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 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
Black Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: GRCr8 - GRCr8 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8920,062,561 - 20,076,074 (+)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl920,062,526 - 20,076,071 (+)EnsemblGRCr8
mRatBN7.2912,564,955 - 12,578,461 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl912,564,920 - 12,578,458 (+)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx921,078,116 - 21,091,657 (+)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0926,144,334 - 26,157,881 (+)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0924,527,382 - 24,540,952 (+)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0914,529,218 - 14,542,731 (+)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl914,529,218 - 14,542,731 (+)Ensemblrn6Rnor6.0
Rnor_5.0913,451,720 - 13,465,233 (+)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.497,947,500 - 7,961,013 (+)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera910,339,525 - 10,352,851 (+)NCBICelera
RGSC_v3.197,947,512 - 7,961,011 (+)NCBI
Cytogenetic Map9q12NCBI
JBrowse:




Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component
nucleoplasm  (IEA,ISO)

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 (+)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl920,062,526 - 20,076,071 (+)EnsemblGRCr8
mRatBN7.2912,564,955 - 12,578,461 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl912,564,920 - 12,578,458 (+)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx921,078,116 - 21,091,657 (+)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0926,144,334 - 26,157,881 (+)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0924,527,382 - 24,540,952 (+)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0914,529,218 - 14,542,731 (+)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl914,529,218 - 14,542,731 (+)Ensemblrn6Rnor6.0
Rnor_5.0913,451,720 - 13,465,233 (+)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.497,947,500 - 7,961,013 (+)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera910,339,525 - 10,352,851 (+)NCBICelera
RGSC_v3.197,947,512 - 7,961,011 (+)NCBI
Cytogenetic Map9q12NCBI
APOBEC2
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38641,053,202 - 41,064,891 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl641,053,201 - 41,064,891 (+)Ensemblhg38GRCh38
GRCh37641,020,941 - 41,032,630 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36641,128,991 - 41,140,233 (+)NCBIBuild 36Build 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 EnsemblGRCm39
GRCm381748,419,231 - 48,432,728 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1748,419,231 - 48,432,930 (-)Ensemblmm10GRCm38
MGSCv371748,558,556 - 48,572,053 (-)NCBIMGSCv37MGSCv37mm9NCBIm37
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 (+)Ensembl
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 (+)EnsemblpanPan2panpan1.1
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 (+)EnsemblcanFam3CanFam3.1
Dog10K_Boxer_Tasha129,838,514 - 9,850,209 (+)NCBIDog10K_Boxer_TashaDog10K_Boxer_Tasha
ROS_Cfam_1.01210,287,773 - 10,299,455 (+)NCBIROS_Cfam_1.0ROS_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_1.0UU_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 (-)EnsemblSpeTri2.0 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 (+)EnsemblsusScr11Sscrofa11.1
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 (-)EnsemblChlSab1.1 EnsemblchlSab2Vervet-AGM
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_1.0 EnsemblhetGla2HetGla_female_1.0 Ensembl
HetGla 1.0NW_00462475417,689,587 - 17,700,318 (-)NCBIHetGla 1.0HetGla 1.0hetGla2
Apobec2
(Rattus rattus - black rat)
Black Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rrattus_CSIRO_v1481,495,010 - 81,508,548 (+)NCBIRrattus_CSIRO_v1

Variants

.
Variants in Apobec2
64 total Variants
miRNA Target Status (No longer updated)

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 (GRCr8)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
2303170Bp332Blood pressure QTL 3323.730.027arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)9671488884474983Rat
631211Bw4Body weight QTL45.31retroperitoneal fat pad mass (VT:0010430)retroperitoneal fat pad weight to body weight ratio (CMO:0000635)9534647950346479Rat
10054141Gmadr4Adrenal mass QTL 42.450.0074adrenal gland mass (VT:0010420)both adrenal glands wet weight (CMO:0000164)9121707400Rat
2303559Gluco54Glucose level QTL 542blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)9875049253750492Rat
7207814Bmd91Bone mineral density QTL 913.5femur size trait (VT:1000369)femoral neck cross-sectional area (CMO:0001697)9131250552Rat
1578675Bss17Bone structure and strength QTL 173.8femur morphology trait (VT:0000559)femoral neck cortical cross-sectional area (CMO:0001702)9360535521031556Rat
9589055Scfw5Subcutaneous fat weight QTL 55.550.001subcutaneous adipose mass (VT:1000472)abdominal subcutaneous fat pad weight (CMO:0002069)949664545496645Rat
1641911Alcrsp13Alcohol response QTL 13response to alcohol trait (VT:0010489)brain neurotensin receptor 1 density (CMO:0002068)9621499551214995Rat
1354650Despr5Despair related QTL 54.010.0017locomotor behavior trait (VT:0001392)amount of time spent in voluntary immobility (CMO:0001043)9875049253750492Rat
1300124Cm4Cardiac mass QTL 43.55heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)9141763315Rat
61425Cia15Collagen induced arthritis QTL 154.6joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)9534647950416711Rat
631643Bp120Blood pressure QTL 12030.004arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)9671488829567695Rat
9589158Gluco65Glucose level QTL 656.820.001blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)949664545496645Rat
7411592Foco8Food consumption QTL 87.40.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)949664545496645Rat
1298088Edpm11Estrogen-dependent pituitary mass QTL 112.5pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)9621499551214995Rat

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

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
15 12 64 96 71 70 39 84 39 6 305 181 10 68 62 86 31 7 7

Sequence


Ensembl Acc Id: ENSRNOT00000016893   ⟹   ENSRNOP00000016893
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl920,062,526 - 20,076,071 (+)Ensembl
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
RefSeq Acc Id: NP_001100353   ⟸   NM_001106883
- UniProtKB: B4F789 (UniProtKB/TrEMBL),   A6JIE5 (UniProtKB/TrEMBL),   F7F9T5 (UniProtKB/TrEMBL)
- Sequence:
Ensembl 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
  ENSRNOT00000016893.9 UniProtKB/TrEMBL
Gene3D-CATH Cytidine Deaminase, domain 2 UniProtKB/TrEMBL
InterPro APOBEC_Cyt_Deaminase UniProtKB/TrEMBL
  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