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

	Submit Data \| Help \| Video Tutorials \| News \| Publications \| Download \| REST API \| Citing RGD \| Contact
	Search RGD Grant Resources Citing RGD About Us Contact Us Genes QTLs Strains Markers Genome Information Ontologies Cell Lines References Download Submit Data OntoMate (Literature Search) JBrowse (Genome Browser) Variant Visualizer Multi-Ontology Enrichment (MOET) Gene-Ortholog Location Finder (GOLF) InterViewer (Protein-Protein Interactions) PhenoMiner (Quatitative Phenotypes) Gene Annotator OLGA (Gene List Generator) RatMine GViewer (Genome Viewer) Overgo Probe Designer ACP Haplotyper Genome Scanner VCMap Aging & Age-Related Disease Cancer Cardiovascular Disease COVID-19 Developmental Disease Diabetes Hematologic Disease Immune & Inflammatory Disease Infectious Disease Liver Disease Neurological Disease Obesity & Metabolic Syndrome Renal Disease Respiratory Disease Sensory Organ Disease Find Models new Genetic Models Autism Models PhenoMiner (Quantitative Phenotypes) Expected Ranges (Quantitative Phenotype) PhenoMiner Term Comparison Hybrid Rat Diversity Panel Phenotypes GERRC (Gene Editing Rat Resource Center) Phenotypes in Other Animal Models Animal Husbandry Strain Medical Records Phylogenetics Strain Availability Calendar Rats 101 Submissions Photo Archive Pathways Rat Community Forum Directory of Rat Laboratories Video Tutorials News RGD Publications RGD Poster Archive Nomenclature Guidelines Resource Links Laboratory Resources Employment Resources
	Advanced Search (OLGA)

Gene: Shox2 (short stature homeobox 2) Rattus norvegicus

Analyze

Symbol:

Shox2

Name:

short stature homeobox 2

RGD ID:

3674

Description:

Predicted to have 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 animal organ development; positive regulation of cell development; and regulation of transcription by RNA polymerase II. Predicted to localize to 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

Also 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)	HGNC	Treefam, OrthoMCL, NCBI, OMA, HomoloGene, Inparanoid, OrthoDB, Ensembl
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 (African 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\|TreeFam)
Homo sapiens (human):	SHOX2 (short stature homeobox 2)	Alliance	DIOPT (Ensembl Compara\|HGNC\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|TreeFam)
Danio rerio (zebrafish):	shox2 (short stature homeobox 2)	Alliance	DIOPT (PhylomeDB\|TreeFam)
Drosophila melanogaster (fruit fly):	CG34367	Alliance	DIOPT (InParanoid\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|TreeFam)

Latest Assembly:

Rnor_6.0 - RGSC Genome Assembly v6.0

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
Rnor_6.0 Ensembl	2	164,118,191 - 164,126,783 (-)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_6.0	2	164,118,175 - 164,126,783 (-)	NCBI	Rnor6.0	Rnor_6.0	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		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)

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)

genistein (ISO)

hydralazine (ISO)

methotrexate (ISO)

morphine (ISO)

nicotine (ISO)

oxaliplatin (EXP)

palbociclib (ISO)

pyridaben (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 (ISO)

cartilage development involved in endochondral bone morphogenesis (ISO)

chondrocyte development (ISO)

chondrocyte differentiation (ISO)

embryonic digestive tract morphogenesis (ISO)

embryonic forelimb morphogenesis (ISO)

embryonic limb morphogenesis (ISO)

embryonic morphogenesis (ISO)

embryonic skeletal joint morphogenesis (ISO)

heart valve development (ISO)

multicellular organism development (IEA)

muscle tissue morphogenesis (ISO)

negative regulation of transcription by RNA polymerase II (ISO)

osteoblast differentiation (ISO)

positive regulation of axonogenesis (ISO)

positive regulation of mesenchymal cell proliferation (ISO)

positive regulation of skeletal muscle fiber development (ISO)

positive regulation of smoothened signaling pathway (ISO)

positive regulation of transcription by RNA polymerase II (ISO)

regulation of branching morphogenesis of a nerve (ISO)

regulation of chondrocyte differentiation (ISO)

regulation of heart rate (ISO)

