DDX53 Gene (Protein Coding)

DEAD-Box Helicase 53

GC0XP022999
GIFtS:
35
This intronless gene encodes a protein which contains several domains found in members of the DEAD-box helicase protein family. Other members of this protein family participate in ATP-dependent RNA unwinding. [provided by RefSeq, Sep 2011] See more...

Aliases for DDX53 Gene

Aliases for DDX53 Gene

  • DEAD-Box Helicase 53 2 3 5
  • Cancer/Testis Antigen 26 2 3 4
  • CAGE 2 3 4
  • CT26 2 3 4
  • DEAD (Asp-Glu-Ala-Asp) Box Polypeptide 53 2 3
  • Probable ATP-Dependent RNA Helicase DDX53 3 4
  • Cancer-Associated Gene Protein 3 4
  • DEAD Box Protein 53 3 4
  • Cancer Associated Gene 2
  • DEAD-Box Protein CAGE 3
  • DEAD Box Protein CAGE 4
  • EC 3.6.4.13 4
  • EC 3.6.1 51
  • DDX53 5

External Ids for DDX53 Gene

Previous GeneCards Identifiers for DDX53 Gene

  • GC0XU900468
  • GC0XP022379
  • GC0XP022777
  • GC0XP022927
  • GC0XP020758
  • GC0XP023018

Summaries for DDX53 Gene

Entrez Gene Summary for DDX53 Gene

  • This intronless gene encodes a protein which contains several domains found in members of the DEAD-box helicase protein family. Other members of this protein family participate in ATP-dependent RNA unwinding. [provided by RefSeq, Sep 2011]

GeneCards Summary for DDX53 Gene

DDX53 (DEAD-Box Helicase 53) is a Protein Coding gene. Diseases associated with DDX53 include Medullary Colon Carcinoma and Gastric Adenosquamous Carcinoma. Gene Ontology (GO) annotations related to this gene include nucleic acid binding and ATP-dependent RNA helicase activity. An important paralog of this gene is DDX43.

Additional gene information for DDX53 Gene

No data available for CIViC Summary , UniProtKB/Swiss-Prot Summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for DDX53 Gene

Genomics for DDX53 Gene

GeneHancer (GH) Regulatory Elements Pubs

Download GeneHancer 2017 data
Promoters and enhancers for DDX53 Gene
GeneHancer (GH) Identifier GH Type GH
Score		 GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites		 Gene Targets
GH0XJ023000 Promoter 0.7 Ensembl 250.7 +0.3 340 0.6 GABPA EHMT2 RFX1 ZBTB40 L3MBTL2 ZNF639 NR2C1 GABPB1 ZFX ATF1 DDX53 HSALNG0136982 ENSG00000288546 PTCHD1-AS PTCHD1
GH0XJ023012 Enhancer 0.6 Ensembl ENCODE 0.4 +12.7 12702 0.7 RCOR1 GATA2 CHD2 piR-42726 piR-36588-482 DDX53 ENSG00000288546 PTCHD1-AS PTCHD1
GH0XJ022950 Enhancer 0.5 Ensembl 0.3 -49.2 -49159 1.6 MAFF NFE2 MAFK IKZF1 SPI1 NFE2L2 EMSY piR-54241-001 piR-41838-037 RF00017-8221 DDX53 ENSG00000288546 PTCHD1-AS CBLL2
GH0XJ022968 Enhancer 0.3 Ensembl ENCODE 0.3 -30.5 -30546 1.2 piR-41838-037 RF00017-8221 DDX53 piR-54241-001 ENSG00000288546 PTCHD1-AS CBLL2
GH0XJ022951 Enhancer 0.3 Ensembl 0.3 -47.8 -47759 0.8 JUND FOS piR-54241-001 piR-41838-037 RF00017-8221 DDX53 ENSG00000288546 PTCHD1-AS CBLL2
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around DDX53 on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for DDX53

Top Transcription factor binding sites by QIAGEN in the DDX53 gene promoter:
  • ATF
  • CUTL1
  • GATA-1
  • HOXA9
  • HOXA9B
  • IRF-1
  • Meis-1
  • Meis-1b
  • RORalpha2
  • STAT1

Genomic Locations for DDX53 Gene

Latest Assembly
chrX:22,999,960-23,003,589
(GRCh38/hg38)
Size:
3,630 bases
Orientation:
Plus strand

Previous Assembly
chrX:23,018,077-23,021,706
(GRCh37/hg19 by Entrez Gene)
Size:
3,630 bases
Orientation:
Plus strand

chrX:23,018,087-23,020,204
(GRCh37/hg19 by Ensembl)
Size:
2,118 bases
Orientation:
Plus strand

Genomic View for DDX53 Gene

Genes around DDX53 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
DDX53 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for DDX53 Gene
GeneLoc Logo Genomic Neighborhood • Exon Structure • Gene Density

