA, U6 small nuclear 600, pseudogene

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • 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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Related articles in PubMed

  1. Syndromic neurodevelopmental disorder associated with de novo variants in DDX23. Burns W, et al. Am J Med Genet A, 2021 Oct. PMID 34050707
  2. RNA Splicing by the Spliceosome. Wilkinson ME, et al. Annu Rev Biochem, 2020 Jun 20. PMID 31794245
  3. A spliceosome intermediate with loosely associated tri-snRNP accumulates in the absence of Prp28 ATPase activity. Boesler C, et al. Nat Commun, 2016 Jul 5. PMID 27377154, Free PMC Article
  4. METTL3 enhances pancreatic ductal adenocarcinoma progression and gemcitabine resistance through modifying DDX23 mRNA N6 adenosine methylation. Lin C, et al. Cell Death Dis, 2023 Mar 28. PMID 36977668, Free PMC Article
  5. Phosphorylation of human PRP28 by SRPK2 is required for integration of the U4/U6-U5 tri-snRNP into the spliceosome. Mathew R, et al. Nat Struct Mol Biol, 2008 May. PMID 18425142

See all (124) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. 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.
  2. Syndromic neurodevelopmental disorder associated with de novo variants in DDX23.
    Title: Syndromic neurodevelopmental disorder associated with de novo variants in DDX23.
  3. RNA Splicing by the Spliceosome.
    Title: RNA Splicing by the Spliceosome.
  4. 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.
  5. 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.
  6. 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.
  7. 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.
Submit: New GeneRIF Correction

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

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

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

Go to the HIV-1, Human Interaction Database

Pathways from PubChem

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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

Homology

Clone Names

  • MGC8416

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 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 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

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)

  1. 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

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000012.12 Reference GRCh38.p14 Primary Assembly

    Range
    48829756..48852163 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060936.1 Alternate T2T-CHM13v2.0

    Range
    48791783..48814355 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q9BUQ8.3 GenPept UniProtKB/Swiss-Prot:Q9BUQ8

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