Crx (cone-rod homeobox) - Rat Genome Database

Name: Crx
Creator: Rat Genome Database
License: Creative Commons CC BY 4.0
Keywords: Rat Gene RGD Genome

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Gene: Crx (cone-rod homeobox) Rattus norvegicus

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Symbol:

Crx

Name:

cone-rod homeobox

RGD ID:

620511

Description:

Enables DNA binding activity. Involved in circadian rhythm and positive regulation of photoreceptor cell differentiation. Predicted to be part of transcription regulator complex. Predicted to be active in nucleus. Human ortholog(s) of this gene implicated in Leber congenital amaurosis 7 and cone-rod dystrophy 2. Orthologous to human CRX (cone-rod homeobox); PARTICIPATES IN retinitis pigmentosa pathway; INTERACTS WITH ammonium chloride; copper atom; copper(0).

Type:

protein-coding

RefSeq Status:

VALIDATED

Previously known as:

cone-rod homeobox containing; cone-rod homeobox containing gene; cone-rod homeobox protein

RGD Orthologs

Alliance Orthologs

More Info

more info ...

More Info

Species	Gene symbol and name	Data Source	Assertion derived from	less info ...
Orthologs ¹				less info ...
Homo sapiens (human):	CRX (cone-rod homeobox)	HGNC	EggNOG, Ensembl, HomoloGene, Inparanoid, NCBI, OMA, OrthoDB, OrthoMCL, Panther, Treefam
Mus musculus (house mouse):	Crx (cone-rod homeobox)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Chinchilla lanigera (long-tailed chinchilla):	Crx (cone-rod homeobox)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Pan paniscus (bonobo/pygmy chimpanzee):	CRX (cone-rod homeobox)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Canis lupus familiaris (dog):	CRX (cone-rod homeobox)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Ictidomys tridecemlineatus (thirteen-lined ground squirrel):	LOC101960714 (cone-rod homeobox protein)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Sus scrofa (pig):	CRX (cone-rod homeobox)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Chlorocebus sabaeus (green monkey):	CRX (cone-rod homeobox)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Heterocephalus glaber (naked mole-rat):	Crx (cone-rod homeobox)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Other homologs ²
Homo sapiens (human):	ARGFX (arginine-fifty homeobox)	HGNC	Treefam
Alliance orthologs ³
Homo sapiens (human):	CRX (cone-rod homeobox)	Alliance	DIOPT (Ensembl Compara\|HGNC\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|SonicParanoid)
Mus musculus (house mouse):	Crx (cone-rod homeobox)	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Danio rerio (zebrafish):	otx5 (orthodenticle homolog 5)	Alliance	DIOPT (Ensembl Compara\|OrthoFinder\|PANTHER)
Danio rerio (zebrafish):	crx (cone-rod homeobox)	Alliance	DIOPT (OMA\|OrthoFinder\|PANTHER)
Caenorhabditis elegans (roundworm):	ceh-37	Alliance	DIOPT (Hieranoid\|OrthoInspector\|PANTHER\|SonicParanoid)
Xenopus tropicalis (tropical clawed frog):	crx	Alliance	DIOPT (Ensembl Compara\|OrthoFinder\|PANTHER)

Latest Assembly:

mRatBN7.2 - mRatBN7.2 Assembly

Position:

Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCr8	1	85,667,971 - 85,681,852 (-)	NCBI		GRCr8
mRatBN7.2	1	76,539,812 - 76,553,694 (-)	NCBI	mRatBN7.2	mRatBN7.2
mRatBN7.2 Ensembl	1	76,540,141 - 76,545,818 (-)	Ensembl		mRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx	1	81,908,471 - 81,914,093 (-)	NCBI	Rnor_SHR	UTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0	1	3,654,790 - 3,660,412 (-)	NCBI	Rnor_SHRSP	UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0	1	83,663,620 - 83,669,242 (-)	NCBI	Rnor_WKY	UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0	1	77,744,593 - 77,758,913 (-)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_6.0 Ensembl	1	77,745,288 - 77,750,960 (-)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_5.0	1	79,009,202 - 79,023,481 (-)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	1	76,190,656 - 76,196,333 (-)	NCBI	RGSC3.4	RGSC_v3.4	rn4	RGSC3.4
RGSC_v3.1	1	76,268,766 - 76,274,444 (-)	NCBI
Celera	1	71,030,638 - 71,036,315 (-)	NCBI		Celera
Cytogenetic Map	1	q21	NCBI

JBrowse:

View Region in Genome Browser (JBrowse)

