Trex2 (three prime repair exonuclease 2) - Rat Genome Database

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Gene: Trex2 (three prime repair exonuclease 2) Rattus norvegicus
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Symbol: Trex2
Name: three prime repair exonuclease 2
RGD ID: 1562245
Description: Predicted to enable several functions, including 3'-5'-DNA exonuclease activity; magnesium ion binding activity; and protein homodimerization activity. Predicted to be involved in DNA catabolic process. Predicted to be located in nucleus. Predicted to be active in cytoplasm. Orthologous to human TREX2 (three prime repair exonuclease 2); INTERACTS WITH 6-propyl-2-thiouracil; bisphenol A; (+)-catechin (ortholog).
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: LOC309275; RGD1562245; similar to 3-5 exonuclease TREX2
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
GRCr8X156,303,203 - 156,304,811 (-)NCBIGRCr8GRCr8GRCr8
GRCr8 EnsemblX156,303,203 - 156,304,811 (-)EnsemblGRCr8
mRatBN7.2X151,151,862 - 151,153,470 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 EnsemblX151,151,864 - 151,153,479 (-)EnsemblmRatBN7.2
UTH_Rnor_SHR_UtxX153,293,024 - 153,294,632 (-)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0X156,856,235 - 156,857,843 (-)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0X154,528,068 - 154,529,676 (-)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0X157,374,305 - 157,375,913 (+)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 EnsemblX157,374,305 - 157,375,913 (+)Ensemblrn6Rnor6.0
Rnor_5.01153,122,389 - 153,123,997 (+)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.4X159,334,472 - 159,336,080 (-)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera1136,736,131 - 136,737,739 (+)NCBICelera
Cytogenetic MapXq37NCBI
JBrowse:




Disease Annotations     Click to see Annotation Detail View

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component
cytoplasm  (IBA)
nucleus  (IEA)

References

References - curated
# Reference Title Reference Citation
1. Differential gene expression pattern of diabetic rat retinas after intravitreal injection of erythropoietin. Chu Q, etal., Clin Experiment Ophthalmol. 2011 Mar;39(2):142-51. doi: 10.1111/j.1442-9071.2010.02437.x.
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
Additional References at PubMed
PMID:11279105  


