RAX2 Gene (Protein Coding)

Retina And Anterior Neural Fold Homeobox 2

GC19M003769
GIFtS:
36
This gene encodes a homeodomain-containing protein that plays a role in eye development. Mutation of this gene causes age-related macular degeneration type 6, an eye disorder resulting in accumulations of protein and lipid beneath the retinal pigment epithelium and within the Bruch's membrane. Defects in this gene can also cause cone-rod dystrophy type 11, a disease characteriz... See more...

Aliases for RAX2 Gene

Aliases for RAX2 Gene

  • Retina And Anterior Neural Fold Homeobox 2 2 3 5
  • Retina And Anterior Neural Fold Homeobox-Like Protein 1 3 4
  • Retina And Anterior Neural Fold Homeobox Protein 2 3 4
  • Retina And Anterior Neural Fold Homeobox Like 1 2 3
  • Q50-Type Retinal Homeobox Protein 3 4
  • CORD11 2 3
  • ARMD6 2 3
  • RAXL1 3 4
  • QRX 3 4
  • MGC15631 2
  • RAX2 5

External Ids for RAX2 Gene

Previous HGNC Symbols for RAX2 Gene

  • RAXL1

Previous GeneCards Identifiers for RAX2 Gene

  • GC19M003449
  • GC19M003498
  • GC19M003499

Summaries for RAX2 Gene

Entrez Gene Summary for RAX2 Gene

  • This gene encodes a homeodomain-containing protein that plays a role in eye development. Mutation of this gene causes age-related macular degeneration type 6, an eye disorder resulting in accumulations of protein and lipid beneath the retinal pigment epithelium and within the Bruch's membrane. Defects in this gene can also cause cone-rod dystrophy type 11, a disease characterized by the initial degeneration of cone photoreceptor cells and resulting in loss of color vision and visual acuity, followed by the degeneration of rod photoreceptor cells, which progresses to night blindness and the loss of peripheral vision. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jan 2016]

GeneCards Summary for RAX2 Gene

RAX2 (Retina And Anterior Neural Fold Homeobox 2) is a Protein Coding gene. Diseases associated with RAX2 include Cone-Rod Dystrophy 11 and Macular Degeneration, Age-Related, 6. Gene Ontology (GO) annotations related to this gene include sequence-specific DNA binding. An important paralog of this gene is RAX.

UniProtKB/Swiss-Prot Summary for RAX2 Gene

  • May be involved in modulating the expression of photoreceptor specific genes. Binds to the Ret-1 and Bat-1 element within the rhodopsin promoter.

Additional gene information for RAX2 Gene

No data available for CIViC Summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for RAX2 Gene

Genomics for RAX2 Gene

GeneHancer (GH) Regulatory Elements Pubs

Download GeneHancer 2017 data
Promoters and enhancers for RAX2 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
GH19J003771 Enhancer 0.7 Ensembl ENCODE 250.7 +0.9 927 0.6 ZNF623 GLI4 ZFP36 ZMYM3 ZFP3 EGR2 KDM1A BCOR ZFHX2 HIC1 RAX2 MRPL54 HSALNG0123304
GH19J003772 Promoter 0.6 EPDnew 250.7 0.0 -20 0.1 VEZF1 MEIS2 EGR2 PKNOX1 ZFHX2 EGR1 RAX2 ENSG00000267148 MATK
GH19J003725 Enhancer 1 Ensembl ENCODE dbSUPER 12 +46.2 46214 1.5 ZIC2 SIN3A ZNF341 SP2 MAZ PKNOX1 GLIS1 ZNF398 ZMYM3 EGR1 MRPL54 APBA3 RAX2 ZFR2 lnc-PIP5K1C-1 TJP3 piR-57460-327
GH19J003727 Enhancer 0.9 Ensembl ENCODE 12 +43.7 43715 1.9 MNT BHLHE40 ZNF639 KLF9 FOSL1 JUND ZBTB33 EGR1 L3MBTL2 SP7 MRPL54 APBA3 RAX2 ZFR2 lnc-PIP5K1C-1 piR-57460-327 TJP3
GH19J003828 Enhancer 0.9 Ensembl ENCODE 11.9 -56.4 -56373 2 CEBPB EP300 FOSL1 TCF7L2 ATF1 NRF1 ZBTB33 EGR1 IKZF1 L3MBTL2 ZFR2 ATCAY RAX2 MRPL54 APBA3 RF00017-2747 MATK RF00017-2748
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around RAX2 on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for RAX2