Model

Annotation Click to see Annotation Detail View

Disease Annotations Click to see Annotation Detail View

Concentric Annular Macular Dystrophy (ISO)

cone-rod dystrophy (ISO)

cone-rod dystrophy 2 (ISO,ISS)

congenital myopathy 1A (ISO)

fundus dystrophy (ISO)

genetic disease (ISO)

Leber congenital amaurosis (ISO)

Leber congenital amaurosis 1 (ISO)

Leber congenital amaurosis 7 (ISO,ISS)

macular degeneration (ISO)

prostate cancer (ISO)

retinal degeneration (ISO)

retinitis pigmentosa (ISO)

Stargardt disease (ISO)

Usher syndrome (ISO)

Gene-Chemical Interaction Annotations Click to see Annotation Detail View

2,3,7,8-tetrachlorodibenzodioxine (ISO)

3,3',5,5'-tetrabromobisphenol A (ISO)

4,4'-sulfonyldiphenol (ISO)

aflatoxin B1 (ISO)

Aflatoxin B2 alpha (ISO)

ammonium chloride (EXP)

benzo[a]pyrene (ISO)

benzo[e]pyrene (ISO)

bisphenol A (ISO)

bisphenol F (ISO)

camptothecin (ISO)

CGP 52608 (ISO)

copper atom (EXP)

copper(0) (EXP)

DDT (EXP)

formaldehyde (ISO)

lead diacetate (EXP,ISO)

lead(0) (ISO)

methapyrilene (ISO)

paracetamol (ISO)

propanal (ISO)

resveratrol (ISO)

triptonide (ISO)

vinclozolin (EXP)

Gene Ontology Annotations Click to see Annotation Detail View

Biological Process

circadian rhythm (IEP)

positive regulation of photoreceptor cell differentiation (IEP)

positive regulation of transcription by RNA polymerase II (ISO)

regulation of DNA-templated transcription (ISO)

regulation of transcription by RNA polymerase II (IBA)

retina development in camera-type eye (ISO)

Cellular Component

nucleus (IBA,ISO)

transcription regulator complex (ISO)

Molecular Function

chromatin binding (ISO)

DNA binding (IDA)

DNA-binding transcription activator activity, RNA polymerase II-specific (ISO)

DNA-binding transcription factor activity (ISO)

DNA-binding transcription factor activity, RNA polymerase II-specific (IBA)

leucine zipper domain binding (ISO)

nuclear receptor binding (ISO)

protein binding (ISO)

RNA polymerase II cis-regulatory region sequence-specific DNA binding (IBA,ISO)

RNA polymerase II transcription regulatory region sequence-specific DNA binding (ISO)

sequence-specific double-stranded DNA binding (ISO)

Molecular Pathway Annotations Click to see Annotation Detail View

retinitis pigmentosa pathway (ISO)

References

References - curated

#	Reference Title	Reference Citation
1.	Genes and mutations causing retinitis pigmentosa.	Daiger SP, etal., Clin Genet. 2013 Aug;84(2):132-41. doi: 10.1111/cge.12203. Epub 2013 Jun 19.
2.	De novo mutations in the CRX homeobox gene associated with Leber congenital amaurosis.	Freund CL, etal., Nat Genet 1998 Apr;18(4):311-2.
3.	Docosahexaenoic acid promotes photoreceptor differentiation without altering Crx expression.	Garelli A, etal., Invest Ophthalmol Vis Sci. 2006 Jul;47(7):3017-27.
4.	Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium.	Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
5.	Rat ISS GO annotations from GOA human gene data--August 2006	GOA data from the GO Consortium
6.	A pineal regulatory element (PIRE) mediates transactivation by the pineal/retina-specific transcription factor CRX.	Li X, etal., Proc Natl Acad Sci U S A. 1998 Feb 17;95(4):1876-81.
7.	Rat ISS GO annotations from MGI mouse gene data--August 2006	MGD data from the GO Consortium
8.	Electronic Transfer of LocusLink and RefSeq Data	NCBI rat LocusLink and RefSeq merged data July 26, 2002
9.	OMIM Disease Annotation Pipeline	OMIM Disease Annotation Pipeline
10.	GOA pipeline	RGD automated data pipeline
11.	ClinVar Automated Import and Annotation Pipeline	RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
12.	Data Import for Chemical-Gene Interactions	RGD automated import pipeline for gene-chemical interactions
13.	Molecular cloning of the cone-rod homeobox gene (Crx) from the rat and its temporal expression pattern in the retina under a daily light-dark cycle.	Sakamoto K, etal., Neurosci Lett 1999 Feb 12;261(1-2):101-4.