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

sinoatrial node cell development (ISO)

sinoatrial node development (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


1.	Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
2.	GOA data from the GO Consortium
3.	Ilse P, etal., Cancer Genomics Proteomics. 2014 Sep-Oct;11(5):251-8.
4.	MGD data from the GO Consortium
5.	NCBI rat LocusLink and RefSeq merged data July 26, 2002
6.	OMIM Disease Annotation Pipeline
7.	RGD automated import pipeline for gene-chemical interactions
8.	Tentative Sequence Data IDs. TIGR Gene Index, Rat Data
9.	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
Rnor_6.0 Ensembl	2	164,118,191 - 164,126,783 (-)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_6.0	2	164,118,175 - 164,126,783 (-)	NCBI	Rnor6.0	Rnor_6.0	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		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.p13 Ensembl	3	158,095,905 - 158,106,420 (-)	Ensembl	GRCh38		hg38	GRCh38
GRCh38.p13 Ensembl	3	158,095,954 - 158,106,503 (-)	Ensembl	GRCh38		hg38	GRCh38
GRCh38	3	158,095,905 - 158,106,420 (-)	NCBI	GRCh38	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		hg18	NCBI36
Build 34	3	159,297,570 - 159,306,541	NCBI
Celera	3	156,237,551 - 156,247,714 (-)	NCBI
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

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		mm39
GRCm39 Ensembl	3	66,879,060 - 66,889,104 (-)	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		mm9	NCBIm37
MGSCv36	3	67,061,195 - 67,069,700 (-)	NCBI			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		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
ROS_Cfam_1.0	23	52,123,573 - 52,131,639 (-)	NCBI
UMICH_Zoey_3.1	23	51,703,428 - 51,711,464 (-)	NCBI
UNSW_CanFamBas_1.0	23	51,755,484 - 51,763,458 (-)	NCBI
UU_Cfam_GSD_1.0	23	52,041,698 - 52,049,712 (-)	NCBI

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
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 - 97,890,447 (-)	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 - African green monkey)

Vervet Assembly	Chr	Position (strand)	Source	Genome Browsers
Vervet Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
ChlSab1.1	15	32,684,598 - 32,694,640 (+)	NCBI
ChlSab1.1 Ensembl	15	32,684,705 - 32,692,699 (+)	Ensembl

Shox2
(Heterocephalus glaber - naked mole-rat)

Molerat Assembly	Chr	Position (strand)	Source	Genome Browsers
Molerat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
HetGla 1.0	NW_004624730	35,826,631 - 35,836,141 (-)	NCBI

Position Markers

D2Got333

Rat Assembly	Chr	Position (strand)	Source	JBrowse
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

QTLs in Region (Rnor_6.0)

The following QTLs overlap with this region.

