Rdh10 (retinol dehydrogenase 10) - Rat Genome Database

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Gene: Rdh10 (retinol dehydrogenase 10) Rattus norvegicus
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Symbol: Rdh10
Name: retinol dehydrogenase 10
RGD ID: 727793
Description: Predicted to enable NAD-retinol dehydrogenase activity. Involved in positive regulation of retinoic acid biosynthetic process. Located in intracellular membrane-bounded organelle. Orthologous to human RDH10 (retinol dehydrogenase 10); PARTICIPATES IN retinoic acid metabolic pathway; retinoid cycle metabolic pathway; retinol metabolic pathway; INTERACTS WITH 1-naphthyl isothiocyanate; 4,4'-diaminodiphenylmethane; acetamide.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: retinol dehydrogenase 10 (all-trans)
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Candidate Gene For: Vetf3
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.253,186,671 - 3,215,572 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl53,188,445 - 3,215,572 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx55,305,902 - 5,332,978 (-)NCBIRnor_SHR
UTH_Rnor_SHRSP_BbbUtx_1.056,944,767 - 6,971,843 (-)NCBIRnor_SHRSP
UTH_Rnor_WKY_Bbb_1.056,641,260 - 6,668,810 (-)NCBIRnor_WKY
Rnor_6.052,605,265 - 2,631,905 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl52,603,505 - 2,632,030 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.052,593,904 - 2,620,243 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.452,286,373 - 2,314,154 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.152,286,372 - 2,314,154 (-)NCBI
Celera52,790,137 - 2,816,729 (-)NCBICelera
Cytogenetic Map5q11NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
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. Key enzymes of the retinoid (visual) cycle in vertebrate retina. Kiser PD, etal., Biochim Biophys Acta. 2012 Jan;1821(1):137-51. Epub 2011 Apr 5.
3. Physiological insights into all-trans-retinoic acid biosynthesis. Napoli JL Biochim Biophys Acta. 2012 Jan;1821(1):152-67. Epub 2011 May 19.
4. NCBI rat LocusLink and RefSeq merged data October 15, 2003 NCBI rat LocusLink and RefSeq merged data October 15, 2003
5. KEGG Annotation Import Pipeline Pipeline to import KEGG annotations from KEGG into RGD
6. GOA pipeline RGD automated data pipeline
7. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
8. Comprehensive gene review and curation RGD comprehensive gene curation
9. Multiple retinol and retinal dehydrogenases catalyze all-trans-retinoic acid biosynthesis in astrocytes. Wang C, etal., J Biol Chem. 2011 Feb 25;286(8):6542-53. Epub 2010 Dec 7.
10. Cloning and characterization of a novel all-trans retinol short-chain dehydrogenase/reductase from the RPE. Wu BX, etal., Invest Ophthalmol Vis Sci 2002 Nov;43(11):3365-72.
11. Identification of RDH10, an All-trans Retinol Dehydrogenase, in Retinal Muller Cells. Wu BX, etal., Invest Ophthalmol Vis Sci. 2004 Nov;45(11):3857-62.
Additional References at PubMed
PMID:17473173   PMID:19458327  