RefSeq DNA sequence for DDX53 Gene

Proteins for DDX53 Gene

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  • Protein details for DDX53 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q86TM3-DDX53_HUMAN
    Recommended name:
    Probable ATP-dependent RNA helicase DDX53
    Protein Accession:
    Q86TM3
    Secondary Accessions:
    • Q0D2N2
    • Q6NVV4

    Protein attributes for DDX53 Gene

    Size:
    631 amino acids
    Molecular mass:
    71154 Da
    Quaternary structure:
    No Data Available

    Three dimensional structures from OCA and Proteopedia for DDX53 Gene

neXtProt entry for DDX53 Gene

Protein Expression for DDX53 Gene

See protein expression from ProteomicsDB, MOPED, PaxDb, and MaxQB

Selected DME Specific Peptides for DDX53 Gene

Q86TM3:
  • VLTPTREL
  • TPTRELA
  • IIATPGR
  • LVIDEAD
  • AQTGTGKT
  • DEADKML
  • IATPGRL

Post-translational modifications for DDX53 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for DDX53 Gene

ENSEMBL proteins:
REFSEQ proteins:

Domains & Families for DDX53 Gene

Gene Families for DDX53 Gene

HGNC:
Human Protein Atlas (HPA):
  • Enzymes
  • Predicted intracellular proteins

Protein Domains for DDX53 Gene

InterPro:
Blocks:
  • KH domain
  • ATP-dependent helicase, DEAD-box
ProtoNet:

Suggested Antigen Peptide Sequences for DDX53 Gene

GenScript: Design optimal peptide antigens:
  • DEAD box protein CAGE (DDX53_HUMAN)

Graphical View of Domain Structure for InterPro Entry

Q86TM3

UniProtKB/Swiss-Prot:

DDX53_HUMAN :
  • Belongs to the DEAD box helicase family.
Family:
  • Belongs to the DEAD box helicase family.
genes like me logo Genes that share domains with DDX53: view

Function for DDX53 Gene

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  6. Cell Lines for research

Molecular function for DDX53 Gene

UniProtKB/Swiss-Prot CatalyticActivity:
Reaction=ATP + H2O = ADP + H(+) + phosphate; Xref=Rhea:RHEA:13065, ChEBI:CHEBI:15377, ChEBI:CHEBI:15378, ChEBI:CHEBI:30616, ChEBI:CHEBI:43474, ChEBI:CHEBI:456216; EC=3.6.4.13;.

Enzyme Numbers (IUBMB) for DDX53 Gene

Phenotypes From GWAS Catalog for DDX53 Gene

Gene Ontology (GO) - Molecular Function for DDX53 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000166 nucleotide binding IEA --
GO:0003676 nucleic acid binding IEA --
GO:0003723 RNA binding IBA 21873635
GO:0003724 RNA helicase activity IBA 21873635
GO:0004386 helicase activity IEA --
genes like me logo Genes that share ontologies with DDX53: view
genes like me logo Genes that share phenotypes with DDX53: view

Animal Models for research

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for DDX53

No data available for Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for DDX53 Gene

Localization for DDX53 Gene

Subcellular locations from UniProtKB/Swiss-Prot for DDX53 Gene

Nucleus.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for DDX53 gene
Compartment Confidence
nucleus 5
cytosol 5
extracellular 3
plasma membrane 2
cytoskeleton 2
mitochondrion 2
endoplasmic reticulum 2
endosome 2
lysosome 2
golgi apparatus 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Nucleoplasm (3)
  • Cytosol (2)
  • Nucleoli (2)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for DDX53 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IEA --
GO:0005654 nucleoplasm IDA --
GO:0005730 nucleolus IDA --
GO:0005829 cytosol IDA --
GO:0043231 intracellular membrane-bounded organelle IDA --
genes like me logo Genes that share ontologies with DDX53: view

Pathways & Interactions for DDX53 Gene

PathCards logo

SuperPathways for DDX53 Gene

No Data Available

Gene Ontology (GO) - Biological Process for DDX53 Gene

None

No data available for Pathways by source and SIGNOR curated interactions for DDX53 Gene

Drugs & Compounds for DDX53 Gene

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  1. Drug products for research

(3) Drugs for DDX53 Gene - From: HMDB

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Water Approved Pharma 0
Phosphate Experimental Pharma 0
ATP Investigational Nutra 0

(1) Additional Compounds for DDX53 Gene - From: HMDB

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
ADP
  • 5'-Adenylphosphoric acid
  • Adenosine 5'-diphosphate
  • ADENOSINE-5'-diphosphATE
  • H3ADP
  • 5'-Adenylphosphate
 58-64-0
genes like me logo Genes that share compounds with DDX53: view

