Human Gene RDH10 (uc003xzi.3)
  Description: Homo sapiens retinol dehydrogenase 10 (all-trans) (RDH10), mRNA.
RefSeq Summary (NM_172037): This gene encodes a retinol dehydrogenase, which converts all-trans-retinol to all-trans-retinal, with preference for NADP as a cofactor. Studies in mice suggest that this protein is essential for synthesis of embryonic retinoic acid and is required for limb, craniofacial, and organ development. [provided by RefSeq, Dec 2011].
Transcript (Including UTRs)
   Position: hg19 chr8:74,206,837-74,237,520 Size: 30,684 Total Exon Count: 6 Strand: +
Coding Region
   Position: hg19 chr8:74,207,525-74,235,271 Size: 27,747 Coding Exon Count: 6 

Page IndexSequence and LinksUniProtKB CommentsPrimersGenetic AssociationsMalaCards
CTDGene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein Structure
Other SpeciesGO AnnotationsmRNA DescriptionsPathwaysOther NamesModel Information
Methods
Data last updated at UCSC: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr8:74,206,837-74,237,520)mRNA (may differ from genome)Protein (341 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
GeneNetworkHGNCHPRDLynxMalacardsMGI
neXtProtOMIMPubMedReactomeTreefamUniProtKB
BioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: RDH10_HUMAN
DESCRIPTION: RecName: Full=Retinol dehydrogenase 10; EC=1.1.1.300;
FUNCTION: Retinol dehydrogenase with a clear preference for NADP. Converts all-trans-retinol to all-trans-retinal. Has no detectable activity towards 11-cis-retinol, 9-cis-retinol and 13-cis-retinol.
CATALYTIC ACTIVITY: All-trans-retinol + NADP(+) = all-trans- retinal + NADPH.
PATHWAY: Cofactor metabolism; retinol metabolism.
SUBCELLULAR LOCATION: Microsome membrane; Single-pass membrane protein (Potential). Endoplasmic reticulum membrane; Single-pass membrane protein (Potential).
TISSUE SPECIFICITY: Detected in retina, kidney, liver, small intestine, placenta, lung, heart and skeletal muscle.
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


-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): RDH10
CDC HuGE Published Literature: RDH10
Positive Disease Associations: Attention Deficit Disorder with Hyperactivity , Body Mass Index , Body Weight Changes , Multiple Sclerosis
Related Studies:
  1. Attention Deficit Disorder with Hyperactivity
    Jessica Lasky-Su et al. American journal of medical genetics. Part B, Neuropsychiatric genetics 2008, Genome-wide association scan of quantitative traits for attention deficit hyperactivity disorder identifies novel associations and confirms candidate gene associations., American journal of medical genetics. Part B, Neuropsychiatric genetics : the official publication of the International Society of Psychiatric Genetic. [PubMed 18821565]
  2. Body Mass Index
    Caroline S Fox et al. BMC medical genetics 2007, Genome-wide association to body mass index and waist circumference: the Framingham Heart Study 100K project., BMC medical genetics. [PubMed 17903300]
    Adiposity traits are associated with SNPs on the Affymetrix 100K SNP GeneChip. Replication of these initial findings is necessary. These data will serve as a resource for replication as more genes become identified with BMI and WC.
  3. Body Mass Index
    Caroline S Fox et al. BMC medical genetics 2007, Genome-wide association to body mass index and waist circumference: the Framingham Heart Study 100K project., BMC medical genetics. [PubMed 17903300]
    Adiposity traits are associated with SNPs on the Affymetrix 100K SNP GeneChip. Replication of these initial findings is necessary. These data will serve as a resource for replication as more genes become identified with BMI and WC.
           more ... click here to view the complete list

-  MalaCards Disease Associations
  MalaCards Gene Search: RDH10
Diseases sorted by gene-association score: choanal atresia, posterior (7), total anomalous pulmonary venous return 1 (7)

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

+  Common Gene Haplotype Alleles
  Press "+" in the title bar above to open this section.

