This gene encodes a homeobox-containing transcription factor that functions in eye development. The gene is expressed early in the eye primordia, and is required for retinal cell fate determination and also regulates stem cell proliferation. Mutations in this gene have been reported in patients with defects in ocular development, including microphthalmia, anophthalmia, and colo... See more...

Aliases for RAX Gene

Aliases for RAX Gene

  • Retina And Anterior Neural Fold Homeobox 2 3 5
  • RX 2 3 4
  • Retina And Anterior Neural Fold Homeobox Protein 3 4
  • Retinal Homeobox Protein Rx 3 4
  • MCOP3 3
  • RAX 5

External Ids for RAX Gene

Previous GeneCards Identifiers for RAX Gene

  • GC18M056767
  • GC18M056909
  • GC18M056720
  • GC18M055083
  • GC18M055084
  • GC18M055085
  • GC18M053643

Summaries for RAX Gene

Entrez Gene Summary for RAX Gene

  • This gene encodes a homeobox-containing transcription factor that functions in eye development. The gene is expressed early in the eye primordia, and is required for retinal cell fate determination and also regulates stem cell proliferation. Mutations in this gene have been reported in patients with defects in ocular development, including microphthalmia, anophthalmia, and coloboma.[provided by RefSeq, Oct 2009]

GeneCards Summary for RAX Gene

RAX (Retina And Anterior Neural Fold Homeobox) is a Protein Coding gene. Diseases associated with RAX include Microphthalmia, Isolated 3 and Microphthalmia. Gene Ontology (GO) annotations related to this gene include RNA polymerase II proximal promoter sequence-specific DNA binding and proximal promoter DNA-binding transcription activator activity, RNA polymerase II-specific. An important paralog of this gene is RAX2.

UniProtKB/Swiss-Prot Summary for RAX Gene

  • Plays a critical role in eye formation by regulating the initial specification of retinal cells and/or their subsequent proliferation. Binds to the photoreceptor conserved element-I (PCE-1/Ret 1) in the photoreceptor cell-specific arrestin promoter.

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

Genomics for RAX Gene

GeneHancer (GH) Regulatory Elements Pubs

Promoters and enhancers for RAX Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH18J059277 Promoter/Enhancer 1.2 EPDnew Ensembl ENCODE 250.7 +0.8 777 0.6 CTCF YY1 TAF1 SP1 SP3 EZH2 ZNF143 KDM1A ZNF335 lnc-CPLX4-2 RAX GRP
GH18J059276 Enhancer 0.5 Ensembl ENCODE 250.7 0.0 -48 0.4 EZH2 ZNF335 lnc-CPLX4-2 RAX HSALNG0121862 CPLX4
GH18J059308 Enhancer 0.8 ENCODE 11.3 -34.6 -34578 0.2 IKZF1 ZNF600 ZIC2 ZBTB10 REST TRIM22 ZNF341 KLF7 CTCF SMAD4 RAX piR-57460-320 CPLX4 HSALNG0121862
GH18J059221 Promoter 1.2 EPDnew Ensembl 0.2 +53.4 53385 1.8 ZNF600 ZIC2 ZBTB10 ZNF341 ZBTB48 CBX8 SCRT1 GLIS1 CTCF ZNF366 GRP NONHSAG023981.2 RAX
GH18J059249 Enhancer 0.7 Ensembl ENCODE 0.4 +24.7 24683 0.6 ZNF654 CEBPB REST CTCF MAFF RAD21 SMC3 ZNF316 MAFK ATF4 lnc-RAX-1 HSALNG0121860 piR-50308-299 RAX GRP
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

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

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

Top Transcription factor binding sites by QIAGEN in the RAX gene promoter:
  • C/EBPalpha
  • GATA-1
  • MyoD
  • Pax-5
  • Spz1
  • STAT1
  • STAT1alpha
  • STAT1beta
  • XBP-1

Genomic Locations for RAX Gene

Latest Assembly
chr18:59,267,035-59,274,086
(GRCh38/hg38)
Size:
7,052 bases
Orientation:
Minus strand

