Shox2 (short stature homeobox 2) - Rat Genome Database

Name: Shox2
Creator: Rat Genome Database
License: Creative Commons CC BY 4.0
Keywords: Rat Gene RGD Genome

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Gene: Shox2 (short stature homeobox 2) Rattus norvegicus

Analyze

Symbol:

Shox2

Name:

short stature homeobox 2

RGD ID:

3674

Description:

Predicted to enable DNA-binding transcription factor activity, RNA polymerase II-specific and sequence-specific double-stranded DNA binding activity. Predicted to be involved in several processes, including heart development; positive regulation of cell development; and regulation of branching morphogenesis of a nerve. Predicted to act upstream of or within several processes, including positive regulation of cell population proliferation; regulation of transcription by RNA polymerase II; and skeletal system development. Predicted to be active in nucleus. Human ortholog(s) of this gene implicated in lung cancer. Orthologous to human SHOX2 (short stature homeobox 2); INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; 2,3,7,8-Tetrachlorodibenzofuran; 3-chloropropane-1,2-diol.

Type:

protein-coding

RefSeq Status:

VALIDATED

Previously known as:

paired family homeodomain protein Prx3; short stature homeobox protein 2

RGD Orthologs

Human

Mouse

Chinchilla

Bonobo

Dog

Squirrel

Pig

Green Monkey

Naked Mole-Rat

Alliance Genes

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):	SHOX2 (short stature homeobox 2)	HGNC	Ensembl, HomoloGene, Inparanoid, NCBI, OMA, OrthoDB, OrthoMCL, Treefam
Mus musculus (house mouse):	Shox2 (short stature homeobox 2)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Chinchilla lanigera (long-tailed chinchilla):	Shox2 (short stature homeobox 2)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Pan paniscus (bonobo/pygmy chimpanzee):	SHOX2 (short stature homeobox 2)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Canis lupus familiaris (dog):	SHOX2 (short stature homeobox 2)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Ictidomys tridecemlineatus (thirteen-lined ground squirrel):	Shox2 (short stature homeobox 2)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Sus scrofa (pig):	SHOX2 (short stature homeobox 2)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Chlorocebus sabaeus (green monkey):	SHOX2 (short stature homeobox 2)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Heterocephalus glaber (naked mole-rat):	Shox2 (short stature homeobox 2)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Alliance orthologs ³
Mus musculus (house mouse):	Shox2 (short stature homeobox 2)	Alliance	DIOPT (Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Homo sapiens (human):	SHOX2 (short stature homeobox 2)	Alliance	DIOPT (Ensembl Compara\|HGNC\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Danio rerio (zebrafish):	shox2 (short stature homeobox 2)	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Drosophila melanogaster (fruit fly):	CG34367	Alliance	DIOPT (InParanoid\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)

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
mRatBN7.2	2	151,217,049 - 151,227,180 (-)	NCBI	mRatBN7.2	mRatBN7.2
mRatBN7.2 Ensembl	2	151,217,552 - 151,227,143 (-)	Ensembl		mRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx	2	158,353,974 - 158,363,583 (-)	NCBI	Rnor_SHR
UTH_Rnor_SHRSP_BbbUtx_1.0	2	156,404,472 - 156,414,073 (-)	NCBI	Rnor_SHRSP
UTH_Rnor_WKY_Bbb_1.0	2	151,037,220 - 151,046,824 (-)	NCBI	Rnor_WKY
Rnor_6.0	2	164,118,175 - 164,126,783 (-)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_6.0 Ensembl	2	164,118,191 - 164,126,783 (-)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_5.0	2	183,469,813 - 183,478,421 (-)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	2	156,881,044 - 156,889,653 (-)	NCBI	RGSC3.4	RGSC_v3.4	rn4	RGSC3.4
RGSC_v3.1	2	156,831,006 - 156,839,616 (-)	NCBI
Celera	2	145,597,026 - 145,605,637 (-)	NCBI		Celera
Cytogenetic Map	2	q31	NCBI

JBrowse:

View Region in Genome Browser (JBrowse)

Model

Annotation Click to see Annotation Detail View

Disease Annotations Click to see Annotation Detail View

cleft palate (ISO)

Leri-Weill dyschondrosteosis (ISS)

lung cancer (ISO)

Gene-Chemical Interaction Annotations Click to see Annotation Detail View

(S)-nicotine (ISO)

17beta-estradiol (ISO)

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

2,3,7,8-Tetrachlorodibenzofuran (EXP)

2-methylcholine (ISO)

3,4-methylenedioxymethamphetamine (ISO)

3-chloropropane-1,2-diol (EXP)

4,4'-sulfonyldiphenol (ISO)

