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    DDX59 DEAD-box helicase 59 [ Homo sapiens (human) ]

    Gene ID: 83479, updated on 27-Dec-2024

    Summary

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    Official Symbol
    DDX59provided by HGNC
    Official Full Name
    DEAD-box helicase 59provided by HGNC
    Primary source
    HGNC:HGNC:25360
    See related
    Ensembl:ENSG00000118197 MIM:615464; AllianceGenome:HGNC:25360
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    OFD5; ZNHIT5
    Summary
    Predicted to enable RNA helicase activity and mRNA binding activity. Predicted to be involved in chromatin looping and chromatin remodeling. Predicted to be located in cytoplasm; membrane; and nucleus. Implicated in orofaciodigital syndrome V. [provided by Alliance of Genome Resources, Dec 2024]
    Expression
    Ubiquitous expression in bone marrow (RPKM 2.6), thyroid (RPKM 2.3) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See DDX59 in Genome Data Viewer
    Location:
    1q32.1
    Exon count:
    13
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (200640805..200669907, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (199897729..199926835, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (200609933..200639035, complement)

    Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC107985459 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1672 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1673 Neighboring gene kinesin family member 14 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:200589147-200589648 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1674 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:200607918-200608633 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr1:200608609-200609808 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2301 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1675 Neighboring gene DDX59 antisense RNA 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2302 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1676 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1677 Neighboring gene MPRA-validated peak646 silencer Neighboring gene calmodulin regulated spectrin associated protein family member 2 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:200735945-200736445 Neighboring gene ribosomal protein L34 pseudogene 6

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: Tissue-specific circular RNA induction during human fetal development
    • Description: 35 human fetal samples from 6 tissues (3 - 7 replicates per tissue) collected between 10 and 20 weeks gestational time were sequenced using Illumina TruSeq Stranded Total RNA
    • BioProject: PRJNA270632
    • Publication: PMID 26076956
    • Analysis date: Mon Apr 2 22:54:59 2018

    Bibliography

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    Related articles in PubMed

    1. DDX59 promotes DNA replication in lung adenocarcinoma. You J, et al. Cell Death Discov, 2017. PMID 28090355, Free PMC Article
    2. Confirmation that mutations in DDX59 cause an autosomal recessive form of oral-facial-digital syndrome: Further delineation of the DDX59 phenotype in two new families. Faily S, et al. Eur J Med Genet, 2017 Oct. PMID 28711741
    3. Mutations in DDX59 implicate RNA helicase in the pathogenesis of orofaciodigital syndrome. Shamseldin HE, et al. Am J Hum Genet, 2013 Sep 5. PMID 23972372, Free PMC Article
    4. A loss-of-function homozygous mutation in DDX59 implicates a conserved DEAD-box RNA helicase in nervous system development and function. Salpietro V, et al. Hum Mutat, 2018 Feb. PMID 29127725, Free PMC Article
    5. EGFR and Ras regulate DDX59 during lung cancer development. Yang L, et al. Gene, 2018 Feb 5. PMID 29133145

    See all (33) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. MicroRNA-628-5p inhibits cell proliferation in glioma by targeting DDX59.
      Title: MicroRNA-628-5p inhibits cell proliferation in glioma by targeting DDX59.
    2. Analysis of human brain gene expression provides evidence that DDX59 is enriched in oligodendrocytes and might act within pathways of leukoencephalopathies-associated genes.
      Title: A loss-of-function homozygous mutation in DDX59 implicates a conserved DEAD-box RNA helicase in nervous system development and function.
    3. Study presents evidence that DDX59 protein can be upregulated by MEK/ERK/MAP kinase pathway downstream of EGFR and Ras signaling. Increased expression of DDX59 mediates the tumorigenecity of EGFR and Ras in lung cancer.
      Title: EGFR and Ras regulate DDX59 during lung cancer development.
    4. The novel DDX59 mutation is associated with oral-facial-digital syndrome.
      Title: Confirmation that mutations in DDX59 cause an autosomal recessive form of oral-facial-digital syndrome: Further delineation of the DDX59 phenotype in two new families.
    5. These data strongly implicate DDX59 RNA helicase family member in the pathogenesis of orofaciodigital syndrome.
      Title: Mutations in DDX59 implicate RNA helicase in the pathogenesis of orofaciodigital syndrome.
    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

    Associated conditions

    Description Tests
    Orofaciodigital syndrome V
    MedGen: C1868118 OMIM: 174300 GeneReviews: Not available
    		Compare labs

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    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

    • DKFZp564B1023

    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 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
    		  
    enables metal ion binding IEA
    Inferred from Electronic Annotation
    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 cytoplasm IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in nucleus IEA
    Inferred from Electronic Annotation
    more info
    		  

