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Gene: Cdx2 (caudal type homeo box 2) Rattus norvegicus

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Symbol:

Cdx2

Name:

caudal type homeo box 2

RGD ID:

621234

Description:

Enables DNA-binding transcription factor activity and double-stranded DNA binding activity. Involved in positive regulation of DNA-templated transcription and positive regulation of cell population proliferation. Located in nucleus. Orthologous to human CDX2 (caudal type homeobox 2); INTERACTS WITH 1,2-dimethylhydrazine; 2,3,7,8-tetrachlorodibenzodioxine; beta-naphthoflavone.

Type:

protein-coding

RefSeq Status:

PROVISIONAL

Previously known as:

homeobox protein CDX-2

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):	CDX2 (caudal type homeobox 2)	HGNC	EggNOG, Ensembl, HomoloGene, Inparanoid, NCBI, OMA, OrthoDB, OrthoMCL, Panther, Treefam
Mus musculus (house mouse):	Cdx2 (caudal type homeobox 2)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Chinchilla lanigera (long-tailed chinchilla):	Cdx2 (caudal type homeobox 2)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Pan paniscus (bonobo/pygmy chimpanzee):	CDX2 (caudal type homeobox 2)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Canis lupus familiaris (dog):	CDX2 (caudal type homeobox 2)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Ictidomys tridecemlineatus (thirteen-lined ground squirrel):	Cdx2 (caudal type homeobox 2)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Sus scrofa (pig):	CDX2 (caudal type homeobox 2)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Chlorocebus sabaeus (green monkey):	CDX2 (caudal type homeobox 2)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Heterocephalus glaber (naked mole-rat):	Cdx2 (caudal type homeobox 2)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Alliance orthologs ³
Homo sapiens (human):	CDX2 (caudal type homeobox 2)	Alliance	DIOPT (Ensembl Compara\|HGNC\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Mus musculus (house mouse):	Cdx2 (caudal type homeobox 2)	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Danio rerio (zebrafish):	cdx1b (caudal type homeobox 1 b)	Alliance	DIOPT (InParanoid\|OMA\|OrthoInspector\|PANTHER\|SonicParanoid)
Drosophila melanogaster (fruit fly):	cad	Alliance	DIOPT (InParanoid\|OrthoFinder\|OrthoInspector\|PANTHER\|SonicParanoid)
Caenorhabditis elegans (roundworm):	pal-1	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|OrthoFinder\|OrthoInspector\|PANTHER\|SonicParanoid)
Xenopus tropicalis (tropical clawed frog):	cdx1	Alliance	DIOPT (InParanoid\|OrthoInspector\|PANTHER\|SonicParanoid)

Latest Assembly:

GRCr8 - GRCr8 Assembly

Position:

Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCr8	12	12,762,769 - 12,769,246 (+)	NCBI		GRCr8
mRatBN7.2	12	7,726,798 - 7,733,142 (+)	NCBI	mRatBN7.2	mRatBN7.2
mRatBN7.2 Ensembl	12	7,726,798 - 7,733,142 (+)	Ensembl		mRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx	12	8,411,731 - 8,418,073 (+)	NCBI	Rnor_SHR	UTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0	12	9,034,882 - 9,041,224 (+)	NCBI	Rnor_SHRSP	UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0	12	8,062,897 - 8,069,239 (+)	NCBI	Rnor_WKY	UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0	12	9,464,026 - 9,470,565 (+)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_6.0 Ensembl	12	9,464,026 - 9,470,565 (+)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_5.0	12	11,578,762 - 11,585,434 (+)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	12	8,296,103 - 8,303,643 (+)	NCBI	RGSC3.4	RGSC_v3.4	rn4	RGSC3.4
RGSC_v3.1	12	8,326,030 - 8,333,571 (+)	NCBI
Celera	12	9,464,881 - 9,471,223 (+)	NCBI		Celera
Cytogenetic Map	12	p11	NCBI

JBrowse:

View Region in Genome Browser (JBrowse)

Model

Annotation Click to see Annotation Detail View

Disease Annotations Click to see Annotation Detail View

Adenomatous Polyps (ISO)

Anorectal Malformations (ISO)

Barrett's esophagus (ISO)

caudal regression syndrome (ISO)

Colonic Neoplasms (ISO)

Ectromelia (ISO)

pre-malignant neoplasm (ISO)

Stomach Neoplasms (ISO)

Gene-Chemical Interaction Annotations Click to see Annotation Detail View

1,2-dimethylhydrazine (EXP,ISO)

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

2-palmitoylglycerol (ISO)

3-\{1-[3-(dimethylamino)propyl]-1H-indol-3-yl\}-4-(1H-indol-3-yl)-1H-pyrrole-2,5-dione (ISO)

