O43186 (CRX_HUMAN) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
Cone-rod homeobox protein

Gene names

Name:	CRX
Synonyms:	CORD2

Organism

Homo sapiens (Human) [Reference proteome]

Taxonomic identifier

9606 [NCBI]

Taxonomic lineage

cellular organisms › Eukaryota › Opisthokonta › Metazoa › Eumetazoa › Bilateria › Deuterostomia › Chordata › Craniata › Vertebrata › Gnathostomata › Teleostomi › Euteleostomi › Sarcopterygii › Tetrapoda › Amniota › Mammalia › Theria › Eutheria › Euarchontoglires › Primates › Haplorrhini › Simiiformes › Catarrhini › Hominoidea › Hominidae › Homininae › Homo

Protein attributes

Sequence length	299 AA.
Sequence status	Complete.
Protein existence	Evidence at protein level

General annotation (Comments)

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. Ref.5
Subunit structure	Interacts with SCA7 By similarity. Interacts with RAX2. Interacts (via the homeobox) with NRL (via the leucine-zipper domain). Interacts with PDC. Ref.6 Ref.7
Subcellular location	Nucleus By similarity.
Tissue specificity	Retina.
Involvement in disease	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. Note: The disease is caused by mutations affecting the gene represented in this entry. Ref.6 Ref.9 Ref.10 Ref.13 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. Note: The disease is caused by mutations affecting the gene represented in this entry. Ref.1 Ref.6 Ref.8 Ref.9 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. Note: The disease is caused by mutations affecting the gene represented in this entry. Ref.8 Ref.9
Sequence similarities	Belongs to the paired homeobox family. Contains 1 homeobox DNA-binding domain.

Ontologies

Keywords
Biological process	Sensory transduction Transcription Transcription regulation Vision
Cellular component	Nucleus
Coding sequence diversity	Polymorphism
Disease	Cone-rod dystrophy Disease mutation Leber congenital amaurosis Retinitis pigmentosa
Domain	Homeobox
Ligand	DNA-binding
Molecular function	Activator
Technical term	Complete proteome Reference proteome
Gene Ontology (GO)
Biological_process	organ morphogenesis Traceable author statement Ref.1. Source: ProtInc positive regulation of transcription from RNA polymerase II promoter Inferred from electronic annotation. Source: Compara response to stimulus Inferred from electronic annotation. Source: UniProtKB-KW retina development in camera-type eye Inferred from electronic annotation. Source: Compara transcription, DNA-dependent Inferred from electronic annotation. Source: UniProtKB-KW visual perception Traceable author statement Ref.1. Source: ProtInc
Cellular_component	transcription factor complex Inferred from electronic annotation. Source: Compara
Molecular_function	chromatin binding Inferred from electronic annotation. Source: Compara sequence-specific DNA binding Inferred from electronic annotation. Source: InterPro sequence-specific DNA binding transcription factor activity Non-traceable author statement Ref.1. Source: ProtInc
Complete GO annotation...

Sequence annotation (Features)

	Feature key	Position(s)	Length	Description	Graphical view	Feature identifier
Molecule processing
	Chain	1 – 299	299	Cone-rod homeobox protein		PRO_0000048862
Regions
	DNA binding	39 – 98	60	Homeobox
Natural variations
	Natural variant	41	1	R → Q in RP. Ref.8 Ref.9		VAR_007946
	Natural variant	41	1	R → W in CORD2; exhibits reduced DNA binding, transcriptional synergy and interaction with NRL. Ref.6 Ref.8		VAR_003750
	Natural variant	42	1	E → K Found in a patient with LCA7. Ref.14		VAR_067189
	Natural variant	80	1	E → A in CORD2. Ref.1 Ref.9 Corresponds to variant rs28939682 [ dbSNP | Ensembl ].		VAR_003751
	Natural variant	88	1	K → N in LCA7; reduces NRL transactivation and reduces steady state levels of CRX and NRL; altered localization to the cytoplasm. Ref.13		VAR_063919
	Natural variant	90	1	R → W in LCA7; reduced DNA-binding ability, transcriptional synergy and interaction with NRL. Ref.6 Ref.10		VAR_008714
	Natural variant	122	1	G → D in RP.		VAR_008282
	Natural variant	141	1	S → F in a breast cancer sample; somatic mutation. Ref.11		VAR_036438
	Natural variant	146 – 149	4	Missing in LCA7.		VAR_007947
	Natural variant	154	1	T → A. Ref.12		VAR_067190
	Natural variant	158	1	A → T. Ref.8		VAR_007948
	Natural variant	242	1	V → M in CORD2. Ref.8		VAR_007949

