Apobec2 (apolipoprotein B mRNA editing enzyme catalytic subunit 2) - Rat Genome Database

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Gene: Apobec2 (apolipoprotein B mRNA editing enzyme catalytic subunit 2) Rattus norvegicus
Analyze
Symbol: Apobec2
Name: apolipoprotein B mRNA editing enzyme catalytic subunit 2
RGD ID: 1308727
Description: Predicted to enable RNA binding activity; cytidine deaminase activity; and identical protein binding activity. Predicted to be involved in DNA demethylation; cytidine to uridine editing; and positive regulation of gene expression via chromosomal CpG island demethylation. Predicted to act upstream of or within mRNA modification. Predicted to be active in cytoplasm and nucleus. Orthologous to human APOBEC2 (apolipoprotein B mRNA editing enzyme catalytic subunit 2); INTERACTS WITH 17beta-estradiol; 2,3,7,8-tetrachlorodibenzodioxine; 2,3,7,8-Tetrachlorodibenzofuran.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: apolipoprotein B editing complex 2; apolipoprotein B mRNA editing enzyme, catalytic polypeptide-like 2; C->U-editing enzyme APOBEC-2; LOC301226; probable C->U-editing enzyme APOBEC-2
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
GRCr8920,062,561 - 20,076,074 (+)NCBIGRCr8
mRatBN7.2912,564,955 - 12,578,461 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl912,564,920 - 12,578,458 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx921,078,116 - 21,091,657 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0926,144,334 - 26,157,881 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0924,527,382 - 24,540,952 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0914,529,218 - 14,542,731 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl914,529,218 - 14,542,731 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0913,451,720 - 13,465,233 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.497,947,500 - 7,961,013 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.197,947,512 - 7,961,011 (+)NCBI
Celera910,339,525 - 10,352,851 (+)NCBICelera
Cytogenetic Map9q12NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component
cytoplasm  (IBA)
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. Rat ISS GO annotations from MGI mouse gene data--August 2006 MGD data from the GO Consortium
4. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:8626621   PMID:10403781   PMID:12477932   PMID:17187054   PMID:21496894  


