Human Gene CRX (ENST00000221996.12) from GENCODE V44
  Description: Homo sapiens cone-rod homeobox (CRX), mRNA. (from RefSeq NM_000554)
RefSeq Summary (NM_000554): 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]. Sequence Note: This RefSeq record was created from transcript and genomic sequence data to make the sequence consistent with the reference genome assembly. The genomic coordinates used for the transcript record were based on transcript alignments.
Gencode Transcript: ENST00000221996.12
Gencode Gene: ENSG00000105392.17
Transcript (Including UTRs)
   Position: hg38 chr19:47,821,937-47,843,324 Size: 21,388 Total Exon Count: 4 Strand: +
Coding Region
   Position: hg38 chr19:47,834,444-47,839,967 Size: 5,524 Coding Exon Count: 3 

Page IndexSequence and LinksUniProtKB CommentsPrimersMalaCardsCTD
RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesGO Annotations
mRNA DescriptionsOther NamesGeneReviewsMethods
Data last updated at UCSC: 2023-08-18 00:09:47

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr19:47,821,937-47,843,324)mRNA (may differ from genome)Protein (299 aa)
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HGNCHPRDLynxMalacardsMGIneXtProt
OMIMPubMedUniProtKBWikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: CRX_HUMAN
DESCRIPTION: RecName: Full=Cone-rod homeobox protein;
FUNCTION: 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, e.g. NRL and RX, to regulate photoreceptor cell-specific gene transcription. Essential for the maintenance of mammalian photoreceptors.
SUBUNIT: Interacts with SCA7 (By similarity). Interacts with RAX2. Interacts (via the homeobox) with NRL (via the leucine-zipper domain). Interacts with PDC.
SUBCELLULAR LOCATION: Nucleus (By similarity).
TISSUE SPECIFICITY: Retina.
DISEASE: Defects in CRX are the cause of Leber congenital amaurosis type 7 (LCA7) [MIM:613829]. LCA designates a clinically and genetically heterogeneous group of childhood retinal degenerations, generally inherited in an autosomal recessive manner. Affected infants have little or no retinal photoreceptor function as tested by electroretinography. LCA represents the most common genetic cause of congenital visual impairment in infants and children.
DISEASE: Defects in CRX are the cause of cone-rod dystrophy type 2 (CORD2) [MIM:120970]; also known as cone-rod retinal dystrophy 2 (CRD2). CORDs are inherited retinal dystrophies belonging to the group of pigmentary retinopathies. CORDs are 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.
DISEASE: Defects in CRX are a cause of retinitis pigmentosa (RP) [MIM:268000]. RP leads to degeneration of retinal photoreceptor cells. 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.
SIMILARITY: Belongs to the paired homeobox family.
SIMILARITY: Contains 1 homeobox DNA-binding domain.
WEB RESOURCE: Name=Mutations of the CRX gene; Note=Retina International's Scientific Newsletter; URL="http://www.retina-international.org/files/sci-news/crxmut.htm";
WEB RESOURCE: Name=GeneReviews; URL="http://www.ncbi.nlm.nih.gov/sites/GeneTests/lab/gene/CRX";

-  Primer design for this transcript
 

Primer3Plus can design qPCR Primers that straddle exon-exon-junctions, which amplify only cDNA, not genomic DNA.
Click here to load the transcript sequence and exon structure into Primer3Plus

Exonprimer can design one pair of Sanger sequencing primers around every exon, located in non-genic sequence.
Click here to open Exonprimer with this transcript

To design primers for a non-coding sequence, zoom to a region of interest and select from the drop-down menu: View > In External Tools > Primer3


-  MalaCards Disease Associations
  MalaCards Gene Search: CRX
Diseases sorted by gene-association score: cone-rod dystrophy* (1371), leber congenital amaurosis 7* (1230), retinitis pigmentosa* (1097), macular dystrophy, concentric annular* (283), leber congenital amaurosis* (141), crx-related leber congenital amaurosis* (100), crx-related retinitis pigmentosa* (100), rhyns syndrome* (83), enhanced s-cone syndrome (12), intraocular retinoblastoma (11), rpe65-related leber congenital amaurosis (11), spinocerebellar ataxia 7 (7), retinoschisis (7), stargardt disease 1 (7), retinal disease (7), keratoconus (7), axenfeld-rieger syndrome, type 1 (6), leber congenital amaurosis 4 (5), retinal degeneration (5), bradyopsia (5), leber congenital amaurosis 9 (5), achromatopsia 3 (4), fundus dystrophy (3), macular degeneration, age-related, 1 (1)
* = Manually curated disease association

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 0.06 RPKM in Testis
Total median expression: 0.09 RPKM



View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
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-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -36.10109-0.331 Picture PostScript Text
3' UTR -1441.903357-0.430 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  InterPro Domains: Graphical view of domain structure
IPR017970 - Homeobox_CS
IPR001356 - Homeodomain
IPR009057 - Homeodomain-like
IPR013851 - Otx_TF_C

