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Aliases for RDH13 Gene

Aliases for RDH13 Gene

  • Retinol Dehydrogenase 13 2 3 5
  • Short Chain Dehydrogenase/Reductase Family 7C Member 3 3 4
  • Retinol Dehydrogenase 13 (All-Trans And 9-Cis) 2 3
  • Retinol Dehydrogenase 13 (All-Trans/9-Cis) 2 3
  • SDR7C3 3 4
  • Short Chain Dehydrogenase/Reductase Family 7C, Member 3 2
  • EC 1.1.1.- 4

External Ids for RDH13 Gene

Previous GeneCards Identifiers for RDH13 Gene

  • GC19M055979
  • GC19M060231
  • GC19M060247
  • GC19M055556
  • GC19M051879

Summaries for RDH13 Gene

Entrez Gene Summary for RDH13 Gene

  • This gene encodes a mitochondrial short-chain dehydrogenase/reductase, which catalyzes the reduction and oxidation of retinoids. The encoded enzyme may function in retinoic acid production and may also protect the mitochondria against oxidative stress. Alternatively spliced transcript variants have been described. [provided by RefSeq, Mar 2009]

GeneCards Summary for RDH13 Gene

RDH13 (Retinol Dehydrogenase 13) is a Protein Coding gene. Among its related pathways are Visual Cycle in Retinal Rods and Signaling by Retinoic Acid. GO annotations related to this gene include oxidoreductase activity and coenzyme binding. An important paralog of this gene is RDH11.

UniProtKB/Swiss-Prot for RDH13 Gene

  • Does not exhibit retinol dehydrogenase (RDH) activity in vitro.

Additional gene information for RDH13 Gene

No data available for CIViC summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for RDH13 Gene

Genomics for RDH13 Gene

Regulatory Elements for RDH13 Gene

Enhancers for RDH13 Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH19H055111 1.8 FANTOM5 ENCODE dbSUPER 29.2 -44.1 -44092 8 HDGF ARNT ARID4B SIN3A YBX1 FEZF1 DMAP1 ZNF2 YY1 ZNF766 EPS8L1 RDH13 U2AF2 LENG8-AS1 LENG8 ENSG00000235681 CNOT3 ENSG00000267523 ZNF580 KMT5C
GH19H055027 1.4 Ensembl ENCODE dbSUPER 22.1 +43.3 43318 1.1 ATF1 PTBP1 ARNT ZBTB40 GATA2 EGR1 ATF7 ETV6 CREM SMARCA5 RDH13 ENSG00000267265 EPS8L1 ENSG00000243494 NLRP7 NLRP2 GP6
GH19H055041 1.4 Ensembl ENCODE dbSUPER 20.4 +29.3 29334 1.3 HDAC1 PKNOX1 ATF1 TBL1XR1 NFRKB TCF12 GATA2 EGR1 ETV6 ATF7 RDH13 NLRP7 NLRP2 GP6 ENSG00000267149
GH19H055062 1 ENCODE 25.5 +8.4 8412 1.7 HDGF PKNOX1 ATF1 ARNT SIN3A DMAP1 BRCA1 GTF3C2 GLIS2 ELK1 CNOT3 ENSG00000235681 LENG8 LENG8-AS1 U2AF2 ZNF581 ENSG00000267523 RDH13 PRPF31 ENSG00000267265
GH19H055036 1 dbSUPER 24.5 +33.1 33098 2.8 HDGF PKNOX1 ATF1 ARNT TCF12 ZNF766 GATA2 ELK1 ATF7 ZC3H11A RDH13 U2AF2 CNOT3 PRPF31 ZNF628 ENSG00000267523 LENG8 LENG8-AS1 ZNF581 ENSG00000267096
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around RDH13 on UCSC Golden Path with GeneCards custom track

Genomic Locations for RDH13 Gene

Genomic Locations for RDH13 Gene
chr19:55,039,108-55,071,291
(GRCh38/hg38)
Size:
32,184 bases
Orientation:
Minus strand
chr19:55,550,476-55,582,659
(GRCh37/hg19)

Genomic View for RDH13 Gene

Genes around RDH13 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
RDH13 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for RDH13 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for RDH13 Gene

Proteins for RDH13 Gene

  • Protein details for RDH13 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q8NBN7-RDH13_HUMAN
    Recommended name:
    Retinol dehydrogenase 13
    Protein Accession:
    Q8NBN7
    Secondary Accessions:
    • Q6UX79
    • Q96G88

