Hoxd9 (homeo box D9) - Rat Genome Database

Name: Hoxd9
Creator: Rat Genome Database
License: Creative Commons CC BY 4.0
Keywords: Rat Gene RGD Genome

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Gene: Hoxd9 (homeo box D9) Rattus norvegicus

Analyze

Symbol:

Hoxd9

Name:

homeo box D9

RGD ID:

1582908

Description:

Predicted to have DNA-binding transcription repressor 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 animal organ development; limb morphogenesis; and regulation of transcription by RNA polymerase II. Predicted to localize to nucleolus and nucleoplasm. Orthologous to human HOXD9 (homeobox D9); INTERACTS WITH bisphenol A; dibutyl phthalate; (+)-catechin (ortholog).

Type:

protein-coding

RefSeq Status:

PROVISIONAL

Also known as:

homeobox Hox-D9; homeobox protein Hox-D9; LOC366083; LOC688999; MGC189507; similar to Homeobox protein Hox-D8 (Hox-4.3) (Hox-5.4)

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):	HOXD9 (homeobox D9)	HGNC	Ensembl, HomoloGene, Inparanoid, NCBI, OrthoDB, Panther, Treefam
Mus musculus (house mouse):	Hoxd9 (homeobox D9)	HGNC	Treefam, NCBI, HomoloGene, Inparanoid, Panther, OrthoDB, Ensembl
Chinchilla lanigera (long-tailed chinchilla):	Hoxd9 (homeobox D9)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Pan paniscus (bonobo/pygmy chimpanzee):	HOXD9 (homeobox D9)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Canis lupus familiaris (dog):	HOXD9 (homeobox D9)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Ictidomys tridecemlineatus (thirteen-lined ground squirrel):	Hoxd9 (homeobox D9)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Sus scrofa (pig):	HOXD9 (homeobox D9)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Chlorocebus sabaeus (African green monkey):	HOXD9 (homeobox D9)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Heterocephalus glaber (naked mole-rat):	Hoxd9 (homeobox D9)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Alliance orthologs ³
Homo sapiens (human):	HOXD9 (homeobox D9)	Alliance	DIOPT (Ensembl Compara\|HGNC\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB)
Mus musculus (house mouse):	Hoxd9 (homeobox D9)	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB)
Danio rerio (zebrafish):	hoxd9a (homeobox D9a)	Alliance	DIOPT (Ensembl Compara\|OMA\|OrthoFinder\|PANTHER\|PhylomeDB)

Latest Assembly:

Rnor_6.0 - RGSC Genome Assembly v6.0

Position:

Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
mRatBN7.2	3	59,600,575 - 59,602,755 (+)	NCBI
Rnor_6.0 Ensembl	3	61,620,192 - 61,622,359 (+)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_6.0	3	61,620,192 - 61,622,360 (+)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_5.0	3	68,086,528 - 68,088,228 (+)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
Celera	3	59,122,389 - 59,124,566 (+)	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

Colorectal Neoplasms (ISO)

hepatocellular carcinoma (ISO)

mucinous adenocarcinoma (ISO)

Neoplastic Processes (ISO)

Ovarian Neoplasms (ISO)

Gene-Chemical Interaction Annotations Click to see Annotation Detail View

(+)-catechin (ISO)

1,1-dichloroethene (ISO)

17beta-estradiol (ISO)

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

4-hydroxyphenyl retinamide (ISO)

aflatoxin B1 (ISO)

atrazine (ISO)

benzo[a]pyrene (ISO)

bisphenol A (EXP,ISO)

choline (ISO)

dibutyl phthalate (EXP)

folic acid (ISO)

L-methionine (ISO)

lead(0) (ISO)

lead(2+) (ISO)

potassium dichromate (ISO)

triclosan (ISO)

tunicamycin (ISO)

vanadyl sulfate (ISO)

Gene Ontology Annotations Click to see Annotation Detail View

Biological Process

adult locomotory behavior (IEA,ISO)

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

embryonic forelimb morphogenesis (IEA,ISO)

embryonic skeletal system development (ISO)

embryonic skeletal system morphogenesis (IBA,IEA,ISO)

forelimb morphogenesis (ISO)

hindlimb morphogenesis (IEA,ISO)

mammary gland development (IEA,ISO)

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

peripheral nervous system neuron development (IEA,ISO)

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

proximal/distal pattern formation (IBA,IEA,ISO)

regulation of gene expression (ISO)

regulation of transcription by RNA polymerase II (IBA)

single fertilization (IEA,ISO)

skeletal muscle tissue development (IEA,ISO)

transcription, DNA-templated (IEA)

Cellular Component

nucleolus (IEA,ISO)

nucleoplasm (IEA,ISO)

nucleus (IBA,ISO)

Molecular Function

DNA binding (ISO)

DNA-binding transcription factor activity (IBA,ISO)

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

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

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

sequence-specific double-stranded 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.	RGD automated import pipeline for gene-chemical interactions

Additional References at PubMed

PMID:1756725	PMID:2568311	PMID:8625797	PMID:9892669	PMID:10642795	PMID:12477932	PMID:17626057	PMID:23760953

Genomics

Comparative Map Data

Hoxd9
(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	59,600,575 - 59,602,755 (+)	NCBI
Rnor_6.0 Ensembl	3	61,620,192 - 61,622,359 (+)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_6.0	3	61,620,192 - 61,622,360 (+)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_5.0	3	68,086,528 - 68,088,228 (+)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
Celera	3	59,122,389 - 59,124,566 (+)	NCBI		Celera
Cytogenetic Map	3	q23	NCBI

