Xrn1 (5'-3' exoribonuclease 1) - Rat Genome Database

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Gene: Xrn1 (5'-3' exoribonuclease 1) Rattus norvegicus
Analyze
Symbol: Xrn1
Name: 5'-3' exoribonuclease 1
RGD ID: 1309713
Description: Predicted to enable 5'-3' RNA exonuclease activity and nucleic acid binding activity. Involved in several processes, including cellular response to cycloheximide; cellular response to puromycin; and response to testosterone. Located in P-body; dendrite; and neuronal cell body. Human ortholog(s) of this gene implicated in Alzheimer's disease. Orthologous to human XRN1 (5'-3' exoribonuclease 1); PARTICIPATES IN ribosome biogenesis pathway; RNA degradation pathway; INTERACTS WITH 17alpha-ethynylestradiol; 2,3,7,8-tetrachlorodibenzodioxine; 3,4-methylenedioxymethamphetamine.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: 5'-3' exoribonuclease 1-like; LOC100911537; LOC300944; RGD1309713; similar to 5-3 exonuclease
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr88105,407,785 - 105,516,967 (+)NCBIGRCr8
mRatBN7.2896,527,871 - 96,637,385 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl896,528,195 - 96,632,739 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx8102,194,582 - 102,298,640 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.08100,393,834 - 100,497,894 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0898,232,779 - 98,336,841 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.08103,774,125 - 103,883,563 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl8103,774,358 - 103,878,899 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.08103,224,942 - 103,334,089 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.48101,018,972 - 101,124,770 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera895,973,269 - 96,077,718 (+)NCBICelera
Cytogenetic Map8q31NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component
cytoplasm  (ISO)
cytosol  (IEA,ISO)
dendrite  (IDA)
neuronal cell body  (IDA)
nucleus  (IBA)
P-body  (IDA,ISO)
plasma membrane  (IEA,ISO)

Molecular Function

Molecular Pathway Annotations     Click to see Annotation Detail View
References

References - curated
# Reference Title Reference Citation
1. A dual yet opposite growth-regulating function of miR-204 and its target XRN1 in prostate adenocarcinoma cells and neuroendocrine-like prostate cancer cells. Ding M, etal., Oncotarget. 2015 Apr 10;6(10):7686-700.
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. Synaptic control of mRNA translation by reversible assembly of XRN1 bodies. Luchelli L, etal., J Cell Sci. 2015 Apr 15;128(8):1542-54. doi: 10.1242/jcs.163295. Epub 2015 Mar 3.
4. Rat ISS GO annotations from MGI mouse gene data--August 2006 MGD data from the GO Consortium
5. KEGG Annotation Import Pipeline Pipeline to import KEGG annotations from KEGG into RGD
6. GOA pipeline RGD automated data pipeline
7. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
8. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
9. Comprehensive gene review and curation RGD comprehensive gene curation
10. Beta-amyloid toxicity modifier genes and the risk of Alzheimer's disease. Rosenthal SL, etal., Am J Neurodegener Dis. 2012;1(2):191-8.
11. A monoclonal antibody against p53 cross-reacts with processing bodies. Thomas MG, etal., PLoS One. 2012;7(5):e36447. doi: 10.1371/journal.pone.0036447. Epub 2012 May 10.
12. Genome wide association study of SNP-, gene-, and pathway-based approaches to identify genes influencing susceptibility to Staphylococcus aureus infections. Ye Z, etal., Front Genet. 2014 May 9;5:125. doi: 10.3389/fgene.2014.00125. eCollection 2014.
Additional References at PubMed
PMID:9049243   PMID:17545563   PMID:18172165   PMID:18625844   PMID:19946888   PMID:20368444   PMID:22658674   PMID:22681889   PMID:26950371  