Pfam Domains:
PF00046 - Homeobox domain
PF03529 - Otx1 transcription factor

ModBase Predicted Comparative 3D Structure on O43186
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-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
Genome BrowserGenome BrowserNo orthologNo orthologNo orthologNo ortholog
Gene Details     
Gene Sorter     
MGIRGD    
Protein SequenceProtein Sequence    
AlignmentAlignment    

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0000978 RNA polymerase II core promoter proximal region sequence-specific DNA binding
GO:0000981 RNA polymerase II transcription factor activity, sequence-specific DNA binding
GO:0001077 transcriptional activator activity, RNA polymerase II core promoter proximal region sequence-specific binding
GO:0003677 DNA binding
GO:0003700 transcription factor activity, sequence-specific DNA binding
GO:0005515 protein binding
GO:0035257 nuclear hormone receptor binding
GO:0043522 leucine zipper domain binding
GO:0043565 sequence-specific DNA binding

Biological Process:
GO:0006351 transcription, DNA-templated
GO:0006355 regulation of transcription, DNA-templated
GO:0006366 transcription from RNA polymerase II promoter
GO:0007275 multicellular organism development
GO:0007399 nervous system development
GO:0007601 visual perception
GO:0007623 circadian rhythm
GO:0009887 animal organ morphogenesis
GO:0030154 cell differentiation
GO:0045944 positive regulation of transcription from RNA polymerase II promoter
GO:0046534 positive regulation of photoreceptor cell differentiation
GO:0050896 response to stimulus

Cellular Component:
GO:0005634 nucleus


-  Descriptions from all associated GenBank mRNAs
  AH012061 - Homo sapiens cone rod homeobox protein (CRX) mRNA, partial sequence.
BC016664 - Homo sapiens cone-rod homeobox, mRNA (cDNA clone MGC:9387 IMAGE:3869862), complete cds.
BC053672 - Homo sapiens cone-rod homeobox, mRNA (cDNA clone MGC:61499 IMAGE:6144191), complete cds.
DQ340179 - Homo sapiens CRX like homeobox 1 mRNA, complete cds.
DQ426868 - Homo sapiens cone-rod homeobox (CRX) mRNA, partial cds, alternatively spliced.
DQ426867 - Homo sapiens cone-rod homeobox (CRX) mRNA, 5' UTR.
AB529176 - Synthetic construct DNA, clone: pF1KB7607, Homo sapiens CRX gene for cone-rod homeobox protein, without stop codon, in Flexi system.
DQ894239 - Synthetic construct Homo sapiens clone IMAGE:100008699; FLH168938.01L; RZPDo839E1093D cone-rod homeobox (CRX) gene, encodes complete protein.
KJ896645 - Synthetic construct Homo sapiens clone ccsbBroadEn_06039 CRX gene, encodes complete protein.
KR709699 - Synthetic construct Homo sapiens clone CCSBHm_00005249 CRX (CRX) mRNA, encodes complete protein.
KR709700 - Synthetic construct Homo sapiens clone CCSBHm_00005251 CRX (CRX) mRNA, encodes complete protein.
KR709701 - Synthetic construct Homo sapiens clone CCSBHm_00005253 CRX (CRX) mRNA, encodes complete protein.
KR709702 - Synthetic construct Homo sapiens clone CCSBHm_00005262 CRX (CRX) mRNA, encodes complete protein.
DQ893564 - Synthetic construct clone IMAGE:100006194; FLH168942.01X; RZPDo839E1094D cone-rod homeobox (CRX) gene, encodes complete protein.
BT007364 - Homo sapiens cone-rod homeobox mRNA, complete cds.
EF432655 - Homo sapiens cone-rod homeobox protein (CRX) mRNA, partial cds.
JD395600 - Sequence 376624 from Patent EP1572962.
JD118759 - Sequence 99783 from Patent EP1572962.
JD112244 - Sequence 93268 from Patent EP1572962.
JD375910 - Sequence 356934 from Patent EP1572962.
JD496996 - Sequence 478020 from Patent EP1572962.
JD404836 - Sequence 385860 from Patent EP1572962.
BC009045 - Homo sapiens, clone IMAGE:3871392, mRNA.

-  Other Names for This Gene
  Alternate Gene Symbols: CORD2, CRX_HUMAN, ENST00000221996.1, ENST00000221996.10, ENST00000221996.11, ENST00000221996.2, ENST00000221996.3, ENST00000221996.4, ENST00000221996.5, ENST00000221996.6, ENST00000221996.7, ENST00000221996.8, ENST00000221996.9, NM_000554, O43186, uc002phq.1, uc002phq.2, uc002phq.3, uc002phq.4, uc002phq.5, uc002phq.6
UCSC ID: ENST00000221996.12
RefSeq Accession: NM_000554
Protein: O43186 (aka CRX_HUMAN)
CCDS: CCDS12706.1

-  GeneReviews for This Gene
  GeneReviews article(s) related to gene CRX:
lca-ov (Leber Congenital Amaurosis / Early-Onset Severe Retinal Dystrophy Overview)
rp-overview (Nonsyndromic Retinitis Pigmentosa Overview)

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.