RGD1564999 (similar to isopentenyl-diphosphate delta isomerase 2) - Rat Genome Database

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Pathways
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Gene: RGD1564999 (similar to isopentenyl-diphosphate delta isomerase 2) Rattus norvegicus
Analyze
No known orthologs.
Symbol: RGD1564999
Name: similar to isopentenyl-diphosphate delta isomerase 2
RGD ID: 1564999
Description: Predicted to be involved in cholesterol biosynthetic process and dimethylallyl diphosphate biosynthetic process. Predicted to be located in peroxisome; PARTICIPATES IN terpenoid biosynthetic pathway; INTERACTS WITH acrylamide; bisphenol A; cefaloridine.
Type: protein-coding
RefSeq Status: MODEL
Previously known as: isopentenyl-diphosphate delta-isomerase 2-like; LOC291266
RGD Orthologs
Alliance Genes
More Info homologs ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21761,518,138 - 61,535,484 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1761,519,390 - 61,531,603 (-)EnsemblmRatBN7.2 Ensembl
Rnor_6.01757,935,992 - 57,954,998 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.01759,740,356 - 59,759,713 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41772,412,210 - 72,417,701 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera1754,388,870 - 54,395,044 (-)NCBICelera
Cytogenetic Map17q12.1NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component
cytoplasm  (IBA)
peroxisome  (IEA)

Molecular Function

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. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
5. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions

Genomics

Variants

.
Variants in RGD1564999
119 total Variants

QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1354581Bp247Blood pressure QTL 2474.5arterial blood pressure trait (VT:2000000)pulse pressure (CMO:0000292)17169599340Rat
1354662Rf49Renal function QTL 492.9blood creatinine amount (VT:0005328)plasma creatinine level (CMO:0000537)17169599340Rat
1354630Cm34Cardiac mass QTL 348.7heart left ventricle mass (VT:0007031)heart left ventricle wet weight (CMO:0000071)17429913069599340Rat
1354638Insul1Insulin level QTL 14.8blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)17429913069599340Rat
1354651Lmblg2Limb length QTL 26tibia length (VT:0004357)tibia length (CMO:0000450)17429913069599340Rat
7394837Memor18Memory QTL 18exploratory behavior trait (VT:0010471)measurement of voluntary locomotion into, out of or within a discrete space in an experimental apparatus (CMO:0000957)171864018263640182Rat
12903978Cm118Cardiac mass QTL 1180.001heart mass (VT:0007028)heart wet weight to body weight ratio (CMO:0002408)172365318468653184Rat
12903979Cm119Cardiac mass QTL 1190.001heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)172365318468653184Rat
12903980Cm120Cardiac mass QTL 1200.002heart right ventricle mass (VT:0007033)heart right ventricle weight to body weight ratio (CMO:0000914)172365318468653184Rat
12903981Am17Aortic mass QTL 170.001aorta mass (VT:0002845)aorta weight to aorta length to body weight ratio (CMO:0002722)172365318468653184Rat
1559055Bp278Blood pressure QTL 2780.04arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)172365318468653184Rat
12903982Kidm70Kidney mass QTL 700.001kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)172365318470974005Rat
1354619Bp242Blood pressure QTL 2426.3arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)172459934069599340Rat
8552928Pigfal9Plasma insulin-like growth factor 1 level QTL 99blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)172840914773409147Rat
9590107Sffal7Serum free fatty acids level QTL 74.810.001blood free fatty acid amount (VT:0001553)plasma free fatty acids level (CMO:0000546)172840914773409147Rat
10450503Bp386Blood pressure QTL 3860.28arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)173136839162109574Rat
2324621Coatc5Coat color QTL 5coat/hair pigmentation trait (VT:0010463)pigmented ventral coat/hair area to total ventral coat/hair area ratio (CMO:0001812)173136839173951021Rat
724549Niddm56Non-insulin dependent diabetes mellitus QTL 560.03blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)173199078476990784Rat
1354663Bvd5Brain ventricular dilatation QTL 53.510.001brain ventricle morphology trait (VT:0000822)hydrocephalus severity score (CMO:0001881)173199078481292925Rat
1300148Bp192Blood pressure QTL 1923.47arterial blood pressure trait (VT:2000000)blood pressure time series experimental set point of the baroreceptor response (CMO:0002593)173455084373951021Rat
724528Uae4Urinary albumin excretion QTL 44.90.0001urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)173583708569599340Rat
2301412Kidm40Kidney mass QTL 400.001kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)173747984782479847Rat
2317054Aia12Adjuvant induced arthritis QTL 124.24joint integrity trait (VT:0010548)left rear ankle joint diameter (CMO:0002149)173828150983281509Rat
2317060Aia26Adjuvant induced arthritis QTL 263.22joint integrity trait (VT:0010548)right rear ankle joint diameter (CMO:0002150)173828150983281509Rat
1598871Memor5Memory QTL 55.3exploratory behavior trait (VT:0010471)total horizontal distance resulting from voluntary locomotion in an experimental apparatus (CMO:0001443)174054004180387013Rat
1358295Aocep1Aortic cell protein QTL 16.10.00000071thoracic aorta cellular protein amount (VT:0010598)aortic cell percentage174099000585990005Rat
1354635Bp245Blood pressure QTL 2456arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)174207316069599340Rat
1354635Bp245Blood pressure QTL 2456arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)174207316069599340Rat
7411575Bw140Body weight QTL 14030.20.001body mass (VT:0001259)body weight gain (CMO:0000420)174856093586533673Rat
8694181Bw151Body weight QTL 1514.360.001body mass (VT:0001259)body weight gain (CMO:0000420)174856093586533673Rat
2317038Ginf3Gastrointestinal inflammation QTL 32.890.005liver integrity trait (VT:0010547)liver granuloma severity score (CMO:0002157)174992015486533673Rat
2303580Gluco49Glucose level QTL 492blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)175004027186533673Rat
4889894Eae33Experimental allergic encephalomyelitis QTL 335.20.0001nervous system integrity trait (VT:0010566)experimental autoimmune encephalomyelitis severity score (CMO:0001419)175090909986022412Rat
1354588Bvd4Brain ventricular dilatation QTL 45.310.001brain ventricle morphology trait (VT:0000822)hydrocephalus severity score (CMO:0001881)175349882882479847Rat
70210Cm15Cardiac mass QTL 156.5heart right ventricle mass (VT:0007033)heart right ventricle wet weight (CMO:0000072)175724672370156904Rat
1600398Edcs5Endometrial carcinoma susceptibility QTL 52.2uterus morphology trait (VT:0001120)percentage of study population developing endometrioid carcinoma during a period of time (CMO:0001759)175724672370852846Rat
2302365Gluco40Glucose level QTL 404.79blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)175724684382046127Rat
7488963Bp369Blood pressure QTL 3690.001arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)175900564977910000Rat
2317045Aia11Adjuvant induced arthritis QTL 114.06joint integrity trait (VT:0010548)left rear ankle joint diameter (CMO:0002149)176078142686533673Rat


