RXRB Gene (Protein Coding)

Retinoid X Receptor Beta

GC06M033193
GIFtS:
48
This gene encodes a member of the retinoid X receptor (RXR) family of nuclear receptors which are involved in mediating the effects of retinoic acid (RA). The encoded protein forms homodimers with the retinoic acid, thyroid hormone, and vitamin D receptors, increasing both DNA binding and transcriptional function on their respective response elements. This gene lies within the ... See more...

Aliases for RXRB Gene

Aliases for RXRB Gene

  • Retinoid X Receptor Beta 2 3 4 5
  • Nuclear Receptor Subfamily 2 Group B Member 2 2 3 4
  • NR2B2 2 3 4
  • Retinoic Acid Receptor RXR-Beta 3 4
  • H-2RIIBP 2 3
  • RCoR-1 2 3
  • MHC Class I Promoter Binding Protein 3
  • Retinoid X Receptor, Beta 2
  • DAUDI6 3
  • RXRB 5

External Ids for RXRB Gene

Previous GeneCards Identifiers for RXRB Gene

  • GC06M033164
  • GC06M033208
  • GC06M033270
  • GC06M033161
  • GC06M032877

Summaries for RXRB Gene

Entrez Gene Summary for RXRB Gene

  • This gene encodes a member of the retinoid X receptor (RXR) family of nuclear receptors which are involved in mediating the effects of retinoic acid (RA). The encoded protein forms homodimers with the retinoic acid, thyroid hormone, and vitamin D receptors, increasing both DNA binding and transcriptional function on their respective response elements. This gene lies within the major histocompatibility complex (MHC) class II region on chromosome 6. Alternatively spliced transcript variants encoding multiple isoforms have been observed for this gene. [provided by RefSeq, Jul 2012]

GeneCards Summary for RXRB Gene

RXRB (Retinoid X Receptor Beta) is a Protein Coding gene. Diseases associated with RXRB include Granulomatosis With Polyangiitis and Vasculitis. Among its related pathways are Signaling by Retinoic Acid and Signaling by GPCR. Gene Ontology (GO) annotations related to this gene include DNA-binding transcription factor activity and sequence-specific DNA binding. An important paralog of this gene is RXRA.

UniProtKB/Swiss-Prot Summary for RXRB Gene

  • Receptor for retinoic acid. Retinoic acid receptors bind as heterodimers to their target response elements in response to their ligands, all-trans or 9-cis retinoic acid, and regulate gene expression in various biological processes. The RAR/RXR heterodimers bind to the retinoic acid response elements (RARE).

Tocris Summary for RXRB Gene

  • Retinoid X receptors (RXR) are members of the NR2B nuclear receptor family and are common binding partners to many other nuclear receptors, including PPARs, liver X receptors (LXRs) and vitamin D receptors (VDRs). There are three RXR subtypes; alpha, beta and gamma.

Gene Wiki entry for RXRB Gene

Additional gene information for RXRB Gene

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

Genomics for RXRB Gene

GeneHancer (GH) Regulatory Elements Pubs

Download GeneHancer 2017 data
Promoters and enhancers for RXRB 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 RXRB on the GeneHancer Hub at the UCSC Golden Path

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

Top Transcription factor binding sites by QIAGEN in the RXRB gene promoter:
  • Sp1

Genomic Locations for RXRB Gene

Latest Assembly
chr6:33,193,588-33,200,991
(GRCh38/hg38)
Size:
7,404 bases
Orientation:
Minus strand

Previous Assembly
chr6:33,161,365-33,168,630
(GRCh37/hg19 by Entrez Gene)
Size:
7,266 bases
Orientation:
Minus strand

chr6:33,161,365-33,168,630
(GRCh37/hg19 by Ensembl)
Size:
7,266 bases
Orientation:
Minus strand

Alternative Locations (GRCh38/hg38)