Genomics

Comparative Map Data
Xrn1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr88105,407,785 - 105,516,967 (+)NCBIGRCr8
mRatBN7.2896,527,871 - 96,637,385 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl896,528,195 - 96,632,739 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx8102,194,582 - 102,298,640 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.08100,393,834 - 100,497,894 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0898,232,779 - 98,336,841 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.08103,774,125 - 103,883,563 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl8103,774,358 - 103,878,899 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.08103,224,942 - 103,334,089 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.48101,018,972 - 101,124,770 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera895,973,269 - 96,077,718 (+)NCBICelera
Cytogenetic Map8q31NCBI
XRN1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh383142,306,610 - 142,448,037 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl3142,306,607 - 142,448,062 (-)EnsemblGRCh38hg38GRCh38
GRCh373142,025,452 - 142,166,879 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 363143,508,139 - 143,649,543 (-)NCBINCBI36Build 36hg18NCBI36
Build 343143,508,149 - 143,649,551NCBI
Celera3140,448,929 - 140,590,249 (-)NCBICelera
Cytogenetic Map3q23NCBI
HuRef3139,398,527 - 139,539,986 (-)NCBIHuRef
CHM1_13141,988,482 - 142,129,875 (-)NCBICHM1_1
T2T-CHM13v2.03145,053,903 - 145,195,321 (-)NCBIT2T-CHM13v2.0
Xrn1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39995,836,803 - 95,939,859 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl995,836,813 - 95,939,856 (+)EnsemblGRCm39 Ensembl
GRCm38995,954,750 - 96,057,806 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl995,954,760 - 96,057,803 (+)EnsemblGRCm38mm10GRCm38
MGSCv37995,855,179 - 95,953,453 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv36995,764,221 - 95,861,980 (+)NCBIMGSCv36mm8
Celera995,521,247 - 95,619,349 (+)NCBICelera
Cytogenetic Map9E3.3NCBI
Xrn1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049555083,441,683 - 3,561,805 (+)EnsemblChiLan1.0
ChiLan1.0NW_0049555083,441,540 - 3,561,896 (+)NCBIChiLan1.0ChiLan1.0
XRN1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v22140,215,062 - 140,359,614 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan13140,219,799 - 140,364,357 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v03139,337,337 - 139,481,479 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.13146,930,988 - 147,073,827 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl3146,930,988 - 147,073,827 (-)Ensemblpanpan1.1panPan2
XRN1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.12338,031,633 - 38,131,413 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl2338,032,841 - 38,131,293 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha2338,020,211 - 38,058,721 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.02338,560,332 - 38,663,551 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl2338,564,712 - 38,663,541 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.12338,242,400 - 38,345,593 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.02338,319,385 - 38,422,540 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.02338,563,654 - 38,666,694 (-)NCBIUU_Cfam_GSD_1.0
Xrn1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440560277,219,073 - 77,333,675 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049365403,963,387 - 4,073,322 (-)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_0049365403,959,156 - 4,073,785 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
XRN1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1383,065,957 - 83,174,477 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11383,063,810 - 83,174,497 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21390,871,657 - 90,977,467 (-)NCBISscrofa10.2Sscrofa10.2susScr3
XRN1
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11548,174,262 - 48,310,527 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl1548,174,316 - 48,305,641 (+)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366604121,109,515 - 21,245,814 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Xrn1
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_00462473018,907,959 - 19,020,724 (-)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_00462473018,903,506 - 19,021,392 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Xrn1
318 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:187
Count of miRNA genes:132
Interacting mature miRNAs:145
Transcripts:ENSRNOT00000014481, ENSRNOT00000074705
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 (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
12879878Bw183Body weight QTL 1830.001body mass (VT:0001259)body weight (CMO:0000012)84329616998968765Rat
1300177Cm2Cardiac mass QTL 23.65heart mass (VT:0007028)heart weight (CMO:0000017)854259986100382532Rat
1549909Stresp11Stress response QTL 116.830.0019stress-related behavior trait (VT:0010451)number of approaches toward negative stimulus before onset of defensive burying response (CMO:0001960)873473045118473045Rat
12879879Cm99Cardiac mass QTL 990.001heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)84329616998968765Rat
1554321Bmd3Bone mineral density QTL 37.90.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)840952565123900184Rat