    Protein attributes for RDH13 Gene

    Size:
    331 amino acids
    Molecular mass:
    35932 Da
    Quaternary structure:
    No Data Available

    Alternative splice isoforms for RDH13 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for RDH13 Gene

Post-translational modifications for RDH13 Gene

  • Ubiquitination at Lys102
  • Modification sites at PhosphoSitePlus

No data available for DME Specific Peptides for RDH13 Gene

Domains & Families for RDH13 Gene

Gene Families for RDH13 Gene

HGNC:
Human Protein Atlas (HPA):
  • Predicted intracellular proteins
  • Predicted secreted proteins

Suggested Antigen Peptide Sequences for RDH13 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

Q8NBN7

UniProtKB/Swiss-Prot:

RDH13_HUMAN :
  • Belongs to the short-chain dehydrogenases/reductases (SDR) family.
Family:
  • Belongs to the short-chain dehydrogenases/reductases (SDR) family.
genes like me logo Genes that share domains with RDH13: view

Function for RDH13 Gene

Molecular function for RDH13 Gene

UniProtKB/Swiss-Prot Function:
Does not exhibit retinol dehydrogenase (RDH) activity in vitro.

Enzyme Numbers (IUBMB) for RDH13 Gene

Phenotypes From GWAS Catalog for RDH13 Gene

Gene Ontology (GO) - Molecular Function for RDH13 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0016491 oxidoreductase activity IEA --
GO:0052650 NADP-retinol dehydrogenase activity TAS --
genes like me logo Genes that share ontologies with RDH13: view
genes like me logo Genes that share phenotypes with RDH13: view

Animal Models for RDH13 Gene

MGI Knock Outs for RDH13:

miRNA for RDH13 Gene

miRTarBase miRNAs that target RDH13

Clone Products

No data available for Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for RDH13 Gene

Localization for RDH13 Gene

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for RDH13 gene
Compartment Confidence
mitochondrion 5
nucleus 2
cytosol 2
extracellular 1
peroxisome 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Mitochondria (3)
  • Cytosol (2)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for RDH13 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005743 mitochondrial inner membrane TAS --
genes like me logo Genes that share ontologies with RDH13: view

No data available for Subcellular locations from UniProtKB/Swiss-Prot for RDH13 Gene

Pathways & Interactions for RDH13 Gene

genes like me logo Genes that share pathways with RDH13: view

Pathways by source for RDH13 Gene

1 Qiagen pathway for RDH13 Gene

Gene Ontology (GO) - Biological Process for RDH13 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0009644 response to high light intensity IEA --
GO:0010842 retina layer formation IEA --
GO:0042462 eye photoreceptor cell development IEA --
GO:0042572 retinol metabolic process IEA --
GO:0055114 oxidation-reduction process IEA --
genes like me logo Genes that share ontologies with RDH13: view

No data available for SIGNOR curated interactions for RDH13 Gene

Drugs & Compounds for RDH13 Gene

(3) Drugs for RDH13 Gene - From: DrugBank and HMDB

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Vitamin A Approved, Vet_approved Nutra Target 511
1-Butanol Experimental Pharma 0
Pyruvaldehyde Experimental Pharma 0

