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

Gene ID: 8449, updated on 3-Apr-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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Location:
6p21.33
Exon count:
24
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 6 NC_000006.12 (30653127..30673006, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (30517301..30537211, complement)
105.20220307 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: 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. 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
  2. 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
  3. 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
  4. Paralog Studies Augment Gene Discovery: DDX and DHX Genes. Paine I, et al. Am J Hum Genet, 2019 Aug 1. PMID 31256877, Free PMC Article
  5. GPKOW is essential for pre-mRNA splicing in vitro and suppresses splicing defect caused by dominant-negative DHX16 mutation in vivo. Zang S, et al. Biosci Rep, 2014 Dec 12. PMID 25296192, Free PMC Article

See all (86) 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)

Genotypes

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 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 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 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 
is_active_in intracellular anatomical structure IBA
Inferred from Biological aspect of Ancestor
more info
  
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_2023_10

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

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

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

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

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

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

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

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

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