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SDR16C5 short chain dehydrogenase/reductase family 16C member 5 [ Homo sapiens (human) ]

Gene ID: 195814, updated on 3-Nov-2024

Summary

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Official Symbol
SDR16C5provided by HGNC
Official Full Name
short chain dehydrogenase/reductase family 16C member 5provided by HGNC
Primary source
HGNC:HGNC:30311
See related
Ensembl:ENSG00000170786 MIM:608989; AllianceGenome:HGNC:30311
Gene type
protein coding
RefSeq status
VALIDATED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
RDH#2; RDHE2; EPHD-2; RDH-E2; retSDR2
Summary
This gene encodes a member of the short-chain alcohol dehydrogenase/reductase superfamily of proteins and is involved in the oxidation of retinol to retinaldehyde. The encoded protein is associated with the endoplasmic reticulum and is predicted to contain three transmembrane helices, suggesting that it is an integral membrane protein. It recognizes all-trans-retinol and all-trans-retinaldehyde as substrates and exhibits a strong preference for NAD(+)/NADH as cofactors. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Dec 2015]
Expression
Biased expression in skin (RPKM 15.8), esophagus (RPKM 9.7) and 7 other tissues See more
Orthologs
all
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Genomic context

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See SDR16C5 in Genome Data Viewer
Location:
8q12.1
Exon count:
8
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 8 NC_000008.11 (56300005..56320175, complement)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 8 NC_060932.1 (56677119..56697312, complement)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 8 NC_000008.10 (57212564..57232734, complement)

Chromosome 8 - NC_000008.11Genomic Context describing neighboring genes Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr8:57079228-57080427 Neighboring gene PLAG1 zinc finger Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27399 Neighboring gene MPRA-validated peak7026 silencer Neighboring gene ReSE screen-validated silencer GRCh37_chr8:57124219-57124444 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27400 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:57126097-57126596 Neighboring gene coiled-coil-helix-coiled-coil-helix domain containing 7 Neighboring gene MPRA-validated peak7027 silencer Neighboring gene NANOG hESC enhancer GRCh37_chr8:57208438-57208939 Neighboring gene short chain dehydrogenase/reductase family 16C member 6, pseudogene Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr8:57302182-57303381 Neighboring gene uncharacterized LOC105375849 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:57327640-57328140 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:57328141-57328641

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: HPA RNA-seq normal tissues HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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Related articles in PubMed

  1. hRDH-E2 gene polymorphisms, variable transcriptional start sites, and psoriasis. Matsuzaka Y, et al. Mamm Genome, 2004 Aug. PMID 15457346
  2. Identification of the hRDH-E2 gene, a novel member of the SDR family, and its increased expression in psoriatic lesion. Matsuzaka Y, et al. Biochem Biophys Res Commun, 2002 Oct 11. PMID 12372410
  3. Biochemical characterization of human epidermal retinol dehydrogenase 2. Lee SA, et al. Chem Biol Interact, 2009 Mar 16. PMID 18926804, Free PMC Article
  4. LRG1 and SDR16C5 protein expressions differ according to HPV status in oropharyngeal squamous cell carcinoma. Randén-Brady R, et al. Sci Rep, 2024 Jun 19. PMID 38898137, Free PMC Article
  5. Characterization of key residues and membrane association domains in retinol dehydrogenase 10. Takahashi Y, et al. Biochem J, 2009 Apr 1. PMID 19102727, Free PMC Article

See all (23) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. LRG1 and SDR16C5 protein expressions differ according to HPV status in oropharyngeal squamous cell carcinoma.
    Title: LRG1 and SDR16C5 protein expressions differ according to HPV status in oropharyngeal squamous cell carcinoma.
  2. Clinical trial of gene-disease association and gene-environment interaction. (HuGE Navigator)
    Title: Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score.
  3. Observational study of gene-disease association. (HuGE Navigator)
    Title: The role of height-associated loci identified in genome wide association studies in the determination of pediatric stature.
  4. mapped to chromosome 8; may be involved in the pathogenesis of psoriasis through its critical role in retinol metabolism in keratinocyte proliferation
    Title: Identification of the hRDH-E2 gene, a novel member of the SDR family, and its increased expression in psoriatic lesion.
Submit: New GeneRIF Correction

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

EBI GWAS Catalog

Description
Genome-wide meta-analysis identifies 11 new loci for anthropometric traits and provides insights into genetic architecture.
EBI GWAS Catalog
Hundreds of variants clustered in genomic loci and biological pathways affect human height.
EBI GWAS Catalog
Identification of ten loci associated with height highlights new biological pathways in human growth.
EBI GWAS Catalog
Many sequence variants affecting diversity of adult human height.
EBI GWAS Catalog
Meta-analysis of genome-wide association studies of adult height in East Asians identifies 17 novel loci.
EBI GWAS Catalog