  • chr6(ALT_REF_LOCI_2):4,605,095-4,612,358 (-)
  • chr6(ALT_REF_LOCI_3):4,437,087-4,444,352 (-)
  • chr6(ALT_REF_LOCI_4):4,613,060-4,620,326 (-)
  • chr6(ALT_REF_LOCI_5):4,629,544-4,636,806 (-)
  • chr6(ALT_REF_LOCI_6):4,387,991-4,395,257 (-)

Genomic View for RXRB Gene

Genes around RXRB on UCSC Golden Path with GeneCards custom track

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

Proteins for RXRB Gene

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

    Protein Symbol:
    P28702-RXRB_HUMAN
    Recommended name:
    Retinoic acid receptor RXR-beta
    Protein Accession:
    P28702
    Secondary Accessions:
    • P28703
    • Q59G65
    • Q5JP92
    • Q5STQ1

    Protein attributes for RXRB Gene

    Size:
    533 amino acids
    Molecular mass:
    56922 Da
    Quaternary structure:
    • Homodimer (in vitro) (PubMed:11782480). Heterodimer with other retinoic acid receptor family members. Binds DNA preferentially as a RAR/RXR heterodimer (PubMed:1310259). Interacts with NR1H3 (PubMed:12970175). Interacts with AKAP13 (By similarity).
    SequenceCaution:
    • Sequence=BAD92481.1; Type=Erroneous initiation; Note=Extended N-terminus.; Evidence={ECO:0000305};

    Three dimensional structures from OCA and Proteopedia for RXRB Gene

    Alternative splice isoforms for RXRB Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for RXRB Gene

Protein Expression for RXRB Gene

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

Post-translational modifications for RXRB Gene

  • Ubiquitination at Lys452
  • Modification sites at PhosphoSitePlus

Other Protein References for RXRB Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for RXRB Gene

Domains & Families for RXRB Gene

Gene Families for RXRB Gene

HGNC:
IUPHAR :
Human Protein Atlas (HPA):
  • Cancer-related genes
  • FDA approved drug targets
  • Nuclear receptors
  • Predicted intracellular proteins
  • Transcription factors

Protein Domains for RXRB Gene

InterPro:
Blocks:
  • Steroid hormone receptor signature
  • Retinoic acid receptor signature

Suggested Antigen Peptide Sequences for RXRB Gene

GenScript: Design optimal peptide antigens:
  • Retinoid X receptor, beta (A2ABB0_HUMAN)
  • cDNA FLJ50538, highly similar to Retinoic acid receptor RXR-beta (B7Z3E4_HUMAN)
  • Retinoid X receptor, beta (Q5STP9_HUMAN)
  • Retinoid X receptor beta (RXRB_HUMAN)

Graphical View of Domain Structure for InterPro Entry

P28702

UniProtKB/Swiss-Prot:

RXRB_HUMAN :
  • Composed of three domains: a modulating N-terminal domain, a DNA-binding domain and a C-terminal ligand-binding domain.
  • Belongs to the nuclear hormone receptor family. NR2 subfamily.
Domain:
  • Composed of three domains: a modulating N-terminal domain, a DNA-binding domain and a C-terminal ligand-binding domain.
Family:
  • Belongs to the nuclear hormone receptor family. NR2 subfamily.
genes like me logo Genes that share domains with RXRB: view

Function for RXRB Gene

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Molecular function for RXRB Gene

UniProtKB/Swiss-Prot Function:
Receptor for retinoic acid. Retinoic acid receptors bind as heterodimers to their target response elements in response to their ligands, all-trans or 9-cis retinoic acid, and regulate gene expression in various biological processes. The RAR/RXR heterodimers bind to the retinoic acid response elements (RARE).
UniProtKB/Swiss-Prot Induction:
Down-regulated by aging.
GENATLAS Biochemistry:
retinoic acid X receptor binding and activated by 9-cis-retinoic acid,only (9-cis-RA),beta subunit,obligate member of heterodimeric nuclear receptors,steroid/thyroid/retinoic receptor superfamily

