Rexo4 (REX4 homolog, 3'-5' exonuclease) - Rat Genome Database

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Gene: Rexo4 (REX4 homolog, 3'-5' exonuclease) Rattus norvegicus
Analyze
Symbol: Rexo4
Name: REX4 homolog, 3'-5' exonuclease
RGD ID: 1306220
Description: Predicted to enable DNA binding activity and nuclease activity. Predicted to be involved in DNA catabolic process; DNA repair; and RNA processing. Predicted to be located in nuclear speck and nucleolus. Predicted to be active in nucleus. Orthologous to human REXO4 (REX4 homolog, 3'-5' exonuclease); INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; 2,4-dinitrotoluene; 2,6-dinitrotoluene.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: LOC311826; REX4, RNA exonuclease 4 homolog; REX4, RNA exonuclease 4 homolog (S. cerevisiae); RNA exonuclease 4; XPMC2 prevents mitotic catastrophe 2 homolog; XPMC2 prevents mitotic catastrophe 2 homolog (Xenopus laevis); Xpmc2h
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
GRCr8330,678,729 - 30,692,376 (-)NCBIGRCr8
mRatBN7.2310,280,654 - 10,291,003 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl310,280,654 - 10,290,996 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx313,340,652 - 13,350,990 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0321,926,053 - 21,936,391 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0320,181,354 - 20,191,692 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.035,500,578 - 5,510,908 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl35,500,589 - 5,510,908 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0310,862,783 - 10,873,113 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.435,849,494 - 5,859,824 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.135,849,797 - 5,865,854 (-)NCBI
Celera35,078,684 - 5,089,014 (-)NCBICelera
Cytogenetic Map3p13-p12NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component
nuclear speck  (IEA,ISO)
nucleolus  (IEA,ISO)
nucleoplasm  (ISO)
nucleus  (IBA)

Molecular Function

References

References - curated
# Reference Title Reference Citation
1. 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.
2. Rat ISS GO annotations from GOA human gene data--August 2006 GOA data from the GO Consortium
3. GOA pipeline RGD automated data pipeline
4. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
5. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:8889548   PMID:12477932   PMID:21602889   PMID:22658674   PMID:22681889  


