Rdh16 (retinol dehydrogenase 16) - Rat Genome Database

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Gene: Rdh16 (retinol dehydrogenase 16) Mus musculus
Analyze
Symbol: Rdh16
Name: retinol dehydrogenase 16
RGD ID: 1623284
MGI Page MGI
Description: Enables all-trans-retinol dehydrogenase (NAD+) activity and identical protein binding activity. Involved in retinoid metabolic process and steroid metabolic process. Acts upstream of or within 9-cis-retinoic acid biosynthetic process. Located in endoplasmic reticulum lumen and endoplasmic reticulum membrane. Is expressed in alimentary system; embryo; future spinal cord; liver; and salivary gland. Orthologous to human RDH16 (retinol dehydrogenase 16).
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: cis-retinol/androgen dehydrogenase 1; CRA; CRAD; CRAD1; MGC107668; Rdh; Rdh6; retinol dehydrogenase 6; retinol dehydrogenase type 6
RGD Orthologs
Human
Bonobo
Alliance Orthologs
More Info more info ...
Latest Assembly: GRCm39 - Mouse Genome Assembly GRCm39
Position:
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm3910127,636,959 - 127,651,715 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl10127,637,021 - 127,682,434 (+)EnsemblGRCm39 Ensembl
GRCm3810127,801,090 - 127,815,846 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl10127,801,152 - 127,846,565 (+)EnsemblGRCm38mm10GRCm38
MGSCv3710127,238,209 - 127,252,895 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv3610127,204,103 - 127,218,788 (+)NCBIMGSCv36mm8
Celera10130,195,773 - 130,210,462 (+)NCBICelera
Cytogenetic Map10D3NCBI
cM Map1075.7NCBI
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
(1->4)-beta-D-glucan  (EXP)
1,1-dichloroethene  (EXP)
1,2-dichloroethane  (EXP)
17beta-estradiol  (EXP,ISO)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,ISO)
2,4,6-trinitrobenzenesulfonic acid  (EXP)
2,4-dibromophenyl 2,4,5-tribromophenyl ether  (EXP)
3,4-methylenedioxymethamphetamine  (EXP)
4-hydroxyphenyl retinamide  (EXP)
aflatoxin B1  (ISO)
benzo[a]pyrene  (EXP,ISO)
bis(2-ethylhexyl) phthalate  (EXP)
bisphenol A  (ISO)
buta-1,3-diene  (EXP)
carnosic acid  (EXP)
chenodeoxycholic acid  (ISO)
chromium(6+)  (EXP)
clofibrate  (EXP)
cyclosporin A  (ISO)
DDE  (ISO)
deoxycholic acid  (ISO)
dibenzofurans  (EXP)
Dibutyl phosphate  (ISO)
dichloroacetic acid  (EXP)
dimethylarsinic acid  (EXP)
fenofibrate  (EXP)
fenthion  (EXP)
glycochenodeoxycholic acid  (ISO)
glycocholic acid  (ISO)
glycodeoxycholic acid  (ISO)
inulin  (EXP)
Lasiocarpine  (ISO)
methylarsonic acid  (EXP)
monosodium L-glutamate  (EXP)
N-Nitrosopyrrolidine  (ISO)
NAD zwitterion  (ISO)
NAD(+)  (ISO)
nefazodone  (ISO)
O-methyleugenol  (ISO)
paracetamol  (EXP,ISO)
perfluorononanoic acid  (ISO)
perfluorooctane-1-sulfonic acid  (EXP)
permethrin  (EXP)
phenobarbital  (EXP)
pirinixic acid  (EXP)
pregnenolone 16alpha-carbonitrile  (EXP)
progesterone  (EXP)
sodium arsenate  (EXP)
sodium arsenite  (EXP,ISO)
Sunset Yellow FCF  (ISO)
tartrazine  (ISO)
testosterone  (EXP)
tetrachloroethene  (EXP)
tetrachloromethane  (EXP)
tetracycline  (EXP)
thiram  (ISO)
trichloroethene  (EXP)
triptonide  (EXP)
troglitazone  (EXP)
valproic acid  (ISO)
vancomycin  (EXP)

Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

Molecular Pathway Annotations     Click to see Annotation Detail View
Phenotype Annotations     Click to see Annotation Detail View

Mammalian Phenotype
References

References - curated
# Reference Title Reference Citation
1. KEGG Annotation Import Pipeline Pipeline to import KEGG annotations from KEGG into RGD
2. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:9407098   PMID:10349636   PMID:10753524   PMID:11042159   PMID:11076861   PMID:11125038   PMID:11217851   PMID:11747070   PMID:11876656   PMID:12466851   PMID:12477932   PMID:14681479  
PMID:15355969   PMID:15765518   PMID:16141072   PMID:16141073   PMID:16223484   PMID:17270348   PMID:21267068   PMID:21677750   PMID:21873635   PMID:30973865   PMID:38355793  


Genomics

Comparative Map Data
Rdh16
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm3910127,636,959 - 127,651,715 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl10127,637,021 - 127,682,434 (+)EnsemblGRCm39 Ensembl
GRCm3810127,801,090 - 127,815,846 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl10127,801,152 - 127,846,565 (+)EnsemblGRCm38mm10GRCm38
MGSCv3710127,238,209 - 127,252,895 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv3610127,204,103 - 127,218,788 (+)NCBIMGSCv36mm8
Celera10130,195,773 - 130,210,462 (+)NCBICelera
Cytogenetic Map10D3NCBI
cM Map1075.7NCBI
RDH16
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381256,951,431 - 56,957,608 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1256,951,431 - 56,959,374 (-)EnsemblGRCh38hg38GRCh38
GRCh371257,345,215 - 57,351,392 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361255,631,482 - 55,637,685 (-)NCBINCBI36Build 36hg18NCBI36
Celera1256,999,103 - 57,005,306 (-)NCBICelera
Cytogenetic Map12q13.3NCBI
HuRef1254,383,970 - 54,390,173 (-)NCBIHuRef
CHM1_11257,312,965 - 57,319,168 (-)NCBICHM1_1
T2T-CHM13v2.01256,919,300 - 56,925,477 (-)NCBIT2T-CHM13v2.0
RDH16
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v21037,345,736 - 37,380,367 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan11237,369,988 - 37,377,137 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v01231,958,385 - 31,966,319 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.11232,211,691 - 32,219,624 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1232,212,746 - 32,219,624 (+)Ensemblpanpan1.1panPan2