3-methyladenine (ISO)

4,4'-sulfonyldiphenol (ISO)

5-aza-2'-deoxycytidine (ISO)

5-fluorouracil (ISO)

acetic acid (ISO)

acetic acid [2-[[(5-nitro-2-thiazolyl)amino]-oxomethyl]phenyl] ester (ISO)

amosite asbestos (ISO)

arsenous acid (ISO)

benzo[a]pyrene (ISO)

benzo[e]pyrene (ISO)

beta-naphthoflavone (EXP)

bis(2-ethylhexyl) phthalate (ISO)

bisphenol A (EXP,ISO)

bromochloroacetic acid (ISO)

CGP 52608 (ISO)

chenodeoxycholic acid (ISO)

choline (ISO)

crocidolite asbestos (ISO)

curcumin (EXP,ISO)

dextran sulfate (ISO)

diarsenic trioxide (ISO)

flavonoids (EXP)

folic acid (ISO)

furan (EXP)

gentamycin (EXP)

GS-441524 (ISO)

hydrogen peroxide (ISO)

indole-3-methanol (ISO)

L-methionine (ISO)

lipopolysaccharide (ISO)

LY294002 (EXP)

methapyrilene (ISO)

methyl methanesulfonate (ISO)

methylmercury chloride (EXP)

N-methyl-4-phenylpyridinium (ISO)

N-nitrosodiethylamine (EXP)

nitric oxide (ISO)

Octicizer (ISO)

paracetamol (EXP)

perfluorooctane-1-sulfonic acid (EXP)

phenytoin (EXP)

poly(I:C) (ISO)

remdesivir (ISO)

retinyl acetate (ISO)

SB 431542 (ISO)

serpentine asbestos (ISO)

silibinin (EXP)

sirolimus (ISO)

Theaflavin 3,3'-digallate (ISO)

titanium dioxide (ISO)

trichloroethene (EXP)

trichostatin A (ISO)

valproic acid (ISO)

Gene Ontology Annotations Click to see Annotation Detail View

Biological Process

anterior/posterior axis specification (IBA)

anterior/posterior pattern specification (IEA,ISO)

blastocyst development (IEA,ISO)

blood vessel development (IEA,ISO)

cell differentiation (IBA)

digestive tract development (IBA)

embryonic pattern specification (IBA)

endosome to lysosome transport (IEA,ISO)

establishment or maintenance of epithelial cell apical/basal polarity (IEA,ISO)

intestinal epithelial cell differentiation (IEA,ISO)

labyrinthine layer development (IEA,ISO)

negative regulation of transcription by RNA polymerase II (IEA,ISO)

pattern specification process (IEA,ISO)

placenta development (IEA,ISO)

positive regulation of cell differentiation (IEA,ISO)

positive regulation of cell population proliferation (IDA)

positive regulation of DNA-templated transcription (IDA)

positive regulation of transcription by RNA polymerase II (IEA,ISO)

regulation of DNA-templated transcription (IEA)

regulation of somitogenesis (IEA,ISO)

regulation of transcription by RNA polymerase II (IBA,IEA,ISO)

somatic stem cell population maintenance (IEA,ISO)

stem cell differentiation (IEA,ISO)

trophectodermal cell differentiation (IEA,ISO)

Cellular Component

condensed nuclear chromosome (IEA,ISO)

nucleoplasm (IEA,ISO)

nucleus (IBA,IDA,IEA,ISO)

protein-containing complex (IEA,ISO)

transcription repressor complex (IEA,ISO)

Molecular Function

DNA binding (IEA)

DNA-binding transcription factor activity (IBA,IDA,IEA,ISO)

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

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

double-stranded DNA binding (IDA)

methyl-CpG binding (IEA,ISO)

protein binding (ISO)

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

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

sequence-specific DNA binding (IEA,ISO)

sequence-specific double-stranded DNA binding (IEA,ISO)