    General protein information

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    Preferred Names
    probable ATP-dependent RNA helicase DDX59
    Names
    DEAD (Asp-Glu-Ala-Asp) box polypeptide 59
    DEAD box protein 59
    zinc finger HIT domain-containing protein 5
    zinc finger HIT-type containing 5
    NP_001026895.2
    NP_001307110.1
    NP_001307111.1
    NP_001336728.1
    NP_001336729.1
    NP_001336730.1
    NP_001336731.1
    NP_001336732.1
    NP_001336733.1
    XP_016857921.1
    XP_047287414.1
    XP_047287415.1
    XP_047287417.1
    XP_047287422.1
    XP_047287424.1
    XP_047287427.1
    XP_047287428.1
    XP_047287431.1
    XP_047287433.1
    XP_047287436.1
    XP_054194941.1
    XP_054194942.1
    XP_054194943.1
    XP_054194944.1
    XP_054194945.1
    XP_054194946.1
    XP_054194947.1
    XP_054194948.1
    XP_054194949.1
    XP_054194950.1
    XP_054194951.1
    XP_054194952.1

    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_053192.2 RefSeqGene

      Range
      5000..30870
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001031725.6 → NP_001026895.2  probable ATP-dependent RNA helicase DDX59 isoform 1

      See identical proteins and their annotated locations for NP_001026895.2

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (1). Variants 1, 4 and 5 all encode the same isoform (1).
      Source sequence(s)
      AL445483
      Consensus CDS
      CCDS30964.1
      UniProtKB/Swiss-Prot
      Q5T1V6, Q6PJL2, Q8IVW3, Q9H0W3
      Related
      ENSP00000330460.6, ENST00000331314.11
      Conserved Domains (1) summary
      cl26939
      Location:89 → 592
      DEXDc; DEAD-like helicases superfamily

    2. NM_001320181.2 → NP_001307110.1  probable ATP-dependent RNA helicase DDX59 isoform 2

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) differs in the 3' UTR and coding sequence compared to variant 1. The resulting isoform (2) has a shorter and distinct C-terminus compared to isoform 1.
      Source sequence(s)
      AL445483
      UniProtKB/TrEMBL
      B7Z5N6
      Conserved Domains (4) summary
      smart00487
      Location:218 → 413
      DEXDc; DEAD-like helicases superfamily
      cd00079
      Location:416 → 531
      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 ...
      cd00268
      Location:205 → 405
      DEADc; DEAD-box helicases. A diverse family of proteins involved in ATP-dependent RNA unwinding, needed in a variety of cellular processes including splicing, ribosome biogenesis and RNA degradation. The name derives from the sequence of the Walker B motif ...
      pfam04438
      Location:105 → 132
      zf-HIT; HIT zinc finger

    3. NM_001320182.1 → NP_001307111.1  probable ATP-dependent RNA helicase DDX59 isoform 3

      Status: VALIDATED

      Description
      Transcript Variant: This variant (3) lacks two alternate in-frame exons compared to variant 1. The resulting isoform (3) has the same N- and C-termini but is shorter compared to isoform 1. The first exon (5' UTR) of this variant has not been determined.
      Source sequence(s)
      AL445483, BC041801, BU621052, BU754283
      UniProtKB/Swiss-Prot
      Q5T1V6
      Conserved Domains (4) summary
      PLN00206
      Location:89 → 478
      PLN00206; DEAD-box ATP-dependent RNA helicase; Provisional
      cd00079
      Location:319 → 434
      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 ...
      pfam04438
      Location:105 → 132
      zf-HIT; HIT zinc finger
      cl21455
      Location:205 → 321
      P-loop_NTPase; P-loop containing Nucleoside Triphosphate Hydrolases

    4. NM_001349799.3 → NP_001336728.1  probable ATP-dependent RNA helicase DDX59 isoform 1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (4), as well as variants 1 and 5, encodes isoform 1.
      Source sequence(s)
      AL445483
      Consensus CDS
      CCDS30964.1
      UniProtKB/Swiss-Prot
      Q5T1V6, Q6PJL2, Q8IVW3, Q9H0W3
      Conserved Domains (1) summary
      cl26939
      Location:89 → 592
      DEXDc; DEAD-like helicases superfamily

    5. NM_001349800.3 → NP_001336729.1  probable ATP-dependent RNA helicase DDX59 isoform 1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (5), as well as variants 1 and 4, encodes isoform 1.
      Source sequence(s)
      AL445483
      Consensus CDS
      CCDS30964.1
      UniProtKB/Swiss-Prot
      Q5T1V6, Q6PJL2, Q8IVW3, Q9H0W3
      Conserved Domains (1) summary
      cl26939
      Location:89 → 592
      DEXDc; DEAD-like helicases superfamily

    6. NM_001349801.3 → NP_001336730.1  probable ATP-dependent RNA helicase DDX59 isoform 4

      Status: VALIDATED

      Description
      Transcript Variant: This variant (6) encodes isoform 4.
      Source sequence(s)
      AL445483
      Conserved Domains (1) summary
      cl26939
      Location:89 → 549
      DEXDc; DEAD-like helicases superfamily

