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Aliases for CRX Gene

Aliases for CRX Gene

  • Cone-Rod Homeobox 2 3
  • CORD2 3 4 6
  • Orthodenticle Homeobox 3 2 3
  • LCA7 3 6
  • CRD 3 6
  • Cone-Rod Homeobox Protein 3
  • OTX3 3

External Ids for CRX Gene

Previous Symbols for CRX Gene

  • CORD2

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 leber congenital amaurosis 7 and cone-rod dystrophy. GO annotations related to this gene include sequence-specific DNA binding transcription factor activity and chromatin binding. An important paralog of this gene is PITX3.

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

Genomic Location for CRX Gene

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

UCSC Golden Path with GeneCards custom track
Cytogenetic band:
Genomic Location for CRX Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for CRX Gene

Regulatory Elements 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

Proteomics data for CRX Gene at MOPED

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 for CRX Gene

Gene Families for CRX Gene

HGNC:
  • PRD :Homeoboxes / PRD class

Protein Domains for CRX Gene

UniProtKB/Swiss-Prot:

CRX_HUMAN
Domain:
  • Contains 1 homeobox DNA-binding domain.:
    • O43186
Family:
  • Belongs to the paired homeobox family.:
    • O43186
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:0000977 RNA polymerase II regulatory region sequence-specific DNA binding --
GO:0000978 RNA polymerase II core promoter proximal region sequence-specific DNA binding IDA 10625658
GO:0001077 RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription IDA 10625658
GO:0003677 DNA binding --
GO:0003682 chromatin binding IEA --
genes like me logo Genes that share ontologies with CRX: view
genes like me logo Genes that share phenotypes with CRX: view

Animal Models for CRX Gene

MGI Knock Outs for CRX:
Targeting motifs for CRX Gene
HOMER Transcription Factor Regulatory Elements motif CRX
  • Consensus sequence: GCTAATCC Submotif: canonical Cell Type: Retina GeoId: GSE20012

No data available for Enzyme Numbers (IUBMB) , miRNA and Transcription Factor Targeting 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 3
cytoskeleton 1

Gene Ontology (GO) - Cellular Components for CRX Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus ISS --
GO:0005667 transcription factor complex IEA --
genes like me logo Genes that share ontologies with CRX: view

Pathways 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:0007275 multicellular organismal development --
GO:0007601 visual perception IEA --
GO:0007623 circadian rhythm IEA --
genes like me logo Genes that share ontologies with CRX: view

No data available for Pathways by source for CRX Gene

Compounds for CRX Gene

(3) Novoseek inferred chemical compound relationships for CRX Gene

Compound -log(P) Hits PubMed IDs
retinoid 49 2
leucine 44.9 3
zinc 6.33 1
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 :

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 for CRX Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

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

This gene is overexpressed in Liver (21.0), Testis (12.1), and Brain - Hippocampus (5.8).

Integrated Proteomics: protein expression from ProteomicsDB, PaxDb, and MOPED for CRX Gene

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 expressions with CRX: view

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 36
  • 99.11 (n)
  • 99.67 (a)
cow
(Bos Taurus)
Mammalia CRX 36
  • 89.97 (n)
  • 97.66 (a)
CRX 37
  • 98 (a)
OneToOne
dog
(Canis familiaris)
Mammalia CRX 36
  • 88.63 (n)
  • 95.65 (a)
CRX 37
  • 97 (a)
OneToOne
mouse
(Mus musculus)
Mammalia Crx 36
  • 87.85 (n)
  • 96.66 (a)
Crx 16
Crx 37
  • 89 (a)
OneToOne
oppossum
(Monodelphis domestica)
Mammalia CRX 37
  • 54 (a)
OneToOne
rat
(Rattus norvegicus)
Mammalia Crx 36
  • 88.29 (n)
  • 97.32 (a)
lizard
(Anolis carolinensis)
Reptilia -- 37
  • 57 (a)
ManyToMany
zebrafish
(Danio rerio)
Actinopterygii crx 37
  • 54 (a)
ManyToMany
fruit fly
(Drosophila melanogaster)
Insecta oc 37
  • 21 (a)
OneToMany
worm
(Caenorhabditis elegans)
Secernentea ceh-37 37
  • 28 (a)
ManyToMany
sea squirt
(Ciona savignyi)
Ascidiacea CS-OTX 37
  • 30 (a)
OneToMany
Species with no ortholog for CRX:
  • 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

Selected SIMAP similar genes for CRX Gene using alignment to 3 proteins:

Pseudogenes.org Pseudogenes for CRX Gene

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 MAF
rs1862482 -- 47,829,983(+) TACTG(C/T)CCAGC intron-variant
rs1862483 -- 47,830,268(+) aacgc(C/T)gctgc intron-variant
rs1862484 -- 47,830,279(+) actcc(A/G)gcctg intron-variant
rs1974815 -- 47,821,690(+) GAGTA(A/G)GGGCT upstream-variant-2KB
rs2340995 -- 47,824,751(+) CAGTG(A/G)GTGCC intron-variant

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

Variant ID Type Subtype PubMed ID
nsv428367 CNV Gain+Loss 18775914
nsv458715 CNV Gain 19166990
esv2662621 CNV Deletion 23128226
esv2718668 CNV Deletion 23290073

Relevant External Links for CRX Gene

HapMap Linkage Disequilibrium report
CRX
Human Gene Mutation Database (HGMD)
CRX
Locus Specific Mutation Databases (LSDB)
CRX

Disorders for CRX Gene

(2) OMIM Diseases for CRX Gene (602225)

UniProtKB/Swiss-Prot

CRX_HUMAN
  • 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:9792858, ECO:0000269 PubMed:9931337}. Note=The disease is caused by mutations affecting the gene represented in this entry.
  • 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.
  • 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:9427255, ECO:0000269 PubMed:9792858}. Note=The disease is caused by mutations affecting the gene represented in this entry.

(4) University of Copenhagen DISEASES for CRX Gene

(9) Novoseek inferred disease relationships for CRX Gene

Disease -log(P) Hits PubMed IDs
lebers congenital amaurosis 95.9 16
cone-rod dystrophy 93.5 21
retinitis pigmentosa 82.8 8
blindness congenital 77.5 1
retinal degeneration 68.3 6

Relevant External Links for CRX

GeneTests
CRX
GeneReviews
CRX
Genetic Association Database (GAD)
CRX
Human Genome Epidemiology (HuGE) Navigator
CRX
genes like me logo Genes that share disorders with CRX: view

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 23 49
  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 23
  3. 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 23
  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 23
  5. 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 23

Products for CRX Gene

Sources for CRX Gene

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