Ogfod2 (2-oxoglutarate and iron-dependent oxygenase domain containing 2) - Rat Genome Database

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Gene: Ogfod2 (2-oxoglutarate and iron-dependent oxygenase domain containing 2) Rattus norvegicus
Analyze
Symbol: Ogfod2
Name: 2-oxoglutarate and iron-dependent oxygenase domain containing 2
RGD ID: 1310594
Description: Orthologous to human OGFOD2 (2-oxoglutarate and iron dependent oxygenase domain containing 2); INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; 2,3,7,8-Tetrachlorodibenzofuran; 6-propyl-2-thiouracil.
Type: protein-coding (Ensembl: pseudogene)
RefSeq Status: VALIDATED
Previously known as: 2-oxoglutarate and iron-dependent oxygenase domain-containing protein 2; LOC288657; RGD1310594; similar to RIKEN cDNA 5730405M13
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
NCBI Annotation Information: Annotation category: suggests misassembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21232,482,377 - 32,485,687 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1232,482,377 - 32,485,673 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1233,662,542 - 33,665,843 (-)NCBIRnor_SHR
UTH_Rnor_SHRSP_BbbUtx_1.01234,273,886 - 34,277,187 (-)NCBIRnor_SHRSP
UTH_Rnor_WKY_Bbb_1.01233,325,784 - 33,329,085 (-)NCBIRnor_WKY
Rnor_6.01237,907,130 - 37,910,446 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1237,907,130 - 37,910,439 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01239,779,493 - 39,782,802 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41233,606,538 - 33,609,847 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.11233,470,506 - 33,473,221 (-)NCBI
Celera1234,170,636 - 34,173,945 (-)NCBICelera
Cytogenetic Map12q15NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

Molecular Function

References

References - curated
# Reference Title Reference Citation
1. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:8889548   PMID:12477932   PMID:14701905  