Additional References at PubMed

PMID:10625658	PMID:10887186	PMID:12407160	PMID:14613968	PMID:15689355	PMID:16539743	PMID:16574740	PMID:20026326	PMID:21052544	PMID:24877634	PMID:30803008

Genomics

Comparative Map Data

Crx
(Rattus norvegicus - Norway rat)

Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCr8	1	85,667,971 - 85,681,852 (-)	NCBI		GRCr8
mRatBN7.2	1	76,539,812 - 76,553,694 (-)	NCBI	mRatBN7.2	mRatBN7.2
mRatBN7.2 Ensembl	1	76,540,141 - 76,545,818 (-)	Ensembl		mRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx	1	81,908,471 - 81,914,093 (-)	NCBI	Rnor_SHR	UTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0	1	3,654,790 - 3,660,412 (-)	NCBI	Rnor_SHRSP	UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0	1	83,663,620 - 83,669,242 (-)	NCBI	Rnor_WKY	UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0	1	77,744,593 - 77,758,913 (-)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_6.0 Ensembl	1	77,745,288 - 77,750,960 (-)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_5.0	1	79,009,202 - 79,023,481 (-)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	1	76,190,656 - 76,196,333 (-)	NCBI	RGSC3.4	RGSC_v3.4	rn4	RGSC3.4
RGSC_v3.1	1	76,268,766 - 76,274,444 (-)	NCBI
Celera	1	71,030,638 - 71,036,315 (-)	NCBI		Celera
Cytogenetic Map	1	q21	NCBI

CRX
(Homo sapiens - human)

Human Assembly	Chr	Position (strand)	Source	Genome Browsers
Human Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCh38	19	47,821,937 - 47,843,324 (+)	NCBI	GRCh38	GRCh38	hg38	GRCh38
GRCh38.p14 Ensembl	19	47,819,779 - 47,843,330 (+)	Ensembl	GRCh38		hg38	GRCh38
GRCh37	19	48,325,194 - 48,346,581 (+)	NCBI	GRCh37	GRCh37	hg19	GRCh37
Build 36	19	53,016,911 - 53,038,393 (+)	NCBI	NCBI36	Build 36	hg18	NCBI36
Build 34	19	53,016,975 - 53,038,392	NCBI
Celera	19	45,130,795 - 45,152,290 (+)	NCBI		Celera
Cytogenetic Map	19	q13.33	NCBI
HuRef	19	44,751,798 - 44,773,295 (+)	NCBI		HuRef
CHM1_1	19	48,327,266 - 48,348,759 (+)	NCBI		CHM1_1
T2T-CHM13v2.0	19	50,652,778 - 50,674,184 (+)	NCBI		T2T-CHM13v2.0

Crx
(Mus musculus - house mouse)

Mouse Assembly	Chr	Position (strand)	Source	Genome Browsers
Mouse Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCm39	7	15,599,872 - 15,613,880 (-)	NCBI	GRCm39	GRCm39	mm39
GRCm39 Ensembl	7	15,599,872 - 15,613,893 (-)	Ensembl		GRCm39 Ensembl
GRCm38	7	15,865,947 - 15,879,955 (-)	NCBI	GRCm38	GRCm38	mm10	GRCm38
GRCm38.p6 Ensembl	7	15,865,947 - 15,879,968 (-)	Ensembl	GRCm38		mm10	GRCm38
MGSCv37	7	16,451,296 - 16,465,304 (-)	NCBI	GRCm37	MGSCv37	mm9	NCBIm37
MGSCv36	7	15,024,471 - 15,038,416 (-)	NCBI		MGSCv36	mm8
Celera	7	13,064,380 - 13,078,683 (-)	NCBI		Celera
Cytogenetic Map	7	A2	NCBI
cM Map	7	8.6	NCBI

Crx
(Chinchilla lanigera - long-tailed chinchilla)

Chinchilla Assembly	Chr	Position (strand)	Source	Genome Browsers
Chinchilla Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
ChiLan1.0 Ensembl	NW_004955574	1,544,917 - 1,548,912 (+)	Ensembl	ChiLan1.0
ChiLan1.0	NW_004955574	1,544,917 - 1,548,912 (+)	NCBI	ChiLan1.0	ChiLan1.0

CRX
(Pan paniscus - bonobo/pygmy chimpanzee)

Bonobo Assembly	Chr	Position (strand)	Source	Genome Browsers
Bonobo Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
NHGRI_mPanPan1-v2	20	53,983,564 - 53,999,402 (+)	NCBI		NHGRI_mPanPan1-v2
NHGRI_mPanPan1	19	55,853,180 - 55,869,032 (+)	NCBI		NHGRI_mPanPan1
Mhudiblu_PPA_v0	19	44,828,119 - 44,856,284 (+)	NCBI	Mhudiblu_PPA_v0	Mhudiblu_PPA_v0	panPan3
PanPan1.1	19	53,451,064 - 53,485,267 (+)	NCBI	panpan1.1	PanPan1.1	panPan2

