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Aliases for CRX Gene

Aliases for CRX Gene

  • Cone-Rod Homeobox 2 3 5
  • Orthodenticle Homeobox 3 2 3
  • CORD2 3 4
  • Cone-Rod Homeobox Protein 3
  • LCA7 3
  • OTX3 3
  • CRD 3

External Ids for CRX Gene

Previous HGNC Symbols for CRX Gene

  • CORD2

Previous GeneCards Identifiers for CRX Gene

  • GC19P048971
  • GC19P048716
  • GC19P053001
  • GC19P053016
  • GC19P048325
  • GC19P044751
  • GC19P048327
  • GC19P048337
  • GC19P048347
  • GC19P048359

Summaries for CRX Gene

Entrez Gene Summary for CRX Gene

  • 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]

GeneCards Summary for CRX Gene

CRX (Cone-Rod Homeobox) is a Protein Coding gene. Diseases associated with CRX include Cone-Rod Dystrophy and Leber Congenital Amaurosis 7. GO annotations related to this gene include transcription factor activity, sequence-specific DNA binding and RNA polymerase II core promoter proximal region sequence-specific DNA binding. An important paralog of this gene is OTX2.

UniProtKB/Swiss-Prot for CRX Gene

  • Transcription factor that binds and transactivates the sequence 5-TAATC[CA]-3 which is found upstream of several photoreceptor-specific genes, including the opsin genes. Acts synergistically with other transcription factors, such as NRL, RORB and RAX, to regulate photoreceptor cell-specific gene transcription. Essential for the maintenance of mammalian photoreceptors.

Gene Wiki entry for CRX Gene

No data available for Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for CRX Gene

Genomics for CRX Gene

Regulatory Elements for CRX Gene

Enhancers for CRX 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
GH19F047789 1.2 FANTOM5 Ensembl ENCODE 22.9 -29.3 -29254 1.1 CTCF KLF1 RAD21 ZNF664 ZNF121 ZFHX2 ZNF366 PATZ1 ZNF143 SMC3 CABP5 CRX GLTSCR2 ENSG00000271150 GC19P047784
GH19F047798 0.6 FANTOM5 17.5 -21.6 -21627 0.2 CABP5 CRX SNORD23 GLTSCR2 SULT2A1 RPL23AP80 TPRX1
GH19F047799 0.8 FANTOM5 15.1 -20.7 -20689 0.2 ZNF366 YBX1 ZBTB17 CRX SNORD23 GLTSCR2 SULT2A1 CABP5 RPL23AP80 TPRX1
GH19F048061 0.3 FANTOM5 7.3 +241.5 241450 0.4 MLLT1 CABP5 KCNJ14 CRX PLA2G4C-AS1
- Elite enhancer/Elite enhancer-gene association Download Table
Download GeneHancer data dump

Enhancers around CRX on UCSC Golden Path with GeneCards custom track

Genomic Location for CRX Gene

Chromosome:
19
Start:
47,819,779 bp from pter
End:
47,843,330 bp from pter
Size:
23,552 bases
Orientation:
Plus strand

Genomic View for CRX Gene

Genes around CRX on UCSC Golden Path with GeneCards custom track

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

RefSeq DNA sequence for CRX Gene

Proteins for CRX Gene

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

    Protein Symbol:
    O43186-CRX_HUMAN
    Recommended name:
    Cone-rod homeobox protein
    Protein Accession:
    O43186
    Secondary Accessions:
    • Q0QD45

    Protein attributes for CRX Gene

    Size:
    299 amino acids
    Molecular mass:
    32261 Da
    Quaternary structure:
    • Interacts (via the homeobox) with NRL (via the leucine-zipper domain). Interacts with PDC, RAX2, RORB and SCA7.

neXtProt entry for CRX Gene

Post-translational modifications for CRX Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for CRX Gene

No data available for DME Specific Peptides for CRX Gene

Domains & Families for CRX Gene

Gene Families for CRX Gene

Protein Domains for CRX Gene

Suggested Antigen Peptide Sequences for CRX Gene

Graphical View of Domain Structure for InterPro Entry

O43186

UniProtKB/Swiss-Prot:

CRX_HUMAN :
  • Contains 1 homeobox DNA-binding domain.
  • Belongs to the paired homeobox family.
Domain:
  • Contains 1 homeobox DNA-binding domain.
Family:
  • Belongs to the paired homeobox family.
genes like me logo Genes that share domains with CRX: view

Function for CRX Gene

Molecular function for CRX Gene

GENATLAS Biochemistry:
phosphoreceptor (cone,rod) specific paired-like homeo domain protein,expressed in developing and mature phosphoreceptor cells,binding and transactivating rhodopsin,homolog to Drosophila orthodenticle (Otx)
UniProtKB/Swiss-Prot Function:
Transcription factor that binds and transactivates the sequence 5-TAATC[CA]-3 which is found upstream of several photoreceptor-specific genes, including the opsin genes. Acts synergistically with other transcription factors, such as NRL, RORB and RAX, to regulate photoreceptor cell-specific gene transcription. Essential for the maintenance of mammalian photoreceptors.

