KDSR Gene (Protein Coding)

3-Ketodihydrosphingosine Reductase

GC18M063327
GIFtS:
42
The protein encoded by this gene catalyzes the reduction of 3-ketodihydrosphingosine to dihydrosphingosine. The putative active site residues of the encoded protein are found on the cytosolic side of the endoplasmic reticulum membrane. A chromosomal rearrangement involving this gene is a cause of follicular lymphoma, also known as type II chronic lymphatic leukemia. The mutatio... See more...

Aliases for KDSR Gene

Aliases for KDSR Gene

  • 3-Ketodihydrosphingosine Reductase 2 3 4 5
  • 3-Dehydrosphinganine Reductase 2 3 4
  • SDR35C1 2 3 4
  • Short Chain Dehydrogenase/Reductase Family 35C Member 1 3 4
  • Follicular Lymphoma Variant Translocation 1 2 3
  • Follicular Variant Translocation Protein 1 3 4
  • KDS Reductase 3 4
  • FVT-1 3 4
  • DHSR 2 3
  • FVT1 3 4
  • Short Chain Dehydrogenase/Reductase Family 35C, Member 1 2
  • EC 1.1.1.102 4
  • EKVP4 3
  • KDSR 5

External Ids for KDSR Gene

Previous HGNC Symbols for KDSR Gene

  • FVT1

Previous GeneCards Identifiers for KDSR Gene

  • GC18M059145
  • GC18M060994
  • GC18M057693

Summaries for KDSR Gene

Entrez Gene Summary for KDSR Gene

  • The protein encoded by this gene catalyzes the reduction of 3-ketodihydrosphingosine to dihydrosphingosine. The putative active site residues of the encoded protein are found on the cytosolic side of the endoplasmic reticulum membrane. A chromosomal rearrangement involving this gene is a cause of follicular lymphoma, also known as type II chronic lymphatic leukemia. The mutation of a conserved residue in the bovine ortholog causes spinal muscular atrophy. [provided by RefSeq, Jul 2008]

GeneCards Summary for KDSR Gene

KDSR (3-Ketodihydrosphingosine Reductase) is a Protein Coding gene. Diseases associated with KDSR include Erythrokeratodermia Variabilis Et Progressiva 4 and Distal Chromosome 18Q Deletion Syndrome. Among its related pathways are Sphingolipid metabolism and Metabolism. Gene Ontology (GO) annotations related to this gene include oxidoreductase activity and 3-dehydrosphinganine reductase activity. An important paralog of this gene is RDH13.

UniProtKB/Swiss-Prot Summary for KDSR Gene

  • Catalyzes the reduction of 3-ketodihydrosphingosine (KDS) to dihydrosphingosine (DHS).

Gene Wiki entry for KDSR Gene

Additional gene information for KDSR Gene

No data available for CIViC Summary , Tocris Summary , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for KDSR Gene

Genomics for KDSR Gene

GeneHancer (GH) Regulatory Elements Pubs

Download GeneHancer 2017 data
Promoters and enhancers for KDSR Gene
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around KDSR on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for KDSR

Top Transcription factor binding sites by QIAGEN in the KDSR gene promoter:
  • FOXL1
  • GATA-3
  • HNF-4alpha1
  • HNF-4alpha2
  • STAT1beta
  • STAT2
  • STAT3
  • STAT4
  • STAT5A
  • STAT5B

Genomic Locations for KDSR Gene

Latest Assembly
chr18:63,327,726-63,367,234
(GRCh38/hg38)
Size:
39,509 bases
Orientation:
Minus strand

Previous Assembly
chr18:60,994,959-61,034,439
(GRCh37/hg19 by Entrez Gene)
Size:
39,481 bases
Orientation:
Minus strand

chr18:60,994,959-61,034,743
(GRCh37/hg19 by Ensembl)
Size:
39,785 bases
Orientation:
Minus strand

Genomic View for KDSR Gene

Genes around KDSR on UCSC Golden Path with GeneCards custom track

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

RefSeq DNA sequence for KDSR Gene

Proteins for KDSR Gene

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

    Protein Symbol:
    Q06136-KDSR_HUMAN
    Recommended name:
    3-ketodihydrosphingosine reductase
    Protein Accession:
    Q06136
    Secondary Accessions:
    • B2R5Y1
    • B4DMX0