Variants

.
Variants in Rdh16
383 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:2044
Count of miRNA genes:727
Interacting mature miRNAs:896
Transcripts:ENSMUST00000071646, ENSMUST00000125163, ENSMUST00000155739
Prediction methods:Miranda, Rnahybrid
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 (GRCm39)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
4142461Bmd25_mbone mineral density 25 (mouse)Not determined1097217101130530862Mouse
1301968Estq4_mestradiol regulated response QTL 4 (mouse)Not determined10100986516130530862Mouse
12904001Opfaq10_mopen field activity QTL 10 (mouse)10125633671129466375Mouse
12879490Frct3_mfear conditioning traits 3 (mouse)10122785970129466996Mouse
11049570Lmr25b_mleishmaniasis resistance 25b (mouse)10108575094130530862Mouse
27226772Tibl13_mtibia length 13, 10 week (mouse)1018875748129635869Mouse
4141361Cfmq3_mcystic fibrosis modifier QTL 3 (mouse)Not determined10101497164130530862Mouse
11533921Mvb2_mmodifier of vibrator 2 (mouse)1097217101130530862Mouse
4141487Tgq21_mtriglyceride QTL 21 (mouse)Not determined104110021130530862Mouse
27226764Tibl19_mtibia length 19, 16 week (mouse)1039175996129635869Mouse
1301895Exq1_mexploratory and excitability QTL 1 (mouse)Not determined10102847852130530862Mouse
1300679Nociq2_mnociceptive sensitivity inflammatory QTL 2 (mouse)Not determined10105041304130530862Mouse
1300678Leg2_mlongevity extending gene 2 (mouse)Not determined10102506908130530862Mouse
14746996Manh69_mmandible shape 69 (mouse)10104763638130530862Mouse
12880413V125Dq9_mvitamin D active form serum level QTL 9 (mouse)1097535905130530862Mouse
1301901Im5_mimmunoregulatory 5 (mouse)Not determined10101497164130530862Mouse
4141153Ltgq2_mliver triglyceride QTL 2 (mouse)Not determined108515907130530862Mouse
11039496Ltpr5b_mLeishmania tropica response 5b (mouse)10108575094130530862Mouse
1357744Cfbw4_mcystic fibrosis body weight 4 (mouse)Not determined10100986516130530862Mouse
4141402T2dm1sa_mtype 2 diabetes mellitus 1 in SMXA RI mice (mouse)Not determined97758644130530862Mouse
11041664Lmr25_mleishmaniasis resistance 25 (mouse)10108575094130530862Mouse
1302200Sle12_msystematic lupus erythematosus susceptibility 12 (mouse)Not determined10105041304130530862Mouse
26884405Huml2_mhumerus length 2, 5 week (mouse)1069735830130430862Mouse
4141007Obrq10_mobesity resistance QTL 10 (mouse)Not determined103243727130530862Mouse
11533919Mvb4_mmodifier of vibrator 4 (mouse)397217101130530862Mouse
12911220Frct3c_mfear conditioning traits 3c (mouse)10122785970129466996Mouse
11049563Lmr25a_mleishmaniasis resistance 25a (mouse)10108575094130530862Mouse
4142089Obrq9_mobesity resistance QTL 9 (mouse)Not determined108515907130530862Mouse
12911218Frct3a_mfear conditioning traits 3a (mouse)10122785970129466996Mouse
14696727Kidrq2_mkidney weight, right QTL 2 (mouse)10102902508130530862Mouse
11040593Lmr5e_mleishmaniasis resistance 5e (mouse)1099220635130530862Mouse
27095911Pglq15_mpelvic girdle length QTL 15, 16 week (mouse)1039175996129635869Mouse
11040594Lmr5f_mleishmaniasis resistance 5f (mouse)10105179713130530862Mouse
11040595Lmr5c_mleishmaniasis resistance 5c (mouse)1099220635130530862Mouse
1357544Vtbt10_mvertebral trabecular bone trait 10 (mouse)Not determined1097217101130530862Mouse
11040596Lmr5d_mleishmaniasis resistance 5d (mouse)10105179713130530862Mouse
11040597Lmr5a_mleishmaniasis resistance 5a (mouse)1099220635130530862Mouse
1357482Nhdlq4_mnon-HDL QTL 4 (mouse)Not determined10105041304130530862Mouse
11040598Lmr5b_mleishmaniasis resistance 5b (mouse)10105179713130530862Mouse

Markers in Region
Rdh6  
Mouse AssemblyChrPosition (strand)SourceJBrowse
GRCm3810127,812,857 - 127,813,471UniSTSGRCm38
GRCm3810127,876,322 - 127,876,932UniSTSGRCm38
MGSCv3710127,249,913 - 127,250,527UniSTSGRCm37
MGSCv3710127,313,378 - 127,313,988UniSTSGRCm37
Celera10130,270,974 - 130,271,584UniSTS
Celera10130,207,479 - 130,208,093UniSTS
Cytogenetic Map10D3UniSTS
cM Map10 UniSTS
AF030513  
Mouse AssemblyChrPosition (strand)SourceJBrowse
GRCm3810127,815,419 - 127,815,556UniSTSGRCm38
MGSCv3710127,252,475 - 127,252,612UniSTSGRCm37
Celera10130,210,042 - 130,210,179UniSTS
Cytogenetic Map10D3UniSTS
Whitehead/MRC_RH101381.42UniSTS


