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

Gene ID: 57696, updated on 3-May-2020

Summary

Official Symbol
DDX55provided by HGNC
Official Full Name
DEAD-box helicase 55provided by HGNC
Primary source
HGNC:HGNC:20085
See related
Ensembl:ENSG00000111364
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

Genomic context

See DDX55 in Genome Data Viewer
Location:
12q24.31
Exon count:
15
Annotation release Status Assembly Chr Location
109.20200228 current GRCh38.p13 (GCF_000001405.39) 12 NC_000012.12 (123602089..123620943)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 12 NC_000012.11 (124086650..124105482)

Chromosome 12 - NC_000012.12Genomic Context describing neighboring genes Neighboring gene TMED2 divergent transcript Neighboring gene transmembrane p24 trafficking protein 2 Neighboring gene uncharacterized LOC105370041 Neighboring gene small nucleolar RNA, H/ACA box 9B Neighboring gene eukaryotic translation initiation factor 2B subunit alpha Neighboring gene general transcription factor IIH subunit 3 Neighboring gene tectonic family member 2

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

Phenotypes

NHGRI GWAS Catalog

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

HIV-1 interactions

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

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Clone Names

  • FLJ16577, KIAA1595, MGC33209

Gene Ontology Provided by GOA

Function Evidence Code Pubs
ATP binding IEA
Inferred from Electronic Annotation
more info
 
RNA binding HDA PubMed 
RNA binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
RNA helicase activity IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
Component Evidence Code Pubs
cytosol IDA
Inferred from Direct Assay
more info
 
membrane HDA PubMed 
nucleolus IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
nucleolus IDA
Inferred from Direct Assay
more info
 
nucleoplasm IDA
Inferred from Direct Assay
more info
 

General protein information

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_016875202.1
XP_016875203.1
XP_016875204.1
XP_016875205.1
XP_016875206.1
XP_016875207.1
XP_016875208.1
XP_016875209.1
XP_016875210.1
XP_024304870.1
XP_024304871.1
XP_024304872.1
XP_024304873.1

NCBI Reference Sequences (RefSeq)

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_020936.3NP_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
    Q8NHQ9
    UniProtKB/TrEMBL
    A0A024RBS0
    Related
    ENSP00000238146.3, ENST00000238146.9
    Conserved Domains (4) summary
    smart00487
    Location:24228
    DEXDc; DEAD-like helicases superfamily
    cd00079
    Location:242371
    HELICc; Helicase superfamily c-terminal domain; associated with DEXDc-, DEAD-, and DEAH-box proteins, yeast initiation factor 4A, Ski2p, and Hepatitis C virus NS3 helicases; this domain is found in a wide variety of helicases and helicase related proteins; may ...
    cd00268
    Location:9224
    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 ...
    pfam13959
    Location:403462
    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: Homo sapiens Updated Annotation Release 109.

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

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000012.12 Reference GRCh38.p13 Primary Assembly

    Range
    123602089..123620943
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011538608.3XP_011536910.1  ATP-dependent RNA helicase DDX55 isoform X10

    Conserved Domains (3) summary
    smart00487
    Location:24228
    DEXDc; DEAD-like helicases superfamily
    cd00268
    Location:9224
    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:252366
    Helicase_C; Helicase conserved C-terminal domain
  2. XM_017019715.1XP_016875204.1  ATP-dependent RNA helicase DDX55 isoform X5

  3. XM_017019721.1XP_016875210.1  ATP-dependent RNA helicase DDX55 isoform X12

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

  5. XM_017019716.1XP_016875205.1  ATP-dependent RNA helicase DDX55 isoform X6

  6. XM_017019714.1XP_016875203.1  ATP-dependent RNA helicase DDX55 isoform X4

  7. XM_024449102.1XP_024304870.1  ATP-dependent RNA helicase DDX55 isoform X7

    Conserved Domains (2) summary
    COG0513
    Location:16280
    SrmB; Superfamily II DNA and RNA helicase [Replication, recombination and repair]
    pfam13959
    Location:274333
    DUF4217; Domain of unknown function (DUF4217)
  8. XM_024449104.1XP_024304872.1  ATP-dependent RNA helicase DDX55 isoform X8

    Conserved Domains (2) summary
    COG0513
    Location:16262
    SrmB; Superfamily II DNA and RNA helicase [Replication, recombination and repair]
    pfam13959
    Location:256315
    DUF4217; Domain of unknown function (DUF4217)
  9. XM_024449103.1XP_024304871.1  ATP-dependent RNA helicase DDX55 isoform X8

    Conserved Domains (2) summary
    COG0513
    Location:16262
    SrmB; Superfamily II DNA and RNA helicase [Replication, recombination and repair]
    pfam13959
    Location:256315
    DUF4217; Domain of unknown function (DUF4217)
  10. XM_024449105.1XP_024304873.1  ATP-dependent RNA helicase DDX55 isoform X11

    Conserved Domains (2) summary
    cd00079
    Location:6125
    HELICc; Helicase superfamily c-terminal domain; associated with DEXDc-, DEAD-, and DEAH-box proteins, yeast initiation factor 4A, Ski2p, and Hepatitis C virus NS3 helicases; this domain is found in a wide variety of helicases and helicase related proteins; may ...
    pfam13959
    Location:157216
    DUF4217; Domain of unknown function (DUF4217)
  11. XM_017019719.1XP_016875208.1  ATP-dependent RNA helicase DDX55 isoform X11

    Conserved Domains (2) summary
    cd00079
    Location:6125
    HELICc; Helicase superfamily c-terminal domain; associated with DEXDc-, DEAD-, and DEAH-box proteins, yeast initiation factor 4A, Ski2p, and Hepatitis C virus NS3 helicases; this domain is found in a wide variety of helicases and helicase related proteins; may ...
    pfam13959
    Location:157216
    DUF4217; Domain of unknown function (DUF4217)
  12. XM_017019713.1XP_016875202.1  ATP-dependent RNA helicase DDX55 isoform X4

  13. XM_017019717.1XP_016875206.1  ATP-dependent RNA helicase DDX55 isoform X9

  14. XM_017019720.2XP_016875209.1  ATP-dependent RNA helicase DDX55 isoform X11

    Conserved Domains (2) summary
    cd00079
    Location:6125
    HELICc; Helicase superfamily c-terminal domain; associated with DEXDc-, DEAD-, and DEAH-box proteins, yeast initiation factor 4A, Ski2p, and Hepatitis C virus NS3 helicases; this domain is found in a wide variety of helicases and helicase related proteins; may ...
    pfam13959
    Location:157216
    DUF4217; Domain of unknown function (DUF4217)
  15. XM_017019711.1XP_016875200.1  ATP-dependent RNA helicase DDX55 isoform X2

  16. XM_017019712.1XP_016875201.1  ATP-dependent RNA helicase DDX55 isoform X3

  17. XM_017019718.1XP_016875207.1  ATP-dependent RNA helicase DDX55 isoform X9

RNA

  1. XR_001748827.1 RNA Sequence

  2. XR_001748822.1 RNA Sequence

  3. XR_001748824.1 RNA Sequence

  4. XR_001748823.1 RNA Sequence

  5. XR_001748825.1 RNA Sequence

  6. XR_001748821.2 RNA Sequence

  7. XR_001748828.1 RNA Sequence

  8. XR_001748826.1 RNA Sequence

  9. XR_001748829.1 RNA Sequence

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