Pbx3 (PBX homeobox 3) - Rat Genome Database

Name: Pbx3
Creator: Rat Genome Database
License: Creative Commons CC BY 4.0
Keywords: Rat Gene RGD Genome

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Gene: Pbx3 (PBX homeobox 3) Rattus norvegicus

Analyze

Symbol:

Pbx3

Name:

PBX homeobox 3

RGD ID:

1307198

Description:

Predicted to have DNA-binding transcription activator activity, RNA polymerase II-specific and RNA polymerase II cis-regulatory region sequence-specific DNA binding activity. Predicted to be involved in several processes, including adult locomotory behavior; animal organ development; and regulation of respiratory gaseous exchange by nervous system process. Predicted to localize to nuclear chromatin and transcription regulator complex. Orthologous to human PBX3 (PBX homeobox 3); INTERACTS WITH benzo[a]pyrene; bisphenol A; cobalt dichloride.

Type:

protein-coding

RefSeq Status:

PROVISIONAL

Also known as:

LOC311876; pre B-cell leukemia transcription factor 3; pre-B-cell leukemia homeobox 3; pre-B-cell leukemia transcription factor 3

Orthologs:

Homo sapiens (human) : PBX3 (PBX homeobox 3) HGNC Alliance
Mus musculus (house mouse) : Pbx3 (pre B cell leukemia homeobox 3) MGI Alliance
Chinchilla lanigera (long-tailed chinchilla) : Pbx3 (PBX homeobox 3)
Pan paniscus (bonobo/pygmy chimpanzee) : PBX3 (PBX homeobox 3)
Canis lupus familiaris (dog) : PBX3 (PBX homeobox 3)
Ictidomys tridecemlineatus (thirteen-lined ground squirrel) : Pbx3 (PBX homeobox 3)
Sus scrofa (pig) : PBX3 (PBX homeobox 3)
Chlorocebus sabaeus (African green monkey) : PBX3 (PBX homeobox 3)
Heterocephalus glaber (naked mole-rat) : Pbx3 (PBX homeobox 3)

more info ...

Species	Gene symbol and name	Data Source	Assertion derived from	less info ...
Orthologs ¹				less info ...
Homo sapiens (human):	PBX3 (PBX homeobox 3)	HGNC	Ensembl, HomoloGene, Inparanoid, NCBI, OMA, OrthoDB, OrthoMCL, Panther, PhylomeDB, Treefam
Mus musculus (house mouse):	Pbx3 (pre B cell leukemia homeobox 3)	HGNC	Treefam, OrthoMCL, NCBI, OMA, HomoloGene, Inparanoid, Panther, PhylomeDB, OrthoDB, Ensembl
Chinchilla lanigera (long-tailed chinchilla):	Pbx3 (PBX homeobox 3)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Pan paniscus (bonobo/pygmy chimpanzee):	PBX3 (PBX homeobox 3)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Canis lupus familiaris (dog):	PBX3 (PBX homeobox 3)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Ictidomys tridecemlineatus (thirteen-lined ground squirrel):	Pbx3 (PBX homeobox 3)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Sus scrofa (pig):	PBX3 (PBX homeobox 3)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Chlorocebus sabaeus (African green monkey):	PBX3 (PBX homeobox 3)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Heterocephalus glaber (naked mole-rat):	Pbx3 (PBX homeobox 3)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Other homologs ²
Homo sapiens (human):	PBX1 (PBX homeobox 1)	HGNC	OrthoDB, OrthoMCL
Homo sapiens (human):	PBX2 (PBX homeobox 2)	HGNC	OrthoMCL
Alliance orthologs ³
Homo sapiens (human):	PBX3 (PBX homeobox 3)	Alliance	DIOPT (Ensembl Compara\|HGNC\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|TreeFam)
Mus musculus (house mouse):	Pbx3 (pre B cell leukemia homeobox 3)	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|TreeFam)
Danio rerio (zebrafish):	pbx1b (pre-B-cell leukemia homeobox 1b)	Alliance	DIOPT (InParanoid\|OMA\|OrthoInspector)
Danio rerio (zebrafish):	pbx1a (pre-B-cell leukemia homeobox 1a)	Alliance	DIOPT (InParanoid\|OMA\|OrthoInspector)
Danio rerio (zebrafish):	pbx3b (pre-B-cell leukemia homeobox 3b)	Alliance	DIOPT (Ensembl Compara\|OMA\|OrthoFinder\|PANTHER\|PhylomeDB)
Caenorhabditis elegans (roundworm):	F31E3.2	Alliance	DIOPT (Hieranoid\|InParanoid\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB)
Drosophila melanogaster (fruit fly):	exd	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PhylomeDB\|TreeFam)
Caenorhabditis elegans (roundworm):	ceh-40	Alliance	DIOPT (OrthoFinder\|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
Rnor_6.0	3	13,241,031 - 13,436,084 (-)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_6.0 Ensembl	3	13,182,024 - 13,525,983 (-)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_5.0	3	18,569,183 - 18,763,413 (-)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	3	13,200,261 - 13,405,859 (-)	NCBI	RGSC3.4		rn4	RGSC3.4
RGSC_v3.1	3	13,096,449 - 13,311,087 (-)	NCBI
Celera	3	12,211,343 - 12,404,425 (-)	NCBI		Celera
Cytogenetic Map	3	p11	NCBI

