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    DDX50 DExD-box helicase 50 [ Homo sapiens (human) ]

    Gene ID: 79009, updated on 27-Nov-2024

    Summary

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    Official Symbol
    DDX50provided by HGNC
    Official Full Name
    DExD-box helicase 50provided by HGNC
    Primary source
    HGNC:HGNC:17906
    See related
    Ensembl:ENSG00000107625 MIM:610373; AllianceGenome:HGNC:17906
    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
    GU2; GUB; mcdrh; RH-II/GuB
    Summary
    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 DEAD box protein family are believed to be involved in embryogenesis, spermatogenesis, and cellular growth and division. This gene encodes a DEAD box enzyme that may be involved in ribosomal RNA synthesis or processing. This gene and DDX21, also called RH-II/GuA, have similar genomic structures and are in tandem orientation on chromosome 10, suggesting that the two genes arose by gene duplication in evolution. This gene has pseudogenes on chromosomes 2, 3 and 4. Alternative splicing of this gene generates multiple transcript variants, but the full length nature of all the other variants but one has not been defined. [provided by RefSeq, Jul 2008]
    Expression
    Ubiquitous expression in testis (RPKM 10.4), thyroid (RPKM 9.2) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See DDX50 in Genome Data Viewer
    Location:
    10q22.1
    Exon count:
    18
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 10 NC_000010.11 (68901315..68946847)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 10 NC_060934.1 (69770124..69825744)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 10 NC_000010.10 (70661071..70706603)

    Chromosome 10 - NC_000010.11Genomic Context describing neighboring genes Neighboring gene cell division cycle and apoptosis regulator 1 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_16866 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_16874 Neighboring gene small nucleolar RNA, C/D box 98 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_16884 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_16893 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_16897 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_16901 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_16907 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_16918 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2422 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2423 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2424 Neighboring gene storkhead box 1 Neighboring gene RNA, U6 small nuclear 697, pseudogene Neighboring gene MPRA-validated peak1002 silencer Neighboring gene NANOG hESC enhancer GRCh37_chr10:70637959-70638530 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3469 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3470 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3471 Neighboring gene RNA, U6 small nuclear 571, pseudogene Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3472 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:70715903-70716684 Neighboring gene H3K27ac hESC enhancer GRCh37_chr10:70716685-70717465 Neighboring gene DExD-box helicase 21 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3474 Neighboring gene mediator complex subunit 28 pseudogene 1 Neighboring gene kinesin family binding protein

    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. Solution structure of the GUCT domain from human RNA helicase II/Gu beta reveals the RRM fold, but implausible RNA interactions. Ohnishi S, et al. Proteins, 2009 Jan. PMID 18615715
    2. DDX50 inhibits the replication of dengue virus 2 by upregulating IFN-β production. Han P, et al. Arch Virol, 2017 Jun. PMID 28181036
    3. DDX50 Is a Viral Restriction Factor That Enhances IRF3 Activation. Pallett MA, et al. Viruses, 2022 Feb 3. PMID 35215908, Free PMC Article
    4. Genomic structure of newly identified paralogue of RNA helicase II/Gu: detection of pseudogenes and multiple alternatively spliced mRNAs. Valdez BC, et al. Gene, 2002 Feb 6. PMID 11891046
    5. Characterization of Staufen 1 ribonucleoprotein complexes. Brendel C, et al. Biochem J, 2004 Dec 1. PMID 15303970, Free PMC Article

    See all (145) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. DDX50 Is a Viral Restriction Factor That Enhances IRF3 Activation.
      Title: DDX50 Is a Viral Restriction Factor That Enhances IRF3 Activation.
    2. Results provide evidence that DDX50 negatively regulates DENV-2 replication during the early stages of infection by inducing IFN-beta production.
      Title: DDX50 inhibits the replication of dengue virus 2 by upregulating IFN-β production.
    3. Solution structure of the GUCT domain from human RNA helicase II/Gu beta reveals the RRM fold, but implausible RNA interactions.
      Title: Solution structure of the GUCT domain from human RNA helicase II/Gu beta reveals the RRM fold, but implausible RNA interactions.
    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

    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 50 (DDX50) by siRNA inhibits HIV-1 replication in HeLa P4/R5 cells PubMed