Previous Assembly
chr18:56,934,270-56,940,686
(GRCh37/hg19 by Entrez Gene)
Size:
6,417 bases
Orientation:
Minus strand

chr18:56,934,267-56,941,318
(GRCh37/hg19 by Ensembl)
Size:
7,052 bases
Orientation:
Minus strand

Genomic View for RAX Gene

Genes around RAX on UCSC Golden Path with GeneCards custom track

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

RefSeq DNA sequence for RAX Gene

Proteins for RAX Gene

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

    Protein Symbol:
    Q9Y2V3-RX_HUMAN
    Recommended name:
    Retinal homeobox protein Rx
    Protein Accession:
    Q9Y2V3
    Secondary Accessions:
    • Q86V11

    Protein attributes for RAX Gene

    Size:
    346 amino acids
    Molecular mass:
    36676 Da
    Quaternary structure:
    No Data Available

    Alternative splice isoforms for RAX Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for RAX Gene

Post-translational modifications for RAX Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for RAX Gene

No data available for DME Specific Peptides for RAX Gene

Domains & Families for RAX Gene

Gene Families for RAX Gene

HGNC:
Human Protein Atlas (HPA):
  • Disease related genes
  • Predicted intracellular proteins
  • Transcription factors

Protein Domains for RAX Gene

InterPro:
Blocks:
  • Paired-like homeodomain protein, OAR

Suggested Antigen Peptide Sequences for RAX Gene

GenScript: Design optimal peptide antigens:
  • Retina and anterior neural fold homeobox protein (RX_HUMAN)

Graphical View of Domain Structure for InterPro Entry

Q9Y2V3

UniProtKB/Swiss-Prot:

RX_HUMAN :
  • Belongs to the paired homeobox family. Bicoid subfamily.
Family:
  • Belongs to the paired homeobox family. Bicoid subfamily.
genes like me logo Genes that share domains with RAX: view

Function for RAX Gene

Molecular function for RAX Gene

UniProtKB/Swiss-Prot Function:
Plays a critical role in eye formation by regulating the initial specification of retinal cells and/or their subsequent proliferation. Binds to the photoreceptor conserved element-I (PCE-1/Ret 1) in the photoreceptor cell-specific arrestin promoter.

Phenotypes From GWAS Catalog for RAX Gene

Gene Ontology (GO) - Molecular Function for RAX Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000978 RNA polymerase II proximal promoter sequence-specific DNA binding IDA 10625658
GO:0000981 DNA-binding transcription factor activity, RNA polymerase II-specific IEA,ISA --
GO:0001228 DNA-binding transcription activator activity, RNA polymerase II-specific IDA 10625658
GO:0003677 DNA binding IEA --
GO:1990837 sequence-specific double-stranded DNA binding IDA 28473536
genes like me logo Genes that share ontologies with RAX: view
genes like me logo Genes that share phenotypes with RAX: view

Human Phenotype Ontology for RAX Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Models for RAX Gene

MGI Knock Outs for RAX:
  • Rax Rax<tm1.2Lwd>
  • Rax Rax<tm1Mjam>

Inhibitory RNAs for research

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

No data available for Enzyme Numbers (IUBMB) , Transcription Factor Targets and HOMER Transcription for RAX Gene

Localization for RAX Gene

Subcellular locations from UniProtKB/Swiss-Prot for RAX Gene

Nucleus.

