Hoxd3 (homeo box D3) - Rat Genome Database

Name: Hoxd3
Creator: Rat Genome Database
License: Creative Commons CC BY 4.0
Keywords: Rat Gene RGD Genome

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Gene: Hoxd3 (homeo box D3) Rattus norvegicus

Analyze

Symbol:

Hoxd3

Name:

homeo box D3

RGD ID:

1588601

Description:

Predicted to enable 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 Notch signaling pathway; embryonic skeletal system morphogenesis; and positive regulation of macromolecule metabolic process. Predicted to act upstream of or within several processes, including glossopharyngeal nerve morphogenesis; positive regulation of neuron differentiation; and thyroid gland development. Predicted to be located in aggresome and nuclear body. Predicted to be active in nucleus. Orthologous to human HOXD3 (homeobox D3); INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; 2,3,7,8-Tetrachlorodibenzofuran; ammonium chloride.

Type:

protein-coding

RefSeq Status:

VALIDATED

Also known as:

homeo box D3 (mapped); Homeobox gene D3; homeobox protein Hox-D3; homeobox protein R6; Hox4r6; Hoxd3_mapped

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):	HOXD3 (homeobox D3)	HGNC	EggNOG, Ensembl, HomoloGene, NCBI, OMA, OrthoDB, OrthoMCL, Panther
Mus musculus (house mouse):	Hoxd3 (homeobox D3)	HGNC	EggNOG, OrthoMCL, NCBI, OMA, HomoloGene, Panther, OrthoDB, Ensembl
Chinchilla lanigera (long-tailed chinchilla):	Hoxd3 (homeobox D3)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Pan paniscus (bonobo/pygmy chimpanzee):	HOXD3 (homeobox D3)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Canis lupus familiaris (dog):	HOXD3 (homeobox D3)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Ictidomys tridecemlineatus (thirteen-lined ground squirrel):	Hoxd3 (homeobox D3)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Sus scrofa (pig):	HOXD3 (homeobox D3)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Chlorocebus sabaeus (green monkey):	HOXD3 (homeobox D3)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Heterocephalus glaber (naked mole-rat):	Hoxd3 (homeobox D3)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Other homologs ²
Homo sapiens (human):	HOXB3 (homeobox B3)	HGNC	OrthoDB
Homo sapiens (human):	HOXA3 (homeobox A3)	HGNC	OrthoDB
Alliance orthologs ³
Homo sapiens (human):	HOXD3 (homeobox D3)	Alliance	DIOPT (HGNC\|OrthoFinder\|PhylomeDB\|TreeFam)
Mus musculus (house mouse):	Hoxd3 (homeobox D3)	Alliance	DIOPT (OrthoFinder\|PhylomeDB\|TreeFam)
Danio rerio (zebrafish):	hoxd3a (homeobox D3a)	Alliance	DIOPT (OrthoFinder\|PhylomeDB\|TreeFam)

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	3	59,638,708 - 59,650,282 (+)	NCBI	mRatBN7.2
mRatBN7.2 Ensembl	3	59,638,708 - 59,650,282 (+)	Ensembl
Rnor_6.0	3	61,650,569 - 61,670,285 (+)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_6.0 Ensembl	3	61,658,245 - 61,670,282 (+)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_5.0	3	68,119,385 - 68,135,819 (+)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	3	57,358,585 - 57,361,651 (+)	NCBI	RGSC3.4		rn4	RGSC3.4
Celera	3	59,160,179 - 59,171,694 (+)	NCBI		Celera
Cytogenetic Map	3	q23	NCBI

JBrowse:

View Region in Genome Browser (JBrowse)

Model

Annotation Click to see Annotation Detail View

Disease Annotations Click to see Annotation Detail View

Prostatic Neoplasms (ISO)

Gene-Chemical Interaction Annotations Click to see Annotation Detail View

(+)-catechin (ISO)

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

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

4,4'-diaminodiphenylmethane (ISO)

4-hydroxyphenyl retinamide (ISO)

5-aza-2'-deoxycytidine (ISO)

aflatoxin B1 (ISO)

all-trans-retinoic acid (ISO)

ammonium chloride (EXP)

antirheumatic drug (ISO)

arsenite(3-) (ISO)

belinostat (ISO)

benzo[a]pyrene (ISO)

bis(2-chloroethyl) sulfide (ISO)

bis(2-ethylhexyl) phthalate (EXP)

bisphenol A (ISO)

Butylbenzyl phthalate (EXP)

cadmium dichloride (ISO)

chlordecone (ISO)

chlorpyrifos (ISO)

choline (ISO)

copper atom (EXP)

copper(0) (EXP)

Cuprizon (EXP)

dibutyl phthalate (EXP)

diethyl phthalate (EXP)

diisobutyl phthalate (EXP)

diisononyl phthalate (EXP)

disodium selenite (ISO)

ethanol (ISO)

flavonoids (ISO)

folic acid (ISO)

gentamycin (EXP)

glycidol (EXP)

indometacin (ISO)