5-aza-2'-deoxycytidine (ISO)

acetazolamide (ISO)

acrylamide (EXP)

aflatoxin B1 (ISO)

all-trans-retinoic acid (ISO)

ammonium chloride (EXP)

antirheumatic drug (ISO)

aristolochic acid A (ISO)

arsenite(3-) (ISO)

benzo[a]pyrene (ISO)

bisphenol A (EXP,ISO)

bisphenol F (ISO)

calcitriol (ISO)

cisplatin (ISO)

decabromodiphenyl ether (EXP)

dorsomorphin (ISO)

endosulfan (EXP)

ethanol (ISO)

flavonoids (EXP)

fulvestrant (ISO)

genistein (ISO)

gentamycin (EXP)

hydralazine (ISO)

methotrexate (ISO)

morphine (ISO)

nicotine (ISO)

oxaliplatin (EXP)

palbociclib (ISO)

paracetamol (EXP)

pyridaben (ISO)

resveratrol (ISO)

SB 431542 (ISO)

silver atom (ISO)

silver(0) (ISO)

sodium arsenite (ISO)

toluene (EXP)

topotecan (EXP)

triclosan (ISO)

undecane (EXP)

valproic acid (ISO)

vorinostat (ISO)

XL147 (ISO)

Gene Ontology Annotations Click to see Annotation Detail View

Biological Process

cardiac atrium morphogenesis (ISO)

cardiac pacemaker cell differentiation (ISO)

cardiac right atrium morphogenesis (IEA,ISO)

cartilage development involved in endochondral bone morphogenesis (IEA,ISO)

chondrocyte development (IEA,ISO)

chondrocyte differentiation (ISO)

embryonic digestive tract morphogenesis (IEA,ISO)

embryonic forelimb morphogenesis (IEA,ISO)

embryonic limb morphogenesis (ISO)

embryonic morphogenesis (ISO)

embryonic skeletal joint morphogenesis (IEA,ISO)

heart valve development (ISO)

mesenchymal cell proliferation (IEA,ISO)

muscle tissue morphogenesis (IEA,ISO)

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

osteoblast differentiation (IEA,ISO)

positive regulation of axonogenesis (IEA,ISO)

positive regulation of mesenchymal cell proliferation (IEA,ISO)

positive regulation of skeletal muscle fiber development (IEA,ISO)

positive regulation of smoothened signaling pathway (IEA,ISO)

positive regulation of stem cell proliferation (IEA,ISO)

positive regulation of transcription by RNA polymerase II (ISO)

regulation of branching morphogenesis of a nerve (IEA,ISO)

regulation of chondrocyte differentiation (IEA,ISO)

regulation of heart rate (IEA,ISO)

regulation of transcription by RNA polymerase II (IBA)

sinoatrial node cell development (IEA,ISO)

sinoatrial node development (ISO)

sinoatrial valve development (IEA,ISO)

smoothened signaling pathway (IEA,ISO)

stem cell proliferation (IEA,ISO)

Cellular Component

nucleus (IBA,IEA)

Molecular Function

DNA binding (IEA)

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

protein binding (ISO)

sequence-specific DNA binding (ISO)

sequence-specific double-stranded DNA binding (IBA)

References

References - curated

#	Reference Title	Reference Citation
1.	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.
2.	Rat ISS GO annotations from GOA human gene data--August 2006	GOA data from the GO Consortium
3.	Analysis of SHOX2 methylation as an aid to cytology in lung cancer diagnosis.	Ilse P, etal., Cancer Genomics Proteomics. 2014 Sep-Oct;11(5):251-8.
4.	Rat ISS GO annotations from MGI mouse gene data--August 2006	MGD data from the GO Consortium
5.	Electronic Transfer of LocusLink and RefSeq Data	NCBI rat LocusLink and RefSeq merged data July 26, 2002
6.	OMIM Disease Annotation Pipeline	OMIM Disease Annotation Pipeline
7.	Data Import for Chemical-Gene Interactions	RGD automated import pipeline for gene-chemical interactions
8.	Tentative Sequence Identification Numbers	Tentative Sequence Data IDs. TIGR Gene Index, Rat Data
9.	Shox2-deficient mice exhibit a rare type of incomplete clefting of the secondary palate.	Yu L, etal., Development. 2005 Oct;132(19):4397-406. Epub 2005 Sep 1.

