Ogfod1 (2-oxoglutarate and iron-dependent oxygenase domain containing 1) - Rat Genome Database

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Gene: Ogfod1 (2-oxoglutarate and iron-dependent oxygenase domain containing 1) Rattus norvegicus
Analyze
Symbol: Ogfod1
Name: 2-oxoglutarate and iron-dependent oxygenase domain containing 1
RGD ID: 1308848
Description: Predicted to enable peptidyl-proline 3-dioxygenase activity. Predicted to be involved in cell population proliferation; regulation of translational termination; and stress granule assembly. Predicted to be located in cytoplasmic stress granule; cytosol; and nucleoplasm. Predicted to be active in cytoplasm. Orthologous to human OGFOD1 (2-oxoglutarate and iron dependent oxygenase domain containing 1); INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; acrylamide; amphetamine.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: 2-oxoglutarate and iron-dependent oxygenase domain-containing protein 1; LOC307657; prolyl 3-hydroxylase OGFOD1; RGD1308848; similar to mKIAA1612 protein
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
GRCr81910,950,950 - 10,980,519 (-)NCBIGRCr8
mRatBN7.21910,945,031 - 10,974,602 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1910,946,018 - 10,975,119 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1910,918,802 - 10,942,463 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01911,683,973 - 11,707,634 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01910,970,978 - 10,994,643 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.01911,425,301 - 11,451,085 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1911,425,105 - 11,451,278 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01911,399,734 - 11,425,518 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41911,382,885 - 11,412,512 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.11911,391,459 - 11,417,244 (-)NCBI
Celera1910,833,456 - 10,859,240 (-)NCBICelera
Cytogenetic Map19p12NCBI
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
cytoplasm  (IBA)
cytoplasmic stress granule  (ISO)
cytosol  (IEA,ISO)
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. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
3. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:24550447   PMID:24550462  


