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    DHX16 DEAH-box helicase 16 [ Homo sapiens (human) ]

    Gene ID: 8449, updated on 10-Dec-2024

    Summary

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    Official Symbol
    DHX16provided by HGNC
    Official Full Name
    DEAH-box helicase 16provided by HGNC
    Primary source
    HGNC:HGNC:2739
    See related
    Ensembl:ENSG00000204560 MIM:603405; AllianceGenome:HGNC:2739
    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
    DBP2; PRP8; Prp2; DDX16; NMOAS; PRPF2; PRO2014
    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 this family are believed to be involved in embryogenesis, spermatogenesis, and cellular growth and division. This gene encodes a DEAD box protein, which is a functional homolog of fission yeast Prp8 protein involved in cell cycle progression. This gene is mapped to the MHC region on chromosome 6p21.3, a region where many malignant, genetic and autoimmune disease genes are linked. Three transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, May 2018]
    Expression
    Ubiquitous expression in testis (RPKM 17.0), spleen (RPKM 9.0) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See DHX16 in Genome Data Viewer
    Location:
    6p21.33
    Exon count:
    24
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 6 NC_000006.12 (30653127..30673006, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (30517301..30537211, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (30620904..30640783, complement)

    Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene H3K27ac hESC enhancer GRCh37_chr6:30585278-30585846 Neighboring gene mitochondrial ribosomal protein S18B Neighboring gene Sharpr-MPRA regulatory region 13793 Neighboring gene alpha tubulin acetyltransferase 1 Neighboring gene prothymosin alpha pseudogene 1 Neighboring gene chromosome 6 open reading frame 136 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:30638704-30639302 Neighboring gene H3K27ac hESC enhancer GRCh37_chr6:30640498-30641094 Neighboring gene ReSE screen-validated silencer GRCh37_chr6:30642736-30642875 Neighboring gene protein phosphatase 1 regulatory subunit 18 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:30649761-30650650 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:30650651-30651540 Neighboring gene nurim Neighboring gene ribosomal protein L7 pseudogene 4

    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. Infantile onset encephalomyopathy, retinopathy, optic atrophy, and mitochondrial DNA depletion associated with a novel pathogenic DHX16 variant. Hautakangas MR, et al. Clin Genet, 2023 Dec. PMID 37574199
    2. Cloning and characterization of a human DEAH-box RNA helicase, a functional homolog of fission yeast Cdc28/Prp8. Imamura O, et al. Nucleic Acids Res, 1998 May 1. PMID 9547260, Free PMC Article
    3. Nuclear retention of unspliced pre-mRNAs by mutant DHX16/hPRP2, a spliceosomal DEAH-box protein. Gencheva M, et al. J Biol Chem, 2010 Nov 12. PMID 20841358, Free PMC Article
    4. Contribution of DEAH-box protein DHX16 in human pre-mRNA splicing. Gencheva M, et al. Biochem J, 2010 Jul 1. PMID 20423332, Free PMC Article
    5. The mammalian analogue of the yeast PRP8 splicing protein is present in the U4/5/6 small nuclear ribonucleoprotein particle and the spliceosome. Pinto AL, et al. Proc Natl Acad Sci U S A, 1989 Nov. PMID 2479028, Free PMC Article

    See all (100) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Infantile onset encephalomyopathy, retinopathy, optic atrophy, and mitochondrial DNA depletion associated with a novel pathogenic DHX16 variant.
      Title: Infantile onset encephalomyopathy, retinopathy, optic atrophy, and mitochondrial DNA depletion associated with a novel pathogenic DHX16 variant.
    2. The RNA helicase DHX16 recognizes specific viral RNA to trigger RIG-I-dependent innate antiviral immunity.
      Title: The RNA helicase DHX16 recognizes specific viral RNA to trigger RIG-I-dependent innate antiviral immunity.
    3. Missense mutation in DHX16 gene is associated with neurodevelopmental disorder.
      Title: Paralog Studies Augment Gene Discovery: DDX and DHX Genes.
    4. Data show that G patch domain and KOW motifs protein (GPKOW )interacted directly with the DEAH-box protein 16 (DHX16/hPRP2) and with RNA.
      Title: GPKOW is essential for pre-mRNA splicing in vitro and suppresses splicing defect caused by dominant-negative DHX16 mutation in vivo.
    5. Results suggest that mutant DHX16/hPRP2 causes a defective spliceosome to retain unspliced gene transcripts in the nuclei.
      Title: Nuclear retention of unspliced pre-mRNAs by mutant DHX16/hPRP2, a spliceosomal DEAH-box protein.
    6. DHX16 is required for human pre-mRNA splicing after the formation of a pre-catalytic spliceosome.
      Title: Contribution of DEAH-box protein DHX16 in human pre-mRNA splicing.
    7. Observational study of gene-disease association. (HuGE Navigator)
      Title: A Large-scale genetic association study of esophageal adenocarcinoma risk.
    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
    Neuromuscular disease and ocular or auditory anomalies with or without seizures
    MedGen: C5231483 OMIM: 618733 GeneReviews: Not available
    		not available

