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Aliases for RAX Gene

Aliases for RAX Gene

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

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 Rax-Related Anophthalmia/Microphthalmia. GO annotations related to this gene include RNA polymerase II core promoter proximal region sequence-specific DNA binding and transcriptional activator activity, RNA polymerase II core promoter proximal region sequence-specific binding. An important paralog of this gene is ARX.

UniProtKB/Swiss-Prot 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 , fRNAdb sequence ontologies and piRNA Summary for RAX Gene

Genomics for RAX Gene

Regulatory Elements for RAX Gene

Enhancers for RAX Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH18G059308 1.1 Ensembl ENCODE 11.9 -34.5 -34508 0.8 RB1 KLF17 ZNF2 ZNF48 RAD21 GLIS2 SCRT2 KLF7 REST ZNF843 RAX CPLX4
GH18G059273 0.6 ENCODE 0.7 +0.5 543 0.2 ZNF263 CTCF SP3 SUZ12 RBBP5 EZH2 GC18M059272 RAX
GH18G059276 0.6 ENCODE 0.7 +0.9 913 0.1 ZNF263 RING1 SP3 RNF2 SUZ12 MAX CBX2 RBBP5 KDM1A EZH2 GC18M059272 RAX
GH18G059274 0.5 ENCODE 0.7 -0.2 -228 0.1 RNF2 SUZ12 CBX2 EZH2 RAX CPLX4
GH18G059275 0.5 ENCODE 0.7 +0.1 103 0.2 RNF2 SUZ12 CBX2 EZH2 GC18M059272 RAX
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around RAX on UCSC Golden Path with GeneCards custom track

Genomic Location for RAX Gene

Chromosome:
18
Start:
59,267,035 bp from pter
End:
59,274,086 bp from pter
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

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for RAX Gene

Domains & Families for RAX Gene

Gene Families for RAX Gene

Suggested Antigen Peptide Sequences for RAX Gene

GenScript: Design optimal peptide antigens:

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.

Gene Ontology (GO) - Molecular Function for RAX Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000978 RNA polymerase II core promoter proximal region sequence-specific DNA binding IDA 10625658
GO:0001077 transcriptional activator activity, RNA polymerase II core promoter proximal region sequence-specific binding IDA 10625658
GO:0003677 DNA binding IEA --
GO:0003700 transcription factor activity, sequence-specific DNA binding IEA --
GO:0043565 sequence-specific DNA binding IEA --
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:

Animal Model Products

CRISPR Products

Inhibitory RNA Products

Clone Products

  • Applied Biological Materials Clones 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

Gene Ontology (GO) - Cellular Components for RAX Gene

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

Pathways & Interactions for RAX Gene

No Data Available

Gene Ontology (GO) - Biological Process for RAX Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006351 transcription, DNA-templated IEA --
GO:0006355 regulation of transcription, DNA-templated IEA --
GO:0006366 transcription from RNA polymerase II promoter IEA --
GO:0007275 multicellular organism development IEA --
GO:0007389 pattern specification process 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

Unigene Clusters for RAX Gene

Retina and anterior neural fold homeobox:
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

Clone Products

  • Applied Biological Materials Clones 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
ECgene alternative splicing isoforms for
RAX

Expression for RAX Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP 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, PaxDb, and MOPED for RAX Gene



Protein tissue co-expression partners for RAX Gene

NURSA nuclear receptor signaling pathways regulating expression of RAX Gene:

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(4.4)

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

Germ Layers:
  • ectoderm
  • mesoderm
Systems:
  • integumentary
  • nervous
  • reproductive
  • skeletal muscle
Organs:
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

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 34 35
  • 99.23 (n)
cow
(Bos Taurus)
Mammalia RAX 34 35
  • 87.67 (n)
mouse
(Mus musculus)
Mammalia Rax 34 16 35
  • 84.8 (n)
rat
(Rattus norvegicus)
Mammalia Rax 34
  • 84.16 (n)
dog
(Canis familiaris)
Mammalia RAX 34 35
  • 81.87 (n)
oppossum
(Monodelphis domestica)
Mammalia -- 35
  • 69 (a)
ManyToMany
-- 35
  • 16 (a)
ManyToMany
platypus
(Ornithorhynchus anatinus)
Mammalia -- 35
  • 58 (a)
ManyToMany
chicken
(Gallus gallus)
Aves RAX 34
  • 75.87 (n)
RX1 35
  • 61 (a)
ManyToMany
lizard
(Anolis carolinensis)
Reptilia -- 35
  • 62 (a)
OneToMany
tropical clawed frog
(Silurana tropicalis)
Amphibia rax 34
  • 61.11 (n)
zebrafish
(Danio rerio)
Actinopterygii rx3 34
  • 59.25 (n)
rx2 35
  • 49 (a)
ManyToMany
fruit fly
(Drosophila melanogaster)
Insecta Rx 36
  • 96 (a)
worm
(Caenorhabditis elegans)
Secernentea ceh-8 35
  • 30 (a)
OneToMany
sea squirt
(Ciona savignyi)
Ascidiacea -- 35
  • 23 (a)
OneToMany
sea squirt
(Ciona intestinalis)
Ascidiacea Cin.14217 34
Species where no ortholog for RAX was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya 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)

Paralogs for RAX Gene

Paralogs for RAX Gene

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

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

Variants for RAX Gene

Sequence variations from dbSNP and Humsavar for RAX Gene

SNP ID Clin Chr 18 pos Sequence Context AA Info Type
rs121909127 Pathogenic, Microphthalmia, isolated, 3 (MCOP3) [MIM:611038] 59,269,470(-) GTGGC(A/G)GCGGC reference, missense
VAR_075630 Microphthalmia, isolated, 3 (MCOP3) [MIM:611038]
VAR_075631 Microphthalmia, isolated, 3 (MCOP3) [MIM:611038]
VAR_075632 Microphthalmia, isolated, 3 (MCOP3) [MIM:611038]
rs104894663 Pathogenic 59,272,465(-) CGTAC(C/T)AGCTG reference, stop-gained

Variation tolerance for RAX Gene

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

Relevant External Links for RAX Gene

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

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

(6) MalaCards diseases for RAX Gene - From: OMIM, ClinVar, GeneTests, Swiss-Prot, DISEASES, and GeneCards

Disorder Aliases PubMed IDs
microphthalmia, isolated 3
  • isolated microphthalmia 3
rax-related anophthalmia/microphthalmia
isolated microphthalmia
  • microphthalmia, isolated 6
microphthalmia
  • microphthalmos
sclerocornea
  • isolated congenital sclerocornea
- 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 mutations affecting the gene represented in this entry.

Relevant External Links for RAX

Genetic Association Database (GAD)
RAX
Human Genome Epidemiology (HuGE) Navigator
RAX
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
RAX
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 V.A. … Mathers P.H. (Hum. Mol. Genet. 2004) 2 3 4 22 64
  2. Both PCE-1/RX and OTX/CRX interactions are necessary for photoreceptor-specific gene expression. (PMID: 10625658) Kimura A. … Shinohara T. (J. Biol. Chem. 2000) 2 3 4 64
  3. 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. (Invest. Ophthalmol. Vis. Sci. 2011) 3 4 64
  4. 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 J.C. (Br J Ophthalmol 2010) 3 46 64
  5. Mutational screening of 10 genes in Chinese patients with microphthalmia and/or coloboma. (PMID: 20057906) Zhang X. … Zhang Q. (Mol. Vis. 2009) 3 46 64

Products for RAX Gene

Sources for RAX Gene

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