(6) Additional Compounds for RDH13 Gene - From: HMDB

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
13-OxoODE
  • (9Z,11E)-13-Oxooctadeca-9,11-dienoate
  • (9Z,11E)-13-Oxooctadeca-9,11-dienoic acid
  • 13-KODE
3a,7a,12a,24-Tetrahydroxy-5b-cholestanoyl-CoA
  • (24R,25R)-3-alpha,7-alpha,12-alpha,24-tetrahydroxy-5-beta-cholestanoyl-CoA
  • (24R,25R)-3-alpha,7-alpha,12-alpha,24-tetrahydroxy-5-beta-cholestanoyl-Coenzyme A
  • 3a,7a,12a,24-Tetrahydroxy-5b-cholestanoyl-CoA
  • 3a,7a,12a,24-Tetrahydroxy-5b-cholestanoyl-Coenzyme A
  • 3a,7a,12a,24z-Tetrahydroxy-5b-cholestanoyl-CoA
3a,7a,12a-Trihydroxy-5b-24-oxocholestanoyl-CoA
  • (24R,25R)-3-alpha,7-alpha,12-alpha,24-tetrahydroxy-5-beta-cholestan-26-oyl-CoA
  • (24R,25R)-3-alpha,7-alpha,12-alpha,24-tetrahydroxy-5-beta-cholestan-26-oyl-Coenzyme A
  • 24-Oxo-25(R)-trihydroxycoprostanoyl-CoA
  • 24-Oxo-25(R)-trihydroxycoprostanoyl-Coenzyme A
  • 25(R)-24-Oxo-3alpha,7alpha,12alpha-trihydroxycoprostanoyl-CoA
3a,7a,12a-Trihydroxy-5b-cholestanoyl-CoA
  • (25R)-3-alpha,7-alpha,12-alpha-trihydroxy-5-beta-cholestan-26-oyl-CoA
  • (25R)-3-alpha,7-alpha,12-alpha-trihydroxy-5-beta-cholestan-26-oyl-Coenzyme A
  • (25R)-3-alpha,7-alpha,12-alpha-trihydroxy-5-beta-cholestanoyl-CoA
  • (25R)-3-alpha,7-alpha,12-alpha-trihydroxy-5-beta-cholestanoyl-Coenzyme A
  • 25(S)-3alpha,7alpha,12alpha-trihydroxy-5beta-cholestan-26-oyl-CoA
57458-60-3
Butanal
  • 1-Butanal
  • Butaldehyde
  • Butalyde
  • Butan-1-al
  • Butanaldehyde
123-72-8
genes like me logo Genes that share compounds with RDH13: view

Transcripts for RDH13 Gene

Unigene Clusters for RDH13 Gene

Retinol dehydrogenase 13 (all-trans/9-cis):
Representative Sequences:

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for RDH13 Gene

ExUns: 1 ^ 2a · 2b · 2c ^ 3 ^ 4 ^ 5 ^ 6a · 6b ^ 7 ^ 8a · 8b ^ 9 ^ 10a · 10b · 10c ^ 11a · 11b
SP1: - - - - - - - -
SP2: - - - - -
SP3: - - -
SP4: - - -
SP5: - - - -
SP6: - - - - - - - - - -
SP7: -
SP8: -

Relevant External Links for RDH13 Gene

GeneLoc Exon Structure for
RDH13
ECgene alternative splicing isoforms for
RDH13

Expression for RDH13 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for RDH13 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Protein differential expression in normal tissues from HIPED for RDH13 Gene

This gene is overexpressed in Nasal epithelium (10.4), Bone (7.7), and Placenta (7.2).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MaxQB, and MOPED for RDH13 Gene



Protein tissue co-expression partners for RDH13 Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of RDH13 Gene:

RDH13

SOURCE GeneReport for Unigene cluster for RDH13 Gene:

Hs.327631

mRNA Expression by UniProt/SwissProt for RDH13 Gene:

Q8NBN7-RDH13_HUMAN
Tissue specificity: Expressed mostly in eye, pancreas, placenta and lung. In the retina, detected in the inner segment of the photoreceptor cells. Weak signals were observed in a small population of inner nuclear neurons and the inner plexiform layer.

Evidence on tissue expression from TISSUES for RDH13 Gene

  • Liver(4.1)
genes like me logo Genes that share expression patterns with RDH13: view

No data available for mRNA differential expression in normal tissues and Phenotype-based relationships between genes and organs from Gene ORGANizer for RDH13 Gene

Orthologs for RDH13 Gene

This gene was present in the common ancestor of animals.

Orthologs for RDH13 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia RDH13 33 34
  • 99.4 (n)
dog
(Canis familiaris)
Mammalia RDH13 33 34
  • 87.31 (n)
cow
(Bos Taurus)
Mammalia RDH13 33 34
  • 87.01 (n)
rat
(Rattus norvegicus)
Mammalia Rdh13 33
  • 84.27 (n)
mouse
(Mus musculus)
Mammalia Rdh13 33 16 34
  • 84.01 (n)
platypus
(Ornithorhynchus anatinus)
Mammalia RDH13 34
  • 72 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia rdh13 33
  • 66.35 (n)
zebrafish
(Danio rerio)
Actinopterygii si:dkey-23o4.6 33
  • 57.1 (n)
rdh12l 34
  • 52 (a)
ManyToMany
sbcb464 33
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP005980 33
  • 58.33 (n)
fruit fly
(Drosophila melanogaster)
Insecta CG30491 33 34
  • 55.8 (n)
CG2064 34
  • 52 (a)
ManyToMany
CG2065 34
  • 51 (a)
ManyToMany
CG2070 34
  • 51 (a)
ManyToMany
CG30495 34
  • 45 (a)
ManyToMany
CG3842 34
  • 37 (a)
ManyToMany
Species where no ortholog for RDH13 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • chicken (Gallus gallus)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • lizard (Anolis carolinensis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • oppossum (Monodelphis domestica)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea squirt (Ciona intestinalis)
  • sea squirt (Ciona savignyi)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)
  • worm (Caenorhabditis elegans)

