Human Gene RDH16 (ENST00000398138.5) from GENCODE V44
  Description: Homo sapiens retinol dehydrogenase 16 (RDH16), transcript variant 1, mRNA. (from RefSeq NM_003708)
Gencode Transcript: ENST00000398138.5
Gencode Gene: ENSG00000139547.8
Transcript (Including UTRs)
   Position: hg38 chr12:56,951,431-56,957,608 Size: 6,178 Total Exon Count: 4 Strand: -
Coding Region
   Position: hg38 chr12:56,952,029-56,957,462 Size: 5,434 Coding Exon Count: 4 

Page IndexSequence and LinksUniProtKB CommentsPrimersCTDRNA-Seq Expression
Microarray ExpressionRNA StructureProtein StructureOther SpeciesGO AnnotationsmRNA Descriptions
PathwaysOther NamesMethods
Data last updated at UCSC: 2023-08-18 09:09:47

-  Sequence and Links to Tools and Databases
Genomic Sequence (chr12:56,951,431-56,957,608)mRNA (may differ from genome)Protein (317 aa)
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaAlphaFold
BioGPSEnsemblEntrez GeneExonPrimerGencodeGeneCards

-  Comments and Description Text from UniProtKB
DESCRIPTION: RecName: Full=Retinol dehydrogenase 16; EC=1.1.-.-; AltName: Full=Microsomal NAD(+)-dependent retinol dehydrogenase 4; Short=RoDH-4; AltName: Full=Sterol/retinol dehydrogenase;
FUNCTION: Oxidoreductase with a preference for NAD. Oxidizes all- trans-retinol and 13-cis-retinol to the corresponding aldehydes. Has higher activity towards CRBP-bound retinol than with free retinol. Oxidizes 3-alpha-hydroxysteroids. Oxidizes androstanediol and androsterone to dihydrotestosterone and androstanedione. Can also catalyze the reverse reaction.
ENZYME REGULATION: Inhibited by citral, perillyl alcohol, geraniol, farnesol and geranyl geraniol.
BIOPHYSICOCHEMICAL PROPERTIES: Kinetic parameters: KM=0.14 uM for androsterone; KM=0.22 uM for androstanediol; KM=0.80 uM for dihydrotestosterone; KM=0.13 uM for NAD; KM=190 uM for NADP;
SUBCELLULAR LOCATION: Microsome membrane; Single-pass type IV membrane protein. Endoplasmic reticulum membrane; Single-pass type IV membrane protein (Potential).
TISSUE SPECIFICITY: Highly expressed in adult liver (at protein level). Detected in endometrium, liver and foreskin. Detected in the spineous layers of adult skin, and at lower levels in basal and granular skin layers. Detected in fetal liver and lung.
INDUCTION: Transiently up-regulated by retinoic acid.
PTM: Not N-glycosylated.
SIMILARITY: Belongs to the short-chain dehydrogenases/reductases (SDR) family.

-  Primer design for this transcript

Primer3Plus can design qPCR Primers that straddle exon-exon-junctions, which amplify only cDNA, not genomic DNA.
Click here to load the transcript sequence and exon structure into Primer3Plus

Exonprimer can design one pair of Sanger sequencing primers around every exon, located in non-genic sequence.
Click here to open Exonprimer with this transcript

To design primers for a non-coding sequence, zoom to a region of interest and select from the drop-down menu: View > In External Tools > Primer3

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene           more ... click here to view the complete list

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 162.75 RPKM in Liver
Total median expression: 188.15 RPKM

View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
  Press "+" in the title bar above to open this section.