    Protein attributes for KDSR Gene

    Size:
    332 amino acids
    Molecular mass:
    36187 Da
    Quaternary structure:
    No Data Available

    Alternative splice isoforms for KDSR Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for KDSR Gene

Protein Expression for KDSR Gene

See protein expression from ProteomicsDB, MOPED, PaxDb, and MaxQB

Post-translational modifications for KDSR Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for KDSR Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for KDSR Gene

Domains & Families for KDSR Gene

Gene Families for KDSR Gene

HGNC:
Human Protein Atlas (HPA):
  • Cancer-related genes
  • Disease related genes
  • Enzymes
  • Potential drug targets
  • Predicted intracellular proteins
  • Predicted membrane proteins

Protein Domains for KDSR Gene

InterPro:
Blocks:
  • Short-chain dehydrogenase/reductase SDR
  • Glucose/ribitol dehydrogenase family signature
ProtoNet:

Suggested Antigen Peptide Sequences for KDSR Gene

GenScript: Design optimal peptide antigens:
  • cDNA FLJ57536, moderately similar to 3-ketodihydrosphingosine reductase (EC 1.1.1.102) (B4DMX0_HUMAN)
  • Follicular variant translocation protein 1 (KDSR_HUMAN)

Graphical View of Domain Structure for InterPro Entry

Q06136

UniProtKB/Swiss-Prot:

KDSR_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 KDSR: view

Function for KDSR Gene

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  3. miRNA products for research
  4. Inhibitory RNAs for research
  5. Clone products for research
  6. Cell Lines for research

Molecular function for KDSR Gene

UniProtKB/Swiss-Prot Function:
Catalyzes the reduction of 3-ketodihydrosphingosine (KDS) to dihydrosphingosine (DHS).
UniProtKB/Swiss-Prot CatalyticActivity:
Reaction=NADP(+) + sphinganine = 3-oxosphinganine + H(+) + NADPH; Xref=Rhea:RHEA:22640, ChEBI:CHEBI:15378, ChEBI:CHEBI:57783, ChEBI:CHEBI:57817, ChEBI:CHEBI:58299, ChEBI:CHEBI:58349; EC=1.1.1.102; Evidence={ECO:0000269|PubMed:15328338};.

Enzyme Numbers (IUBMB) for KDSR Gene

Phenotypes From GWAS Catalog for KDSR Gene

Gene Ontology (GO) - Molecular Function for KDSR Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005515 protein binding IPI 32814053
GO:0016491 oxidoreductase activity IEA --
GO:0047560 3-dehydrosphinganine reductase activity TAS --
genes like me logo Genes that share ontologies with KDSR: view
genes like me logo Genes that share phenotypes with KDSR: view

Human Phenotype Ontology for KDSR Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Models for research

  • Taconic Biosciences Mouse Models for KDSR

miRNA for KDSR Gene

miRTarBase miRNAs that target KDSR

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for KDSR

No data available for Animal Models , Transcription Factor Targets and HOMER Transcription for KDSR Gene

Localization for KDSR Gene

Subcellular locations from UniProtKB/Swiss-Prot for KDSR Gene

Endoplasmic reticulum membrane. Multi-pass membrane protein.

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 KDSR gene
Compartment Confidence
endoplasmic reticulum 5
extracellular 4
plasma membrane 2
mitochondrion 2
lysosome 2
cytoskeleton 1
nucleus 1
endosome 1
cytosol 1
golgi apparatus 1

Gene Ontology (GO) - Cellular Components for KDSR Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005615 extracellular space TAS 8417785
GO:0005783 endoplasmic reticulum IDA 15364918
GO:0005789 endoplasmic reticulum membrane TAS --
GO:0016020 membrane IEA,HDA 19946888
GO:0016021 integral component of membrane IEA --
genes like me logo Genes that share ontologies with KDSR: view

No data available for Subcellular locations from the Human Protein Atlas (HPA) for KDSR Gene

Pathways & Interactions for KDSR Gene

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

Pathways by source for KDSR Gene

2 BioSystems pathways for KDSR Gene
2 KEGG pathways for KDSR Gene

UniProtKB/Swiss-Prot Q06136-KDSR_HUMAN

  • Pathway: Lipid metabolism; sphingolipid metabolism.

