Ubiad1 (UbiA prenyltransferase domain containing 1) - Rat Genome Database

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Gene: Ubiad1 (UbiA prenyltransferase domain containing 1) Rattus norvegicus
Analyze
Symbol: Ubiad1
Name: UbiA prenyltransferase domain containing 1
RGD ID: 1309588
Description: Predicted to enable antioxidant activity and prenyltransferase activity. Predicted to be involved in circulatory system development; endothelial cell development; and ketone biosynthetic process. Predicted to be located in cytoplasm; membrane; and nucleus. Predicted to be active in Golgi membrane and endoplasmic reticulum. Human ortholog(s) of this gene implicated in Schnyder corneal dystrophy. Orthologous to human UBIAD1 (UbiA prenyltransferase domain containing 1); INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; 2,4-dinitrotoluene; bisphenol A.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: LOC313706; RGD1309588; similar to transitional epithelia response protein; ubiA prenyltransferase domain-containing protein 1
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
GRCr85164,139,714 - 164,167,777 (-)NCBIGRCr8
mRatBN7.25158,856,582 - 158,880,490 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl5158,868,672 - 158,880,271 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx5161,585,431 - 161,597,024 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.05163,407,568 - 163,419,147 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.05163,363,915 - 163,375,494 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.05165,247,630 - 165,259,228 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl5165,247,133 - 165,259,224 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.05168,904,231 - 168,915,829 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.45165,515,219 - 165,526,817 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.15165,527,047 - 165,536,759 (-)NCBI
Celera5157,145,271 - 157,156,869 (-)NCBICelera
Cytogenetic Map5q36NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

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 MGI mouse gene data--August 2006 MGD data from the GO Consortium
3. OMIM Disease Annotation Pipeline OMIM Disease Annotation 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
Additional References at PubMed
PMID:11314041   PMID:20953171   PMID:23169578   PMID:23374346   PMID:25874989   PMID:27846632   PMID:30483777  