    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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    Protein interactions

    Protein Gene Interaction Pubs
    retropepsin gag-pol Positional proteomics analysis identifies the cleavage of human DEAH (Asp-Glu-Ala-His) box polypeptide 16 (DHX16) at amino acid residues 314-315 by the HIV-1 protease PubMed

    Go to the HIV-1, Human Interaction Database

    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

    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 binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables RNA helicase activity TAS
    Traceable Author Statement
    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 helicase activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables molecular adaptor activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables pattern recognition receptor activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables ubiquitin binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in RNA splicing TAS
    Traceable Author Statement
    more info
    		 PubMed 
    involved_in antiviral innate immune response IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    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 IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in mRNA splicing, via spliceosome IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in mRNA splicing, via spliceosome TAS
    Traceable Author Statement
    more info
    		  
    Component Evidence Code Pubs
    part_of U2-type precatalytic spliceosome IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    is_active_in cytoplasm IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in nucleoplasm IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in nucleoplasm TAS
    Traceable Author Statement
    more info
    		  
    located_in nucleus IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    part_of spliceosomal complex IDA
    Inferred from Direct Assay
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    pre-mRNA-splicing factor ATP-dependent RNA helicase DHX16
    Names
    ATP-dependent RNA helicase #3
    DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 16
    DEAD/H box 16
    DEAH (Asp-Glu-Ala-His) box polypeptide 16
    DEAH-box protein 16
    RNA helicase
    pre-mRNA processing factor 2
    putative pre-mRNA-splicing factor ATP-dependent RNA helicase DHX16
    NP_001157711.1
    NP_001350444.1
    NP_003578.2
    XP_011513240.1
    XP_011513241.1
    XP_011513243.1
    XP_054185898.1
    XP_054185899.1
    XP_054185900.1
    XP_054186391.1
    XP_054186392.1
    XP_054186393.1
    XP_054186664.1
    XP_054186665.1
    XP_054186666.1
    XP_054186884.1
    XP_054186885.1
    XP_054186886.1
    XP_054187163.1
    XP_054187164.1
    XP_054187165.1
    XP_054187405.1
    XP_054187406.1
    XP_054187407.1
    XP_054212524.1
    XP_054212525.1
    XP_054212526.1

    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_001164239.2 → NP_001157711.1  pre-mRNA-splicing factor ATP-dependent RNA helicase DHX16 isoform 2

      See identical proteins and their annotated locations for NP_001157711.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) differs in the 5' UTR and coding sequence compared to variant 1. The resulting isoform (2) has a shorter and distinct N-terminus compared to isoform 1.
      Source sequence(s)
      AK302721, BC008825, BQ772493
      UniProtKB/TrEMBL
      A0A1U9X7L6, A0A1U9X7L7
      Conserved Domains (2) summary
      COG1643
      Location:330 → 968
      HrpA; HrpA-like RNA helicase [Translation, ribosomal structure and biogenesis]
      cl26511
      Location:88 → 316
      Neuromodulin_N; Gap junction protein N-terminal region

    2. NM_001363515.2 → NP_001350444.1  pre-mRNA-splicing factor ATP-dependent RNA helicase DHX16 isoform 3

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) contains an alternate exon compared to variant 1. The resulting isoform (3) has a shorter and distinct N-terminus compared to isoform 1.
      Source sequence(s)
      AL662798
      Consensus CDS
      CCDS87382.1
      UniProtKB/TrEMBL
      A0A140T8Y5, Q5SQH5, Q9P186
      Related
      ENSP00000365620.5, ENST00000376437.9
      Conserved Domains (1) summary
      COG1643
      Location:7 → 547
      HrpA; HrpA-like RNA helicase [Translation, ribosomal structure and biogenesis]