-  mRNA Secondary Structure of 3' and 5' UTRs
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -43.50146-0.298 Picture PostScript Text
3' UTR -228.70598-0.382 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  InterPro Domains: Graphical view of domain structure
IPR002198 - DH_sc/Rdtase_SDR
IPR002347 - Glc/ribitol_DH
IPR016040 - NAD(P)-bd_dom
IPR020904 - Sc_DH/Rdtase_CS

Pfam Domains:
PF00106 - short chain dehydrogenase

ModBase Predicted Comparative 3D Structure on O75452
The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
No orthologGenome BrowserGenome BrowserNo orthologGenome BrowserNo ortholog
 RGDEnsembl WormBase 
 Protein SequenceProtein Sequence Protein Sequence 
 AlignmentAlignment Alignment 

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0004745 retinol dehydrogenase activity
GO:0009055 electron carrier activity
GO:0016491 oxidoreductase activity

Biological Process:
GO:0006629 lipid metabolic process
GO:0022900 electron transport chain
GO:0055114 oxidation-reduction process

Cellular Component:
GO:0005783 endoplasmic reticulum
GO:0005789 endoplasmic reticulum membrane
GO:0016020 membrane
GO:0016021 integral component of membrane
GO:0031090 organelle membrane
GO:0043231 intracellular membrane-bounded organelle

-  Descriptions from all associated GenBank mRNAs
  AF086735 - Homo sapiens retinol dehydrogenase mRNA, complete cds.
AB209332 - Homo sapiens mRNA for microsomal NAD+-dependent retinol dehydrogenase 4 variant protein.
JD386829 - Sequence 367853 from Patent EP1572962.
JD110481 - Sequence 91505 from Patent EP1572962.
JD496093 - Sequence 477117 from Patent EP1572962.
JD281534 - Sequence 262558 from Patent EP1572962.
JD496358 - Sequence 477382 from Patent EP1572962.
JD385067 - Sequence 366091 from Patent EP1572962.
JD552913 - Sequence 533937 from Patent EP1572962.
JD335583 - Sequence 316607 from Patent EP1572962.
JD539380 - Sequence 520404 from Patent EP1572962.
JD343783 - Sequence 324807 from Patent EP1572962.
JD215005 - Sequence 196029 from Patent EP1572962.
DQ499468 - Homo sapiens HCV core-binding protein 12-binding protein A (HCBP12BPA) mRNA, complete cds.
JD530856 - Sequence 511880 from Patent EP1572962.
JD087716 - Sequence 68740 from Patent EP1572962.
JD344776 - Sequence 325800 from Patent EP1572962.
AF057034 - Homo sapiens sterol/retinol dehydrogenase mRNA, complete cds.
BC160081 - Synthetic construct Homo sapiens clone IMAGE:100064017, MGC:193196 retinol dehydrogenase 16 (all-trans) (RDH16) mRNA, encodes complete protein.
AK311025 - Homo sapiens cDNA, FLJ18067.
JD124387 - Sequence 105411 from Patent EP1572962.
JD532989 - Sequence 514013 from Patent EP1572962.
JD203014 - Sequence 184038 from Patent EP1572962.

-  Biochemical and Signaling Pathways
  BioCyc Knowledge Library
PWY-6872 - retinoate biosynthesis I

Reactome (by CSHL, EBI, and GO)

Protein O75452 (Reactome details) participates in the following event(s):

R-HSA-5362518 RDH10,16,DHRS9,RDHE2 oxidise atROL to atRAL
R-HSA-2454081 RDH5 oxidises 11cROL to 11cRAL
R-HSA-5365859 RA biosynthesis pathway
R-HSA-2453902 The canonical retinoid cycle in rods (twilight vision)
R-HSA-5362517 Signaling by Retinoic Acid
R-HSA-2187338 Visual phototransduction
R-HSA-9006931 Signaling by Nuclear Receptors
R-HSA-418594 G alpha (i) signalling events
R-HSA-162582 Signal Transduction
R-HSA-388396 GPCR downstream signalling
R-HSA-372790 Signaling by GPCR

-  Other Names for This Gene
  Alternate Gene Symbols: ENST00000398138.1, ENST00000398138.2, ENST00000398138.3, ENST00000398138.4, NM_003708, O75452, Q9UNV2, RDH16_HUMAN, RODH4, uc001smi.1, uc001smi.2, uc001smi.3, uc001smi.4, uc001smi.5, uc001smi.6, uc001smi.7
UCSC ID: ENST00000398138.5
RefSeq Accession: NM_003708
Protein: O75452 (aka RDH16_HUMAN)

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.