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    RAX2 retina and anterior neural fold homeobox 2 [ Homo sapiens (human) ]

    Gene ID: 84839, updated on 27-Nov-2024

    Summary

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    Official Symbol
    RAX2provided by HGNC
    Official Full Name
    retina and anterior neural fold homeobox 2provided by HGNC
    Primary source
    HGNC:HGNC:18286
    See related
    Ensembl:ENSG00000173976 MIM:610362; AllianceGenome:HGNC:18286
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    QRX; RP95; ARMD6; RAXL1; CORD11
    Summary
    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]
    Expression
    Low expression observed in reference dataset See more
    Orthologs
    all
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    Genomic context

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    See RAX2 in Genome Data Viewer
    Location:
    19p13.3
    Exon count:
    3
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 19 NC_000019.10 (3769089..3772228, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 19 NC_060943.1 (3748340..3751481, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 19 NC_000019.9 (3769087..3772226, complement)

    Chromosome 19 - NC_000019.10Genomic Context describing neighboring genes Neighboring gene ReSE screen-validated silencer GRCh37_chr19:3761575-3761892 Neighboring gene uncharacterized LOC105372248 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13744 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:3770519-3771018 Neighboring gene mitochondrial ribosomal protein L54 Neighboring gene MPRA-validated peak3254 silencer Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:3784812-3785807 Neighboring gene ReSE screen-validated silencer GRCh37_chr19:3787338-3787536 Neighboring gene MPRA-validated peak3255 silencer Neighboring gene megakaryocyte-associated tyrosine kinase Neighboring gene ReSE screen-validated silencer GRCh37_chr19:3809153-3809388 Neighboring gene zinc finger RNA binding protein 2 Neighboring gene Sharpr-MPRA regulatory region 15218 Neighboring gene MPRA-validated peak3257 silencer Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13745 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:3831251-3831840 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:3843229-3843728 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:3849523-3850024

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: HPA RNA-seq normal tissues
    • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
    • BioProject: PRJEB4337
    • Publication: PMID 24309898
    • Analysis date: Wed Apr 4 07:08:55 2018

    Bibliography

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    Related articles in PubMed

    1. Autosomal Dominant Retinal Dystrophy With Electronegative Waveform Associated With a Novel RAX2 Mutation. Yang P, et al. JAMA Ophthalmol, 2015 Jun. PMID 25789692, Free PMC Article
    2. QRX, a novel homeobox gene, modulates photoreceptor gene expression. Wang QL, et al. Hum Mol Genet, 2004 May 15. PMID 15028672
    3. New genetic associations detected in a host response study to hepatitis B vaccine. Davila S, et al. Genes Immun, 2010 Apr. PMID 20237496
    4. A census of human transcription factors: function, expression and evolution. Vaquerizas JM, et al. Nat Rev Genet, 2009 Apr. PMID 19274049
    5. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. Strausberg RL, et al. Proc Natl Acad Sci U S A, 2002 Dec 24. PMID 12477932, Free PMC Article

    See all (6) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. A frameshift heterozygous mutation in RAX2 inherited in an autosomal dominant fashion was associated with mixed cone and rod dysfunction.
      Title: Autosomal Dominant Retinal Dystrophy With Electronegative Waveform Associated With a Novel RAX2 Mutation.
    2. Observational study of gene-disease association. (HuGE Navigator)
      Title: New genetic associations detected in a host response study to hepatitis B vaccine.
    Submit: New GeneRIF Correction

    Phenotypes

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    Find tests for this gene in the NIH Genetic Testing Registry (GTR)

    Review eQTL and phenotype association data in this region using PheGenI

    Associated conditions

    Description Tests
    Age related macular degeneration 6
    MedGen: C3151060 OMIM: 613757 GeneReviews: Not available
    		Compare labs
    Cone-rod dystrophy 11
    MedGen: C1835865 OMIM: 610381 GeneReviews: Not available
    		Compare labs
    Retinitis pigmentosa 95
    MedGen: C5774244 OMIM: 620102 GeneReviews: Not available
    		not available

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Homology

    Clone Names

    • MGC15631

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables DNA-binding transcription activator activity, RNA polymerase II-specific IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables DNA-binding transcription factor activity, RNA polymerase II-specific IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables DNA-binding transcription factor activity, RNA polymerase II-specific ISA
    Inferred from Sequence Alignment
    more info
    		  
    enables RNA polymerase II cis-regulatory region sequence-specific DNA binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables RNA polymerase II cis-regulatory region sequence-specific DNA binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in positive regulation of transcription by RNA polymerase II IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in regulation of transcription by RNA polymerase II IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in visual perception IEA
    Inferred from Electronic Annotation
    more info
    		  
    Component Evidence Code Pubs
    located_in chromatin ISA
    Inferred from Sequence Alignment
    more info
    		  
    located_in nucleus IEA
    Inferred from Electronic Annotation
    more info
    		  

    General protein information

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    Preferred Names
    retina and anterior neural fold homeobox protein 2
    Names
    Q50-type retinal homeobox protein
    retina and anterior neural fold homeobox like 1
    retina and anterior neural fold homeobox-like protein 1

    NCBI Reference Sequences (RefSeq)

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    RefSeqs maintained independently of Annotated Genomes

    These reference sequences exist independently of genome builds. Explain

    These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

    Genomic

    1. NG_011565.1 RefSeqGene

      Range
      4994..8133
      Download
      GenBank, FASTA, Sequence Viewer (Graphics), LRG_1200

    mRNA and Protein(s)

    1. NM_001319074.4 → NP_001306003.2  retina and anterior neural fold homeobox protein 2

      Status: REVIEWED

      Source sequence(s)
      AC005777
      Consensus CDS
      CCDS12112.1
      UniProtKB/Swiss-Prot
      Q96IS3
      Related
      ENSP00000450456.3, ENST00000555633.3
      Conserved Domains (1) summary
      pfam00046
      Location:31 → 84
      Homeobox; Homeobox domain

    2. NM_032753.4 → NP_116142.1  retina and anterior neural fold homeobox protein 2

      See identical proteins and their annotated locations for NP_116142.1

      Status: REVIEWED

      Source sequence(s)
      AC005777, AY211277, BC018709
      Consensus CDS
      CCDS12112.1
      UniProtKB/Swiss-Prot
      Q96IS3
      Related
      ENSP00000450687.2, ENST00000555978.5
      Conserved Domains (1) summary
      pfam00046
      Location:31 → 84
      Homeobox; Homeobox domain

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

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

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000019.10 Reference GRCh38.p14 Primary Assembly

      Range
      3769089..3772228 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060943.1 Alternate T2T-CHM13v2.0

      Range
      3748340..3751481 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q96IS3.1 GenPept UniProtKB/Swiss-Prot:Q96IS3

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

    Chemical Information
    Molecular Biology Databases
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