Interacting Proteins for KDSR Gene

Selected Interacting proteins: Q06136-KDSR_HUMAN for KDSR Gene via UniProtKB IID

GPS-Prot Interaction Network for KDSR

Gene Ontology (GO) - Biological Process for KDSR Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006629 lipid metabolic process IEA --
GO:0006665 sphingolipid metabolic process IEA --
GO:0006666 3-keto-sphinganine metabolic process IBA,IDA 15364918
GO:0030148 sphingolipid biosynthetic process TAS --
GO:0055114 oxidation-reduction process IEA --
genes like me logo Genes that share ontologies with KDSR: view

No data available for SIGNOR curated interactions for KDSR Gene

Drugs & Compounds for KDSR Gene

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  1. Drug products for research

(3) Drugs for KDSR Gene - From: HMDB

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
NADP Experimental Pharma 0
NADPH Experimental Pharma 0
sphinganine Pharma 0

(2) Additional Compounds for KDSR Gene - From: HMDB

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
3-Dehydrosphinganine
  • 3-Dehydro-D-sphinganine
  • 3-Ketodihydrosphingosine
  • 3-Ketosphinganine
  • (2S)-2-Amino-1-hydroxyoctadecan-3-one
  • 1-Hydroxy-2-amino-3-oxo-octadecane
 16105-69-4
Hydrogen Ion
  • H+
  • H(+)
  • Hydron
  • Hydrogen cation
  • Proton
genes like me logo Genes that share compounds with KDSR: view

Transcripts for KDSR Gene

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mRNA/cDNA for KDSR Gene

1 REFSEQ mRNAs :
10 NCBI additional mRNA sequence :
13 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for KDSR

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

ExUns: 1 ^ 2 ^ 3 ^ 4 ^ 5a · 5b · 5c ^ 6 ^ 7 ^ 8 ^ 9a · 9b ^ 10 ^ 11 ^ 12a · 12b · 12c
SP1: - - - -
SP2: - - - -
SP3:
SP4: -
SP5: -
SP6:

Relevant External Links for KDSR Gene

GeneLoc Exon Structure for
KDSR

Expression for KDSR Gene

Products:

  1. Primer products for research
  2. Gene Expression Assays for research

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

mRNA expression in normal human tissues for KDSR Gene
mRNA expression by BioGPS for KDSR GenemRNA expression by GTEx for KDSR Gene

Protein differential expression in normal tissues from HIPED for KDSR Gene

This gene is overexpressed in Retina (6.7).

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



Protein tissue co-expression partners for KDSR Gene

- Elite partner

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for KDSR

SOURCE GeneReport for Unigene cluster for KDSR Gene:

Hs.74050

mRNA Expression by UniProt/SwissProt for KDSR Gene:

Q06136-KDSR_HUMAN
Tissue specificity: Expressed in all tissues examined. Highest expression in placenta. High expression in lung, kidney, stomach and small intestine, low expression in heart, spleen and skeletal muscle. Weakly expressed in normal hematopoietic tissues. Higher expression in some T-cell malignancies and PHA-stimulated lymphocytes.

Evidence on tissue expression from TISSUES for KDSR Gene

  • Nervous system(4.9)
  • Heart(4.4)
  • Liver(2.3)
  • Skin(2.2)
  • Kidney(2.1)
genes like me logo Genes that share expression patterns with KDSR: view

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , mRNA differential expression in normal tissues and Phenotype-based relationships between genes and organs from Gene ORGANizer for KDSR Gene

Orthologs for KDSR Gene

This gene was present in the common ancestor of eukaryotes.