Genomics

Comparative Map Data
Rdh10
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.253,186,671 - 3,215,572 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl53,188,445 - 3,215,572 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx55,305,902 - 5,332,978 (-)NCBIRnor_SHR
UTH_Rnor_SHRSP_BbbUtx_1.056,944,767 - 6,971,843 (-)NCBIRnor_SHRSP
UTH_Rnor_WKY_Bbb_1.056,641,260 - 6,668,810 (-)NCBIRnor_WKY
Rnor_6.052,605,265 - 2,631,905 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl52,603,505 - 2,632,030 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.052,593,904 - 2,620,243 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.452,286,373 - 2,314,154 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.152,286,372 - 2,314,154 (-)NCBI
Celera52,790,137 - 2,816,729 (-)NCBICelera
Cytogenetic Map5q11NCBI
RDH10
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38873,294,602 - 73,325,281 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p13 Ensembl873,294,602 - 73,325,281 (+)EnsemblGRCh38hg38GRCh38
GRCh37874,206,837 - 74,237,516 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36874,369,891 - 74,399,347 (+)NCBINCBI36Build 36hg18NCBI36
Build 34874,369,890 - 74,399,345NCBI
Celera870,204,803 - 70,235,112 (+)NCBICelera
Cytogenetic Map8q21.11NCBI
HuRef869,697,681 - 69,728,383 (+)NCBIHuRef
CHM1_1874,259,535 - 74,290,179 (+)NCBICHM1_1
T2T-CHM13v2.0873,724,122 - 73,754,883 (+)NCBIT2T-CHM13v2.0
Rdh10
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39116,176,106 - 16,202,774 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl116,175,998 - 16,203,958 (+)EnsemblGRCm39 Ensembl
GRCm38116,105,882 - 16,132,550 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl116,105,774 - 16,133,734 (+)EnsemblGRCm38mm10GRCm38
MGSCv37116,095,963 - 16,122,631 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv36116,091,096 - 16,117,764 (+)NCBIMGSCv36mm8
Celera116,041,876 - 16,068,353 (+)NCBICelera
Cytogenetic Map1A3NCBI
cM Map14.94NCBI
Rdh10
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554446,878,722 - 6,909,421 (-)EnsemblChiLan1.0
ChiLan1.0NW_0049554446,878,722 - 6,909,421 (-)NCBIChiLan1.0ChiLan1.0
RDH10
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.1871,481,094 - 71,510,689 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl871,481,089 - 71,510,689 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v0869,833,320 - 69,863,536 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
RDH10
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.12921,886,014 - 21,912,451 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl2921,885,012 - 21,911,303 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha2922,150,310 - 22,176,734 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.02921,995,836 - 22,022,275 (+)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl2921,994,920 - 22,022,273 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.12922,053,870 - 22,080,295 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.02922,090,663 - 22,117,118 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.02922,371,574 - 22,398,035 (+)NCBIUU_Cfam_GSD_1.0
Rdh10
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440530357,360,563 - 57,388,453 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049366482,060,125 - 2,088,833 (+)EnsemblSpeTri2.0
SpeTri2.0NW_0049366482,060,131 - 2,088,021 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
RDH10
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl462,569,885 - 62,601,439 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1462,569,877 - 62,600,981 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
RDH10
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1868,903,665 - 68,933,536 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl868,904,352 - 68,933,792 (+)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366603972,438,768 - 72,468,649 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Rdh10
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_00462474417,837,609 - 17,868,431 (-)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_00462474417,838,047 - 17,868,423 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Rdh10
94 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:121
Count of miRNA genes:106
Interacting mature miRNAs:112
Transcripts:ENSRNOT00000009096
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 (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1331756Rf34Renal function QTL 344.16275kidney blood vessel physiology trait (VT:0100012)absolute change in renal blood flow rate (CMO:0001168)5190450412Rat
70212Niddm25Non-insulin dependent diabetes mellitus QTL 253.54blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)51131345958Rat
1331771Rf35Renal function QTL 354.36965kidney blood vessel physiology trait (VT:0100012)absolute change in renal blood flow rate (CMO:0001168)572947086724018Rat
2312562Pur18Proteinuria QTL 182.60.001urine total protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)5213896532656739Rat
1576314Eutr1Estrogen induced uterine response QTL 1uterus integrity trait (VT:0010575)pyometritis severity score (CMO:0002009)52138965166875058Rat
631551Vetf1Vascular elastic tissue fragility QTL 150.0001aorta elastic tissue integrity trait (VT:0010556)artery internal elastic lamina non-tumorous lesion count (CMO:0001913)522822265904428Rat
8662454Vetf3Vascular elastic tissue fragility QTL 327.4artery integrity trait (VT:0010639)number of ruptures of the internal elastic lamina of the abdominal aorta and iliac arteries (CMO:0002562)5228222669540447Rat


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 3 33 33 11 33 48 35 41 11
Low 43 24 8 8 8 8 11 26 8
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000009096   ⟹   ENSRNOP00000009096
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl53,188,445 - 3,215,572 (-)Ensembl
Rnor_6.0 Ensembl52,603,505 - 2,632,030 (-)Ensembl
RefSeq Acc Id: NM_181478   ⟹   NP_852143
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.253,188,445 - 3,215,572 (-)NCBI
Rnor_6.052,605,265 - 2,631,905 (-)NCBI
Rnor_5.052,593,904 - 2,620,243 (-)NCBI
RGSC_v3.452,286,373 - 2,314,154 (-)RGD
Celera52,790,137 - 2,816,729 (-)RGD
Sequence:
RefSeq Acc Id: XM_039110151   ⟹   XP_038966079
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.253,186,671 - 3,215,165 (-)NCBI
Protein Sequences
Protein RefSeqs NP_852143 (Get FASTA)   NCBI Sequence Viewer  
  XP_038966079 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAO31688 (Get FASTA)   NCBI Sequence Viewer  
  EDM11511 (Get FASTA)   NCBI Sequence Viewer  
  EDM11512 (Get FASTA)   NCBI Sequence Viewer  
  Q80ZF7 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: NP_852143   ⟸   NM_181478
- UniProtKB: Q80ZF7 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: ENSRNOP00000009096   ⟸   ENSRNOT00000009096
RefSeq Acc Id: XP_038966079   ⟸   XM_039110151
- Peptide Label: isoform X1

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-Q80ZF7-F1-model_v2 AlphaFold Q80ZF7 1-341 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:727793 AgrOrtholog
BioCyc Gene G2FUF-42304 BioCyc
Ensembl Genes ENSRNOG00000006681 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Protein ENSRNOP00000009096 ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript ENSRNOT00000009096 ENTREZGENE, UniProtKB/Swiss-Prot
InterPro NAD(P)-bd_dom_sf UniProtKB/Swiss-Prot
  RDH10 UniProtKB/Swiss-Prot
  Sc_DH/Rdtase_CS UniProtKB/Swiss-Prot
  SDR_fam UniProtKB/Swiss-Prot
KEGG Report rno:353252 UniProtKB/Swiss-Prot
NCBI Gene 353252 ENTREZGENE
PANTHER PTHR24322:SF731 UniProtKB/Swiss-Prot
Pfam adh_short UniProtKB/Swiss-Prot
PhenoGen Rdh10 PhenoGen
PRINTS GDHRDH UniProtKB/Swiss-Prot
  SDRFAMILY UniProtKB/Swiss-Prot
PROSITE ADH_SHORT UniProtKB/Swiss-Prot
Superfamily-SCOP SSF51735 UniProtKB/Swiss-Prot
UniProt Q80ZF7 ENTREZGENE, UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2016-12-15 Rdh10  retinol dehydrogenase 10  Rdh10  retinol dehydrogenase 10 (all-trans)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2004-09-10 Rdh10  retinol dehydrogenase 10 (all-trans)      Symbol and Name status set to approved 1299863 APPROVED