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Aliases for DXO Gene

Aliases for DXO Gene

  • Decapping Exoribonuclease 2 3 5
  • DOM3Z 3 4
  • DOM3L 3 4
  • NG6 3 4
  • Decapping And Exoribonuclease Protein 3
  • DOM-3 (C. Elegans) Homolog Z 2
  • Dom-3 Homolog Z (C. Elegans) 2
  • Dom-3 Homolog Z 4
  • Protein Dom3Z 3
  • EC 3.1.13.- 4
  • EC 3.6.1.- 4
  • RAI1 3

External Ids for DXO Gene

Previous HGNC Symbols for DXO Gene

  • DOM3Z

Previous GeneCards Identifiers for DXO Gene

  • GC06M031950

Summaries for DXO Gene

Entrez Gene Summary for DXO Gene

  • This gene localizes to the major histocompatibility complex (MHC) class III region on chromosome 6. The function of its protein product is unknown, but its ubiquitous expression and conservation in both simple and complex eukaryotes suggests that this may be a housekeeping gene. [provided by RefSeq, Jul 2008]

GeneCards Summary for DXO Gene

DXO (Decapping Exoribonuclease) is a Protein Coding gene. Diseases associated with DXO include Late-Onset Retinal Degenration and Gyrate Atrophy Of Choroid And Retina. Gene Ontology (GO) annotations related to this gene include nucleotide binding and mRNA binding.

UniProtKB/Swiss-Prot for DXO Gene

  • Ribonuclease that specifically degrades pre-mRNAs with a defective 5 end cap and is part of a pre-mRNA capping quality control. Has decapping, pyrophosphohydrolase and 5-3 exonuclease activities. Has decapping activity toward incomplete 5 end cap mRNAs such as unmethylated 5 end-capped RNA to release GpppN and 5 end monophosphate RNA. The 5 end monophosphate RNA is then degraded by the 5-3 exoribonuclease activity, enabling this enzyme to decap and degrade incompletely capped mRNAs. Also possesses RNA 5-pyrophosphohydrolase activity by hydrolyzing the 5 end triphosphate to release pyrophosphates (By similarity).

Gene Wiki entry for DXO Gene

Additional gene information for DXO Gene

No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for DXO Gene

Genomics for DXO Gene

GeneHancer (GH) Regulatory Elements for DXO Gene

Promoters and enhancers for DXO 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
GH06I031969 Promoter/Enhancer 2.3 EPDnew Ensembl ENCODE dbSUPER 573.5 +0.7 652 4.9 CLOCK MLX ZFP64 FEZF1 DMAP1 IRF4 YY1 SLC30A9 ZNF213 E2F8 DXO STK19 SKIV2L DDX39B BRD2 ATF6B LY6G5B C4A NFKBIL1 LSM2
GH06I032965 Promoter/Enhancer 2.4 EPDnew Ensembl ENCODE dbSUPER 56.9 -998.4 -998377 10.4 ZFP64 DMAP1 IRF4 YY1 SLC30A9 ZNF213 E2F8 ZNF143 ZNF548 ZNF263 BRD2 HLA-DMA ENSG00000223837 LEMD2 VPS52 RXRB ATF6B DAXX HCG25 RING1
GH06I031774 Promoter/Enhancer 2 EPDnew Ensembl ENCODE dbSUPER 54.8 +195.5 195486 3.8 CLOCK MLX DMAP1 IRF4 YY1 SLC30A9 ZNF213 E2F8 ZNF263 SP3 VWA7 GTF2H4 DXO PPT2 EGFL8 ZBTB12 PRRC2A PRRT1 NFKBIL1 C4A
GH06I031725 Promoter/Enhancer 2.5 EPDnew Ensembl ENCODE dbSUPER 33.6 +243.7 243711 5.6 HDGF HNRNPUL1 PKNOX1 CLOCK ARNT ZFP64 ARID4B SIN3A DMAP1 ZNF2 DDAH2 DDX39B LY6G5B ATF6B LSM2 SKIV2L PBX2 NFKBIL1 CSNK2B MSH5
GH06I031662 Promoter/Enhancer 2.3 EPDnew Ensembl ENCODE dbSUPER 34.5 +307.2 307246 5 MLX ZFP64 YBX1 DMAP1 YY1 SLC30A9 E2F8 ZNF143 ZNF263 SP3 CSNK2B GPANK1 ENSG00000201207 ENSG00000263020 GC06P032042 DDX39B LY6G5B ATF6B MDC1 GTF2H4
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around DXO on UCSC Golden Path with GeneCards custom track

