DDX46 DEAD-box helicase 46 [Homo sapiens (human)] - Gene

Summary

Official Symbol: DDX46provided by HGNC
Official Full Name: DEAD-box helicase 46provided by HGNC
Primary source: HGNC:HGNC:18681
See related: Ensembl:ENSG00000145833 MIM:617848; AllianceGenome:HGNC:18681
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: Prp5; PRPF5
Summary: This gene encodes a member of the DEAD box protein family. 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 component of the 17S U2 snRNP complex; it plays an important role in pre-mRNA splicing. Multiple alternatively spliced transcript variants have been found for this gene. [provided by RefSeq, Jul 2014]
Expression: Ubiquitous expression in appendix (RPKM 11.5), lymph node (RPKM 11.4) and 25 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 5q31.1

Exon count:: 25

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	5	NC_000005.10 (134758779..134831121)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	5	NC_060929.1 (135284406..135358072)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	5	NC_000005.9 (134094469..134166811)

Chromosome 5 - NC_000005.10 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 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?

Oncogenic DDX46 promotes pancreatic cancer development and gemcitabine resistance by facilitating the JMJD6/CDK4 signaling pathway.
Title: Oncogenic DDX46 promotes pancreatic cancer development and gemcitabine resistance by facilitating the JMJD6/CDK4 signaling pathway.
Mechanisms of the RNA helicases DDX42 and DDX46 in human U2 snRNP assembly.
Title: Mechanisms of the RNA helicases DDX42 and DDX46 in human U2 snRNP assembly.
The role of DDX46 in breast cancer proliferation and invasiveness: A potential therapeutic target.
Title: The role of DDX46 in breast cancer proliferation and invasiveness: A potential therapeutic target.
Knockdown of DDX46 suppresses the proliferation and invasion of gastric cancer through inactivating Akt/GSK-3beta/beta-catenin pathway.
Title: Knockdown of DDX46 suppresses the proliferation and invasion of gastric cancer through inactivating Akt/GSK-3β/β-catenin pathway.
DDX46 silencing inhibits cell proliferation by activating apoptosis and autophagy in cutaneous squamous cell carcinoma.
Title: DDX46 silencing inhibits cell proliferation by activating apoptosis and autophagy in cutaneous squamous cell carcinoma.
Knockdown of DDX46 inhibited osteosarcoma cell proliferation.
Title: Knockdown of DDX46 Inhibits the Invasion and Tumorigenesis in Osteosarcoma Cells.
DDX46 is critical for ESCC cells proliferation.
Title: Knockdown of DDX46 inhibits proliferation and induces apoptosis in esophageal squamous cell carcinoma cells.
DDX46 is critical for colorectal cancer (CRC) cell proliferation and is a potential therapeutic target for CRC treatment.
Title: Lentiviral DDX46 knockdown inhibits growth and induces apoptosis in human colorectal cancer cells.
Short-term exercise resulted in a significant increase of mRNA expression of genes encoding proteins involved in the formation of precatalytic splisosome: DDX46.
Title: Changed profile of splicing regulator genes expression in response to exercise.
characterization of protein associated with the human 17S U2 snRNP and one of its stable subunits, SF3b; results indicate that Prp5 plays an important role in pre-mRNA splicing, acting during or prior to prespliceosome assembly
Title: Characterization of novel SF3b and 17S U2 snRNP proteins, including a human Prp5p homologue and an SF3b DEAD-box protein.

Submit: New GeneRIF Correction See all GeneRIFs (11)

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

EBI GWAS Catalog

Description
Many sequence variants affecting diversity of adult human height. 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)

HIV-1 interactions

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Protein interactions

Protein	Gene	Interaction	Pubs
Tat	tat	Interaction of HIV-1 Tat with DEXDc in T-cells is identified by a proteomic strategy based on affinity chromatography coupled with mass spectrometry	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

RH65840 (e-PCR)
- UniSTS:50436

RH16381 (e-PCR)
- UniSTS:65564

D5S1766 (e-PCR), detects polymorphism
- UniSTS:16165

DDX46 (e-PCR)
- UniSTS:504905

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 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 U2-type prespliceosome assembly	IDA Inferred from Direct Assay more info	PubMed
involved_in U2-type prespliceosome assembly	NAS Non-traceable Author Statement 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	IBA Inferred from Biological aspect of Ancestor more info
involved_in mRNA splicing, via spliceosome	IDA Inferred from Direct Assay more info	PubMed
involved_in mRNA splicing, via spliceosome	NAS Non-traceable Author Statement more info	PubMed
involved_in mRNA splicing, via spliceosome	TAS Traceable Author Statement more info