Genomics

Comparative Map Data
Rexo4
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8330,678,729 - 30,692,376 (-)NCBIGRCr8
mRatBN7.2310,280,654 - 10,291,003 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl310,280,654 - 10,290,996 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx313,340,652 - 13,350,990 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0321,926,053 - 21,936,391 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0320,181,354 - 20,191,692 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.035,500,578 - 5,510,908 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl35,500,589 - 5,510,908 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0310,862,783 - 10,873,113 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.435,849,494 - 5,859,824 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.135,849,797 - 5,865,854 (-)NCBI
Celera35,078,684 - 5,089,014 (-)NCBICelera
Cytogenetic Map3p13-p12NCBI
REXO4
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh389133,406,058 - 133,418,172 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl9133,406,059 - 133,418,096 (-)EnsemblGRCh38hg38GRCh38
GRCh379136,271,182 - 136,283,292 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 369135,261,007 - 135,272,985 (-)NCBINCBI36Build 36hg18NCBI36
Build 349133,300,741 - 133,312,718NCBI
Celera9106,821,755 - 106,833,737 (-)NCBICelera
Cytogenetic Map9q34.2NCBI
HuRef9105,773,009 - 105,785,123 (-)NCBIHuRef
CHM1_19136,421,689 - 136,433,799 (-)NCBICHM1_1
T2T-CHM13v2.09145,620,490 - 145,632,600 (-)NCBIT2T-CHM13v2.0
Rexo4
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39226,843,575 - 26,854,398 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl226,843,575 - 26,854,398 (-)EnsemblGRCm39 Ensembl
GRCm38226,953,559 - 26,964,386 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl226,953,563 - 26,964,386 (-)EnsemblGRCm38mm10GRCm38
MGSCv37226,809,083 - 26,819,906 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv36226,775,572 - 26,786,395 (-)NCBIMGSCv36mm8
Celera226,663,308 - 26,673,885 (-)NCBICelera
Cytogenetic Map2A3NCBI
cM Map219.13NCBI
Rexo4
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049555132,745,842 - 2,752,792 (-)EnsemblChiLan1.0
ChiLan1.0NW_0049555132,745,220 - 2,754,927 (-)NCBIChiLan1.0ChiLan1.0
REXO4
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v2115,935,794 - 5,947,747 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan195,938,115 - 5,950,083 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v09104,528,838 - 104,540,813 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.19133,140,392 - 133,152,413 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl9133,140,392 - 133,152,413 (-)Ensemblpanpan1.1panPan2
REXO4
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1949,827,584 - 49,834,872 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl949,828,067 - 49,836,632 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha949,108,818 - 49,117,512 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0950,701,335 - 50,710,055 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl950,701,353 - 50,710,040 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1949,463,729 - 49,472,367 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0949,805,229 - 49,813,879 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0949,883,307 - 49,891,968 (-)NCBIUU_Cfam_GSD_1.0
Rexo4
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024404947199,870,382 - 199,894,211 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049366693,481,294 - 3,491,572 (+)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_0049366693,479,778 - 3,504,938 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
REXO4
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1273,011,734 - 273,021,938 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11273,011,736 - 273,021,956 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21306,985,545 - 306,995,759 (-)NCBISscrofa10.2Sscrofa10.2susScr3
REXO4
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1124,718,728 - 4,732,138 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl124,718,799 - 4,731,241 (+)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_023666058253,488 - 270,560 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Rexo4
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046247601,851,877 - 1,859,387 (-)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_0046247601,851,008 - 1,861,370 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Rexo4
20 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:160
Count of miRNA genes:120
Interacting mature miRNAs:147
Transcripts:ENSRNOT00000042289
Prediction methods:Miranda, 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
1358357Srcrtb1Stress Responsive Cort Basal QTL 16.360.002blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)3865816227494778Rat
4889966Bss95Bone structure and strength QTL 954.4tibia area (VT:1000281)tibia-fibula cross-sectional area (CMO:0001718)3136847613Rat
2292615Ept17Estrogen-induced pituitary tumorigenesis QTL 176.7pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)3653764510778823Rat
10401810Kidm53Kidney mass QTL 53kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)3822719447233430Rat
1298526Arunc3Aerobic running capacity QTL 32.2exercise endurance trait (VT:0002332)maximum distance run on treadmill (CMO:0001406)3822719433703538Rat
631545Bp85Blood pressure QTL 853.1arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)3133278763Rat
631679Cm10Cardiac mass QTL 107.340.0001heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)3131158234Rat
2290452Scl56Serum cholesterol level QTL 562.26blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)3191609953Rat
631568Bp92Blood pressure QTL 922.20.005arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)3139874793Rat
70203Gcr2Gastric cancer resistance QTL 22.6stomach morphology trait (VT:0000470)stomach tumor susceptibility score (CMO:0002043)3865816227494778Rat
70202Alc19Alcohol consumption QTL 192.5drinking behavior trait (VT:0001422)ethanol intake volume to total fluid intake volume ratio (CMO:0001591)3127494778Rat
2312664Scl62Serum cholesterol level QTL 620.05blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)3138710544Rat
61468Bp15Blood pressure QTL 154.4blood pressure trait (VT:0000183)pulse pressure (CMO:0000292)3133278763Rat
1358185Ept6Estrogen-induced pituitary tumorigenesis QTL 66.7pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)3653764510778823Rat
631831Alc8Alcohol consumption QTL 82.7consumption behavior trait (VT:0002069)calculated ethanol drink intake rate (CMO:0001615)3133230976Rat

Markers in Region
RH131162  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2310,280,916 - 10,281,115 (+)MAPPERmRatBN7.2
Rnor_6.035,500,841 - 5,501,039NCBIRnor6.0
Rnor_5.0310,863,046 - 10,863,244UniSTSRnor5.0
RGSC_v3.435,849,757 - 5,849,955UniSTSRGSC3.4
Celera35,078,947 - 5,079,145UniSTS
Cytogenetic Map3p12UniSTS
RH140467  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2310,283,214 - 10,283,368 (+)MAPPERmRatBN7.2
Rnor_6.035,503,139 - 5,503,292NCBIRnor6.0
Rnor_5.0310,865,344 - 10,865,497UniSTSRnor5.0
RGSC_v3.435,852,055 - 5,852,208UniSTSRGSC3.4
Celera35,081,245 - 5,081,398UniSTS
Cytogenetic Map3p12UniSTS