Expression

RNA-SEQ Expression


Sequence


Ensembl Acc Id: ENSMUST00000071646   ⟹   ENSMUSP00000071573
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39 Ensembl10127,637,023 - 127,651,708 (+)Ensembl
GRCm38.p6 Ensembl10127,801,154 - 127,815,839 (+)Ensembl
Ensembl Acc Id: ENSMUST00000125163   ⟹   ENSMUSP00000122839
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39 Ensembl10127,637,022 - 127,682,434 (+)Ensembl
GRCm38.p6 Ensembl10127,801,153 - 127,846,565 (+)Ensembl
Ensembl Acc Id: ENSMUST00000155739   ⟹   ENSMUSP00000115993
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39 Ensembl10127,637,021 - 127,651,035 (+)Ensembl
GRCm38.p6 Ensembl10127,801,152 - 127,815,166 (+)Ensembl
RefSeq Acc Id: NM_009040   ⟹   NP_033066
RefSeq Status: VALIDATED
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm3910127,637,022 - 127,651,708 (+)NCBI
GRCm3810127,801,153 - 127,815,839 (+)NCBI
MGSCv3710127,238,209 - 127,252,895 (+)RGD
Celera10130,195,773 - 130,210,462 (+)RGD
cM Map10 ENTREZGENE
Sequence:
RefSeq Acc Id: XM_006513389   ⟹   XP_006513452
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm3910127,636,959 - 127,651,715 (+)NCBI
GRCm3810127,801,090 - 127,815,846 (+)NCBI
Sequence:
RefSeq Acc Id: NP_033066   ⟸   NM_009040
- UniProtKB: O54909 (UniProtKB/TrEMBL),   E9Q9P8 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006513452   ⟸   XM_006513389
- Peptide Label: isoform X1
- UniProtKB: O54909 (UniProtKB/TrEMBL),   E9Q9P8 (UniProtKB/TrEMBL)
- Sequence:
Ensembl Acc Id: ENSMUSP00000122839   ⟸   ENSMUST00000125163
Ensembl Acc Id: ENSMUSP00000071573   ⟸   ENSMUST00000071646
Ensembl Acc Id: ENSMUSP00000115993   ⟸   ENSMUST00000155739

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-O54909-F1-model_v2 AlphaFold O54909 1-317 view protein structure

Promoters
RGD ID:6819795
Promoter ID:MM_KWN:5934
Type:Non-CpG
SO ACC ID:SO:0000170
Source:MPROMDB
Tissues & Cell Lines:Kidney,   Liver
Transcripts:NM_009040,   OTTMUST00000068613,   UC007HKR.1
Position:
Mouse AssemblyChrPosition (strand)Source
MGSCv3610127,238,046 - 127,238,546 (+)MPROMDB
RGD ID:8673540
Promoter ID:EPDNEW_M14801
Type:initiation region
Name:Rdh16_1
Description:Mus musculus retinol dehydrogenase 16 , mRNA.
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Single-end sequencing.
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm3810127,801,152 - 127,801,212EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene MGI:1201375 AgrOrtholog
Ensembl Genes ENSMUSG00000069456 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  ENSMUSG00000099009 UniProtKB/TrEMBL
Ensembl Transcript ENSMUST00000071646 ENTREZGENE
  ENSMUST00000071646.2 UniProtKB/Swiss-Prot
  ENSMUST00000125163.2 UniProtKB/TrEMBL
  ENSMUST00000128247.2 UniProtKB/TrEMBL
  ENSMUST00000155739.2 UniProtKB/TrEMBL
Gene3D-CATH NAD(P)-binding Rossmann-like Domain UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
InterPro NAD(P)-bd_dom_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Sc_DH/Rdtase_CS UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SDR_fam UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report mmu:19683 UniProtKB/Swiss-Prot
MGD MGI:1201375 ENTREZGENE
NCBI Gene 19683 ENTREZGENE
PANTHER CIS-RETINOL/3ALPHA HYDROXYSTEROL SHORT-CHAIN DEHYDROGENASE-LIKE PROTEIN-RELATED UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SHORT-CHAIN DEHYDROGENASE/REDUCTASE FAMILY 9C UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam adh_short UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Rdh16 PhenoGen
PRINTS GDHRDH UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SDRFAMILY UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PROSITE ADH_SHORT UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP SSF51735 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt D6RFQ4_MOUSE UniProtKB/TrEMBL
  D6RFT0_MOUSE UniProtKB/TrEMBL
  E9Q9P8 ENTREZGENE, UniProtKB/TrEMBL
  O54909 ENTREZGENE
  Q3TP45_MOUSE UniProtKB/TrEMBL
  RDH16_MOUSE UniProtKB/Swiss-Prot