Genomics

Comparative Map Data
Apobec2
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8920,062,561 - 20,076,074 (+)NCBIGRCr8
mRatBN7.2912,564,955 - 12,578,461 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl912,564,920 - 12,578,458 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx921,078,116 - 21,091,657 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0926,144,334 - 26,157,881 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0924,527,382 - 24,540,952 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0914,529,218 - 14,542,731 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl914,529,218 - 14,542,731 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0913,451,720 - 13,465,233 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.497,947,500 - 7,961,013 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.197,947,512 - 7,961,011 (+)NCBI
Celera910,339,525 - 10,352,851 (+)NCBICelera
Cytogenetic Map9q12NCBI
APOBEC2
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38641,053,202 - 41,064,891 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl641,053,202 - 41,064,891 (+)EnsemblGRCh38hg38GRCh38
GRCh37641,020,941 - 41,032,630 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36641,128,991 - 41,140,233 (+)NCBINCBI36Build 36hg18NCBI36
Build 34641,128,990 - 41,140,233NCBI
Celera642,573,621 - 42,585,311 (+)NCBICelera
Cytogenetic Map6p21.1NCBI
HuRef640,738,899 - 40,750,382 (+)NCBIHuRef
CHM1_1641,023,446 - 41,035,133 (+)NCBICHM1_1
T2T-CHM13v2.0640,881,766 - 40,893,448 (+)NCBIT2T-CHM13v2.0
Apobec2
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391748,726,259 - 48,739,756 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1748,726,259 - 48,739,958 (-)EnsemblGRCm39 Ensembl
GRCm381748,419,231 - 48,432,728 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1748,419,231 - 48,432,930 (-)EnsemblGRCm38mm10GRCm38
MGSCv371748,558,556 - 48,572,053 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv361747,884,798 - 47,898,295 (-)NCBIMGSCv36mm8
Celera1751,850,648 - 51,864,329 (-)NCBICelera
Cytogenetic Map17CNCBI
cM Map1724.02NCBI
Apobec2
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554377,724,988 - 7,735,893 (+)EnsemblChiLan1.0
ChiLan1.0NW_0049554377,725,092 - 7,735,892 (+)NCBIChiLan1.0ChiLan1.0
APOBEC2
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v2555,549,682 - 55,561,639 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan1651,418,800 - 51,432,812 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v0640,641,211 - 40,652,975 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.1641,950,194 - 41,963,086 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl641,950,194 - 41,963,086 (+)Ensemblpanpan1.1panPan2
APOBEC2
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1129,808,276 - 9,819,973 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl129,808,297 - 9,819,985 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha129,838,514 - 9,850,209 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.01210,287,773 - 10,299,455 (+)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl1210,287,792 - 10,299,468 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1129,820,060 - 9,831,740 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0129,901,879 - 9,913,563 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0129,996,527 - 10,008,237 (+)NCBIUU_Cfam_GSD_1.0
Apobec2
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440494645,190,396 - 45,201,160 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_00493647618,758,582 - 18,769,835 (-)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_00493647618,759,040 - 18,769,815 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
APOBEC2
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl736,364,300 - 36,384,295 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1736,364,258 - 36,381,012 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2741,660,757 - 41,675,416 (+)NCBISscrofa10.2Sscrofa10.2susScr3
APOBEC2
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11731,091,668 - 31,104,534 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl1731,095,184 - 31,103,526 (-)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366604441,053,972 - 41,065,649 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Apobec2
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_00462475417,689,595 - 17,700,316 (-)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_00462475417,689,587 - 17,700,318 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Apobec2
89 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:237
Count of miRNA genes:157
Interacting mature miRNAs:181
Transcripts:ENSRNOT00000016893
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
10054141Gmadr4Adrenal mass QTL 42.450.0074adrenal gland mass (VT:0010420)both adrenal glands wet weight (CMO:0000164)9114209783Rat
70226Eae4Experimental allergic encephalomyelitis QTL 4nervous system integrity trait (VT:0010566)experimental autoimmune encephalomyelitis incidence/prevalence measurement (CMO:0001046)9125661317Rat
9589055Scfw5Subcutaneous fat weight QTL 55.550.001subcutaneous adipose mass (VT:1000472)abdominal subcutaneous fat pad weight (CMO:0002069)9137999212Rat
7411592Foco8Food consumption QTL 87.40.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)9137999212Rat
9589158Gluco65Glucose level QTL 656.820.001blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)9137999212Rat
1300124Cm4Cardiac mass QTL 43.55heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)9140594091Rat
1298088Edpm11Estrogen-dependent pituitary mass QTL 112.5pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)9143718459Rat
1641911Alcrsp13Alcohol response QTL 13response to alcohol trait (VT:0010489)brain neurotensin receptor 1 density (CMO:0002068)9143718459Rat
10054125Srcrt7Stress Responsive Cort QTL 73.330.0011blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)9187073594Rat
1331757Cdexp1CD45RC expression in CD8 T cells QTL 14.3CD8-positive T cell quantity (VT:0008077)blood CD45RC(high) CD8 T cell count to CD45RC(low) CD8 T cell count ratio (CMO:0001990)9102453767509080Rat
1354650Despr5Despair related QTL 54.010.0017locomotor behavior trait (VT:0001392)amount of time spent in voluntary immobility (CMO:0001043)9125408446254084Rat
2303559Gluco54Glucose level QTL 542blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)9125408446254084Rat
1578675Bss17Bone structure and strength QTL 173.8femur morphology trait (VT:0000559)femoral neck cortical cross-sectional area (CMO:0001702)9336865213533896Rat
61425Cia15Collagen induced arthritis QTL 154.6joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)9510982642921101Rat
631211Bw4Body weight QTL45.31retroperitoneal fat pad mass (VT:0010430)retroperitoneal fat pad weight to body weight ratio (CMO:0000635)9510982650109826Rat
11353947Bp392Blood pressure QTL 392arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)9728325252283252Rat
61450Ciaa3CIA Autoantibody QTL 36.5blood autoantibody amount (VT:0003725)calculated serum anti-type 2 collagen antibody titer (CMO:0001279)9795472022071169Rat
9589133Insul26Insulin level QTL 2617.960.001blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)9895256053952560Rat
7411609Foco16Food consumption QTL 1625.60.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)9895256053952560Rat