Genomics

Comparative Map Data
Ogfod2
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21232,482,377 - 32,485,687 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1232,482,377 - 32,485,673 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1233,662,542 - 33,665,843 (-)NCBIRnor_SHR
UTH_Rnor_SHRSP_BbbUtx_1.01234,273,886 - 34,277,187 (-)NCBIRnor_SHRSP
UTH_Rnor_WKY_Bbb_1.01233,325,784 - 33,329,085 (-)NCBIRnor_WKY
Rnor_6.01237,907,130 - 37,910,446 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1237,907,130 - 37,910,439 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01239,779,493 - 39,782,802 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41233,606,538 - 33,609,847 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.11233,470,506 - 33,473,221 (-)NCBI
Celera1234,170,636 - 34,173,945 (-)NCBICelera
Cytogenetic Map12q15NCBI
OGFOD2
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh3812122,974,726 - 122,980,042 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p13 Ensembl12122,974,580 - 122,980,043 (+)EnsemblGRCh38hg38GRCh38
GRCh3712123,459,273 - 123,464,589 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 3612122,025,307 - 122,030,541 (+)NCBINCBI36Build 36hg18NCBI36
Celera12123,052,147 - 123,057,381 (+)NCBICelera
Cytogenetic Map12q24.31NCBI
HuRef12120,420,494 - 120,425,728 (+)NCBIHuRef
CHM1_112123,427,672 - 123,432,906 (+)NCBICHM1_1
T2T-CHM13v2.012122,971,251 - 122,976,567 (+)NCBIT2T-CHM13v2.0
Ogfod2
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm395124,250,384 - 124,253,544 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl5124,250,360 - 124,253,546 (+)EnsemblGRCm39 Ensembl
GRCm385124,112,321 - 124,115,482 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl5124,112,297 - 124,115,483 (+)EnsemblGRCm38mm10GRCm38
MGSCv375124,562,347 - 124,565,485 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv365124,372,956 - 124,376,094 (+)NCBIMGSCv36mm8
Celera5121,188,479 - 121,191,617 (+)NCBICelera
Cytogenetic Map5FNCBI
Ogfod2
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554825,806,187 - 5,812,070 (-)EnsemblChiLan1.0
ChiLan1.0NW_0049554825,807,082 - 5,812,070 (-)NCBIChiLan1.0ChiLan1.0
OGFOD2
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.112124,815,874 - 124,821,224 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl12124,815,870 - 124,821,224 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v012120,581,092 - 120,586,538 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
OGFOD2
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1266,525,655 - 6,530,333 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl266,526,304 - 6,530,286 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha266,687,275 - 6,691,957 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0266,775,661 - 6,780,327 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl266,776,310 - 6,780,284 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1266,708,530 - 6,713,196 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0266,799,982 - 6,804,649 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0266,754,015 - 6,758,697 (-)NCBIUU_Cfam_GSD_1.0
Ogfod2
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024405118157,801,425 - 157,805,961 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049365581,674,026 - 1,677,827 (-)EnsemblSpeTri2.0
SpeTri2.0NW_0049365581,673,464 - 1,678,044 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
OGFOD2
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1429,890,010 - 29,895,405 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11429,890,003 - 29,895,405 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21431,578,547 - 31,583,932 (-)NCBISscrofa10.2Sscrofa10.2susScr3
OGFOD2
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.111118,314,648 - 118,320,082 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl11118,315,252 - 118,319,685 (+)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_023666037126,992,486 - 126,997,659 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Ogfod2
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_00462474722,976,149 - 22,980,145 (+)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_00462474722,975,884 - 22,980,145 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Ogfod2
25 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:98
Count of miRNA genes:78
Interacting mature miRNAs:90
Transcripts:ENSRNOT00000001433
Prediction methods: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
70213Niddm27Non-insulin dependent diabetes mellitus QTL 273.72blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)121983578938193007Rat
2303569Gluco44Glucose level QTL 442blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)121281238546669029Rat
2303575Insul14Insulin level QTL 144blood insulin amount (VT:0001560)blood insulin level (CMO:0000349)12142450532Rat
2302042Pia38Pristane induced arthritis QTL 383.50.001blood immunoglobulin amount (VT:0002460)serum immunoglobulin G1 level (CMO:0002115)12144503507Rat
2302060Pia37Pristane induced arthritis QTL 376.10.001blood immunoglobulin amount (VT:0002460)serum immunoglobulin G1 level (CMO:0002115)121319815746669029Rat
70169Eae13Experimental allergic encephalomyelitis QTL 130.032nervous system integrity trait (VT:0010566)experimental autoimmune encephalomyelitis incidence/prevalence measurement (CMO:0001046)122413920236638073Rat
61324Eae5Experimental allergic encephalomyelitis QTL 514nervous system integrity trait (VT:0010566)percentage of study population developing relapsing-remitting experimental autoimmune encephalomyelitis during a period of time (CMO:0001402)121961087046669029Rat
1331761Bp218Blood pressure QTL 2182.973arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)121107382545055165Rat
737822Alc10Alcohol consumption QTL 102.2consumption behavior trait (VT:0002069)ethanol drink intake rate (CMO:0001407)121961087040218516Rat
1298081Cia25Collagen induced arthritis QTL 254.7joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)121961088935682913Rat
631560Apr1Acute phase response QTL 16.1orosomucoid 1 amount (VT:0010541)plasma orosomucoid 1 level (CMO:0001467)121914436246669029Rat
737979Pia22Pristane induced arthritis QTL 2253.1joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)12144465750Rat
1331787Rf41Renal function QTL 412.998kidney blood vessel physiology trait (VT:0100012)absolute change in renal blood flow rate (CMO:0001168)122806455740218380Rat
631543Bp83Blood pressure QTL 835.8arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)121555082638478808Rat
1300162Bp188Blood pressure QTL 1883.19arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)123210317445899022Rat
1302792Scl21Serum cholesterol level QTL 213.80.0011blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)12719673046669029Rat
1641928Alcrsp5Alcohol response QTL 5response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)121281238546669029Rat
1598855Bp294Blood pressure QTL 2943.5arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)12134851688Rat
2300186Bmd59Bone mineral density QTL 597.10.0001lumbar vertebra mineral mass (VT:0010511)volumetric bone mineral density (CMO:0001553)121047413746669029Rat
2293684Bmd26Bone mineral density QTL 264.40.0002femur mineral mass (VT:0010011)total volumetric bone mineral density (CMO:0001728)121587265332974238Rat
2293699Bss49Bone structure and strength QTL 495.610.0001lumbar vertebra size trait (VT:0010518)lumbar vertebra trabecular cross-sectional area (CMO:0001692)121047413746669029Rat
634350Apr4Acute phase response QTL 46orosomucoid 1 amount (VT:0010541)plasma orosomucoid 1 level (CMO:0001467)12117200546172005Rat
634351Apr5Acute phase response QTL 56.7blood interleukin-6 amount (VT:0008595)plasma interleukin-6 level (CMO:0001927)12144503507Rat
1600386Calcic2Intracellular calcium level QTL 20.001platelet physiology trait (VT:0005464)platelet intracellular calcium level (CMO:0000922)122806443346669029Rat
1300175Cm5Cardiac mass QTL 53.78heart mass (VT:0007028)heart left ventricle weight to body weight ratio (CMO:0000530)122806443345899022Rat
1549902Bp269Blood pressure QTL 269arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)121318273646669029Rat
1549912Bp268Blood pressure QTL 268arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)101318273646669029Rat
1556747Calcic1Intracellular calcium level QTL 13.6platelet calcium amount (VT:0010500)platelet intracellular calcium level (CMO:0000922)122806443340130419Rat
1549829Scl48Serum cholesterol level QTL 485blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)12960327746669029Rat
631829Alc6Alcohol consumption QTL 64.7consumption behavior trait (VT:0002069)ethanol drink intake rate (CMO:0001407)122860752637691617Rat
61404Bw120Body weight QTL 1205.1body mass (VT:0001259)body mass index (BMI) (CMO:0000105)121235161946669029Rat
61421Cia12Collagen induced arthritis QTL 124.6joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)121363552335682913Rat
5684888Pia42Pristane induced arthritis QTL 42joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)121961087042828880Rat
7411660Foco28Food consumption QTL 2810.90.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)12142110980Rat
8552918Pigfal7Plasma insulin-like growth factor 1 level QTL 7blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)12556449546669029Rat
7411547Bw129Body weight QTL 1290.001body mass (VT:0001259)body weight gain (CMO:0000420)6556449546669029Rat
7411597Foco10Food consumption QTL 100.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)12556449546669029Rat
8552912Pigfal6Plasma insulin-like growth factor 1 level QTL 65blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)12556449846669029Rat
9590086Insglur6Insulin/glucose ratio QTL 618.970.001blood insulin amount (VT:0001560)calculated plasma insulin level (CMO:0002170)12142110980Rat
7411641Foco19Food consumption QTL 1927.70.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)12556449546669029Rat
7411643Foco20Food consumption QTL 200.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)122032881946669029Rat
8552964Pigfal17Plasma insulin-like growth factor 1 level QTL 173.5blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)12556449546669029Rat
8694179Bw150Body weight QTL 1502.90.001body mass (VT:0001259)body weight gain (CMO:0000420)12142110980Rat
7411586Foco5Food consumption QTL 55.40.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)12142110980Rat
7411595Foco9Food consumption QTL 940.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)12142110980Rat
7411545Bw128Body weight QTL 1285.20.001body mass (VT:0001259)body weight gain (CMO:0000420)12142110980Rat
7411588Foco6Food consumption QTL 60.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)12556449546669029Rat
9590147Scort7Serum corticosterone level QTL 713.610.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)12142110980Rat
10059594Kidm46Kidney mass QTL 463.790.025kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)12610757946669029Rat