Additional References at PubMed

PMID:9371788	PMID:16537395	PMID:17372176	PMID:17481601	PMID:18514492	PMID:21156168	PMID:22916278	PMID:23332764	PMID:26697824

Genomics

Comparative Map Data

Shox2
(Rattus norvegicus - Norway rat)

Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
mRatBN7.2	2	151,217,049 - 151,227,180 (-)	NCBI	mRatBN7.2	mRatBN7.2
mRatBN7.2 Ensembl	2	151,217,552 - 151,227,143 (-)	Ensembl		mRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx	2	158,353,974 - 158,363,583 (-)	NCBI	Rnor_SHR
UTH_Rnor_SHRSP_BbbUtx_1.0	2	156,404,472 - 156,414,073 (-)	NCBI	Rnor_SHRSP
UTH_Rnor_WKY_Bbb_1.0	2	151,037,220 - 151,046,824 (-)	NCBI	Rnor_WKY
Rnor_6.0	2	164,118,175 - 164,126,783 (-)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_6.0 Ensembl	2	164,118,191 - 164,126,783 (-)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_5.0	2	183,469,813 - 183,478,421 (-)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	2	156,881,044 - 156,889,653 (-)	NCBI	RGSC3.4	RGSC_v3.4	rn4	RGSC3.4
RGSC_v3.1	2	156,831,006 - 156,839,616 (-)	NCBI
Celera	2	145,597,026 - 145,605,637 (-)	NCBI		Celera
Cytogenetic Map	2	q31	NCBI

SHOX2
(Homo sapiens - human)

Human Assembly	Chr	Position (strand)	Source	Genome Browsers
Human Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCh38	3	158,095,905 - 158,106,420 (-)	NCBI	GRCh38	GRCh38	hg38	GRCh38
GRCh38.p13 Ensembl	3	158,095,905 - 158,106,420 (-)	Ensembl	GRCh38		hg38	GRCh38
GRCh37	3	157,813,694 - 157,824,209 (-)	NCBI	GRCh37	GRCh37	hg19	GRCh37
Build 36	3	159,296,494 - 159,306,630 (-)	NCBI	NCBI36	Build 36	hg18	NCBI36
Build 34	3	159,297,570 - 159,306,541	NCBI
Celera	3	156,237,551 - 156,247,714 (-)	NCBI		Celera
Cytogenetic Map	3	q25.32	NCBI
HuRef	3	155,210,551 - 155,220,711 (-)	NCBI		HuRef
CHM1_1	3	157,777,104 - 157,787,273 (-)	NCBI		CHM1_1
T2T-CHM13v2.0	3	160,870,630 - 160,881,158 (-)	NCBI		T2T-CHM13v2.0

Shox2
(Mus musculus - house mouse)

Mouse Assembly	Chr	Position (strand)	Source	Genome Browsers
Mouse Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCm39	3	66,879,056 - 66,889,104 (-)	NCBI	GRCm39	GRCm39	mm39
GRCm39 Ensembl	3	66,879,060 - 66,889,104 (-)	Ensembl		GRCm39 Ensembl
GRCm38	3	66,971,723 - 66,981,771 (-)	NCBI	GRCm38	GRCm38	mm10	GRCm38
GRCm38.p6 Ensembl	3	66,971,727 - 66,981,771 (-)	Ensembl	GRCm38		mm10	GRCm38
MGSCv37	3	66,777,188 - 66,785,693 (-)	NCBI	GRCm37	MGSCv37	mm9	NCBIm37
MGSCv36	3	67,061,195 - 67,069,700 (-)	NCBI		MGSCv36	mm8
Celera	3	67,108,915 - 67,117,391 (-)	NCBI		Celera
Cytogenetic Map	3	E1	NCBI
cM Map	3	30.76	NCBI

Shox2
(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_004955448	8,937,610 - 8,947,890 (-)	Ensembl	ChiLan1.0
ChiLan1.0	NW_004955448	8,937,656 - 8,947,890 (-)	NCBI	ChiLan1.0	ChiLan1.0

SHOX2
(Pan paniscus - bonobo/pygmy chimpanzee)

Bonobo Assembly	Chr	Position (strand)	Source	Genome Browsers
Bonobo Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
PanPan1.1	3	163,190,277 - 163,199,239 (-)	NCBI	panpan1.1	PanPan1.1	panPan2
PanPan1.1 Ensembl	3	163,190,284 - 163,199,239 (-)	Ensembl	panpan1.1		panPan2
Mhudiblu_PPA_v0	3	155,138,969 - 155,149,619 (-)	NCBI	Mhudiblu_PPA_v0	Mhudiblu_PPA_v0	panPan3

SHOX2
(Canis lupus familiaris - dog)

Dog Assembly	Chr	Position (strand)	Source	Genome Browsers
Dog Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
CanFam3.1	23	51,484,696 - 51,492,586 (-)	NCBI	CanFam3.1	CanFam3.1	canFam3	CanFam3.1
CanFam3.1 Ensembl	23	51,484,421 - 51,492,566 (-)	Ensembl	CanFam3.1		canFam3	CanFam3.1
Dog10K_Boxer_Tasha	23	51,357,238 - 51,365,278 (-)	NCBI		Dog10K_Boxer_Tasha
ROS_Cfam_1.0	23	52,123,573 - 52,131,639 (-)	NCBI		ROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl	23	52,123,242 - 52,131,401 (-)	Ensembl		ROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1	23	51,703,428 - 51,711,464 (-)	NCBI		UMICH_Zoey_3.1
UNSW_CanFamBas_1.0	23	51,755,484 - 51,763,458 (-)	NCBI		UNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0	23	52,041,698 - 52,049,712 (-)	NCBI		UU_Cfam_GSD_1.0