    Go to the HIV-1, Human Interaction Database

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • MGC3199

    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 ATP-dependent H2AZ histone chaperone activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables ATP-dependent H3-H4 histone complex chaperone activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables DNA clamp loader activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables RNA binding HDA PubMed 
    enables RNA helicase activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables chromatin extrusion motor activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables cohesin loader activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables mRNA binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Process Evidence Code Pubs
    involved_in chromatin looping IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in chromatin remodeling IEA
    Inferred from Electronic Annotation
    more info
    		  
    Component Evidence Code Pubs
    located_in membrane HDA PubMed 
    is_active_in nucleolus IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in nucleolus IDA
    Inferred from Direct Assay
    more info
    		  
    located_in plasma membrane IDA
    Inferred from Direct Assay
    more info
    		  

    General protein information

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    Preferred Names
    ATP-dependent RNA helicase DDX50
    Names
    DEAD (Asp-Glu-Ala-Asp) box polypeptide 50
    DEAD box protein 50
    DEAD-box helicase 50
    RNA helicase II/Gu beta
    gu-beta
    malignant cell derived RNA helicase
    nucleolar protein GU2
    NP_076950.1
    XP_011538446.1
    XP_047281682.1
    XP_047281683.1
    XP_047281684.1
    XP_054222682.1
    XP_054222683.1
    XP_054222684.1
    XP_054222685.1
    XP_054222686.1

    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.

    Genomic

    1. NG_050683.2 RefSeqGene

      Range
      5002..50534
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_024045.2 → NP_076950.1  ATP-dependent RNA helicase DDX50

      See identical proteins and their annotated locations for NP_076950.1

      Status: REVIEWED

      Source sequence(s)
      AL359844
      Consensus CDS
      CCDS7283.1
      UniProtKB/Swiss-Prot
      Q5VX37, Q8WV76, Q9BQ39, Q9BWI8
      UniProtKB/TrEMBL
      B4DW97
      Related
      ENSP00000362687.3, ENST00000373585.8
      Conserved Domains (3) summary
      COG0513
      Location:108 → 526
      SrmB; Superfamily II DNA and RNA helicase [Replication, recombination and repair]
      cd12936
      Location:568 → 659
      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
      cd17944
      Location:148 → 349
      DEADc_DDX21_DDX50; DEAD-box helicase domain of DEAD box proteins 21 and 50

    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_000010.11 Reference GRCh38.p14 Primary Assembly

      Range
      68901315..68946847
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_011540144.3 → XP_011538446.1  ATP-dependent RNA helicase DDX50 isoform X1

      See identical proteins and their annotated locations for XP_011538446.1

      UniProtKB/TrEMBL
      B4DW97, K0J110
      Conserved Domains (3) summary
      COG0513
      Location:43 → 461
      SrmB; Superfamily II DNA and RNA helicase [Replication, recombination and repair]
      cd12936
      Location:503 → 594
      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
      cd17944
      Location:83 → 284
      DEADc_DDX21_DDX50; DEAD-box helicase domain of DEAD box proteins 21 and 50

    2. XM_047425726.1 → XP_047281682.1  ATP-dependent RNA helicase DDX50 isoform X1

    3. XM_047425727.1 → XP_047281683.1  ATP-dependent RNA helicase DDX50 isoform X1

    4. XM_047425728.1 → XP_047281684.1  ATP-dependent RNA helicase DDX50 isoform X2

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060934.1 Alternate T2T-CHM13v2.0

      Range
      69770124..69825744
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054366710.1 → XP_054222685.1  ATP-dependent RNA helicase DDX50 isoform X1

    2. XM_054366707.1 → XP_054222682.1  ATP-dependent RNA helicase DDX50 isoform X3

      UniProtKB/Swiss-Prot
      Q5VX37, Q8WV76, Q9BQ39, Q9BWI8

    3. XM_054366708.1 → XP_054222683.1  ATP-dependent RNA helicase DDX50 isoform X1

    4. XM_054366709.1 → XP_054222684.1  ATP-dependent RNA helicase DDX50 isoform X1

    5. XM_054366711.1 → XP_054222686.1  ATP-dependent RNA helicase DDX50 isoform X2

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9BQ39.1 GenPept UniProtKB/Swiss-Prot:Q9BQ39

    Gene LinkOut

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

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