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DHX38 DEAH-box helicase 38 [ Homo sapiens (human) ]

Gene ID: 9785, updated on 14-Nov-2024

Summary

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Official Symbol
DHX38provided by HGNC
Official Full Name
DEAH-box helicase 38provided by HGNC
Primary source
HGNC:HGNC:17211
See related
Ensembl:ENSG00000140829 MIM:605584; AllianceGenome:HGNC:17211
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
RP84; DDX38; PRP16; PRPF16
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. The protein encoded by this gene is a member of the DEAD/H box family of splicing factors. This protein resembles yeast Prp16 more closely than other DEAD/H family members. It is an ATPase and essential for the catalytic step II in pre-mRNA splicing process. [provided by RefSeq, Jul 2008]
Expression
Ubiquitous expression in spleen (RPKM 15.5), bone marrow (RPKM 15.1) and 25 other tissues See more
Orthologs
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Genomic context

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See DHX38 in Genome Data Viewer
Location:
16q22.2
Exon count:
27
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 16 NC_000016.10 (72093847..72112912)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 16 NC_060940.1 (77910161..77929227)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 16 NC_000016.9 (72127746..72146811)

Chromosome 16 - NC_000016.10Genomic Context describing neighboring genes Neighboring gene haptoglobin Neighboring gene haptoglobin-related protein Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11089 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11090 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11091 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:72132901-72133401 Neighboring gene thioredoxin like 4B Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr16:72141414-72142613 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11093 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11092 Neighboring gene H3K27ac hESC enhancer GRCh37_chr16:72159455-72159956 Neighboring gene NANOG hESC enhancer GRCh37_chr16:72162293-72163093 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:72163923-72164424 Neighboring gene polyamine modulated factor 1 binding protein 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:72171124-72171624 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11094 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11095 Neighboring gene uncharacterized LOC105371341 Neighboring gene VISTA enhancer hs22 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr16:72257113-72258312 Neighboring gene uncharacterized LOC124903720 Neighboring gene MYC binding protein pseudogene

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. Confirmation of the Role of DHX38 in the Etiology of Early-Onset Retinitis Pigmentosa. Latif Z, et al. Invest Ophthalmol Vis Sci, 2018 Sep 4. PMID 30208423, Free PMC Article
  2. The splicing factor DHX38/PRP16 is required for ovarian clear cell carcinoma tumorigenesis, as revealed by a CRISPR-Cas9 screen. Cona B, et al. FEBS Open Bio, 2022 Mar. PMID 34965029, Free PMC Article
  3. DHX38 restricts chemoresistance by regulating the alternative pre-mRNA splicing of RELL2 in pancreatic ductal adenocarcinoma. Li Z, et al. PLoS Genet, 2023 Jul. PMID 37506056, Free PMC Article
  4. Retinitis pigmentosa-linked mutation in DHX38 modulates its splicing activity. Obuća M, et al. PLoS One, 2022. PMID 35385551, Free PMC Article
  5. PRP16 is an RNA-dependent ATPase that interacts transiently with the spliceosome. Schwer B, et al. Nature, 1991 Feb 7. PMID 1825134

See all (109) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. DHX38 enhances proliferation, metastasis, and EMT progression in NSCLC through the G3BP1-mediated MAPK pathway.
    Title: DHX38 enhances proliferation, metastasis, and EMT progression in NSCLC through the G3BP1-mediated MAPK pathway.
  2. DHX38 restricts chemoresistance by regulating the alternative pre-mRNA splicing of RELL2 in pancreatic ductal adenocarcinoma.
    Title: DHX38 restricts chemoresistance by regulating the alternative pre-mRNA splicing of RELL2 in pancreatic ductal adenocarcinoma.
  3. Retinitis pigmentosa-linked mutation in DHX38 modulates its splicing activity.
    Title: Retinitis pigmentosa-linked mutation in DHX38 modulates its splicing activity.
  4. The splicing factor DHX38/PRP16 is required for ovarian clear cell carcinoma tumorigenesis, as revealed by a CRISPR-Cas9 screen.
    Title: The splicing factor DHX38/PRP16 is required for ovarian clear cell carcinoma tumorigenesis, as revealed by a CRISPR-Cas9 screen.
  5. We identified a second deleterious DHX38 variant that segregates with arRP in two families, providing additional evidence that DHX38 is involved in RP etiology. DHX38 encodes for pre-mRNA splicing factor PRP16, which is important in catalyzing pre-mRNA splicing.
    Title: Confirmation of the Role of DHX38 in the Etiology of Early-Onset Retinitis Pigmentosa.
  6. DHX38 is the first pre-mRNA splicing gene that is putatively associated with autosomal-recessive inherited retinitis pigmentosa.
    Title: A missense mutation in the splicing factor gene DHX38 is associated with early-onset retinitis pigmentosa with macular coloboma.
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
Retinitis pigmentosa 84
MedGen: C4748725 OMIM: 618220 GeneReviews: Not available
Compare labs