Genomic Locations for DXO Gene

Genomic Locations for DXO Gene
chr6:31,969,810-31,972,292
(GRCh38/hg38)
Size:
2,483 bases
Orientation:
Minus strand
chr6:31,937,587-31,940,069
(GRCh37/hg19)

Genomic View for DXO Gene

Genes around DXO on UCSC Golden Path with GeneCards custom track

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

Proteins for DXO Gene

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

    Protein Symbol:
    O77932-DXO_HUMAN
    Recommended name:
    Decapping and exoribonuclease protein
    Protein Accession:
    O77932
    Secondary Accessions:
    • A2CER3
    • B0UZ80
    • O15004
    • O78127
    • O78128
    • Q5ST60
    • Q6IPZ2
    • Q9NPK4

    Protein attributes for DXO Gene

    Size:
    396 amino acids
    Molecular mass:
    44929 Da
    Cofactor:
    Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
    Quaternary structure:
    No Data Available
    SequenceCaution:
    • Sequence=AAB67983.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305}; Sequence=CAB89306.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};

neXtProt entry for DXO Gene

Post-translational modifications for DXO Gene

No Post-translational modifications

Other Protein References for DXO Gene

No data available for DME Specific Peptides for DXO Gene

Domains & Families for DXO Gene

Gene Families for DXO Gene

Human Protein Atlas (HPA):
  • Predicted intracellular proteins

Protein Domains for DXO Gene

InterPro:
Blocks:
ProtoNet:

Suggested Antigen Peptide Sequences for DXO Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

O77932

UniProtKB/Swiss-Prot:

DXO_HUMAN :
  • Belongs to the DXO/Dom3Z family.
Family:
  • Belongs to the DXO/Dom3Z family.
genes like me logo Genes that share domains with DXO: view

Function for DXO Gene

Molecular function for DXO Gene

UniProtKB/Swiss-Prot Function:
Ribonuclease that specifically degrades pre-mRNAs with a defective 5 end cap and is part of a pre-mRNA capping quality control. Has decapping, pyrophosphohydrolase and 5-3 exonuclease activities. Has decapping activity toward incomplete 5 end cap mRNAs such as unmethylated 5 end-capped RNA to release GpppN and 5 end monophosphate RNA. The 5 end monophosphate RNA is then degraded by the 5-3 exoribonuclease activity, enabling this enzyme to decap and degrade incompletely capped mRNAs. Also possesses RNA 5-pyrophosphohydrolase activity by hydrolyzing the 5 end triphosphate to release pyrophosphates (By similarity).

Enzyme Numbers (IUBMB) for DXO Gene

Phenotypes From GWAS Catalog for DXO Gene

Gene Ontology (GO) - Molecular Function for DXO Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000166 nucleotide binding IEA --
GO:0000287 magnesium ion binding ISS --
GO:0003723 RNA binding IEA --
GO:0003729 mRNA binding ISS --
GO:0004518 nuclease activity IEA --
genes like me logo Genes that share ontologies with DXO: view
genes like me logo Genes that share phenotypes with DXO: view

miRNA for DXO Gene

miRTarBase miRNAs that target DXO

Inhibitory RNA Products

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

Localization for DXO Gene

Subcellular locations from UniProtKB/Swiss-Prot for DXO 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 DXO gene
Compartment Confidence
nucleus 5
cytosol 5
plasma membrane 4
extracellular 1
mitochondrion 1
peroxisome 1

