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    DDX28 DEAD-box helicase 28 [ Homo sapiens (human) ]

    Gene ID: 55794, updated on 10-Dec-2024

    Summary

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    Official Symbol
    DDX28provided by HGNC
    Official Full Name
    DEAD-box helicase 28provided by HGNC
    Primary source
    HGNC:HGNC:17330
    See related
    Ensembl:ENSG00000182810 MIM:607618; AllianceGenome:HGNC:17330
    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
    MDDX28
    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 the DEAD box protein family are believed to be involved in embryogenesis, spermatogenesis, and cellular growth and division. This gene is intronless. It encodes an RNA-dependent ATPase. The encoded protein is localized in the mitochondria and the nucleus, and can be transported between the mitochondria and the nucleus. [provided by RefSeq, Jul 2008]
    Orthologs
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    Genomic context

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    See DDX28 in Genome Data Viewer
    Location:
    16q22.1
    Exon count:
    1
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 16 NC_000016.10 (68020916..68023232, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 16 NC_060940.1 (73816696..73819012, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 16 NC_000016.9 (68054819..68057135, complement)

    Chromosome 16 - NC_000016.10Genomic Context describing neighboring genes Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:68055836-68056586 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:68056587-68057337 Neighboring gene RNA, U6 small nuclear 359, pseudogene Neighboring gene DPEP2 neighbor Neighboring gene ReSE screen-validated silencer GRCh37_chr16:68078446-68078635 Neighboring gene dihydrouridine synthase 2 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11003 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11004 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11005 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7638 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7639 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11006 Neighboring gene Sharpr-MPRA regulatory region 7518 Neighboring gene nuclear factor of activated T cells 3 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7640 Neighboring gene H3K27ac hESC enhancer GRCh37_chr16:68197467-68198334 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:68221558-68222058 Neighboring gene small nucleolar RNA SNORA48

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Bibliography

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    Related articles in PubMed

    1. DEAD Box Protein Family Member DDX28 Is a Negative Regulator of Hypoxia-Inducible Factor 2α- and Eukaryotic Initiation Factor 4E2-Directed Hypoxic Translation. Evagelou SL, et al. Mol Cell Biol, 2020 Feb 27. PMID 31907278, Free PMC Article
    2. Cloning and characterization of MDDX28, a putative dead-box helicase with mitochondrial and nuclear localization. Valgardsdottir R, et al. J Biol Chem, 2001 Aug 24. PMID 11350955
    3. Transport signals and transcription-dependent nuclear localization of the putative DEAD-box helicase MDDX28. Valgardsdottir R, et al. J Biol Chem, 2003 Jun 6. PMID 12663657
    4. Identification of RNA helicases in human immunodeficiency virus 1 (HIV-1) replication - a targeted small interfering RNA library screen using pseudotyped and WT HIV-1. Williams CA, et al. J Gen Virol, 2015 Jun. PMID 25701821, Free PMC Article
    5. Mitochondrial RNA Granules Are Centers for Posttranscriptional RNA Processing and Ribosome Biogenesis. Antonicka H, et al. Cell Rep, 2015 Feb 17. PMID 25683715

    See all (66) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. The authors have identified the DEAD box protein family member DDX28 as an interactor and negative regulator of HIF-2alpha that suppresses HIF-2alpha's ability to activate eIF4E2-directed translation.
      Title: DEAD Box Protein Family Member DDX28 Is a Negative Regulator of Hypoxia-Inducible Factor 2α- and Eukaryotic Initiation Factor 4E2-Directed Hypoxic Translation.
    2. Observational study of gene-disease association. (HuGE Navigator)
      Title: Genetic variants in nuclear-encoded mitochondrial genes influence AIDS progression.
    3. Three domains in the N-terminal half of the protein and its RNA binding ability were essential for nucleolar localization as well as transcription-inhibition-dependent localization to nuclear subcompartments and two were the nuclear localization signal
      Title: Transport signals and transcription-dependent nuclear localization of the putative DEAD-box helicase MDDX28.
    Submit: New GeneRIF Correction

    Phenotypes

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    Review eQTL and phenotype association data in this region using PheGenI

    EBI GWAS Catalog

    Description
    Biological insights from 108 schizophrenia-associated genetic loci.
    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)

    HIV-1 interactions

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    Replication interactions

    Interaction Pubs
    siRNA knockdown of DDX28 decreases intra- and extra-cellular HIV CA(p24) from HeLa cells transfected with env-deleted HIV-1 plasmid, a vesicular stomatitis virus glycoprotein plasmid and specific siRNA. Resulting HIV demonstrates decreased infectivity. PubMed

    Protein interactions

    Protein Gene Interaction Pubs
    capsid gag siRNA knockdown of DDX28 decreases intra- and extra-cellular HIV CA(p24) from HeLa cells transfected with env-deleted HIV-1 plasmid, a vesicular stomatitis virus glycoprotein plasmid and specific siRNA. Resulting HIV demonstrates decreased infectivity. 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

    • FLJ11282

    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 IEA
    Inferred from Electronic Annotation
    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 rRNA binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    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
    		  
    involved_in mitochondrial large ribosomal subunit assembly IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in mitochondrial large ribosomal subunit assembly IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    Component Evidence Code Pubs
    located_in cytosol IDA
    Inferred from Direct Assay
    more info
    		  
    located_in mitochondrial nucleoid IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in mitochondrion HTP PubMed 
    is_active_in mitochondrion IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in mitochondrion IDA
    Inferred from Direct Assay
    more info
    		  
    located_in nucleolus IDA
    Inferred from Direct Assay
    more info
    		  
    located_in nucleoplasm IDA
    Inferred from Direct Assay
    more info
    		  
    located_in ribonucleoprotein granule IDA
    Inferred from Direct Assay
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    probable ATP-dependent RNA helicase DDX28
    Names
    DEAD (Asp-Glu-Ala-Asp) box polypeptide 28
    DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 28
    mitochondrial DEAD box protein 28
    mitochondrial DEAD-box polypeptide 28
    NP_060850.2

    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_018380.4 → NP_060850.2  probable ATP-dependent RNA helicase DDX28

      See identical proteins and their annotated locations for NP_060850.2

      Status: REVIEWED

      Source sequence(s)
      AC130462
      Consensus CDS
      CCDS10858.1
      UniProtKB/Swiss-Prot
      Q9NUL7
      Related
      ENSP00000332340.6, ENST00000332395.7
      Conserved Domains (2) summary
      PRK01297
      Location:27 → 538
      PRK01297; ATP-dependent RNA helicase RhlB; Provisional
      cd17948
      Location:137 → 371
      DEADc_DDX28; DEAD-box helicase domain of DEAD box protein 28

    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_000016.10 Reference GRCh38.p14 Primary Assembly

      Range
      68020916..68023232 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060940.1 Alternate T2T-CHM13v2.0

      Range
      73816696..73819012 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9NUL7.2 GenPept UniProtKB/Swiss-Prot:Q9NUL7

    Gene LinkOut

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

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