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    DDX55 DEAD-box helicase 55 [ Homo sapiens (human) ]

    Gene ID: 57696, updated on 10-Dec-2024

    Summary

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    Official Symbol
    DDX55provided by HGNC
    Official Full Name
    DEAD-box helicase 55provided by HGNC
    Primary source
    HGNC:HGNC:20085
    See related
    Ensembl:ENSG00000111364 MIM:620176; AllianceGenome:HGNC:20085
    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
    Summary
    This gene encodes a member of protein family containing a characteristic Asp-Glu-Ala-Asp (DEAD) motif. These proteins are putative RNA helicases, and may be involved in a range of nuclear processes including translational initiation, nuclear and mitochondrial splicing, and ribosome and spliceosome assembly. Multiple alternatively spliced transcript variants have been found for this gene. Pseudogenes have been identified on chromosomes 1 and 12. [provided by RefSeq, Feb 2016]
    Expression
    Ubiquitous expression in lymph node (RPKM 4.3), bone marrow (RPKM 4.0) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See DDX55 in Genome Data Viewer
    Location:
    12q24.31
    Exon count:
    15
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 12 NC_000012.12 (123602099..123620943)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 12 NC_060936.1 (123600963..123619807)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 12 NC_000012.11 (124086646..124105490)

    Chromosome 12 - NC_000012.12Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5047 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7271 Neighboring gene TMED2 divergent transcript Neighboring gene transmembrane p24 trafficking protein 2 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5048 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7272 Neighboring gene uncharacterized LOC105370041 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr12:124105924-124107123 Neighboring gene small nucleolar RNA, H/ACA box 9B Neighboring gene eukaryotic translation initiation factor 2B subunit alpha Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7273 Neighboring gene general transcription factor IIH subunit 3 Neighboring gene ReSE screen-validated silencer GRCh37_chr12:124129599-124129794 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr12:124143885-124145084 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7274 Neighboring gene tectonic family member 2 Neighboring gene ReSE screen-validated silencer GRCh37_chr12:124184156-124184331

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: Tissue-specific circular RNA induction during human fetal development
    • Description: 35 human fetal samples from 6 tissues (3 - 7 replicates per tissue) collected between 10 and 20 weeks gestational time were sequenced using Illumina TruSeq Stranded Total RNA
    • BioProject: PRJNA270632
    • Publication: PMID 26076956
    • Analysis date: Mon Apr 2 22:54:59 2018

    Bibliography

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    Related articles in PubMed

    1. The DExD box ATPase DDX55 is recruited to domain IV of the 28S ribosomal RNA by its C-terminal region. Choudhury P, et al. RNA Biol, 2021 Aug. PMID 33048000, Free PMC Article
    2. D-E-A-D protein family of putative RNA helicases. Schmid SR, et al. Mol Microbiol, 1992 Feb. PMID 1552844
    3. Genome-wide association and longitudinal analyses reveal genetic loci linking pubertal height growth, pubertal timing and childhood adiposity. Cousminer DL, et al. Hum Mol Genet, 2013 Jul 1. PMID 23449627, Free PMC Article
    4. Prediction of the coding sequences of unidentified human genes. XVIII. The complete sequences of 100 new cDNA clones from brain which code for large proteins in vitro. Nagase T, et al. DNA Res, 2000 Aug 31. PMID 10997877
    5. Human Regulatory Protein Ki-1/57 Is a Target of SUMOylation and Affects PML Nuclear Body Formation. Saito Â, et al. J Proteome Res, 2017 Sep 1. PMID 28695742, Free PMC Article

    See all (78) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. The DExD box ATPase DDX55 is recruited to domain IV of the 28S ribosomal RNA by its C-terminal region.
      Title: The DExD box ATPase DDX55 is recruited to domain IV of the 28S ribosomal RNA by its C-terminal region.
    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

    EBI GWAS Catalog

    Description
    Genome-wide association and longitudinal analyses reveal genetic loci linking pubertal height growth, pubertal timing and childhood adiposity.
    EBI GWAS Catalog

    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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    Replication interactions

    Interaction Pubs
    Knockdown of DEAD (Asp-Glu-Ala-Asp) box polypeptide 55 (DDX55) by siRNA inhibits HIV-1 replication in HeLa-derived TZM-bl cells 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

    Homology

    Clone Names

    • FLJ16577, KIAA1595, MGC33209

    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 PubMed 
    enables RNA helicase activity IEA
    Inferred from Electronic Annotation
    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
    		  