JBrowse:

View Region in Genome Browser (JBrowse)

Model

Annotation Click to see Annotation Detail View

Gene-Chemical Interaction Annotations Click to see Annotation Detail View

1,2-dichloroethane (ISO)

17beta-estradiol (ISO)

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

2-hydroxypropanoic acid (ISO)

2-methylcholine (ISO)

3-isobutyl-1-methyl-7H-xanthine (ISO)

4,4'-sulfonyldiphenol (ISO)

4-hydroxyphenyl retinamide (ISO)

5-fluorouracil (ISO)

aflatoxin B1 (ISO)

aflatoxin M1 (ISO)

all-trans-retinoic acid (ISO)

azathioprine (ISO)

benzo[a]pyrene (EXP,ISO)

bisphenol A (EXP)

bisphenol F (ISO)

bortezomib (ISO)

butanal (ISO)

carbamazepine (ISO)

carbon nanotube (ISO)

choline (ISO)

cisplatin (ISO)

cobalt dichloride (EXP)

cocaine (ISO)

crocidolite asbestos (ISO)

cyclosporin A (ISO)

dexamethasone (ISO)

dibutyl phthalate (EXP,ISO)

dorsomorphin (ISO)

doxorubicin (ISO)

endosulfan (EXP)

ethanol (ISO)

folic acid (ISO)

indometacin (ISO)

ketamine (EXP)

L-methionine (ISO)

lead diacetate (ISO)

methapyrilene (EXP)

methyl methanesulfonate (ISO)

methylmercury chloride (ISO)

oxaliplatin (EXP)

paracetamol (ISO)

phenobarbital (ISO)

pirinixic acid (ISO)

quercetin (ISO)

rac-lactic acid (ISO)

SB 431542 (ISO)

sodium arsenite (ISO)

sunitinib (ISO)

tamoxifen (ISO)

tert-butyl hydroperoxide (ISO)

tetrachloromethane (ISO)

thapsigargin (ISO)

toluene (EXP)

topotecan (EXP)

trichostatin A (ISO)

triclosan (ISO)

uranium atom (ISO)

urethane (ISO)

valproic acid (ISO)

Gene Ontology Annotations Click to see Annotation Detail View

Biological Process

adult locomotory behavior (ISO)

animal organ morphogenesis (IBA)

brain development (IBA)

dorsal spinal cord development (ISO)

embryonic organ development (IBA)

eye development (IBA)

neuron development (IBA,ISO)

positive regulation of transcription by RNA polymerase II (ISO)

regulation of respiratory gaseous exchange by nervous system process (ISO)

regulation of transcription by RNA polymerase II (IBA)

respiratory gaseous exchange by respiratory system (ISO)

Cellular Component

nuclear chromatin (IBA)

nucleus (ISO)

transcription regulator complex (ISO)

Molecular Function

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

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

protein binding (ISO)

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

sequence-specific DNA binding (ISO)

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.	MGD data from the GO Consortium
4.	RGD automated data pipeline
5.	RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
6.	RGD automated import pipeline for gene-chemical interactions

Additional References at PubMed

PMID:10381567	PMID:10842069	PMID:15466398	PMID:15527896	PMID:16847320	PMID:18155191

Genomics

Comparative Map Data

Pbx3
(Rattus norvegicus - Norway rat)

Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
Rnor_6.0	3	13,241,031 - 13,436,084 (-)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_6.0 Ensembl	3	13,182,024 - 13,525,983 (-)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_5.0	3	18,569,183 - 18,763,413 (-)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	3	13,200,261 - 13,405,859 (-)	NCBI	RGSC3.4		rn4	RGSC3.4
RGSC_v3.1	3	13,096,449 - 13,311,087 (-)	NCBI
Celera	3	12,211,343 - 12,404,425 (-)	NCBI		Celera
Cytogenetic Map	3	p11	NCBI

PBX3
(Homo sapiens - human)

Human Assembly	Chr	Position (strand)	Source	Genome Browsers
Human Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCh38.p13 Ensembl	9	125,747,345 - 125,967,377 (+)	Ensembl	GRCh38		hg38	GRCh38
GRCh38	9	125,747,372 - 125,967,377 (+)	NCBI	GRCh38	GRCh38	hg38	GRCh38
GRCh37	9	128,509,617 - 128,729,656 (+)	NCBI	GRCh37	GRCh37	hg19	GRCh37
Build 36	9	127,549,487 - 127,769,477 (+)	NCBI	NCBI36		hg18	NCBI36
Build 34	9	125,589,286 - 125,808,921	NCBI
Celera	9	99,158,741 - 99,384,104 (+)	NCBI
Cytogenetic Map	9	q33.3	NCBI
HuRef	9	98,122,353 - 98,347,071 (+)	NCBI		HuRef
CHM1_1	9	128,660,292 - 128,880,307 (+)	NCBI		CHM1_1

Pbx3
(Mus musculus - house mouse)