    3. NM_003587.5 → NP_003578.2  pre-mRNA-splicing factor ATP-dependent RNA helicase DHX16 isoform 1

      See identical proteins and their annotated locations for NP_003578.2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) encodes the longest isoform (1).
      Source sequence(s)
      BC008825, BQ772493, DB072495
      Consensus CDS
      CCDS4685.1
      UniProtKB/Swiss-Prot
      O60231, O60322, Q5JP45, Q969X7, Q96QC1
      UniProtKB/TrEMBL
      A0A1U9X7L6, Q5SQH4
      Related
      ENSP00000365625.3, ENST00000376442.8
      Conserved Domains (2) summary
      PTZ00121
      Location:148 → 376
      PTZ00121; MAEBL; Provisional
      COG1643
      Location:390 → 1028
      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_000006.12 Reference GRCh38.p14 Primary Assembly

      Range
      30653127..30673006 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_011514939.3 → XP_011513241.1  pre-mRNA-splicing factor ATP-dependent RNA helicase DHX16 isoform X1

      See identical proteins and their annotated locations for XP_011513241.1

      Conserved Domains (5) summary
      smart00487
      Location:100 → 282
      DEXDc; DEAD-like helicases superfamily
      smart00847
      Location:499 → 583
      HA2; Helicase associated domain (HA2) Add an annotation
      cd00046
      Location:117 → 256
      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.
      cd00079
      Location:281 → 438
      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 ...
      pfam07717
      Location:618 → 716
      OB_NTP_bind; Oligonucleotide/oligosaccharide-binding (OB)-fold

    2. XM_011514938.3 → XP_011513240.1  pre-mRNA-splicing factor ATP-dependent RNA helicase DHX16 isoform X1

      See identical proteins and their annotated locations for XP_011513240.1

      Conserved Domains (5) summary
      smart00487
      Location:100 → 282
      DEXDc; DEAD-like helicases superfamily
      smart00847
      Location:499 → 583
      HA2; Helicase associated domain (HA2) Add an annotation
      cd00046
      Location:117 → 256
      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.
      cd00079
      Location:281 → 438
      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 ...
      pfam07717
      Location:618 → 716
      OB_NTP_bind; Oligonucleotide/oligosaccharide-binding (OB)-fold

    3. XM_011514941.4 → XP_011513243.1  pre-mRNA-splicing factor ATP-dependent RNA helicase DHX16 isoform X2

      See identical proteins and their annotated locations for XP_011513243.1

      UniProtKB/TrEMBL
      A0A140T8Y5, Q9P186
      Conserved Domains (5) summary
      smart00847
      Location:281 → 365
      HA2; Helicase associated domain (HA2) Add an annotation
      COG1643
      Location:1 → 511
      HrpA; HrpA-like RNA helicase [Translation, ribosomal structure and biogenesis]
      cd00046
      Location:1 → 38
      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.
      cd00079
      Location:63 → 220
      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 ...
      pfam07717
      Location:400 → 498
      OB_NTP_bind; Oligonucleotide/oligosaccharide-binding (OB)-fold

    Reference GRCh38.p14 ALT_REF_LOCI_1

    Genomic

    1. NT_167244.2 Reference GRCh38.p14 ALT_REF_LOCI_1

      Range
      1988954..2002512 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Reference GRCh38.p14 ALT_REF_LOCI_2

    Genomic

    1. NT_113891.3 Reference GRCh38.p14 ALT_REF_LOCI_2

      Range
      2132841..2152750 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054329923.1 → XP_054185898.1  pre-mRNA-splicing factor ATP-dependent RNA helicase DHX16 isoform X1

    2. XM_054329924.1 → XP_054185899.1  pre-mRNA-splicing factor ATP-dependent RNA helicase DHX16 isoform X1

    3. XM_054329925.1 → XP_054185900.1  pre-mRNA-splicing factor ATP-dependent RNA helicase DHX16 isoform X2

      UniProtKB/TrEMBL
      A0A140T8Y5, Q9P186

    Reference GRCh38.p14 ALT_REF_LOCI_3

    Genomic

    1. NT_167245.2 Reference GRCh38.p14 ALT_REF_LOCI_3

      Range
      1908950..1928860 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054330416.1 → XP_054186391.1  pre-mRNA-splicing factor ATP-dependent RNA helicase DHX16 isoform X1

