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

    Gene ID: 9879, updated on 17-Jun-2024

    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
    NEW
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    Genomic context

    See DDX46 in Genome Data Viewer
    Location:
    5q31.1
    Exon count:
    25
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 5 NC_000005.10 (134758779..134831121)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 5 NC_060929.1 (135284406..135358072)
    105.20220307 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 ReSE screen-validated silencer GRCh37_chr5:134064440-134064607 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23161 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23162 Neighboring gene calcium modulating ligand Neighboring gene ribosomal protein L34 pseudogene 13 Neighboring gene H3K27ac hESC enhancer GRCh37_chr5:134181369-134182104 Neighboring gene chromosome 5 open reading frame 24 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23163 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:134210028-134210733 Neighboring gene uncharacterized LOC124901071 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?

    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

    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 TAS
    Traceable Author Statement
    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 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 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

    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
    XP_054209895.1

    NCBI Reference Sequences (RefSeq)

    NEW Try the new Transcript table

    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/TrEMBL
      A0A0C4DG89, A8K6X3
      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
      O94894, Q7L014, Q96EI0, Q9Y658
      UniProtKB/TrEMBL
      A8K6X3
      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: GCF_000001405.40-RS_2023_10

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

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000005.10 Reference GRCh38.p14 Primary Assembly

      Range
      134758779..134831121
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_011543758.3XP_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_948313.4 RNA Sequence

    2. XR_007058668.1 RNA Sequence

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060929.1 Alternate T2T-CHM13v2.0

      Range
      135284406..135358072
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054353920.1XP_054209895.1  probable ATP-dependent RNA helicase DDX46 isoform X1

    RNA

    1. XR_008487209.1 RNA Sequence

    2. XR_008487210.1 RNA Sequence