CRX
(Canis lupus familiaris - dog)

Dog Assembly	Chr	Position (strand)	Source	Genome Browsers
Dog Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
CanFam3.1	1	108,249,911 - 108,261,015 (+)	NCBI	CanFam3.1	CanFam3.1	canFam3	CanFam3.1
CanFam3.1 Ensembl	1	108,249,911 - 108,261,010 (+)	Ensembl	CanFam3.1		canFam3	CanFam3.1
Dog10K_Boxer_Tasha	1	107,732,789 - 107,743,823 (+)	NCBI		Dog10K_Boxer_Tasha
ROS_Cfam_1.0	1	108,775,575 - 108,786,695 (+)	NCBI		ROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl	1	108,775,575 - 108,786,690 (+)	Ensembl		ROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1	1	108,443,942 - 108,454,986 (+)	NCBI		UMICH_Zoey_3.1
UNSW_CanFamBas_1.0	1	108,088,397 - 108,099,501 (+)	NCBI		UNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0	1	108,956,307 - 108,967,430 (+)	NCBI		UU_Cfam_GSD_1.0

LOC101960714
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)

Squirrel Assembly	Chr	Position (strand)	Source	Genome Browsers
Squirrel Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
HiC_Itri_2	NW_024409349	19,791,903 - 19,800,967 (+)	NCBI		HiC_Itri_2
SpeTri2.0 Ensembl	NW_004936664	1,409,229 - 1,419,234 (+)	Ensembl	SpeTri2.0	SpeTri2.0 Ensembl
SpeTri2.0	NW_004936664	1,408,618 - 1,419,096 (+)	NCBI	SpeTri2.0	SpeTri2.0		SpeTri2.0

CRX
(Sus scrofa - pig)

Pig Assembly	Chr	Position (strand)	Source	Genome Browsers
Pig Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
Sscrofa11.1 Ensembl	6	53,506,410 - 53,512,190 (+)	Ensembl	Sscrofa11.1		susScr11	Sscrofa11.1
Sscrofa11.1	6	53,506,410 - 53,509,858 (+)	NCBI	Sscrofa11.1	Sscrofa11.1	susScr11	Sscrofa11.1
Sscrofa10.2	6	49,089,411 - 49,092,899 (+)	NCBI	Sscrofa10.2	Sscrofa10.2	susScr3

CRX
(Chlorocebus sabaeus - green monkey)

Green Monkey Assembly	Chr	Position (strand)	Source	Genome Browsers
Green Monkey Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
ChlSab1.1	6	41,125,912 - 41,133,478 (+)	NCBI	ChlSab1.1	ChlSab1.1	chlSab2
ChlSab1.1 Ensembl	6	41,126,125 - 41,132,951 (+)	Ensembl	ChlSab1.1	ChlSab1.1 Ensembl	chlSab2
Vero_WHO_p1.0	NW_023666073	20,889,919 - 20,895,927 (+)	NCBI	Vero_WHO_p1.0	Vero_WHO_p1.0

Crx
(Heterocephalus glaber - naked mole-rat)

Naked Mole-Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Naked Mole-Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
HetGla_female_1.0 Ensembl	NW_004624832	6,104,229 - 6,108,146 (-)	Ensembl	HetGla_female_1.0	HetGla_female_1.0 Ensembl	hetGla2
HetGla 1.0	NW_004624832	6,103,530 - 6,108,129 (-)	NCBI	HetGla_female_1.0	HetGla 1.0	hetGla2

Variants

Variants in Crx
83 total Variants

miRNA Target Status

Predicted Target Of

	Summary Value
Count of predictions:	71
Count of miRNA genes:	64
Interacting mature miRNAs:	65
Transcripts:	ENSRNOT00000018858
Prediction methods:	Microtar, Miranda, Rnahybrid
Result types:	miRGate_prediction

The detailed report is available here: Full Report CSV TAB Printer

miRNA Target Status data imported from miRGate (http://mirgate.bioinfo.cnio.es/).
For more information about miRGate, see PMID:25858286 or access the full paper here.

QTLs in Region (mRatBN7.2)

The following QTLs overlap with this region.