Genomics

Comparative Map Data
Ogfod1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81910,950,950 - 10,980,519 (-)NCBIGRCr8
mRatBN7.21910,945,031 - 10,974,602 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1910,946,018 - 10,975,119 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1910,918,802 - 10,942,463 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01911,683,973 - 11,707,634 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01910,970,978 - 10,994,643 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.01911,425,301 - 11,451,085 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1911,425,105 - 11,451,278 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01911,399,734 - 11,425,518 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41911,382,885 - 11,412,512 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.11911,391,459 - 11,417,244 (-)NCBI
Celera1910,833,456 - 10,859,240 (-)NCBICelera
Cytogenetic Map19p12NCBI
OGFOD1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381656,451,524 - 56,479,104 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1656,451,521 - 56,479,104 (+)EnsemblGRCh38hg38GRCh38
GRCh371656,485,436 - 56,513,016 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 361655,042,925 - 55,068,908 (+)NCBINCBI36Build 36hg18NCBI36
Celera1640,983,443 - 41,009,426 (+)NCBICelera
Cytogenetic Map16q13NCBI
HuRef1642,355,849 - 42,381,832 (+)NCBIHuRef
CHM1_11657,892,420 - 57,918,407 (+)NCBICHM1_1
T2T-CHM13v2.01662,246,598 - 62,274,175 (+)NCBIT2T-CHM13v2.0
Ogfod1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39894,763,782 - 94,794,550 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl894,763,826 - 94,794,549 (+)EnsemblGRCm39 Ensembl
GRCm38894,037,122 - 94,067,922 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl894,037,198 - 94,067,921 (+)EnsemblGRCm38mm10GRCm38
MGSCv37896,561,098 - 96,591,822 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv36896,926,420 - 96,957,051 (+)NCBIMGSCv36mm8
Celera898,368,451 - 98,399,175 (+)NCBICelera
Cytogenetic Map8C5NCBI
cM Map846.08NCBI
Ogfod1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495543314,234,636 - 14,260,211 (+)EnsemblChiLan1.0
ChiLan1.0NW_00495543314,234,469 - 14,260,211 (+)NCBIChiLan1.0ChiLan1.0
OGFOD1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v21865,933,075 - 65,959,256 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan11671,852,159 - 71,878,109 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v01636,737,753 - 36,763,797 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.11655,870,144 - 55,895,470 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1655,870,144 - 55,895,470 (+)Ensemblpanpan1.1panPan2
OGFOD1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1259,711,440 - 59,736,448 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl259,711,890 - 59,736,216 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha256,345,122 - 56,370,151 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0260,256,515 - 60,281,555 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl260,255,426 - 60,281,048 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1257,086,854 - 57,111,887 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0258,095,694 - 58,120,747 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0258,988,675 - 59,013,708 (-)NCBIUU_Cfam_GSD_1.0
Ogfod1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440934950,808,257 - 50,829,722 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049364758,759,348 - 8,780,841 (+)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_0049364758,759,348 - 8,780,816 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
OGFOD1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl629,312,750 - 29,339,711 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1629,312,741 - 29,339,701 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
OGFOD1
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1542,360,982 - 42,387,201 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl542,360,992 - 42,387,791 (+)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366604733,977,004 - 34,003,909 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Ogfod1
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_00462475791,854 - 115,133 (-)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_00462475792,670 - 116,127 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Ogfod1
155 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:69
Count of miRNA genes:64
Interacting mature miRNAs:68
Transcripts:ENSRNOT00000026118
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
7411590Foco7Food consumption QTL 76.80.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)19124688055Rat
10054132Srcrt9Stress Responsive Cort QTL 92.870.0017blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)19127355345Rat
631678Cm9Cardiac mass QTL 94.270.0001aorta mass (VT:0002845)aorta weight (CMO:0000076)19128982497Rat
631681Cm12Cardiac mass QTL 123.330.00053heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)19128982497Rat
1549847Bss8Bone structure and strength QTL 84lumbar vertebra strength trait (VT:0010574)vertebra ultimate force (CMO:0001678)19131963836Rat
9590298Uminl5Urine mineral level QTL 53.590.001urine mineral amount (VT:0015086)urine electrolyte level (CMO:0000593)19136824771Rat
8552935Pigfal10Plasma insulin-like growth factor 1 level QTL 105.7blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)19136824771Rat
9590250Scort11Serum corticosterone level QTL 1123.450.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)19136824771Rat
9590090Insglur8Insulin/glucose ratio QTL 810.810.001blood insulin amount (VT:0001560)calculated plasma insulin level (CMO:0002170)19136824771Rat
9589102Slep13Serum leptin concentration QTL 134.630.001blood leptin amount (VT:0005667)plasma leptin level (CMO:0000781)1956937445569374Rat
8694186Bw152Body weight QTL 1523.340.001body mass (VT:0001259)body weight gain (CMO:0000420)1956937445569374Rat
7247442Uae39Urinary albumin excretion QTL 39urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)19218792746708701Rat
724566Uae12Urinary albumin excretion QTL 125urine albumin amount (VT:0002871)urine albumin level (CMO:0000130)19218792756457239Rat
61447Tcas1Tongue tumor susceptibility QTL 16.08tongue integrity trait (VT:0010553)squamous cell carcinoma of the tongue maximum tumor diameter (CMO:0001875)19231612147316121Rat
2317848Alcrsp21Alcohol response QTL 211.8999999761581420.05response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)19320477748204777Rat
1331737Uae29Urinary albumin excretion QTL 295.5urine albumin amount (VT:0002871)urine albumin level (CMO:0000130)19409615555283277Rat
724518Uae19Urinary albumin excretion QTL 195.5urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)19745724942983518Rat
724565Tcas5Tongue tumor susceptibility QTL 510.04tongue integrity trait (VT:0010553)number of squamous cell tumors of the tongue with diameter greater than 3 mm (CMO:0001950)19997775339654489Rat
631840Niddm38Non-insulin dependent diabetes mellitus QTL 383.86blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)191032318023069265Rat
61423Cia14Collagen induced arthritis QTL 143joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)191082797043544039Rat

Markers in Region
RH131221  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21910,945,176 - 10,945,387 (+)MAPPERmRatBN7.2
Rnor_6.01911,421,700 - 11,421,910NCBIRnor6.0
Rnor_5.01911,396,133 - 11,396,343UniSTSRnor5.0
RGSC_v3.41911,383,032 - 11,383,242UniSTSRGSC3.4
Celera1910,829,843 - 10,830,053UniSTS
RH 3.4 Map19111.9UniSTS
Cytogenetic Map19p12UniSTS


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 6 12 12 12 52 7
Low 3 36 45 29 19 29 8 11 22 35 34 11 8
Below cutoff 1