9590292Uminl3Urine mineral level QTL 33.620.001urine mineral amount (VT:0015086)urine electrolyte level (CMO:0000593)871888757116888757Rat
1578769Uae31Urinary albumin excretion QTL 313.30.001urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)830848154101699754Rat
12879880Cm100Cardiac mass QTL 1000.001heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)84329616998968765Rat
12879881Cm101Cardiac mass QTL 1010.001heart right ventricle mass (VT:0007033)heart right ventricle weight to body weight ratio (CMO:0000914)84329616998968765Rat
12879882Am8Aortic mass QTL 80.001aorta mass (VT:0002845)aorta weight to aorta length to body weight ratio (CMO:0002722)84329616998968765Rat
12879883Kidm65Kidney mass QTL 650.001kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)84329616998968765Rat
738011Anxrr9Anxiety related response QTL 96.1exploratory behavior trait (VT:0010471)number of entries into a discrete space in an experimental apparatus (CMO:0000960)893535351123900184Rat
8693654Alc32Alcohol consumption QTL 3220.755drinking behavior trait (VT:0001422)calculated ethanol drink intake rate (CMO:0001615)888612425107550209Rat
1358912Bw51Body weight QTL 512.95body mass (VT:0001259)body weight (CMO:0000012)851351728107062046Rat
1578765Klgr1Kidney lesion grade QTL 13.30.0001kidney morphology trait (VT:0002135)organ lesion measurement (CMO:0000677)830848154101699754Rat
738014Anxrr15Anxiety related response QTL 153.60.005locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)895718998123900184Rat
1300171Bp184Blood pressure QTL 1843.66arterial blood pressure trait (VT:2000000)blood pressure time series experimental set point of the baroreceptor response (CMO:0002593)870513503118219066Rat
1578755Pur5Proteinuria QTL 53.30.0001urine total protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)830848154101699754Rat
2313400Anxrr25Anxiety related response QTL 25aggression-related behavior trait (VT:0015014)tameness/aggressiveness composite score (CMO:0002136)889265192114019816Rat
2303171Bp331Blood pressure QTL 3315.570.005arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)861290298119084929Rat
8662823Vetf5Vascular elastic tissue fragility QTL 51.9artery integrity trait (VT:0010639)patent ductus arteriosus score (CMO:0002566)82824291299525068Rat
2293697Bmd39Bone mineral density QTL 39femur strength trait (VT:0010010)femur total energy absorbed before break (CMO:0001677)85404374498968765Rat
631210Bw3Body weight QTL35.9mesenteric fat pad mass (VT:0010427)mesenteric fat pad weight to body weight ratio (CMO:0000654)869349194112783834Rat
1358903Bp252Blood pressure QTL 25270.0001arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)893965141123900184Rat
1358896Bp262Blood pressure QTL 2622.89arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)82720571599103503Rat
1331837Bw23Body weight QTL 234.190.00007body mass (VT:0001259)body weight (CMO:0000012)84653172299083736Rat
1331838Niddm61Non-insulin dependent diabetes mellitus QTL 613.530.0004blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)83646953599083736Rat
8694446Bw170Body weight QTL 17012.070.001retroperitoneal fat pad mass (VT:0010430)retroperitoneal fat pad weight to body weight ratio (CMO:0000635)871888757116888757Rat
631650Stl6Serum triglyceride level QTL 640.0019blood triglyceride amount (VT:0002644)plasma triglyceride level (CMO:0000548)810378157112202585Rat
631653Bp125Blood pressure QTL 1253.3arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)866142385111142385Rat
1581557Eae16Experimental allergic encephalomyelitis QTL 163.8nervous system integrity trait (VT:0010566)experimental autoimmune encephalomyelitis incidence/prevalence measurement (CMO:0001046)88462195110921472Rat
1358907Cm40Cardiac mass QTL 401.89heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)82720571599103503Rat
70197BpQTLcluster8Blood pressure QTL cluster 83.482arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)846531639119088626Rat
2316950Scl66Serum cholesterol level QTL 664.1blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)830848259105647037Rat
2300182Bmd56Bone mineral density QTL 565.4femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)895718998123900184Rat
2300181Bmd55Bone mineral density QTL 555.70.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)876468691121468691Rat
10402857Bp380Blood pressure QTL 3800.95arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)85396876598968765Rat
1358892Kidm26Kidney mass QTL 263.69kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)82720571599103503Rat
2301402Bp316Blood pressure QTL 3160.005arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)85396876598968765Rat
631664Hcar3Hepatocarcinoma resistance QTL 32.90.0005liver integrity trait (VT:0010547)volume of individual liver tumorous lesion (CMO:0001078)85423764499103503Rat
1358893Bp263Blood pressure QTL 2635.01arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)893965141123900184Rat
8694200Abfw4Abdominal fat weight QTL 49.070.001visceral adipose mass (VT:0010063)abdominal fat pad weight to body weight ratio (CMO:0000095)871888757116888757Rat
8694392Bw161Body weight QTL 1618.060.001body lean mass (VT:0010483)lean tissue morphological measurement (CMO:0002184)871888757116888757Rat
61437Cia6Collagen induced arthritis QTL 6joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)882460758122812818Rat

