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rax retina and anterior neural fold homeobox [ Xenopus tropicalis (tropical clawed frog) ]

Gene ID: 100038124, updated on 4-Nov-2024

Summary

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Official Symbol
raxprovided by Xenbase
Official Full Name
retina and anterior neural fold homeoboxprovided by Xenbase
Primary source
Xenbase:XB-GENE-492665
See related
Ensembl:ENSXETG00000021154 AllianceGenome:Xenbase:XB-GENE-492665
Gene type
protein coding
RefSeq status
MODEL
Organism
Xenopus tropicalis
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Amphibia; Batrachia; Anura; Pipoidea; Pipidae; Xenopodinae; Xenopus; Silurana
Also known as
rx; rx1; Rx2A; Xrax; Xrx1; rax1; rx-1; rx1a; Xrx1A; rax-a; rax-b
Summary
Predicted to enable DNA binding activity and DNA-binding transcription factor activity, RNA polymerase II-specific. Predicted to be involved in immune response. Predicted to act upstream of or within positive regulation of transcription by RNA polymerase II. Predicted to be located in nucleus. Predicted to be active in external side of plasma membrane and extracellular space. Is expressed in ectoderm; nervous system; and visual system. Human ortholog(s) of this gene implicated in isolated microphthalmia 3. Orthologous to human RAX (retina and anterior neural fold homeobox). [provided by Alliance of Genome Resources, Nov 2024]
Orthologs
human mouse all
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Genomic context

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See rax in Genome Data Viewer
Location:
chromosome: 1
Exon count:
3
Annotation release Status Assembly Chr Location
104 current UCB_Xtro_10.0 (GCF_000004195.4) 1 NC_030677.2 (201401908..201407707)
103 previous assembly Xenopus_tropicalis_v9.1 (GCF_000004195.3) 1 NC_030677.1 (188150087..188155380)

Chromosome 1 - NC_030677.2Genomic Context describing neighboring genes Neighboring gene lectin, mannose binding 1 Neighboring gene complexin 4 Neighboring gene gastrin releasing peptide Neighboring gene SEC11 homolog C, signal peptidase complex subunit

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Bibliography

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Related articles in PubMed

  1. Autoregulation of retinal homeobox (rax) gene promoter activity through a highly conserved genomic element. Kelly LE, et al. Genesis, 2016 Nov. PMID 27696680, Free PMC Article
  2. Identification of retinal homeobox (rax) gene-dependent genes by a microarray approach: The DNA endoglycosylase neil3 is a major downstream component of the rax genetic pathway. Pan Y, et al. Dev Dyn, 2018 Nov. PMID 30311321, Free PMC Article
  3. Xenopus mutant reveals necessity of rax for specifying the eye field which otherwise forms tissue with telencephalic and diencephalic character. Fish MB, et al. Dev Biol, 2014 Nov 15. PMID 25224223, Free PMC Article
  4. Molecular links among the causative genes for ocular malformation: Otx2 and Sox2 coregulate Rax expression. Danno H, et al. Proc Natl Acad Sci U S A, 2008 Apr 8. PMID 18385377, Free PMC Article
  5. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Gaudet P, et al. Brief Bioinform, 2011 Sep. PMID 21873635, Free PMC Article

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. identified neil3 as a component of the rax genetic pathway necessary for normal retinal progenitor cell development. neil3 is involved in the base excision DNA repair pathway, suggesting that this pathway is essential for normal rax-dependent progenitor cell development in the mature retina.
    Title: Identification of retinal homeobox (rax) gene-dependent genes by a microarray approach: The DNA endoglycosylase neil3 is a major downstream component of the rax genetic pathway.
  2. We found that three ultra-conserved genomic elements (UCEs) flanking the rax coding region regulate expression of a rax promoter-GFP transgene in Xenopus tadpoles.
    Title: Autoregulation of retinal homeobox (rax) gene promoter activity through a highly conserved genomic element.
  3. Rax is necessary for specifying the eye field which otherwise forms tissue with telencephalic and diencephalic character.
    Title: Xenopus mutant reveals necessity of rax for specifying the eye field which otherwise forms tissue with telencephalic and diencephalic character.
  4. direct interaction and interdependence between the Otx2 and Sox2 proteins coordinate Rax expression in eye development, providing molecular linkages among the genes responsible for ocular malformation.
    Title: Molecular links among the causative genes for ocular malformation: Otx2 and Sox2 coregulate Rax expression.
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General gene information

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Homology

Gene Ontology Provided by Xenbase

Function Evidence Code Pubs
enables DNA binding IEA
Inferred from Electronic Annotation
more info
  
enables DNA-binding transcription factor activity, RNA polymerase II-specific IEA
Inferred from Electronic Annotation
more info
  
Process Evidence Code Pubs
involved_in immune response IBA
Inferred from Biological aspect of Ancestor
more info
  
acts_upstream_of_or_within positive regulation of transcription by RNA polymerase II IEA
Inferred from Electronic Annotation
more info
  
Component Evidence Code Pubs
is_active_in external side of plasma membrane IBA
Inferred from Biological aspect of Ancestor
more info
  
is_active_in extracellular space IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in nucleus IEA
Inferred from Electronic Annotation
more info
  

General protein information

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Preferred Names
retinal homeobox protein Rx

NCBI Reference Sequences (RefSeq)

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RefSeqs of Annotated Genomes: Xenopus tropicalis Annotation Release 104 details...Open this link in a new tab

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference UCB_Xtro_10.0 Primary Assembly

Genomic

  1. NC_030677.2 Reference UCB_Xtro_10.0 Primary Assembly

    Range
    201401908..201407707
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_002936669.5 → XP_002936715.1  retinal homeobox protein Rx

    UniProtKB/TrEMBL
    F7CDS7
    Related
    ENSXETP00000045740.3, ENSXETT00000045740.4
    Conserved Domains (2) summary
    pfam00046
    Location:135 → 188
    Homeobox; Homeobox domain
    pfam03826
    Location:299 → 315
    OAR; OAR domain
Nucleotide Protein Strain
Heading Accession and Version

Gene LinkOut

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Molecular Biology Databases
Research Materials