Markers in Region
RH128292  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2912,577,029 - 12,577,235 (+)MAPPERmRatBN7.2
Rnor_6.0914,541,300 - 14,541,505NCBIRnor6.0
Rnor_5.0913,463,802 - 13,464,007UniSTSRnor5.0
RGSC_v3.497,959,582 - 7,959,787UniSTSRGSC3.4
Celera910,351,420 - 10,351,625UniSTS
RH 3.4 Map931.5UniSTS
Cytogenetic Map9q12UniSTS
RH128626  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2912,578,128 - 12,578,330 (+)MAPPERmRatBN7.2
Rnor_6.0914,542,399 - 14,542,600NCBIRnor6.0
Rnor_5.0913,464,901 - 13,465,102UniSTSRnor5.0
RGSC_v3.497,960,681 - 7,960,882UniSTSRGSC3.4
Celera910,352,519 - 10,352,720UniSTS
Cytogenetic Map9q12UniSTS


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 43 8 11 1 7 8
Low 3 31 15 19 15 19 15 29 4
Below cutoff 12 12 12 20 20 7

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000016893   ⟹   ENSRNOP00000016893
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl912,564,920 - 12,578,458 (+)Ensembl
Rnor_6.0 Ensembl914,529,218 - 14,542,731 (+)Ensembl
RefSeq Acc Id: NM_001106883   ⟹   NP_001100353
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8920,062,561 - 20,076,074 (+)NCBI
mRatBN7.2912,564,955 - 12,578,461 (+)NCBI
Rnor_6.0914,529,218 - 14,542,731 (+)NCBI
Rnor_5.0913,451,720 - 13,465,233 (+)NCBI
RGSC_v3.497,947,500 - 7,961,013 (+)RGD
Celera910,339,525 - 10,352,851 (+)RGD
Sequence:
Protein Sequences
Protein RefSeqs NP_001100353 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAI68177 (Get FASTA)   NCBI Sequence Viewer  
  EDM18937 (Get FASTA)   NCBI Sequence Viewer  
  EDM18938 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000016893
  ENSRNOP00000016893.4
Reference Protein Sequences
RefSeq Acc Id: NP_001100353   ⟸   NM_001106883
- UniProtKB: B4F789 (UniProtKB/TrEMBL),   A6JIE5 (UniProtKB/TrEMBL),   F7F9T5 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000016893   ⟸   ENSRNOT00000016893
Protein Domains
CMP/dCMP-type deaminase

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-B4F789-F1-model_v2 AlphaFold B4F789 1-224 view protein structure

Transcriptome

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

Promoters
RGD ID:13696486
Promoter ID:EPDNEW_R7010
Type:multiple initiation site
Name:Apobec2_1
Description:apolipoprotein B mRNA editing enzyme catalytic subunit 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_6.0914,529,216 - 14,529,276EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1308727 AgrOrtholog
BioCyc Gene G2FUF-28311 BioCyc
Ensembl Genes ENSRNOG00000012303 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000016893 ENTREZGENE
  ENSRNOT00000016893.8 UniProtKB/TrEMBL
Gene3D-CATH Cytidine Deaminase, domain 2 UniProtKB/TrEMBL
InterPro CMP_dCMP_Zn-bd UniProtKB/TrEMBL
  Cytidine_deaminase-like UniProtKB/TrEMBL
KEGG Report rno:301226 UniProtKB/TrEMBL
NCBI Gene 301226 ENTREZGENE
PANTHER C-U-EDITING ENZYME APOBEC-2 UniProtKB/TrEMBL
  MRNA EDITING ENZYME UniProtKB/TrEMBL
Pfam APOBEC2 UniProtKB/TrEMBL
PhenoGen Apobec2 PhenoGen
PROSITE CYT_DCMP_DEAMINASES_2 UniProtKB/TrEMBL
RatGTEx ENSRNOG00000012303 RatGTEx
Superfamily-SCOP SSF53927 UniProtKB/TrEMBL
UniProt A6JIE5 ENTREZGENE, UniProtKB/TrEMBL
  B4F789 ENTREZGENE
  F7F9T5 ENTREZGENE, UniProtKB/TrEMBL
UniProt Secondary B4F789 UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2016-03-15 Apobec2  apolipoprotein B mRNA editing enzyme catalytic subunit 2  Apobec2  apolipoprotein B mRNA editing enzyme, catalytic polypeptide-like 2  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-09-25 Apobec2  apolipoprotein B mRNA editing enzyme, catalytic polypeptide-like 2  Apobec2  apolipoprotein B editing complex 2   Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-04-30 Apobec2  apolipoprotein B editing complex 2   Apobec2_predicted  apolipoprotein B editing complex 2 (predicted)  'predicted' is removed 2292626 APPROVED
2005-01-12 Apobec2_predicted  apolipoprotein B editing complex 2 (predicted)      Symbol and Name status set to approved 70820 APPROVED