Shox2
(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_024405602	84,914,738 - 84,925,145 (+)	NCBI		HiC_Itri_2
SpeTri2.0 Ensembl	NW_004936519	4,809,687 - 4,818,792 (-)	Ensembl	SpeTri2.0
SpeTri2.0	NW_004936519	4,810,777 - 4,818,733 (-)	NCBI	SpeTri2.0	SpeTri2.0		SpeTri2.0

SHOX2
(Sus scrofa - pig)

Pig Assembly	Chr	Position (strand)	Source	Genome Browsers
Pig Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
Sscrofa11.1 Ensembl	13	97,879,281 - 97,889,785 (-)	Ensembl	Sscrofa11.1		susScr11	Sscrofa11.1
Sscrofa11.1	13	97,879,586 - 97,892,276 (-)	NCBI	Sscrofa11.1	Sscrofa11.1	susScr11	Sscrofa11.1
Sscrofa10.2	13	106,074,270 - 106,084,447 (-)	NCBI	Sscrofa10.2	Sscrofa10.2	susScr3

SHOX2
(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	15	32,684,598 - 32,694,640 (+)	NCBI	ChlSab1.1	ChlSab1.1	chlSab2
ChlSab1.1 Ensembl	15	32,684,705 - 32,692,699 (+)	Ensembl	ChlSab1.1	ChlSab1.1 Ensembl	chlSab2
Vero_WHO_p1.0	NW_023666041	5,251,405 - 5,261,933 (+)	NCBI	Vero_WHO_p1.0	Vero_WHO_p1.0

Shox2
(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_004624730	35,825,922 - 35,835,756 (-)	Ensembl	HetGla_female_1.0	HetGla_female_1.0 Ensembl	hetGla2
HetGla 1.0	NW_004624730	35,826,631 - 35,836,141 (-)	NCBI	HetGla_female_1.0	HetGla 1.0	hetGla2