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 RAX gene
Compartment Confidence
nucleus 5
cytoskeleton 1

Gene Ontology (GO) - Cellular Components for RAX Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000785 chromatin ISA --
GO:0005634 nucleus IEA --
genes like me logo Genes that share ontologies with RAX: view

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

Pathways & Interactions for RAX Gene

PathCards logo

SuperPathways for RAX Gene

No Data Available

Gene Ontology (GO) - Biological Process for RAX 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:0007275 multicellular organism development IEA --
GO:0007389 pattern specification process IEA --
GO:0007420 brain development IEA --
genes like me logo Genes that share ontologies with RAX: view

No data available for Pathways by source and SIGNOR curated interactions for RAX Gene

Drugs & Compounds for RAX Gene

No Compound Related Data Available

Transcripts for RAX Gene

mRNA/cDNA for RAX Gene

1 REFSEQ mRNAs :
3 NCBI additional mRNA sequence :
4 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 RAX

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

ExUns: 1a · 1b ^ 2 ^ 3a · 3b
SP1:
SP2: -

Relevant External Links for RAX Gene

GeneLoc Exon Structure for
RAX

Expression for RAX Gene

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

mRNA differential expression in normal tissues according to GTEx for RAX Gene

This gene is overexpressed in Pituitary (x31.9) and Skin - Not Sun Exposed (Suprapubic) (x4.2).

Protein differential expression in normal tissues from HIPED for RAX Gene

This gene is overexpressed in Retina (69.0).

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



Protein tissue co-expression partners for RAX Gene

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

SOURCE GeneReport for Unigene cluster for RAX Gene:

Hs.278957

mRNA Expression by UniProt/SwissProt for RAX Gene:

Q9Y2V3-RX_HUMAN
Tissue specificity: Expressed in the developing eye and weakly expressed in the adult retina.

Evidence on tissue expression from TISSUES for RAX Gene

  • Eye(4.5)

Phenotype-based relationships between genes and organs from Gene ORGANizer for RAX Gene

Germ Layers:
  • ectoderm
  • mesoderm
Systems:
  • integumentary
  • nervous
  • reproductive
  • skeletal muscle
Regions:
Head and neck:
  • brain
  • cranial nerve
  • eye
  • eyelid
  • face
  • head
Pelvis:
  • testicle
General:
  • peripheral nervous system
  • skin
genes like me logo Genes that share expression patterns with RAX: view

Primer products for research

Orthologs for RAX Gene

This gene was present in the common ancestor of animals.

Orthologs for RAX Gene

Organism Taxonomy Gene Similarity Type Details
Chimpanzee
(Pan troglodytes)
Mammalia RAX 29 30
  • 99.23 (n)
OneToOne
Cow
(Bos Taurus)
Mammalia RAX 29 30
  • 87.67 (n)
OneToOne
Mouse
(Mus musculus)
Mammalia Rax 29 16 30
  • 84.8 (n)
OneToOne
Rat
(Rattus norvegicus)
Mammalia Rax 29
  • 84.16 (n)
Dog
(Canis familiaris)
Mammalia RAX 29 30
  • 81.87 (n)
OneToOne
Oppossum
(Monodelphis domestica)
Mammalia -- 30
  • 69 (a)
ManyToMany
-- 30
  • 16 (a)
ManyToMany
Platypus
(Ornithorhynchus anatinus)
Mammalia -- 30
  • 58 (a)
ManyToMany
Chicken
(Gallus gallus)
Aves RAX 29
  • 75.87 (n)
RX1 30
  • 61 (a)
ManyToMany
Lizard
(Anolis carolinensis)
Reptilia -- 30
  • 62 (a)
OneToMany
Tropical Clawed Frog
(Silurana tropicalis)
Amphibia rax 29
  • 61.11 (n)
Zebrafish
(Danio rerio)
Actinopterygii rx3 29
  • 59.25 (n)
rx2 30
  • 49 (a)
ManyToMany
Fruit Fly
(Drosophila melanogaster)
Insecta Rx 31
  • 96 (a)
Worm
(Caenorhabditis elegans)
Secernentea ceh-8 30
  • 30 (a)
OneToMany
Sea Squirt
(Ciona savignyi)
Ascidiacea -- 30
  • 23 (a)
OneToMany
Sea Vase
(Ciona intestinalis)
Ascidiacea Cin.14217 29
Species where no ortholog for RAX 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)
  • 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 (Oryza sativa)
  • Rice Blast Fungus (Magnaporthe grisea)
  • Schistosome Parasite (Schistosoma mansoni)
  • Sea Anemone (Nematostella vectensis)
  • 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 RAX Gene