    2. XM_054330417.1 → XP_054186392.1  pre-mRNA-splicing factor ATP-dependent RNA helicase DHX16 isoform X1

    3. XM_054330418.1 → XP_054186393.1  pre-mRNA-splicing factor ATP-dependent RNA helicase DHX16 isoform X2

      UniProtKB/TrEMBL
      A0A140T8Y5, Q9P186

    Reference GRCh38.p14 ALT_REF_LOCI_4

    Genomic

    1. NT_167246.2 Reference GRCh38.p14 ALT_REF_LOCI_4

      Range
      1963351..1983259 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054330689.1 → XP_054186664.1  pre-mRNA-splicing factor ATP-dependent RNA helicase DHX16 isoform X1

    2. XM_054330690.1 → XP_054186665.1  pre-mRNA-splicing factor ATP-dependent RNA helicase DHX16 isoform X1

    3. XM_054330691.1 → XP_054186666.1  pre-mRNA-splicing factor ATP-dependent RNA helicase DHX16 isoform X2

      UniProtKB/TrEMBL
      A0A140T8Y5, Q9P186

    Reference GRCh38.p14 ALT_REF_LOCI_5

    Genomic

    1. NT_167247.2 Reference GRCh38.p14 ALT_REF_LOCI_5

      Range
      1997177..2017083 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054330909.1 → XP_054186884.1  pre-mRNA-splicing factor ATP-dependent RNA helicase DHX16 isoform X1

    2. XM_054330910.1 → XP_054186885.1  pre-mRNA-splicing factor ATP-dependent RNA helicase DHX16 isoform X1

    3. XM_054330911.1 → XP_054186886.1  pre-mRNA-splicing factor ATP-dependent RNA helicase DHX16 isoform X2

      UniProtKB/TrEMBL
      A0A140T8Y5, Q9P186

    Reference GRCh38.p14 ALT_REF_LOCI_6

    Genomic

    1. NT_167248.2 Reference GRCh38.p14 ALT_REF_LOCI_6

      Range
      1908209..1928119 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054331188.1 → XP_054187163.1  pre-mRNA-splicing factor ATP-dependent RNA helicase DHX16 isoform X1

    2. XM_054331189.1 → XP_054187164.1  pre-mRNA-splicing factor ATP-dependent RNA helicase DHX16 isoform X1

    3. XM_054331190.1 → XP_054187165.1  pre-mRNA-splicing factor ATP-dependent RNA helicase DHX16 isoform X2

      UniProtKB/TrEMBL
      A0A140T8Y5

    Reference GRCh38.p14 ALT_REF_LOCI_7

    Genomic

    1. NT_167249.2 Reference GRCh38.p14 ALT_REF_LOCI_7

      Range
      1953878..1973789 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054331430.1 → XP_054187405.1  pre-mRNA-splicing factor ATP-dependent RNA helicase DHX16 isoform X1

    2. XM_054331431.1 → XP_054187406.1  pre-mRNA-splicing factor ATP-dependent RNA helicase DHX16 isoform X1

    3. XM_054331432.1 → XP_054187407.1  pre-mRNA-splicing factor ATP-dependent RNA helicase DHX16 isoform X2

      UniProtKB/TrEMBL
      A0A140T8Y5, Q9P186

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060930.1 Alternate T2T-CHM13v2.0

      Range
      30517301..30537211 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054356549.1 → XP_054212524.1  pre-mRNA-splicing factor ATP-dependent RNA helicase DHX16 isoform X1

    2. XM_054356550.1 → XP_054212525.1  pre-mRNA-splicing factor ATP-dependent RNA helicase DHX16 isoform X1

    3. XM_054356551.1 → XP_054212526.1  pre-mRNA-splicing factor ATP-dependent RNA helicase DHX16 isoform X2

      UniProtKB/TrEMBL
      A0A140T8Y5, Q9P186
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    O60231.2 GenPept UniProtKB/Swiss-Prot:O60231

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