Phenotypes From GWAS Catalog for RXRB Gene

Gene Ontology (GO) - Molecular Function for RXRB Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000977 RNA polymerase II regulatory region sequence-specific DNA binding IDA 12767074
GO:0000978 RNA polymerase II proximal promoter sequence-specific DNA binding IBA 21873635
GO:0000981 DNA-binding transcription factor activity, RNA polymerase II-specific ISA --
GO:0001228 DNA-binding transcription activator activity, RNA polymerase II-specific IDA 12767074
GO:0003677 DNA binding IEA --
genes like me logo Genes that share ontologies with RXRB: view
genes like me logo Genes that share phenotypes with RXRB: view

Animal Models for RXRB Gene

MGI Knock Outs for RXRB:

Animal Models for research

miRNA for RXRB Gene

miRTarBase miRNAs that target RXRB

Inhibitory RNAs for research

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No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for RXRB Gene

Localization for RXRB Gene

Subcellular locations from UniProtKB/Swiss-Prot for RXRB Gene

Nucleus. Cytoplasm.

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 RXRB gene
Compartment Confidence
nucleus 5
peroxisome 2
cytosol 2
plasma membrane 1
extracellular 1
cytoskeleton 1
mitochondrion 1
endoplasmic reticulum 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Nucleoplasm (3)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for RXRB Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000785 chromatin ISA --
GO:0005634 nucleus IDA 7990953
GO:0005654 nucleoplasm TAS --
GO:0005737 cytoplasm IEA --
GO:0090575 RNA polymerase II transcription factor complex IBA 21873635
genes like me logo Genes that share ontologies with RXRB: view

Pathways & Interactions for RXRB Gene

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

Pathways by source for RXRB Gene

1 GeneGo (Thomson Reuters) pathway for RXRB Gene
  • Transcription Sin3 and NuRD in transcription regulation
3 Qiagen pathways for RXRB Gene
  • Nuclear Receptor Activation by Vitamin-A
  • Oct4 in Mammalian ESC Pluripotency
  • PPAR Pathway

SIGNOR curated interactions for RXRB Gene

Activates:
Is activated by:

Gene Ontology (GO) - Biological Process for RXRB Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006355 regulation of transcription, DNA-templated IEA --
GO:0006357 regulation of transcription by RNA polymerase II IBA 21873635
GO:0006367 transcription initiation from RNA polymerase II promoter TAS --
GO:0030154 cell differentiation IBA 21873635
GO:0032526 response to retinoic acid IBA 21873635
genes like me logo Genes that share ontologies with RXRB: view

Drugs & Compounds for RXRB Gene

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(28) Drugs for RXRB Gene - From: DrugBank, ApexBio, DGIdb, IUPHAR, HMDB, Tocris, and Novoseek

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Bexarotene Approved, Investigational Pharma Agonist, Target Potent and selective RXR agonist, Others 45
Adapalene Approved Pharma Target, agonist, binder RAR尾 and RAR纬 agonist 92
Alitretinoin Approved, Investigational Pharma Target, agonist 18
Tazarotene Approved, Investigational Pharma Target, agonist, binder Topical retinoid;antiproliferative;inducer of TIG3 tumor suppressor 51
Tretinoin Approved, Investigational Nutra Target, agonist, binder 288

(3) Additional Compounds for RXRB Gene - From: Novoseek

Name Synonyms Role CAS Number PubChem IDs PubMed IDs

(4) Tocris Compounds for RXRB Gene

Compound Action Cas Number
Bexarotene Potent and selective RXR agonist 153559-49-0
CD 3254 Potent and selective RXRalpha agonist. 196961-43-0
HX 531 Potent RXR antagonist 188844-34-0
LG 100754 RXR:PPAR agonist 180713-37-5