RGD ID	Symbol	Name	LOD	P Value	Trait	Sub Trait	Chr	Start	Stop	Species
10755499	Bp389	Blood pressure QTL 389	2.61		arterial blood pressure trait (VT:2000000)	diastolic blood pressure (CMO:0000005)	2	16679272	245624402	Rat
1358894	Kidm24	Kidney mass QTL 24	4.03		kidney mass (VT:0002707)	both kidneys wet weight to body weight ratio (CMO:0000340)	2	23837491	169852800	Rat
1358899	Kidm23	Kidney mass QTL 23	3.88		kidney mass (VT:0002707)	both kidneys wet weight to body weight ratio (CMO:0000340)	2	23837491	169852800	Rat
1358901	Cm38	Cardiac mass QTL 38	2		heart mass (VT:0007028)	heart weight to body weight ratio (CMO:0000074)	2	23837491	169852800	Rat
1358904	Cm39	Cardiac mass QTL 39	2.26		heart mass (VT:0007028)	heart weight to body weight ratio (CMO:0000074)	2	23837491	169852800	Rat
1358910	Kidm27	Kidney mass QTL 27	5.77		kidney mass (VT:0002707)	both kidneys wet weight to body weight ratio (CMO:0000340)	2	23837491	169852800	Rat
1358911	Kidm28	Kidney mass QTL 28	5.42		kidney mass (VT:0002707)	both kidneys wet weight to body weight ratio (CMO:0000340)	2	23837491	169852800	Rat
1358913	Cm41	Cardiac mass QTL 41	2.73		heart mass (VT:0007028)	heart weight to body weight ratio (CMO:0000074)	2	23837491	218957222	Rat
1358917	Cm42	Cardiac mass QTL 42	2.82		heart mass (VT:0007028)	heart weight to body weight ratio (CMO:0000074)	2	23837491	218957222	Rat
1358887	Bw50	Body weight QTL 50	2.39		body mass (VT:0001259)	body weight (CMO:0000012)	2	23837719	169852670	Rat
1358908	Bw49	Body weight QTL 49	3.36		body mass (VT:0001259)	body weight (CMO:0000012)	2	23837719	169852670	Rat
2293835	Kiddil5	Kidney dilation QTL 5	3.8		kidney pelvis morphology trait (VT:0004194)	hydronephrosis severity score (CMO:0001208)	2	42776916	169852800	Rat
2293843	Kiddil6	Kidney dilation QTL 6	3.1		kidney pelvis morphology trait (VT:0004194)	hydronephrosis severity score (CMO:0001208)	2	42776916	195645082	Rat
1298085	Bp165	Blood pressure QTL 165		0.0006	arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	2	42776916	217498710	Rat
1298074	Bp164	Blood pressure QTL 164		0.003	arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	2	42776916	217498710	Rat
61467	Bp14	Blood pressure QTL 14	2.2		arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	2	43133606	217498545	Rat
61467	Bp14	Blood pressure QTL 14	2.2		arterial blood pressure trait (VT:2000000)	diastolic blood pressure (CMO:0000005)	2	43133606	217498545	Rat
1354601	Slep1	Serum leptin concentration QTL 1	5.39		blood leptin amount (VT:0005667)	serum leptin level (CMO:0000780)	2	43149788	198704485	Rat
631266	Bp132	Blood pressure QTL 132		0.0005	arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	2	46537589	217498710	Rat
1331760	Bp206	Blood pressure QTL 206	3.62454		arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	2	56244671	217498710	Rat
1298080	Bp163	Blood pressure QTL 163		0.02	arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	2	66828049	217498710	Rat
1354648	Bp239	Blood pressure QTL 239		0.001	arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	2	66828236	243550655	Rat
1358900	Bw48	Body weight QTL 48	4.88		body mass (VT:0001259)	body weight (CMO:0000012)	2	68865414	169852800	Rat
1354605	Rf48	Renal function QTL 48	2.9		blood creatinine amount (VT:0005328)	plasma creatinine level (CMO:0000537)	2	75687495	221880419	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	78321410	217498710	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	83754907	237610852	Rat
1354622	Kidm16	Kidney mass QTL 16	3		kidney mass (VT:0002707)	left kidney wet weight (CMO:0000083)	2	83819608	239166203	Rat
1354649	Kidm17	Kidney mass QTL 17	2.9		kidney mass (VT:0002707)	calculated kidney weight (CMO:0000160)	2	83819608	243901375	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	93995316	169852800	Rat
631507	Bp105	Blood pressure QTL 105		0.001	arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	2	116075644	228737869	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	116075644	228737869	Rat
1359030	Bp277	Blood pressure QTL 277			arterial blood pressure trait (VT:2000000)	diastolic blood pressure (CMO:0000005)	2	118446646	200453484	Rat