Subcellular locations from the

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

Gene Ontology (GO) - Cellular Components for DXO Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IDA --
GO:0005829 cytosol IDA --
GO:0005886 plasma membrane IDA --
genes like me logo Genes that share ontologies with DXO: view

Pathways & Interactions for DXO Gene

No Data Available

Gene Ontology (GO) - Biological Process for DXO Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006402 mRNA catabolic process ISS --
GO:0008152 metabolic process ISS --
GO:0050779 RNA destabilization ISS --
GO:0071028 nuclear mRNA surveillance ISS --
GO:0090305 nucleic acid phosphodiester bond hydrolysis ISS --
genes like me logo Genes that share ontologies with DXO: view

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

Drugs & Compounds for DXO Gene

No Compound Related Data Available

Transcripts for DXO Gene

CRISPR Products

Inhibitory RNA Products

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

No ASD Table

Relevant External Links for DXO Gene

GeneLoc Exon Structure for
DXO
ECgene alternative splicing isoforms for
DXO

Expression for DXO Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for DXO Gene

Protein differential expression in normal tissues from HIPED for DXO Gene

This gene is overexpressed in Testis (29.9), Peripheral blood mononuclear cells (21.0), NK cells (10.0), and Fetal ovary (8.1).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MaxQB, and MOPED for DXO Gene



Protein tissue co-expression partners for DXO Gene

NURSA nuclear receptor signaling pathways regulating expression of DXO Gene:

DXO

mRNA Expression by UniProt/SwissProt for DXO Gene:

O77932-DXO_HUMAN
Tissue specificity: Ubiquitously expressed.
genes like me logo Genes that share expression patterns with DXO: view

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , mRNA differential expression in normal tissues , Evidence on tissue expression from TISSUES and Phenotype-based relationships between genes and organs from Gene ORGANizer for DXO Gene

Orthologs for DXO Gene

This gene was present in the common ancestor of eukaryotes.

Orthologs for DXO Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia DOM3Z 33
  • 99.33 (n)
DXO 34
  • 99 (a)
OneToOne
dog
(Canis familiaris)
Mammalia DXO 34 33
  • 90.41 (n)
OneToOne
cow
(Bos Taurus)
Mammalia DOM3Z 34 33
  • 89.29 (n)
OneToOne
rat
(Rattus norvegicus)
Mammalia Dxo 33
  • 87.56 (n)
mouse
(Mus musculus)
Mammalia Dxo 16 34 33
  • 86.7 (n)
oppossum
(Monodelphis domestica)
Mammalia DXO 34
  • 68 (a)
OneToOne
lizard
(Anolis carolinensis)
Reptilia DXO 34
  • 58 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia dxo 33
  • 56.14 (n)
zebrafish
(Danio rerio)
Actinopterygii zgc:92781 33
  • 59.51 (n)
DXO 34
  • 50 (a)
OneToOne
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP007205 33
  • 43.2 (n)
fruit fly
(Drosophila melanogaster)
Insecta CG9125 33 34
  • 42.96 (n)
cuff 34
  • 20 (a)
OneToMany
worm
(Caenorhabditis elegans)
Secernentea math-43 34 33
  • 45.32 (n)
OneToMany
dom-3 34
  • 26 (a)
OneToMany
A. gosspyii yeast
(Ashbya gossypii)
Saccharomycetes AGOS_AFR263C 33
  • 45.05 (n)
K. lactis yeast
(Kluyveromyces lactis)
Saccharomycetes KLLA0E12893g 33
  • 38.83 (n)
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes RAI1 33 34 36
  • 38.69 (n)
thale cress
(Arabidopsis thaliana)
eudicotyledons AT4G17620 33
  • 42.24 (n)
bread mold
(Neurospora crassa)
Ascomycetes NCU04191 33
  • 48.7 (n)
fission yeast
(Schizosaccharomyces pombe)
Schizosaccharomycetes din1 33
  • 42.02 (n)
sea squirt
(Ciona savignyi)
Ascidiacea -- 34
  • 39 (a)
OneToOne
Species where no ortholog for DXO was found in the sources mined by GeneCards:
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • chicken (Gallus gallus)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • platypus (Ornithorhynchus anatinus)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)