L-methionine (ISO)

nickel atom (ISO)

potassium dichromate (ISO)

silicon dioxide (ISO)

sodium arsenite (ISO)

testosterone (ISO)

valproic acid (ISO)

vorinostat (ISO)

Gene Ontology Annotations Click to see Annotation Detail View

Biological Process

anterior/posterior pattern specification (IBA,IEA,ISO)

cartilage development (IEA,ISO)

cell-matrix adhesion (ISO)

embryonic skeletal system morphogenesis (IBA,IEA,ISO)

glossopharyngeal nerve morphogenesis (IEA,ISO)

Notch signaling pathway (ISO)

positive regulation of gene expression (ISO)

positive regulation of neuron differentiation (IEA,ISO)

positive regulation of transcription by RNA polymerase II (ISO)

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

thyroid gland development (IEA,ISO)

transcription, DNA-templated (ISO)

Cellular Component

aggresome (ISO)

nuclear body (ISO)

nucleoplasm (ISO)

nucleus (IBA,IEA)

Molecular Function

DNA binding (IEA)

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

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

protein binding (ISO)

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

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

sequence-specific double-stranded DNA binding (ISO)

References

References - curated


1.	Chung SY, etal., Mamm Genome 1993 Sep;4(9):537-40.
2.	Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
3.	RGD automated data pipeline
4.	RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
5.	RGD automated import pipeline for gene-chemical interactions

Additional References at PubMed

PMID:2907739	PMID:7742539	PMID:7910549	PMID:7913519	PMID:7913891	PMID:9441667	PMID:9520319	PMID:12836255	PMID:14610084	PMID:18164701

Genomics

Comparative Map Data

Hoxd3
(Rattus norvegicus - Norway rat)

Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
mRatBN7.2	3	59,638,708 - 59,650,282 (+)	NCBI	mRatBN7.2
mRatBN7.2 Ensembl	3	59,638,708 - 59,650,282 (+)	Ensembl
Rnor_6.0	3	61,650,569 - 61,670,285 (+)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_6.0 Ensembl	3	61,658,245 - 61,670,282 (+)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_5.0	3	68,119,385 - 68,135,819 (+)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	3	57,358,585 - 57,361,651 (+)	NCBI	RGSC3.4		rn4	RGSC3.4
Celera	3	59,160,179 - 59,171,694 (+)	NCBI		Celera
Cytogenetic Map	3	q23	NCBI

HOXD3
(Homo sapiens - human)

Human Assembly	Chr	Position (strand)	Source	Genome Browsers
Human Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCh38.p13 Ensembl	2	176,136,612 - 176,173,102 (+)	Ensembl	GRCh38		hg38	GRCh38
GRCh38	2	176,157,307 - 176,173,102 (+)	NCBI	GRCh38	GRCh38	hg38	GRCh38
GRCh37	2	177,022,035 - 177,037,826 (+)	NCBI	GRCh37	GRCh37	hg19	GRCh37
Build 36	2	176,737,051 - 176,746,072 (+)	NCBI	NCBI36		hg18	NCBI36
Build 34	2	176,854,311 - 176,863,333	NCBI
Celera	2	170,637,984 - 170,647,006 (+)	NCBI
Cytogenetic Map	2	q31.1	NCBI
HuRef	2	168,905,653 - 168,914,773 (+)	NCBI		HuRef
CHM1_1	2	177,034,674 - 177,043,694 (+)	NCBI		CHM1_1

Hoxd3
(Mus musculus - house mouse)

Mouse Assembly	Chr	Position (strand)	Source	Genome Browsers
Mouse Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCm39	2	74,542,337 - 74,578,615 (+)	NCBI	GRCm39		mm39
GRCm39 Ensembl	2	74,542,271 - 74,578,786 (+)	Ensembl
GRCm38	2	74,711,993 - 74,748,271 (+)	NCBI	GRCm38	GRCm38	mm10	GRCm38
GRCm38.p6 Ensembl	2	74,711,927 - 74,748,442 (+)	Ensembl	GRCm38		mm10	GRCm38
MGSCv37	2	74,550,050 - 74,586,328 (+)	NCBI	GRCm37		mm9	NCBIm37
MGSCv36	2	74,544,767 - 74,548,445 (+)	NCBI			mm8
Celera	2	76,382,118 - 76,418,402 (+)	NCBI		Celera
Cytogenetic Map	2	C3	NCBI
cM Map	2	44.13	NCBI

Hoxd3
(Chinchilla lanigera - long-tailed chinchilla)

Chinchilla Assembly	Chr	Position (strand)	Source	Genome Browsers
Chinchilla Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
ChiLan1.0	NW_004955403	20,489,663 - 20,496,021 (-)	NCBI	ChiLan1.0	ChiLan1.0