Evolution for RDH13 Gene

ENSEMBL:
Gene Tree for RDH13 (if available)
TreeFam:
Gene Tree for RDH13 (if available)

Paralogs for RDH13 Gene

Paralogs for RDH13 Gene

(9) SIMAP similar genes for RDH13 Gene using alignment to 5 proteins:

genes like me logo Genes that share paralogs with RDH13: view

Variants for RDH13 Gene

Sequence variations from dbSNP and Humsavar for RDH13 Gene

SNP ID Clin Chr 19 pos Sequence Context AA Info Type
rs1045062629 -- 55,043,336(+) AGTGA(A/G)CTGTG intron-variant, downstream-variant-500B
rs118024102 -- 55,043,351(+) CACTG(C/T)ACTCC intron-variant, downstream-variant-500B
rs147994397 -- 55,043,388(+) TCTCT(A/G)AAAAA intron-variant, downstream-variant-500B
rs1654440 -- 55,043,343(+) tgtga(C/T)ggcac intron-variant, downstream-variant-500B
rs183851439 -- 55,043,381(+) GACCT(C/T)GTCTC intron-variant, downstream-variant-500B

Structural Variations from Database of Genomic Variants (DGV) for RDH13 Gene

Variant ID Type Subtype PubMed ID
nsv9770 CNV loss 18304495
nsv833880 CNV loss 17160897
nsv817874 CNV loss 17921354
nsv580342 CNV loss 21841781
nsv580341 CNV loss 21841781
nsv1150276 OTHER inversion 26484159
nsv1134812 CNV deletion 24896259
nsv1123280 CNV deletion 24896259
nsv1109218 CNV deletion 24896259
nsv1079034 OTHER inversion 25765185
nsv1063883 CNV gain 25217958
esv9070 CNV loss 19470904
esv3644835 CNV loss 21293372
esv3644834 CNV loss 21293372
esv3644831 CNV gain 21293372
esv3644830 CNV loss 21293372
esv3644829 CNV gain 21293372
esv34356 CNV gain 17911159
esv2763211 CNV gain 21179565
esv2762052 CNV gain 21179565
esv2758772 CNV gain 17122850
esv2718944 CNV deletion 23290073
esv2718872 CNV deletion 23290073
esv2672890 CNV deletion 23128226
esv2671441 CNV deletion 23128226
esv2667609 CNV deletion 23128226
dgv1819n106 OTHER inversion 24896259

Variation tolerance for RDH13 Gene

Residual Variation Intolerance Score: 84.7% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 5.90; 74.32% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for RDH13 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
RDH13

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for RDH13 Gene

Disorders for RDH13 Gene

Relevant External Links for RDH13

Genetic Association Database (GAD)
RDH13
Human Genome Epidemiology (HuGE) Navigator
RDH13
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
RDH13

No disorders were found for RDH13 Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for RDH13 Gene

Publications for RDH13 Gene

  1. Dual-substrate specificity short chain retinol dehydrogenases from the vertebrate retina. (PMID: 12226107) Haeseleer F … Palczewski K (The Journal of biological chemistry 2002) 2 3 4 60
  2. Genetic variants in nuclear-encoded mitochondrial genes influence AIDS progression. (PMID: 20877624) Hendrickson SL … O'Brien SJ (PloS one 2010) 3 45 60
  3. The SDR (short-chain dehydrogenase/reductase and related enzymes) nomenclature initiative. (PMID: 19027726) Persson B … Oppermann U (Chemico-biological interactions 2009) 2 3 60
  4. Human retinol dehydrogenase 13 (RDH13) is a mitochondrial short-chain dehydrogenase/reductase with a retinaldehyde reductase activity. (PMID: 18039331) Belyaeva OV … Kedishvili NY (The FEBS journal 2008) 3 22 60
  5. Signal sequence and keyword trap in silico for selection of full-length human cDNAs encoding secretion or membrane proteins from oligo-capped cDNA libraries. (PMID: 16303743) Otsuki T … Isogai T (DNA research : an international journal for rapid publication of reports on genes and genomes 2005) 3 4 60

Products for RDH13 Gene

Sources for RDH13 Gene

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