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

Gene ID: 8449, updated on 12-Aug-2018

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; Vega:OTTHUMG00000031060
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; 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

Genomic context

See DHX16 in Genome Data Viewer
Location:
6p21.33
Exon count:
24
Annotation release Status Assembly Chr Location
109 current GRCh38.p12 (GCF_000001405.38) 6 NC_000006.12 (30653119..30673053, complement)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (30620896..30640830, complement)

Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene protein phosphatase 1 regulatory subunit 10 Neighboring gene mitochondrial ribosomal protein S18B Neighboring gene alpha tubulin acetyltransferase 1 Neighboring gene prothymosin alpha pseudogene 1 Neighboring gene chromosome 6 open reading frame 136 Neighboring gene protein phosphatase 1 regulatory subunit 18 Neighboring gene nurim

Genomic regions, transcripts, and products

Expression

  • 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 Jun 15 11:32:44 2016

Bibliography

GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

HIV-1 interactions

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 BioSystems

  • Gene Expression, organism-specific biosystem (from REACTOME)
    Gene Expression, organism-specific biosystemGene Expression covers the pathways by which genomic DNA is transcribed to yield RNA, the regulation of these transcription processes, and the pathways by which newly-made RNA Transcripts are process...
  • Processing of Capped Intron-Containing Pre-mRNA, organism-specific biosystem (from REACTOME)
    Processing of Capped Intron-Containing Pre-mRNA, organism-specific biosystemCo-transcriptional pre-mRNA splicing is not obligatory. Pre-mRNA splicing begins co-transcriptionally and often continues post-transcriptionally. Human genes contain an average of nine introns per ge...
  • Spliceosome, organism-specific biosystem (from KEGG)
    Spliceosome, organism-specific biosystemAfter transcription, eukaryotic mRNA precursors contain protein-coding exons and noncoding introns. In the following splicing, introns are excised and exons are joined by a macromolecular complex, th...
  • Spliceosome, conserved biosystem (from KEGG)
    Spliceosome, conserved biosystemAfter transcription, eukaryotic mRNA precursors contain protein-coding exons and noncoding introns. In the following splicing, introns are excised and exons are joined by a macromolecular complex, th...
  • mRNA Processing, organism-specific biosystem (from WikiPathways)
    mRNA Processing, organism-specific biosystemThis process describes the conversion of precursor messenger RNA into mature messenger RNA (mRNA). The pre-mRNA molecule undergoes three main modifications. These modifications are 5' capping, 3' po...
  • mRNA Splicing, organism-specific biosystem (from REACTOME)
    mRNA Splicing, organism-specific biosystemThe process in which excision of introns from the primary transcript of messenger RNA (mRNA) is followed by ligation of the two exon termini exposed by removal of each intron, is called mRNA splicing...
  • mRNA Splicing - Major Pathway, organism-specific biosystem (from REACTOME)
    mRNA Splicing - Major Pathway, organism-specific biosystemThe splicing of pre-mRNA occurs within a large, very dynamic complex, designated the 'spliceosome'. The 50-60S spliceosomes are estimated to be 40-60 nm in diameter, and have molecular weights in the...

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
ATP binding IEA
Inferred from Electronic Annotation
more info
 
ATP-dependent 3'-5' RNA helicase activity IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
ATPase activity EXP
Inferred from Experiment
more info
PubMed 
RNA binding HDA PubMed 
RNA binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
RNA helicase activity TAS
Traceable Author Statement
more info
PubMed 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
Process Evidence Code Pubs
RNA splicing TAS
Traceable Author Statement
more info
PubMed 
mRNA splicing, via spliceosome IMP
Inferred from Mutant Phenotype
more info
PubMed 
mRNA splicing, via spliceosome TAS
Traceable Author Statement
more info
 
Component Evidence Code Pubs
nucleoplasm IDA
Inferred from Direct Assay
more info
PubMed 
nucleoplasm TAS
Traceable Author Statement
more info
 
nucleus IDA
Inferred from Direct Assay
more info
PubMed 
spliceosomal complex IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
spliceosomal complex IDA
Inferred from Direct Assay
more info
PubMed 

General protein information

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
putative pre-mRNA-splicing factor ATP-dependent RNA helicase DHX16
NP_001157711.1
NP_003578.2
XP_011513240.1
XP_011513241.1
XP_011513242.1
XP_011513243.1

NCBI Reference Sequences (RefSeq)