HOXD3
(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	2B	181,141,538 - 181,161,604 (+)	NCBI	panpan1.1	PanPan1.1	panPan2
PanPan1.1 Ensembl	2B	181,141,538 - 181,161,604 (+)	Ensembl	panpan1.1		panPan2
Mhudiblu_PPA_v0	2B	63,432,720 - 63,452,816 (+)	NCBI	Mhudiblu_PPA_v0		panPan3

HOXD3
(Canis lupus familiaris - dog)

Dog Assembly	Chr	Position (strand)	Source	Genome Browsers
Dog Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
CanFam3.1	36	19,961,393 - 19,981,672 (+)	NCBI	CanFam3.1	CanFam3.1	canFam3	CanFam3.1
CanFam3.1 Ensembl	36	19,960,761 - 19,980,525 (+)	Ensembl	CanFam3.1		canFam3	CanFam3.1
Dog10K_Boxer_Tasha	36	19,981,411 - 19,991,206 (+)	NCBI
ROS_Cfam_1.0	36	20,112,859 - 20,122,679 (+)	NCBI
UMICH_Zoey_3.1	36	20,186,809 - 20,196,601 (+)	NCBI
UNSW_CanFamBas_1.0	36	20,187,489 - 20,197,280 (+)	NCBI
UU_Cfam_GSD_1.0	36	20,299,340 - 20,309,132 (+)	NCBI

Hoxd3
(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_024405303	137,094,251 - 137,107,421 (+)	NCBI
SpeTri2.0	NW_004936509	5,654,737 - 5,659,937 (+)	NCBI	SpeTri2.0	SpeTri2.0		SpeTri2.0

HOXD3
(Sus scrofa - pig)

Pig Assembly	Chr	Position (strand)	Source	Genome Browsers
Pig Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
Sscrofa11.1 Ensembl	15	81,953,834 - 81,973,816 (+)	Ensembl	Sscrofa11.1		susScr11	Sscrofa11.1
Sscrofa11.1	15	81,969,482 - 81,974,893 (+)	NCBI	Sscrofa11.1	Sscrofa11.1	susScr11	Sscrofa11.1
Sscrofa10.2	15	91,436,839 - 91,442,273 (+)	NCBI	Sscrofa10.2	Sscrofa10.2	susScr3

HOXD3
(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	10	61,739,589 - 61,754,845 (+)	NCBI	ChlSab1.1		chlSab2
ChlSab1.1 Ensembl	10	61,744,967 - 61,748,121 (+)	Ensembl	ChlSab1.1		chlSab2
Vero_WHO_p1.0	NW_023666040	137,860,734 - 137,882,021 (-)	NCBI	Vero_WHO_p1.0

Hoxd3
(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 1.0	NW_004624787	13,308,406 - 13,312,770 (+)	NCBI	HetGla_female_1.0		hetGla2

Position Markers

BB104313

Rat Assembly	Chr	Position (strand)	Source	JBrowse
mRatBN7.2	3	59,650,073 - 59,650,218 (+)	MAPPER	mRatBN7.2
Rnor_6.0	3	61,670,074 - 61,670,218	NCBI	Rnor6.0
Rnor_5.0	3	68,135,611 - 68,135,755	UniSTS	Rnor5.0
RGSC_v3.4	3	57,362,290 - 57,362,434	UniSTS	RGSC3.4
Celera	3	59,171,486 - 59,171,630	UniSTS
Cytogenetic Map	3	q23	UniSTS

UniSTS:467540

Rat Assembly	Chr	Position (strand)	Source	JBrowse
mRatBN7.2	3	59,648,676 - 59,649,334 (+)	MAPPER	mRatBN7.2
Rnor_6.0	3	61,668,677 - 61,669,334	NCBI	Rnor6.0
Rnor_5.0	3	68,134,214 - 68,134,871	UniSTS	Rnor5.0
RGSC_v3.4	3	57,360,893 - 57,361,550	UniSTS	RGSC3.4
Celera	3	59,170,135 - 59,170,746	UniSTS
Cytogenetic Map	3	q23	UniSTS

