Dxo (decapping exoribonuclease) - Rat Genome Database

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Gene: Dxo (decapping exoribonuclease) Rattus norvegicus
Analyze
Symbol: Dxo
Name: decapping exoribonuclease
RGD ID: 1303267
Description: Predicted to enable several functions, including 5'-3' exonuclease activity; hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides; and magnesium ion binding activity. Predicted to be involved in NAD-cap decapping; RNA destabilization; and nuclear mRNA surveillance. Predicted to be located in nucleoplasm and plasma membrane. Predicted to be active in cytosol and nucleus. Orthologous to human DXO (decapping exoribonuclease); PARTICIPATES IN 3'-end pre-mRNA processing pathway; RNA polymerase II transcription termination pathway; INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; 2,4,6-trinitrotoluene; 2,6-dinitrotoluene.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: 5'-3' exoribonuclease DXO; decapping and exoribonuclease protein; deNADding enzyme DXO; DOM-3 homolog Z; DOM-3 homolog Z (C. elegans); Dom3z; MGC95256; NAD-capped RNA hydrolase DXO
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Black Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: GRCr8 - GRCr8 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8203,997,953 - 4,000,115 (-)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl203,997,955 - 4,000,037 (-)EnsemblGRCr8
mRatBN7.2203,993,322 - 3,995,484 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl203,993,327 - 3,995,494 (-)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx204,693,280 - 4,695,364 (-)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0204,055,028 - 4,057,112 (-)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0204,592,209 - 4,594,293 (-)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0204,517,307 - 4,519,391 (+)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl204,517,307 - 4,519,389 (+)Ensemblrn6Rnor6.0
Rnor_5.0206,597,106 - 6,599,190 (+)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.4204,093,718 - 4,095,802 (-)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera204,035,291 - 4,037,375 (+)NCBICelera
RGSC_v3.1204,093,893 - 4,096,049 (-)NCBI
Cytogenetic Map20p12NCBI
JBrowse:




Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component
cytosol  (IBA)
nucleoplasm  (IEA,ISO)
nucleus  (IBA,IEA,ISO,ISS)

Molecular Function

Molecular Pathway Annotations     Click to see Annotation Detail View
References

References - curated
# Reference Title Reference Citation
1. Pre-mRNA 3'-end processing complex assembly and function. Chan S, etal., Wiley Interdiscip Rev RNA. 2011 May-Jun;2(3):321-35. doi: 10.1002/wrna.54. Epub 2010 Oct 18.
2. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
3. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
4. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
5. Comprehensive gene review and curation RGD comprehensive gene curation
6. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. Strausberg RL, etal., Proc Natl Acad Sci U S A. 2002 Dec 24;99(26):16899-903. Epub 2002 Dec 11.
Additional References at PubMed
PMID:15060004   PMID:15489334   PMID:23523372   PMID:28283058   PMID:29601584   PMID:30180947   PMID:31101919  


