DXO decapping exoribonuclease [Homo sapiens (human)] - Gene

Summary

Official Symbol: DXOprovided by HGNC
Official Full Name: decapping exoribonucleaseprovided by HGNC
Primary source: HGNC:HGNC:2992
See related: Ensembl:ENSG00000204348 MIM:605996; AllianceGenome:HGNC:2992
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: NG6; RAI1; DOM3L; DOM3Z
Summary: 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]
Expression: Ubiquitous expression in testis (RPKM 17.8), adrenal (RPKM 16.9) and 25 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 6p21.33

Exon count:: 7

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	6	NC_000006.12 (31969815..31972138, complement)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	6	NC_060930.1 (31823020..31825343, complement)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	6	NC_000006.11 (31937592..31939915, complement)

Chromosome 6 - NC_000006.12 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: HPA RNA-seq normal tissues 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

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

DOM3Z limits both miR-122-dependent and miR-122-independent Hepatitis C RNA accumulation.
Title: miR-122 does not impact recognition of the HCV genome by innate sensors of RNA but rather protects the 5' end from the cellular pyrophosphatases, DOM3Z and DUSP11.
Study showed that DXO is a multifunctional enzyme that possesses both decapping and 5'-3' exoribonuclease activities toward non-2'-O-methylated RNA transcripts. DXO is directly involved in the mRNA quality control mechanism by degrading mRNAs with abnormal cap structures.
Title: 2'-O-methylation of the mRNA cap protects RNAs from decapping and degradation by DXO.
Observational study of gene-disease association, gene-environment interaction, and pharmacogenomic / toxicogenomic. (HuGE Navigator)
Title: Variation at the NFATC2 locus increases the risk of thiazolidinedione-induced edema in the Diabetes REduction Assessment with ramipril and rosiglitazone Medication (DREAM) study.
Observational study of gene-disease association. (HuGE Navigator)
Title: Gene-centric association signals for lipids and apolipoproteins identified via the HumanCVD BeadChip.

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
GWAS of blood cell traits identifies novel associated loci and epistatic interactions in Caucasian and African-American children. EBI GWAS Catalog EBI GWAS CatalogPubMed
Risk HLA-DQA1 and PLA(2)R1 alleles in idiopathic membranous nephropathy. EBI GWAS Catalog EBI GWAS CatalogPubMed

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

WI-16314 (e-PCR)
- UniSTS:65600

DOM3Z (e-PCR)
- UniSTS:519098

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables 5'-3' exonuclease activity	ISS Inferred from Sequence or Structural Similarity more info
enables RNA NAD+-cap (NAD+-forming) hydrolase activity	ISS Inferred from Sequence or Structural Similarity more info
enables mRNA 5'-diphosphatase activity	IBA Inferred from Biological aspect of Ancestor more info
enables mRNA 5'-diphosphatase activity	ISS Inferred from Sequence or Structural Similarity more info
enables mRNA binding	ISS Inferred from Sequence or Structural Similarity more info
enables magnesium ion binding	ISS Inferred from Sequence or Structural Similarity more info
enables nucleotide binding	IEA Inferred from Electronic Annotation more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed

Process	Evidence Code	Pubs
involved_in NAD-cap decapping	IBA Inferred from Biological aspect of Ancestor more info
involved_in NAD-cap decapping	IDA Inferred from Direct Assay more info	PubMed
involved_in RNA destabilization	ISS Inferred from Sequence or Structural Similarity more info
involved_in mRNA catabolic process	IDA Inferred from Direct Assay more info	PubMed
involved_in mRNA catabolic process	ISS Inferred from Sequence or Structural Similarity more info
involved_in nuclear mRNA surveillance	ISS Inferred from Sequence or Structural Similarity more info
involved_in nuclear-transcribed mRNA catabolic process	IBA Inferred from Biological aspect of Ancestor more info
involved_in nucleic acid metabolic process	ISS Inferred from Sequence or Structural Similarity more info