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
2290452	Scl56	Serum cholesterol level QTL 56	2.26		blood cholesterol amount (VT:0000180)	plasma total cholesterol level (CMO:0000585)	3	1	91609953	Rat
1358905	Hrtrt17	Heart rate QTL 17	5.9	0.000014	heart pumping trait (VT:2000009)	heart rate (CMO:0000002)	3	10861912	89878372	Rat
1358885	Bp251	Blood pressure QTL 251	3.8		arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	3	14489145	121056321	Rat
1358888	Bp264	Blood pressure QTL 264	4.43		arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	3	14489145	121056321	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	15005422	76927699	Rat
631676	Cm8	Cardiac mass QTL 8	7.03	0.0001	aorta mass (VT:0002845)	aorta weight (CMO:0000076)	3	16954708	61954708	Rat
10450804	Scl70	Serum cholesterol level QTL 70	4.7	0.001	blood LDL cholesterol amount (VT:0000181)	blood low density lipoprotein cholesterol level (CMO:0000053)	3	20714090	65714090	Rat
10450794	Scl69	Serum cholesterol level QTL 69	6.3	0.001	blood LDL cholesterol amount (VT:0000181)	blood low density lipoprotein cholesterol level (CMO:0000053)	3	20714090	65714090	Rat
2302055	Pia30	Pristane induced arthritis QTL 30	3.5	0.001	blood autoantibody amount (VT:0003725)	serum immunoglobulin M-type rheumatoid factor level relative to an arbitrary reference serum (CMO:0002111)	3	27936919	72936919	Rat
9590286	Uminl1	Urine mineral level QTL 1	3.5	0.001	urine mineral amount (VT:0015086)	urine electrolyte level (CMO:0000593)	3	28249687	73249687	Rat
8694196	Abfw2	Abdominal fat weight QTL 2	16.58	0.001	visceral adipose mass (VT:0010063)	abdominal fat pad weight to body weight ratio (CMO:0000095)	3	28249687	73249687	Rat
8694386	Bw159	Body weight QTL 159	4.52	0.001	body lean mass (VT:0010483)	lean tissue morphological measurement (CMO:0002184)	3	28249687	73249687	Rat
8552950	Pigfal12	Plasma insulin-like growth factor 1 level QTL 12	7.3		blood insulin-like growth factor amount (VT:0010479)	plasma insulin-like growth factor 1 level (CMO:0001299)	3	28249687	73249687	Rat
9590136	Scort3	Serum corticosterone level QTL 3	23.37	0.001	blood corticosterone amount (VT:0005345)	plasma corticosterone level (CMO:0001173)	3	28249687	73249687	Rat
2303593	Gluco46	Glucose level QTL 46	3		blood glucose amount (VT:0000188)	blood glucose level (CMO:0000046)	3	28468571	73468571	Rat
1354590	Despr11	Despair related QTL 11		0.000031	locomotor behavior trait (VT:0001392)	amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)	3	28468571	73468571	Rat
737818	Hcar12	Hepatocarcinoma resistance QTL 12	2.6		liver integrity trait (VT:0010547)	volume of individual liver tumorous lesion (CMO:0001078)	3	29463235	118376539	Rat
61419	Cia11	Collagen induced arthritis QTL 11	5.6		joint integrity trait (VT:0010548)	joint inflammation composite score (CMO:0000919)	3	30356773	98535386	Rat
61356	Bp37	Blood pressure QTL 37	3		blood pressure trait (VT:0000183)	systolic blood pressure (CMO:0000004)	3	30684642	75684642	Rat
631647	Bp122	Blood pressure QTL 122	6.2		arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	3	30684642	75684642	Rat
70216	Cm14	Cardiac mass QTL 14	2.1		heart mass (VT:0007028)	heart wet weight (CMO:0000069)	3	31172320	163586636	Rat
11565451	Bw177	Body weight QTL 177		0.002	body mass (VT:0001259)	body weight (CMO:0000012)	3	31426403	70668733	Rat
11565452	Kidm57	Kidney mass QTL 57		0.001	kidney mass (VT:0002707)	both kidneys wet weight to body weight ratio (CMO:0000340)	3	31426403	70668733	Rat
12879866	Cm94	Cardiac mass QTL 94		0.001	heart left ventricle mass (VT:0007031)	heart left ventricle weight to body weight ratio (CMO:0000530)	3	31426403	70668733	Rat
12879867	Cm95	Cardiac mass QTL 95		0.047	heart right ventricle mass (VT:0007033)	heart right ventricle weight to body weight ratio (CMO:0000914)	3	31426403	70668733	Rat
12879868	Am6	Aortic mass QTL 6		0.001	aorta mass (VT:0002845)	aorta weight to aorta length to body weight ratio (CMO:0002722)	3	31426403	70668733	Rat
2301400	Cm68	Cardiac mass QTL 68		0.001	heart mass (VT:0007028)	heart wet weight to body weight ratio (CMO:0002408)	3	31426403	70668733	Rat