    7. NM_001349802.3 → NP_001336731.1  probable ATP-dependent RNA helicase DDX59 isoform 5

      Status: VALIDATED

      Description
      Transcript Variant: This variant (7) encodes isoform 5.
      Source sequence(s)
      AL445483
      Related
      ENSP00000394367.2, ENST00000447706.6
      Conserved Domains (1) summary
      cl26939
      Location:89 → 532
      DEXDc; DEAD-like helicases superfamily

    8. NM_001349803.3 → NP_001336732.1  probable ATP-dependent RNA helicase DDX59 isoform 6

      Status: VALIDATED

      Description
      Transcript Variant: This variant (8) encodes isoform 6.
      Source sequence(s)
      AL445483
      Conserved Domains (1) summary
      cl26939
      Location:89 → 508
      DEXDc; DEAD-like helicases superfamily

    9. NM_001349804.2 → NP_001336733.1  probable ATP-dependent RNA helicase DDX59 isoform 7

      Status: VALIDATED

      Description
      Transcript Variant: This variant (9) encodes isoform 7.
      Source sequence(s)
      AL445483
      Conserved Domains (1) summary
      cl26939
      Location:89 → 355
      DEXDc; DEAD-like helicases superfamily

    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_000001.11 Reference GRCh38.p14 Primary Assembly

      Range
      200640805..200669907 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047431475.1 → XP_047287431.1  probable ATP-dependent RNA helicase DDX59 isoform X7

    2. XM_047431471.1 → XP_047287427.1  probable ATP-dependent RNA helicase DDX59 isoform X6

    3. XM_047431472.1 → XP_047287428.1  probable ATP-dependent RNA helicase DDX59 isoform X6

    4. XM_047431461.1 → XP_047287417.1  probable ATP-dependent RNA helicase DDX59 isoform X3

    5. XM_047431468.1 → XP_047287424.1  probable ATP-dependent RNA helicase DDX59 isoform X5

    6. XM_017002432.3 → XP_016857921.1  probable ATP-dependent RNA helicase DDX59 isoform X1

      UniProtKB/Swiss-Prot
      Q5T1V6, Q6PJL2, Q8IVW3, Q9H0W3
      Conserved Domains (1) summary
      cl26939
      Location:89 → 592
      DEXDc; DEAD-like helicases superfamily

    7. XM_047431466.1 → XP_047287422.1  probable ATP-dependent RNA helicase DDX59 isoform X4

    8. XM_047431459.1 → XP_047287415.1  probable ATP-dependent RNA helicase DDX59 isoform X2

    9. XM_047431458.1 → XP_047287414.1  probable ATP-dependent RNA helicase DDX59 isoform X2

    10. XM_047431477.1 → XP_047287433.1  probable ATP-dependent RNA helicase DDX59 isoform X8

    11. XM_047431480.1 → XP_047287436.1  probable ATP-dependent RNA helicase DDX59 isoform X9

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060925.1 Alternate T2T-CHM13v2.0

      Range
      199897729..199926835 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054338975.1 → XP_054194950.1  probable ATP-dependent RNA helicase DDX59 isoform X7

    2. XM_054338973.1 → XP_054194948.1  probable ATP-dependent RNA helicase DDX59 isoform X6

    3. XM_054338974.1 → XP_054194949.1  probable ATP-dependent RNA helicase DDX59 isoform X6

    4. XM_054338970.1 → XP_054194945.1  probable ATP-dependent RNA helicase DDX59 isoform X3

    5. XM_054338972.1 → XP_054194947.1  probable ATP-dependent RNA helicase DDX59 isoform X5

    6. XM_054338967.1 → XP_054194942.1  probable ATP-dependent RNA helicase DDX59 isoform X1

      UniProtKB/Swiss-Prot
      Q5T1V6, Q6PJL2, Q8IVW3, Q9H0W3

    7. XM_054338971.1 → XP_054194946.1  probable ATP-dependent RNA helicase DDX59 isoform X4

    8. XM_054338969.1 → XP_054194944.1  probable ATP-dependent RNA helicase DDX59 isoform X2

    9. XM_054338968.1 → XP_054194943.1  probable ATP-dependent RNA helicase DDX59 isoform X2

    10. XM_054338966.1 → XP_054194941.1  probable ATP-dependent RNA helicase DDX59 isoform X1

      UniProtKB/Swiss-Prot
      Q5T1V6, Q6PJL2, Q8IVW3, Q9H0W3

    11. XM_054338976.1 → XP_054194951.1  probable ATP-dependent RNA helicase DDX59 isoform X8

    12. XM_054338977.1 → XP_054194952.1  probable ATP-dependent RNA helicase DDX59 isoform X9

    Suppressed Reference Sequence(s)

    The following Reference Sequences have been suppressed. Explain

    1. NM_031306.2: Suppressed sequence

      Description
      NM_031306.2: This RefSeq was permanently suppressed because currently there is insufficient support for the transcript and the protein.
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q5T1V6.1 GenPept UniProtKB/Swiss-Prot:Q5T1V6

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