Variants

Variants in Shox2
41 total Variants

miRNA Target Status

Predicted Target Of

	Summary Value
Count of predictions:	105
Count of miRNA genes:	77
Interacting mature miRNAs:	88
Transcripts:	ENSRNOT00000016843
Prediction methods:	Miranda, Rnahybrid, Targetscan
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
1358894	Kidm24	Kidney mass QTL 24	4.03		kidney mass (VT:0002707)	both kidneys wet weight to body weight ratio (CMO:0000340)	2	25413423	157142209	Rat
1358899	Kidm23	Kidney mass QTL 23	3.88		kidney mass (VT:0002707)	both kidneys wet weight to body weight ratio (CMO:0000340)	2	25413423	157142209	Rat
1358901	Cm38	Cardiac mass QTL 38	2		heart mass (VT:0007028)	heart weight to body weight ratio (CMO:0000074)	2	25413423	157142209	Rat
1358904	Cm39	Cardiac mass QTL 39	2.26		heart mass (VT:0007028)	heart weight to body weight ratio (CMO:0000074)	2	25413423	157142209	Rat
1358910	Kidm27	Kidney mass QTL 27	5.77		kidney mass (VT:0002707)	both kidneys wet weight to body weight ratio (CMO:0000340)	2	25413423	157142209	Rat
1358911	Kidm28	Kidney mass QTL 28	5.42		kidney mass (VT:0002707)	both kidneys wet weight to body weight ratio (CMO:0000340)	2	25413423	157142209	Rat
1358913	Cm41	Cardiac mass QTL 41	2.73		heart mass (VT:0007028)	heart weight to body weight ratio (CMO:0000074)	2	25413423	203928301	Rat
1358917	Cm42	Cardiac mass QTL 42	2.82		heart mass (VT:0007028)	heart weight to body weight ratio (CMO:0000074)	2	25413423	203928301	Rat
1358887	Bw50	Body weight QTL 50	2.39		body mass (VT:0001259)	body weight (CMO:0000012)	2	25413652	157142078	Rat
1358908	Bw49	Body weight QTL 49	3.36		body mass (VT:0001259)	body weight (CMO:0000012)	2	25413652	157142078	Rat
2293835	Kiddil5	Kidney dilation QTL 5	3.8		kidney pelvis morphology trait (VT:0004194)	hydronephrosis severity score (CMO:0001208)	2	42804607	157142209	Rat
2293843	Kiddil6	Kidney dilation QTL 6	3.1		kidney pelvis morphology trait (VT:0004194)	hydronephrosis severity score (CMO:0001208)	2	42804607	182042367	Rat
1298074	Bp164	Blood pressure QTL 164		0.003	arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	2	42804607	202447032	Rat
1298085	Bp165	Blood pressure QTL 165		0.0006	arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	2	42804607	202447032	Rat
61467	Bp14	Blood pressure QTL 14	2.2		arterial blood pressure trait (VT:2000000)	diastolic blood pressure (CMO:0000005)	2	43154682	202446871	Rat
61467	Bp14	Blood pressure QTL 14	2.2		arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	2	43154682	202446871	Rat
1354601	Slep1	Serum leptin concentration QTL 1	5.39		blood leptin amount (VT:0005667)	serum leptin level (CMO:0000780)	2	43171017	184114403	Rat
631266	Bp132	Blood pressure QTL 132		0.0005	arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	2	46123260	202447032	Rat
1331760	Bp206	Blood pressure QTL 206	3.62454		arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	2	56043031	202447032	Rat
1298080	Bp163	Blood pressure QTL 163		0.02	arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	2	66118275	202447032	Rat
1354648	Bp239	Blood pressure QTL 239		0.001	arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	2	66118463	226797303	Rat
1558653	Prcr1	Prostate cancer resistance QTL 1	5		prostate integrity trait (VT:0010571)	area of ventral prostate occupied by tumorous lesions to total ventral prostate area ratio (CMO:0000899)	2	72532993	157142209	Rat
1354605	Rf48	Renal function QTL 48	2.9		blood creatinine amount (VT:0005328)	plasma creatinine level (CMO:0000537)	2	74786664	206665859	Rat
61374	Edpm2	Estrogen-dependent pituitary mass QTL 2	4.42	0.86	pituitary gland mass (VT:0010496)	pituitary gland wet weight (CMO:0000853)	2	76539322	202447032	Rat
1581569	Uae32	Urinary albumin excretion QTL 32		0.0001	urine protein amount (VT:0005160)	urine albumin excretion rate (CMO:0000757)	2	78665619	219826953	Rat
724534	Uae6	Urinary albumin excretion QTL 6	10		urine albumin amount (VT:0002871)	urine albumin level (CMO:0000130)	2	78665619	249053267	Rat
8662832	Vetf7	Vascular elastic tissue fragility QTL 7	3.5		aorta elastin amount (VT:0003905)	aorta wall extracellular elastin dry weight to aorta wall dry weight ratio (CMO:0002002)	2	81689826	221035911	Rat
1354622	Kidm16	Kidney mass QTL 16	3		kidney mass (VT:0002707)	left kidney wet weight (CMO:0000083)	2	81754530	222436696	Rat
1354649	Kidm17	Kidney mass QTL 17	2.9		kidney mass (VT:0002707)	calculated kidney weight (CMO:0000160)	2	81754530	227146641	Rat
631507	Bp105	Blood pressure QTL 105		0.001	arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	2	112456140	212696837	Rat
634308	Sach6	Saccharin preference QTL 6	4.9		taste sensitivity trait (VT:0001986)	saccharin intake volume to total fluid intake volume ratio (CMO:0001601)	2	112456140	212696837	Rat
1354594	Despr10	Despair related QTL 10		0.00000249	locomotor behavior trait (VT:0001392)	amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)	2	114654253	159654253	Rat
1359030	Bp277	Blood pressure QTL 277			arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	2	114837527	185876470	Rat