1300169	Bp177	Blood pressure QTL 177	2.96		arterial blood pressure trait (VT:2000000)	blood pressure time series experimental set point of the baroreceptor response (CMO:0002593)	3	33703347	61017857	Rat
1354589	Bw31	Body weight QTL 31	3.3		body mass (VT:0001259)	body weight (CMO:0000012)	3	33703347	78196190	Rat
1354604	Bw36	Body weight QTL 36	2.9		body mass (VT:0001259)	body weight (CMO:0000012)	3	33703347	104104347	Rat
1358362	Srcrt2	Stress Responsive Cort QTL 2	2.78		blood corticosterone amount (VT:0005345)	plasma corticosterone level (CMO:0001173)	3	38192233	133483320	Rat
738019	Anxrr10	Anxiety related response QTL 10	3.9		exploratory behavior trait (VT:0010471)	number of entries into a discrete space in an experimental apparatus (CMO:0000960)	3	38517803	83517803	Rat
2302276	Bw82	Body weight QTL 82	4.32		body mass (VT:0001259)	body weight (CMO:0000012)	3	39454637	62951183	Rat
1331777	Bw24	Body weight QTL 24	3.503		body mass (VT:0001259)	body weight (CMO:0000012)	3	39454637	89115240	Rat
1331795	Rf30	Renal function QTL 30	3.708		urine potassium amount (VT:0010539)	urine potassium level (CMO:0000128)	3	39454637	89115240	Rat
1354597	Kidm13	Kidney mass QTL 13	2.9		kidney mass (VT:0002707)	right kidney wet weight (CMO:0000082)	3	41874578	104104347	Rat
2301970	Bw81	Body weight QTL 81	5.19		body mass (VT:0001259)	body weight (CMO:0000012)	3	41874578	155617519	Rat
2301971	Cm71	Cardiac mass QTL 71	4.63		heart left ventricle mass (VT:0007031)	heart left ventricle weight (CMO:0000776)	3	41874578	155617519	Rat
1300178	Hrtrt4	Heart rate QTL 4	3.74		heart pumping trait (VT:2000009)	heart rate (CMO:0000002)	3	43827364	90905114	Rat
1581503	Cm58	Cardiac mass QTL 58	2.7	0.05	heart left ventricle mass (VT:0007031)	heart left ventricle weight to body weight ratio (CMO:0000530)	3	43827364	121056321	Rat
1559282	Emca5	Estrogen-induced mammary cancer QTL 5	3.9		mammary gland integrity trait (VT:0010552)	percentage of study population developing mammary tumors during a period of time (CMO:0000948)	3	43827364	169034231	Rat
2292591	Esta4	Estrogen-induced thymic atrophy QTL 4			thymus mass (VT:0004954)	thymus wet weight (CMO:0000855)	3	47233211	147415807	Rat
1358186	Ept2	Estrogen-induced pituitary tumorigenesis QTL 2	8.3		pituitary gland mass (VT:0010496)	pituitary gland wet weight (CMO:0000853)	3	47233430	110362260	Rat
2292613	Ept16	Estrogen-induced pituitary tumorigenesis QTL 16	8.3		pituitary gland mass (VT:0010496)	pituitary gland wet weight (CMO:0000853)	3	47233430	110362260	Rat
631665	Bw8	Body weight QTL 8	5.5		body mass (VT:0001259)	body weight (CMO:0000012)	3	50437042	119183768	Rat
724523	Tsu1	Thymus enlargement suppressive QTL 1	3.84		thymus mass (VT:0004954)	thymus weight to body weight ratio (CMO:0000612)	3	50437504	115638231	Rat
1582249	Bw77	Body weight QTL 77	3.2	0.0025	epididymal fat pad mass (VT:0010421)	epididymal fat pad weight to body weight ratio (CMO:0000658)	3	53184593	64655484	Rat
1582218	Bw74	Body weight QTL 74	3.9	0.0021	body mass (VT:0001259)	body weight (CMO:0000012)	3	53184593	115665732	Rat
1582238	Bw68	Body weight QTL 68	3.2	0.0064	body mass (VT:0001259)	body weight (CMO:0000012)	3	53184593	115665732	Rat
1582239	Epfw1	Epididymal fat weight QTL 1	4.5	0.0006	epididymal fat pad mass (VT:0010421)	epididymal fat pad weight to body weight ratio (CMO:0000658)	3	53184593	115665732	Rat
61377	Edpm3	Estrogen-dependent pituitary mass QTL 3	7.05	0.038	pituitary gland mass (VT:0010496)	pituitary gland wet weight (CMO:0000853)	3	53184692	89878207	Rat
731180	Bp152	Blood pressure QTL 152		0.03	arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	3	53781112	91609953	Rat
731180	Bp152	Blood pressure QTL 152		0.03	arterial blood pressure trait (VT:2000000)	diastolic blood pressure (CMO:0000005)	3	53781112	91609953	Rat
731180	Bp152	Blood pressure QTL 152		0.03	arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	3	53781112	91609953	Rat
1581568	Rf53	Renal function QTL 53			total urine protein amount (VT:0000032)	urine protein excretion rate to body weight ratio (CMO:0001099)	3	56395968	161299569	Rat
8662816	Vetf4	Vascular elastic tissue fragility QTL 4	4		renal artery integrity trait (VT:0010642)	number of ruptures of the internal elastic lamina of the renal arteries (CMO:0002563)	3	59242096	157323038	Rat