Mouse Assembly	Chr	Position (strand)	Source	Genome Browsers
Mouse Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCm39	2	34,061,469 - 34,262,375 (-)	NCBI
GRCm38	2	34,171,457 - 34,372,045 (-)	NCBI	GRCm38	GRCm38	mm10	GRCm38
GRCm38.p6 Ensembl	2	34,171,457 - 34,373,142 (-)	Ensembl	GRCm38		mm10	GRCm38
MGSCv37	2	34,027,429 - 34,227,556 (-)	NCBI	GRCm37		mm9	NCBIm37
MGSCv36	2	33,993,918 - 34,194,045 (-)	NCBI			mm8
Celera	2	33,869,694 - 34,069,148 (-)	NCBI		Celera
Cytogenetic Map	2	B	NCBI
cM Map	2	22.84	NCBI

Pbx3
(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_004955419	2,419,029 - 2,627,607 (-)	Ensembl	ChiLan1.0
ChiLan1.0	NW_004955419	2,419,081 - 2,624,299 (-)	NCBI	ChiLan1.0	ChiLan1.0

PBX3
(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	9	125,379,110 - 125,599,634 (+)	NCBI	panpan1.1	PanPan1.1	panPan2
PanPan1.1 Ensembl	9	125,379,489 - 125,598,178 (+)	Ensembl	panpan1.1		panPan2
Mhudiblu_PPA_v0	9	96,867,140 - 97,089,205 (+)	NCBI

PBX3
(Canis lupus familiaris - dog)

Dog Assembly	Chr	Position (strand)	Source	Genome Browsers
Dog Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
CanFam3.1 Ensembl	9	57,199,812 - 57,429,811 (-)	Ensembl	CanFam3.1		canFam3	CanFam3.1
CanFam3.1	9	57,198,531 - 57,429,820 (-)	NCBI	CanFam3.1	CanFam3.1	canFam3	CanFam3.1

Pbx3
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)

Squirrel Assembly	Chr	Position (strand)	Source	Genome Browsers
Squirrel Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
SpeTri2.0	NW_004936487	13,779,999 - 13,986,617 (+)	NCBI	SpeTri2.0	SpeTri2.0		SpeTri2.0

PBX3
(Sus scrofa - pig)

Pig Assembly	Chr	Position (strand)	Source	Genome Browsers
Pig Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
Sscrofa11.1 Ensembl	1	266,382,640 - 266,610,646 (+)	Ensembl	Sscrofa11.1		susScr11	Sscrofa11.1
Sscrofa11.1	1	266,383,311 - 266,610,646 (+)	NCBI	Sscrofa11.1	Sscrofa11.1	susScr11	Sscrofa11.1
Sscrofa10.2	1	300,208,202 - 300,433,688 (+)	NCBI	Sscrofa10.2	Sscrofa10.2	susScr3

PBX3
(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	12	12,174,407 - 12,400,184 (-)	NCBI

Pbx3
(Heterocephalus glaber - naked mole-rat)

No map positions available.

Position Markers

D3Chm7

Rat Assembly	Chr	Position (strand)	Source	JBrowse
Rnor_6.0	3	13,352,601 - 13,352,827	NCBI	Rnor6.0
Rnor_5.0	3	18,680,823 - 18,681,049	UniSTS	Rnor5.0
RGSC_v3.4	3	13,312,545 - 13,312,772	RGD	RGSC3.4
RGSC_v3.4	3	13,312,546 - 13,312,772	UniSTS	RGSC3.4
Celera	3	12,322,409 - 12,322,635	UniSTS
Cytogenetic Map	3	p11	UniSTS

RH133967

Rat Assembly	Chr	Position (strand)	Source	JBrowse
Rnor_6.0	3	13,426,211 - 13,426,416	NCBI	Rnor6.0
Rnor_6.0	3	14,159,612 - 14,159,817	NCBI	Rnor6.0
Rnor_5.0	3	19,478,517 - 19,478,722	UniSTS	Rnor5.0
Rnor_5.0	3	18,753,576 - 18,753,781	UniSTS	Rnor5.0
RGSC_v3.4	3	13,396,073 - 13,396,278	UniSTS	RGSC3.4
Celera	3	12,394,614 - 12,394,819	UniSTS
Cytogenetic Map	3	p11	UniSTS

