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

    Gene ID: 9416, updated on 28-Oct-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
    mouse all
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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_2024_08 current GRCh38.p14 (GCF_000001405.40) 12 NC_000012.12 (48829756..48852163, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 12 NC_060936.1 (48791783..48814355, complement)
    RS_2024_09 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 adipose secreted signaling protein 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 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. RNA Splicing by the Spliceosome. Wilkinson ME, et al. Annu Rev Biochem, 2020 Jun 20. PMID 31794245
    2. Syndromic neurodevelopmental disorder associated with de novo variants in DDX23. Burns W, et al. Am J Med Genet A, 2021 Oct. PMID 34050707
    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. SRSF1 interactome determined by proximity labeling reveals direct interaction with spliceosomal RNA helicase DDX23. Segovia D, et al. Proc Natl Acad Sci U S A, 2024 May 21. PMID 38743621,
    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 (144) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. SRSF1 interactome determined by proximity labeling reveals direct interaction with spliceosomal RNA helicase DDX23.
      Title: SRSF1 interactome determined by proximity labeling reveals direct interaction with spliceosomal RNA helicase DDX23.
    2. 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.
    3. Syndromic neurodevelopmental disorder associated with de novo variants in DDX23.
      Title: Syndromic neurodevelopmental disorder associated with de novo variants in DDX23.
    4. RNA Splicing by the Spliceosome.
      Title: RNA Splicing by the Spliceosome.
    5. 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.
    6. 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.
    7. 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.
    8. 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 
    located_in 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_2024_08

    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

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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