Apex2 (apurinic/apyrimidinic endodeoxyribonuclease 2) - Rat Genome Database

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Gene: Apex2 (apurinic/apyrimidinic endodeoxyribonuclease 2) Rattus norvegicus
Analyze
Symbol: Apex2
Name: apurinic/apyrimidinic endodeoxyribonuclease 2
RGD ID: 1565983
Description: Predicted to enable DNA-(apurinic or apyrimidinic site) endonuclease activity; double-stranded DNA 3'-5' DNA exonuclease activity; and phosphoric diester hydrolase activity. Predicted to be involved in base-excision repair. Predicted to be located in fibrillar center; mitochondrial inner membrane; and nucleoplasm. Predicted to be active in nucleus. Orthologous to human APEX2 (apurinic/apyrimidinic endodeoxyribonuclease 2); PARTICIPATES IN base excision repair pathway; INTERACTS WITH (R,R,R)-alpha-tocopherol; 2,3,7,8-tetrachlorodibenzodioxine; acrylamide.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: APEX nuclease (apurinic/apyrimidinic endonuclease) 2; DNA-(apurinic or apyrimidinic site) endonuclease 2; DNA-(apurinic or apyrimidinic site) lyase 2; hypothetical protein LOC317628; LOC317628; MGC156784; RGD1565983; similar to apurinic/apyrimidinic endonuclease 2; uncharacterized protein LOC317628
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8X22,914,943 - 22,937,713 (-)NCBIGRCr8
mRatBN7.2X19,425,684 - 19,508,459 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 EnsemblX19,487,419 - 19,508,439 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_UtxX16,917,014 - 16,943,392 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0X23,180,186 - 23,207,908 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0X20,000,651 - 20,021,638 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0X23,146,085 - 23,166,676 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 EnsemblX23,146,085 - 23,166,675 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0X23,566,192 - 23,586,783 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4X39,811,484 - 39,832,225 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
CeleraX19,761,515 - 19,779,599 (-)NCBICelera
Cytogenetic MapXq12NCBI
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

Biological Process

Cellular Component

Molecular Pathway Annotations     Click to see Annotation Detail View
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. KEGG Annotation Import Pipeline Pipeline to import KEGG annotations from KEGG into RGD
3. GOA pipeline RGD automated data pipeline
4. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:12477932   PMID:12573260   PMID:14651853   PMID:15319281   PMID:18614015  


Genomics

Comparative Map Data
Apex2
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8X22,914,943 - 22,937,713 (-)NCBIGRCr8
mRatBN7.2X19,425,684 - 19,508,459 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 EnsemblX19,487,419 - 19,508,439 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_UtxX16,917,014 - 16,943,392 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0X23,180,186 - 23,207,908 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0X20,000,651 - 20,021,638 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0X23,146,085 - 23,166,676 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 EnsemblX23,146,085 - 23,166,675 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0X23,566,192 - 23,586,783 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4X39,811,484 - 39,832,225 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
CeleraX19,761,515 - 19,779,599 (-)NCBICelera
Cytogenetic MapXq12NCBI
APEX2
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38X55,000,363 - 55,009,057 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 EnsemblX55,000,363 - 55,009,057 (+)EnsemblGRCh38hg38GRCh38
GRCh37X55,026,796 - 55,035,490 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36X55,043,505 - 55,050,937 (+)NCBINCBI36Build 36hg18NCBI36
Build 34X54,909,800 - 54,917,232NCBI
CeleraX58,861,923 - 58,869,355 (+)NCBICelera
Cytogenetic MapXp11.21NCBI
HuRefX52,077,699 - 52,085,248 (+)NCBIHuRef
CHM1_1X55,016,795 - 55,024,345 (+)NCBICHM1_1
T2T-CHM13v2.0X54,293,489 - 54,302,183 (+)NCBIT2T-CHM13v2.0
Apex2
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39X149,286,625 - 149,371,175 (-)NCBIGRCm39GRCm39mm39
GRCm39 EnsemblX149,302,515 - 149,372,864 (-)EnsemblGRCm39 Ensembl
GRCm38X150,426,974 - 150,588,206 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 EnsemblX150,519,519 - 150,589,868 (-)EnsemblGRCm38mm10GRCm38
MGSCv37X147,006,050 - 147,022,692 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv36X145,912,223 - 145,928,865 (-)NCBIMGSCv36mm8
CeleraX133,818,627 - 133,835,339 (+)NCBICelera
Cytogenetic MapXF3NCBI
cM MapX68.46NCBI
Apex2
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554752,344,087 - 2,359,906 (+)EnsemblChiLan1.0
ChiLan1.0NW_0049554752,343,992 - 2,359,492 (+)NCBIChiLan1.0ChiLan1.0
APEX2
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v2X56,396,084 - 56,403,908 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan1X56,399,691 - 56,407,515 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v0X47,210,552 - 47,218,320 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.1X55,442,599 - 55,450,402 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 EnsemblX55,442,599 - 55,450,402 (+)Ensemblpanpan1.1panPan2
APEX2
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1X46,692,667 - 46,703,309 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 EnsemblX46,693,191 - 46,702,195 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_TashaX38,028,054 - 38,038,942 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0X46,981,068 - 46,991,960 (+)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 EnsemblX46,981,563 - 46,997,086 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1X46,490,847 - 46,501,736 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0X46,957,419 - 46,968,304 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0X46,899,682 - 46,910,572 (+)NCBIUU_Cfam_GSD_1.0
Apex2
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2X39,468,146 - 39,477,569 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049367511,807,867 - 1,819,272 (+)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_0049367511,807,867 - 1,817,780 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
APEX2
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 EnsemblX47,862,667 - 47,871,184 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1X47,862,682 - 47,870,579 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2X53,798,823 - 53,806,723 (+)NCBISscrofa10.2Sscrofa10.2susScr3
APEX2
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1X51,077,496 - 51,084,787 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 EnsemblX51,077,025 - 51,084,783 (+)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_0236660865,055,784 - 5,063,231 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Apex2
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_004624910382,244 - 400,714 (+)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_004624910382,144 - 398,151 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Apex2
311 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:31
Count of miRNA genes:28
Interacting mature miRNAs:30
Transcripts:ENSRNOT00000068703
Prediction methods:Miranda, Pita, 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
731181Uae27Urinary albumin excretion QTL 272.70.0059urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)X143491017Rat
634325Bw13Body weight QTL 130body mass (VT:0001259)body weight (CMO:0000012)X144797220991088Rat
70165Bp64Blood pressure QTL 645.2arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)X144812931706553Rat
631204Gluco15Glucose level QTL 150.001blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)X162371522646544Rat
1298071Edpm12Estrogen-dependent pituitary mass QTL 123.2pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)X292789847927898Rat
10755455Coatc13Coat color QTL 130coat/hair pigmentation trait (VT:0010463)pigmented ventral coat/hair area to total ventral coat/hair area ratio (CMO:0001812)7440600049406000Rat
631666Iddm5Insulin dependent diabetes mellitus QTL 5blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)X449454949494549Rat
61430Cia18Collagen induced arthritis QTL 183.1joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)X14843113120568734Rat
71116Niddm16Non-insulin dependent diabetes mellitus QTL 167.81blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)X1529780260297802Rat