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


Ensembl Acc Id: ENSRNOT00000042289   ⟹   ENSRNOP00000043432
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl310,280,654 - 10,290,996 (-)Ensembl
Rnor_6.0 Ensembl35,500,589 - 5,510,908 (-)Ensembl
RefSeq Acc Id: NM_001033884   ⟹   NP_001029056
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8330,678,729 - 30,689,059 (-)NCBI
mRatBN7.2310,280,654 - 10,290,984 (-)NCBI
Rnor_6.035,500,578 - 5,510,908 (-)NCBI
Rnor_5.0310,862,783 - 10,873,113 (-)NCBI
RGSC_v3.435,849,494 - 5,859,824 (-)RGD
Celera35,078,684 - 5,089,014 (-)RGD
Sequence:
RefSeq Acc Id: XR_010064643
Type: NON-CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8330,681,611 - 30,692,376 (-)NCBI
Protein Sequences
Protein RefSeqs NP_001029056 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAI61820 (Get FASTA)   NCBI Sequence Viewer  
  EDL93449 (Get FASTA)   NCBI Sequence Viewer  
  EDL93450 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000043432.4
RefSeq Acc Id: NP_001029056   ⟸   NM_001033884
- UniProtKB: B1WBN4 (UniProtKB/TrEMBL),   F7ESM1 (UniProtKB/TrEMBL)
- Sequence:
Ensembl Acc Id: ENSRNOP00000043432   ⟸   ENSRNOT00000042289
Protein Domains
Exonuclease

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-B1WBN4-F1-model_v2 AlphaFold B1WBN4 1-409 view protein structure

Transcriptome

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

Promoters
RGD ID:13691919
Promoter ID:EPDNEW_R2444
Type:initiation region
Name:Rexo4_1
Description:REX4 homolog, 3'-5' exonuclease
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_6.035,510,862 - 5,510,922EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1306220 AgrOrtholog
BioCyc Gene G2FUF-50316 BioCyc
Ensembl Genes ENSRNOG00000027867 Ensembl, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000042289.6 UniProtKB/TrEMBL
Gene3D-CATH 3.30.420.10 UniProtKB/TrEMBL
IMAGE_CLONE IMAGE:9088929 IMAGE-MGC_LOAD
InterPro Exonuclease_RNaseT/DNA_pol3 UniProtKB/TrEMBL
  PolynucTfrase_RNaseH_fold UniProtKB/TrEMBL
  REX4_DEDDh_dom UniProtKB/TrEMBL
  REXO1/3/4-like UniProtKB/TrEMBL
  RNaseH_sf UniProtKB/TrEMBL
KEGG Report rno:311826 UniProtKB/TrEMBL
MGC_CLONE MGC:187273 IMAGE-MGC_LOAD
NCBI Gene 311826 ENTREZGENE
PANTHER RNA EXONUCLEASE 4 UniProtKB/TrEMBL
  RNA EXONUCLEASE REXO1 / RECO3 FAMILY MEMBER-RELATED UniProtKB/TrEMBL
Pfam Exonuc_X-T UniProtKB/TrEMBL
PhenoGen Rexo4 PhenoGen
RatGTEx ENSRNOG00000027867 RatGTEx
SMART EXOIII UniProtKB/TrEMBL
Superfamily-SCOP RNaseH_fold UniProtKB/TrEMBL
UniProt A6JTJ7_RAT UniProtKB/TrEMBL
  A6JTJ8_RAT UniProtKB/TrEMBL
  B1WBN4 ENTREZGENE, UniProtKB/TrEMBL
  F7ESM1 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2015-07-17 Rexo4  REX4 homolog, 3'-5' exonuclease  Rexo4  REX4, RNA exonuclease 4 homolog (S. cerevisiae)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2006-03-30 Rexo4  REX4, RNA exonuclease 4 homolog (S. cerevisiae)  Xpmc2h  XPMC2 prevents mitotic catastrophe 2 homolog (Xenopus laevis)  Symbol and Name updated 1299863 APPROVED
2005-12-06 Xpmc2h  XPMC2 prevents mitotic catastrophe 2 homolog (Xenopus laevis)  Xpmc2h_predicted  XPMC2 prevents mitotic catastrophe 2 homolog (Xenopus laevis) (predicted)  Symbol and Name updated 1559027 APPROVED
2005-01-12 Xpmc2h_predicted  XPMC2 prevents mitotic catastrophe 2 homolog (Xenopus laevis) (predicted)      Symbol and Name status set to approved 70820 APPROVED