References

References - curated

#	Reference Title	Reference Citation
1.	Homeosis and intestinal tumours in Cdx2 mutant mice.	Chawengsaksophak K, etal., Nature 1997 Mar 6;386(6620):84-7.
2.	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.
3.	Rat ISS GO annotations from GOA human gene data--August 2006	GOA data from the GO Consortium
4.	AGR2 gene function requires a unique endoplasmic reticulum localization motif.	Gupta A, etal., J Biol Chem. 2012 Feb 10;287(7):4773-82. doi: 10.1074/jbc.M111.301531. Epub 2011 Dec 19.
5.	Rat ISS GO annotations from MGI mouse gene data--August 2006	MGD data from the GO Consortium
6.	Electronic Transfer of LocusLink and RefSeq Data	NCBI rat LocusLink and RefSeq merged data July 26, 2002
7.	GOA pipeline	RGD automated data pipeline
8.	Data Import for Chemical-Gene Interactions	RGD automated import pipeline for gene-chemical interactions
9.	CDX2, COX2 and MUC2 expressions in Barrett's esophagus: can they be useful in determination of the dysplasia?	Turkmen IC, etal., Turk Patoloji Derg. 2012;28(3):251-8. doi: 10.5146/tjpath.2012.01132.
10.	Heparin-binding EGF-like growth factor gene transcription regulated by Cdx2 in the intestinal epithelium.	Uesaka T, etal., Am J Physiol Gastrointest Liver Physiol 2002 Oct;283(4):G840-7.

Additional References at PubMed

PMID:11959827	PMID:15019784	PMID:15509711	PMID:15677472	PMID:15788452	PMID:16239403	PMID:16325584	PMID:16396910	PMID:17138661	PMID:17212918	PMID:17347684	PMID:17404613
PMID:17417665	PMID:18313392	PMID:18423437	PMID:19664209	PMID:19796622	PMID:19853565	PMID:20404091	PMID:20551175	PMID:20676102	PMID:21530438	PMID:22015720	PMID:22190642
PMID:22529382	PMID:22573614	PMID:22948967	PMID:23824537	PMID:24036311	PMID:24268575	PMID:24315442	PMID:25397698	PMID:26268420	PMID:28473536

Genomics

Comparative Map Data

Cdx2
(Rattus norvegicus - Norway rat)

Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCr8	12	12,762,769 - 12,769,246 (+)	NCBI		GRCr8
mRatBN7.2	12	7,726,798 - 7,733,142 (+)	NCBI	mRatBN7.2	mRatBN7.2
mRatBN7.2 Ensembl	12	7,726,798 - 7,733,142 (+)	Ensembl		mRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx	12	8,411,731 - 8,418,073 (+)	NCBI	Rnor_SHR	UTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0	12	9,034,882 - 9,041,224 (+)	NCBI	Rnor_SHRSP	UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0	12	8,062,897 - 8,069,239 (+)	NCBI	Rnor_WKY	UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0	12	9,464,026 - 9,470,565 (+)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_6.0 Ensembl	12	9,464,026 - 9,470,565 (+)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_5.0	12	11,578,762 - 11,585,434 (+)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	12	8,296,103 - 8,303,643 (+)	NCBI	RGSC3.4	RGSC_v3.4	rn4	RGSC3.4
RGSC_v3.1	12	8,326,030 - 8,333,571 (+)	NCBI
Celera	12	9,464,881 - 9,471,223 (+)	NCBI		Celera
Cytogenetic Map	12	p11	NCBI

CDX2
(Homo sapiens - human)

Human Assembly	Chr	Position (strand)	Source	Genome Browsers
Human Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCh38	13	27,960,918 - 27,969,315 (-)	NCBI	GRCh38	GRCh38	hg38	GRCh38
GRCh38.p14 Ensembl	13	27,960,918 - 27,969,315 (-)	Ensembl	GRCh38		hg38	GRCh38
GRCh37	13	28,535,055 - 28,543,452 (-)	NCBI	GRCh37	GRCh37	hg19	GRCh37
Build 36	13	27,434,278 - 27,441,317 (-)	NCBI	NCBI36	Build 36	hg18	NCBI36
Build 34	13	27,434,278 - 27,441,317	NCBI
Celera	13	9,611,324 - 9,618,360 (-)	NCBI		Celera
Cytogenetic Map	13	q12.2	NCBI
HuRef	13	9,356,889 - 9,364,186 (-)	NCBI		HuRef
CHM1_1	13	28,504,663 - 28,511,974 (-)	NCBI		CHM1_1
T2T-CHM13v2.0	13	27,182,310 - 27,190,703 (-)	NCBI		T2T-CHM13v2.0

Cdx2
(Mus musculus - house mouse)

Mouse Assembly	Chr	Position (strand)	Source	Genome Browsers
Mouse Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCm39	5	147,237,710 - 147,244,059 (-)	NCBI	GRCm39	GRCm39	mm39
GRCm39 Ensembl	5	147,237,615 - 147,244,080 (-)	Ensembl		GRCm39 Ensembl
GRCm38	5	147,300,900 - 147,307,249 (-)	NCBI	GRCm38	GRCm38	mm10	GRCm38
GRCm38.p6 Ensembl	5	147,300,805 - 147,307,270 (-)	Ensembl	GRCm38		mm10	GRCm38
MGSCv37	5	148,112,476 - 148,118,825 (-)	NCBI	GRCm37	MGSCv37	mm9	NCBIm37
MGSCv36	5	147,611,249 - 147,617,598 (-)	NCBI		MGSCv36	mm8
Celera	5	145,292,162 - 145,298,512 (-)	NCBI		Celera
Cytogenetic Map	5	G3	NCBI
cM Map	5	86.86	NCBI

