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

Gene ID: 9416, updated on 10-Oct-2019

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
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

Genomic context

See DDX23 in Genome Data Viewer
Location:
12q13.12
Exon count:
17
Annotation release Status Assembly Chr Location
109.20190905 current GRCh38.p13 (GCF_000001405.39) 12 NC_000012.12 (48829756..48852163, complement)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 12 NC_000012.11 (49223539..49245957, complement)

Chromosome 12 - NC_000012.12Genomic Context describing neighboring genes Neighboring gene chromosome 20 open reading frame 27 pseudogene Neighboring gene uncharacterized LOC101927241 Neighboring gene calcium voltage-gated channel auxiliary subunit beta 3 Neighboring gene uncharacterized LOC105369755 Neighboring gene Rho family GTPase 1 Neighboring gene RNA, U6 small nuclear 600, pseudogene

Genomic regions, transcripts, and products

Expression

  • 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

Phenotypes

NHGRI GWAS Catalog

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

HIV-1 interactions

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 BioSystems

  • Gene Expression, organism-specific biosystem (from REACTOME)
    Gene Expression, organism-specific biosystemGene Expression covers the pathways by which genomic DNA is transcribed to yield RNA, the regulation of these transcription processes, and the pathways by which newly-made RNA Transcripts are process...
  • Processing of Capped Intron-Containing Pre-mRNA, organism-specific biosystem (from REACTOME)
    Processing of Capped Intron-Containing Pre-mRNA, organism-specific biosystemCo-transcriptional pre-mRNA splicing is not obligatory. Pre-mRNA splicing begins co-transcriptionally and often continues post-transcriptionally. Human genes contain an average of nine introns per ge...
  • Spliceosome, organism-specific biosystem (from KEGG)
    Spliceosome, organism-specific biosystemAfter transcription, eukaryotic mRNA precursors contain protein-coding exons and noncoding introns. In the following splicing, introns are excised and exons are joined by a macromolecular complex, th...
  • Spliceosome, conserved biosystem (from KEGG)
    Spliceosome, conserved biosystemAfter transcription, eukaryotic mRNA precursors contain protein-coding exons and noncoding introns. In the following splicing, introns are excised and exons are joined by a macromolecular complex, th...
  • Spliceosome, U4/U6.U5 tri-snRNP, organism-specific biosystem (from KEGG)
    Spliceosome, U4/U6.U5 tri-snRNP, organism-specific biosystemStructural complex; Genetic information processing; Spliceosome
  • Spliceosome, U4/U6.U5 tri-snRNP, conserved biosystem (from KEGG)
    Spliceosome, U4/U6.U5 tri-snRNP, conserved biosystemStructural complex; Genetic information processing; Spliceosome
  • mRNA Splicing, organism-specific biosystem (from REACTOME)
    mRNA Splicing, organism-specific biosystemThe process in which excision of introns from the primary transcript of messenger RNA (mRNA) is followed by ligation of the two exon termini exposed by removal of each intron, is called mRNA splicing...
  • mRNA Splicing - Major Pathway, organism-specific biosystem (from REACTOME)
    mRNA Splicing - Major Pathway, organism-specific biosystemThe splicing of pre-mRNA occurs within a large, very dynamic complex, designated the 'spliceosome'. The 50-60S spliceosomes are estimated to be 40-60 nm in diameter, and have molecular weights in the...
  • mRNA Splicing - Minor Pathway, organism-specific biosystem (from REACTOME)
    mRNA Splicing - Minor Pathway, organism-specific biosystemThe splicing of a subset of pre-mRNA introns occurs by a second pathway, designated the AT-AC or U12-dependent splicing pathway. AT-AC introns have highly conserved, non-canonical splice sites that ...

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Clone Names

  • MGC8416

Gene Ontology Provided by GOA

Function Evidence Code Pubs
ATP binding IEA
Inferred from Electronic Annotation
more info
 
RNA binding HDA PubMed 
RNA binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
RNA helicase activity TAS
Traceable Author Statement
more info
PubMed 
NOT helicase activity IDA
Inferred from Direct Assay
more info
PubMed 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
Process Evidence Code Pubs
RNA splicing TAS
Traceable Author Statement
more info
PubMed 
RNA splicing, via transesterification reactions TAS
Traceable Author Statement
more info
PubMed 
cis assembly of pre-catalytic spliceosome IC
Inferred by Curator
more info
PubMed 
mRNA splicing, via spliceosome IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
mRNA splicing, via spliceosome IC
Inferred by Curator
more info
PubMed 
mRNA splicing, via spliceosome TAS
Traceable Author Statement
more info
 
Component Evidence Code Pubs
U5 snRNP IDA
Inferred from Direct Assay
more info
PubMed 
catalytic step 2 spliceosome IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
catalytic step 2 spliceosome IDA
Inferred from Direct Assay
more info
PubMed 
extracellular exosome HDA PubMed 
nucleolus IDA
Inferred from Direct Assay
more info
 
nucleoplasm IDA
Inferred from Direct Assay
more info
 
nucleoplasm TAS
Traceable Author Statement
more info
 
nucleus TAS
Traceable Author Statement
more info
PubMed 

General protein information

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
NP_004809.2

NCBI Reference Sequences (RefSeq)

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_004818.3NP_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
    Q9BUQ8
    UniProtKB/TrEMBL
    A0A024R0Z3, B3KY11
    Related
    ENSP00000310723.2, ENST00000308025.8
    Conserved Domains (3) summary
    COG0513
    Location:379783
    SrmB; Superfamily II DNA and RNA helicase [Replication, recombination and repair]
    cl25887
    Location:80210
    RRM; RNA recognition motif (RRM) domain [Translation, ribosomal structure and biogenesis]
    cl26511
    Location:4351
    Neuromodulin_N; Gap junction protein N-terminal region

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109.20190905

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

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000012.12 Reference GRCh38.p13 Primary Assembly

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