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    CRX cone-rod homeobox [ Homo sapiens (human) ]

    Gene ID: 1406, updated on 9-Dec-2024

    Summary

    Official Symbol
    CRXprovided by HGNC
    Official Full Name
    cone-rod homeoboxprovided by HGNC
    Primary source
    HGNC:HGNC:2383
    See related
    Ensembl:ENSG00000105392 MIM:602225; AllianceGenome:HGNC:2383
    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
    CRD; LCA7; OTX3; CORD2
    Summary
    The protein encoded by this gene is a photoreceptor-specific transcription factor which plays a role in the differentiation of photoreceptor cells. This homeodomain protein is necessary for the maintenance of normal cone and rod function. Mutations in this gene are associated with photoreceptor degeneration, Leber congenital amaurosis type III and the autosomal dominant cone-rod dystrophy 2. Several alternatively spliced transcript variants of this gene have been described, but the full-length nature of some variants has not been determined. [provided by RefSeq, Jul 2008]
    Expression
    Low expression observed in reference dataset See more
    Orthologs
    NEW
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    Genomic context

    See CRX in Genome Data Viewer
    Location:
    19q13.33
    Exon count:
    4
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 19 NC_000019.10 (47821937..47843324)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 19 NC_060943.1 (50652778..50674184)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 19 NC_000019.9 (48325194..48346581)

    Chromosome 19 - NC_000019.10Genomic Context describing neighboring genes Neighboring gene ribosomal protein L23a pseudogene 80 Neighboring gene tetrapeptide repeat homeobox 1 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:48342812-48343337 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr19:48352354-48353156 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr19:48353157-48353960 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:48366933-48367434 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:48367435-48367934 Neighboring gene tetrapeptide repeat homeobox 2 Neighboring gene long intergenic non-protein coding RNA 1595

    Genomic regions, transcripts, and products

    Expression

    • 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

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?

    Pathways from PubChem

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables DNA-binding transcription activator activity ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    enables DNA-binding transcription activator activity, RNA polymerase II-specific IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables DNA-binding transcription factor activity ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    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 
    enables RNA polymerase II transcription regulatory region sequence-specific DNA binding ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    enables RNA polymerase II-specific DNA-binding transcription factor binding ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    enables leucine zipper domain binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    enables nuclear receptor binding ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    enables sequence-specific double-stranded DNA binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    Process Evidence Code Pubs
    involved_in animal organ morphogenesis TAS
    Traceable Author Statement
    more info
    PubMed 
    involved_in cell differentiation IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in nervous system development IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in positive regulation of transcription by RNA polymerase II IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in positive regulation of transcription by RNA polymerase II ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in regulation of DNA-templated transcription ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    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
    part_of RNA polymerase II transcription regulator complex ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    located_in chromatin ISA
    Inferred from Sequence Alignment
    more info
     
    located_in chromatin ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    is_active_in nucleus IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    located_in nucleus ISS
    Inferred from Sequence or Structural Similarity
    more info
     

    General protein information

    Preferred Names
    cone-rod homeobox protein
    Names
    orthodenticle homeobox 3

    NCBI Reference Sequences (RefSeq)

    NEW Try the new Transcript table

    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_008605.1 RefSeqGene

      Range
      5096..26483
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_000554.6NP_000545.1  cone-rod homeobox protein

      See identical proteins and their annotated locations for NP_000545.1

      Status: REVIEWED

      Source sequence(s)
      AC008745, BE782215, BG396702, BQ423938, BU736672
      Consensus CDS
      CCDS12706.1
      UniProtKB/Swiss-Prot
      O43186, Q0QD45
      Related
      ENSP00000221996.5, ENST00000221996.12
      Conserved Domains (2) summary
      pfam00046
      Location:4393
      Homeobox; Homeobox domain
      pfam03529
      Location:166249
      TF_Otx; Otx1 transcription factor

    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
      47821937..47843324
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060943.1 Alternate T2T-CHM13v2.0

      Range
      50652778..50674184
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)