RGD ID	Symbol	Name	LOD	P Value	Trait	Sub Trait	Chr	Start	Stop	Species
1331732	Srn4	Serum renin concentration QTL 4	4.467		renin activity (VT:0005581)	plasma renin activity level (CMO:0000116)	1	35239598	78430678	Rat
2313059	Bss55	Bone structure and strength QTL 55	3.2	0.0001	tibia size trait (VT:0100001)	tibia midshaft cross-sectional area (CMO:0001717)	1	43284731	118944897	Rat
631688	Hcas2	Hepatocarcinoma susceptibility QTL 2	3	0.0001	liver integrity trait (VT:0010547)	liver tumorous lesion number (CMO:0001068)	1	5925874	115540829	Rat
1578649	Bmd8	Bone mineral density QTL 8	4.9		femur mineral mass (VT:0010011)	trabecular volumetric bone mineral density (CMO:0001729)	1	49393172	94393172	Rat
1358359	Sradr1	Stress Responsive Adrenal Weight QTL 1	4.74		adrenal gland mass (VT:0010420)	both adrenal glands wet weight (CMO:0000164)	1	30882023	123479925	Rat
634314	Niddm44	Non-insulin dependent diabetes mellitus QTL 44			blood glucose amount (VT:0000188)	blood glucose level (CMO:0000046)	1	49393289	199050459	Rat
4889929	Bss87	Bone structure and strength QTL 87	6.7		tibia area (VT:1000281)	tibia-fibula cortical bone endosteal cross-sectional area (CMO:0001722)	1	53895117	82174945	Rat
1331792	Rf29	Renal function QTL 29	4.589		urine potassium amount (VT:0010539)	urine potassium level (CMO:0000128)	1	35239598	78430678	Rat
2313062	Bmd73	Bone mineral density QTL 73	3.9	0.0001	tibia mineral mass (VT:1000283)	compact volumetric bone mineral density (CMO:0001730)	1	11481312	82174945	Rat
8552900	Pigfal1	Plasma insulin-like growth factor 1 level QTL 1	7.4		blood insulin-like growth factor amount (VT:0010479)	plasma insulin-like growth factor 1 level (CMO:0001299)	1	34836858	79836858	Rat
1578654	Bss10	Bone structure and strength QTL 10	4		femur morphology trait (VT:0000559)	femoral neck cortical cross-sectional area (CMO:0001702)	1	49393172	159356837	Rat
1554320	Bmd1	Bone mineral density QTL 1	12.2	0.0001	femur mineral mass (VT:0010011)	volumetric bone mineral density (CMO:0001553)	1	509108	86060548	Rat
1354643	Foco2	Food consumption QTL 2	7.17	0.0001	eating behavior trait (VT:0001431)	food intake rate (CMO:0000427)	1	33449848	78449848	Rat
2302059	Pia36	Pristane induced arthritis QTL 36	3.8	0.001	blood immunoglobulin amount (VT:0002460)	serum immunoglobulin G1 level (CMO:0002115)	1	43333002	88333002	Rat
2313065	Bss67	Bone structure and strength QTL 67	3.1	0.0001	tibia area (VT:1000281)	tibia total energy absorbed before break (CMO:0001736)	1	11481312	82174945	Rat
1300121	Hrtrt1	Heart rate QTL 1	3.7		heart pumping trait (VT:2000009)	heart rate (CMO:0000002)	1	65789093	115540829	Rat
7421628	Bp361	Blood pressure QTL 361		0.001	arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	1	66023617	118608521	Rat
2313069	Bss68	Bone structure and strength QTL 68	2.9	0.0001	tibia size trait (VT:0100001)	tibia total energy absorbed before break (CMO:0001736)	1	11481312	82174945	Rat
631495	Bp96	Blood pressure QTL 96	4.52		arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	1	22340647	102268831	Rat
2313075	Bss66	Bone structure and strength QTL 66	3.4	0.0001	tibia length (VT:0004357)	tibia length (CMO:0000450)	1	11481312	82174945	Rat
70225	Bp58	Blood pressure QTL 58	3.3		arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	1	32356093	162846471	Rat
631512	Scl6	Serum cholesterol level QTL 6	9.6		blood cholesterol amount (VT:0000180)	serum total cholesterol level (CMO:0000363)	1	72197680	90508767	Rat
2298545	Neuinf8	Neuroinflammation QTL 8	4.6		nervous system integrity trait (VT:0010566)	spinal cord beta-2 microglobulin mRNA level (CMO:0002125)	1	57336763	151090257	Rat