Sequences

	Sequence		Length	Mass (Da)
	O43186 [UniParc]. Last modified June 1, 1998. Version 1. Checksum: 46747C09277A0864	FASTA	299	32,261
	10 20 30 40 50 60 MMAYMNPGPH YSVNALALSG PSVDLMHQAV PYPSAPRKQR RERTTFTRSQ LEELEALFAK 70 80 90 100 110 120 TQYPDVYARE EVALKINLPE SRVQVWFKNR RAKCRQQRQQ QKQQQQPPGG QAKARPAKRK 130 140 150 160 170 180 AGTSPRPSTD VCPDPLGISD SYSPPLPGPS GSPTTAVATV SIWSPASESP LPEAQRAGLV 190 200 210 220 230 240 ASGPSLTSAP YAMTYAPASA FCSSPSAYGS PSSYFSGLDP YLSPMVPQLG GPALSPLSGP 250 260 270 280 290 SVGPSLAQSP TSLSGQSYGA YSPVDSLEFK DPTGTWKFTY NPMDPLDYKD QSAWKFQIL

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"Cone-rod dystrophy due to mutations in a novel photoreceptor-specific homeobox gene (CRX) essential for maintenance of the photoreceptor." Freund C.L., Gregory-Evans C.Y., Furukawa T., Papaioannou M., Looser J., Ploder L., Bellingham J., Ng D., Herbrick J.-A.S., Duncan A., Scherer S.W., Tsui L.-C., Loutradis-Anagnostou A., Jacobson S.G., Cepko C.L., Bhattacharya S.S., McInnes R.R. Cell 91:543-553(1997) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], VARIANT CORD2 ALA-80.
[2]	"Cloning of human full-length CDSs in BD Creator(TM) system donor vector." Kalnine N., Chen X., Rolfs A., Halleck A., Hines L., Eisenstein S., Koundinya M., Raphael J., Moreira D., Kelley T., LaBaer J., Lin Y., Phelan M., Farmer A. Submitted (MAY-2003) to the EMBL/GenBank/DDBJ databases Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
[3]	"The DNA sequence and biology of human chromosome 19." Grimwood J., Gordon L.A., Olsen A.S., Terry A., Schmutz J., Lamerdin J.E., Hellsten U., Goodstein D., Couronne O., Tran-Gyamfi M., Aerts A., Altherr M., Ashworth L., Bajorek E., Black S., Branscomb E., Caenepeel S., Carrano A.V. , Caoile C., Chan Y.M., Christensen M., Cleland C.A., Copeland A., Dalin E., Dehal P., Denys M., Detter J.C., Escobar J., Flowers D., Fotopulos D., Garcia C., Georgescu A.M., Glavina T., Gomez M., Gonzales E., Groza M., Hammon N., Hawkins T., Haydu L., Ho I., Huang W., Israni S., Jett J., Kadner K., Kimball H., Kobayashi A., Larionov V., Leem S.-H., Lopez F., Lou Y., Lowry S., Malfatti S., Martinez D., McCready P.M., Medina C., Morgan J., Nelson K., Nolan M., Ovcharenko I., Pitluck S., Pollard M., Popkie A.P., Predki P., Quan G., Ramirez L., Rash S., Retterer J., Rodriguez A., Rogers S., Salamov A., Salazar A., She X., Smith D., Slezak T., Solovyev V., Thayer N., Tice H., Tsai M., Ustaszewska A., Vo N., Wagner M., Wheeler J., Wu K., Xie G., Yang J., Dubchak I., Furey T.S., DeJong P., Dickson M., Gordon D., Eichler E.E., Pennacchio L.A., Richardson P., Stubbs L., Rokhsar D.S., Myers R.M., Rubin E.M., Lucas S.M. Nature 428:529-535(2004) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
[4]	"The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC)." The MGC Project Team Genome Res. 14:2121-2127(2004) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA]. Tissue: Eye.
[5]	"Both PCE-1/RX and OTX/CRX interactions are necessary for photoreceptor-specific gene expression." Kimura A., Singh D., Wawrousek E.F., Kikuchi M., Nakamura M., Shinohara T. J. Biol. Chem. 275:1152-1160(2000) [PubMed] [Europe PMC] [Abstract] Cited for: FUNCTION.