Component	Evidence Code	Pubs
is_active_in cytosol	IBA Inferred from Biological aspect of Ancestor more info
located_in cytosol	IDA Inferred from Direct Assay more info
located_in nucleoplasm	IDA Inferred from Direct Assay more info
is_active_in nucleus	IBA Inferred from Biological aspect of Ancestor more info
located_in nucleus	IDA Inferred from Direct Assay more info	PubMed
located_in plasma membrane	IDA Inferred from Direct Assay more info

General protein information

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Preferred Names: decapping and exoribonuclease protein

Names: 5'-3' exoribonuclease DXO; NAD-capped RNA hydrolase DXO; deNADding enzyme DXO; protein Dom3Z

NCBI Reference Sequences (RefSeq)

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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)

NM_001371205.1 → NP_001358134.1 decapping and exoribonuclease protein isoform 1

Status: REVIEWED

Description

Transcript Variant: This variant (1) represents the longest transcript. Both variants 1 and 3 encode the same protein.

Source sequence(s)

AL645922

UniProtKB/TrEMBL

H7C5D2

Conserved Domains (1) summary

pfam08652
Location:51 → 118

RAI1; RAI1 like PD-(D/E)XK nuclease
NM_001371206.1 → NP_001358135.1 decapping and exoribonuclease protein isoform 1

Status: REVIEWED

Description

Transcript Variant: This variant (2) differs in the 5' UTR compared to variant 1. Both variants 1 and 3 encode the same protein.

Source sequence(s)

AL645922

UniProtKB/TrEMBL

H7C5D2

Related

ENST00000474587.1

Conserved Domains (1) summary

pfam08652
Location:51 → 118

RAI1; RAI1 like PD-(D/E)XK nuclease
NM_005510.4 → NP_005501.2 decapping and exoribonuclease protein isoform 2

See identical proteins and their annotated locations for NP_005501.2

Status: REVIEWED

Source sequence(s)

AF059252, BC019083

Consensus CDS

CCDS4732.1

UniProtKB/Swiss-Prot

A2CER3, B0UZ80, O15004, O77932, O78127, O78128, Q5ST60, Q6IPZ2, Q9NPK4

UniProtKB/TrEMBL

A0A024RCW8, A0A1U9X7P1

Related

ENSP00000337759.5, ENST00000337523.10

Conserved Domains (1) summary

pfam08652
Location:235 → 302

RAI1; RAI1 like PD-(D/E)XK nuclease

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

NC_000006.12 Reference GRCh38.p14 Primary Assembly

Range

31969815..31972138 complement

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_006715005.4 → XP_006715068.1 decapping and exoribonuclease protein isoform X1

See identical proteins and their annotated locations for XP_006715068.1

UniProtKB/Swiss-Prot

A2CER3, B0UZ80, O15004, O77932, O78127, O78128, Q5ST60, Q6IPZ2, Q9NPK4

UniProtKB/TrEMBL

A0A024RCW8, A0A1U9X7P1

Related

ENSP00000364498.3, ENST00000375349.7

Conserved Domains (1) summary

pfam08652
Location:235 → 302

RAI1; RAI1 like PD-(D/E)XK nuclease
XM_047418262.1 → XP_047274218.1 decapping and exoribonuclease protein isoform X1

UniProtKB/Swiss-Prot

A2CER3, B0UZ80, O15004, O77932, O78127, O78128, Q5ST60, Q6IPZ2, Q9NPK4

UniProtKB/TrEMBL

A0A024RCW8

Related

ENSP00000364505.3, ENST00000375356.7
XM_047418263.1 → XP_047274219.1 decapping and exoribonuclease protein isoform X2
XM_047418264.1 → XP_047274220.1 decapping and exoribonuclease protein isoform X3

UniProtKB/TrEMBL

F8WC68

Related

ENSP00000418632.1, ENST00000480240.5

Reference GRCh38.p14 ALT_REF_LOCI_2

Genomic

NT_113891.3 Reference GRCh38.p14 ALT_REF_LOCI_2

Range

3447242..3449565 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_054329744.1 → XP_054185719.1 decapping and exoribonuclease protein isoform X1