2313072	Bss53	Bone structure and strength QTL 53	4.3	0.0001	tibia length (VT:0004357)	tibia length (CMO:0000450)	1	43284731	118944897	Rat
10059597	Bp377	Blood pressure QTL 377	3.42	0.025	arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	1	32737458	199368955	Rat
2313078	Bss54	Bone structure and strength QTL 54	3.5	0.0001	tibia area (VT:1000281)	tibia midshaft cross-sectional area (CMO:0001717)	1	43284731	118944897	Rat
2313077	Bss69	Bone structure and strength QTL 69	3.5	0.0001	tibia strength trait (VT:1000284)	bone polar moment of inertia (CMO:0001558)	1	11481312	82174945	Rat
1331778	Rf28	Renal function QTL 28	4.66		urine potassium amount (VT:0010539)	urine potassium excretion rate (CMO:0000761)	1	45803140	78430678	Rat
2313402	Anxrr24	Anxiety related response QTL 24			aggression-related behavior trait (VT:0015014)	tameness/aggressiveness composite score (CMO:0002136)	1	48963584	144267916	Rat
1331785	Rf27	Renal function QTL 27	4.643		urine sodium amount (VT:0006274)	urine sodium level (CMO:0000129)	1	28879780	78430678	Rat
61342	Bp27	Blood pressure QTL 27	3.4	0.0006	arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	1	56732668	98773277	Rat
1300172	Bp172	Blood pressure QTL 172	3.56		arterial blood pressure trait (VT:2000000)	diastolic blood pressure (CMO:0000005)	1	32737273	90665040	Rat
4889962	Bss94	Bone structure and strength QTL 94	3.8		tibia area (VT:1000281)	tibia-fibula cortical bone endosteal cross-sectional area (CMO:0001722)	1	49361465	82174945	Rat
2313094	Bss58	Bone structure and strength QTL 58	3.7	0.0001	tibia strength trait (VT:1000284)	tibia total energy absorbed before break (CMO:0001736)	1	43284731	118944897	Rat
6903308	Scl36	Serum cholesterol QTL 36	2	0.0125	blood cholesterol amount (VT:0000180)	plasma total cholesterol level (CMO:0000585)	1	53863041	90532583	Rat
2313092	Bmd72	Bone mineral density QTL 72	2.5	0.0001	tibia mineral mass (VT:1000283)	total volumetric bone mineral density (CMO:0001728)	1	11481312	82174945	Rat
2300164	Bmd44	Bone mineral density QTL 44	5.4	0.0001	lumbar vertebra mineral mass (VT:0010511)	volumetric bone mineral density (CMO:0001553)	1	56949932	101949932	Rat
2313099	Bss56	Bone structure and strength QTL 56	2.4	0.0001	tibia size trait (VT:0100001)	tibia midshaft endosteal cross-sectional area (CMO:0001716)	1	43284731	118944897	Rat
2313098	Bmd70	Bone mineral density QTL 70	3.6	0.0001	tibia mineral mass (VT:1000283)	compact volumetric bone mineral density (CMO:0001730)	1	43284731	118944897	Rat
2313097	Bss70	Bone structure and strength QTL 70	3.5	0.0001	tibia strength trait (VT:1000284)	tibia total energy absorbed before break (CMO:0001736)	1	11481312	82174945	Rat
9589820	Insglur3	Insulin/glucose ratio QTL 3	10.75	0.001	blood insulin amount (VT:0001560)	calculated plasma insulin level (CMO:0002170)	1	34836858	79836858	Rat
152025249	Scl82	Serum cholesterol level QTL 82	4.77		blood cholesterol amount (VT:0000180)		1	50343510	99980958	Rat
1354599	Bw29	Body weight QTL 29	3.46	0.001	body mass (VT:0001259)	body weight (CMO:0000012)	1	33449848	78449848	Rat
4889919	Bss86	Bone structure and strength QTL 86	4.1		tibia area (VT:1000281)	tibia midshaft total cross-sectional area (CMO:0001715)	1	53895117	82174945	Rat
8552948	Pigfal11	Plasma insulin-like growth factor 1 level QTL 11	4.7		blood insulin-like growth factor amount (VT:0010479)	plasma insulin-like growth factor 1 level (CMO:0001299)	1	34836858	79836858	Rat
2313051	Bss57	Bone structure and strength QTL 57	3.7	0.0001	tibia strength trait (VT:1000284)	bone polar moment of inertia (CMO:0001558)	1	43284731	118944897	Rat