Gene Ontology (GO) - Molecular Function for CRX 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,ISS --
GO:0005515 protein binding IPI 16189514
genes like me logo Genes that share ontologies with CRX: view
genes like me logo Genes that share phenotypes with CRX: view

Human Phenotype Ontology for CRX Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Models for CRX Gene

MGI Knock Outs for CRX:

Animal Model Products

Targeted motifs for CRX Gene
HOMER Transcription Factor Regulatory Elements motif CRX
  • Consensus sequence: GCTAATCC Submotif: canonical Cell Type: Retina GEO ID: GSE20012

Inhibitory RNA Products

Clone Products

Flow Cytometry Products

No data available for Enzyme Numbers (IUBMB) and Transcription Factor Targets for CRX Gene

Localization for CRX Gene

Subcellular locations from UniProtKB/Swiss-Prot for CRX Gene

Nucleus.

Subcellular locations from

COMPARTMENTS
Jensen Localization Image for CRX Gene COMPARTMENTS Subcellular localization image for CRX gene
Compartment Confidence
nucleus 5
cytoskeleton 2

Gene Ontology (GO) - Cellular Components for CRX Gene

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

Pathways & Interactions for CRX Gene

SuperPathways for CRX Gene

No Data Available

Gene Ontology (GO) - Biological Process for CRX Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006351 transcription, DNA-templated IEA --
GO:0006355 regulation of transcription, DNA-templated ISS --
GO:0006366 transcription from RNA polymerase II promoter IEA --
GO:0007275 multicellular organism development IEA --
GO:0007399 nervous system development IEA --
genes like me logo Genes that share ontologies with CRX: view

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

Drugs & Compounds for CRX Gene

(2) Drugs for CRX Gene - From: Novoseek

Name Status Disease Links Group Role Mechanism of Action Clinical Trials

(1) Additional Compounds for CRX Gene - From: Novoseek

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
genes like me logo Genes that share compounds with CRX: view

Transcripts for CRX Gene

mRNA/cDNA for CRX Gene

(1) REFSEQ mRNAs :
(1) Selected AceView cDNA sequences:
(7) Ensembl transcripts including schematic representations, and UCSC links where relevant :

Inhibitory RNA Products

Clone Products

Flow Cytometry Products

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

No ASD Table

Relevant External Links for CRX Gene

GeneLoc Exon Structure for
CRX
ECgene alternative splicing isoforms for
CRX

Expression for CRX Gene

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

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

This gene is overexpressed in Liver (x21.0), Testis (x12.1), and Brain - Hippocampus (x5.8).

Protein differential expression in normal tissues from HIPED for CRX 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 CRX Gene



Protein tissue co-expression partners for CRX Gene

NURSA nuclear receptor signaling pathways regulating expression of CRX Gene:

CRX

SOURCE GeneReport for Unigene cluster for CRX Gene:

Hs.617342

mRNA Expression by UniProt/SwissProt for CRX Gene:

O43186-CRX_HUMAN
Tissue specificity: Retina.
genes like me logo Genes that share expression patterns with CRX: view

Primer Products

Orthologs for CRX Gene

This gene was present in the common ancestor of animals.

Orthologs for CRX Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia CRX 34
  • 99.11 (n)
cow
(Bos Taurus)
Mammalia CRX 34 35
  • 89.97 (n)
dog
(Canis familiaris)
Mammalia CRX 34 35
  • 88.63 (n)
rat
(Rattus norvegicus)
Mammalia Crx 34
  • 88.29 (n)
mouse
(Mus musculus)
Mammalia Crx 34 16 35
  • 87.85 (n)
oppossum
(Monodelphis domestica)
Mammalia CRX 35
  • 54 (a)
OneToOne
lizard
(Anolis carolinensis)
Reptilia -- 35
  • 57 (a)
ManyToMany
zebrafish
(Danio rerio)
Actinopterygii crx 35
  • 54 (a)
ManyToMany
fruit fly
(Drosophila melanogaster)
Insecta oc 35
  • 21 (a)
OneToMany
worm
(Caenorhabditis elegans)
Secernentea ceh-37 35
  • 28 (a)
ManyToMany
sea squirt
(Ciona savignyi)
Ascidiacea CS-OTX 35
  • 30 (a)
OneToMany
Species where no ortholog for CRX 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)
  • chicken (Gallus gallus)
  • 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)
  • platypus (Ornithorhynchus anatinus)
  • 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)
  • tropical clawed frog (Silurana tropicalis)
  • wheat (Triticum aestivum)

Evolution for CRX Gene

ENSEMBL:
Gene Tree for CRX (if available)
TreeFam:
Gene Tree for CRX (if available)

Paralogs for CRX Gene

Paralogs for CRX Gene

(4) SIMAP similar genes for CRX Gene using alignment to 3 proteins:

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

Variants for CRX Gene

Sequence variations from dbSNP and Humsavar for CRX Gene

SNP ID Clin Chr 19 pos Sequence Context AA Info Type
rs104894672 Cone-rod dystrophy 2 (CORD2) [MIM:120970], Pathogenic 47,836,263(+) AGCGG(C/T)GGGAG reference, missense
rs104894673 Leber congenital amaurosis 7 (LCA7) [MIM:613829], Pathogenic 47,839,335(+) AGAAC(C/T)GGAGG reference, missense
rs28939682 Cone-rod dystrophy 2 (CORD2) [MIM:120970]
rs61748436 Retinitis pigmentosa (RP) [MIM:268000], Pathogenic 47,836,264(+) GCGGC(A/G)GGAGC reference, missense
rs61748459 Cone-rod dystrophy 2 (CORD2) [MIM:120970], untested 47,839,791(+) CCTCC(A/G)TGGGA reference, missense

Structural Variations from Database of Genomic Variants (DGV) for CRX Gene

Variant ID Type Subtype PubMed ID
esv2662621 CNV deletion 23128226
esv2718668 CNV deletion 23290073
esv3644559 CNV gain 21293372
nsv1058622 CNV gain 25217958
nsv1066097 CNV gain 25217958
nsv1066782 CNV loss 25217958
nsv1078445 CNV duplication 25765185
nsv1132476 CNV duplication 24896259
nsv1147845 CNV duplication 26484159
nsv428367 CNV gain+loss 18775914
nsv458715 CNV gain 19166990
nsv579897 CNV gain 21841781

Variation tolerance for CRX Gene

Residual Variation Intolerance Score: 60.7% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 2.94; 49.20% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for CRX Gene

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

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

Disorders for CRX Gene

MalaCards: The human disease database

(24) MalaCards diseases for CRX Gene - From: OMIM, ClinVar, GeneTests, Orphanet, Swiss-Prot, DISEASES, Novoseek, and GeneCards

Disorder Aliases PubMed IDs
cone-rod dystrophy
  • cone-rod retinal dystrophy-2
leber congenital amaurosis 7
  • lca7
retinitis pigmentosa
  • retinitis pigmentosa 1
macular dystrophy, concentric annular
  • maculopathy, bull's eye
leber congenital amaurosis
  • lca
- elite association - COSMIC cancer census association via MalaCards
Search CRX in MalaCards View complete list of genes associated with diseases

UniProtKB/Swiss-Prot

CRX_HUMAN
  • Cone-rod dystrophy 2 (CORD2) [MIM:120970]: 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. {ECO:0000269 PubMed:9390563, ECO:0000269 PubMed:9427255, ECO:0000269 PubMed:9792858}. Note=The disease is caused by mutations affecting the gene represented in this entry.
  • Leber congenital amaurosis 7 (LCA7) [MIM:613829]: A severe dystrophy of the retina, typically becoming evident in the first years of life. Visual function is usually poor and often accompanied by nystagmus, sluggish or near-absent pupillary responses, photophobia, high hyperopia and keratoconus. {ECO:0000269 PubMed:20513135, ECO:0000269 PubMed:21602930, ECO:0000269 PubMed:9792858, ECO:0000269 PubMed:9931337}. Note=The disease is caused by mutations affecting the gene represented in this entry.
  • Retinitis pigmentosa (RP) [MIM:268000]: A retinal dystrophy belonging to the group of pigmentary retinopathies. Retinitis pigmentosa is characterized by retinal pigment deposits visible on fundus examination and primary loss of rod photoreceptor cells followed by secondary loss of cone photoreceptors. Patients typically have night vision blindness and loss of midperipheral visual field. As their condition progresses, they lose their far peripheral visual field and eventually central vision as well. {ECO:0000269 PubMed:11139241, ECO:0000269 PubMed:9427255, ECO:0000269 PubMed:9792858}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Relevant External Links for CRX

Genetic Association Database (GAD)
CRX
Human Genome Epidemiology (HuGE) Navigator
CRX
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
CRX
genes like me logo Genes that share disorders with CRX: view

No data available for Genatlas for CRX Gene

Publications for CRX Gene

  1. A range of clinical phenotypes associated with mutations in CRX, a photoreceptor transcription-factor gene. (PMID: 9792858) Sohocki M.M. … Daiger S.P. (Am. J. Hum. Genet. 1998) 3 4 22 46 64
  2. Cone-rod dystrophy due to mutations in a novel photoreceptor-specific homeobox gene (CRX) essential for maintenance of the photoreceptor. (PMID: 9390563) Freund C.L. … McInnes R.R. (Cell 1997) 2 3 4 22 64
  3. 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) 3 4 22 64
  4. Leber congenital amaurosis caused by a homozygous mutation (R90W) in the homeodomain of the retinal transcription factor CRX: direct evidence for the involvement of CRX in the development of photoreceptor function. (PMID: 9931337) Swaroop A. … Sieving P.A. (Hum. Mol. Genet. 1999) 3 4 22 64
  5. Mutations in the cone-rod homeobox gene are associated with the cone- rod dystrophy photoreceptor degeneration. (PMID: 9427255) Swain P.K. … Zack D.J. (Neuron 1997) 3 4 22 64

Products for CRX Gene

Sources for CRX Gene

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