Rdh8 (retinol dehydrogenase 8) - Rat Genome Database

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Gene: Rdh8 (retinol dehydrogenase 8) Rattus norvegicus
Analyze
Symbol: Rdh8
Name: retinol dehydrogenase 8
RGD ID: 1589829
Description: Predicted to enable all-trans-retinol dehydrogenase (NAD+) activity. Predicted to be involved in retinol metabolic process. Predicted to act upstream of or within visual perception. Predicted to be located in cytoplasm and membrane. Predicted to be active in cytosol. Orthologous to human RDH8 (retinol dehydrogenase 8); PARTICIPATES IN retinoid cycle metabolic pathway; retinol metabolic pathway; vitamin A deficiency pathway; INTERACTS WITH bisphenol A; 1,2-dichloroethane (ortholog); 4,4'-sulfonyldiphenol (ortholog).
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: LOC690953; retinol dehydrogenase 8 (all-trans); similar to retinol dehydrogenase 8
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Black Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: GRCr8 - GRCr8 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8827,629,380 - 27,636,651 (+)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl827,629,380 - 27,636,651 (+)EnsemblGRCr8
mRatBN7.2819,353,191 - 19,360,462 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl819,353,191 - 19,360,462 (+)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx823,372,628 - 23,379,896 (+)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0821,670,471 - 21,677,742 (+)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0819,582,880 - 19,590,157 (+)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0821,835,065 - 21,842,374 (+)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl821,835,103 - 21,842,374 (+)Ensemblrn6Rnor6.0
Rnor_5.0821,891,192 - 21,898,463 (+)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.4819,837,679 - 19,844,950 (+)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera820,748,500 - 20,755,674 (+)NCBICelera
Cytogenetic Map8q13NCBI
JBrowse:




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

Biological Process

Cellular Component
cytoplasm  (IEA)
cytosol  (IBA)
membrane  (IEA)

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. KEGG Annotation Import Pipeline Pipeline to import KEGG annotations from KEGG into RGD
4. SMPDB Annotation Import Pipeline Pipeline to import SMPDB annotations from SMPDB into RGD
5. GOA pipeline RGD automated data pipeline
6. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
7. Comprehensive gene review and curation RGD comprehensive gene curation
Additional References at PubMed
PMID:15755727  


Genomics

Comparative Map Data
Rdh8
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8827,629,380 - 27,636,651 (+)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl827,629,380 - 27,636,651 (+)EnsemblGRCr8
mRatBN7.2819,353,191 - 19,360,462 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl819,353,191 - 19,360,462 (+)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx823,372,628 - 23,379,896 (+)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0821,670,471 - 21,677,742 (+)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0819,582,880 - 19,590,157 (+)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0821,835,065 - 21,842,374 (+)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl821,835,103 - 21,842,374 (+)Ensemblrn6Rnor6.0
Rnor_5.0821,891,192 - 21,898,463 (+)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.4819,837,679 - 19,844,950 (+)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera820,748,500 - 20,755,674 (+)NCBICelera
Cytogenetic Map8q13NCBI
RDH8
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381910,013,483 - 10,022,279 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1910,013,249 - 10,022,279 (+)Ensemblhg38GRCh38
GRCh371910,124,159 - 10,132,955 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36199,984,925 - 9,993,954 (+)NCBIBuild 36Build 36hg18NCBI36
Build 34199,984,924 - 9,993,954NCBI
Celera1910,019,397 - 10,028,442 (+)NCBICelera
Cytogenetic Map19p13.2NCBI
HuRef199,704,402 - 9,713,196 (+)NCBIHuRef
CHM1_11910,123,733 - 10,132,768 (+)NCBICHM1_1
T2T-CHM13v2.01910,139,673 - 10,148,469 (+)NCBIT2T-CHM13v2.0
Rdh8
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39920,729,790 - 20,739,354 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl920,729,799 - 20,737,413 (+)EnsemblGRCm39 EnsemblGRCm39
GRCm38920,818,494 - 20,828,058 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl920,818,503 - 20,826,117 (+)Ensemblmm10GRCm38
MGSCv37920,622,948 - 20,630,607 (+)NCBIMGSCv37MGSCv37mm9NCBIm37
MGSCv36920,568,906 - 20,576,565 (+)NCBIMGSCv36mm8
Celera918,087,214 - 18,094,873 (+)NCBICelera
Cytogenetic Map9A3NCBI
cM Map97.64NCBI
Rdh8
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554951,388,424 - 1,392,552 (+)Ensembl
ChiLan1.0NW_0049554951,388,385 - 1,393,209 (+)NCBIChiLan1.0ChiLan1.0
RDH8
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v22014,932,689 - 14,941,498 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan11913,932,907 - 13,941,820 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v0199,565,918 - 9,575,017 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.11910,226,185 - 10,235,114 (+)NCBIPanPan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1910,226,185 - 10,235,114 (+)EnsemblpanPan2panpan1.1
RDH8
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.12051,029,633 - 51,035,910 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl2051,029,609 - 51,035,951 (-)EnsemblcanFam3CanFam3.1
Dog10K_Boxer_Tasha2050,896,101 - 50,902,410 (-)NCBIDog10K_Boxer_TashaDog10K_Boxer_Tasha
ROS_Cfam_1.02051,551,591 - 51,557,900 (-)NCBIROS_Cfam_1.0ROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl2051,551,596 - 51,557,940 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.12050,759,378 - 50,765,691 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.02051,186,311 - 51,192,625 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.02051,427,359 - 51,433,667 (-)NCBIUU_Cfam_GSD_1.0UU_Cfam_GSD_1.0
Rdh8
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024405118209,909,060 - 209,915,152 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_004936659439,557 - 445,298 (+)EnsemblSpeTri2.0 Ensembl
SpeTri2.0NW_004936659439,541 - 445,645 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
RDH8
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl268,871,707 - 68,877,675 (+)EnsemblsusScr11Sscrofa11.1
Sscrofa11.1268,871,707 - 68,878,222 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2269,199,776 - 69,206,290 (+)NCBISscrofa10.2Sscrofa10.2susScr3
RDH8
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.169,096,680 - 9,102,770 (+)NCBIChlSab1.1ChlSab1.1chlSab2
Vero_WHO_p1.0NW_02366607410,969,558 - 10,974,970 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Rdh8
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046248282,253,995 - 2,260,315 (+)EnsemblHetGla_female_1.0 EnsemblhetGla2HetGla_female_1.0 Ensembl
HetGla 1.0NW_0046248282,254,570 - 2,259,512 (+)NCBIHetGla 1.0HetGla 1.0hetGla2
Rdh8
(Rattus rattus - black rat)
Black Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rrattus_CSIRO_v1817,082,016 - 17,088,215 (+)NCBIRrattus_CSIRO_v1

