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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 2 and Leber Congenital Amaurosis 7. Among its related pathways are Circadian rythm related genes. Gene Ontology (GO) annotations related to this gene include DNA binding transcription factor activity and RNA polymerase II proximal promoter 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

Additional gene information for CRX Gene

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

Genomics for CRX Gene

GeneHancer (GH) Regulatory Elements for CRX Gene

Promoters and enhancers for CRX Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH19I047819 Enhancer 0.5 ENCODE 550.8 +0.1 108 0.8 SP1 GLIS1 IKZF1 IRF4 SPI1 CRX GC19P047820 GC19P047821 TPRX1 GC19P047825 GC19P047824 GC19P047823 GC19P047822 LINC01595 GC19P047842
GH19I047821 Promoter 0.5 EPDnew 550.8 +2.1 2139 0.1 CRX CCDC114 GC19P047821 GC19P047824 GC19P047839 GC19P047842
GH19I047827 Promoter 0.5 EPDnew 550.4 +8.0 8033 0.1 CRX GC19P047824 GC19P047821 GC19P047842 GC19P047839
GH19I047789 Enhancer 1 FANTOM5 ENCODE 22.9 -29.3 -29254 1.1 CTCF KLF1 SIN3A RAD21 ZFHX2 ZNF366 POLR2A PATZ1 VEZF1 ZNF143 CABP5 CRX ZC3H4 NOP53-AS1 GRWD1 RASIP1 BICRA NOP53 ENSG00000271150 GC19P047784
GH19I047798 Enhancer 0.3 FANTOM5 17.6 -21.6 -21627 0.2 CABP5 CRX SNORD23 NOP53 SULT2A1 RPL23AP80 TPRX1
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around CRX on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the CRX gene promoter:

Genomic Locations for CRX Gene

Genomic Locations for CRX Gene
chr19:47,819,779-47,843,330
(GRCh38/hg38)
Size:
23,552 bases
Orientation:
Plus strand
chr19:48,322,703-48,346,587
(GRCh37/hg19)

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

HGNC:
Human Protein Atlas (HPA):
  • Disease related genes
  • Predicted intracellular proteins
  • Transcription factors

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 :
  • Belongs to the paired homeobox family.
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.

Phenotypes From GWAS Catalog for CRX Gene

Gene Ontology (GO) - Molecular Function for CRX Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000978 RNA polymerase II proximal promoter sequence-specific DNA binding IDA 10625658
GO:0001077 transcriptional activator activity, RNA polymerase II proximal promoter sequence-specific DNA binding IDA 10625658
GO:0003677 DNA binding IEA --
GO:0003700 DNA binding transcription factor activity ISS,NAS --
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

CRISPR 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

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
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
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

No data available for Subcellular locations from the Human Protein Atlas (HPA) for CRX Gene

Pathways & Interactions for CRX Gene

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

Pathways by source for CRX Gene

1 BioSystems pathway for CRX Gene

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 by RNA polymerase II 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 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 :

CRISPR Products

Inhibitory RNA Products

Clone 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 CGAP 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.

Evidence on tissue expression from TISSUES for CRX Gene

  • Eye(4.9)
  • Nervous system(3)

Phenotype-based relationships between genes and organs from Gene ORGANizer for CRX Gene

