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    DHX40 DEAH-box helicase 40 [ Homo sapiens (human) ]

    Gene ID: 79665, updated on 14-Nov-2024

    Summary

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    Official Symbol
    DHX40provided by HGNC
    Official Full Name
    DEAH-box helicase 40provided by HGNC
    Primary source
    HGNC:HGNC:18018
    See related
    Ensembl:ENSG00000108406 MIM:607570; AllianceGenome:HGNC:18018
    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
    PAD; DDX40; ARG147
    Summary
    This gene encodes a member of the DExH/D box family of ATP-dependent RNA helicases that have an essential role in RNA metabolism. Alternate splicing results in multiple transcript variants. A pseudogene of this gene is found on chromosome 17.[provided by RefSeq, Oct 2009]
    Expression
    Ubiquitous expression in testis (RPKM 20.7), thyroid (RPKM 19.9) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See DHX40 in Genome Data Viewer
    Location:
    17q23.1
    Exon count:
    18
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 17 NC_000017.11 (59565610..59608345)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 17 NC_060941.1 (60434369..60477103)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 17 NC_000017.10 (57642971..57685706)

    Chromosome 17 - NC_000017.11Genomic Context describing neighboring genes Neighboring gene long intergenic non-protein coding RNA 1476 Neighboring gene uncharacterized LOC105371845 Neighboring gene uncharacterized LOC105371847 Neighboring gene RNA, U4 small nuclear 13, pseudogene Neighboring gene H3K27ac hESC enhancer GRCh37_chr17:57642652-57643194 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8781 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:57695690-57696502 Neighboring gene Sharpr-MPRA regulatory region 22 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8782 Neighboring gene clathrin heavy chain Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr17:57760547-57761746 Neighboring gene Sharpr-MPRA regulatory region 12460 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12513 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:57780642-57781146 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:57781147-57781650 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:57784605-57785260 Neighboring gene peptidyl-tRNA hydrolase 2

    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 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. Identification of a novel human DDX40gene, a new member of the DEAH-box protein family. Xu J, et al. J Hum Genet, 2002. PMID 12522690
    2. Molecular and functional characterization of the p62 complex, an assembly of nuclear pore complex glycoproteins. Hu T, et al. J Cell Biol, 1996 Aug. PMID 8707840, Free PMC Article
    3. Identification and Characterization of USP7 Targets in Cancer Cells. Georges A, et al. Sci Rep, 2018 Oct 26. PMID 30367141, Free PMC Article
    4. USP7 Regulates Cytokinesis through FBXO38 and KIF20B. Georges A, et al. Sci Rep, 2019 Feb 25. PMID 30804394, Free PMC Article
    5. Proteomic Analysis Reveals a Role for RSK in p120-catenin Phosphorylation and Melanoma Cell-Cell Adhesion. Méant A, et al. Mol Cell Proteomics, 2020 Jan. PMID 31678930, Free PMC Article

    See all (68) citations in PubMed

    GeneRIFs: Gene References Into Functions

    Phenotypes

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    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)

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • FLJ22060, FLJ34015

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables 3'-5' RNA helicase activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    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 IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    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 protein binding IPI
    Inferred from Physical Interaction
    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 mRNA splicing, via spliceosome IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Component Evidence Code Pubs
    part_of spliceosomal complex IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  

    General protein information

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    Preferred Names
    probable ATP-dependent RNA helicase DHX40
    Names
    DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 40 (RNA helicase)
    DEAH (Asp-Glu-Ala-His) box polypeptide 40
    DEAH box protein 40
    NP_001159773.1
    NP_078888.4
    XP_006722146.1
    XP_011523555.1
    XP_016880569.1
    XP_047292714.1
    XP_054173201.1
    XP_054173202.1
    XP_054173203.1
    XP_054173204.1

    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.

    mRNA and Protein(s)