1359030	Bp277	Blood pressure QTL 277			arterial blood pressure trait (VT:2000000)	diastolic blood pressure (CMO:0000005)	2	114837527	185876470	Rat
1578648	Bss11	Bone structure and strength QTL 11	4.7		femur morphology trait (VT:0000559)	femoral neck cortical cross-sectional area (CMO:0001702)	2	114837527	211674221	Rat
1554319	Bmd2	Bone mineral density QTL 2	13.4	0.0001	lumbar vertebra area (VT:0010570)	lumbar vertebra cross-sectional area (CMO:0001689)	2	114837675	212549332	Rat
1582257	Gluco21	Glucose level QTL 21	3.1	0.0035	blood glucose amount (VT:0000188)	blood glucose level (CMO:0000046)	2	118111229	157142209	Rat
738007	Anxrr7	Anxiety related response QTL 7	4.4		exploratory behavior trait (VT:0010471)	number of entries into a discrete space in an experimental apparatus (CMO:0000960)	2	118189491	163189491	Rat
1358360	Sradr2	Stress Responsive Adrenal Weight QTL 2	10.24		adrenal gland mass (VT:0010420)	both adrenal glands wet weight (CMO:0000164)	2	129164097	152195315	Rat
6907363	Bp357	Blood pressure QTL 357	4.1	0.002	arterial blood pressure trait (VT:2000000)	diastolic blood pressure (CMO:0000005)	2	129540907	174540907	Rat
1300165	Rf9	Renal function QTL 9	3.28		kidney glomerulus integrity trait (VT:0010546)	index of glomerular damage (CMO:0001135)	2	133914684	202447032	Rat
70175	BpQTLCluster3	Blood pressure QTL cluster 3	4.128		arterial blood pressure trait (VT:2000000)	diastolic blood pressure (CMO:0000005)	2	135552573	202446871	Rat
70175	BpQTLCluster3	Blood pressure QTL cluster 3	4.128		arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	2	135552573	202446871	Rat
70175	BpQTLCluster3	Blood pressure QTL cluster 3	4.128		arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	2	135552573	202446871	Rat
70175	BpQTLCluster3	Blood pressure QTL cluster 3	4.128		arterial blood pressure trait (VT:2000000)	pulse pressure (CMO:0000292)	2	135552573	202446871	Rat
70175	BpQTLCluster3	Blood pressure QTL cluster 3	4.128		arterial blood pressure trait (VT:2000000)	absolute change in systolic blood pressure (CMO:0000607)	2	135552573	202446871	Rat
1298076	Bp166	Blood pressure QTL 166		0.0009	arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	2	136445150	202447032	Rat
1581502	Esta3	Estrogen-induced thymic atrophy QTL 3			thymus mass (VT:0004954)	thymus wet weight (CMO:0000855)	2	136916935	189599348	Rat
1359022	Ppulsi1	Prepulse inhibition QTL 1	3.63		prepulse inhibition trait (VT:0003088)	acoustic startle response measurement (CMO:0001519)	2	136916935	213594495	Rat
1331794	Bp202	Blood pressure QTL 202	3.66819		arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	2	141194931	223265385	Rat
1331805	Cm29	Cardiac mass QTL 29	3.50746		heart mass (VT:0007028)	heart wet weight (CMO:0000069)	2	141194931	223265385	Rat
71113	Cari2	Carrageenan-induced inflammation QTL 2	2.7	0.009	hypodermis integrity trait (VT:0010550)	inflammatory exudate volume (CMO:0001429)	2	141596551	202447032	Rat
724568	Uae13	Urinary albumin excretion QTL 13	4.4		urine albumin amount (VT:0002871)	urine albumin excretion rate (CMO:0000757)	2	143157029	210020885	Rat
10043136	Iddm54	Insulin dependent diabetes mellitus QTL 54	3.4	0.0001	blood glucose amount (VT:0000188)	blood glucose level (CMO:0000046)	2	143657411	190602963	Rat
10043136	Iddm54	Insulin dependent diabetes mellitus QTL 54	3.4	0.0001	blood glucose amount (VT:0000188)	age at onset/diagnosis of type 1 diabetes mellitus (CMO:0001140)	2	143657411	190602963	Rat
6903312	Bw112	Body weight QTL 112	3.2	0.0013	body mass (VT:0001259)	body weight (CMO:0000012)	2	143657569	184114274	Rat
61401	Niddm2	Non-insulin dependent diabetes mellitus QTL 2	4.54		blood glucose amount (VT:0000188)	blood glucose level (CMO:0000046)	2	144599348	189599348	Rat
631520	Bp73	Blood pressure QTL 73		0.0001	arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	2	147686913	168355276	Rat
1598833	Bp295	Blood pressure QTL 295	3.5		arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	2	147798556	192798556	Rat
1641925	Alcrsp2	Alcohol response QTL 2			response to alcohol trait (VT:0010489)	duration of loss of righting reflex (CMO:0002289)	2	149559561	221167075	Rat
1641891	Alcrsp17	Alcohol response QTL 17			response to alcohol trait (VT:0010489)	duration of loss of righting reflex (CMO:0002289)	2	149559561	249053267	Rat
1598805	Memor8	Memory QTL 8	3		exploratory behavior trait (VT:0010471)	average horizontal distance between subject and target during voluntary locomotion in an experimental apparatus (CMO:0002674)	2	150341585	189039377	Rat
631501	Bp101	Blood pressure QTL 101	2.4		arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	2	150341684	202446871	Rat
2301966	Bp322	Blood pressure QTL 322	3.58		arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	2	150540301	202447032	Rat
1354609	Niddm62	Non-insulin dependent diabetes mellitus QTL 62	4.72	0.000006	insulin secretion trait (VT:0003564)	plasma insulin level (CMO:0000342)	2	150540301	202447032	Rat

