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

Gene ID: 9879, updated on 23-Nov-2021

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
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
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Genomic context

See DDX46 in Genome Data Viewer
Location:
5q31.1
Exon count:
25
Annotation release Status Assembly Chr Location
109.20211119 current GRCh38.p13 (GCF_000001405.39) 5 NC_000005.10 (134758778..134831121)
105.20201022 previous assembly GRCh37.p13 (GCF_000001405.25) 5 NC_000005.9 (134094469..134166811)

Chromosome 5 - NC_000005.10Genomic Context describing neighboring genes Neighboring gene SEC24 homolog A, COPII coat complex component Neighboring gene RNA, U6 small nuclear 757, pseudogene Neighboring gene calcium modulating ligand Neighboring gene ribosomal protein L34 pseudogene 13 Neighboring gene chromosome 5 open reading frame 24 Neighboring gene thioredoxin domain containing 15

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 Apr 4 07:08:55 2018

Bibliography

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Phenotypes

Associated conditions

Description Tests
Many sequence variants affecting diversity of adult human height.
GeneReviews: Not available

HIV-1 interactions

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

Pathways from PubChem

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Clone Names

  • MGC9936, FLJ25329, KIAA0801

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 RNA binding HDA PubMed 
enables RNA helicase activity IEA
Inferred from Electronic Annotation
more info
 
Process Evidence Code Pubs
involved_in mRNA splicing, via spliceosome IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
Component Evidence Code Pubs
located_in Cajal body IEA
Inferred from Electronic Annotation
more info
 
located_in fibrillar center IDA
Inferred from Direct Assay
more info
 
located_in membrane IEA
Inferred from Electronic Annotation
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 PubMed 
is_active_in nucleus IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 

General protein information

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
NP_055644.2
XP_011542060.1

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.

mRNA and Protein(s)

  1. NM_001300860.2NP_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/Swiss-Prot
    Q7L014
    UniProtKB/TrEMBL
    A0A0C4DG89
    Related
    ENSP00000416534.2, ENST00000452510.7
    Conserved Domains (2) summary
    COG0513
    Location:344826
    SrmB; Superfamily II DNA and RNA helicase [Replication, recombination and repair]
    cd17953
    Location:361582
    DEADc_DDX46; DEAD-box helicase domain of DEAD box protein 46
  2. NM_014829.4NP_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
    Q7L014
    Related
    ENSP00000346236.4, ENST00000354283.8
    Conserved Domains (3) summary
    COG0513
    Location:344826
    SrmB; Superfamily II DNA and RNA helicase [Replication, recombination and repair]
    cd17953
    Location:361582
    DEADc_DDX46; DEAD-box helicase domain of DEAD box protein 46
    cd22473
    Location:9281030
    KH-I_DDX46; type I K homology (KH) RNA-binding domain found in DEAD box protein 46 (DDX46) and similar proteins

RNA

  1. 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: Homo sapiens Updated Annotation Release 109.20211119

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

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000005.10 Reference GRCh38.p13 Primary Assembly

    Range
    134758778..134831121
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011543758.2XP_011542060.1  probable ATP-dependent RNA helicase DDX46 isoform X1

    Related
    ENSP00000487025.1, ENST00000628477.2
    Conserved Domains (1) summary
    cl21455
    Location:378510
    P-loop_NTPase; P-loop containing Nucleoside Triphosphate Hydrolases

RNA

  1. XR_948314.2 RNA Sequence

  2. XR_948313.3 RNA Sequence

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