    1. NM_001166301.2 → NP_001159773.1  probable ATP-dependent RNA helicase DHX40 isoform 2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) has multiple differences in the coding region compared to variant 1. The encoded isoform (2) is shorter than isoform 1.
      Source sequence(s)
      AC004167, AF319521, AF461690, AK299151, AL832510
      Consensus CDS
      CCDS54150.1
      UniProtKB/TrEMBL
      B4DR88
      Related
      ENSP00000388749.3, ENST00000425628.7
      Conserved Domains (1) summary
      COG1643
      Location:24 → 673
      HrpA; HrpA-like RNA helicase [Translation, ribosomal structure and biogenesis]

    2. NM_024612.5 → NP_078888.4  probable ATP-dependent RNA helicase DHX40 isoform 1

      See identical proteins and their annotated locations for NP_078888.4

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).
      Source sequence(s)
      AF319521, BC024187
      Consensus CDS
      CCDS11617.1
      UniProtKB/Swiss-Prot
      B3KTJ5, C9JR60, Q5JPH4, Q8IX18, Q8TC86, Q8WY53, Q9BXM1, Q9H6M9
      UniProtKB/TrEMBL
      B4DR88
      Related
      ENSP00000251241.4, ENST00000251241.9
      Conserved Domains (1) summary
      COG1643
      Location:16 → 770
      HrpA; HrpA-like RNA helicase [Translation, ribosomal structure and biogenesis]

    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_000017.11 Reference GRCh38.p14 Primary Assembly

      Range
      59565610..59608345
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_006722083.4 → XP_006722146.1  probable ATP-dependent RNA helicase DHX40 isoform X1

      UniProtKB/TrEMBL
      B4DR88
      Conserved Domains (5) summary
      smart00490
      Location:312 → 399
      HELICc; helicase superfamily c-terminal domain
      smart00847
      Location:448 → 530
      HA2; Helicase associated domain (HA2) Add an annotation
      COG1643
      Location:16 → 743
      HrpA; HrpA-like RNA helicase [Translation, ribosomal structure and biogenesis]
      cd00046
      Location:78 → 213
      DEXDc; DEAD-like helicases superfamily. A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
      pfam07717
      Location:564 → 672
      OB_NTP_bind; Oligonucleotide/oligosaccharide-binding (OB)-fold

    2. XM_011525253.4 → XP_011523555.1  probable ATP-dependent RNA helicase DHX40 isoform X3

      Conserved Domains (5) summary
      smart00847
      Location:408 → 496
      HA2; Helicase associated domain (HA2) Add an annotation
      COG1643
      Location:16 → 709
      HrpA; HrpA-like RNA helicase [Translation, ribosomal structure and biogenesis]
      cd00046
      Location:78 → 213
      DEXDc; DEAD-like helicases superfamily. A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
      pfam07717
      Location:530 → 638
      OB_NTP_bind; Oligonucleotide/oligosaccharide-binding (OB)-fold
      cl21455
      Location:257 → 362
      P-loop_NTPase; P-loop containing Nucleoside Triphosphate Hydrolases

    3. XM_017025080.3 → XP_016880569.1  probable ATP-dependent RNA helicase DHX40 isoform X2

      UniProtKB/TrEMBL
      B4DR88
      Conserved Domains (1) summary
      COG1643
      Location:38 → 694
      HrpA; HrpA-like RNA helicase [Translation, ribosomal structure and biogenesis]

    4. XM_047436758.1 → XP_047292714.1  probable ATP-dependent RNA helicase DHX40 isoform X4

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060941.1 Alternate T2T-CHM13v2.0

      Range
      60434369..60477103
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054317226.1 → XP_054173201.1  probable ATP-dependent RNA helicase DHX40 isoform X1

    2. XM_054317228.1 → XP_054173203.1  probable ATP-dependent RNA helicase DHX40 isoform X3

    3. XM_054317227.1 → XP_054173202.1  probable ATP-dependent RNA helicase DHX40 isoform X2

    4. XM_054317229.1 → XP_054173204.1  probable ATP-dependent RNA helicase DHX40 isoform X4

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q8IX18.2 GenPept UniProtKB/Swiss-Prot:Q8IX18

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