Markers in Region
RH133436  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2896,632,348 - 96,632,540 (+)MAPPERmRatBN7.2
Rnor_6.08103,878,527 - 103,878,718NCBIRnor6.0
Rnor_5.08103,329,053 - 103,329,244UniSTSRnor5.0
RGSC_v3.48101,124,199 - 101,124,390UniSTSRGSC3.4
Celera896,077,315 - 96,077,506UniSTS
RH 3.4 Map81052.7UniSTS
Cytogenetic Map8q31UniSTS


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
nervous system
renal system
reproductive system
respiratory system
9 11 49 113 91 90 59 25 59 6 218 97 93 45 60 31

Sequence

Nucleotide Sequences
RefSeq Transcripts NM_001305240 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006243594 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006243596 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006243598 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006243599 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008766573 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017595581 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039081170 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039081171 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039081172 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039081173 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_063265209 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_063265210 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_063265211 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_063265212 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_217233 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XR_010053953 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XR_594087 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide CH473954 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ225473 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  JAXUCZ010000008 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Ensembl Acc Id: ENSRNOT00000014481   ⟹   ENSRNOP00000014481
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl896,528,195 - 96,632,739 (+)Ensembl
Rnor_6.0 Ensembl8103,774,358 - 103,878,899 (+)Ensembl
Ensembl Acc Id: ENSRNOT00000102470   ⟹   ENSRNOP00000077966
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl896,528,292 - 96,584,614 (+)Ensembl
RefSeq Acc Id: NM_001305240   ⟹   NP_001292169
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr88105,407,785 - 105,512,334 (+)NCBI
mRatBN7.2896,528,195 - 96,632,752 (+)NCBI
Rnor_6.08103,774,378 - 103,878,930 (+)NCBI
Celera895,973,269 - 96,077,718 (+)NCBI
Sequence:
RefSeq Acc Id: XM_006243594   ⟹   XP_006243656
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr88105,407,863 - 105,516,967 (+)NCBI
mRatBN7.2896,527,875 - 96,637,385 (+)NCBI
Rnor_6.08103,774,127 - 103,883,563 (+)NCBI
Rnor_5.08103,224,942 - 103,334,089 (+)NCBI
Sequence:
RefSeq Acc Id: XM_006243596   ⟹   XP_006243658
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr88105,407,863 - 105,516,967 (+)NCBI
mRatBN7.2896,527,871 - 96,637,385 (+)NCBI
Rnor_6.08103,774,126 - 103,883,563 (+)NCBI
Rnor_5.08103,224,942 - 103,334,089 (+)NCBI
Sequence:
RefSeq Acc Id: XM_006243598   ⟹   XP_006243660
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr88105,407,863 - 105,516,967 (+)NCBI
mRatBN7.2896,527,873 - 96,637,385 (+)NCBI
Rnor_6.08103,774,127 - 103,883,563 (+)NCBI
Rnor_5.08103,224,942 - 103,334,089 (+)NCBI
Sequence:
RefSeq Acc Id: XM_008766573   ⟹   XP_008764795
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr88105,407,863 - 105,459,010 (+)NCBI
mRatBN7.2896,527,874 - 96,579,513 (+)NCBI
Rnor_6.08103,774,384 - 103,825,662 (+)NCBI
Sequence:
RefSeq Acc Id: XM_039081170   ⟹   XP_038937098
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr88105,407,863 - 105,516,967 (+)NCBI
mRatBN7.2896,527,873 - 96,637,385 (+)NCBI
RefSeq Acc Id: XM_039081171   ⟹   XP_038937099
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr88105,407,863 - 105,516,967 (+)NCBI
mRatBN7.2896,527,875 - 96,637,385 (+)NCBI
RefSeq Acc Id: XM_039081172   ⟹   XP_038937100
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr88105,407,863 - 105,485,552 (+)NCBI
mRatBN7.2896,527,872 - 96,605,961 (+)NCBI
RefSeq Acc Id: XM_039081173   ⟹   XP_038937101
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr88105,436,854 - 105,516,967 (+)NCBI
mRatBN7.2896,557,267 - 96,637,385 (+)NCBI
RefSeq Acc Id: XM_063265209   ⟹   XP_063121279
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr88105,407,863 - 105,516,967 (+)NCBI
RefSeq Acc Id: XM_063265210   ⟹   XP_063121280
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr88105,407,863 - 105,516,967 (+)NCBI
RefSeq Acc Id: XM_063265211   ⟹   XP_063121281
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr88105,422,079 - 105,516,967 (+)NCBI
RefSeq Acc Id: XM_063265212   ⟹   XP_063121282
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr88105,407,863 - 105,459,010 (+)NCBI
RefSeq Acc Id: XM_217233   ⟹   XP_217233
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr88105,407,863 - 105,516,967 (+)NCBI
mRatBN7.2896,527,879 - 96,637,385 (+)NCBI
Rnor_6.08103,774,127 - 103,883,563 (+)NCBI
Rnor_5.08103,224,942 - 103,334,089 (+)NCBI
RGSC_v3.48101,018,972 - 101,124,770 (+)RGD
Sequence:
RefSeq Acc Id: XR_010053953
Type: NON-CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr88105,407,863 - 105,440,738 (+)NCBI
RefSeq Acc Id: XP_217233   ⟸   XM_217233
- Peptide Label: isoform X4
- UniProtKB: D4ABN8 (UniProtKB/TrEMBL),   A6I270 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006243656   ⟸   XM_006243594
- Peptide Label: isoform X1
- UniProtKB: A6I270 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006243658   ⟸   XM_006243596
- Peptide Label: isoform X3
- UniProtKB: A6I270 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006243660   ⟸   XM_006243598
- Peptide Label: isoform X6
- UniProtKB: A6I270 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_008764795   ⟸   XM_008766573
- Peptide Label: isoform X12
- UniProtKB: A0A8I5XWP1 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: NP_001292169   ⟸   NM_001305240
- UniProtKB: A6I270 (UniProtKB/TrEMBL)
- Sequence:
Ensembl Acc Id: ENSRNOP00000014481   ⟸   ENSRNOT00000014481
RefSeq Acc Id: XP_038937100   ⟸   XM_039081172
- Peptide Label: isoform X10
RefSeq Acc Id: XP_038937098   ⟸   XM_039081170
- Peptide Label: isoform X2
- UniProtKB: A6I270 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_038937099   ⟸   XM_039081171
- Peptide Label: isoform X7
- UniProtKB: A6I270 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_038937101   ⟸   XM_039081173
- Peptide Label: isoform X11
Ensembl Acc Id: ENSRNOP00000077966   ⟸   ENSRNOT00000102470
RefSeq Acc Id: XP_063121280   ⟸   XM_063265210
- Peptide Label: isoform X8
- UniProtKB: A6I270 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_063121279   ⟸   XM_063265209
- Peptide Label: isoform X5
- UniProtKB: A6I270 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_063121282   ⟸   XM_063265212
- Peptide Label: isoform X13
RefSeq Acc Id: XP_063121281   ⟸   XM_063265211
- Peptide Label: isoform X9
- UniProtKB: A6I270 (UniProtKB/TrEMBL)
Protein Domains
5'-3' exoribonuclease 1 D1   5'-3' exoribonuclease 1 SH3-like   Exoribonuclease Xrn1 D2/D3   Xrn1 helical   Xrn1 N-terminal