Markers in Region

D2Got333

Rat Assembly	Chr	Position (strand)	Source	JBrowse
mRatBN7.2	2	151,223,786 - 151,223,949 (+)	MAPPER	mRatBN7.2
Rnor_6.0	2	164,123,866 - 164,124,028	NCBI	Rnor6.0
Rnor_5.0	2	183,475,504 - 183,475,666	UniSTS	Rnor5.0
RGSC_v3.4	2	156,886,736 - 156,886,898	UniSTS	RGSC3.4
Celera	2	145,602,714 - 145,602,882	UniSTS
Cytogenetic Map	2	q31	UniSTS

Expression

RNA-SEQ Expression

High: > 1000 TPM value Medium: Between 11 and 1000 TPM
Low: Between 0.5 and 10 TPM Below Cutoff: < 0.5 TPM

	alimentary part of gastrointestinal system	circulatory system	endocrine system	exocrine system	hemolymphoid system	hepatobiliary system	integumental system	musculoskeletal system	nervous system	renal system	reproductive system	respiratory system	appendage
High
Medium		4							30
Low		30	13	4	7	4	8	10	38	31	23	8	8
Below cutoff	1	7	11	7	9	7		1	4	4	15	1

View RNA-SEQ Expression Data

Sequence

Nucleotide Sequences


RefSeq Transcripts	NM_013028	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_039101799	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
GenBank Nucleotide	AJ002258	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	AJ002259	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	AJ002260	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	CH473976	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	JACYVU010000069	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles

Reference Sequences

RefSeq Acc Id:

ENSRNOT00000016843 ⟹ ENSRNOP00000016843

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2 Ensembl	2	151,217,552 - 151,227,143 (-)	Ensembl
Rnor_6.0 Ensembl	2	164,118,191 - 164,126,783 (-)	Ensembl

RefSeq Acc Id:

NM_013028 ⟹ NP_037160

RefSeq Status:

VALIDATED

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2	2	151,217,552 - 151,227,143 (-)	NCBI
Rnor_6.0	2	164,118,175 - 164,126,783 (-)	NCBI
Rnor_5.0	2	183,469,813 - 183,478,421 (-)	NCBI
RGSC_v3.4	2	156,881,044 - 156,889,653 (-)	RGD
Celera	2	145,597,026 - 145,605,637 (-)	RGD

Sequence:

show sequence

GGAATTCGGCACGAGCCGGGAGCTGGACATGGGAGCCGCGGAGCGGAGCAGGGAGCCCGGCAGC
CCGCGGCTGACGGAGGTGTCCCCTGAACTGAAGGATCGCAAAGAGGATGCGAAAGGGATGGAGG
ACGAAGGCCAGACCAAAATCAAGCAGCGGCGAAGTCGGACCAATTTTACCCTGGAACAACTCAA
CGAGCTGGAGAGGCTTTTCGATGAGACCCACTATCCAGACGCTTTTATGCGCGAGGAACTGAGC
CAGCGACTGGGGCTATCTGAGGCCCGAGTACAGGTTTGGTTTCAAAATCGAAGAGCTAAGTGTA
GAAAACAGGAAAATCAACTTCATAAAGGTGTCCTTATAGGGGCTGCTAGCCAGTTTGAAGCTTG
TAGAGTTGCACCCTATGTCAACGTAGGTGCTTTAAGGATGCCATTTCAGCAGGATAGTCATTGC
AACGTGACGCCCTTGTCCTTTCAGGTTCAGGCGCACGTGCAGCTGGACAGCGCCGTGCGAGCCG
CGCACCACCACCTGCATCCGCACCTGGCCGCGCACGGCCCTTACATGATGTTCCCGGCACCGCC
CTTCGGACTGCCGCTGGCCACGCTGGCGGCGGACTCGGCCTCCGCCGCCTCGGTGGTGGCTGCC
GCCGCCGCCGCCAAGACCACCAGCAAGAACTCCAGCATCGCGGATCTCAGACTGAAAGCTAAAA
AGCACGCGGCCGCCCTGGGTCTGTGACGCCGGCGCCACGGCCACGGTCGGTGGAGCCTTCTATG
CGGCGCGACCCCGCACGCTCTCCGCGACCGGCTGCTTCTCCCGCACCCGCTTCGGACCGACTAA
GCCTGTCCCTTCCCCGCTGACTGCCGCCTTTTCTTTCTGCACCCTGGATCCCTAGGGCGGGACT
CTGCGCTGGACCCGGGATCCCACGAGGACCACCAGCCCGGGCTCCTGCCACCCGCCCTTGGGAC
TAAAATTCGGCTTTGTAGGAGCGGGTTTGGGGAAGTCTGGATAGAGACTGGACAAAGGAGTGTG
GCAACAGTGACCACAGCTGCGGCGACGGACTCGTTCATAGGAATAAAATCTTGCTAACAACAAA
TGAGCAAAAACAAAAAAGGATAGAGAACAAACTAAAAAAAGAAAATGAGAAAGGGGGCTTGTTT
CTTATTGCTATTTGGCTGGAATTAGAGAGAGAACGATGAAGCAAAACAATTCTTAAAATTATTT
TGTACATAAAAATACGGAAAAATAACCTGGATGAATCTTGAGAGAAAGGGGGGAGGGATTTACC
AACTAAAATGTATGTTTTTTTTTAAATGGTCCAAGGAAACAAAACAGAAGGAAGAGGTATACTA
TTTAAGAATTAAGATGAAAAAAAAAAGCGCAGCTGGGAAGTTCACAGGTTTTGAAGCTGACCTT
TTTCTGCGAAGTTCACTTTAATACGAGACATTTGATAAGAGAGGCGGGCCTCCTTTTACGTTGA
ATCTGATGCTTTGAGTTTTAAAACACCATGTTTGGAAGAGCAAGAAGAGGGAAGACAGTGTGGA
AACGAGGAGGGAAAAAAGGACGTTCATACAAAAAAAAAAAAAAAAACTCGAG