Orthologs for KDSR Gene

Organism Taxonomy Gene Similarity Type Details
Chimpanzee
(Pan troglodytes)
 Mammalia KDSR 30 31
  • 100 (n)
 OneToOne
Dog
(Canis familiaris)
 Mammalia KDSR 30 31
  • 89.75 (n)
 OneToOne
Oppossum
(Monodelphis domestica)
 Mammalia KDSR 31
  • 89 (a)
 OneToOne
Cow
(Bos Taurus)
 Mammalia KDSR 30 31
  • 88.65 (n)
 OneToOne
Mouse
(Mus musculus)
 Mammalia Kdsr 30 17 31
  • 88.19 (n)
 OneToOne
Rat
(Rattus norvegicus)
 Mammalia Kdsr 30
  • 87.45 (n)
Platypus
(Ornithorhynchus anatinus)
 Mammalia KDSR 31
  • 85 (a)
 OneToOne
Chicken
(Gallus gallus)
 Aves KDSR 31
  • 85 (a)
 OneToOne
Lizard
(Anolis carolinensis)
 Reptilia KDSR 31
  • 71 (a)
 OneToOne
Tropical Clawed Frog
(Silurana tropicalis)
 Amphibia kdsr 30
  • 75.34 (n)
African clawed frog
(Xenopus laevis)
 Amphibia Xl.16086 30
Zebrafish
(Danio rerio)
 Actinopterygii kdsr 30 31
  • 73.57 (n)
 OneToOne
zgc55947 30
African malaria mosquito
(Anopheles gambiae)
 Insecta AgaP_AGAP003984 30
  • 50.11 (n)
Fruit Fly
(Drosophila melanogaster)
 Insecta CG10425 30 31
  • 49.05 (n)
 OneToOne
Worm
(Caenorhabditis elegans)
 Secernentea Y37E11AM.3 31
  • 37 (a)
 OneToOne
Baker's yeast
(Saccharomyces cerevisiae)
 Saccharomycetes TSC10 33
Thale Cress
(Arabidopsis thaliana)
 eudicotyledons AT5G19200 30
  • 45.61 (n)
Rice
(Oryza sativa)
 Liliopsida Os02g0701900 30
  • 48.77 (n)
Sea Squirt
(Ciona savignyi)
 Ascidiacea -- 31
  • 52 (a)
 OneToOne
Species where no ortholog for KDSR was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Eremothecium gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • Alicante grape (Vitis vinifera)
  • Alpha proteobacteria (Wolbachia pipientis)
  • Amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • Barley (Hordeum vulgare)
  • Beta proteobacteria (Neisseria meningitidis)
  • Bread mold (Neurospora crassa)
  • 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)
  • Loblloly Pine (Pinus taeda)
  • Malaria Parasite (Plasmodium falciparum)
  • Medicago Trunc (Medicago Truncatula)
  • Moss (Physcomitrella patens)
  • Orangutan (Pongo pygmaeus)
  • Pig (Sus scrofa)
  • Rainbow Trout (Oncorhynchus mykiss)
  • Rice Blast Fungus (Magnaporthe grisea)
  • Schistosome Parasite (Schistosoma mansoni)
  • Sea Anemone (Nematostella vectensis)
  • Sea Vase (Ciona intestinalis)
  • Sea Urchin (Strongylocentrotus purpuratus)
  • Sorghum (Sorghum bicolor)
  • Soybean (Glycine max)
  • Stem Rust Fungus (Puccinia graminis)
  • Sugarcane (Saccharum officinarum)
  • Tomato (Lycopersicon esculentum)
  • Toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • Wheat (Triticum aestivum)

Evolution for KDSR Gene

ENSEMBL:
Gene Tree for KDSR (if available)
TreeFam:
Gene Tree for KDSR (if available)
Aminode:
Evolutionary constrained regions (ECRs) for KDSR: view image

Paralogs for KDSR Gene

Paralogs for KDSR Gene

(1) SIMAP similar genes for KDSR Gene using alignment to 4 proteins:

  • KDSR_HUMAN
  • B4DMX0_HUMAN
  • K7EQS7_HUMAN
  • K7ERC8_HUMAN
genes like me logo Genes that share paralogs with KDSR: view

Variants for KDSR Gene

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  1. SNP Genotyping and Copy Number Assays for research

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for KDSR Gene

SNP ID Clinical significance and condition Chr 18 pos Variation AA Info Type
rs1114167450 Pathogenic: Erythrokeratodermia variabilis et progressiva 4 63,362,810(-) CCTT/C
NM_002035.4(KDSR):c.164_166del (p.Gln55_Gly56delinsArg) 		INFRAME_INDEL
rs1114167451 Pathogenic: Erythrokeratodermia variabilis et progressiva 4 63,355,565(-) T/G
NM_002035.4(KDSR):c.256-2A>C 		SPLICE_ACCEPTOR
rs1114167452 Pathogenic: Erythrokeratodermia variabilis et progressiva 4. Erythrokeratodermia variabilis et progressiva 4 (EKVP4) [MIM:617526] 63,350,940(-) T/Ap.Tyr186Phe
NM_002035.4(KDSR):c.557A>T (p.Tyr186Phe) 		MISSENSE
rs749446295 Benign: not provided 63,338,803(-) G/A
NM_002035.4(KDSR):c.774C>T (p.Ala258=) 		SYNONYMOUS
rs752611378 Pathogenic: Erythrokeratodermia variabilis et progressiva 4 63,335,257(-) C/T
NM_002035.4(KDSR):c.879G>A (p.Gln293=) 		SYNONYMOUS

dbSNP identifiers (rs#s) for variants without ClinVar clinical significance for KDSR Gene

All consequence types are included: molecular consequences (e.g. missense, synonymous), and location-based (e.g. intron, upstream).