1359030	Bp277	Blood pressure QTL 277			arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	2	118446646	200453484	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	118446646	227707979	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	118446793	228582621	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	119789823	164789823	Rat
1582257	Gluco21	Glucose level QTL 21	3.1	0.0035	blood glucose amount (VT:0000188)	blood glucose level (CMO:0000046)	2	121750419	169852800	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	123456539	168456539	Rat
1358360	Sradr2	Stress Responsive Adrenal Weight QTL 2	10.24		adrenal gland mass (VT:0010420)	both adrenal glands wet weight (CMO:0000164)	2	133399373	173020198	Rat
1300165	Rf9	Renal function QTL 9	3.28		kidney glomerulus integrity trait (VT:0010546)	index of glomerular damage (CMO:0001135)	2	138901276	217498710	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	140566078	217498545	Rat
70175	BpQTLCluster3	Blood pressure QTL cluster 3	4.128		arterial blood pressure trait (VT:2000000)	pulse pressure (CMO:0000292)	2	140566078	217498545	Rat
70175	BpQTLCluster3	Blood pressure QTL cluster 3	4.128		arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	2	140566078	217498545	Rat
70175	BpQTLCluster3	Blood pressure QTL cluster 3	4.128		arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	2	140566078	217498545	Rat
70175	BpQTLCluster3	Blood pressure QTL cluster 3	4.128		arterial blood pressure trait (VT:2000000)	diastolic blood pressure (CMO:0000005)	2	140566078	217498545	Rat
1298076	Bp166	Blood pressure QTL 166		0.0009	arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	2	141583337	217498710	Rat
1581502	Esta3	Estrogen-induced thymic atrophy QTL 3			thymus mass (VT:0004954)	thymus wet weight (CMO:0000855)	2	142053350	204585731	Rat
1359022	Ppulsi1	Prepulse inhibition QTL 1	3.63		prepulse inhibition trait (VT:0003088)	acoustic startle response measurement (CMO:0001519)	2	142053350	228984665	Rat
6907363	Bp357	Blood pressure QTL 357	4.1	0.002	arterial blood pressure trait (VT:2000000)	diastolic blood pressure (CMO:0000005)	2	143447078	188447078	Rat
1331794	Bp202	Blood pressure QTL 202	3.66819		arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	2	147122993	240020001	Rat
1331805	Cm29	Cardiac mass QTL 29	3.50746		heart mass (VT:0007028)	heart wet weight (CMO:0000069)	2	147122993	240020001	Rat
71113	Cari2	Carrageenan-induced inflammation QTL 2	2.7	0.009	hypodermis integrity trait (VT:0010550)	inflammatory exudate volume (CMO:0001429)	2	147522550	217498710	Rat
724568	Uae13	Urinary albumin excretion QTL 13	4.4		urine albumin amount (VT:0002871)	urine albumin excretion rate (CMO:0000757)	2	149114878	225501939	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	149614466	205573168	Rat
10043136	Iddm54	Insulin dependent diabetes mellitus QTL 54	3.4	0.0001	blood glucose amount (VT:0000188)	blood glucose level (CMO:0000046)	2	149614466	205573168	Rat
6903312	Bw112	Body weight QTL 112	3.2	0.0013	body mass (VT:0001259)	body weight (CMO:0000012)	2	149614623	198704357	Rat
631520	Bp73	Blood pressure QTL 73		0.0001	arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	2	153799203	181987474	Rat
1641925	Alcrsp2	Alcohol response QTL 2			response to alcohol trait (VT:0010489)	duration of loss of righting reflex (CMO:0002289)	2	155965557	237742948	Rat
1641891	Alcrsp17	Alcohol response QTL 17			response to alcohol trait (VT:0010489)	duration of loss of righting reflex (CMO:0002289)	2	155965557	254121739	Rat
1598805	Memor8	Memory QTL 8	3		exploratory behavior trait (VT:0010471)	average horizontal distance in proximity to the target during voluntary locomotion in an experimental apparatus (CMO:0002674)	2	157914311	204022555	Rat
631501	Bp101	Blood pressure QTL 101	2.4		arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	2	157914409	217498545	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	158159186	217498710	Rat
2301966	Bp322	Blood pressure QTL 322	3.58		arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	2	158159186	217498710	Rat
61401	Niddm2	Non-insulin dependent diabetes mellitus QTL 2	4.54		blood glucose amount (VT:0000188)	blood glucose level (CMO:0000046)	2	159585731	204585731	Rat
1598833	Bp295	Blood pressure QTL 295	3.5		arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	2	161745602	206745602	Rat