Expression


Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000044132   ⟹   ENSRNOP00000049372
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1761,519,390 - 61,531,603 (-)Ensembl
RefSeq Acc Id: XM_039096375   ⟹   XP_038952303
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21761,518,138 - 61,535,484 (-)NCBI
Protein Sequences
Protein RefSeqs XP_038952303 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: XP_038952303   ⟸   XM_039096375
RefSeq Acc Id: ENSRNOP00000049372   ⟸   ENSRNOT00000044132
Protein Domains
Nudix hydrolase

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-D3ZVY0-F1-model_v2 AlphaFold D3ZVY0 1-249 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)
BioCyc Gene G2FUF-8887 BioCyc
Ensembl Genes ENSRNOG00000067140 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000049372 ENTREZGENE
  ENSRNOP00000049372.5 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000044132 ENTREZGENE
  ENSRNOT00000044132.6 UniProtKB/TrEMBL
Gene3D-CATH Nucleoside Triphosphate Pyrophosphohydrolase UniProtKB/TrEMBL
InterPro IsopentenylPP_isomerase_typ1 UniProtKB/TrEMBL
  NUDIX_hydrolase-like_dom_sf UniProtKB/TrEMBL
  NUDIX_hydrolase_dom UniProtKB/TrEMBL
NCBI Gene 291266 ENTREZGENE
PANTHER ISOPENTENYL-DIPHOSPHATE DELTA-ISOMERASE UniProtKB/TrEMBL
  ISOPENTENYL-DIPHOSPHATE DELTA-ISOMERASE 2 UniProtKB/TrEMBL
Pfam NUDIX UniProtKB/TrEMBL
PhenoGen RGD1564999 PhenoGen
PROSITE NUDIX UniProtKB/TrEMBL
Superfamily-SCOP SSF55811 UniProtKB/TrEMBL
TIGRFAMs IPP_isom_1 UniProtKB/TrEMBL
UniProt D3ZVY0_RAT UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2022-06-02 RGD1564999  similar to isopentenyl-diphosphate delta isomerase 2  RGD1564999  similar to isopentenyl-diphosphate delta isomerase 2  Data Merged 737654 PROVISIONAL
2021-08-09 RGD1564999  similar to isopentenyl-diphosphate delta isomerase 2      Symbol and Name status set to provisional 45752 PROVISIONAL
2012-07-02 RGD1564999  similar to isopentenyl-diphosphate delta isomerase 2  LOC689872  similar to isopentenyl-diphosphate delta isomerase 2  Data Merged 1643240 APPROVED
2008-04-30 RGD1564999  similar to isopentenyl-diphosphate delta isomerase 2   RGD1564999_predicted  similar to isopentenyl-diphosphate delta isomerase 2 (predicted)  'predicted' is removed 2292626 APPROVED
2006-11-19 LOC689872  similar to isopentenyl-diphosphate delta isomerase 2      Symbol and Name status set to provisional 70820 PROVISIONAL
2006-03-07 RGD1564999_predicted  similar to isopentenyl-diphosphate delta isomerase 2 (predicted)  LOC291266  similar to isopentenyl-diphosphate delta isomerase 2  Symbol and Name status set to approved 1299863 APPROVED
2006-02-09 LOC291266  similar to isopentenyl-diphosphate delta isomerase 2      Symbol and Name status set to provisional 70820 PROVISIONAL