(11) ApexBio Compounds for RXRB Gene

Compound Action Cas Number
Acitretin Metabolite of etretinate 55079-83-9
Adapalene RAR尾 and RAR纬 agonist 106685-40-9
Bexarotene 153559-49-0
Fluorobexarotene 1190848-23-7
HX 531 188844-34-0
HX 630 188844-52-2
LG 100754 180713-37-5
LG 101506 331248-11-4
PA 452 457657-34-0
SR 11237 146670-40-8
UVI 3003 847239-17-2
genes like me logo Genes that share compounds with RXRB: view

Drug products for research

Transcripts for RXRB Gene

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mRNA/cDNA for RXRB Gene

3 REFSEQ mRNAs :
23 NCBI additional mRNA sequence :
5 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 RXRB

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

No ASD Table

Relevant External Links for RXRB Gene

GeneLoc Exon Structure for
RXRB

Expression for RXRB Gene

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  1. Primer products for research
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mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for RXRB Gene

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

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Protein differential expression in normal tissues from HIPED for RXRB Gene

This gene is overexpressed in Blymphocyte (27.3), Peripheral blood mononuclear cells (12.2), Placenta (10.6), and Ovary (6.6).

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



Protein tissue co-expression partners for RXRB Gene

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

SOURCE GeneReport for Unigene cluster for RXRB Gene:

Hs.388034

mRNA Expression by UniProt/SwissProt for RXRB Gene:

P28702-RXRB_HUMAN
Tissue specificity: Expressed in aortic endothelial cells (at protein level) (PubMed:28167758). Expressed in monocytes (PubMed:26463675). Expressed in a variety of tumor cell lines.

Evidence on tissue expression from TISSUES for RXRB Gene

  • Nervous system(4.8)
  • Liver(4.5)
  • Thyroid gland(2.4)
  • Skin(2.2)
  • Kidney(2.1)
  • Intestine(2.1)
  • Muscle(2)
genes like me logo Genes that share expression patterns with RXRB: view

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

Orthologs for RXRB Gene

This gene was present in the common ancestor of animals.

Orthologs for RXRB Gene

Organism Taxonomy Gene Similarity Type Details
Chimpanzee
(Pan troglodytes)
 Mammalia RXRB 29 30
  • 99.69 (n)
 OneToOne
Dog
(Canis familiaris)
 Mammalia RXRB 29 30
  • 95.21 (n)
 OneToOne
Cow
(Bos Taurus)
 Mammalia RXRB 29 30
  • 93.11 (n)
 OneToOne
Oppossum
(Monodelphis domestica)
 Mammalia RXRB 30
  • 93 (a)
 OneToOne
Mouse
(Mus musculus)
 Mammalia Rxrb 29 16 30
  • 91.67 (n)
 OneToOne
Rat
(Rattus norvegicus)
 Mammalia Rxrb 29
  • 90.35 (n)
Lizard
(Anolis carolinensis)
 Reptilia RXRB 30
  • 64 (a)
 OneToOne
Tropical Clawed Frog
(Silurana tropicalis)
 Amphibia rxrb 29
  • 73.24 (n)
Zebrafish
(Danio rerio)
 Actinopterygii rxrba 29 30
  • 73.12 (n)
 OneToMany
rxrbb 30
  • 70 (a)
 OneToMany
-- 29
Fruit Fly
(Drosophila melanogaster)
 Insecta usp 30 31
  • 40 (a)
 OneToMany
Worm
(Caenorhabditis elegans)
 Secernentea nhr-69 31
  • 34 (a)
nhr-14 31
  • 33 (a)
Species where no ortholog for RXRB was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Eremothecium gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • 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)
  • Loblloly Pine (Pinus taeda)
  • Malaria Parasite (Plasmodium falciparum)
  • Medicago Trunc (Medicago Truncatula)
  • Moss (Physcomitrella patens)
  • Orangutan (Pongo pygmaeus)
  • Pig (Sus scrofa)
  • Platypus (Ornithorhynchus anatinus)
  • Rainbow Trout (Oncorhynchus mykiss)
  • Rice (Oryza sativa)
  • Rice Blast Fungus (Magnaporthe grisea)
  • Schistosome Parasite (Schistosoma mansoni)
  • Sea Anemone (Nematostella vectensis)
  • Sea Vase (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)