G07093

Rat Assembly	Chr	Position (strand)	Source	JBrowse
Rnor_6.0	3	13,241,552 - 13,241,658	NCBI	Rnor6.0
Rnor_5.0	3	18,569,704 - 18,569,810	UniSTS	Rnor5.0
RGSC_v3.4	3	13,200,336 - 13,200,442	UniSTS	RGSC3.4
Celera	3	12,211,418 - 12,211,524	UniSTS
Cytogenetic Map	3	p11	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
631679	Cm10	Cardiac mass QTL 10	7.34	0.0001	heart left ventricle mass (VT:0007031)	heart left ventricle weight to body weight ratio (CMO:0000530)	3	1	25786001	Rat
70202	Alc19	Alcohol consumption QTL 19	2.5		drinking behavior trait (VT:0001422)	ethanol intake volume to total fluid intake volume ratio (CMO:0001591)	3	1	28136884	Rat
631545	Bp85	Blood pressure QTL 85	3.1		arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	3	1	28500807	Rat
61468	Bp15	Blood pressure QTL 15	4.4		blood pressure trait (VT:0000183)	diastolic blood pressure (CMO:0000005)	3	1	28500807	Rat
61468	Bp15	Blood pressure QTL 15	4.4		blood pressure trait (VT:0000183)	systolic blood pressure (CMO:0000004)	3	1	28500807	Rat
61468	Bp15	Blood pressure QTL 15	4.4		blood pressure trait (VT:0000183)	pulse pressure (CMO:0000292)	3	1	28500807	Rat
631831	Alc8	Alcohol consumption QTL 8	2.7		consumption behavior trait (VT:0002069)	calculated ethanol drink intake rate (CMO:0001615)	3	1	32972944	Rat
4889966	Bss95	Bone structure and strength QTL 95	4.4		tibia area (VT:1000281)	tibia-fibula cross-sectional area (CMO:0001718)	3	1	37891710	Rat
2312664	Scl62	Serum cholesterol level QTL 62		0.05	blood cholesterol amount (VT:0000180)	serum total cholesterol level (CMO:0000363)	3	1	39773425	Rat
2290452	Scl56	Serum cholesterol level QTL 56	2.26		blood cholesterol amount (VT:0000180)	plasma total cholesterol level (CMO:0000585)	3	1	95176874	Rat
1298526	Arunc3	Aerobic running capacity QTL 3	2.2		exercise endurance trait (VT:0002332)	maximum distance run on treadmill (CMO:0001406)	3	2631421	33477544	Rat
10401810	Kidm53	Kidney mass QTL 53			kidney mass (VT:0002707)	both kidneys wet weight to body weight ratio (CMO:0000340)	3	2631421	48562146	Rat
70203	Gcr2	Gastric cancer resistance QTL 2	2.6		stomach morphology trait (VT:0000470)	stomach tumor susceptibility score (CMO:0002043)	3	3285929	28136884	Rat
1358357	Srcrtb1	Stress Responsive Cort Basal QTL 1	6.36	0.002	blood corticosterone amount (VT:0005345)	plasma corticosterone level (CMO:0001173)	3	3285929	28136884	Rat
8693641	Alc30	Alcohol consumption QTL 30	2	0.739	drinking behavior trait (VT:0001422)	calculated ethanol drink intake rate (CMO:0001615)	3	5654639	25105730	Rat
1558654	Bw56	Body weight QTL 56	4.5	0.0000171	body mass (VT:0001259)	body weight (CMO:0000012)	3	6000748	34394365	Rat
6893355	Bw101	Body weight QTL 101	0.4	0.38	body mass (VT:0001259)	body weight (CMO:0000012)	3	6000748	34394365	Rat
6893363	Bw105	Body weight QTL 105	2.6	0.0036	body mass (VT:0001259)	body weight (CMO:0000012)	3	6000748	34394365	Rat
70191	BpQTLcluster4	Blood pressure QTL cluster 4	3		arterial blood pressure trait (VT:2000000)	absolute change in mean arterial blood pressure (CMO:0000533)	3	6000748	51687917	Rat
70191	BpQTLcluster4	Blood pressure QTL cluster 4	3		arterial blood pressure trait (VT:2000000)	absolute change in systolic blood pressure (CMO:0000607)	3	6000748	51687917	Rat
1558647	Cm46	Cardiac mass QTL 46	5.4	0.0000055	heart mass (VT:0007028)	heart wet weight (CMO:0000069)	3	6000866	34394121	Rat
1558650	Cm48	Cardiac mass QTL 48	4	0.0001	heart mass (VT:0007028)	heart weight to body weight ratio (CMO:0000074)	3	6000866	34394121	Rat
1558657	Cm43	Cardiac mass QTL 43	6.6	0.0000000293	heart mass (VT:0007028)	heart wet weight (CMO:0000069)	3	6000866	34394121	Rat
1358905	Hrtrt17	Heart rate QTL 17	5.9	0.000014	heart pumping trait (VT:2000009)	heart rate (CMO:0000002)	3	10094081	93415837	Rat
2298542	Neuinf11	Neuroinflammation QTL 11	3.9		nervous system integrity trait (VT:0010566)	spinal cord complement component 1, q subcomponent, B chain mRNA level (CMO:0002126)	3	10119318	79772001	Rat
1358885	Bp251	Blood pressure QTL 251	3.8		arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	3	10639528	127023997	Rat
1358888	Bp264	Blood pressure QTL 264	4.43		arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	3	10639528	127023997	Rat
11528620	Bss113	Bone structure and strength QTL 113	9.75	0.00000000017	femur morphology trait (VT:0000559)	femoral neck width (CMO:0001695)	3	12236221	15217668	Rat
634306	Bp140	Blood pressure QTL 140	3.3	0.0013	arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	3	13126914	36600143	Rat
634306	Bp140	Blood pressure QTL 140	3.3	0.0013	arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	3	13126914	36600143	Rat
634306	Bp140	Blood pressure QTL 140	3.3	0.0013	arterial blood pressure trait (VT:2000000)	diastolic blood pressure (CMO:0000005)	3	13126914	36600143	Rat
634306	Bp140	Blood pressure QTL 140	3.3	0.0013	arterial blood pressure trait (VT:2000000)	diastolic blood pressure (CMO:0000005)	3	13126914	36600143	Rat
634306	Bp140	Blood pressure QTL 140	3.3	0.0013	arterial blood pressure trait (VT:2000000)	heart rate (CMO:0000002)	3	13126914	36600143	Rat
634306	Bp140	Blood pressure QTL 140	3.3	0.0013	arterial blood pressure trait (VT:2000000)	heart rate (CMO:0000002)	3	13126914	36600143	Rat
634306	Bp140	Blood pressure QTL 140	3.3	0.0013	arterial blood pressure trait (VT:2000000)	body weight (CMO:0000012)	3	13126914	36600143	Rat
634306	Bp140	Blood pressure QTL 140	3.3	0.0013	arterial blood pressure trait (VT:2000000)	body weight (CMO:0000012)	3	13126914	36600143	Rat
631568	Bp92	Blood pressure QTL 92	2.2	0.005	arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	3	13126914	41510346	Rat