Variants

.
Variants in Rdh8
82 total Variants
miRNA Target Status (No longer updated)

Predicted Target Of
Summary Value
Count of predictions:48
Count of miRNA genes:45
Interacting mature miRNAs:48
Transcripts:ENSRNOT00000032076
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 (GRCr8)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1357398Slep3Serum leptin concentration QTL 33.43blood leptin amount (VT:0005667)serum leptin level (CMO:0000780)81799410550763951Rat
2317030Wbc5White blood cell count QTL 53.210.005leukocyte quantity (VT:0000217)white blood cell count (CMO:0000027)81699464261994642Rat
12880044Am9Aortic mass QTL 90.007aorta mass (VT:0002845)aorta weight to aorta length to body weight ratio (CMO:0002722)81038254055382540Rat
2317032Ginf2Gastrointestinal inflammation QTL 23.210.005liver integrity trait (VT:0010547)liver granuloma severity score (CMO:0002157)81296416557964165Rat
2301416Bp315Blood pressure QTL 3150.008arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)81595227960952279Rat
2317036Livw3Liver weight QTL 32.430.01liver mass (VT:0003402)liver weight to body weight ratio (CMO:0000633)81296416557964165Rat
1598824Memor4Memory QTL 42.5exploratory behavior trait (VT:0010471)total horizontal distance resulting from voluntary locomotion in an experimental apparatus (CMO:0001443)81799386262252873Rat
12880023Bw184Body weight QTL 1840.001body mass (VT:0001259)body weight (CMO:0000012)81038254055382540Rat
9590084Insglur5Insulin/glucose ratio QTL 518.540.001blood insulin amount (VT:0001560)calculated plasma insulin level (CMO:0002170)8132882639Rat
12880028Cm103Cardiac mass QTL 1030.02heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)81038254055382540Rat
2317051Aia18Adjuvant induced arthritis QTL 182.42joint integrity trait (VT:0010548)left rear ankle joint diameter (CMO:0002149)81699464261994642Rat
2317048Ginf1Gastrointestinal inflammation QTL 13.520.005cecum mucosa thickness (VT:0010234)enterocolitis severity score (CMO:0002138)81296416557964165Rat
2302367Slep5Serum leptin concentration QTL 53.43blood leptin amount (VT:0005667)serum leptin level (CMO:0000780)81799410550763951Rat
12880025Cm102Cardiac mass QTL 1020.044heart mass (VT:0007028)heart wet weight to body weight ratio (CMO:0002408)81038254055382540Rat