[6]	"The leucine zipper of NRL interacts with the CRX homeodomain. A possible mechanism of transcriptional synergy in rhodopsin regulation." Mitton K.P., Swain P.K., Chen S., Xu S., Zack D.J., Swaroop A. J. Biol. Chem. 275:29794-29799(2000) [PubMed] [Europe PMC] [Abstract] Cited for: INTERACTION WITH NRL, CHARACTERIZATION OF VARIANT CORD2 TRP-41, CHARACTERIZATION OF VARIANT LCA7 TRP-90.
[7]	"QRX, a novel homeobox gene, modulates photoreceptor gene expression." Wang Q.-L., Chen S., Esumi N., Swain P.K., Haines H.S., Peng G., Melia B.M., McIntosh I., Heckenlively J.R., Jacobson S.G., Stone E.M., Swaroop A., Zack D.J. Hum. Mol. Genet. 13:1025-1040(2004) [PubMed] [Europe PMC] [Abstract] Cited for: INTERACTION WITH RAX2.
[8]	"Mutations in the cone-rod homeobox gene are associated with the cone-rod dystrophy photoreceptor degeneration." Swain P.K., Chen S., Wang Q.-L., Affatigato L.M., Coats C.L., Brady K.D., Fishman G.A., Jacobson S.G., Swaroop A., Stone E., Sieving P.A., Zack D.J. Neuron 19:1329-1336(1997) [PubMed] [Europe PMC] [Abstract] Cited for: VARIANTS CORD2 TRP-41 AND MET-242, VARIANT RP GLN-41, VARIANT THR-158.
[9]	"A range of clinical phenotypes associated with mutations in CRX, a photoreceptor transcription-factor gene." Sohocki M.M., Sullivan L.S., Mintz-Hittner H.A., Birch D., Heckenlively J.R., Freund C.L., McInnes R.R., Daiger S.P. Am. J. Hum. Genet. 63:1307-1315(1998) [PubMed] [Europe PMC] [Abstract] Cited for: VARIANT RP GLN-41, VARIANT CORD2 ALA-80, VARIANT LCA7 146-LEU--PRO-149 DEL.
[10]	"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." Swaroop A., Wang Q.-L., Wu W., Cook J., Coats C., Xu S., Chen S., Zack D.J., Sieving P.A. Hum. Mol. Genet. 8:299-305(1999) [PubMed] [Europe PMC] [Abstract] Cited for: VARIANT LCA7 TRP-90.
[11]	"The consensus coding sequences of human breast and colorectal cancers." Sjoeblom T., Jones S., Wood L.D., Parsons D.W., Lin J., Barber T.D., Mandelker D., Leary R.J., Ptak J., Silliman N., Szabo S., Buckhaults P., Farrell C., Meeh P., Markowitz S.D., Willis J., Dawson D., Willson J.K.V. , Gazdar A.F., Hartigan J., Wu L., Liu C., Parmigiani G., Park B.H., Bachman K.E., Papadopoulos N., Vogelstein B., Kinzler K.W., Velculescu V.E. Science 314:268-274(2006) [PubMed] [Europe PMC] [Abstract] Cited for: VARIANT [LARGE SCALE ANALYSIS] PHE-141.
[12]	"Molecular characterization of Leber congenital amaurosis in Koreans." Seong M.W., Kim S.Y., Yu Y.S., Hwang J.M., Kim J.Y., Park S.S. Mol. Vis. 14:1429-1436(2008) [PubMed] [Europe PMC] [Abstract] Cited for: VARIANT ALA-154.
[13]	"Two novel CRX mutant proteins causing autosomal dominant Leber congenital amaurosis interact differently with NRL." Nichols L.L. II, Alur R.P., Boobalan E., Sergeev Y.V., Caruso R.C., Stone E.M., Swaroop A., Johnson M.A., Brooks B.P. Hum. Mutat. 31:E1472-E1483(2010) [PubMed] [Europe PMC] [Abstract] Cited for: VARIANT LCA7 ASN-88, CHARACTERIZATION OF VARIANT LCA7 ASN-88.
[14]	"Detection of variants in 15 genes in 87 unrelated Chinese patients with Leber congenital amaurosis." Li L., Xiao X., Li S., Jia X., Wang P., Guo X., Jiao X., Zhang Q., Hejtmancik J.F. PLoS ONE 6:E19458-E19458(2011) [PubMed] [Europe PMC] [Abstract] Cited for: VARIANT LYS-42.
+	Additional computationally mapped references.