Top Transcription factor binding sites by QIAGEN in the RAX2 gene promoter:
  • AML1a
  • AREB6
  • ATF6
  • CREB
  • deltaCREB
  • GR
  • GR-alpha
  • p300
  • PPAR-gamma1
  • PPAR-gamma2

Genomic Locations for RAX2 Gene

Latest Assembly
chr19:3,769,089-3,772,228
(GRCh38/hg38)
Size:
3,140 bases
Orientation:
Minus strand

Previous Assembly
chr19:3,769,087-3,772,226
(GRCh37/hg19 by Entrez Gene)
Size:
3,140 bases
Orientation:
Minus strand

chr19:3,769,087-3,772,233
(GRCh37/hg19 by Ensembl)
Size:
3,147 bases
Orientation:
Minus strand

Genomic View for RAX2 Gene

Genes around RAX2 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
RAX2 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for RAX2 Gene
GeneLoc Logo Genomic Neighborhood • Exon Structure • Gene Density

RefSeq DNA sequence for RAX2 Gene

Proteins for RAX2 Gene

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  2. Protein products for research
  3. Assay products for research

  • Protein details for RAX2 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q96IS3-RAX2_HUMAN
    Recommended name:
    Retina and anterior neural fold homeobox protein 2
    Protein Accession:
    Q96IS3

    Protein attributes for RAX2 Gene

    Size:
    184 amino acids
    Molecular mass:
    20086 Da
    Quaternary structure:
    • Interacts with CRX.

neXtProt entry for RAX2 Gene

Protein Expression for RAX2 Gene

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

Post-translational modifications for RAX2 Gene

No Post-translational modifications

Other Protein References for RAX2 Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for RAX2 Gene

Domains & Families for RAX2 Gene

Gene Families for RAX2 Gene

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

Protein Domains for RAX2 Gene

InterPro:
ProtoNet:

Suggested Antigen Peptide Sequences for RAX2 Gene

GenScript: Design optimal peptide antigens:
  • Retina and anterior neural fold homeobox-like protein 1 (RAX2_HUMAN)

Graphical View of Domain Structure for InterPro Entry

Q96IS3

UniProtKB/Swiss-Prot:

RAX2_HUMAN :
  • The Homeobox transactivates the Ret-1 element in the presence of CRX and NRL.
Domain:
  • The Homeobox transactivates the Ret-1 element in the presence of CRX and NRL.
genes like me logo Genes that share domains with RAX2: view

Function for RAX2 Gene

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  1. Animal Models for research
  2. CRISPR products for research
  3. miRNA products for research
  4. Inhibitory RNAs for research
  5. Clone products for research
  6. Cell Lines for research

Molecular function for RAX2 Gene

UniProtKB/Swiss-Prot Function:
May be involved in modulating the expression of photoreceptor specific genes. Binds to the Ret-1 and Bat-1 element within the rhodopsin promoter.

Phenotypes From GWAS Catalog for RAX2 Gene

Gene Ontology (GO) - Molecular Function for RAX2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000978 RNA polymerase II proximal promoter sequence-specific DNA binding IDA 15028672
GO:0000981 DNA-binding transcription factor activity, RNA polymerase II-specific ISA --
GO:0001228 DNA-binding transcription activator activity, RNA polymerase II-specific IDA 15028672
GO:0003677 DNA binding IEA --
genes like me logo Genes that share ontologies with RAX2: view
genes like me logo Genes that share phenotypes with RAX2: view

Human Phenotype Ontology for RAX2 Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Models for research

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for RAX2

No data available for Enzyme Numbers (IUBMB) , Animal Models , miRNA , Transcription Factor Targets and HOMER Transcription for RAX2 Gene

Localization for RAX2 Gene

Subcellular locations from UniProtKB/Swiss-Prot for RAX2 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 RAX2 gene
Compartment Confidence
nucleus 4
extracellular 1
cytoskeleton 1
mitochondrion 1
golgi apparatus 1

Gene Ontology (GO) - Cellular Components for RAX2 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 RAX2: view

No data available for Subcellular locations from the Human Protein Atlas (HPA) for RAX2 Gene

Pathways & Interactions for RAX2 Gene

PathCards logo

SuperPathways for RAX2 Gene

No Data Available

Gene Ontology (GO) - Biological Process for RAX2 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:0007601 visual perception IEA --
GO:0045944 positive regulation of transcription by RNA polymerase II IDA 15028672
GO:0050896 response to stimulus IEA --
genes like me logo Genes that share ontologies with RAX2: view

No data available for Pathways by source and SIGNOR curated interactions for RAX2 Gene