miRNA Target Status

Predicted Target Of

	Summary Value
Count of predictions:	388
Count of miRNA genes:	213
Interacting mature miRNAs:	246
Transcripts:	ENSRNOT00000029600
Prediction methods:	Microtar, 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	3	30	18	18	11	18			74	26	33	11
Low		13	39	23	8	23	8	11		9	8		8
Below cutoff

View RNA-SEQ Expression Data

Sequence

Nucleotide Sequences


RefSeq Transcripts	NM_001107834	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_006233975	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
GenBank Nucleotide	AABR07051471	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	AABR07051472	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	AABR07051473	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	AABR07051474	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	AAHX01020862	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	AAHX01020863	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	AAHX01020864	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	AAHX01020865	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	AAHX01020866	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	CH474001	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles

Reference Sequences

RefSeq Acc Id:

ENSRNOT00000029600 ⟹ ENSRNOP00000029846

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
Rnor_6.0 Ensembl	3	13,240,999 - 13,435,979 (-)	Ensembl

RefSeq Acc Id:

ENSRNOT00000082036 ⟹ ENSRNOP00000075035

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
Rnor_6.0 Ensembl	3	13,182,024 - 13,525,983 (-)	Ensembl

RefSeq Acc Id:

NM_001107834 ⟹ NP_001101304

RefSeq Status:

PROVISIONAL

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
Rnor_6.0	3	13,241,477 - 13,436,022 (-)	NCBI
Rnor_5.0	3	18,569,183 - 18,763,413 (-)	NCBI
RGSC_v3.4	3	13,200,261 - 13,405,859 (-)	RGD
Celera	3	12,211,343 - 12,404,425 (-)	RGD

Sequence:

show sequence

CTTCGCCTCCGCCGCCGCCGCCCGCTCCCGCCCGCGCGCGGCGGGATGGACGATCAATCCAGGA
TGCTGCAGACTCTGGCCGGGGTGAACCTGGCCGGCCACTCGGTCCAAGGGGGTATGGCTCTGCC
GCCTCCCCCTCACGGCCACGAAGGGGCGGACGGCGACGGCAGGAAGCAGGACATCGGCGACATC
CTCCACCAGATCATGACCATCACCGACCAGAGCTTGGACGAGGCGCAAGCAAAGAAACATGCTC
TGAACTGTCACAGAATGAAACCGGCGCTCTTCAGCGTCTTGTGTGAGATCAAAGAGAAAACAGG
TCTCAGCATCAGAGGAGCCCAGGAGGAAGACCCTCCCGACCCCCAGCTAATGAGACTGGACAAT
ATGCTTTTGGCAGAAGGGGTTTCAGGTCCTGAGAAAGGTGGGGGATCGGCGGCAGCAGCTGCAG
CCGCGGCAGCCTCTGGAGGTTCTTCAGATAACTCTATTGAACACTCAGATTACAGAGCCAAATT
GACCCAGATCAGACAAATCTATCACACAGAACTGGAGAAATATGAACAGGCATGTAATGAATTC
ACAACACACGTGATGAACCTTCTCCGAGAACAGAGTAGAACGCGTCCCATTTCCCCGAAAGAGA
TCGAAAGGATGGTGGGCATCATCCACAGGAAGTTTAGCTCCATCCAAATGCAGCTCAAGCAGAG
CACGTGTGAAGCAGTCATGATTTTAAGATCAAGGTTCCTTGATGCCAGACGGAAAAGGCGTAAC
TTCAGTAAACAGGCTACAGAAATCTTGAATGAATATTTTTACTCACACCTCAGCAACCCCTACC
CCAGTGAAGAAGCCAAAGAGGAGCTGGCCAAGAAATGCAGCATCACAGTATCACAGGTATCCAA
CTGGTTTGGCAACAAACGAATCAGGTACAAGAAGAACATCGGCAAATTTCAAGAGGAGGCCAAT
CTCTATGCTGCAAAAACAGCCGTGACAGCCGCACACGCAGTGGCCGCAGCCGTGCAGAACAACC
AGACCAACTCACCCACCACGCCAAACTCTGGTTCTTCTGGTTCTTTTAACCTCCCAAATTCTGG
GGACATGTTCATGAACATGCAGAGTCTGAATGGGGATTCTTACCAAGGGTCCCAAGTCGGAGCC
AATGTGCAGTCACAGGTGGATACCCTCCGTCATGTTATCAATCAGACGGGAGGCTACAGTGACG
GCCTTGGAGCAAACTCACTGTACAGTCCGCATAACTTAAACGCTAATGGAGGCTGGCAGGACGC
AACAACTCCATCTTCTGTGACTTCTCCTACGGAAGGCCCGGGCAGCGTGCACTCGGATACCTCT
AACTAATCCTGGCCTCTCCCAGCTGTCATGCCTTGACAAGCGCATTCGGAGCAATAGGAGGAGG
AGGGAAGCGTTTTGTAACCCACCACCTACAGCTTTACTGTAAACCCTGTCTTCTTAGAGAACTC
GGGAAACCTGTTTTTTAAGGAATCATAACCATTTGTATTTAAACTTAAGACACACGTTTAAAGG
AAAGCACTTTATCCGATTAGGCCGAGACGTAACATTGTTGACAGTTCTTAACTGTCTCATCCTA
ATTTATTATTACATTTTACAGTAATGGTTCCACAGTTGCCAGTTCCTTGGCCTTAAGGGTAAGA
AGTACCATCTATGCTAGACCCCAATTATAGAGCAGGCAAGGTTCACCCTGCCTACGCTGAGCCC
TGGCGGATTTCCATGCAGGCTCTCATCGTTCTCACGTCACGGATGGGCTTGGAGGGAAGGCGAT
GTCTGCCTGTCTTCTTAAGGAAGGCATTTCAGAACTTCCCTCGCCATGTTTGTGTTGCCATCTC
TTATGTTGTAATTAGGTCAAAGACTGGTGGCCTCCTTTCTCCCTCTGAAGTACCAGAGCCCGGA
GTCTGCGCTAATGAGACCATGGATCCAGATTGCCCTGAGATGAAGATCTTGCTGCTACAGAGGT
GAAAACAAGACCTGTCTGGGGTTTGACCGTGTGCGCTGGGTGCTGCACAGACTTGTCAAGGTGT
GCTCTTCCTCTGGGCAGCCTGGAAAGGCCCTGCTCTCTGGAGTGCTGTATATAGTGTAGCAAAA
GAGTATTTATACATCCCACCAATCAAAACACAGCTTTATTACCTCATGCGAACTCATACAAACC
AATAGAATCCCAACATGTTCTGTAGCTTAGAGCGCTCACTTACTACCTCTGAACAATACTCACG
CTGTAGTTCGTCTCTTTCTTATCTTTTTGCATCTTGTAATTAACTCTTTGTTTCCCTTCACAAA
ATGTAATGTACATT

hide sequence

RefSeq Acc Id:

XM_006233975 ⟹ XP_006234037

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
Rnor_6.0	3	13,241,031 - 13,436,084 (-)	NCBI
Rnor_5.0	3	18,569,183 - 18,763,413 (-)	NCBI

Sequence:

show sequence

CTCCCCCTCCCCCTAACCCCTCCTTTCTTCTCCTCCCTCGCCGCCGCCGCCGCCGCCTCAGCCT
TCGCCTCCGCCGCCGCCGCCCGCTCCCGCCCGCGCGCGGCGGGATGGACGATCAATCCAGGATG
CTGCAGACTCTGGCCGGGGTGAACCTGGCCGGCCACTCGGTCCAAGGGGGTATGGCTCTGCCGC
CTCCCCCTCACGGCCACGAAGGGGCGGACGGCGACGGCAGGAAGCAGGACATCGGCGACATCCT
CCACCAGATCATGACCATCACCGACCAGAGCTTGGACGAGGCGCAAGCAAAGAAACATGCTCTG
AACTGTCACAGAATGAAACCGGCGCTCTTCAGCGTCTTGTGTGAGATCAAAGAGAAAACAGGTC
TCAGCATCAGAGGAGCCCAGGAGGAAGACCCTCCCGACCCCCAGCTAATGAGACTGGACAATAT
GCTTTTGGCAGAAGGGGTTTCAGGTCCTGAGAAAGGTGGGGGATCGGCGGCAGCAGCTGCAGCC
GCGGCAGCCTCTGGAGGTTCTTCAGATAACTCTATTGAACACTCAGATTACAGAGCCAAATTGA
CCCAGATCAGACAAATCTATCACACAGAACTGGAGAAATATGAACAGGCATGTAATGAATTCAC
AACACACGTGATGAACCTTCTCCGAGAACAGAGTAGAACGCGTCCCATTTCCCCGAAAGAGATC
GAAAGGATGGTGGGCATCATCCACAGGAAGTTTAGCTCCATCCAAATGCAGCTCAAGCAGAGCA
CGTGTGAAGCAGTCATGATTTTAAGATCAAGGTTCCTTGATGCCAGACGGAAAAGGCGTAACTT
CAGTAAACAGGCTACAGAAATCTTGAATGAATATTTTTACTCACACCTCAGCAACCCCTACCCC
AGTGAAGAAGCCAAAGAGGAGCTGGCCAAGAAATGCAGCATCACAGTATCACAGGTATCCAACT
GGTTTGGCAACAAACGAATCAGGTACAAGAAGAACATCGGCAAATTTCAAGAGGAGGCCAATCT
CTATGCTGCAAAAACAGCCGTGACAGCCGCACACGCAGTGGCCGCAGCCGTGCAGAACAACCAG
ACCAACTCACCCACCACGCCAAACTCTGGTGGATACCCTCCGTCATGTTATCAATCAGACGGGA
GGCTACAGTGACGGCCTTGGAGCAAACTCACTGTACAGTCCGCATAACTTAAACGCTAATGGAG
GCTGGCAGGACGCAACAACTCCATCTTCTGTGACTTCTCCTACGGAAGGCCCGGGCAGCGTGCA
CTCGGATACCTCTAACTAATCCTGGCCTCTCCCAGCTGTCATGCCTTGACAAGCGCATTCGGAG
CAATAGGAGGAGGAGGGAAGCGTTTTGTAACCCACCACCTACAGCTTTACTGTAAACCCTGTCT
TCTTAGAGAACTCGGGAAACCTGTTTTTTAAGGAATCATAACCATTTGTATTTAAACTTAAGAC
ACACGTTTAAAGGAAAGCACTTTATCCGATTAGGCCGAGACGTAACATTGTTGACAGTTCTTAA
CTGTCTCATCCTAATTTATTATTACATTTTACAGTAATGGTTCCACAGTTGCCAGTTCCTTGGC
CTTAAGGGTAAGAAGTACCATCTATGCTAGACCCCAATTATAGAGCAGGCAAGGTTCACCCTGC
CTACGCTGAGCCCTGGCGGATTTCCATGCAGGCTCTCATCGTTCTCACGTCACGGATGGGCTTG
GAGGGAAGGCGATGTCTGCCTGTCTTCTTAAGGAAGGCATTTCAGAACTTCCCTCGCCATGTTT
GTGTTGCCATCTCTTATGTTGTAATTAGGTCAAAGACTGGTGGCCTCCTTTCTCCCTCTGAAGT
ACCAGAGCCCGGAGTCTGCGCTAATGAGACCATGGATCCAGATTGCCCTGAGATGAAGATCTTG
CTGCTACAGAGGTGAAAACAAGACCTGTCTGGGGTTTGACCGTGTGCGCTGGGTGCTGCACAGA
CTTGTCAAGGTGTGCTCTTCCTCTGGGCAGCCTGGAAAGGCCCTGCTCTCTGGAGTGCTGTATA
TAGTGTAGCAAAAGAGTATTTATACATCCCACCAATCAAAACACAGCTTTATTACCTCATGCGA
ACTCATACAAACCAATAGAATCCCAACATGTTCTGTAGCTTAGAGCGCTCACTTACTACCTCTG
AACAATACTCACGCTGTAGTTCGTCTCTTTCTTATCTTTTTGCATCTTGTAATTAACTCTTTGT
TTCCCTTCACAAAATGTAATGTACATTGTAATCTTTTAAAAGAAAACTCAGGGTTGCATTTGCA
ACCCTTAAAAAGCCCAGATCGGCAACATTGGGTCTGACTCCTAACACGGACCATCCCAGCTGTT
GTAAATACTGAGACGCGTGTTGAATGTTCTTCATCTTGTTACTAATCCATATGAAGAAAAAGGA
AAAAAGAAAAAAAAAAAGGCGGGTTCTTGTGATGCGTTCAGATTCAGTACTCAGCACTGTACAT
TTCACCCTGTGTGGCGGGCCCTCTCCTCCTCTTTTTGTATTGTATGCGATTCTGAAACTGACTG
GGTCGTGACAATAATTCGTGGCGGTGATTCTGATGTATTAAAAGCGTTCCGTGTTCCTTTCTAC
TGGCTCACACCCTGGATTGAAAAGTCTTCCTTGTGGTAGTTATATGTAGTTTCAAACATGAATA
AACTTTGCTTTCCTGATTAAACCTA

hide sequence

Protein Sequences


Protein RefSeqs	NP_001101304	(Get FASTA)	NCBI Sequence Viewer
	XP_006234037	(Get FASTA)	NCBI Sequence Viewer
GenBank Protein	EDL93176	(Get FASTA)	NCBI Sequence Viewer

Reference Sequences

RefSeq Acc Id:

NP_001101304 ⟸ NM_001107834

- UniProtKB:

D4AB31 (UniProtKB/TrEMBL)

- Sequence:

show sequence

MDDQSRMLQTLAGVNLAGHSVQGGMALPPPPHGHEGADGDGRKQDIGDILHQIMTITDQSLDEA
QAKKHALNCHRMKPALFSVLCEIKEKTGLSIRGAQEEDPPDPQLMRLDNMLLAEGVSGPEKGGG
SAAAAAAAAASGGSSDNSIEHSDYRAKLTQIRQIYHTELEKYEQACNEFTTHVMNLLREQSRTR
PISPKEIERMVGIIHRKFSSIQMQLKQSTCEAVMILRSRFLDARRKRRNFSKQATEILNEYFYS
HLSNPYPSEEAKEELAKKCSITVSQVSNWFGNKRIRYKKNIGKFQEEANLYAAKTAVTAAHAVA
AAVQNNQTNSPTTPNSGSSGSFNLPNSGDMFMNMQSLNGDSYQGSQVGANVQSQVDTLRHVINQ
TGGYSDGLGANSLYSPHNLNANGGWQDATTPSSVTSPTEGPGSVHSDTSN

hide sequence

RefSeq Acc Id:

XP_006234037 ⟸ XM_006233975

- Peptide Label:

isoform X1

- Sequence:

show sequence

MDDQSRMLQTLAGVNLAGHSVQGGMALPPPPHGHEGADGDGRKQDIGDILHQIMTITDQSLDEA
QAKKHALNCHRMKPALFSVLCEIKEKTGLSIRGAQEEDPPDPQLMRLDNMLLAEGVSGPEKGGG
SAAAAAAAAASGGSSDNSIEHSDYRAKLTQIRQIYHTELEKYEQACNEFTTHVMNLLREQSRTR
PISPKEIERMVGIIHRKFSSIQMQLKQSTCEAVMILRSRFLDARRKRRNFSKQATEILNEYFYS
HLSNPYPSEEAKEELAKKCSITVSQVSNWFGNKRIRYKKNIGKFQEEANLYAAKTAVTAAHAVA
AAVQNNQTNSPTTPNSGGYPPSCYQSDGRLQ

hide sequence

RefSeq Acc Id:

ENSRNOP00000075035 ⟸ ENSRNOT00000082036

RefSeq Acc Id:

ENSRNOP00000029846 ⟸ ENSRNOT00000029600

Protein Domains

Homeobox

Transcriptome

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

Promoters

RGD ID:

13692003

Promoter ID:

EPDNEW_R2528

Type:

single initiation site

Name:

Pbx3_1

Description:

PBX homeobox 3

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	3	13,436,058 - 13,436,118	EPDNEW

Strain Variation

Strain Sequence Variants (Rnor 6.0)

ACI/EurMcwi (MCW)

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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)

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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)

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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)

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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)

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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)

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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)

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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)

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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)

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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)

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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)

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CSV

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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)

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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)

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CSV

TAB

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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)

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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)

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CSV

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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)

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CSV

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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)

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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)

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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)

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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)

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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)

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CSV

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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)

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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)

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CSV

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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)

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CSV

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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)

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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)

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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)

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CSV

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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)

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CSV

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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)

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CSV

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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)

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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)

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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)

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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)

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CSV

TAB

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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)

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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)

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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)

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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)

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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)

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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)

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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)

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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)

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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)

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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

Damaging Variants

Assembly: Rnor_6.0

Chromosome	Start Pos	End Pos	Reference Nucleotide	Variant Nucleotide	Variant Type	Strain
3	13288522	13288523	G	A	snv	CDR

Additional Information

External Database Links

Database	Acc Id	Source(s)
AGR Gene	RGD:1307198	AgrOrtholog
Ensembl Genes	ENSRNOG00000022162	Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein	ENSRNOP00000029846	ENTREZGENE, UniProtKB/TrEMBL
	ENSRNOP00000075035	ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript	ENSRNOT00000029600	ENTREZGENE, UniProtKB/TrEMBL
	ENSRNOT00000082036	ENTREZGENE, UniProtKB/TrEMBL
InterPro	Homeobox	UniProtKB/TrEMBL
	Homeobox_CS	UniProtKB/TrEMBL
	Homeodomain-like	UniProtKB/TrEMBL
	PBX	UniProtKB/TrEMBL
KEGG Report	rno:311876	UniProtKB/TrEMBL
NCBI Gene	311876	ENTREZGENE
Pfam	Homeobox	UniProtKB/TrEMBL
	PBC	UniProtKB/TrEMBL
PhenoGen	Pbx3	PhenoGen
PROSITE	HOMEOBOX_1	UniProtKB/TrEMBL
	HOMEOBOX_2	UniProtKB/TrEMBL
SMART	HOX	UniProtKB/TrEMBL
Superfamily-SCOP	Homeodomain_like	UniProtKB/TrEMBL
UniGene	Rn.162662	ENTREZGENE
UniProt	A0A0G2K9K8_RAT	UniProtKB/TrEMBL
	D4AB31	ENTREZGENE, UniProtKB/TrEMBL

Nomenclature History

Date	Current Symbol	Current Name	Previous Symbol	Previous Name	Description	Reference	Status
2016-05-26	Pbx3	PBX homeobox 3	Pbx3	pre-B-cell leukemia homeobox 3	Nomenclature updated to reflect human and mouse nomenclature	1299863	APPROVED
2008-10-30	Pbx3	pre-B-cell leukemia homeobox 3	Pbx3	pre B-cell leukemia transcription factor 3	Nomenclature updated to reflect human and mouse nomenclature	1299863	APPROVED
2008-04-30	Pbx3	pre B-cell leukemia transcription factor 3	Pbx3_predicted	pre B-cell leukemia transcription factor 3 (predicted)	'predicted' is removed	2292626	APPROVED
2005-01-12	Pbx3_predicted	pre B-cell leukemia transcription factor 3 (predicted)			Symbol and Name status set to approved	70820	APPROVED

RGD is funded by grant HL64541 from the National Heart, Lung, and Blood Institute on behalf of the NIH.

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)