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

Summary

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

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_000006.12 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

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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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

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.
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.
Missense mutation in DHX16 gene is associated with neurodevelopmental disorder.
Title: Paralog Studies Augment Gene Discovery: DDX and DHX Genes.
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.
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.
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.
Observational study of gene-disease association. (HuGE Navigator)
Title: A Large-scale genetic association study of esophageal adenocarcinoma risk.

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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

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

MARC_4697-4698:996679616:1 (e-PCR)
- UniSTS:269421

STS-N98554 (e-PCR)
- UniSTS:51059

D6S1533E (e-PCR)
- UniSTS:153978

MARC_3797-3798:991937626:7 (e-PCR)
- UniSTS:231059

MARC_23735-23736:1032274434:1 (e-PCR)
- UniSTS:268761

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 more info	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

EC 3.6.4.13

NP_001350444.1

EC 3.6.4.13

NP_003578.2

EC 3.6.4.13

XP_011513240.1

EC 3.6.4.13

XP_011513241.1

EC 3.6.4.13

XP_011513243.1

EC 3.6.4.13

XP_054185898.1

EC 3.6.4.13

XP_054185899.1

EC 3.6.4.13

XP_054185900.1

EC 3.6.4.13

XP_054186391.1

EC 3.6.4.13

XP_054186392.1

EC 3.6.4.13

XP_054186393.1

EC 3.6.4.13

XP_054186664.1

EC 3.6.4.13

XP_054186665.1

EC 3.6.4.13

XP_054186666.1

EC 3.6.4.13

XP_054186884.1

EC 3.6.4.13

XP_054186885.1

EC 3.6.4.13

XP_054186886.1

EC 3.6.4.13

XP_054187163.1

EC 3.6.4.13

XP_054187164.1

EC 3.6.4.13

XP_054187165.1

EC 3.6.4.13

XP_054187405.1

EC 3.6.4.13

XP_054187406.1

EC 3.6.4.13

XP_054187407.1

EC 3.6.4.13

XP_054212524.1

EC 3.6.4.13

XP_054212525.1

EC 3.6.4.13

XP_054212526.1

EC 3.6.4.13

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)

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
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]
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

NC_000006.12 Reference GRCh38.p14 Primary Assembly

Range

30653127..30673006 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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
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
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

NT_167244.2 Reference GRCh38.p14 ALT_REF_LOCI_1

Range

1988954..2002512 complement

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GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p14 ALT_REF_LOCI_2

Genomic

NT_113891.3 Reference GRCh38.p14 ALT_REF_LOCI_2

Range

2132841..2152750 complement

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_054329923.1 → XP_054185898.1 pre-mRNA-splicing factor ATP-dependent RNA helicase DHX16 isoform X1
XM_054329924.1 → XP_054185899.1 pre-mRNA-splicing factor ATP-dependent RNA helicase DHX16 isoform X1
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

NT_167245.2 Reference GRCh38.p14 ALT_REF_LOCI_3

Range

1908950..1928860 complement

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_054330416.1 → XP_054186391.1 pre-mRNA-splicing factor ATP-dependent RNA helicase DHX16 isoform X1
XM_054330417.1 → XP_054186392.1 pre-mRNA-splicing factor ATP-dependent RNA helicase DHX16 isoform X1
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

NT_167246.2 Reference GRCh38.p14 ALT_REF_LOCI_4

Range

1963351..1983259 complement

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_054330689.1 → XP_054186664.1 pre-mRNA-splicing factor ATP-dependent RNA helicase DHX16 isoform X1
XM_054330690.1 → XP_054186665.1 pre-mRNA-splicing factor ATP-dependent RNA helicase DHX16 isoform X1
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

NT_167247.2 Reference GRCh38.p14 ALT_REF_LOCI_5

Range

1997177..2017083 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_054330909.1 → XP_054186884.1 pre-mRNA-splicing factor ATP-dependent RNA helicase DHX16 isoform X1
XM_054330910.1 → XP_054186885.1 pre-mRNA-splicing factor ATP-dependent RNA helicase DHX16 isoform X1
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

NT_167248.2 Reference GRCh38.p14 ALT_REF_LOCI_6

Range

1908209..1928119 complement

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_054331188.1 → XP_054187163.1 pre-mRNA-splicing factor ATP-dependent RNA helicase DHX16 isoform X1
XM_054331189.1 → XP_054187164.1 pre-mRNA-splicing factor ATP-dependent RNA helicase DHX16 isoform X1
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

NT_167249.2 Reference GRCh38.p14 ALT_REF_LOCI_7

Range

1953878..1973789 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_054331430.1 → XP_054187405.1 pre-mRNA-splicing factor ATP-dependent RNA helicase DHX16 isoform X1
XM_054331431.1 → XP_054187406.1 pre-mRNA-splicing factor ATP-dependent RNA helicase DHX16 isoform X1
XM_054331432.1 → XP_054187407.1 pre-mRNA-splicing factor ATP-dependent RNA helicase DHX16 isoform X2

Alternate T2T-CHM13v2.0

Genomic

NC_060930.1 Alternate T2T-CHM13v2.0

Range

30517301..30537211 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_054356549.1 → XP_054212524.1 pre-mRNA-splicing factor ATP-dependent RNA helicase DHX16 isoform X1
XM_054356550.1 → XP_054212525.1 pre-mRNA-splicing factor ATP-dependent RNA helicase DHX16 isoform X1
XM_054356551.1 → XP_054212526.1 pre-mRNA-splicing factor ATP-dependent RNA helicase DHX16 isoform X2