Markers in Region
DXWox4  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2X19,510,955 - 19,511,180 (-)MAPPERmRatBN7.2
mRatBN7.2X19,510,955 - 19,511,090 (-)MAPPERmRatBN7.2
Rnor_6.0X23,143,401 - 23,143,535NCBIRnor6.0
Rnor_6.0X23,143,256 - 23,143,535NCBIRnor6.0
Rnor_5.0X23,563,363 - 23,563,642UniSTSRnor5.0
Rnor_5.0X23,563,508 - 23,563,642UniSTSRnor5.0
RGSC_v3.4X39,834,775 - 39,834,909UniSTSRGSC3.4
RGSC_v3.4X39,834,774 - 39,834,909RGDRGSC3.4
RGSC_v3.1X39,888,243 - 39,888,378RGD
CeleraX19,782,149 - 19,782,283UniSTS
RH 3.4 MapX209.72UniSTS
RH 3.4 MapX209.72RGD
RH 2.0 Map21201.6RGD
Cytogenetic MapXq22-q31UniSTS
Cytogenetic MapXq21UniSTS
BI294000  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2X19,507,840 - 19,507,992 (-)MAPPERmRatBN7.2
Rnor_6.0X23,146,499 - 23,146,650NCBIRnor6.0
Rnor_5.0X23,566,606 - 23,566,757UniSTSRnor5.0
RGSC_v3.4X39,831,660 - 39,831,811UniSTSRGSC3.4
CeleraX19,779,034 - 19,779,185UniSTS
RH 3.4 MapX209.72UniSTS
Cytogenetic MapXq21UniSTS
BE104231  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2X19,487,501 - 19,487,652 (-)MAPPERmRatBN7.2
Rnor_6.0X23,166,443 - 23,166,593NCBIRnor6.0
Rnor_5.0X23,586,550 - 23,586,700UniSTSRnor5.0
RGSC_v3.4X39,811,567 - 39,811,717UniSTSRGSC3.4
CeleraX19,761,598 - 19,761,748UniSTS
RH 3.4 MapX210.13UniSTS
Cytogenetic MapXq21UniSTS


Expression


RNA-SEQ Expression
High: > 1000 TPM value   Medium: Between 11 and 1000 TPM
Low: Between 0.5 and 10 TPM   Below Cutoff: < 0.5 TPM

alimentary part of gastrointestinal system circulatory system endocrine system exocrine system hemolymphoid system hepatobiliary system integumental system musculoskeletal system nervous system renal system reproductive system respiratory system appendage
High
Medium 2 10 24 18 12 18 39 20 32 5
Low 1 33 33 23 7 23 8 11 35 15 9 6 8
Below cutoff