Markers in Region
RH138929  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21232,483,822 - 32,484,014 (+)MAPPERmRatBN7.2
Rnor_6.01237,908,575 - 37,908,766NCBIRnor6.0
Rnor_5.01239,780,938 - 39,781,129UniSTSRnor5.0
RGSC_v3.41233,607,983 - 33,608,174UniSTSRGSC3.4
Celera1234,172,081 - 34,172,272UniSTS
RH 3.4 Map12570.7UniSTS
Cytogenetic Map12q15UniSTS


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 1 10 3 9 2
Low 2 43 57 41 19 41 8 11 64 32 32 9 8
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000001433   ⟹   ENSRNOP00000001433
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1232,482,377 - 32,485,673 (-)Ensembl
Rnor_6.0 Ensembl1237,907,130 - 37,910,439 (-)Ensembl
RefSeq Acc Id: NM_001105927   ⟹   NP_001099397
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21232,482,377 - 32,485,687 (-)NCBI
Rnor_6.01237,907,130 - 37,910,439 (-)NCBI
Rnor_5.01239,779,493 - 39,782,802 (-)NCBI
RGSC_v3.41233,606,538 - 33,609,847 (-)RGD
Celera1234,170,636 - 34,173,945 (-)RGD
Sequence:
Protein Sequences
Protein RefSeqs NP_001099397 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein EDM13605 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: NP_001099397   ⟸   NM_001105927
- UniProtKB: D3ZU70 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000001433   ⟸   ENSRNOT00000001433

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-D3ZU70-F1-model_v2 AlphaFold D3ZU70 1-349 view protein structure

Transcriptome

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

Promoters
RGD ID:13698618
Promoter ID:EPDNEW_R9143
Type:single initiation site
Name:Ogfod2_1
Description:2-oxoglutarate and iron-dependent oxygenase domain containing2
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_6.01237,910,442 - 37,910,502EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1310594 AgrOrtholog
BioCyc Gene G2FUF-19344 BioCyc
Ensembl Genes ENSRNOG00000001081 Ensembl, ENTREZGENE
Ensembl Transcript ENSRNOT00000001433 ENTREZGENE
NCBI Gene 288657 ENTREZGENE
PhenoGen Ogfod2 PhenoGen
UniProt D3ZU70 ENTREZGENE


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2008-02-27 Ogfod2  2-oxoglutarate and iron-dependent oxygenase domain containing 2  RGD1310594_predicted  similar to RIKEN cDNA 5730405M13 (predicted)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2005-01-20 RGD1310594_predicted  similar to RIKEN cDNA 5730405M13 (predicted)  LOC288657_predicted    Symbol and Name status set to approved 1331353 APPROVED
2005-01-12 LOC288657_predicted  similar to RIKEN cDNA 5730405M13 (predicted)      Symbol and Name status set to provisional 70820 PROVISIONAL