Genomics

Comparative Map Data
Trex2
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8X156,303,203 - 156,304,811 (-)NCBIGRCr8GRCr8GRCr8
GRCr8 EnsemblX156,303,203 - 156,304,811 (-)EnsemblGRCr8
mRatBN7.2X151,151,862 - 151,153,470 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 EnsemblX151,151,864 - 151,153,479 (-)EnsemblmRatBN7.2
UTH_Rnor_SHR_UtxX153,293,024 - 153,294,632 (-)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0X156,856,235 - 156,857,843 (-)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0X154,528,068 - 154,529,676 (-)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0X157,374,305 - 157,375,913 (+)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 EnsemblX157,374,305 - 157,375,913 (+)Ensemblrn6Rnor6.0
Rnor_5.01153,122,389 - 153,123,997 (+)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.4X159,334,472 - 159,336,080 (-)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera1136,736,131 - 136,737,739 (+)NCBICelera
Cytogenetic MapXq37NCBI
TREX2
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38X153,444,473 - 153,446,056 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 EnsemblX153,444,473 - 153,470,587 (-)Ensemblhg38GRCh38
GRCh37X152,709,931 - 152,711,514 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36X152,363,372 - 152,365,139 (-)NCBIBuild 36Build 36hg18NCBI36
Build 34X152,231,024 - 152,231,735NCBI
CeleraX152,943,888 - 152,945,655 (-)NCBICelera
Cytogenetic MapXq28NCBI
HuRefX141,369,186 - 141,370,953 (-)NCBIHuRef
CHM1_1X152,584,603 - 152,586,370 (-)NCBICHM1_1
T2T-CHM13v2.0X151,718,056 - 151,719,639 (-)NCBIT2T-CHM13v2.0
Trex2
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39X72,477,311 - 72,478,949 (-)NCBIGRCm39GRCm39mm39
GRCm39 EnsemblX72,477,311 - 72,478,950 (-)EnsemblGRCm39 EnsemblGRCm39
GRCm38X73,433,705 - 73,435,343 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 EnsemblX73,433,705 - 73,435,344 (-)Ensemblmm10GRCm38
MGSCv37X70,679,044 - 70,680,682 (-)NCBIMGSCv37MGSCv37mm9NCBIm37
MGSCv36X69,686,425 - 69,688,050 (-)NCBIMGSCv36mm8
CeleraX64,687,545 - 64,689,183 (-)NCBICelera
Cytogenetic MapXA7.3NCBI
cM MapX37.31NCBI
Trex2
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_004955580207,903 - 209,426 (-)Ensembl
ChiLan1.0NW_004955580207,903 - 209,426 (-)NCBIChiLan1.0ChiLan1.0
TREX2
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v2X153,484,903 - 153,485,860 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan1X153,488,507 - 153,489,464 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v0X142,995,051 - 142,998,178 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.1X152,881,479 - 152,884,584 (-)NCBIPanPan1.1PanPan1.1panPan2
TREX2
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1X121,263,341 - 121,265,009 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 EnsemblX121,258,646 - 121,264,555 (-)EnsemblcanFam3CanFam3.1
Dog10K_Boxer_TashaX106,593,265 - 106,595,819 (-)NCBIDog10K_Boxer_TashaDog10K_Boxer_Tasha
Trex2
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2X118,580,535 - 118,584,104 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_004936809318,548 - 319,258 (-)EnsemblSpeTri2.0 Ensembl
SpeTri2.0NW_004936809317,655 - 319,293 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
TREX2
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 EnsemblX124,234,738 - 124,238,598 (-)EnsemblsusScr11Sscrofa11.1
Sscrofa11.1X124,234,736 - 124,244,193 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2X141,798,112 - 141,800,794 (-)NCBISscrofa10.2Sscrofa10.2susScr3
TREX2
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1X127,878,891 - 127,882,019 (-)NCBIChlSab1.1ChlSab1.1chlSab2
Vero_WHO_p1.0NW_02366606565,740,629 - 65,743,712 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Trex2
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_004624946187,056 - 210,497 (-)EnsemblHetGla_female_1.0 EnsemblhetGla2HetGla_female_1.0 Ensembl
HetGla 1.0NW_004624946187,147 - 188,805 (-)NCBIHetGla 1.0HetGla 1.0hetGla2
Trex2
(Rattus rattus - black rat)
Black Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rrattus_CSIRO_v1X129,056,510 - 129,058,093 (-)NCBIRrattus_CSIRO_v1

miRNA Target Status (No longer updated)

Predicted Target Of
Summary Value
Count of predictions:207
Count of miRNA genes:130
Interacting mature miRNAs:145
Transcripts:ENSRNOT00000023245
Prediction methods:Microtar, Miranda, Rnahybrid
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
738025Stresp3Stress response QTL 34.610.0066stress-related behavior trait (VT:0010451)defensive burying - approachX105359969157758123Rat
10059603Bw174Body weight QTL 1743.40.025body mass (VT:0001259)body weight (CMO:0000012)X118973754157758123Rat

Markers in Region
BF418169  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2X151,151,971 - 151,152,065 (-)MAPPERmRatBN7.2
Rnor_6.0X157,375,710 - 157,375,803NCBIRnor6.0
Rnor_5.01153,123,794 - 153,123,887UniSTSRnor5.0
RGSC_v3.4X159,334,582 - 159,334,675UniSTSRGSC3.4
Celera1136,737,536 - 136,737,629UniSTS
Cytogenetic MapXq37UniSTS