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_001164239.1NP_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, DB072495
    UniProtKB/Swiss-Prot
    O60231
    UniProtKB/TrEMBL
    A0A1U9X7L7, B4DZ28
    Conserved Domains (2) summary
    COG1643
    Location:330968
    HrpA; HrpA-like RNA helicase [Translation, ribosomal structure and biogenesis]
    cl26511
    Location:88316
    Neuromodulin_N; Gap junction protein N-terminal region
  2. NM_001363515.1NP_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
    Conserved Domains (1) summary
    COG1643
    Location:7547
    HrpA; HrpA-like RNA helicase [Translation, ribosomal structure and biogenesis]
  3. NM_003587.4NP_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
    UniProtKB/TrEMBL
    Q5SQH4
    Related
    ENSP00000365625.3, OTTHUMP00000029071, ENST00000376442.7, OTTHUMT00000076076
    Conserved Domains (6) summary
    smart00487
    Location:399581
    DEXDc; DEAD-like helicases superfamily
    smart00847
    Location:798882
    HA2; Helicase associated domain (HA2) Add an annotation
    cd00046
    Location:416555
    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:580737
    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 ...
    pfam05416
    Location:156285
    Peptidase_C37; Southampton virus-type processing peptidase
    pfam07717
    Location:9171015
    OB_NTP_bind; Oligonucleotide/oligosaccharide-binding (OB)-fold

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109 details...Open this link in a new tab

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p12 Primary Assembly

Genomic

  1. NC_000006.12 Reference GRCh38.p12 Primary Assembly

    Range
    30653119..30673053 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011514940.2XP_011513242.1  pre-mRNA-splicing factor ATP-dependent RNA helicase DHX16 isoform X2

    UniProtKB/TrEMBL
    Q5SQH5
    Related
    ENSP00000365620.5, OTTHUMP00000029072, ENST00000376437.9, OTTHUMT00000076077
    Conserved Domains (1) summary
    COG1643
    Location:7547
    HrpA; HrpA-like RNA helicase [Translation, ribosomal structure and biogenesis]
  2. XM_011514939.2XP_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:100282
    DEXDc; DEAD-like helicases superfamily
    smart00847
    Location:499583
    HA2; Helicase associated domain (HA2) Add an annotation
    cd00046
    Location:117256
    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:281438
    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:618716
    OB_NTP_bind; Oligonucleotide/oligosaccharide-binding (OB)-fold
  3. XM_011514938.2XP_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:100282
    DEXDc; DEAD-like helicases superfamily
    smart00847
    Location:499583
    HA2; Helicase associated domain (HA2) Add an annotation
    cd00046
    Location:117256
    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:281438
    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:618716
    OB_NTP_bind; Oligonucleotide/oligosaccharide-binding (OB)-fold
  4. XM_011514941.3XP_011513243.1  pre-mRNA-splicing factor ATP-dependent RNA helicase DHX16 isoform X3

    See identical proteins and their annotated locations for XP_011513243.1

    Conserved Domains (5) summary
    smart00847
    Location:281365
    HA2; Helicase associated domain (HA2) Add an annotation
    COG1643
    Location:1511
    HrpA; HrpA-like RNA helicase [Translation, ribosomal structure and biogenesis]
    cd00046
    Location:138
    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:63220
    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:400498
    OB_NTP_bind; Oligonucleotide/oligosaccharide-binding (OB)-fold

RNA

  1. XR_001743678.2 RNA Sequence

Reference GRCh38.p12 ALT_REF_LOCI_1

Genomic

  1. NT_167244.2 Reference GRCh38.p12 ALT_REF_LOCI_1

    Range
    1988954..2002559 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p12 ALT_REF_LOCI_2

Genomic

  1. NT_113891.3 Reference GRCh38.p12 ALT_REF_LOCI_2

    Range
    2132833..2152797 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p12 ALT_REF_LOCI_3

Genomic

  1. NT_167245.2 Reference GRCh38.p12 ALT_REF_LOCI_3

    Range
    1908942..1928907 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p12 ALT_REF_LOCI_4

Genomic

  1. NT_167246.2 Reference GRCh38.p12 ALT_REF_LOCI_4

    Range
    1963343..1983306 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p12 ALT_REF_LOCI_5

Genomic

  1. NT_167247.2 Reference GRCh38.p12 ALT_REF_LOCI_5

    Range
    1997169..2017130 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p12 ALT_REF_LOCI_6

Genomic

  1. NT_167248.2 Reference GRCh38.p12 ALT_REF_LOCI_6

    Range
    1908201..1928166 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p12 ALT_REF_LOCI_7

Genomic

  1. NT_167249.2 Reference GRCh38.p12 ALT_REF_LOCI_7

    Range
    1953870..1973836 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
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