Cdx2
(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	NW_004955497	7,316,372 - 7,321,627 (-)	NCBI	ChiLan1.0	ChiLan1.0

CDX2
(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	14	27,548,318 - 27,556,707 (-)	NCBI		NHGRI_mPanPan1-v2
NHGRI_mPanPan1	13	18,652,989 - 18,661,365 (-)	NCBI		NHGRI_mPanPan1
Mhudiblu_PPA_v0	13	9,241,856 - 9,250,297 (-)	NCBI	Mhudiblu_PPA_v0	Mhudiblu_PPA_v0	panPan3
PanPan1.1	13	27,585,194 - 27,593,632 (-)	NCBI	panpan1.1	PanPan1.1	panPan2
PanPan1.1 Ensembl	13	27,586,340 - 27,593,632 (-)	Ensembl	panpan1.1		panPan2

CDX2
(Canis lupus familiaris - dog)

Dog Assembly	Chr	Position (strand)	Source	Genome Browsers
Dog Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
CanFam3.1	25	11,701,134 - 11,707,883 (+)	NCBI	CanFam3.1	CanFam3.1	canFam3	CanFam3.1
CanFam3.1 Ensembl	25	11,700,779 - 11,707,127 (+)	Ensembl	CanFam3.1		canFam3	CanFam3.1
Dog10K_Boxer_Tasha	25	11,764,347 - 11,771,858 (+)	NCBI		Dog10K_Boxer_Tasha
ROS_Cfam_1.0	25	11,830,047 - 11,837,557 (+)	NCBI		ROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl	25	11,830,188 - 11,836,088 (+)	Ensembl		ROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1	25	11,724,391 - 11,732,134 (+)	NCBI		UMICH_Zoey_3.1
UNSW_CanFamBas_1.0	25	11,716,837 - 11,724,610 (+)	NCBI		UNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0	25	11,761,010 - 11,768,541 (+)	NCBI		UU_Cfam_GSD_1.0

Cdx2
(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_024404945	172,810,950 - 172,815,170 (+)	NCBI		HiC_Itri_2
SpeTri2.0	NW_004936472	23,137,936 - 23,141,205 (-)	NCBI	SpeTri2.0	SpeTri2.0		SpeTri2.0

CDX2
(Sus scrofa - pig)

Pig Assembly	Chr	Position (strand)	Source	Genome Browsers
Pig Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
Sscrofa11.1 Ensembl	11	5,339,716 - 5,346,057 (-)	Ensembl	Sscrofa11.1		susScr11	Sscrofa11.1
Sscrofa11.1	11	5,339,727 - 5,346,081 (-)	NCBI	Sscrofa11.1	Sscrofa11.1	susScr11	Sscrofa11.1
Sscrofa10.2	11	5,113,685 - 5,120,021 (+)	NCBI	Sscrofa10.2	Sscrofa10.2	susScr3

CDX2
(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	3	7,080,142 - 7,088,010 (-)	NCBI	ChlSab1.1	ChlSab1.1	chlSab2
ChlSab1.1 Ensembl	3	7,078,503 - 7,087,285 (-)	Ensembl	ChlSab1.1	ChlSab1.1 Ensembl	chlSab2
Vero_WHO_p1.0	NW_023666057	37,301,589 - 37,309,900 (+)	NCBI	Vero_WHO_p1.0	Vero_WHO_p1.0

Cdx2
(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_004624776	10,551,503 - 10,556,845 (+)	Ensembl	HetGla_female_1.0	HetGla_female_1.0 Ensembl	hetGla2
HetGla 1.0	NW_004624776	10,551,503 - 10,556,987 (+)	NCBI	HetGla_female_1.0	HetGla 1.0	hetGla2

Variants

Variants in Cdx2
16 total Variants

miRNA Target Status (No longer updated)

Predicted Target Of

	Summary Value
Count of predictions:	111
Count of miRNA genes:	99
Interacting mature miRNAs:	104
Transcripts:	ENSRNOT00000048188
Prediction methods:	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 (GRCr8)

The following QTLs overlap with this region.