Markers in Region
D8Got20  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2819,356,230 - 19,356,439 (+)MAPPERmRatBN7.2
Rnor_6.0821,838,143 - 21,838,351NCBIRnor6.0
Rnor_5.0821,894,232 - 21,894,440UniSTSRnor5.0
RGSC_v3.4819,840,718 - 19,840,927RGDRGSC3.4
RGSC_v3.4819,840,719 - 19,840,927UniSTSRGSC3.4
Celera820,751,443 - 20,751,651UniSTS
RGSC_v3.1819,840,718 - 19,840,927RGD
Cytogenetic Map8q13UniSTS


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
sensory system
visual system
7 3 11 48 35 36 11 24 11 4 82 49 34 13 57 25 13 13

Sequence


Ensembl Acc Id: ENSRNOT00000032076   ⟹   ENSRNOP00000033991
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl827,629,380 - 27,636,651 (+)Ensembl
mRatBN7.2 Ensembl819,353,191 - 19,360,462 (+)Ensembl
Rnor_6.0 Ensembl821,835,103 - 21,842,374 (+)Ensembl
RefSeq Acc Id: NM_001168593   ⟹   NP_001162065
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8827,629,380 - 27,636,651 (+)NCBI
mRatBN7.2819,353,191 - 19,360,462 (+)NCBI
Rnor_6.0821,835,103 - 21,842,374 (+)NCBI
Rnor_5.0821,891,192 - 21,898,463 (+)NCBI
RGSC_v3.4819,837,679 - 19,844,950 (+)RGD
Celera820,748,500 - 20,755,674 (+)RGD
Sequence:
Protein Sequences
Protein RefSeqs NP_001162065 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein EDL78350 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000033991
  ENSRNOP00000033991.4
RefSeq Acc Id: NP_001162065   ⟸   NM_001168593
- UniProtKB: D4A8D2 (UniProtKB/TrEMBL),   A6JNL6 (UniProtKB/TrEMBL)
- Sequence:
Ensembl Acc Id: ENSRNOP00000033991   ⟸   ENSRNOT00000032076

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-D4A8D2-F1-model_v2 AlphaFold D4A8D2 1-312 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:1589829 AgrOrtholog
BioCyc Gene G2FUF-31458 BioCyc
BioCyc Pathway PWY-6857 [retinol biosynthesis] BioCyc
  PWY-6861 [the visual cycle I (vertebrates)] BioCyc
BioCyc Pathway Image PWY-6857 BioCyc
  PWY-6861 BioCyc
Ensembl Genes ENSRNOG00000025767 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000032076 ENTREZGENE
  ENSRNOT00000032076.6 UniProtKB/TrEMBL
Gene3D-CATH NAD(P)-binding Rossmann-like Domain UniProtKB/TrEMBL
InterPro 17beta_DH UniProtKB/TrEMBL
  Glc/ribitol_DH UniProtKB/TrEMBL
  NAD(P)-bd_dom_sf UniProtKB/TrEMBL
  Sc_DH/Rdtase_CS UniProtKB/TrEMBL
KEGG Report rno:690953 UniProtKB/TrEMBL
NCBI Gene 690953 ENTREZGENE
PANTHER RETINOL DEHYDROGENASE 8 UniProtKB/TrEMBL
  RETINOL DEHYDROGENASE-RELATED UniProtKB/TrEMBL
Pfam adh_short UniProtKB/TrEMBL
PhenoGen Rdh8 PhenoGen
PIRSF 17beta-HSD UniProtKB/TrEMBL
PRINTS GDHRDH UniProtKB/TrEMBL
  SDRFAMILY UniProtKB/TrEMBL
PROSITE ADH_SHORT UniProtKB/TrEMBL
RatGTEx ENSRNOG00000025767 RatGTEx
Superfamily-SCOP SSF51735 UniProtKB/TrEMBL
UniProt A6JNL6 ENTREZGENE, UniProtKB/TrEMBL
  D4A8D2 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2018-02-19 Rdh8  retinol dehydrogenase 8  Rdh8  retinol dehydrogenase 8 (all-trans)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-09-24 Rdh8  retinol dehydrogenase 8 (all-trans)  Rdh8  retinol dehydrogenase 8  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-03-06 Rdh8  retinol dehydrogenase 8  LOC690953  similar to retinol dehydrogenase 8  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-01-09 LOC690953  similar to retinol dehydrogenase 8  LOC687099  similar to retinol dehydrogenase 8  Data merged from RGD:1590070 1643240 APPROVED
2006-11-20 LOC690953  similar to retinol dehydrogenase 8      Symbol and Name status set to provisional 70820 PROVISIONAL
2006-11-20 LOC687099  similar to retinol dehydrogenase 8      Symbol and Name status set to provisional 70820 PROVISIONAL