Web resources

Mutations of the CRX gene

Retina International's Scientific Newsletter

GeneReviews

Cross-references

Sequence databases
EMBL GenBank DDBJ	AF024711 Genomic DNA. Translation: AAB88418.1. BT007364 mRNA. Translation: AAP36028.1. AC008745 Genomic DNA. No translation available. BC016664 mRNA. No translation available. BC053672 mRNA. No translation available.
IPI	IPI00011226.
RefSeq	NP_000545.1. NM_000554.4.
UniGene	Hs.617342. Hs.633434. Hs.639114.
3D structure databases
ProteinModelPortal	O43186.
ModBase	Search...
Protein-protein interaction databases
IntAct	O43186. 3 interactions.
MINT	MINT-1442706.
STRING	9606.ENSP00000221996.
PTM databases
PhosphoSite	O43186.
Proteomic databases
PaxDb	O43186.
PRIDE	O43186.
Protocols and materials databases
DNASU	1406.
StructuralBiologyKnowledgebase	Search...
Genome annotation databases
Ensembl	ENST00000221996; ENSP00000221996; ENSG00000105392. ENST00000539067; ENSP00000445565; ENSG00000105392. ENST00000556900; ENSP00000450582; ENSG00000105392. ENST00000557738; ENSP00000450840; ENSG00000105392.
GeneID	1406.
KEGG	hsa:1406.
UCSC	uc002phq.4. human.
Organism-specific databases
CTD	1406.
GeneCards	GC19P048327.
HGNC	HGNC:2383. CRX.
HPA	HPA036762. HPA036763.
MIM	120970. phenotype. 268000. phenotype. 602225. gene. 613829. phenotype.
neXtProt	NX_O43186.
Orphanet	1872. Cone rod dystrophy. 65. Leber congenital amaurosis. 791. Retinitis pigmentosa.
PharmGKB	PA26903.
GenAtlas	Search...
Phylogenomic databases
eggNOG	NOG324074.
HOGENOM	HOG000082677.
HOVERGEN	HBG004028.
InParanoid	O43186.
KO	K09337.
OMA	QTKARPA.
OrthoDB	EOG4NKBWG.
PhylomeDB	O43186.
Gene expression databases
ArrayExpress	O43186.
Bgee	O43186.
CleanEx	HS_CRX.
Genevestigator	O43186.
GermOnline	ENSG00000105392. Homo sapiens.
Family and domain databases
Gene3D	1.10.10.60. 1 hit.
InterPro	IPR017970. Homeobox_CS. IPR001356. Homeodomain. IPR009057. Homeodomain-like. IPR013851. Otx_TF_C. [Graphical view]
Pfam	PF00046. Homeobox. 1 hit. PF03529. TF_Otx. 1 hit. [Graphical view]
SMART	SM00389. HOX. 1 hit. [Graphical view]
SUPFAM	SSF46689. Homeodomain_like. 1 hit.
PROSITE	PS00027. HOMEOBOX_1. 1 hit. PS50071. HOMEOBOX_2. 1 hit. [Graphical view]
ProtoNet	Search...
Other
ChiTaRS	CRX. human.
GenomeRNAi	1406.
NextBio	5749.
SOURCE	Search...

Entry information

Entry name

CRX_HUMAN

Accession

Primary (citable) accession number: O43186

Entry history

Integrated into UniProtKB/Swiss-Prot:	July 15, 1998
Last sequence update:	June 1, 1998
Last modified:	May 1, 2013
This is version 131 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Chordata Protein Annotation Program

Disclaimer

Any medical or genetic information present in this entry is provided for research, educational and informational purposes only. It is not in any way intended to be used as a substitute for professional medical advice, diagnosis, treatment or care.