RGD ID	Symbol	Name	LOD	P Value	Trait	Sub Trait	Chr	Start	Stop	Species
2312418	Kidm41	Kidney mass QTL 41	3.7	0.0001	kidney mass (VT:0002707)	single kidney wet weight to body weight ratio (CMO:0000622)	12	1	19611090	Rat
8552964	Pigfal17	Plasma insulin-like growth factor 1 level QTL 17	3.5		blood insulin-like growth factor amount (VT:0010479)	plasma insulin-like growth factor 1 level (CMO:0001299)	12	5564495	46669029	Rat
7411641	Foco19	Food consumption QTL 19	27.7	0.001	eating behavior trait (VT:0001431)	feed conversion ratio (CMO:0001312)	12	5564495	46669029	Rat
9590147	Scort7	Serum corticosterone level QTL 7	13.61	0.001	blood corticosterone amount (VT:0005345)	plasma corticosterone level (CMO:0001173)	12	1	42110980	Rat
8552912	Pigfal6	Plasma insulin-like growth factor 1 level QTL 6	5		blood insulin-like growth factor amount (VT:0010479)	plasma insulin-like growth factor 1 level (CMO:0001299)	12	5564498	46669029	Rat
10059594	Kidm46	Kidney mass QTL 46	3.79	0.025	kidney mass (VT:0002707)	both kidneys wet weight to body weight ratio (CMO:0000340)	12	6107579	46669029	Rat
1581516	Cm56	Cardiac mass QTL 56	4.2	0.05	heart left ventricle mass (VT:0007031)	heart left ventricle weight to body weight ratio (CMO:0000530)	12	1	29333307	Rat
9590086	Insglur6	Insulin/glucose ratio QTL 6	18.97	0.001	blood insulin amount (VT:0001560)	calculated plasma insulin level (CMO:0002170)	12	1	42110980	Rat
8552918	Pigfal7	Plasma insulin-like growth factor 1 level QTL 7			blood insulin-like growth factor amount (VT:0010479)	plasma insulin-like growth factor 1 level (CMO:0001299)	12	5564495	46669029	Rat
6893681	Bw109	Body weight QTL 109	2.3	0.004	body mass (VT:0001259)	body weight (CMO:0000012)	12	1	23297788	Rat
1302792	Scl21	Serum cholesterol level QTL 21	3.8	0.0011	blood cholesterol amount (VT:0000180)	plasma total cholesterol level (CMO:0000585)	12	7196730	46669029	Rat
1300174	Bw15	Body weight QTL 15	2.93		body mass (VT:0001259)	body weight loss (CMO:0001399)	12	1	9318387	Rat
1598855	Bp294	Blood pressure QTL 294	3.5		arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	12	1	34851688	Rat
1600391	Edcs2	Endometrial carcinoma susceptibility QTL2	3.5	0.01	uterus morphology trait (VT:0001120)	percentage of study population developing endometrioid carcinoma during a period of time (CMO:0001759)	12	6833190	17870186	Rat
10755457	Coatc14	Coat color QTL 14		0.01759	coat/hair pigmentation trait (VT:0010463)	pigmented ventral coat/hair area to total ventral coat/hair area ratio (CMO:0001812)	12	1	22591684	Rat
724526	Uae3	Urinary albumin excretion QTL 3	4.9	0.0001	urine albumin amount (VT:0002871)	urine albumin excretion rate (CMO:0000757)	12	3906969	10373166	Rat
634351	Apr5	Acute phase response QTL 5	6.7		blood interleukin-6 amount (VT:0008595)	plasma interleukin-6 level (CMO:0001927)	12	1	44503507	Rat
8694179	Bw150	Body weight QTL 150	2.9	0.001	body mass (VT:0001259)	body weight gain (CMO:0000420)	12	1	42110980	Rat
634350	Apr4	Acute phase response QTL 4	6		orosomucoid 1 amount (VT:0010541)	plasma orosomucoid 1 level (CMO:0001467)	12	1172005	46172005	Rat
7411545	Bw128	Body weight QTL 128	5.2	0.001	body mass (VT:0001259)	body weight gain (CMO:0000420)	12	1	42110980	Rat
7411547	Bw129	Body weight QTL 129		0.001	body mass (VT:0001259)	body weight gain (CMO:0000420)	6	5564495	46669029	Rat
7387292	Kidm42	Kidney mass QTL 42	3.03	0.0004	kidney mass (VT:0002707)	left kidney wet weight (CMO:0000083)	12	1	36247923	Rat
737979	Pia22	Pristane induced arthritis QTL 22	53.1		joint integrity trait (VT:0010548)	joint inflammation composite score (CMO:0000919)	12	1	44465750	Rat
7411586	Foco5	Food consumption QTL 5	5.4	0.001	eating behavior trait (VT:0001431)	feed conversion ratio (CMO:0001312)	12	1	42110980	Rat
2303575	Insul14	Insulin level QTL 14	4		blood insulin amount (VT:0001560)	blood insulin level (CMO:0000349)	12	1	42450532	Rat
7411588	Foco6	Food consumption QTL 6		0.001	eating behavior trait (VT:0001431)	feed conversion ratio (CMO:0001312)	12	5564495	46669029	Rat
7243862	Mcs30	Mammary carcinoma susceptibility QTL 30	8.62		mammary gland integrity trait (VT:0010552)	mammary tumor number (CMO:0000343)	12	797729	8525593	Rat
2302042	Pia38	Pristane induced arthritis QTL 38	3.5	0.001	blood immunoglobulin amount (VT:0002460)	serum immunoglobulin G1 level (CMO:0002115)	12	1	44503507	Rat
7411595	Foco9	Food consumption QTL 9	4	0.001	eating behavior trait (VT:0001431)	feed conversion ratio (CMO:0001312)	12	1	42110980	Rat
7411597	Foco10	Food consumption QTL 10		0.001	eating behavior trait (VT:0001431)	feed conversion ratio (CMO:0001312)	12	5564495	46669029	Rat
7411660	Foco28	Food consumption QTL 28	10.9	0.001	eating behavior trait (VT:0001431)	feed conversion ratio (CMO:0001312)	12	1	42110980	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.