    Component Evidence Code Pubs
    located_in cytosol IDA
    Inferred from Direct Assay
    more info
    		  
    located_in membrane HDA PubMed 
    is_active_in nucleolus IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in nucleolus IDA
    Inferred from Direct Assay
    more info
    		  
    located_in nucleoplasm IDA
    Inferred from Direct Assay
    more info
    		  

    General protein information

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    Preferred Names
    ATP-dependent RNA helicase DDX55
    Names
    DEAD (Asp-Glu-Ala-Asp) box polypeptide 55
    DEAD box protein 55
    epididymis secretory sperm binding protein
    NP_065987.1
    XP_011536910.1
    XP_016875199.1
    XP_016875200.1
    XP_016875201.1
    XP_016875204.1
    XP_016875205.1
    XP_016875210.1
    XP_047285177.1
    XP_047285178.1
    XP_047285179.1
    XP_047285180.1
    XP_047285181.1
    XP_047285182.1
    XP_047285183.1
    XP_047285184.1
    XP_047285185.1
    XP_054228667.1
    XP_054228668.1
    XP_054228669.1
    XP_054228670.1
    XP_054228671.1
    XP_054228672.1
    XP_054228673.1
    XP_054228674.1
    XP_054228675.1
    XP_054228676.1
    XP_054228677.1
    XP_054228678.1
    XP_054228679.1
    XP_054228680.1
    XP_054228681.1
    XP_054228682.1
    XP_054228683.1
    XP_054228684.1

    NCBI Reference Sequences (RefSeq)

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    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_020936.3 → NP_065987.1  ATP-dependent RNA helicase DDX55

      See identical proteins and their annotated locations for NP_065987.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) encodes the protein.
      Source sequence(s)
      AA403154, AB046815, AC055713, BC030020, BU619784
      Consensus CDS
      CCDS9251.1
      UniProtKB/Swiss-Prot
      Q658L6, Q8IYH0, Q8NHQ9, Q9HCH7
      UniProtKB/TrEMBL
      A0A384N652
      Related
      ENSP00000238146.3, ENST00000238146.9
      Conserved Domains (3) summary
      cd18787
      Location:242 → 372
      SF2_C_DEAD; C-terminal helicase domain of the DEAD box helicases
      cd17960
      Location:20 → 224
      DEADc_DDX55; DEAD-box helicase domain of DEAD box protein 55
      pfam13959
      Location:405 → 462
      DUF4217; Domain of unknown function (DUF4217)

    RNA

    1. NR_135104.2 RNA Sequence

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) uses an alternate internal splice site compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
      Source sequence(s)
      AA403154, AB046815, AC117503, AK301043, BU619784, DA806426

    2. NR_135105.2 RNA Sequence

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) uses an alternate internal splice site compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
      Source sequence(s)
      AC055713, AC117503

    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_000012.12 Reference GRCh38.p14 Primary Assembly

      Range
      123602099..123620943
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047429221.1 → XP_047285177.1  ATP-dependent RNA helicase DDX55 isoform X3

      UniProtKB/TrEMBL
      A0A384N652

    2. XM_047429222.1 → XP_047285178.1  ATP-dependent RNA helicase DDX55 isoform X4

      UniProtKB/TrEMBL
      A0A384N652

    3. XM_017019711.2 → XP_016875200.1  ATP-dependent RNA helicase DDX55 isoform X2

      UniProtKB/TrEMBL
      A0A384N652

    4. XM_017019710.2 → XP_016875199.1  ATP-dependent RNA helicase DDX55 isoform X1

      UniProtKB/TrEMBL
      A0A384N652

    5. XM_017019715.2 → XP_016875204.1  ATP-dependent RNA helicase DDX55 isoform X5

      UniProtKB/TrEMBL
      F5H5U2

    6. XM_017019716.2 → XP_016875205.1  ATP-dependent RNA helicase DDX55 isoform X6

      UniProtKB/TrEMBL
      F5H5U2

    7. XM_047429227.1 → XP_047285183.1  ATP-dependent RNA helicase DDX55 isoform X11

      UniProtKB/TrEMBL
      B4DVE4

    8. XM_047429224.1 → XP_047285180.1  ATP-dependent RNA helicase DDX55 isoform X8

      UniProtKB/TrEMBL
      B4DVE4

    9. XM_011538608.4 → XP_011536910.1  ATP-dependent RNA helicase DDX55 isoform X14

      UniProtKB/TrEMBL
      Q8TEC9
      Conserved Domains (3) summary
      smart00487
      Location:24 → 228
      DEXDc; DEAD-like helicases superfamily
      cd00268
      Location:9 → 224
      DEADc; DEAD-box helicases. A diverse family of proteins involved in ATP-dependent RNA unwinding, needed in a variety of cellular processes including splicing, ribosome biogenesis and RNA degradation. The name derives from the sequence of the Walker B motif ...
      pfam00271
      Location:252 → 366
      Helicase_C; Helicase conserved C-terminal domain