Genomics

Comparative Map Data
Ubiad1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr85164,139,714 - 164,167,777 (-)NCBIGRCr8
mRatBN7.25158,856,582 - 158,880,490 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl5158,868,672 - 158,880,271 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx5161,585,431 - 161,597,024 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.05163,407,568 - 163,419,147 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.05163,363,915 - 163,375,494 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.05165,247,630 - 165,259,228 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl5165,247,133 - 165,259,224 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.05168,904,231 - 168,915,829 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.45165,515,219 - 165,526,817 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.15165,527,047 - 165,536,759 (-)NCBI
Celera5157,145,271 - 157,156,869 (-)NCBICelera
Cytogenetic Map5q36NCBI
UBIAD1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38111,273,198 - 11,299,574 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl111,273,198 - 11,296,049 (+)EnsemblGRCh38hg38GRCh38
GRCh37111,333,255 - 11,359,631 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36111,255,866 - 11,268,929 (+)NCBINCBI36Build 36hg18NCBI36
Celera110,445,515 - 10,460,752 (+)NCBICelera
Cytogenetic Map1p36.22NCBI
HuRef110,484,571 - 10,499,808 (+)NCBIHuRef
CHM1_1111,321,582 - 11,336,819 (+)NCBICHM1_1
T2T-CHM13v2.0110,814,791 - 10,841,185 (+)NCBIT2T-CHM13v2.0
Ubiad1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm394148,518,952 - 148,529,217 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl4148,518,952 - 148,529,228 (-)EnsemblGRCm39 Ensembl
GRCm384148,434,495 - 148,444,760 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl4148,434,495 - 148,444,771 (-)EnsemblGRCm38mm10GRCm38
MGSCv374147,808,606 - 147,818,860 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv364147,278,297 - 147,288,551 (-)NCBIMGSCv36mm8
Celera4150,694,934 - 150,705,296 (-)NCBICelera
Cytogenetic Map4E2NCBI
cM Map478.76NCBI
Ubiad1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554862,472,035 - 2,481,975 (-)EnsemblChiLan1.0
ChiLan1.0NW_0049554862,472,035 - 2,481,975 (-)NCBIChiLan1.0ChiLan1.0
UBIAD1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v21216,825,270 - 216,947,504 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan11215,471,658 - 215,593,828 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v0110,039,415 - 10,161,005 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.1111,260,412 - 11,283,070 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl111,260,412 - 11,281,381 (+)Ensemblpanpan1.1panPan2
UBIAD1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1284,803,338 - 84,813,030 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl284,804,935 - 84,813,344 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha281,333,812 - 81,343,426 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0285,465,002 - 85,474,235 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl285,465,558 - 85,474,643 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1282,213,915 - 82,223,567 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0283,215,697 - 83,225,323 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0284,278,162 - 84,287,802 (-)NCBIUU_Cfam_GSD_1.0
Ubiad1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440505834,459,827 - 34,468,386 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_004936474284,569 - 295,572 (+)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_004936474284,630 - 293,090 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
UBIAD1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl671,419,602 - 71,433,210 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1671,419,559 - 71,431,275 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2665,324,184 - 65,335,891 (+)NCBISscrofa10.2Sscrofa10.2susScr3
UBIAD1
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.120120,499,210 - 120,512,759 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl20120,496,075 - 120,512,748 (-)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366605424,407,273 - 24,421,040 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Ubiad1
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046248181,554,084 - 1,565,383 (-)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_0046248181,555,751 - 1,565,281 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Ubiad1
61 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:254
Count of miRNA genes:168
Interacting mature miRNAs:199
Transcripts:ENSRNOT00000012692
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
10053720Scort26Serum corticosterone level QTL 262.060.0147blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)5124965598166875058Rat
631272Lanf1Left ventricular atrial natriuretic factor QTL 112heart left ventricle natriuretic peptide A amount (VT:0010596)heart left ventricle natriuretic peptide A level (CMO:0002165)5151113452166875058Rat
1576314Eutr1Estrogen induced uterine response QTL 1uterus integrity trait (VT:0010575)pyometritis severity score (CMO:0002009)52138965166875058Rat
2302369Scl60Serum cholesterol level QTL 603.13blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)5143608201161165651Rat
631562Apr2Acute phase response QTL 23.7blood murinoglobulin 1 amount (VT:0010597)plasma murinoglobulin 1 level (CMO:0001931)5135927956166875058Rat
634349Bp139Blood pressure QTL 1390.001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)5128924607166875058Rat
61444Strs2Sensitivity to stroke QTL 24.7cerebrum integrity trait (VT:0010549)post-insult time to onset of cerebrovascular lesion (CMO:0002343)5135929696166875058Rat
724525Bp147Blood pressure QTL 1474.30.0001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)5126424772166875058Rat
1549904Neuinf1Neuroinflammation QTL 130nervous system integrity trait (VT:0010566)blood T lymphocyte count (CMO:0000110)5154828214166875058Rat
738018Anxrr4Anxiety related response QTL 45.1exploratory behavior trait (VT:0010471)percentage of entries into a discrete space in an experimental apparatus (CMO:0000961)5130130159166875058Rat
2313096Bmd78Bone mineral density QTL 783.10.0001tibia mineral mass (VT:1000283)total volumetric bone mineral density (CMO:0001728)5144377876161317411Rat
8552908Pigfal4Plasma insulin-like growth factor 1 level QTL 46.6blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)5128506074166875058Rat
61393Bp7Blood pressure QTL 74.50.0001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)560293434161481680Rat
7794791Mcs33Mammary carcinoma susceptibility QTL 331.93mammary gland integrity trait (VT:0010552)mammary tumor incidence/prevalence measurement (CMO:0000946)5131345754166875058Rat
1354631Swd2Spike wave discharge measurement QTL 23.640.0002brain electrophysiology trait (VT:0010557)brain total spike-and-wave discharge duration (CMO:0001740)5151113452164465185Rat
1302790Scl20Serum cholesterol level QTL 206.40.0001blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)582394392166664054Rat
1598861Cm64Cardiac mass QTL 642.9heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)5127798274166875058Rat
1578766Tcas11Tongue tumor susceptibility QTL 114.12tongue integrity trait (VT:0010553)number of squamous cell tumors of the tongue with diameter greater than 3 mm (CMO:0001950)546711509161317411Rat
631505Bp103Blood pressure QTL 1033.2arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)5132717196165560427Rat
1641920Colcs1Colorectal carcinoma susceptibility QTL 12.990.0055intestine integrity trait (VT:0010554)benign colorectal tumor surface area measurement (CMO:0001799)5121846814166846814Rat
1298090Bp155Blood pressure QTL 1553.8arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)5151006154161165494Rat
1598819Bp292Blood pressure QTL 2924.3arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)5127798274166875058Rat
8694169Bw148Body weight QTL 14850.001body mass (VT:0001259)body weight gain (CMO:0000420)5128506074166875058Rat
1331721Bp210Blood pressure QTL 2103.413arterial blood pressure trait (VT:2000000)blood pressure time series experimental set point of the baroreceptor response (CMO:0002593)5143069996166846814Rat

Markers in Region
RH129718  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.25158,868,705 - 158,868,905 (+)MAPPERmRatBN7.2
Rnor_6.05165,247,664 - 165,247,863NCBIRnor6.0
Rnor_5.05168,904,265 - 168,904,464UniSTSRnor5.0
RGSC_v3.45165,515,253 - 165,515,452UniSTSRGSC3.4
Celera5157,145,305 - 157,145,504UniSTS
RH 3.4 Map51105.1UniSTS
Cytogenetic Map5q36UniSTS


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
nervous system
renal system
reproductive system
respiratory system
9 11 49 113 91 90 59 25 59 6 218 97 93 45 60 31

