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

Summary

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: mouse all
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Genomic context

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_000016.10 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
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?

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.
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.
Retinitis pigmentosa-linked mutation in DHX38 modulates its splicing activity.
Title: Retinitis pigmentosa-linked mutation in DHX38 modulates its splicing activity.
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.
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.
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 EBI GWAS CatalogPubMed
Novel Loci for metabolic networks and multi-tissue expression studies reveal genes for atherosclerosis. EBI GWAS Catalog EBI GWAS CatalogPubMed

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

SHGC-32168 (e-PCR)
- UniSTS:21510

D16S2867 (e-PCR)
- UniSTS:153437

SHGC-61046 (e-PCR)
- UniSTS:53369

RH102302 (e-PCR)
- UniSTS:96636

RH45493 (e-PCR)
- UniSTS:14717

RH44725 (e-PCR)
- UniSTS:86435

G62063 (e-PCR)
- UniSTS:139177

RH80727 (e-PCR)
- UniSTS:91109

SHGC-60761 (e-PCR)
- UniSTS:65786

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 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 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 more info	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

EC 3.6.4.13

XP_011521786.1

EC 3.6.4.13

XP_016879402.1

EC 3.6.4.13

XP_047290941.1

EC 3.6.4.13

XP_047290942.1

EC 3.6.4.13

XP_054170516.1

EC 3.6.4.13

XP_054170517.1

EC 3.6.4.13

XP_054170518.1

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.

Genomic

NG_034207.1 RefSeqGene

Range

5132..24197

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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

NC_000016.10 Reference GRCh38.p14 Primary Assembly

Range

72093847..72112912

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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

Alternate T2T-CHM13v2.0

Genomic

NC_060940.1 Alternate T2T-CHM13v2.0

Range

77910161..77929227

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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
XM_054314542.1 → XP_054170517.1 pre-mRNA-splicing factor ATP-dependent RNA helicase PRP16 isoform X2
XM_054314543.1 → XP_054170518.1 pre-mRNA-splicing factor ATP-dependent RNA helicase PRP16 isoform X3