hide sequence

RefSeq Acc Id:

XM_039101799 ⟹ XP_038957727

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2	2	151,217,049 - 151,227,180 (-)	NCBI

Protein Sequences


Protein RefSeqs	NP_037160	(Get FASTA)	NCBI Sequence Viewer
	XP_038957727	(Get FASTA)	NCBI Sequence Viewer
GenBank Protein	CAA05283	(Get FASTA)	NCBI Sequence Viewer
	CAA05284	(Get FASTA)	NCBI Sequence Viewer
	CAA05285	(Get FASTA)	NCBI Sequence Viewer
	EDM00930	(Get FASTA)	NCBI Sequence Viewer
	EDM00931	(Get FASTA)	NCBI Sequence Viewer
	EDM00932	(Get FASTA)	NCBI Sequence Viewer
	O35750	(Get FASTA)	NCBI Sequence Viewer

Reference Sequences

RefSeq Acc Id:

NP_037160 ⟸ NM_013028

- UniProtKB:

G3V7M9 (UniProtKB/TrEMBL)

- Sequence:

show sequence

MGAAERSREPGSPRLTEVSPELKDRKEDAKGMEDEGQTKIKQRRSRTNFTLEQLNELERLFDET
HYPDAFMREELSQRLGLSEARVQVWFQNRRAKCRKQENQLHKGVLIGAASQFEACRVAPYVNVG
ALRMPFQQDSHCNVTPLSFQVQAHVQLDSAVRAAHHHLHPHLAAHGPYMMFPAPPFGLPLATLA
ADSASAASVVAAAAAAKTTSKNSSIADLRLKAKKHAAALGL

hide sequence

RefSeq Acc Id:

ENSRNOP00000016843 ⟸ ENSRNOT00000016843

RefSeq Acc Id:	XP_038957727 ⟸ XM_039101799
- Peptide Label:	isoform X1

Protein Domains

Homeobox OAR

Protein Structures

Name	Modeler	Protein Id	AA Range	Protein Structure
AF-O35750-F1-model_v2	AlphaFold	O35750	1-237	view protein structure

Transcriptome

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

Promoters

RGD ID:

13691363

Promoter ID:

EPDNEW_R1888

Type:

single initiation site

Name:

Shox2_1

Description:

short stature homeobox 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	2	164,126,708 - 164,126,768	EPDNEW

Additional Information

External Database Links

Database	Acc Id	Source(s)
AGR Gene	RGD:3674	AgrOrtholog
BioCyc Gene	G2FUF-52872	BioCyc
Ensembl Genes	ENSRNOG00000012478	Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein	ENSRNOP00000016843	ENTREZGENE
	ENSRNOP00000016843.5	UniProtKB/TrEMBL
Ensembl Transcript	ENSRNOT00000016843	ENTREZGENE
	ENSRNOT00000016843.6	UniProtKB/TrEMBL
InterPro	Homeobox-like_sf	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	Homeobox_CS	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	Homeobox_dom	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	HTH_motif	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	OAR_dom	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report	rno:25546	UniProtKB/Swiss-Prot
NCBI Gene	25546	ENTREZGENE
Pfam	Homeodomain	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	OAR	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen	Shox2	PhenoGen
PRINTS	HTHREPRESSR	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PROSITE	HOMEOBOX_1	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	HOMEOBOX_2	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	OAR	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
SMART	HOX	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP	SSF46689	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
TIGR	TC228946
UniProt	G3V7M9	ENTREZGENE, UniProtKB/TrEMBL
	O35750	ENTREZGENE, UniProtKB/Swiss-Prot
UniProt Secondary	O35749	UniProtKB/Swiss-Prot
	O35751	UniProtKB/Swiss-Prot

Nomenclature History

Date	Current Symbol	Current Name	Previous Symbol	Previous Name	Description	Reference	Status
2002-06-10	Shox2	Short stature homeobox 2			Symbol and Name status set to approved	70586	APPROVED

RGD Curation Notes

Note Type	Note	Reference
gene_process	human homolog encodes putative homeobox gene involved in embryonic development	704404

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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Imported Disease Annotations - MGI