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
9 3 27 62 38 42 21 39 21 6 140 74 1 50 33 72 21 1 1

Sequence


Ensembl Acc Id: ENSRNOT00000081973   ⟹   ENSRNOP00000075461
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 EnsemblX156,303,203 - 156,304,811 (-)Ensembl
mRatBN7.2 EnsemblX151,151,864 - 151,153,479 (-)Ensembl
Rnor_6.0 EnsemblX157,374,305 - 157,375,913 (+)Ensembl
RefSeq Acc Id: NM_001107580   ⟹   NP_001101050
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8X156,303,203 - 156,304,811 (-)NCBI
mRatBN7.2X151,151,862 - 151,153,470 (-)NCBI
Rnor_6.0X157,374,305 - 157,375,913 (+)NCBI
Rnor_5.01153,122,389 - 153,123,997 (+)NCBI
RGSC_v3.4X159,334,472 - 159,336,080 (-)RGD
Celera1136,736,131 - 136,737,739 (+)NCBI
Sequence:
Protein Sequences
Protein RefSeqs NP_001101050 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein EDL85052 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000075461
  ENSRNOP00000075461.1
RefSeq Acc Id: NP_001101050   ⟸   NM_001107580
- UniProtKB: D4A3I6 (UniProtKB/TrEMBL),   A6KRY6 (UniProtKB/TrEMBL)
- Sequence:
Ensembl Acc Id: ENSRNOP00000075461   ⟸   ENSRNOT00000081973
Protein Domains
Exonuclease

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-D4A3I6-F1-model_v2 AlphaFold D4A3I6 1-236 view protein structure

Transcriptome

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

Promoters
RGD ID:13702061
Promoter ID:EPDNEW_R12585
Type:single initiation site
Name:Trex2_1
Description:three prime repair exonuclease 2
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_6.0X157,374,282 - 157,374,342EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1562245 AgrOrtholog
BioCyc Gene G2FUF-676 BioCyc
Ensembl Genes ENSRNOG00000056983 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000081973 ENTREZGENE
  ENSRNOT00000081973.3 UniProtKB/TrEMBL
Gene3D-CATH 3.30.420.10 UniProtKB/TrEMBL
InterPro Exonuclease_RNaseT/DNA_pol3 UniProtKB/TrEMBL
  PolynucTfrase_RNaseH_fold UniProtKB/TrEMBL
  RNaseH_sf UniProtKB/TrEMBL
  TREX1/2 UniProtKB/TrEMBL
KEGG Report rno:309275 UniProtKB/TrEMBL
NCBI Gene 309275 ENTREZGENE
PANTHER PTHR13058 UniProtKB/TrEMBL
  PTHR13058:SF24 UniProtKB/TrEMBL
Pfam RNase_T UniProtKB/TrEMBL
PhenoGen Trex2 PhenoGen
RatGTEx ENSRNOG00000056983 RatGTEx
SMART EXOIII UniProtKB/TrEMBL
Superfamily-SCOP RNaseH_fold UniProtKB/TrEMBL
UniProt A6KRY6 ENTREZGENE, UniProtKB/TrEMBL
  D4A3I6 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2008-04-30 Trex2  three prime repair exonuclease 2   Trex2_predicted  three prime repair exonuclease 2 (predicted)  'predicted' is removed 2292626 APPROVED
2006-03-30 Trex2_predicted  three prime repair exonuclease 2 (predicted)  RGD1562245_predicted  similar to 3-5 exonuclease TREX2 (predicted)  Symbol and Name updated 1299863 APPROVED
2006-03-07 RGD1562245_predicted  similar to 3-5 exonuclease TREX2 (predicted)  LOC309275  similar to 3-5 exonuclease TREX2  Symbol and Name status set to approved 1299863 APPROVED
2006-02-09 LOC309275  similar to 3-5 exonuclease TREX2      Symbol and Name status set to provisional 70820 PROVISIONAL