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.

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
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

- 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

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

Strain Variation

Strain Sequence Variants (Rnor 6.0)

ACI/EurMcwi (MCW)

Visual

CSV

TAB

Printer

Sequenced By:	Medical College of Wisconsin (Dr. Howard Jacob)
Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA v0.7.7 and GATK v3.2-2
Breeder:	Medical College of Wisconsin
Description:	Provided by the Medical College of Wisconsin (Dr. Howard Jacob)

ACI/EurMcwi (RGD)

Visual

CSV

TAB

Printer

Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

ACI/N (MCW)

Visual

CSV

TAB

Printer

Sequenced By:	Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen) Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform:	SOLiD 4 and 5500
Secondary Analysis:	liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder:	National Institutes of Health
Description:	Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin

BBDP/Wor (RGD)

Visual

CSV

TAB

Printer

Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

BN/SsN (MCW)

Visual

CSV

TAB

Printer

Sequenced By:	Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen) Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform:	SOLiD 4 and 5500
Secondary Analysis:	liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder:	National Institutes of Health
Description:	Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin

Buf/N (MCW)

Visual

CSV

TAB

Printer

Sequenced By:	Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen) Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform:	SOLiD 4 and 5500
Secondary Analysis:	liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder:	National Institutes of Health
Description:	Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin

COP/CrCrl (MCW & UW)

Visual

CSV

TAB

Printer

Sequenced By:	Medical College of Wisconsin (Dr. Howard Jacob) University of Wisconsin (Dr. James Shull)
Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA v0.7.7 and GATK v3.2-2
Breeder:	Charles River Laboratories
Description:	Provided by the Medical College of Wisconsin (Dr. Howard Jacob) and UW Madison (Dr. James Shull)

F344/NCrl (RGD)

Visual

CSV

TAB

Printer

Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

F344/NRrrc (MCW)

Visual

CSV

TAB

Printer

Sequenced By:	Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen) Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform:	SOLiD 4 and 5500
Secondary Analysis:	liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder:	National Institutes of Health
Description:	Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin

FHH/EurMcwi (MCW)

Visual

CSV

TAB

Printer

Sequenced By:	Medical College of Wisconsin (Dr. Howard Jacob)
Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA v0.7.7 and GATK v3.2-2
Breeder:	Medical College of Wisconsin
Description:	Provided by the Medical College of Wisconsin (Dr. Howard Jacob)

FHH/EurMcwi (RGD)

Visual

CSV

TAB

Printer

Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

FHL/EurMcwi (MCW)

Visual

CSV

TAB

Printer

Sequenced By:	Medical College of Wisconsin (Dr. Howard Jacob)
Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA v0.7.7 and GATK v3.2-2
Breeder:	Medical College of Wisconsin
Description:	Provided by the Medical College of Wisconsin (Dr. Howard Jacob)

FHL/EurMcwi (RGD)

Visual

CSV

TAB

Printer

Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

GH/OmrMcwi (MCW)

Visual

CSV

TAB

Printer

Sequenced By:	Medical College of Wisconsin (Dr. Howard Jacob)
Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA v0.7.7 and GATK v3.2-2
Breeder:	Medical College of Wisconsin
Description:	Provided by the Medical College of Wisconsin (Dr. Howard Jacob)

GK/Ox (RGD)

Visual

CSV

TAB

Printer

Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

LE/Stm (RGD)

Visual

CSV

TAB

Printer

Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

LEW/Crl (RGD)