miRNA Target Status

Predicted Target Of

	Summary Value
Count of predictions:	63
Count of miRNA genes:	61
Interacting mature miRNAs:	63
Transcripts:	ENSRNOT00000033511
Prediction methods:	Miranda, Rnahybrid
Result types:	miRGate_prediction

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

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

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									1	10	18
Low	2	8	13	4	1	4			16	25	16
Below cutoff	1	10	7	2	8	2	7	8	11		5	1	7

View RNA-SEQ Expression Data

Sequence

Nucleotide Sequences


RefSeq Transcripts	NM_001271038	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_008761881	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_039104414	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
GenBank Nucleotide	CH473949	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	JACYVU010000115	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	M37569	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles

Reference Sequences

RefSeq Acc Id:

ENSRNOT00000033511 ⟹ ENSRNOP00000034938

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2 Ensembl	3	59,638,708 - 59,650,282 (+)	Ensembl
Rnor_6.0 Ensembl	3	61,658,245 - 61,670,282 (+)	Ensembl

RefSeq Acc Id:

NM_001271038 ⟹ NP_001257967

RefSeq Status:

VALIDATED

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2	3	59,638,708 - 59,650,282 (+)	NCBI
Rnor_6.0	3	61,658,245 - 61,670,282 (+)	NCBI
Rnor_5.0	3	68,119,385 - 68,135,819 (+)	NCBI
Celera	3	59,160,179 - 59,171,694 (+)	NCBI

Sequence:

show sequence

GCCGCTTTGGGCCTGGGAGCCGACCGGCGGGCGGGTGGACCGACCAGCGAGCAGCGCAGGCGAA
GCCAGCTTGGGGACTACAAACTCGTTCCTCCAGCGTTTATTGGTAGTTGAACCTCAGCCTGGTT
CCGTTCTACCGGGAATTCCGTGTACTCTGGTATATGGCCGAGTCTGCAAGCGCGCAAGACCAGG
GTTGGGACACTGTTGTCTGCAGACAAAGGGGGAAGGCTAGCTCTGCCCCCCACTGGCGCCCACT
CTGAGACCGAGGACACCAGGTTTATGATAAATTGGGATCCAGGTTACCTGGAGCTTGGAAACTG
GCCCAGCTCTCTCAAGATTAGCAGACACTGGCCTTGGTGGAGAAGGAGACAGTGGTAGTCAATG
TTATTTGAGCAGGGTCAGCAGGCCCTGGAGCTTCCTGAGTGCACCATGCAGAAGGCTGCATACT
ATGAGAACCCAGGACTCTTTGGAGGCTATGGATACAGCAAAGCCACTGATGCATATGGCTATAG
CACTCCTCATCAACCCTACCCACCCCCTGCTGCTGCCAACTCCCTGGACAGTGATTACCCAAGT
TCTGCCTGCTCCATCCAGAGTTCTGCACCTCTTCGAGCCCCAGCCCACAAAGGAGCGGAACTCA
ACGGTAGCTGCATGCGGCCTGGCACTGGGAACAGCCAGGGTGGGGGTGGAGGCAACCAACCTCC
TGGCCTGAACTCAGAGCAGCAGCCACCGCAACCTCCCCCTCCACCACCCACCCTGCCCCCATCC
TCACCCACCAATCCCGGAAGCGGAGTGCCTGCCAAGAAGACCAAGGGTGGGCCCAATGCTTCTA
GCTCTTCCTCTACCATCAGCAAGCAGATCTTCCCCTGGATGAAGGAATCCCGACAGAACTCAAA
GCAGAAGAACAGCTGTGCCACTTCAGGAGAGAACTGCGAGGACAAGAGCCCACCGGGCCCGGCA
TCCAAGAGGGTGCGCACGGCGTACACGAGTGCTCAGCTGGTAGAGCTGGAGAAGGAGTTCCACT
TCAACCGCTACCTGTGCCGGCCGCGCCGCGTGGAGATGGCTAACCTGCTGAACCTCACCGAACG
CCAGATCAAGATCTGGTTCCAGAACCGTCGCATGAAGTACAAGAAGGACCAGAAGGCCAAGGGC
ATCCTGCATTCTCCCGCAGGCCAGTCCCCGGAGCGCAGCCCACCTCTTGGAGGAGCGGCGGGCC
ACGTGGCCTACTCCGGCCAGCTGCCGCCCGTGCCCGGCCTGGCCTACGACGCACCCTCGCCGCC
GGCTTTCGCTAAATCGCAGCCCAATATGTACGGCCTGGCCGCCTACACGGCGCCTCTCAGTAGC
TGCCTGCCGCAGCAGAAGCGTTACGCGGCGCCCGAGTTCGAGCCCCACCCCATGGCGAGCAACG
GCGGCGGCTTCGCCAGCGCCAACCTGCAGGGCAGCCCGGTGTACGTAGGTGGCAACTTCGTCGA
CTCCATGGCGCCCGCGTCCGGGCCGGTCTTCAATCTGGGTCACCTCTCGCACCCGTCTTCGGCC
AGCGTGGACTACAGCTGCGCCGCGCAAATCCCTGGCAACCATCACCACGGACCGTGCGACCCTC
ATCCCACCTACACAGATCTCTCGGCTCACCACACGTCTCAGGGACGCCTGCCCGAGGCCCCCAA
ACTGACACATCTGTAGCGGTTGCCGCCGGCCTGGCGCAATTACCTCTCTGGTTTTGGTGGCAGG
GGTGGTGGCGGGGCGGGGCCCGAAAGGCAGTTTAGGGGAACCCCCCTCCCTGATCTGGCCTGGC
AGATGCCACACGAGTTTCGGGCTTCCAGCGGCCGAGGCTGACGCGACTGGGCCTCCCCTCCAGG
CGTGTCCTCCTTTGGGTGACTCGCTATAAATCAGCCGCAAGGATCCTCCCCTGTAAACCTGACA
GTGCCATAAACTGCGGACCGAGGGACTCTAATCTGGTAATGGTGTCCCTAAGGTAAGTCCTAGA
CCTATCCGTGGCGTGTCCTGAAGAGAGGGACTAGAGCCTGGAGAACCCCGGGCCTGGCCCTTCT
GTCTAGCTTAGTTTCAGAGACCTTAATTTATAATGCTCCTTCCCTTCCTGTAAAGATTGCATCG
GACTAAACAATCTGTATTTATTATTTGAAGCGAGTAATTTCGTTTCCCTGATTATTTATCCTAG
TCTTAATGTATTTATGTGTATATTTGTAGAATTCTGCAGCCGGGCCTAGGTACTCGCTCCCAGG
CCTTTTGGGGGGGGGGCATATTTCATCTCTTTAGTCCCCTTGGTCTGAACTAGTTGAGAGAATA
GTCTTGAACAGTTGTAACCGTGGCTGGTGTCTGTAGTTGTTGTAAAGGACTGAGATCACAAATG
GTCCTTCATGGGTAGAGTCAGGCAGCCCGGTGGCATAGCGCGACTCAAGCGAGTCGTTTCTCAA
CAGCCGAAGCCCTCACCACTCGACACAGCTTACTGATTTCAAATTGTCTGGTACTATTTGAACA
AACATTTAGAATAAAACATTTTTTTCAGTTG