Drugs & Compounds for RAX2 Gene

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  1. Drug products for research
No Compound Related Data Available

Transcripts for RAX2 Gene

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mRNA/cDNA for RAX2 Gene

2 REFSEQ mRNAs :
4 NCBI additional mRNA sequence :
2 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 RAX2

Alternative Splicing Database (ASD) splice patterns (SP) for RAX2 Gene

No ASD Table

Relevant External Links for RAX2 Gene

GeneLoc Exon Structure for
RAX2

Expression for RAX2 Gene

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

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for RAX2 Gene

mRNA expression in normal human tissues for RAX2 Gene
mRNA expression by BioGPS for RAX2 GenemRNA expression by GTEx for RAX2 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

  • Eye (Sensory Organs)

mRNA differential expression in normal tissues according to GTEx for RAX2 Gene

This gene is overexpressed in Pituitary (x19.3), Uterus (x10.0), and Fallopian Tube (x5.2).

Protein differential expression in normal tissues from HIPED for RAX2 Gene

This gene is overexpressed in Retina (69.0).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB and MOPED for RAX2 Gene



Protein tissue co-expression partners for RAX2 Gene

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for RAX2

SOURCE GeneReport for Unigene cluster for RAX2 Gene:

Hs.532691

Evidence on tissue expression from TISSUES for RAX2 Gene

  • Eye(4.6)

Phenotype-based relationships between genes and organs from Gene ORGANizer for RAX2 Gene

Germ Layers:
  • ectoderm
  • endoderm
  • mesoderm
Systems:
  • cardiovascular
  • endocrine
  • immune
  • integumentary
  • nervous
  • reproductive
  • skeletal muscle
  • skeleton
Regions:
Head and neck:
  • brain
  • cerebellum
  • cranial nerve
  • ear
  • eye
  • head
  • lacrimal apparatus
  • pituitary gland
Thorax:
  • breast
Pelvis:
  • ovary
  • penis
  • prostate
  • testicle
  • uterus
  • vagina
  • vulva
Limb:
  • arm
  • digit
  • foot
  • forearm
  • hand
  • lower limb
  • shin
  • thigh
  • toe
  • upper limb
General:
  • blood
  • blood vessel
  • hair
  • peripheral nerve
  • peripheral nervous system
  • skin
  • spinal cord
genes like me logo Genes that share expression patterns with RAX2: view

Primer products for research

No data available for mRNA Expression by UniProt/SwissProt for RAX2 Gene

Orthologs for RAX2 Gene

This gene was present in the common ancestor of animals.

Orthologs for RAX2 Gene

Organism Taxonomy Gene Similarity Type Details
Chimpanzee
(Pan troglodytes)
 Mammalia RAX2 30 31
  • 99.46 (n)
 OneToOne
Dog
(Canis familiaris)
 Mammalia RAX2 30 31
  • 88.22 (n)
 OneToOne
Cow
(Bos Taurus)
 Mammalia RAX2 30 31
  • 87.58 (n)
 OneToOne
Oppossum
(Monodelphis domestica)
 Mammalia RAX2 31
  • 60 (a)
 OneToOne
Platypus
(Ornithorhynchus anatinus)
 Mammalia -- 31
  • 28 (a)
 OneToMany
Chicken
(Gallus gallus)
 Aves RAX1 31
  • 29 (a)
 OneToMany
Lizard
(Anolis carolinensis)
 Reptilia -- 31
  • 29 (a)
 OneToMany
Zebrafish
(Danio rerio)
 Actinopterygii rx3 31
  • 33 (a)
 OneToMany
Fruit Fly
(Drosophila melanogaster)
 Insecta hbn 31
  • 15 (a)
 ManyToMany
Worm
(Caenorhabditis elegans)
 Secernentea ceh-8 31
  • 23 (a)
 OneToMany
Sea Squirt
(Ciona savignyi)
 Ascidiacea -- 31
  • 17 (a)
 OneToMany
Species where no ortholog for RAX2 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)
  • Mouse (Mus musculus)
  • Orangutan (Pongo pygmaeus)
  • Pig (Sus scrofa)
  • Rainbow Trout (Oncorhynchus mykiss)
  • Rat (Rattus norvegicus)
  • Rice (Oryza sativa)
  • 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)
  • Thale Cress (Arabidopsis thaliana)
  • Tomato (Lycopersicon esculentum)
  • Toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • Tropical Clawed Frog (Silurana tropicalis)
  • Wheat (Triticum aestivum)

Evolution for RAX2 Gene

ENSEMBL:
Gene Tree for RAX2 (if available)
TreeFam:
Gene Tree for RAX2 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for RAX2: view image