Component	Evidence Code	Pubs
located_in Cajal body	IEA Inferred from Electronic Annotation more info
part_of U2 snRNP	NAS Non-traceable Author Statement more info	PubMed
part_of U2-type spliceosomal complex	IDA Inferred from Direct Assay more info	PubMed
located_in fibrillar center	IDA Inferred from Direct Assay more info
located_in nuclear speck	IDA Inferred from Direct Assay more info
located_in nucleoplasm	TAS Traceable Author Statement more info
located_in nucleus	HDA more info	PubMed
is_active_in nucleus	IBA Inferred from Biological aspect of Ancestor more info
located_in nucleus	NAS Non-traceable Author Statement more info	PubMed
part_of spliceosomal complex	NAS Non-traceable Author Statement more info	PubMed

General protein information

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Preferred Names: probable ATP-dependent RNA helicase DDX46

Names: DEAD (Asp-Glu-Ala-Asp) box polypeptide 46; DEAD box protein 46; PRP5 homolog; Prp5-like DEAD-box protein; RNA helicase

NP_001287789.1

EC 3.6.4.13

NP_055644.2

EC 3.6.4.13

XP_011542060.1

EC 3.6.4.13

XP_054209895.1

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_001300860.2 → NP_001287789.1 probable ATP-dependent RNA helicase DDX46 isoform 1

See identical proteins and their annotated locations for NP_001287789.1

Status: REVIEWED

Description

Transcript Variant: This variant (1) encodes the longer isoform (1).

Source sequence(s)

AC010301, BF244218, BK000565, BU608108

Consensus CDS

CCDS75306.1

UniProtKB/TrEMBL

A0A0C4DG89, A8K6X3

Related

ENSP00000416534.2, ENST00000452510.7

Conserved Domains (2) summary

COG0513
Location:344 → 826

SrmB; Superfamily II DNA and RNA helicase [Replication, recombination and repair]

cd17953
Location:361 → 582

DEADc_DDX46; DEAD-box helicase domain of DEAD box protein 46
NM_014829.4 → NP_055644.2 probable ATP-dependent RNA helicase DDX46 isoform 2

See identical proteins and their annotated locations for NP_055644.2

Status: REVIEWED

Description

Transcript Variant: This variant (2) has an alternate splice site in the coding region but maintains the reading frame, compared to variant 1. The resulting isoform (2) lacks an internal aa, compared to isoform 1.

Source sequence(s)

AC010301, BC012304, BF244218, BU608108

Consensus CDS

CCDS34240.1

UniProtKB/Swiss-Prot

O94894, Q7L014, Q96EI0, Q9Y658

UniProtKB/TrEMBL

A8K6X3

Related

ENSP00000346236.4, ENST00000354283.8

Conserved Domains (3) summary

COG0513
Location:344 → 826

SrmB; Superfamily II DNA and RNA helicase [Replication, recombination and repair]

cd17953
Location:361 → 582

DEADc_DDX46; DEAD-box helicase domain of DEAD box protein 46

cd22473
Location:928 → 1030

KH-I_DDX46; type I K homology (KH) RNA-binding domain found in DEAD box protein 46 (DDX46) and similar proteins

RNA

NR_125341.2 RNA Sequence

Status: REVIEWED

Description

Transcript Variant: This variant (3) lacks an internal exon in the 5' region and has an additional exon in the central region, compared to variant 1. This variant is represented as non-coding because use of the 5'-most expected translation start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).

Source sequence(s)

AC010301, AK126011, BU608108

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_000005.10 Reference GRCh38.p14 Primary Assembly

Range

134758779..134831121

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_011543758.3 → XP_011542060.1 probable ATP-dependent RNA helicase DDX46 isoform X1

Related

ENSP00000487025.1, ENST00000628477.2

Conserved Domains (1) summary

cl21455
Location:378 → 510

P-loop_NTPase; P-loop containing Nucleoside Triphosphate Hydrolases