Visual

CSV

TAB

Printer

Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

LEW/NCrlBR (RGD)

Visual

CSV

TAB

Printer

Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

LH/MavRrrc (RGD)

Visual

CSV

TAB

Printer

Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

LL/MavRrrc (RGD)

Visual

CSV

TAB

Printer

Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

LN/MavRrrc (RGD)

Visual

CSV

TAB

Printer

Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

M520/N (MCW)

Visual

CSV

TAB

Printer

Sequenced By:	Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen) Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform:	SOLiD 4 and 5500
Secondary Analysis:	liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder:	National Institutes of Health
Description:	Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin

MHS/Gib (RGD)

Visual

CSV

TAB

Printer

Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

MNS/Gib (RGD)

Visual

CSV

TAB

Printer

Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

MR/N (MCW)

Visual

CSV

TAB

Printer

Sequenced By:	Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen) Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform:	SOLiD 4 and 5500
Secondary Analysis:	liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder:	National Institutes of Health
Description:	Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin

SBH/Ygl (MCW)

Visual

CSV

TAB

Printer

Sequenced By:	Medical College of Wisconsin (Dr. Howard Jacob)
Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA v0.7.7 and GATK v3.2-2
Breeder:	Medical College of Wisconsin
Description:	SBH/Ygl sequenced by MCW

SBH/Ygl (RGD)

Visual

CSV

TAB

Printer

Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

SBN/Ygl (MCW)

Visual

CSV

TAB

Printer

Sequenced By:	Medical College of Wisconsin (Dr. Howard Jacob)
Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA v0.7.7 and GATK v3.2-2
Breeder:	Medical College of Wisconsin
Description:	SBN/Ygl sequenced by MCW

SBN/Ygl (RGD)

Visual

CSV

TAB

Printer

Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

SHR/NHsd (RGD)

Visual

CSV

TAB

Printer

Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

SHRSP/Gcrc (RGD)

Visual

CSV

TAB

Printer

Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

SR/JrHsd (MCW)

Visual

CSV

TAB

Printer

Sequenced By:	Medical College of Wisconsin (Dr. Howard Jacob)
Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA v0.7.7 and GATK v3.2-2
Breeder:	Harlan Laboratories
Description:	Provided by the Medical College of Wisconsin (Dr. Howard Jacob)

SR/JrHsd (RGD)

Visual

CSV

TAB

Printer

Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

SS/Jr (RGD)

Visual

CSV

TAB

Printer

Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

SS/JrHsdMcwi (MCW)

Visual

CSV

TAB

Printer

Sequenced By:	Medical College of Wisconsin (Dr. Howard Jacob)
Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA v0.7.7 and GATK v3.2-2
Breeder:	Medical College of Wisconsin
Description:	Provided by the Medical College of Wisconsin (Dr. Howard Jacob)

SS/JrHsdMcwi (RGD)

Visual

CSV

TAB

Printer

Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

WAG/Rij (RGD)

Visual

CSV

TAB

Printer

Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

WKY/Gcrc (RGD)

Visual

CSV

TAB

Printer

Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

WKY/N (MCW)

Visual

CSV

TAB

Printer

Sequenced By:	Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen) Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform:	SOLiD 4 and 5500
Secondary Analysis:	liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder:	National Institutes of Health
Description:	Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin

WKY/NCrl (RGD)

Visual

CSV

TAB

Printer

Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

WKY/NHsd (RGD)

Visual

CSV

TAB

Printer

Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

WN/N (MCW)

Visual

CSV

TAB

Printer

Sequenced By:	Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen) Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform:	SOLiD 4 and 5500
Secondary Analysis:	liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder:	National Institutes of Health
Description:	Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin

Additional Information

External Database Links

Database	Acc Id	Source(s)
AGR Gene	RGD:3674	AgrOrtholog
Ensembl Genes	ENSRNOG00000012478	Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein	ENSRNOP00000016843	ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript	ENSRNOT00000016843	ENTREZGENE, 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_RAT	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)

Send us a Message

Imported Disease Annotations - MGI