Germ Layers:
  • ectoderm
  • endoderm
  • mesoderm
Systems:
  • cardiovascular
  • digestive
  • endocrine
  • immune
  • integumentary
  • nervous
  • reproductive
  • respiratory
  • skeletal muscle
  • skeleton
Regions:
Head and neck:
  • brain
  • cerebellum
  • cranial nerve
  • ear
  • eye
  • eyelid
  • face
  • head
  • lacrimal apparatus
  • middle ear
  • nose
  • olfactory bulb
  • outer ear
  • pituitary gland
  • skull
Thorax:
  • breast
Abdomen:
  • liver
Pelvis:
  • ovary
  • penis
  • prostate
  • testicle
  • uterus
  • vagina
  • vulva
General:
  • blood
  • blood vessel
  • hair
  • peripheral nerve
  • peripheral nervous system
  • red blood cell
  • skin
  • spinal cord
genes like me logo Genes that share expression patterns 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 33
  • 99.11 (n)
cow
(Bos Taurus)
Mammalia CRX 33 34
  • 89.97 (n)
dog
(Canis familiaris)
Mammalia CRX 33 34
  • 88.63 (n)
rat
(Rattus norvegicus)
Mammalia Crx 33
  • 88.29 (n)
mouse
(Mus musculus)
Mammalia Crx 33 16 34
  • 87.85 (n)
oppossum
(Monodelphis domestica)
Mammalia CRX 34
  • 54 (a)
OneToOne
lizard
(Anolis carolinensis)
Reptilia -- 34
  • 57 (a)
ManyToMany
zebrafish
(Danio rerio)
Actinopterygii crx 34
  • 54 (a)
ManyToMany
fruit fly
(Drosophila melanogaster)
Insecta oc 34
  • 21 (a)
OneToMany
worm
(Caenorhabditis elegans)
Secernentea ceh-37 34
  • 28 (a)
ManyToMany
sea squirt
(Ciona savignyi)
Ascidiacea CS-OTX 34
  • 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 Variation AA Info Type
rs1012989722 uncertain-significance, Retinitis Pigmentosa, Dominant, Leber congenital amaurosis, Cone-Rod Dystrophy, Dominant 47,841,726(+) G/T 3_prime_UTR_variant
rs10418215 benign, Cone-Rod Dystrophy, Dominant, Leber congenital amaurosis, Retinitis Pigmentosa, Dominant 47,821,930(+) T/C 5_prime_UTR_variant
rs10418834 benign, Cone-Rod Dystrophy, Dominant, Retinitis Pigmentosa, Dominant, Leber congenital amaurosis 47,841,422(+) T/A 3_prime_UTR_variant
rs104894671 pathogenic, not-provided, Cone-rod dystrophy 2, not provided, Cone-rod dystrophy 2 (CORD2) [MIM:120970] 47,836,381(+) A/C coding_sequence_variant, missense_variant
rs104894672 pathogenic, not-provided, Cone-rod dystrophy 2, not provided, Cone-rod dystrophy 2 (CORD2) [MIM:120970] 47,836,263(+) C/T coding_sequence_variant, missense_variant

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)

Additional Variant Information for CRX Gene

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

SNP Genotyping and Copy Number Assay Products

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

Disorders for CRX Gene

MalaCards: The human disease database

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

- 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, due to cone photoreceptors degenerating at a higher rate than rod photoreceptors. {ECO:0000269 PubMed:10887186, 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:10887186, 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.

Additional Disease Information for CRX

Genetic Association Database
(GAD)
Human Genome Epidemiology Navigator
(HuGE)
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
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 MM … Daiger SP (American journal of human genetics 1998) 3 4 22 44 58
  2. Cone-rod dystrophy due to mutations in a novel photoreceptor-specific homeobox gene (CRX) essential for maintenance of the photoreceptor. (PMID: 9390563) Freund CL … McInnes RR (Cell 1997) 2 3 4 22 58
  3. Both PCE-1/RX and OTX/CRX interactions are necessary for photoreceptor-specific gene expression. (PMID: 10625658) Kimura A … Shinohara T (The Journal of biological chemistry 2000) 3 4 22 58
  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 PA (Human molecular genetics 1999) 3 4 22 58
  5. Mutations in the cone-rod homeobox gene are associated with the cone-rod dystrophy photoreceptor degeneration. (PMID: 9427255) Swain PK … Zack DJ (Neuron 1997) 3 4 22 58

Products for CRX Gene

Sources for CRX Gene

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