Download All Expressed Objects for this Gene

alimentary part of gastrointestinal system	circulatory system	ectoderm	endocrine system	endoderm	exocrine system	hemolymphoid system	hepatobiliary system	integumental system	mesenchyme	mesoderm	nervous system	renal system	reproductive system	respiratory system
9	5	21	44	41	24	23	24	6	84	37	10	14	27	17

Sequence

Nucleotide Sequences


RefSeq Transcripts	NM_023963	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_008768999	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_063271647	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
GenBank Nucleotide	AF104031	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	AJ278466	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	AJ278467	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	CH474012	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	JAXUCZ010000012	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles

Ensembl Acc Id:

ENSRNOT00000048188 ⟹ ENSRNOP00000045045

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2 Ensembl	12	7,726,798 - 7,733,142 (+)	Ensembl
Rnor_6.0 Ensembl	12	9,464,026 - 9,470,565 (+)	Ensembl

RefSeq Acc Id:

NM_023963 ⟹ NP_076453

RefSeq Status:

PROVISIONAL

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
GRCr8	12	12,762,904 - 12,769,246 (+)	NCBI
mRatBN7.2	12	7,726,798 - 7,733,142 (+)	NCBI
Rnor_6.0	12	9,464,026 - 9,470,565 (+)	NCBI
Rnor_5.0	12	11,578,762 - 11,585,434 (+)	NCBI
RGSC_v3.4	12	8,296,103 - 8,303,643 (+)	RGD
Celera	12	9,464,881 - 9,471,223 (+)	RGD

Sequence:

show sequence

CAGTAATCAGCTACCTTTATCCCTAGCCCCCTGCGCCCCGCGCCCCTGGCAGCCTTCAACGCTT
GTCCCCAGGCAGTATGGTGAGGTCTGCTCTGGGTCCCTCGCCACCATGTACGTGAGCTACCTTC
TGGACAAGGACGTGAGCATGTACCCTAGCTCCGTGCGCCACTCCGGCGGCCTCAACCTGGCGCC
GCAGAACTTTGTCAGTCCCCCGCAGTACCCGGACTACGGTGGTTACCACGTGGCGGCCGCCGCT
GCTGCGGCGGCGAACTTGGACAGCGCTCAGTCCCCAGGGCCATCCTGGCCCACCGCGTACGGCG
CCCCTCTCCGCGAGGACTGGAATGGCTACGCACCCGGGGGCGCTGCCGCAGCCAACGCGGTAGC
CCACGGCCTCAATGGTGGCTCCCCGGCCGCCGCTATGGGCTACAGCAGCCCCGCCGAATACCAC
GCACACCATCACCCGCATCATCACCCTCACCATCCGGCCGCTGCGCCGTCCTGCGCCTCCGGAT
TGCTGCAGACGCTCAACCCCGGCCCTCCAGGGCCCGCAGCCACCGCCGCCGCAGAACAGCTGTC
CCCCAGCGGCCAGCGGCGAAACCTTTGTGAATGGATGAGGAAGCCAGCTCAGCCGTCCCTAGGA
AGCCAAGTGAAAACCAGGACGAAAGACAAATACCGGGTGGTGTACACAGACCATCAGCGGCTGG
AGCTGGAGAAGGAATTTCACTATAGTCGATACATCACCATCAGGAGGAAAGCTGAGTTGGCCGC
CACACTCGGGCTCTCGGAGAGGCAGGTTAAAATTTGGTTTCAGAACCGCAGAGCCAAGGAAAGG
AAAATCAACAAAAAGAAGTTGCAACAGCAGCAGCAGCAGCAGCCTCCCGCACCGCCGCCACCAC
AGCCTTCCCAGCCTCAGTCCGGTGCATTGCGGAGCGTGCCGGAGCCCTTGAGTCCTGTGACCTC
CTTGCAAGGCTCGGTGCCTGGTTCTGTTCCTGGGGTTCTGGGGCCAGCTGGAGGGGTTTTAAAC
TCCACTGTCACCCAGTGACCCCTCCTGTGGCCTGAAGTGGCGGTGGCTCAGCAATCCCAGGCTG
AGCCATGAGGAGCACGGACACTGTGAGAAACCTCAGAAGAGACCCCTCTTCTCCTACCCACAAA
CAACACCTACAGATGGAGATCGAGGACAGAGGGCAGAAGACGAGTGGGATTGTGGACCTCAGGA
GAAGATATGGTTTAGATTTTTTTTTTAAATTTTTCCCGTTCTGACTTTTCCTGTCAGCAAAGGA
AGTGATTCCTGGGGCTTCTTCATTCATGCTCCTTGCCAGGACTGGCTACAGGCACCAAGCTTTC
AGCTTCTTTTGCCTCAGCTCTTTGCCTCCAAAAAAAAAGAGACTGTATTTCTGTTTGGAGCTGA
GGAGAGATAGAGTGTGAGGCCGGAGTTGGGGGTTGGGGCGGGCGGGGCAAGCAACACTTGAGCC
AAGATGGCTGTTTCCTGCTGACTGCTTTCTGAGAACCAGCTGGCCATCCTGCCTCAGGGGCAGG
GACTGTTGAAACTTACTTGAGCCAGAGGCAGCTAAGACAGAAAGCTGGATTGACCGAAGTCTGC
AGAACCTTCCCCCCCTCAGGTGGTCTGTGCTTTCTTCTCTGTCCACAGATCAGGAAGGGGTGGT
GGGTTCAGGGACCATCGTGTGAGAGGAGGGGGGGTGGTTAGCCAACTCCAGGCCCCTGCGACAA
GGGCTTGTTTAGAAAGCCTGTCACCAGAGCTGCTGTAGGCTGAATGTATGTCTGTGTCGTAAAT
GCCAGAGCCAACCTGGACTTCCTGTCCCTTCCCTCGTCTTTGGCTGAAGAAGACCGGAATTGCT
GCTGTTCGAGTCACTGGTCTGTGTAACAAGCCAAACAAGCCTTTTAAAAAGCCTTCTGGATCCA
TGGGTAGAGAGAGAGAGTGAGAGACGTTGTATGGTGAAGGGAAGTGGGGAGGGGGATATCTGAA
CACAGTTGACTTTTATTTTGTAAAAAGACAAAAGATATAAAAGGAGCTTTACAGATTTCAGATC
CTAAAAAAAAAAAAAAAAAAAAAA

hide sequence

RefSeq Acc Id:

XM_063271647 ⟹ XP_063127717

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
GRCr8	12	12,762,769 - 12,769,240 (+)	NCBI

Protein Sequences


Protein RefSeqs	NP_076453	(Get FASTA)	NCBI Sequence Viewer
	XP_063127717	(Get FASTA)	NCBI Sequence Viewer
GenBank Protein	AAD17915	(Get FASTA)	NCBI Sequence Viewer
	CAC03735	(Get FASTA)	NCBI Sequence Viewer
	EDL89564	(Get FASTA)	NCBI Sequence Viewer
Ensembl Protein	ENSRNOP00000045045
	ENSRNOP00000045045.4

RefSeq Acc Id:

NP_076453 ⟸ NM_023963

- UniProtKB:

Q9ESV7 (UniProtKB/TrEMBL), F1M7G8 (UniProtKB/TrEMBL), A0A9K3Y7D3 (UniProtKB/TrEMBL)

- Sequence:

show sequence

MYVSYLLDKDVSMYPSSVRHSGGLNLAPQNFVSPPQYPDYGGYHVAAAAAAAANLDSAQSPGPS
WPTAYGAPLREDWNGYAPGGAAAANAVAHGLNGGSPAAAMGYSSPAEYHAHHHPHHHPHHPAAA
PSCASGLLQTLNPGPPGPAATAAAEQLSPSGQRRNLCEWMRKPAQPSLGSQVKTRTKDKYRVVY
TDHQRLELEKEFHYSRYITIRRKAELAATLGLSERQVKIWFQNRRAKERKINKKKLQQQQQQQP
PAPPPPQPSQPQSGALRSVPEPLSPVTSLQGSVPGSVPGVLGPAGGVLNSTVTQ

hide sequence

Ensembl Acc Id:

ENSRNOP00000045045 ⟸ ENSRNOT00000048188

RefSeq Acc Id:	XP_063127717 ⟸ XM_063271647
- Peptide Label:	isoform X1

Protein Domains

Homeobox

Protein Structures

Name	Modeler	Protein Id	AA Range	Protein Structure
AF-Q9ESV7-F1-model_v2	AlphaFold	Q9ESV7	1-310	view protein structure

Transcriptome

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

Promoters

RGD ID:

13698402

Promoter ID:

EPDNEW_R8927

Type:

initiation region

Name:

Cdx2_1

Description:

caudal type homeo box 2

SO ACC ID:

SO:0000170

Source:

EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)

Experiment Methods:

Single-end sequencing.

Position:

Rat Assembly	Chr	Position (strand)	Source
Rnor_6.0	12	9,463,987 - 9,464,047	EPDNEW

Additional Information

External Database Links

Database	Acc Id	Source(s)
AGR Gene	RGD:621234	AgrOrtholog
BioCyc Gene	G2FUF-20116	BioCyc
Ensembl Genes	ENSRNOG00000032759	Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript	ENSRNOT00000048188	ENTREZGENE
	ENSRNOT00000048188.6	UniProtKB/TrEMBL
Gene3D-CATH	Homeodomain-like	UniProtKB/TrEMBL
InterPro	Caudal_activation_dom	UniProtKB/TrEMBL
	Caudal_homeobox	UniProtKB/TrEMBL
	Homeobox_CS	UniProtKB/TrEMBL
	Homeobox_metazoa	UniProtKB/TrEMBL
	Homeodomain	UniProtKB/TrEMBL
	Homeodomain-like	UniProtKB/TrEMBL
	HTH_motif	UniProtKB/TrEMBL
KEGG Report	rno:66019	UniProtKB/TrEMBL
NCBI Gene	66019	ENTREZGENE
PANTHER	HOMEOBOX PROTEIN CDX	UniProtKB/TrEMBL
	HOMEOBOX PROTEIN CDX-2	UniProtKB/TrEMBL
Pfam	Caudal_act	UniProtKB/TrEMBL
	Homeobox	UniProtKB/TrEMBL
PhenoGen	Cdx2	PhenoGen
PRINTS	HOMEOBOX	UniProtKB/TrEMBL
	HTHREPRESSR	UniProtKB/TrEMBL
PROSITE	HOMEOBOX_1	UniProtKB/TrEMBL
	HOMEOBOX_2	UniProtKB/TrEMBL
RatGTEx	ENSRNOG00000032759	RatGTEx
SMART	HOX	UniProtKB/TrEMBL
Superfamily-SCOP	Homeodomain_like	UniProtKB/TrEMBL
UniProt	A0A9K3Y7D3	ENTREZGENE, UniProtKB/TrEMBL
	F1M7G8	ENTREZGENE
	Q9ESV7	ENTREZGENE, UniProtKB/TrEMBL
UniProt Secondary	F1M7G8	UniProtKB/TrEMBL

Nomenclature History

Date	Current Symbol	Current Name	Previous Symbol	Previous Name	Description	Reference	Status
2005-01-20	Cdx2	caudal type homeo box 2			Symbol and Name status set to approved	1299863	APPROVED
2002-08-07	Cdx2	caudal type homeo box 2			Symbol and Name status set to provisional	70820	PROVISIONAL

RGD Curation Notes

Note Type	Note	Reference
gene_expression	expression is restricted to the intestine	625733
gene_physical_interaction	interacts with DNA elements that have an AT-rich consensus sequence (TTTAC/T)	625733
gene_process	induces expression of heparin-binding EGF-like growth factor (HB-EGF)	625733
gene_process	activates transcription of heparin-binding EGF-like growth factor (HB-EGF) in intestinal epithetial cells (IEC)-6	625733
gene_process	activates several genes that are not involved in cell proliferation, including sucrase-isomaltase (SI), lactase-phlorizin hydrolase, lactase, apolipoprotein B, carbonic anhydrase 1, calbindin-D9K, and clusterin	625733
gene_process	mediates cell proliferation and migration by activation of gene transcription	625733
gene_product	member of the caudal-related homeobox gene family	625733
gene_regulation	function inhibited partially by an EGF receptor-specific tyrosine kinase inhibitor, PD-153035	625733

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)

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