hide sequence

RefSeq Acc Id:

XM_039104414 ⟹ XP_038960342

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2	3	59,645,660 - 59,650,282 (+)	NCBI

Protein Sequences


Protein RefSeqs	NP_001257967	(Get FASTA)	NCBI Sequence Viewer
	XP_038960342	(Get FASTA)	NCBI Sequence Viewer
GenBank Protein	AAA41345	(Get FASTA)	NCBI Sequence Viewer
	EDL79188	(Get FASTA)	NCBI Sequence Viewer
	EDL79189	(Get FASTA)	NCBI Sequence Viewer
	P18867	(Get FASTA)	NCBI Sequence Viewer

Reference Sequences

RefSeq Acc Id:

NP_001257967 ⟸ NM_001271038

- UniProtKB:

D3Z957 (UniProtKB/TrEMBL)

- Sequence:

show sequence

MLFEQGQQALELPECTMQKAAYYENPGLFGGYGYSKATDAYGYSTPHQPYPPPAAANSLDSDYP
SSACSIQSSAPLRAPAHKGAELNGSCMRPGTGNSQGGGGGNQPPGLNSEQQPPQPPPPPPTLPP
SSPTNPGSGVPAKKTKGGPNASSSSSTISKQIFPWMKESRQNSKQKNSCATSGENCEDKSPPGP
ASKRVRTAYTSAQLVELEKEFHFNRYLCRPRRVEMANLLNLTERQIKIWFQNRRMKYKKDQKAK
GILHSPAGQSPERSPPLGGAAGHVAYSGQLPPVPGLAYDAPSPPAFAKSQPNMYGLAAYTAPLS
SCLPQQKRYAAPEFEPHPMASNGGGFASANLQGSPVYVGGNFVDSMAPASGPVFNLGHLSHPSS
ASVDYSCAAQIPGNHHHGPCDPHPTYTDLSAHHTSQGRLPEAPKLTHL

hide sequence

RefSeq Acc Id:

ENSRNOP00000034938 ⟸ ENSRNOT00000033511

RefSeq Acc Id:	XP_038960342 ⟸ XM_039104414
- Peptide Label:	isoform X1

Protein Domains

Homeobox

Transcriptome

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

Strain Variation

Strain Sequence Variants (Rnor 6.0)