Sequence


Ensembl Acc Id: ENSRNOT00000012692   ⟹   ENSRNOP00000012691
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl5158,868,672 - 158,880,271 (-)Ensembl
Rnor_6.0 Ensembl5165,247,133 - 165,259,224 (-)Ensembl
RefSeq Acc Id: NM_001107993   ⟹   NP_001101463
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr85164,151,802 - 164,163,400 (-)NCBI
mRatBN7.25158,868,672 - 158,880,271 (-)NCBI
Rnor_6.05165,247,630 - 165,259,228 (-)NCBI
Rnor_5.05168,904,231 - 168,915,829 (-)NCBI
RGSC_v3.45165,515,219 - 165,526,817 (-)RGD
Celera5157,145,271 - 157,156,869 (-)RGD
Sequence:
RefSeq Acc Id: XM_039110098   ⟹   XP_038966026
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr85164,153,808 - 164,164,296 (-)NCBI
mRatBN7.25158,870,681 - 158,880,490 (-)NCBI
RefSeq Acc Id: XM_039110099   ⟹   XP_038966027
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr85164,139,714 - 164,164,290 (-)NCBI
mRatBN7.25158,856,582 - 158,880,483 (-)NCBI
RefSeq Acc Id: XM_063287833   ⟹   XP_063143903
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr85164,151,801 - 164,167,777 (-)NCBI
RefSeq Acc Id: NP_001101463   ⟸   NM_001107993
- UniProtKB: D3ZG27 (UniProtKB/Swiss-Prot)
- Sequence:
Ensembl Acc Id: ENSRNOP00000012691   ⟸   ENSRNOT00000012692
RefSeq Acc Id: XP_038966027   ⟸   XM_039110099
- Peptide Label: isoform X2
RefSeq Acc Id: XP_038966026   ⟸   XM_039110098
- Peptide Label: isoform X1
RefSeq Acc Id: XP_063143903   ⟸   XM_063287833
- Peptide Label: isoform X3

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-D3ZG27-F1-model_v2 AlphaFold D3ZG27 1-338 view protein structure

Transcriptome

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

Promoters
RGD ID:13694260
Promoter ID:EPDNEW_R4785
Type:multiple initiation site
Name:Ubiad1_1
Description:UbiA prenyltransferase domain containing 1
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_6.05165,259,225 - 165,259,285EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1309588 AgrOrtholog
BioCyc Gene G2FUF-39166 BioCyc
Ensembl Genes ENSRNOG00000009575 Ensembl, UniProtKB/Swiss-Prot
  ENSRNOG00055022876 UniProtKB/Swiss-Prot
  ENSRNOG00060030393 UniProtKB/Swiss-Prot
  ENSRNOG00065010719 UniProtKB/Swiss-Prot
Ensembl Transcript ENSRNOT00000012692.6 UniProtKB/Swiss-Prot
  ENSRNOT00055039273 UniProtKB/Swiss-Prot
  ENSRNOT00060052781 UniProtKB/Swiss-Prot
  ENSRNOT00065017372 UniProtKB/Swiss-Prot
Gene3D-CATH 1.10.357.140 UniProtKB/Swiss-Prot
InterPro UbiA_prenyltransferase UniProtKB/Swiss-Prot
  UbiA_sf UniProtKB/Swiss-Prot
  UBIAD1 UniProtKB/Swiss-Prot
KEGG Report rno:313706 UniProtKB/Swiss-Prot
NCBI Gene 313706 ENTREZGENE
PANTHER PTHR13929 UniProtKB/Swiss-Prot
  UBIA PRENYLTRANSFERASE DOMAIN-CONTAINING PROTEIN 1 UniProtKB/Swiss-Prot
Pfam UbiA UniProtKB/Swiss-Prot
PhenoGen Ubiad1 PhenoGen
PIRSF UBIAD1 UniProtKB/Swiss-Prot
RatGTEx ENSRNOG00000009575 RatGTEx
  ENSRNOG00055022876 RatGTEx
  ENSRNOG00060030393 RatGTEx
  ENSRNOG00065010719 RatGTEx
UniProt D3ZG27 ENTREZGENE, UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2008-04-30 Ubiad1  UbiA prenyltransferase domain containing 1   Ubiad1_predicted  UbiA prenyltransferase domain containing 1 (predicted)  'predicted' is removed 2292626 APPROVED
2006-03-30 Ubiad1_predicted  UbiA prenyltransferase domain containing 1 (predicted)  RGD1309588_predicted  similar to transitional epithelia response protein (predicted)  Symbol and Name updated 1299863 APPROVED
2005-01-20 RGD1309588_predicted  similar to transitional epithelia response protein (predicted)  LOC313706_predicted    Symbol and Name status set to approved 1331353 APPROVED
2005-01-12 LOC313706_predicted  similar to transitional epithelia response protein (predicted)      Symbol and Name status set to provisional 70820 PROVISIONAL