EBI GWAS Catalog

Description
Biological, clinical and population relevance of 95 loci for blood lipids.
EBI GWAS Catalog
Novel Loci for metabolic networks and multi-tissue expression studies reveal genes for atherosclerosis.
EBI GWAS Catalog

Variation

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See Variation Viewer (GRCh37.p13)

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

Clone Names

  • KIAA0224

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 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 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
  
involved_in mRNA splicing, via spliceosome IC
Inferred by Curator
more info
 PubMed 
involved_in mRNA splicing, via spliceosome IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in mRNA splicing, via spliceosome TAS
Traceable Author Statement
more info
  
Component Evidence Code Pubs
part_of catalytic step 2 spliceosome IDA
Inferred from Direct Assay
more info
 PubMed 
located_in membrane HDA PubMed 
located_in nucleoplasm TAS
Traceable Author Statement
more info
  
located_in nucleus NAS
Non-traceable Author Statement
more info
 PubMed 
part_of spliceosomal complex IBA
Inferred from Biological aspect of Ancestor
more info
  

General protein information

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Preferred Names
pre-mRNA-splicing factor ATP-dependent RNA helicase PRP16
Names
ATP-dependent RNA helicase DHX38
DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 38
DEAH (Asp-Glu-Ala-His) box polypeptide 38
DEAH box protein 38
PRP16 homolog of S.cerevisiae
pre-mRNA processing factor 16
NP_054722.2
XP_011521786.1
XP_016879402.1
XP_047290941.1
XP_047290942.1
XP_054170516.1
XP_054170517.1
XP_054170518.1

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.

Genomic

  1. NG_034207.1 RefSeqGene

    Range
    5132..24197
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_014003.4 → NP_054722.2  pre-mRNA-splicing factor ATP-dependent RNA helicase PRP16

    See identical proteins and their annotated locations for NP_054722.2

    Status: REVIEWED

    Source sequence(s)
    AA126451, BC008340, BG719187, BM473438
    Consensus CDS
    CCDS10907.1
    UniProtKB/Swiss-Prot
    B4DVG8, D3DWS7, O75212, Q92620, Q96HN7
    UniProtKB/TrEMBL
    A8K6G9
    Related
    ENSP00000268482.3, ENST00000268482.8
    Conserved Domains (1) summary
    COG1643
    Location:515 → 1146
    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_000016.10 Reference GRCh38.p14 Primary Assembly

    Range
    72093847..72112912
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011523484.3 → XP_011521786.1  pre-mRNA-splicing factor ATP-dependent RNA helicase PRP16 isoform X1

    See identical proteins and their annotated locations for XP_011521786.1

    UniProtKB/Swiss-Prot
    B4DVG8, D3DWS7, O75212, Q92620, Q96HN7
    UniProtKB/TrEMBL
    A8K6G9
    Conserved Domains (1) summary
    COG1643
    Location:515 → 1146
    HrpA; HrpA-like RNA helicase [Translation, ribosomal structure and biogenesis]

  2. XM_017023913.3 → XP_016879402.1  pre-mRNA-splicing factor ATP-dependent RNA helicase PRP16 isoform X2

    UniProtKB/TrEMBL
    A8K6G9
    Conserved Domains (5) summary
    smart00490
    Location:723 → 826
    HELICc; helicase superfamily c-terminal domain
    smart00487
    Location:491 → 678
    DEXDc; DEAD-like helicases superfamily
    smart00847
    Location:895 → 977
    HA2; Helicase associated domain (HA2) Add an annotation
    cd00046
    Location:516 → 652
    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:1028 → 1111
    OB_NTP_bind; Oligonucleotide/oligosaccharide-binding (OB)-fold

  3. XM_047434985.1 → XP_047290941.1  pre-mRNA-splicing factor ATP-dependent RNA helicase PRP16 isoform X1

    UniProtKB/Swiss-Prot
    B4DVG8, D3DWS7, O75212, Q92620, Q96HN7

  4. XM_047434986.1 → XP_047290942.1  pre-mRNA-splicing factor ATP-dependent RNA helicase PRP16 isoform X3

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060940.1 Alternate T2T-CHM13v2.0

    Range
    77910161..77929227
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054314541.1 → XP_054170516.1  pre-mRNA-splicing factor ATP-dependent RNA helicase PRP16 isoform X1

    UniProtKB/Swiss-Prot
    B4DVG8, D3DWS7, O75212, Q92620, Q96HN7

  2. XM_054314542.1 → XP_054170517.1  pre-mRNA-splicing factor ATP-dependent RNA helicase PRP16 isoform X2

  3. XM_054314543.1 → XP_054170518.1  pre-mRNA-splicing factor ATP-dependent RNA helicase PRP16 isoform X3

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q92620.2 GenPept UniProtKB/Swiss-Prot:Q92620

Gene LinkOut

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