ACI/EurMcwi (2019)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	MCW
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

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 (2020)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	NIH
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

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-Lx/CubMcwi (2019)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	MCW
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

BN/NHsdMcwi (2019)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	MCW
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

BN/NHsdMcwi (2020)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	MCW
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

BN/SsN (2020)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	NIH
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

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 (2020)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	NIH
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

BXH2/CubMcwi (2020)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	MCW
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

BXH3/CubMcwi (2020)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	MCW
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

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)

DA/OlaHsd (2019)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	Envigo
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

F344/DuCrl (2019)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	Charles River
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

F344/N (2020)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	NIH
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

F344/NCrl (2019)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	Charles River
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

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

F344/Stm (2019)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	Japan
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

FHH/EurMcwi (2019)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	MCW
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

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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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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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

FXLE16/Stm (2020)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	Japan
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

FXLE18/Stm (2020)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	Japan
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

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/FarMcwi (2019)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	MCW
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

GK/Ox (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

HXB10/IpcvMcwi (2019)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	MCW
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

HXB2/IpcvMcwi (2019)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	MCW
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

HXB20/IpcvMcwi (2020)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	MCW
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

HXB31/IpcvMcwi (2019)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	MCW
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

HXB4/IpcvMcwi (2020)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	MCW
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

LE/Stm (2019)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	Japan
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

LE/Stm (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/Crl (2019)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	Charles River
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

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

LEXF10A/StmMcwi (2020)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	MCW
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

LEXF11/Stm (2020)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	Japan
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

LEXF1A/Stm (2019)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	Japan
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

LEXF1C/Stm (2019)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	Japan
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

LEXF2B/Stm (2019)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	Japan
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

LEXF3/Stm (2020)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	Japan
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

LEXF4/Stm (2020)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	Japan
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

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

LH/MavRrrcAek (2020)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	Kwitek
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

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

LL/MavRrrcAek (2020)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	Kwitek
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

LN/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/MavRrrcAek (2020)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	Kwitek
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

M520/N (2020)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	NIH
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

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

M520/NRrrcMcwi (2019)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	MCW
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

MHS/Gib (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

MNS/Gib (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

MR/N (2020)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	NIH
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

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

MWF/Hsd (2019)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	MCW
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

PVG/Seac (2019)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	Japan
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

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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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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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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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

SHR/OlalpcvMcwi (2019)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	MCW
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

SHRSP/A3NCrl (2019)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	Charles River
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

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 (2020)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	Envigo
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

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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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 (2019)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	MCW
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

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

WAG/RijCrl (2020)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	Charles River
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

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 (2020)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	NIH
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

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 (2019)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	Charles River
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

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 (2020)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	NIH
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

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

Additional Information

External Database Links

Database	Acc Id	Source(s)
AGR Gene	RGD:1588601	AgrOrtholog
Ensembl Genes	ENSRNOG00000001577	Ensembl, UniProtKB/TrEMBL
Ensembl Protein	ENSRNOP00000034938	UniProtKB/TrEMBL
Ensembl Transcript	ENSRNOT00000033511	UniProtKB/TrEMBL
InterPro	DUF4074	UniProtKB/TrEMBL
	Homeobox-like_sf	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	Homeobox_Antennapedia_CS	UniProtKB/TrEMBL
	Homeobox_CS	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	Homeobox_dom	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	Homeobox_metazoa	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report	rno:288152	UniProtKB/TrEMBL
NCBI Gene	288152	ENTREZGENE
Pfam	DUF4074	UniProtKB/TrEMBL
	Homeodomain	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen	Hoxd3	PhenoGen
PRINTS	HOMEOBOX	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PROSITE	ANTENNAPEDIA	UniProtKB/TrEMBL
	HOMEOBOX_1	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	HOMEOBOX_2	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
SMART	HOX	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP	SSF46689	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt	D3Z957	ENTREZGENE, UniProtKB/TrEMBL
	HXD3_RAT	UniProtKB/Swiss-Prot, ENTREZGENE

Nomenclature History

Date	Current Symbol	Current Name	Previous Symbol	Previous Name	Description	Reference	Status
2007-04-13		homeo box D3	Hoxd3	homeo box D3 (mapped)	Name updated	737654	APPROVED
2007-04-11	Hoxd3	homeo box D3 (mapped)	Hoxd3_mapped	homeo box D3 (mapped)	Data Merged	737654	APPROVED
2006-11-19	Hoxd3	homeo box D3 (mapped)			Symbol and Name status set to provisional	70820	PROVISIONAL
2005-11-17	Hoxd3_mapped	homeo box D3 (mapped)	Hoxd3	homeo box D3	Symbol and Name updated	1556543	APPROVED
2002-06-10	Hoxd3	Homeobox gene D3			Symbol and Name status set to approved	70586	APPROVED

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 - CTD