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-D4ABN8-F1-model_v2 AlphaFold D4ABN8 1-1723 view protein structure

Transcriptome

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

Promoters
RGD ID:13696189
Promoter ID:EPDNEW_R6714
Type:initiation region
Name:Xrn1_1
Description:5'-3' exoribonuclease 1
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_6.08103,774,421 - 103,774,481EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1309713 AgrOrtholog
BioCyc Gene G2FUF-29468 BioCyc
Ensembl Genes ENSRNOG00000042951 Ensembl, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000014481.9 UniProtKB/TrEMBL
  ENSRNOT00000102470.1 UniProtKB/TrEMBL
Gene3D-CATH 1.25.40.1050 UniProtKB/TrEMBL
  2.170.260.40 UniProtKB/TrEMBL
  2.30.30.750 UniProtKB/TrEMBL
  3.40.50.12390 UniProtKB/TrEMBL
InterPro 5_3_exoribonuclease UniProtKB/TrEMBL
  5_3_exoribonuclease_1 UniProtKB/TrEMBL
  Put_53exo UniProtKB/TrEMBL
  SH3_12 UniProtKB/TrEMBL
  XRN1_D1 UniProtKB/TrEMBL
  XRN1_D1_sf UniProtKB/TrEMBL
  XRN1_D2_D3 UniProtKB/TrEMBL
  Xrn1_helical UniProtKB/TrEMBL
  XRN1_SH3_sf UniProtKB/TrEMBL
NCBI Gene 300944 ENTREZGENE
PANTHER 5'-3' EXORIBONUCLEASE 1 UniProtKB/TrEMBL
  PTHR12341 UniProtKB/TrEMBL
Pfam SH3_12 UniProtKB/TrEMBL
  XRN1_D1 UniProtKB/TrEMBL
  XRN1_D2_D3 UniProtKB/TrEMBL
  XRN_M UniProtKB/TrEMBL
  XRN_N UniProtKB/TrEMBL
PhenoGen Xrn1 PhenoGen
PIRSF Exonuclease_Xnr1 UniProtKB/TrEMBL
RatGTEx ENSRNOG00000042951 RatGTEx
Superfamily-SCOP dsRNA-binding domain-like UniProtKB/TrEMBL
UniProt A0A8I5XWP1 ENTREZGENE, UniProtKB/TrEMBL
  A6I270 ENTREZGENE, UniProtKB/TrEMBL
  D4ABN8 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2021-03-09 Xrn1  5'-3' exoribonuclease 1  LOC100911537  5'-3' exoribonuclease 1-like  Data merged from RGD:6492433 737654 PROVISIONAL
2012-07-05 LOC100911537  5'-3' exoribonuclease 1-like      Symbol and Name status set to provisional 70820 PROVISIONAL
2008-04-30 Xrn1  5'-3' exoribonuclease 1   Xrn1_predicted  5'-3' exoribonuclease 1 (predicted)  'predicted' is removed 2292626 APPROVED
2006-03-30 Xrn1_predicted  5'-3' exoribonuclease 1 (predicted)  RGD1309713_predicted  similar to 5-3 exonuclease (predicted)  Symbol and Name updated 1299863 APPROVED
2005-01-20 RGD1309713_predicted  similar to 5-3 exonuclease (predicted)  LOC300944_predicted    Symbol and Name status set to approved 1331353 APPROVED
2005-01-12 LOC300944_predicted  similar to 5-3 exonuclease (predicted)      Symbol and Name status set to provisional 70820 PROVISIONAL