Transcripts for DDX53 Gene

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mRNA/cDNA for DDX53 Gene

1 REFSEQ mRNAs :
3 NCBI additional mRNA sequence :
1 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for DDX53

Alternative Splicing Database (ASD) splice patterns (SP) for DDX53 Gene

No ASD Table

Relevant External Links for DDX53 Gene

GeneLoc Exon Structure for
DDX53

Expression for DDX53 Gene

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  1. Primer products for research
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mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for DDX53 Gene

mRNA expression in normal human tissues for DDX53 Gene
mRNA expression by GTEx for DDX53 GenemRNA expression by BioGPS for DDX53 Gene

mRNA differential expression in normal tissues according to GTEx for DDX53 Gene

This gene is overexpressed in Testis (x51.7).

Protein differential expression in normal tissues from HIPED for DDX53 Gene

This gene is overexpressed in Testis (24.9), NK cells (21.7), Ovary (9.5), Liver (6.7), and Adipocyte (6.2).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB and MOPED for DDX53 Gene



Protein tissue co-expression partners for DDX53 Gene

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for DDX53

SOURCE GeneReport for Unigene cluster for DDX53 Gene:

Hs.434416

mRNA Expression by UniProt/SwissProt for DDX53 Gene:

Q86TM3-DDX53_HUMAN
Tissue specificity: Expressed in testis. Wide expression in various cancer tissues and cancer cell lines.

Evidence on tissue expression from TISSUES for DDX53 Gene

  • Intestine(2.8)
  • Blood(2.7)
  • Spleen(2.7)
  • Kidney(2.5)
  • Lymph node(2.5)
  • Bone marrow(2.5)
  • Liver(2.5)
  • Lung(2.4)
  • Stomach(2.2)
  • Skin(2.2)
  • Heart(2.2)
  • Nervous system(2.1)
  • Muscle(2)
genes like me logo Genes that share expression patterns with DDX53: view

Primer products for research

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery and Phenotype-based relationships between genes and organs from Gene ORGANizer for DDX53 Gene

Orthologs for DDX53 Gene

This gene was present in the common ancestor of animals and fungi.

Orthologs for DDX53 Gene

Organism Taxonomy Gene Similarity Type Details
Chimpanzee
(Pan troglodytes)
 Mammalia DDX53 30 31
  • 98.57 (n)
 OneToOne
Dog
(Canis familiaris)
 Mammalia DDX53 30
  • 77.67 (n)
Cow
(Bos Taurus)
 Mammalia DDX53 31
  • 68 (a)
 OneToOne
Platypus
(Ornithorhynchus anatinus)
 Mammalia -- 31
  • 63 (a)
 ManyToMany
-- 31
  • 60 (a)
 ManyToMany
Oppossum
(Monodelphis domestica)
 Mammalia -- 31
  • 56 (a)
 ManyToMany
-- 31
  • 56 (a)
 ManyToMany
Chicken
(Gallus gallus)
 Aves -- 31
  • 54 (a)
 OneToMany
Lizard
(Anolis carolinensis)
 Reptilia -- 31
  • 55 (a)
 OneToMany
Zebrafish
(Danio rerio)
 Actinopterygii ddx43 31
  • 46 (a)
 OneToMany
Fruit Fly
(Drosophila melanogaster)
 Insecta CG7878 31
  • 39 (a)
 OneToMany
Worm
(Caenorhabditis elegans)
 Secernentea Y54G11A.3 31
  • 38 (a)
 OneToMany
Baker's yeast
(Saccharomyces cerevisiae)
 Saccharomycetes DBP2 31
  • 35 (a)
 OneToMany
Species where no ortholog for DDX53 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Eremothecium gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • Alpha proteobacteria (Wolbachia pipientis)
  • Amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • Barley (Hordeum vulgare)
  • Beta proteobacteria (Neisseria meningitidis)
  • Bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • Common water flea (Daphnia pulex)
  • Corn (Zea mays)
  • E. coli (Escherichia coli)
  • Filamentous fungi (Aspergillus nidulans)
  • Firmicute Bacteria (Streptococcus pneumoniae)
  • Fission Yeast (Schizosaccharomyces pombe)
  • Green Algae (Chlamydomonas reinhardtii)
  • Honey Bee (Apis mellifera)
  • K. Lactis Yeast (Kluyveromyces lactis)
  • Loblloly Pine (Pinus taeda)
  • Malaria Parasite (Plasmodium falciparum)
  • Medicago Trunc (Medicago Truncatula)
  • Moss (Physcomitrella patens)
  • Mouse (Mus musculus)
  • Orangutan (Pongo pygmaeus)
  • Pig (Sus scrofa)
  • Rainbow Trout (Oncorhynchus mykiss)
  • Rat (Rattus norvegicus)
  • Rice (Oryza sativa)
  • Rice Blast Fungus (Magnaporthe grisea)
  • Schistosome Parasite (Schistosoma mansoni)
  • Sea Anemone (Nematostella vectensis)
  • Sea Vase (Ciona intestinalis)
  • Sea Squirt (Ciona savignyi)
  • Sea Urchin (Strongylocentrotus purpuratus)
  • Sorghum (Sorghum bicolor)
  • Soybean (Glycine max)
  • Stem Rust Fungus (Puccinia graminis)
  • Sugarcane (Saccharum officinarum)
  • Thale Cress (Arabidopsis thaliana)
  • Tomato (Lycopersicon esculentum)
  • Toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • Tropical Clawed Frog (Silurana tropicalis)
  • Wheat (Triticum aestivum)