Genomics

Comparative Map Data
Dxo
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8203,997,953 - 4,000,115 (-)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl203,997,955 - 4,000,037 (-)EnsemblGRCr8
mRatBN7.2203,993,322 - 3,995,484 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl203,993,327 - 3,995,494 (-)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx204,693,280 - 4,695,364 (-)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0204,055,028 - 4,057,112 (-)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0204,592,209 - 4,594,293 (-)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0204,517,307 - 4,519,391 (+)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl204,517,307 - 4,519,389 (+)Ensemblrn6Rnor6.0
Rnor_5.0206,597,106 - 6,599,190 (+)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.4204,093,718 - 4,095,802 (-)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera204,035,291 - 4,037,375 (+)NCBICelera
RGSC_v3.1204,093,893 - 4,096,049 (-)NCBI
Cytogenetic Map20p12NCBI
DXO
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38631,969,815 - 31,972,138 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl631,969,810 - 31,972,509 (-)Ensemblhg38GRCh38
GRCh37631,937,592 - 31,939,915 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36632,045,567 - 32,048,011 (-)NCBIBuild 36Build 36hg18NCBI36
Build 34632,045,566 - 32,048,011NCBI
Celera633,537,350 - 33,539,794 (-)NCBICelera
Cytogenetic Map6p21.33NCBI
HuRef631,724,525 - 31,726,969 (-)NCBIHuRef
CHM1_1631,939,669 - 31,942,113 (-)NCBICHM1_1
T2T-CHM13v2.0631,823,020 - 31,825,343 (-)NCBIT2T-CHM13v2.0
Dxo
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391735,055,998 - 35,058,162 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1735,055,995 - 35,058,209 (+)EnsemblGRCm39 EnsemblGRCm39
GRCm381734,836,996 - 34,839,187 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1734,837,019 - 34,839,233 (+)Ensemblmm10GRCm38
MGSCv371734,973,964 - 34,976,131 (+)NCBIMGSCv37MGSCv37mm9NCBIm37
MGSCv361734,445,139 - 34,447,289 (+)NCBIMGSCv36mm8
Celera1737,932,348 - 37,934,515 (+)NCBICelera
Cytogenetic Map17B1NCBI
cM Map1718.39NCBI
Dxo
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_004955437481,554 - 484,989 (-)Ensembl
ChiLan1.0NW_004955437482,866 - 484,989 (-)NCBIChiLan1.0ChiLan1.0
DXO
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v2546,446,379 - 46,448,629 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan1642,407,867 - 42,410,121 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v0631,630,523 - 31,632,363 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.1632,517,086 - 32,519,566 (-)NCBIPanPan1.1PanPan1.1panPan2
PanPan1.1 Ensembl632,517,086 - 32,519,566 (-)EnsemblpanPan2panpan1.1
DXO
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1121,424,584 - 1,426,275 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl121,424,591 - 1,426,452 (-)EnsemblcanFam3CanFam3.1
Dog10K_Boxer_Tasha121,559,785 - 1,562,016 (-)NCBIDog10K_Boxer_TashaDog10K_Boxer_Tasha
ROS_Cfam_1.0121,566,885 - 1,568,996 (-)NCBIROS_Cfam_1.0ROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl121,566,892 - 1,568,726 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1121,424,344 - 1,426,575 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0121,492,527 - 1,494,758 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0121,559,127 - 1,561,358 (-)NCBIUU_Cfam_GSD_1.0UU_Cfam_GSD_1.0
Dxo
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440494635,982,182 - 35,984,452 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049367271,576,886 - 1,579,154 (+)EnsemblSpeTri2.0 Ensembl
SpeTri2.0NW_0049367271,576,823 - 1,579,158 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
DXO
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl724,056,525 - 24,060,011 (-)EnsemblsusScr11Sscrofa11.1
Sscrofa11.1724,057,670 - 24,060,108 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2727,752,093 - 27,754,531 (+)NCBISscrofa10.2Sscrofa10.2susScr3
DXO
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11740,049,679 - 40,052,114 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl1740,050,257 - 40,052,050 (+)EnsemblChlSab1.1 EnsemblchlSab2Vervet-AGM
Vero_WHO_p1.0NW_02366604431,886,210 - 31,888,644 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Dxo
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_00462475424,281,101 - 24,287,647 (+)EnsemblHetGla_female_1.0 EnsemblhetGla2HetGla_female_1.0 Ensembl
HetGla 1.0NW_00462475424,281,099 - 24,283,403 (+)NCBIHetGla 1.0HetGla 1.0hetGla2
Dxo
(Rattus rattus - black rat)
Black Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rrattus_CSIRO_v1187,429,918 - 7,432,056 (+)NCBIRrattus_CSIRO_v1

Variants

.
Variants in Dxo
7 total Variants
miRNA Target Status (No longer updated)

Predicted Target Of
Summary Value
Count of predictions:158
Count of miRNA genes:118
Interacting mature miRNAs:130
Transcripts:ENSRNOT00000000483
Prediction methods:Microtar, Miranda, Rnahybrid, Targetscan
Result types:miRGate_prediction

The detailed report is available here: Full Report CSV TAB Printer

miRNA Target Status data imported from miRGate (http://mirgate.bioinfo.cnio.es/).
For more information about miRGate, see PMID:25858286 or access the full paper here.


