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

Gene ID: 83479, updated on 11-Apr-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 binding activity and RNA helicase activity. Predicted to be located in cytoplasm and nucleus. Predicted to be integral component of membrane. Implicated in orofaciodigital syndrome V. [provided by Alliance of Genome Resources, Apr 2022]
Expression
Ubiquitous expression in bone marrow (RPKM 2.6), thyroid (RPKM 2.3) and 25 other tissues See more
Orthologs
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Genomic context

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Location:
1q32.1
Exon count:
13
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (200640805..200669907, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (199897729..199926835, complement)
105.20220307 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: 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. 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
  2. DDX59 promotes DNA replication in lung adenocarcinoma. You J, et al. Cell Death Discov, 2017. PMID 28090355, Free PMC Article
  3. MicroRNA-628-5p inhibits cell proliferation in glioma by targeting DDX59. Xie P, et al. J Cell Biochem, 2019 Oct. PMID 31111544
  4. EGFR and Ras regulate DDX59 during lung cancer development. Yang L, et al. Gene, 2018 Feb 5. PMID 29133145
  5. 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

See all (31) 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
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Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

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 RNA helicase activity IBA
Inferred from Biological aspect of Ancestor
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
  
Component Evidence Code Pubs
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_2023_10

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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