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

Gene ID: 195814, updated on 1-Jun-2020

Summary

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
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

Genomic context

See SDR16C5 in Genome Data Viewer
Location:
8q12.1
Exon count:
8
Annotation release Status Assembly Chr Location
109.20200522 current GRCh38.p13 (GCF_000001405.39) 8 NC_000008.11 (56299648..56320776, complement)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 8 NC_000008.10 (57212570..57233335, complement)

Chromosome 8 - NC_000008.11Genomic Context describing neighboring genes Neighboring gene PLAG1 zinc finger Neighboring gene coiled-coil-helix-coiled-coil-helix domain containing 7 Neighboring gene short chain dehydrogenase/reductase family 16C member 6, pseudogene Neighboring gene uncharacterized LOC105375849

Genomic regions, transcripts, and products

Expression

  • Project title: 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

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Phenotypes

NHGRI GWAS Catalog

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

Pathways from PubChem

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Clone Names

  • FLJ33105

Gene Ontology Provided by GOA

Function Evidence Code Pubs
activating transcription factor binding IPI
Inferred from Physical Interaction
more info
PubMed 
oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
retinol dehydrogenase activity IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
retinol dehydrogenase activity IDA
Inferred from Direct Assay
more info
PubMed 
transcription corepressor activity IDA
Inferred from Direct Assay
more info
PubMed 
transcription factor binding IPI
Inferred from Physical Interaction
more info
PubMed 
Process Evidence Code Pubs
keratinocyte proliferation IMP
Inferred from Mutant Phenotype
more info
PubMed 
negative regulation of histone acetylation IDA
Inferred from Direct Assay
more info
PubMed 
negative regulation of transcription by RNA polymerase II IMP
Inferred from Mutant Phenotype
more info
PubMed 
oxidation-reduction process IEA
Inferred from Electronic Annotation
more info
 
positive regulation of histone deacetylation IDA
Inferred from Direct Assay
more info
PubMed 
retinal metabolic process IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
retinal metabolic process IDA
Inferred from Direct Assay
more info
PubMed 
retinol metabolic process IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
retinol metabolic process IDA
Inferred from Direct Assay
more info
PubMed 
retinol metabolic process IEA
Inferred from Electronic Annotation
more info
 
Component Evidence Code Pubs
colocalizes_with chromatin IDA
Inferred from Direct Assay
more info
PubMed 
colocalizes_with endoplasmic reticulum IDA
Inferred from Direct Assay
more info
PubMed 
endoplasmic reticulum membrane IDA
Inferred from Direct Assay
more info
PubMed 
endoplasmic reticulum membrane TAS
Traceable Author Statement
more info
 
integral component of membrane IEA
Inferred from Electronic Annotation
more info
 
lipid droplet IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
nucleus IDA
Inferred from Direct Assay
more info
PubMed 
colocalizes_with plasma membrane IDA
Inferred from Direct Assay
more info
PubMed 
transcriptional repressor complex IDA
Inferred from Direct Assay
more info
PubMed 

General protein information

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
XP_011515781.1

NCBI Reference Sequences (RefSeq)

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_001318049.1NP_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)
    AB083038, AC103849, AK095159, BC037219, BC064525
    Consensus CDS
    CCDS83296.1
    UniProtKB/Swiss-Prot
    Q8N3Y7
    UniProtKB/TrEMBL
    B3KT84, G3V145
    Related
    ENSP00000431010.1, ENST00000522671.1
    Conserved Domains (2) summary
    cd05339
    Location:42280
    17beta-HSDXI-like_SDR_c; human 17-beta-hydroxysteroid dehydrogenase XI-like, classical (c) SDRs
    pfam00106
    Location:41231
    adh_short; short chain dehydrogenase
  2. NM_001318050.1NP_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)
    AB083038, AC103849, AK095159, AY444559, BC064525
    Consensus CDS
    CCDS83295.1
    UniProtKB/Swiss-Prot
    Q8N3Y7
    UniProtKB/TrEMBL
    B3KT84
    Related
    ENSP00000379947.2, ENST00000396721.6
    Conserved Domains (2) summary
    cd05339
    Location:42240
    17beta-HSDXI-like_SDR_c; human 17-beta-hydroxysteroid dehydrogenase XI-like, classical (c) SDRs
    PRK05650
    Location:43240
    PRK05650; short chain dehydrogenase; Provisional
  3. NM_138969.3NP_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)
    AB083038, AC103849, AK095159, BC037219, BC064525
    Consensus CDS
    CCDS6167.1
    UniProtKB/Swiss-Prot
    Q8N3Y7
    UniProtKB/TrEMBL
    B3KT84
    Related
    ENSP00000307607.3, ENST00000303749.7
    Conserved Domains (1) summary
    cd05339
    Location:42284
    17beta-HSDXI-like_SDR_c; human 17-beta-hydroxysteroid dehydrogenase XI-like, classical (c) SDRs

RefSeqs of Annotated Genomes: Homo sapiens Updated Annotation Release 109.

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

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000008.11 Reference GRCh38.p13 Primary Assembly

    Range
    56299648..56320776 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011517479.2XP_011515781.1  epidermal retinol dehydrogenase 2 isoform X1

    Conserved Domains (2) summary
    PRK06172
    Location:36221
    PRK06172; short chain dehydrogenase; Provisional
    cd05339
    Location:42236
    17beta-HSDXI-like_SDR_c; human 17-beta-hydroxysteroid dehydrogenase XI-like, classical (c) SDRs
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