Expression

RNA-SEQ Expression

Click on a value in the shaded box below the category label to view a detailed expression data table for that system.

alimentary part of gastrointestinal system	ectoderm	endocrine system	endoderm	exocrine system	hepatobiliary system	mesenchyme	nervous system	reproductive system
1	9	1	1	1	1	2	9	15

Sequence

Nucleotide Sequences


RefSeq Transcripts	NM_021855	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_006228354	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_017589643	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
GenBank Nucleotide	AB021129	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	AF135838	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	CH473979	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	JAXUCZ010000001	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles

Ensembl Acc Id:

ENSRNOT00000018858 ⟹ ENSRNOP00000018858

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2 Ensembl	1	76,540,141 - 76,545,818 (-)	Ensembl
Rnor_6.0 Ensembl	1	77,745,288 - 77,750,960 (-)	Ensembl

RefSeq Acc Id:

NM_021855 ⟹ NP_068627

RefSeq Status:

VALIDATED

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
GRCr8	1	85,667,971 - 85,681,852 (-)	NCBI
mRatBN7.2	1	76,539,812 - 76,553,694 (-)	NCBI
Rnor_6.0	1	77,745,288 - 77,750,960 (-)	NCBI
Rnor_5.0	1	79,009,202 - 79,023,481 (-)	NCBI
RGSC_v3.4	1	76,190,656 - 76,196,333 (-)	RGD
Celera	1	71,030,638 - 71,036,315 (-)	RGD

Sequence:

show sequence

ATGATGGCGTATATGAACCCGGGACCTCACTATTCGGTCAATGCCTTGGCCCTGAGTGGCCCCA
GTGTGGACCTGATGCACCAGGCTGTCCCATACTCAAGTGCCCCTAGGAAGCAGAGGCGGGAGCG
GACCACGTTCACCAGGAGCCAGCTGGAGGAGCTGGAGGCCCTGTTTGCCAAGACCCAGTACCCG
GATGTGTATGCACGTGAGGAGGTTGCTCTCAAGATCAACCTGCCTGAGTCCAGGGTCCAGGTCT
GGTTCAAGAATCGCAGGGCGAAATGCAGACAGCAGAGGCAGCAGCAGAAACAGCAGCAGCAGCC
CCCAGGGGTACAAGCCAAGGCTCGTCCTGCGAAGAGGAAGGCAGGCACATCCCCGAGACCCTCT
ACAGATGTTTGTACAGATCCTTTGGGCATCTCAGATTCCTACAGCCCATCTCTGCCTGGTCCCT
CAGGTTCACCTACCACAGCAGTGGCCACCGTATCCATCTGGAGTCCGGCCTCAGAGTCTCCTTT
GCCTGAGGCCCAGAGAGCTGGCCTAGTGGCTTCAGGGTCCTCTCTCACCTCAGCCCCTTATGCC
ATGACCTATGCCCCTGCTTCTGCTTTCTGTTCTTCACCTTCAGCTTATGCATCTCCAAGCTCCT
ATTTCAGTGGGTTGGATCCATACCTTTCTCCCATGGTGCCCCAGCTAGGGGGTCCGGCTCTCAG
CCCCCTCTCGGGCCCCTCTGTGGGGCCATCCTTGGCCCAGTCCCCCACCTCCTTGTCAGGCCAG
AGCTATAGCACCTACAGCCCCGTGGACAGCCTGGAATTCAAGGACCCTACAGGCACCTGGAAAT
TCACCTACAATCCCATGGACCCTCTGGACTACAAAGATCAGAGTGCCTGGAAGTTTCAGATCTT
GTAG

hide sequence

Protein Sequences


Protein RefSeqs	NP_068627	(Get FASTA)	NCBI Sequence Viewer
GenBank Protein	AAF61630	(Get FASTA)	NCBI Sequence Viewer
	BAA76666	(Get FASTA)	NCBI Sequence Viewer
	EDM08352	(Get FASTA)	NCBI Sequence Viewer
Ensembl Protein	ENSRNOP00000018858.3

RefSeq Acc Id:

NP_068627 ⟸ NM_021855

- UniProtKB:

F1LPR9 (UniProtKB/TrEMBL), Q9WTQ9 (UniProtKB/TrEMBL), A0A9K3Y7X4 (UniProtKB/TrEMBL)

- Sequence:

show sequence

MMAYMNPGPHYSVNALALSGPSVDLMHQAVPYSSAPRKQRRERTTFTRSQLEELEALFAKTQYP
DVYAREEVALKINLPESRVQVWFKNRRAKCRQQRQQQKQQQQPPGVQAKARPAKRKAGTSPRPS
TDVCTDPLGISDSYSPSLPGPSGSPTTAVATVSIWSPASESPLPEAQRAGLVASGSSLTSAPYA
MTYAPASAFCSSPSAYASPSSYFSGLDPYLSPMVPQLGGPALSPLSGPSVGPSLAQSPTSLSGQ
SYSTYSPVDSLEFKDPTGTWKFTYNPMDPLDYKDQSAWKFQIL

hide sequence

Ensembl Acc Id:

ENSRNOP00000018858 ⟸ ENSRNOT00000018858

Protein Domains

Homeobox

Protein Structures

Name	Modeler	Protein Id	AA Range	Protein Structure
AF-Q9WTQ9-F1-model_v2	AlphaFold	Q9WTQ9	1-299	view protein structure

Transcriptome

eQTL		View at Phenogen
WGCNA		View at Phenogen
Tissue/Strain Expression		View at Phenogen

Additional Information

External Database Links

Database	Acc Id	Source(s)
AGR Gene	RGD:620511	AgrOrtholog
BioCyc Gene	G2FUF-60640	BioCyc
Ensembl Genes	ENSRNOG00000013890	Ensembl, UniProtKB/TrEMBL
Ensembl Transcript	ENSRNOT00000018858.5	UniProtKB/TrEMBL
Gene3D-CATH	Homeodomain-like	UniProtKB/TrEMBL
InterPro	Homeobox	UniProtKB/TrEMBL
	Homeobox_CS	UniProtKB/TrEMBL
	Homeodomain-like	UniProtKB/TrEMBL
	Otx_TF_C	UniProtKB/TrEMBL
KEGG Report	rno:60446	UniProtKB/TrEMBL
NCBI Gene	60446	ENTREZGENE
PANTHER	CONE-ROD HOMEOBOX PROTEIN	UniProtKB/TrEMBL
	HOMEOBOX PROTEIN	UniProtKB/TrEMBL
Pfam	Homeobox	UniProtKB/TrEMBL
	TF_Otx	UniProtKB/TrEMBL
PhenoGen	Crx	PhenoGen
PROSITE	HOMEOBOX_1	UniProtKB/TrEMBL
	HOMEOBOX_2	UniProtKB/TrEMBL
RatGTEx	ENSRNOG00000013890	RatGTEx
SMART	HOX	UniProtKB/TrEMBL
Superfamily-SCOP	Homeodomain_like	UniProtKB/TrEMBL
UniProt	A0A9K3Y7X4	ENTREZGENE, UniProtKB/TrEMBL
	F1LPR9	ENTREZGENE
	Q9JLT8_RAT	UniProtKB/TrEMBL
	Q9WTQ9	ENTREZGENE, UniProtKB/TrEMBL
UniProt Secondary	F1LPR9	UniProtKB/TrEMBL

Nomenclature History

Date	Current Symbol	Current Name	Previous Symbol	Previous Name	Description	Reference	Status
2008-10-15	Crx	cone-rod homeobox	Crx	cone-rod homeobox containing gene	Nomenclature updated to reflect human and mouse nomenclature	1299863	APPROVED
2008-02-22	Crx	cone-rod homeobox containing gene	Crx	cone-rod homeobox protein	Nomenclature updated to reflect human and mouse nomenclature	1299863	APPROVED
2005-01-20	Crx	cone-rod homeobox protein			Symbol and Name status set to approved	1299863	APPROVED
2002-08-07	Crx	cone-rod homeobox protein			Symbol and Name status set to provisional	70820	PROVISIONAL

RGD Curation Notes

Note Type	Note	Reference
gene_expression	mRNA levels in the rat retina were constant under a daily light-dark cycle	632541

Gene Annotator (Functional Annotation) unavailable	Gene Annotator (Annotation Distribution) unavailable	Variant Visualizer (Genomic Variants) unavailble Variant Visualizer (Genomic Variants) unavailable
Gene Annotator (Functional Annotation)	Gene Annotator (Annotation Distribution)	Variant Visualizer (Genomic Variants)

InterViewer (Protein-Protein Interactions) unavailable	Gviewer (Genome Viewer) unavailable	Variant Visualizer (Damaging Variants) unavailble Variant Visualizer (Damaging Variants) unavailable
InterViewer (Protein-Protein Interactions)	GViewer (Genome Viewer)	Variant Visualizer (Damaging Variants)

Gene Annotator (Annotation Comparison) unavailable	OLGA (Gene List Generator) unavailable
Gene Annotator (Annotation Comparison)	OLGA (Gene List Generator)	Excel (Download)

MOET (Multi-Ontology Enrichement) unavailable	GOLF (Gene-Ortholog Location Finder) unavailable
MOET (Multi-Ontology Enrichement)	GOLF (Gene-Ortholog Location Finder)

Imported Disease Annotations - ClinVar

Imported Disease Annotations - CTD

Imported Disease Annotations - MGI

Imported Disease Annotations - OMIM

RGD Manual Annotations

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