QTLs in Region (GRCr8)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
2306850Pia40Pristane induced arthritis QTL 400.0001joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)2015332005306452Rat
61474Eae1Experimental allergic encephalomyelitis QTL 13nervous system integrity trait (VT:0010566)experimental autoimmune encephalomyelitis severity score (CMO:0001419)2016693431Rat
2317057Aia27Adjuvant induced arthritis QTL 272.83joint integrity trait (VT:0010548)right rear ankle joint diameter (CMO:0002150)20126925056Rat
1641915Colcr9Colorectal carcinoma resistance QTL 92.970.0024intestine integrity trait (VT:0010554)benign colorectal tumor number (CMO:0001795)20133724594Rat
7387283Uae44Urinary albumin excretion QTL 440.1712urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)20126128279Rat
7411668Foco32Food consumption QTL 3280.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)20136600300Rat
2305926Iddm37Insulin dependent diabetes mellitus QTL 376blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)20153308346533083Rat
1354642Despr15Despair related QTL 150.0027locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)20124164241Rat
1558640Prcs2Prostate cancer susceptibility QTL 23.3prostate integrity trait (VT:0010571)percentage of study population developing ventral prostate tumorous lesions during a period of time (CMO:0000943)20134066551Rat
1331772Cdexp2CD45RC expression in CD8 T cells QTL 25.7CD8-positive T cell quantity (VT:0008077)blood CD45RC(high) CD8 T cell count to CD45RC(low) CD8 T cell count ratio (CMO:0001990)20362632310078622Rat
8694189Bw153Body weight QTL 1533.130.001body mass (VT:0001259)body weight gain (CMO:0000420)20129193376Rat
70154Insul2Insulin level QTL 23.75blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)2016693431Rat
4889857Pur27Proteinuria QTL 2712.20.001urine total protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)20127341128Rat
1300152Bp195Blood pressure QTL 1953.46arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)2036263239244918Rat
9590109Sffal8Serum free fatty acids level QTL 85.320.01blood free fatty acid amount (VT:0001553)plasma free fatty acids level (CMO:0000546)20129193376Rat
9589155Insul32Insulin level QTL 326.380.001blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)20129193376Rat
9590275Scort15Serum corticosterone level QTL 153.480.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)20129193376Rat
7411650Foco23Food consumption QTL 2320.70.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)20129193376Rat
61432Cia1Collagen induced arthritis QTL 1joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)20114100378Rat
2317851Alcrsp22Alcohol response QTL 223.20.05response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)20127341128Rat
1641893Alcrsp7Alcohol response QTL 7response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)20127341128Rat
6893685Bw111Body weight QTL 1112.70.004body mass (VT:0001259)body weight (CMO:0000012)20132578510Rat
9590252Scort12Serum corticosterone level QTL 1220.460.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)20136600300Rat

Markers in Region
RH128323  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2203,993,011 - 3,993,203 (-)MAPPERmRatBN7.2
Rnor_6.0204,519,515 - 4,519,706NCBIRnor6.0
Rnor_5.0206,599,314 - 6,599,505UniSTSRnor5.0
RGSC_v3.4204,093,403 - 4,093,594UniSTSRGSC3.4
Celera204,037,499 - 4,037,690UniSTS
RH 3.4 Map2052.5UniSTS
Cytogenetic Map20p12UniSTS


Expression

RNA-SEQ Expression

alimentary part of gastrointestinal system
appendage
circulatory system
ectoderm
endocrine system
endoderm
exocrine system
hemolymphoid system
hepatobiliary system
integumental system
mesenchyme
mesoderm
musculoskeletal system
nervous system
renal system
reproductive system
respiratory system
sensory system
visual system
16 12 67 162 91 90 59 92 59 6 356 192 11 141 81 92 31 17 17