Sequence


RefSeq Acc Id: ENSRNOT00000068703   ⟹   ENSRNOP00000060925
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 EnsemblX19,487,419 - 19,508,439 (-)Ensembl
Rnor_6.0 EnsemblX23,146,085 - 23,166,675 (+)Ensembl
RefSeq Acc Id: NM_001079892   ⟹   NP_001073361
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8X22,914,943 - 22,935,930 (-)NCBI
mRatBN7.2X19,487,419 - 19,508,406 (-)NCBI
Rnor_6.0X23,146,085 - 23,166,676 (+)NCBI
Rnor_5.0X23,566,192 - 23,586,783 (+)NCBI
RGSC_v3.4X39,811,484 - 39,832,225 (-)RGD
CeleraX19,761,515 - 19,779,599 (-)RGD
Sequence:
RefSeq Acc Id: XM_063280109   ⟹   XP_063136179
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8X22,914,943 - 22,937,713 (-)NCBI
Protein Sequences
Protein RefSeqs NP_001073361 (Get FASTA)   NCBI Sequence Viewer  
  XP_063136179 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAI27531 (Get FASTA)   NCBI Sequence Viewer  
  EDL86343 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000060925
  ENSRNOP00000060925.4
RefSeq Acc Id: NP_001073361   ⟸   NM_001079892
- UniProtKB: A1L132 (UniProtKB/TrEMBL),   D3ZPZ3 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000060925   ⟸   ENSRNOT00000068703
RefSeq Acc Id: XP_063136179   ⟸   XM_063280109
- Peptide Label: isoform X1
Protein Domains
GRF-type

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-D3ZPZ3-F1-model_v2 AlphaFold D3ZPZ3 1-514 view protein structure

Transcriptome

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

Promoters
RGD ID:13701776
Promoter ID:EPDNEW_R12300
Type:initiation region
Name:Apex2_1
Description:apurinic/apyrimidinic endodeoxyribonuclease 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_6.0X23,146,036 - 23,146,096EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1565983 AgrOrtholog
BioCyc Gene G2FUF-2812 BioCyc
Ensembl Genes ENSRNOG00000000166 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000068703 ENTREZGENE
  ENSRNOT00000068703.4 UniProtKB/TrEMBL
Gene3D-CATH 3.60.10.10 UniProtKB/TrEMBL
IMAGE_CLONE IMAGE:7126449 IMAGE-MGC_LOAD
InterPro AP_endonuclease_F1_BS UniProtKB/TrEMBL
  Endo/exonu/phosph_ase_sf UniProtKB/TrEMBL
  Endo/exonuclease/phosphatase UniProtKB/TrEMBL
  exoDNase_III UniProtKB/TrEMBL
  Znf_GRF UniProtKB/TrEMBL
KEGG Report rno:317628 UniProtKB/TrEMBL
MGC_CLONE MGC:156784 IMAGE-MGC_LOAD
NCBI Gene 317628 ENTREZGENE
PANTHER DNA-(APURINIC OR APYRIMIDINIC SITE) ENDONUCLEASE 2 UniProtKB/TrEMBL
  ExoIII_xth UniProtKB/TrEMBL
Pfam Exo_endo_phos UniProtKB/TrEMBL
  zf-GRF UniProtKB/TrEMBL
PhenoGen Apex2 PhenoGen
PROSITE AP_NUCLEASE_F1_1 UniProtKB/TrEMBL
  AP_NUCLEASE_F1_4 UniProtKB/TrEMBL
  ZF_GRF UniProtKB/TrEMBL
RatGTEx ENSRNOG00000000166 RatGTEx
Superfamily-SCOP Exo_endo_phos UniProtKB/TrEMBL
UniProt A1L132 ENTREZGENE, UniProtKB/TrEMBL
  D3ZPZ3 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2016-03-15 Apex2  apurinic/apyrimidinic endodeoxyribonuclease 2  Apex2  APEX nuclease (apurinic/apyrimidinic endonuclease) 2  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2012-10-12 Apex2  APEX nuclease (apurinic/apyrimidinic endonuclease) 2  RGD1565983  similar to apurinic/apyrimidinic endonuclease 2  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-04-30 RGD1565983  similar to apurinic/apyrimidinic endonuclease 2   RGD1565983_predicted  similar to apurinic/apyrimidinic endonuclease 2 (predicted)  'predicted' is removed 2292626 APPROVED
2006-03-07 RGD1565983_predicted  similar to apurinic/apyrimidinic endonuclease 2 (predicted)  LOC317628  similar to apurinic/apyrimidinic endonuclease 2  Symbol and Name status set to approved 1299863 APPROVED
2006-02-09 LOC317628  similar to apurinic/apyrimidinic endonuclease 2      Symbol and Name status set to provisional 70820 PROVISIONAL