    10. XM_017019721.2 → XP_016875210.1  ATP-dependent RNA helicase DDX55 isoform X15

      UniProtKB/TrEMBL
      Q8TEC9

    11. XM_047429229.1 → XP_047285185.1  ATP-dependent RNA helicase DDX55 isoform X13

      UniProtKB/TrEMBL
      Q8TEC9

    12. XM_047429225.1 → XP_047285181.1  ATP-dependent RNA helicase DDX55 isoform X9

      UniProtKB/TrEMBL
      B4DVE4

    13. XM_047429226.1 → XP_047285182.1  ATP-dependent RNA helicase DDX55 isoform X10

      UniProtKB/TrEMBL
      B4DVE4

    14. XM_047429228.1 → XP_047285184.1  ATP-dependent RNA helicase DDX55 isoform X12

      UniProtKB/TrEMBL
      B4DVE4

    15. XM_017019712.2 → XP_016875201.1  ATP-dependent RNA helicase DDX55 isoform X3

      UniProtKB/TrEMBL
      A0A384N652

    16. XM_047429223.1 → XP_047285179.1  ATP-dependent RNA helicase DDX55 isoform X7

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060936.1 Alternate T2T-CHM13v2.0

      Range
      123600963..123619807
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054372693.1 → XP_054228668.1  ATP-dependent RNA helicase DDX55 isoform X3

      UniProtKB/TrEMBL
      A0A384N652

    2. XM_054372696.1 → XP_054228671.1  ATP-dependent RNA helicase DDX55 isoform X4

      UniProtKB/TrEMBL
      A0A384N652

    3. XM_054372701.1 → XP_054228676.1  ATP-dependent RNA helicase DDX55 isoform X16

    4. XM_054372699.1 → XP_054228674.1  ATP-dependent RNA helicase DDX55 isoform X7

    5. XM_054372694.1 → XP_054228669.1  ATP-dependent RNA helicase DDX55 isoform X3

      UniProtKB/TrEMBL
      A0A384N652

    6. XM_054372692.1 → XP_054228667.1  ATP-dependent RNA helicase DDX55 isoform X1

      UniProtKB/TrEMBL
      A0A384N652

    7. XM_054372697.1 → XP_054228672.1  ATP-dependent RNA helicase DDX55 isoform X5

      UniProtKB/TrEMBL
      F5H5U2

    8. XM_054372698.1 → XP_054228673.1  ATP-dependent RNA helicase DDX55 isoform X6

      UniProtKB/TrEMBL
      F5H5U2

    9. XM_054372704.1 → XP_054228679.1  ATP-dependent RNA helicase DDX55 isoform X11

      UniProtKB/TrEMBL
      B4DVE4

    10. XM_054372708.1 → XP_054228683.1  ATP-dependent RNA helicase DDX55 isoform X17

    11. XM_054372700.1 → XP_054228675.1  ATP-dependent RNA helicase DDX55 isoform X8

      UniProtKB/TrEMBL
      B4DVE4

    12. XM_054372709.1 → XP_054228684.1  ATP-dependent RNA helicase DDX55 isoform X15

      UniProtKB/TrEMBL
      Q8TEC9

    13. XM_054372707.1 → XP_054228682.1  ATP-dependent RNA helicase DDX55 isoform X14

      UniProtKB/TrEMBL
      Q8TEC9

    14. XM_054372706.1 → XP_054228681.1  ATP-dependent RNA helicase DDX55 isoform X13

      UniProtKB/TrEMBL
      Q8TEC9

    15. XM_054372702.1 → XP_054228677.1  ATP-dependent RNA helicase DDX55 isoform X9

      UniProtKB/TrEMBL
      B4DVE4

    16. XM_054372703.1 → XP_054228678.1  ATP-dependent RNA helicase DDX55 isoform X10

      UniProtKB/TrEMBL
      B4DVE4

    17. XM_054372705.1 → XP_054228680.1  ATP-dependent RNA helicase DDX55 isoform X12

      UniProtKB/TrEMBL
      B4DVE4

    18. XM_054372695.1 → XP_054228670.1  ATP-dependent RNA helicase DDX55 isoform X3

      UniProtKB/TrEMBL
      A0A384N652
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q8NHQ9.3 GenPept UniProtKB/Swiss-Prot:Q8NHQ9

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