Evolution for DXO Gene

ENSEMBL:
Gene Tree for DXO (if available)
TreeFam:
Gene Tree for DXO (if available)

Paralogs for DXO Gene

No data available for Paralogs for DXO Gene

Variants for DXO Gene

Sequence variations from dbSNP and Humsavar for DXO Gene

SNP ID Clin Chr 06 pos Variation AA Info Type
rs142860816 uncertain-significance, Trichohepatoenteric syndrome 31,969,640(-) G/A downstream_transcript_variant
rs146401600 uncertain-significance, Trichohepatoenteric syndrome 31,969,310(-) C/A/T
rs2075702 likely-benign, Trichohepatoenteric syndrome 31,969,734(-) T/C downstream_transcript_variant
rs267600971 likely-pathogenic, Malignant melanoma of skin, Squamous cell carcinoma of the skin 31,972,346(-) G/A upstream_transcript_variant
rs565424838 uncertain-significance, Trichohepatoenteric syndrome 31,969,685(-) C/A/G/T downstream_transcript_variant

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

Variant ID Type Subtype PubMed ID
dgv10403n54 CNV loss 21841781
dgv10404n54 CNV loss 21841781
dgv10463n54 CNV loss 21841781
esv2759415 CNV gain+loss 17122850
nsv1073969 CNV deletion 25765185
nsv1112900 CNV deletion 24896259
nsv1126749 CNV deletion 24896259
nsv284 CNV deletion 15895083
nsv428141 CNV gain+loss 18775914
nsv5247 CNV deletion 18451855
nsv601970 CNV loss 21841781
nsv601971 CNV gain 21841781
nsv830628 CNV loss 17160897

Variation tolerance for DXO Gene

Residual Variation Intolerance Score: 79.9% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 6.44; 77.29% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for DXO Gene

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

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

Disorders for DXO Gene

MalaCards: The human disease database

(4) MalaCards diseases for DXO Gene - From: HGMD and DISEASES

Disorder Aliases PubMed IDs
late-onset retinal degenration
  • lord
gyrate atrophy of choroid and retina
  • gacr
choroid disease
  • abnormality of the choroid
asphyxiating thoracic dystrophy
  • jeune syndrome
- elite association - COSMIC cancer census association via MalaCards
Search DXO in MalaCards View complete list of genes associated with diseases
genes like me logo Genes that share disorders with DXO: view

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

Publications for DXO Gene

  1. Four ubiquitously expressed genes, RD (D6S45)-SKI2W (SKIV2L)-DOM3Z-RP1 (D6S60E), are present between complement component genes factor B and C4 in the class III region of the HLA. (PMID: 9799600) Yang Z … Yu CY (Genomics 1998) 2 3 4 58
  2. A mammalian pre-mRNA 5' end capping quality control mechanism and an unexpected link of capping to pre-mRNA processing. (PMID: 23523372) Jiao X … Kiledjian M (Molecular cell 2013) 2 3 58
  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 58
  4. The DNA sequence and analysis of human chromosome 6. (PMID: 14574404) Mungall AJ … Beck S (Nature 2003) 3 4 58
  5. Analysis of the gene-dense major histocompatibility complex class III region and its comparison to mouse. (PMID: 14656967) Xie T … Hood L (Genome research 2003) 3 4 58

Products for DXO Gene

Sources for DXO Gene

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