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Pathways from PubChem

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Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Clone Names

  • FLJ33105

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables DNA-binding transcription factor binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables RNA polymerase II-specific DNA-binding transcription factor binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables all-trans-retinol dehydrogenase (NAD+) activity IBA
Inferred from Biological aspect of Ancestor
more info
  
enables all-trans-retinol dehydrogenase (NAD+) activity IDA
Inferred from Direct Assay
more info
 PubMed 
enables all-trans-retinol dehydrogenase (NAD+) activity TAS
Traceable Author Statement
more info
  
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables transcription corepressor activity IDA
Inferred from Direct Assay
more info
 PubMed 
Process Evidence Code Pubs
involved_in keratinocyte proliferation IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in negative regulation of gene expression, epigenetic IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in negative regulation of transcription by RNA polymerase II IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in retinal metabolic process IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in retinal metabolic process IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in retinol metabolic process IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in retinol metabolic process IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in retinol metabolic process IEA
Inferred from Electronic Annotation
more info
  
Component Evidence Code Pubs
located_in chromatin IDA
Inferred from Direct Assay
more info
 PubMed 
colocalizes_with endoplasmic reticulum IDA
Inferred from Direct Assay
more info
 PubMed 
located_in endoplasmic reticulum membrane IDA
Inferred from Direct Assay
more info
 PubMed 
located_in endoplasmic reticulum membrane TAS
Traceable Author Statement
more info
  
is_active_in lipid droplet IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in nucleus IDA
Inferred from Direct Assay
more info
 PubMed 
colocalizes_with plasma membrane IDA
Inferred from Direct Assay
more info
 PubMed 
part_of transcription repressor complex IDA
Inferred from Direct Assay
more info
 PubMed 

General protein information

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Preferred Names
epidermal retinol dehydrogenase 2
Names
epidermal retinal dehydrogenase 2
retinal short chain dehydrogenase reductase
retinal short-chain dehydrogenase reductase 2
NP_001304978.1
NP_001304979.1
NP_620419.2

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

mRNA and Protein(s)

  1. NM_001318049.2 → NP_001304978.1  epidermal retinol dehydrogenase 2 isoform 1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (1).
    Source sequence(s)
    AC103849
    Consensus CDS
    CCDS83296.1
    UniProtKB/TrEMBL
    G3V145
    Related
    ENSP00000431010.1, ENST00000522671.1
    Conserved Domains (2) summary
    cd05339
    Location:42 → 280
    17beta-HSDXI-like_SDR_c; human 17-beta-hydroxysteroid dehydrogenase XI-like, classical (c) SDRs
    pfam00106
    Location:41 → 231
    adh_short; short chain dehydrogenase

  2. NM_001318050.2 → NP_001304979.1  epidermal retinol dehydrogenase 2 isoform 3

    Status: VALIDATED

    Description
    Transcript Variant: This variant (3) lacks an alternate in-frame exon in the 5' coding region and an alternate exon in the 3' coding region compared to variant 1. It encodes isoform 3, which is shorter than and has a distinct C-terminus compared to isoform 1.
    Source sequence(s)
    AC103849
    Consensus CDS
    CCDS83295.1
    UniProtKB/Swiss-Prot
    Q8N3Y7
    UniProtKB/TrEMBL
    B3KT84
    Related
    ENSP00000379947.2, ENST00000396721.6
    Conserved Domains (2) summary
    cd05339
    Location:42 → 240
    17beta-HSDXI-like_SDR_c; human 17-beta-hydroxysteroid dehydrogenase XI-like, classical (c) SDRs
    PRK05650
    Location:43 → 240
    PRK05650; short chain dehydrogenase; Provisional

  3. NM_138969.4 → NP_620419.2  epidermal retinol dehydrogenase 2 isoform 2

    See identical proteins and their annotated locations for NP_620419.2

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) lacks an alternate exon in the 3' coding region compared to variant 1. It encodes isoform 2, which is shorter than and has a distinct C-terminus compared to isoform 1.
    Source sequence(s)
    AC103849
    Consensus CDS
    CCDS6167.1
    UniProtKB/Swiss-Prot
    B4DGK2, Q330K3, Q8N3Y7, Q8TDV9, Q96LX1
    Related
    ENSP00000307607.3, ENST00000303749.8
    Conserved Domains (1) summary
    cd05339
    Location:42 → 284
    17beta-HSDXI-like_SDR_c; human 17-beta-hydroxysteroid dehydrogenase XI-like, classical (c) SDRs

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000008.11 Reference GRCh38.p14 Primary Assembly

    Range
    56300005..56320175 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060932.1 Alternate T2T-CHM13v2.0

    Range
    56677119..56697312 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q8N3Y7.2 GenPept UniProtKB/Swiss-Prot:Q8N3Y7

Gene LinkOut

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