Paralogs for RAX2 Gene

Paralogs for RAX2 Gene

(27) SIMAP similar genes for RAX2 Gene using alignment to 1 proteins:

  • RAX2_HUMAN
genes like me logo Genes that share paralogs with RAX2: view

Variants for RAX2 Gene

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Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for RAX2 Gene

SNP ID Clinical significance and condition Chr 19 pos Variation AA Info Type
834258 Uncertain Significance: Age-related macular degeneration 6; not provided 3,770,940(-) C/T
NM_001319074.4(RAX2):c.236G>A (p.Arg79Gln) 		MISSENSE
834260 Conflicting Interpretations: Retinal dystrophy; not provided 3,771,588(-) G/C
NM_001319074.4(RAX2):c.155C>G (p.Pro52Arg) 		MISSENSE
836937 Uncertain Significance: not provided 3,771,534(-) C/T
NM_001319074.4(RAX2):c.209G>A (p.Arg70His) 		MISSENSE
853992 Uncertain Significance: not provided 3,770,632(-) G/A
NM_001319074.4(RAX2):c.544C>T (p.Pro182Ser) 		MISSENSE
856647 Uncertain Significance: not provided 3,770,926(-) G/A
NM_001319074.4(RAX2):c.250C>T (p.Arg84Cys) 		MISSENSE

dbSNP identifiers (rs#s) for variants without ClinVar clinical significance for RAX2 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 RAX2 Gene

Variant ID Type Subtype PubMed ID
nsv470114 CNV loss 18288195
nsv509718 CNV insertion 20534489

Variation tolerance for RAX2 Gene

Gene Damage Index Score: 1.63; 31.23% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for RAX2 Gene

Human Gene Mutation Database (HGMD)
RAX2
SNPedia medical, phenotypic, and genealogical associations of SNPs for
RAX2

SNP Genotyping and Copy Number Assays for research

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for RAX2 Gene

Disorders for RAX2 Gene

MalaCards: The human disease database

(11) MalaCards diseases for RAX2 Gene - From: OMI, CVR, GTR, ORP, SWI, COP, and GCD

- elite association - COSMIC cancer census association via MalaCards
Search RAX2 in MalaCards View complete list of genes associated with diseases

UniProtKB/Swiss-Prot

RAX2_HUMAN
  • Macular degeneration, age-related, 6 (ARMD6) [MIM:613757]: A form of age-related macular degeneration, a multifactorial eye disease and the most common cause of irreversible vision loss in the developed world. In most patients, the disease is manifest as ophthalmoscopically visible yellowish accumulations of protein and lipid that lie beneath the retinal pigment epithelium and within an elastin-containing structure known as Bruch membrane. {ECO:0000269 PubMed:15028672}. Note=Disease susceptibility is associated with variants affecting the gene represented in this entry.
  • Cone-rod dystrophy 11 (CORD11) [MIM:610381]: An inherited retinal dystrophy characterized by retinal pigment deposits visible on fundus examination, predominantly in the macular region, and initial loss of cone photoreceptors followed by rod degeneration. This leads to decreased visual acuity and sensitivity in the central visual field, followed by loss of peripheral vision. Severe loss of vision occurs earlier than in retinitis pigmentosa, due to cone photoreceptors degenerating at a higher rate than rod photoreceptors. {ECO:0000269 PubMed:15028672}. Note=The disease is caused by variants affecting the gene represented in this entry.

Additional Disease Information for RAX2

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 RAX2: view

No data available for Genatlas for RAX2 Gene

Publications for RAX2 Gene

  1. QRX, a novel homeobox gene, modulates photoreceptor gene expression. (PMID: 15028672) Wang QL … Zack DJ (Human molecular genetics 2004) 3 4 74
  2. Autosomal Dominant Retinal Dystrophy With Electronegative Waveform Associated With a Novel RAX2 Mutation. (PMID: 25789692) Yang P … Pennesi ME (JAMA ophthalmology 2015) 3
  3. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. (PMID: 21873635) Gaudet P … Thomas PD (Briefings in bioinformatics 2011) 3
  4. New genetic associations detected in a host response study to hepatitis B vaccine. (PMID: 20237496) Davila S … Seielstad M (Genes and immunity 2010) 3
  5. A census of human transcription factors: function, expression and evolution. (PMID: 19274049) Vaquerizas JM … Luscombe NM (Nature reviews. Genetics 2009) 3

ExternalLinks

View latest publications for RAX2 gene in Mastermind

Products for RAX2 Gene

Sources for RAX2 Gene