Evolution for DDX53 Gene

ENSEMBL:
Gene Tree for DDX53 (if available)
TreeFam:
Gene Tree for DDX53 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for DDX53: view image

Paralogs for DDX53 Gene

Paralogs for DDX53 Gene

(15) SIMAP similar genes for DDX53 Gene using alignment to 1 proteins:

  • DDX53_HUMAN

Pseudogenes.org Pseudogenes for DDX53 Gene

genes like me logo Genes that share paralogs with DDX53: view

Variants for DDX53 Gene

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Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for DDX53 Gene

SNP ID Clinical significance and condition Chr 0X pos Variation AA Info Type
rs1057518429 Uncertain Significance: not specified 23,000,869(+) G/A
NM_182699.4(DDX53):c.812G>A (p.Gly271Glu) 		MISSENSE
rs1064795781 Uncertain Significance: not provided 23,000,545(+) G/A
NM_182699.4(DDX53):c.488G>A (p.Cys163Tyr) 		MISSENSE
rs139415880 Benign: not provided 23,000,170(+) A/G
NM_182699.4(DDX53):c.113A>G (p.His38Arg) 		MISSENSE
rs141158062 Benign: not provided 23,000,372(+) C/T
NM_182699.4(DDX53):c.315C>T (p.Ala105=) 		SYNONYMOUS
rs143131443 Likely Benign: not provided 23,000,547(+) G/A
NM_182699.4(DDX53):c.490G>A (p.Glu164Lys) 		MISSENSE

dbSNP identifiers (rs#s) for variants without ClinVar clinical significance for DDX53 Gene

All consequence types are included: molecular consequences (e.g. missense, synonymous), and location-based (e.g. intron, upstream).

Structural Variations from Database of Genomic Variants (DGV) for DDX53 Gene

Variant ID Type Subtype PubMed ID
esv3573648 CNV loss 25503493

Variation tolerance for DDX53 Gene

Residual Variation Intolerance Score: 72.8% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 8.38; 85.49% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for DDX53 Gene

Human Gene Mutation Database (HGMD)
DDX53
SNPedia medical, phenotypic, and genealogical associations of SNPs for
DDX53

SNP Genotyping and Copy Number Assays for research

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for DDX53 Gene

Disorders for DDX53 Gene

MalaCards: The human disease database

(5) MalaCards diseases for DDX53 Gene - From: COP

Disorder Aliases PubMed IDs
medullary colon carcinoma
gastric adenosquamous carcinoma
  • adenosquamous carcinoma of stomach
colorectal cancer
  • crc
breast fibrosarcoma
  • fibrosarcoma of the breast
colonic disease
  • colon disorder
- elite association - COSMIC cancer census association via MalaCards
Search DDX53 in MalaCards View complete list of genes associated with diseases

Additional Disease Information for DDX53

Genetic Association Database
(GAD)
Human Genome Epidemiology Navigator
(HuGE)
Atlas
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
Open Targets Platform
Open Targets Platform
genes like me logo Genes that share disorders with DDX53: view

No data available for UniProtKB/Swiss-Prot and Genatlas for DDX53 Gene

Publications for DDX53 Gene

  1. Comparative structural analysis of human DEAD-box RNA helicases. (PMID: 20941364) Schütz P … Schüler H (PloS one 2010) 3 4
  2. Functional impact of global rare copy number variation in autism spectrum disorders. (PMID: 20531469) Pinto D … Betancur C (Nature 2010) 3 41
  3. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PMID: 15489334) Gerhard DS … MGC Project Team (Genome research 2004) 3 4
  4. Identification and characterization of a novel cancer/testis antigen gene CAGE. (PMID: 11922625) Cho B … Jeoung DI (Biochemical and biophysical research communications 2002) 3 4
  5. Role of DDX53 in taxol-resistance of cervix cancer cells in vitro. (PMID: 30454700) Park SY … Kim Y (Biochemical and biophysical research communications 2018) 3

ExternalLinks

View latest publications for DDX53 gene in Mastermind

Products for DDX53 Gene

Sources for DDX53 Gene