Evolution for RXRB Gene

ENSEMBL:
Gene Tree for RXRB (if available)
TreeFam:
Gene Tree for RXRB (if available)
Aminode:
Evolutionary constrained regions (ECRs) for RXRB: view image
Alliance of Genome Resources:
Additional Orthologs for RXRB

Paralogs for RXRB Gene

Paralogs for RXRB Gene

(46) SIMAP similar genes for RXRB Gene using alignment to 6 proteins:

  • RXRB_HUMAN
  • B7Z3E4_HUMAN
  • E9PK75_HUMAN
  • E9PK95_HUMAN
  • J3JS70_HUMAN
  • J3JS71_HUMAN
genes like me logo Genes that share paralogs with RXRB: view

Variants for RXRB Gene

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

SNP ID Clinical significance and condition Chr 06 pos Variation AA Info Type
rs143154990 Benign: not provided 33,194,833(-) G/GGGTGGA
NM_021976.5(RXRB):c.1455-10_1455-5dup 		INTRON

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

Variant ID Type Subtype PubMed ID
dgv10609n54 CNV loss 21841781
nsv1073969 CNV deletion 25765185
nsv1112900 CNV deletion 24896259
nsv1119076 CNV deletion 24896259
nsv522719 CNV loss 19592680
nsv830634 CNV loss 17160897

Variation tolerance for RXRB Gene

Residual Variation Intolerance Score: 18.1% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 2.02; 37.17% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for RXRB Gene

Human Gene Mutation Database (HGMD)
RXRB
SNPedia medical, phenotypic, and genealogical associations of SNPs for
RXRB
Leiden Open Variation Database (LOVD)
RXRB

SNP Genotyping and Copy Number Assays for research

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

Disorders for RXRB Gene

MalaCards: The human disease database

(3) MalaCards diseases for RXRB Gene - From: COP and GCD

Disorder Aliases PubMed IDs
granulomatosis with polyangiitis
  • gpa
vasculitis
  • angiitis
lung cancer
  • lung cancer, susceptibility to
- elite association - COSMIC cancer census association via MalaCards
Search RXRB in MalaCards View complete list of genes associated with diseases

Additional Disease Information for RXRB

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 RXRB: view

No data available for UniProtKB/Swiss-Prot and Genatlas for RXRB Gene

Publications for RXRB Gene

  1. Retinoid X receptor beta polymorphisms do not explain functional differences in vitamins D and A response in Antineutrophil cytoplasmic antibody associated vasculitis patients. (PMID: 19811264) Kälsch AI … Yard BA (Autoimmunity 2009) 3 22 40
  2. Mutation analysis of the retinoid X receptor beta, nuclear-related receptor 1, and peroxisome proliferator-activated receptor alpha genes in schizophrenia and alcohol dependence: possible haplotype association of nuclear-related receptor 1 gene to alcohol dependence. (PMID: 11840500) Ishiguro H … Arinami T (American journal of medical genetics 2002) 3 22 40
  3. Cloning and chromosome mapping of human retinoid X receptor beta: selective amino acid sequence conservation of a nuclear hormone receptor in mammals. (PMID: 8381386) Fleischhauer K … Yang SY (Human genetics 1993) 3 4 22
  4. Mapping of RXRB to human chromosome 6p21.3. (PMID: 8257090) Fitzgibbon J … Povey S (Annals of human genetics 1993) 2 3 22
  5. Purification, cloning, and RXR identity of the HeLa cell factor with which RAR or TR heterodimerizes to bind target sequences efficiently. (PMID: 1310259) Leid M … Mader S (Cell 1992) 3 4 22

ExternalLinks

View latest publications for RXRB gene in Mastermind

Products for RXRB Gene