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

Variant ID Type Subtype PubMed ID
esv1455992 CNV insertion 17803354
esv2657702 CNV deletion 23128226
esv2671992 CNV deletion 23128226
esv2717201 CNV deletion 23290073
esv3305878 CNV mobile element insertion 20981092
esv3325049 CNV insertion 20981092
esv3642768 CNV loss 21293372
esv3642769 CNV gain 21293372
esv3642770 CNV loss 21293372
nsv1066552 CNV gain 25217958
nsv577096 CNV loss 21841781

Variation tolerance for KDSR Gene

Residual Variation Intolerance Score: 15% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 0.56; 12.15% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for KDSR Gene

Human Gene Mutation Database (HGMD)
KDSR
SNPedia medical, phenotypic, and genealogical associations of SNPs for
KDSR

SNP Genotyping and Copy Number Assays for research

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

Disorders for KDSR Gene

MalaCards: The human disease database

(15) MalaCards diseases for KDSR Gene - From: OMI, CVR, GTR, ORP, SWI, COP, and GCD

- elite association - COSMIC cancer census association via MalaCards
Search KDSR in MalaCards View complete list of genes associated with diseases

UniProtKB/Swiss-Prot

KDSR_HUMAN
  • Note=A chromosomal aberration involving KDSR is a cause of follicular lymphoma; also known as type II chronic lymphatic leukemia. Translocation t(2;18)(p11;q21) with a Ig J kappa chain region (PubMed:8417785). {ECO:0000269 PubMed:8417785}.
  • Erythrokeratodermia variabilis et progressiva 4 (EKVP4) [MIM:617526]: A form of erythrokeratodermia variabilis et progressiva, a genodermatosis characterized by the coexistence of two independent skin lesions: transient erythema and hyperkeratosis that is usually localized but occasionally occurs in its generalized form. Clinical presentation varies significantly within a family and from one family to another. Palmoplantar keratoderma is present in around 50% of cases. {ECO:0000269 PubMed:28575652}. Note=The disease is caused by variants affecting the gene represented in this entry.

Additional Disease Information for KDSR

Genetic Association Database
(GAD)
Human Genome Epidemiology Navigator
(HuGE)
Atlas
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
Open Targets Platform
Open Targets Platform
genes like me logo Genes that share disorders with KDSR: view

No data available for Genatlas for KDSR Gene

Publications for KDSR Gene

  1. FVT-1 is a mammalian 3-ketodihydrosphingosine reductase with an active site that faces the cytosolic side of the endoplasmic reticulum membrane. (PMID: 15328338) Kihara A … Igarashi Y (The Journal of biological chemistry 2004) 2 3 4 23
  2. FVT-1, a novel human transcription unit affected by variant translocation t(2;18)(p11;q21) of follicular lymphoma. (PMID: 8417785) Rimokh R … Magaud JP (Blood 1993) 2 3 4 23
  3. Mutations in KDSR Cause Recessive Progressive Symmetric Erythrokeratoderma. (PMID: 28575652) Boyden LM … Choate KA (American journal of human genetics 2017) 3 4 74
  4. A missense mutation in the 3-ketodihydrosphingosine reductase FVT1 as candidate causal mutation for bovine spinal muscular atrophy. (PMID: 17420465) Krebs S … Förster M (Proceedings of the National Academy of Sciences of the United States of America 2007) 2 3 23
  5. The SDR (short-chain dehydrogenase/reductase and related enzymes) nomenclature initiative. (PMID: 19027726) Persson B … Oppermann U (Chemico-biological interactions 2009) 2 3

ExternalLinks

View latest publications for KDSR gene in Mastermind

Products for KDSR Gene

Sources for KDSR Gene