UniProtKB/Swiss-Prot

A2CER3, B0UZ80, O15004, O77932, O78127, O78128, Q5ST60, Q6IPZ2, Q9NPK4

UniProtKB/TrEMBL

A0A024RCW8
XM_054329745.1 → XP_054185720.1 decapping and exoribonuclease protein isoform X2
XM_054329746.1 → XP_054185721.1 decapping and exoribonuclease protein isoform X3

UniProtKB/TrEMBL

F8WC68

Reference GRCh38.p14 ALT_REF_LOCI_3

Genomic

NT_167245.2 Reference GRCh38.p14 ALT_REF_LOCI_3

Range

3217590..3219913 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_054330237.1 → XP_054186212.1 decapping and exoribonuclease protein isoform X1

UniProtKB/TrEMBL

A0A1U9X7N5
XM_054330238.1 → XP_054186213.1 decapping and exoribonuclease protein isoform X3

UniProtKB/TrEMBL

F8WC68

Reference GRCh38.p14 ALT_REF_LOCI_5

Genomic

NT_167247.2 Reference GRCh38.p14 ALT_REF_LOCI_5

Range

3311851..3314174 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_054330779.1 → XP_054186754.1 decapping and exoribonuclease protein isoform X1

UniProtKB/Swiss-Prot

A2CER3, B0UZ80, O15004, O77932, O78127, O78128, Q5ST60, Q6IPZ2, Q9NPK4

UniProtKB/TrEMBL

A0A024RCW8
XM_054330780.1 → XP_054186755.1 decapping and exoribonuclease protein isoform X2
XM_054330781.1 → XP_054186756.1 decapping and exoribonuclease protein isoform X3

UniProtKB/TrEMBL

F8WC68

Reference GRCh38.p14 ALT_REF_LOCI_6

Genomic

NT_167248.2 Reference GRCh38.p14 ALT_REF_LOCI_6

Range

3225785..3228108 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_054331015.1 → XP_054186990.1 decapping and exoribonuclease protein isoform X1

UniProtKB/Swiss-Prot

A2CER3, B0UZ80, O15004, O77932, O78127, O78128, Q5ST60, Q6IPZ2, Q9NPK4

UniProtKB/TrEMBL

A0A024RCW8
XM_054331016.1 → XP_054186991.1 decapping and exoribonuclease protein isoform X2
XM_054331017.1 → XP_054186992.1 decapping and exoribonuclease protein isoform X3

UniProtKB/TrEMBL

F8WC68

Reference GRCh38.p14 ALT_REF_LOCI_7

Genomic

NT_167249.2 Reference GRCh38.p14 ALT_REF_LOCI_7

Range

3271004..3273327 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_054331281.1 → XP_054187256.1 decapping and exoribonuclease protein isoform X1

UniProtKB/Swiss-Prot

A2CER3, B0UZ80, O15004, O77932, O78127, O78128, Q5ST60, Q6IPZ2, Q9NPK4

UniProtKB/TrEMBL

A0A024RCW8
XM_054331282.1 → XP_054187257.1 decapping and exoribonuclease protein isoform X2
XM_054331283.1 → XP_054187258.1 decapping and exoribonuclease protein isoform X3

UniProtKB/TrEMBL

F8WC68

Alternate T2T-CHM13v2.0

Genomic

NC_060930.1 Alternate T2T-CHM13v2.0

Range

31823020..31825343 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_054354416.1 → XP_054210391.1 decapping and exoribonuclease protein isoform X1

UniProtKB/Swiss-Prot

A2CER3, B0UZ80, O15004, O77932, O78127, O78128, Q5ST60, Q6IPZ2, Q9NPK4

UniProtKB/TrEMBL

A0A024RCW8
XM_054354417.1 → XP_054210392.1 decapping and exoribonuclease protein isoform X2
XM_054354418.1 → XP_054210393.1 decapping and exoribonuclease protein isoform X2
XM_054354419.1 → XP_054210394.1 decapping and exoribonuclease protein isoform X3

UniProtKB/TrEMBL

F8WC68