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 27.50 RPKM in Nerve - Tibial
Total median expression: 339.06 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 -409.50688-0.595 Picture PostScript Text
3' UTR -597.632249-0.266 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
PF08659 - KR domain
PF13561 - Enoyl-(Acyl carrier protein) reductase

SCOP Domains:
51735 - NAD(P)-binding Rossmann-fold domains

ModBase Predicted Comparative 3D Structure on Q8IZV5
FrontTopSide
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 orthologNo orthologNo ortholog
Gene DetailsGene Details    
Gene SorterGene Sorter    
 RGDEnsembl   
 Protein SequenceProtein Sequence   
 AlignmentAlignment   

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0004745 retinol dehydrogenase activity
GO:0016491 oxidoreductase activity
GO:0052650 NADP-retinol dehydrogenase activity

Biological Process:
GO:0001523 retinoid metabolic process
GO:0001656 metanephros development
GO:0001701 in utero embryonic development
GO:0002138 retinoic acid biosynthetic process
GO:0007601 visual perception
GO:0008406 gonad development
GO:0009887 animal organ morphogenesis
GO:0014032 neural crest cell development
GO:0031076 embryonic camera-type eye development
GO:0035115 embryonic forelimb morphogenesis
GO:0042572 retinol metabolic process
GO:0042574 retinal metabolic process
GO:0043583 ear development
GO:0043584 nose development
GO:0048568 embryonic organ development
GO:0048703 embryonic viscerocranium morphogenesis
GO:0055114 oxidation-reduction process
GO:0060431 primary lung bud formation
GO:0060449 bud elongation involved in lung branching

Cellular Component:
GO:0005737 cytoplasm
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
GO:0044297 cell body
GO:0005634 nucleus


-  Descriptions from all associated GenBank mRNAs
  AF456765 - Homo sapiens retinol dehydrogenase 10 (RDH10) mRNA, complete cds.
BC067131 - Homo sapiens retinol dehydrogenase 10 (all-trans), mRNA (cDNA clone MGC:70403 IMAGE:6153778), complete cds.
JD470804 - Sequence 451828 from Patent EP1572962.
JD443992 - Sequence 425016 from Patent EP1572962.
JD462602 - Sequence 443626 from Patent EP1572962.
JD407234 - Sequence 388258 from Patent EP1572962.
JD461606 - Sequence 442630 from Patent EP1572962.
JD462932 - Sequence 443956 from Patent EP1572962.
AY358270 - Homo sapiens clone DNA213097 RDH10 (UNQ9375) mRNA, complete cds.
AX721306 - Sequence 266 from Patent WO0220754.
JD171397 - Sequence 152421 from Patent EP1572962.
JD550899 - Sequence 531923 from Patent EP1572962.
JD297015 - Sequence 278039 from Patent EP1572962.
JD450724 - Sequence 431748 from Patent EP1572962.
JD287046 - Sequence 268070 from Patent EP1572962.

-  Biochemical and Signaling Pathways
  KEGG - Kyoto Encyclopedia of Genes and Genomes
hsa00830 - Retinol metabolism
hsa01100 - Metabolic pathways

Reactome (by CSHL, EBI, and GO)

Protein Q8IZV5 (Reactome details) participates in the following event(s):

R-HSA-74872 RDH10,11 oxidise 11cROL to 11cRAL
R-HSA-5362518 RDH10,16,DHRS9,RDHE2 oxidise atROL to atRAL
R-HSA-2453902 The canonical retinoid cycle in rods (twilight vision)
R-HSA-5365859 RA biosynthesis pathway
R-HSA-2187338 Visual phototransduction
R-HSA-5362517 Signaling by Retinoic Acid
R-HSA-418594 G alpha (i) signalling events
R-HSA-9006931 Signaling by Nuclear Receptors
R-HSA-388396 GPCR downstream signalling
R-HSA-162582 Signal Transduction
R-HSA-372790 Signaling by GPCR

-  Other Names for This Gene
  Alternate Gene Symbols: NM_172037, NP_742034, Q8IZV5, RDH10_HUMAN, UNQ9375/PRO34191
UCSC ID: uc003xzi.3
RefSeq Accession: NM_172037
Protein: Q8IZV5 (aka RDH10_HUMAN)
CCDS: CCDS6213.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_172037.4
exon count: 6CDS single in 3' UTR: no RNA size: 3981
ORF size: 1026CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 2228.00frame shift in genome: no % Coverage: 99.55
has start codon: yes stop codon in genome: no # of Alignments: 1
has end codon: yes retained intron: no # AT/AC introns 0
selenocysteine: no end bleed into intron: 0# strange splices: 0
Click here for a detailed description of the fields of the table above.

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