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

Paralogs for RAX Gene

(3) SIMAP similar genes for RAX Gene using alignment to 2 proteins:

  • RX_HUMAN
  • G3V2C8_HUMAN
genes like me logo Genes that share paralogs with RAX: view

Variants for RAX Gene

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

SNP ID Clinical significance and condition Chr 18 pos Variation AA Info Type
889050 Uncertain Significance: Microphthalmia, isolated 3 59,267,209(-) G/A
NM_013435.3(RAX):c.*1795C>T
THREE_PRIME_UTR
889051 Uncertain Significance: Microphthalmia, isolated 3 59,267,233(-) C/T
NM_013435.3(RAX):c.*1771G>A
THREE_PRIME_UTR
889052 Uncertain Significance: Microphthalmia, isolated 3 59,267,330(-) T/C
NM_013435.3(RAX):c.*1674A>G
THREE_PRIME_UTR
889107 Uncertain Significance: Microphthalmia, isolated 3 59,268,207(-) C/G
NM_013435.3(RAX):c.*797G>C
THREE_PRIME_UTR
889108 Uncertain Significance: Microphthalmia, isolated 3 59,268,293(-) C/T
NM_013435.3(RAX):c.*711G>A
THREE_PRIME_UTR

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

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

Variation tolerance for RAX Gene

Gene Damage Index Score: 8.12; 84.58% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for RAX Gene

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

SNP Genotyping and Copy Number Assays for research

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot and Structural Variations from Database of Genomic Variants (DGV) for RAX Gene

Disorders for RAX Gene

MalaCards: The human disease database

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

Disorder Aliases PubMed IDs
microphthalmia, isolated 3
  • mcop3
microphthalmia
  • microphthalmos
colobomatous microphthalmia
  • mac
sclerocornea
  • isolated congenital sclerocornea
microphthalmia, syndromic 8
  • mcops8
- elite association - COSMIC cancer census association via MalaCards
Search RAX in MalaCards View complete list of genes associated with diseases

UniProtKB/Swiss-Prot

RX_HUMAN
  • Microphthalmia, isolated, 3 (MCOP3) [MIM:611038]: A disorder of eye formation, ranging from small size of a single eye to complete bilateral absence of ocular tissues. Ocular abnormalities like opacities of the cornea and lens, scaring of the retina and choroid, and other abnormalities may also be present. {ECO:0000269 PubMed:14662654, ECO:0000269 PubMed:24033328}. Note=The disease is caused by variants affecting the gene represented in this entry.

Additional Disease Information for RAX

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 RAX: view

No data available for Genatlas for RAX Gene

Publications for RAX Gene

  1. Mutations in the human RAX homeobox gene in a patient with anophthalmia and sclerocornea. (PMID: 14662654) Voronina VA … Mathers PH (Human molecular genetics 2004) 2 3 4 22 72
  2. Both PCE-1/RX and OTX/CRX interactions are necessary for photoreceptor-specific gene expression. (PMID: 10625658) Kimura A … Shinohara T (The Journal of biological chemistry 2000) 2 3 4
  3. Molecular findings and clinical data in a cohort of 150 patients with anophthalmia/microphthalmia. (PMID: 24033328) Chassaing N … Calvas P (Clinical genetics 2014) 4 72
  4. Full-length transcriptome analysis of human retina-derived cell lines ARPE-19 and Y79 using the vector-capping method. (PMID: 21697133) Oshikawa M … Kato S (Investigative ophthalmology & visual science 2011) 3 4
  5. Mutational screening of CHX10, GDF6, OTX2, RAX and SOX2 genes in 50 unrelated microphthalmia-anophthalmia-coloboma (MAC) spectrum cases. (PMID: 20494911) Gonzalez-Rodriguez J … Zenteno JC (The British journal of ophthalmology 2010) 3 40

Products for RAX Gene

Sources for RAX Gene