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    DDX56 DEAD-box helicase 56 [ Homo sapiens (human) ]

    Gene ID: 54606, updated on 27-Nov-2024

    Summary

    Official Symbol
    DDX56provided by HGNC
    Official Full Name
    DEAD-box helicase 56provided by HGNC
    Primary source
    HGNC:HGNC:18193
    See related
    Ensembl:ENSG00000136271 MIM:608023; AllianceGenome:HGNC:18193
    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
    DDX21; DDX26; NOH61
    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 shows ATPase activity in the presence of polynucleotides and associates with nucleoplasmic 65S preribosomal particles. This gene may be involved in ribosome synthesis, most likely during assembly of the large 60S ribosomal subunit. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Mar 2012]
    Expression
    Ubiquitous expression in thyroid (RPKM 15.8), lymph node (RPKM 15.1) and 25 other tissues See more
    Orthologs
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    Genomic context

    See DDX56 in Genome Data Viewer
    Location:
    7p13
    Exon count:
    14
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 7 NC_000007.14 (44565804..44573908, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 7 NC_060931.1 (44725568..44733672, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 7 NC_000007.13 (44605403..44613507, complement)

    Chromosome 7 - NC_000007.14Genomic Context describing neighboring genes Neighboring gene ribosomal protein L36a pseudogene 27 Neighboring gene NPC1 like intracellular cholesterol transporter 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25941 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:44579601-44580222 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:44600956-44601850 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:44605263-44605762 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25942 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18145 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18146 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25943 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25944 Neighboring gene transmembrane p24 trafficking protein 4 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25945 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18147 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:44646637-44647200 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25947 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18148 Neighboring gene oxoglutarate dehydrogenase Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25948 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25949 Neighboring gene ReSE screen-validated silencer GRCh37_chr7:44674956-44675111 Neighboring gene OGDH intron CAGE-defined high expression enhancer Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25951 Neighboring gene H3K27ac hESC enhancer GRCh37_chr7:44679045-44679572 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:44685039-44685539 Neighboring gene ReSE screen-validated silencer GRCh37_chr7:44717745-44717958 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:44740093-44740593

    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

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?

    HIV-1 interactions

    Protein interactions

    Protein Gene Interaction Pubs
    Rev rev DDX56 interacts with HIV-1 Rev and enhances the Rev function. DDX56 alters the subcellular localization of Rev from nucleolus to nucleus and co-localizes with Rev in the nucleus PubMed

    Go to the HIV-1, Human Interaction Database

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Potential readthrough

    Included gene: TMED4

    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 RNA stem-loop binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables chromatin extrusion motor activity IEA
    Inferred from Electronic Annotation
    more info
     
    enables cohesin loader activity IEA
    Inferred from Electronic Annotation
    more info
     
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    enables protein sequestering activity IDA
    Inferred from Direct Assay
    more info
    PubMed 
    Component Evidence Code Pubs
    located_in cytosol IDA
    Inferred from Direct Assay
    more info
    PubMed 
    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
    PubMed 
    is_active_in nucleus IDA
    Inferred from Direct Assay
    more info
    PubMed 

    General protein information

    Preferred Names
    probable ATP-dependent RNA helicase DDX56
    Names
    61-kd nucleolar helicase
    ATP-dependent 61 kDa nucleolar RNA helicase
    DEAD (Asp-Glu-Ala-Asp) box helicase 56
    DEAD (Asp-Glu-Ala-Asp) box polypeptide 56
    DEAD box protein 21
    DEAD box protein 56
    DEAD-box RNA helicase
    nucleolar helicase of 61 kDa
    putative nucleolar RNA helicase
    NP_001244118.1
    NP_061955.1

    NCBI Reference Sequences (RefSeq)

    NEW Try the new Transcript table

    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_001257189.2NP_001244118.1  probable ATP-dependent RNA helicase DDX56 isoform 2

      See identical proteins and their annotated locations for NP_001244118.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) lacks an alternate in-frame exon compared to variant 1. The resulting protein (isoform 2) is shorter compared to isoform 1.
      Source sequence(s)
      AC004938, AK315363, CA423604
      Consensus CDS
      CCDS59053.1
      UniProtKB/TrEMBL
      Q53HB9
      Related
      ENSP00000393488.1, ENST00000431640.5
      Conserved Domains (3) summary
      COG0513
      Location:9473
      SrmB; Superfamily II DNA and RNA helicase [Replication, recombination and repair]
      cd00079
      Location:234348
      HELICc; Helicase superfamily c-terminal domain; associated with DEXDc-, DEAD-, and DEAH-box proteins, yeast initiation factor 4A, Ski2p, and Hepatitis C virus NS3 helicases; this domain is found in a wide variety of helicases and helicase related proteins; may ...
      cl21455
      Location:9219
      P-loop_NTPase; P-loop containing Nucleoside Triphosphate Hydrolases
    2. NM_019082.4NP_061955.1  probable ATP-dependent RNA helicase DDX56 isoform 1

      See identical proteins and their annotated locations for NP_061955.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) represents the longer transcript and encodes the longer protein (isoform 1).
      Source sequence(s)
      AK125595, BC001235
      Consensus CDS
      CCDS5492.1
      UniProtKB/Swiss-Prot
      A4D2K9, C9JV95, Q6IAE2, Q9H9I8, Q9NY93
      UniProtKB/TrEMBL
      Q53HB9
      Related
      ENSP00000258772.5, ENST00000258772.10
      Conserved Domains (2) summary
      COG0513
      Location:9513
      SrmB; Superfamily II DNA and RNA helicase [Replication, recombination and repair]
      cd17961
      Location:14220
      DEADc_DDX56; DEAD-box helicase domain of DEAD box protein 56

    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_000007.14 Reference GRCh38.p14 Primary Assembly

      Range
      44565804..44573908 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060931.1 Alternate T2T-CHM13v2.0

      Range
      44725568..44733672 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)