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000026118   ⟹   ENSRNOP00000026118
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1910,946,018 - 10,975,119 (-)Ensembl
Rnor_6.0 Ensembl1911,425,105 - 11,451,278 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000112630   ⟹   ENSRNOP00000086113
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1910,946,018 - 10,975,119 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000115629   ⟹   ENSRNOP00000090572
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1910,946,018 - 10,975,119 (-)Ensembl
RefSeq Acc Id: NM_001107411   ⟹   NP_001100881
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81910,950,950 - 10,980,519 (-)NCBI
mRatBN7.21910,945,031 - 10,974,602 (-)NCBI
Rnor_6.01911,425,301 - 11,451,085 (-)NCBI
Rnor_5.01911,399,734 - 11,425,518 (-)NCBI
RGSC_v3.41911,382,885 - 11,412,512 (-)RGD
Celera1910,833,456 - 10,859,240 (-)NCBI
Sequence:
RefSeq Acc Id: XM_063277995   ⟹   XP_063134065
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81910,950,950 - 10,979,761 (-)NCBI
Protein Sequences
Protein RefSeqs NP_001100881 (Get FASTA)   NCBI Sequence Viewer  
  XP_063134065 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein EDL87355 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000026118
  ENSRNOP00000026118.5
  ENSRNOP00000086113.1
  ENSRNOP00000090572.1
Reference Protein Sequences
RefSeq Acc Id: NP_001100881   ⟸   NM_001107411
- UniProtKB: D4ACB4 (UniProtKB/TrEMBL),   A6JY77 (UniProtKB/TrEMBL),   A0A8I6A1K6 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000026118   ⟸   ENSRNOT00000026118
RefSeq Acc Id: ENSRNOP00000086113   ⟸   ENSRNOT00000112630
RefSeq Acc Id: ENSRNOP00000090572   ⟸   ENSRNOT00000115629
RefSeq Acc Id: XP_063134065   ⟸   XM_063277995
- Peptide Label: isoform X1
Protein Domains
Fe2OG dioxygenase   Prolyl 4-hydroxylase alpha subunit

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-D4ACB4-F1-model_v2 AlphaFold D4ACB4 1-545 view protein structure

Transcriptome

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


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1308848 AgrOrtholog
BioCyc Gene G2FUF-6470 BioCyc
Ensembl Genes ENSRNOG00000019288 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000026118 ENTREZGENE
  ENSRNOT00000026118.8 UniProtKB/TrEMBL
  ENSRNOT00000112630.1 UniProtKB/TrEMBL
  ENSRNOT00000115629.1 UniProtKB/TrEMBL
Gene3D-CATH q2cbj1_9rhob like domain UniProtKB/TrEMBL
InterPro Oxoglu/Fe-dep_dioxygenase UniProtKB/TrEMBL
  Oxoglutarate/Fe-dep_Oase_C UniProtKB/TrEMBL
  Pro_4_hyd_alph UniProtKB/TrEMBL
  TPA1/OFD1_N UniProtKB/TrEMBL
KEGG Report rno:307657 UniProtKB/TrEMBL
NCBI Gene 307657 ENTREZGENE
PANTHER HISTONE ACETYLTRANSFERASE COMPLEX UniProtKB/TrEMBL
  PROLYL 3-HYDROXYLASE OGFOD1 UniProtKB/TrEMBL
Pfam 2OG-FeII_Oxy_4 UniProtKB/TrEMBL
  Ofd1_CTDD UniProtKB/TrEMBL
PhenoGen Ogfod1 PhenoGen
PROSITE FE2OG_OXY UniProtKB/TrEMBL
RatGTEx ENSRNOG00000019288 RatGTEx
SMART P4Hc UniProtKB/TrEMBL
UniProt A0A8I6A1K6 ENTREZGENE, UniProtKB/TrEMBL
  A0A8I6ANI0_RAT UniProtKB/TrEMBL
  A6JY77 ENTREZGENE, UniProtKB/TrEMBL
  D4ACB4 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2008-02-26 Ogfod1  2-oxoglutarate and iron-dependent oxygenase domain containing 1  RGD1308848_predicted  similar to mKIAA1612 protein (predicted)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2005-01-20 RGD1308848_predicted  similar to mKIAA1612 protein (predicted)  LOC307657_predicted    Symbol and Name status set to approved 1331353 APPROVED
2005-01-12 LOC307657_predicted  similar to mKIAA1612 protein (predicted)      Symbol and Name status set to provisional 70820 PROVISIONAL