Sequence


Ensembl Acc Id: ENSRNOT00000000483   ⟹   ENSRNOP00000000483
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl203,997,955 - 4,000,037 (-)Ensembl
mRatBN7.2 Ensembl203,993,327 - 3,995,494 (-)Ensembl
Rnor_6.0 Ensembl204,517,307 - 4,519,389 (+)Ensembl
Ensembl Acc Id: ENSRNOT00000096572   ⟹   ENSRNOP00000092315
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl203,997,955 - 3,999,735 (-)Ensembl
mRatBN7.2 Ensembl203,993,327 - 3,995,109 (-)Ensembl
RefSeq Acc Id: NM_212497   ⟹   NP_997662
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8203,997,953 - 4,000,037 (-)NCBI
mRatBN7.2203,993,327 - 3,995,411 (-)NCBI
Rnor_6.0204,517,307 - 4,519,391 (+)NCBI
Rnor_5.0206,597,106 - 6,599,190 (+)NCBI
RGSC_v3.4204,093,718 - 4,095,802 (-)RGD
Celera204,035,291 - 4,037,375 (+)RGD
Sequence:
RefSeq Acc Id: XM_039098809   ⟹   XP_038954737
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8203,998,437 - 4,000,115 (-)NCBI
mRatBN7.2203,993,811 - 3,995,484 (-)NCBI
RefSeq Acc Id: NP_997662   ⟸   NM_212497
- UniProtKB: Q6MG77 (UniProtKB/Swiss-Prot),   A6KTK3 (UniProtKB/TrEMBL),   A6KTK4 (UniProtKB/TrEMBL)
- Sequence:
Ensembl Acc Id: ENSRNOP00000000483   ⟸   ENSRNOT00000000483
RefSeq Acc Id: XP_038954737   ⟸   XM_039098809
- Peptide Label: isoform X1
- UniProtKB: A6KTK5 (UniProtKB/TrEMBL)
Ensembl Acc Id: ENSRNOP00000092315   ⟸   ENSRNOT00000096572
Protein Domains
RAI1-like

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-Q6MG77-F1-model_v2 AlphaFold Q6MG77 1-397 view protein structure

Transcriptome

eQTL   View at Phenogen
WGCNA   View at Phenogen
Tissue/Strain Expression   View at Phenogen

Promoters
RGD ID:13701353
Promoter ID:EPDNEW_R11876
Type:initiation region
Name:Dxo_1
Description:decapping exoribonuclease
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Single-end sequencing.
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0204,517,245 - 4,517,305EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1303267 AgrOrtholog
BioCyc Gene G2FUF-4599 BioCyc
Ensembl Genes ENSRNOG00000000422 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript ENSRNOT00000000483 ENTREZGENE
  ENSRNOT00000000483.5 UniProtKB/Swiss-Prot
IMAGE_CLONE IMAGE:7133445 IMAGE-MGC_LOAD
InterPro RAI1 UniProtKB/Swiss-Prot
  RAI1-like_fam UniProtKB/Swiss-Prot
KEGG Report rno:361799 UniProtKB/Swiss-Prot
MGC_CLONE MGC:95256 IMAGE-MGC_LOAD
NCBI Gene 361799 ENTREZGENE
PANTHER DECAPPING AND EXORIBONUCLEASE PROTEIN UniProtKB/Swiss-Prot
  PTHR12395 UniProtKB/Swiss-Prot
Pfam RAI1 UniProtKB/Swiss-Prot
PhenoGen Dxo PhenoGen
RatGTEx ENSRNOG00000000422 RatGTEx
UniProt A0A8I6AGB1_RAT UniProtKB/TrEMBL
  A6KTK3 ENTREZGENE, UniProtKB/TrEMBL
  A6KTK4 ENTREZGENE, UniProtKB/TrEMBL
  A6KTK5 ENTREZGENE, UniProtKB/TrEMBL
  DXO_RAT UniProtKB/Swiss-Prot, ENTREZGENE


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2013-09-18 Dxo  decapping exoribonuclease  Dom3z  DOM-3 homolog Z (C. elegans)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2006-03-30 Dom3z  DOM-3 homolog Z (C. elegans)    DOM-3 homolog Z  Name updated 1299863 APPROVED
2005-09-30 Dom3z        Symbol and Name status set to provisional 70820 PROVISIONAL