HOXD9
(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	176,122,719 - 176,124,937 (+)	Ensembl	GRCh38		hg38	GRCh38
GRCh38	2	176,122,719 - 176,124,937 (+)	NCBI	GRCh38	GRCh38	hg38	GRCh38
GRCh37	2	176,987,447 - 176,989,665 (+)	NCBI	GRCh37	GRCh37	hg19	GRCh37
Build 36	2	176,695,334 - 176,697,770 (+)	NCBI	NCBI36		hg18	NCBI36
Build 34	2	176,812,594 - 176,815,031	NCBI
Celera	2	170,596,564 - 170,598,796 (+)	NCBI
Cytogenetic Map	2	q31.1	NCBI
HuRef	2	168,864,337 - 168,866,570 (+)	NCBI		HuRef
CHM1_1	2	176,993,281 - 176,995,514 (+)	NCBI		CHM1_1

Hoxd9
(Mus musculus - house mouse)

Mouse Assembly	Chr	Position (strand)	Source	Genome Browsers
Mouse Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCm39	2	74,528,107 - 74,530,552 (+)	NCBI	GRCm39		mm39
GRCm39 Ensembl	2	74,528,071 - 74,530,552 (+)	Ensembl
GRCm38	2	74,697,763 - 74,700,208 (+)	NCBI	GRCm38	GRCm38	mm10	GRCm38
GRCm38.p6 Ensembl	2	74,697,727 - 74,700,208 (+)	Ensembl	GRCm38		mm10	GRCm38
MGSCv37	2	74,535,820 - 74,538,265 (+)	NCBI	GRCm37		mm9	NCBIm37
MGSCv36	2	74,498,602 - 74,501,047 (+)	NCBI			mm8
Celera	2	76,367,886 - 76,370,331 (+)	NCBI		Celera
Cytogenetic Map	2	C3	NCBI
cM Map	2	44.13	NCBI

Hoxd9
(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_004955451	12,619,722 - 12,621,320 (+)	NCBI	ChiLan1.0	ChiLan1.0

HOXD9
(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	181,111,939 - 181,114,176 (+)	NCBI	panpan1.1	PanPan1.1	panPan2
PanPan1.1 Ensembl	2B	181,112,002 - 181,113,415 (+)	Ensembl	panpan1.1		panPan2
Mhudiblu_PPA_v0	2B	63,401,813 - 63,404,731 (+)	NCBI	Mhudiblu_PPA_v0		panPan3

HOXD9
(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	19,929,479 - 19,932,861 (+)	NCBI	CanFam3.1	CanFam3.1	canFam3	CanFam3.1
Dog10K_Boxer_Tasha	36	19,940,306 - 19,942,693 (+)	NCBI
ROS_Cfam_1.0	36	20,071,501 - 20,073,894 (+)	NCBI
UMICH_Zoey_3.1	36	20,145,703 - 20,148,083 (+)	NCBI
UNSW_CanFamBas_1.0	36	20,146,398 - 20,148,785 (+)	NCBI
UU_Cfam_GSD_1.0	36	20,258,243 - 20,260,602 (+)	NCBI

Hoxd9
(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	137,055,383 - 137,058,040 (+)	NCBI
SpeTri2.0	NW_004936509	5,609,744 - 5,611,943 (+)	NCBI	SpeTri2.0	SpeTri2.0		SpeTri2.0

HOXD9
(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	81,924,142 - 81,926,274 (+)	Ensembl	Sscrofa11.1		susScr11	Sscrofa11.1
Sscrofa11.1	15	81,910,415 - 81,926,276 (+)	NCBI	Sscrofa11.1	Sscrofa11.1	susScr11	Sscrofa11.1

HOXD9
(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	10	61,695,065 - 61,699,936 (+)	NCBI
ChlSab1.1 Ensembl	10	61,697,271 - 61,699,933 (+)	Ensembl

Hoxd9
(Heterocephalus glaber - naked mole-rat)

Molerat Assembly	Chr	Position (strand)	Source	Genome Browsers
Molerat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
HetGla 1.0	NW_004624787	13,263,020 - 13,265,538 (+)	NCBI

Position Markers

D2Mit38

Rat Assembly	Chr	Position (strand)	Source	JBrowse
mRatBN7.2	3	59,599,917 - 59,600,088 (+)	MAPPER
Rnor_6.0	3	61,619,535 - 61,619,705	NCBI	Rnor6.0
Rnor_5.0	3	68,085,871 - 68,086,041	UniSTS	Rnor5.0
RGSC_v3.4	3	57,311,466 - 57,311,636	UniSTS	RGSC3.4
Celera	3	59,121,732 - 59,121,902	UniSTS
Cytogenetic Map	3	q23	UniSTS

RH129262

Rat Assembly	Chr	Position (strand)	Source	JBrowse
mRatBN7.2	3	59,602,535 - 59,602,726 (+)	MAPPER
Rnor_6.0	3	61,622,141 - 61,622,331	NCBI	Rnor6.0
Rnor_5.0	3	68,088,009 - 68,088,199	UniSTS	Rnor5.0
RGSC_v3.4	3	57,314,291 - 57,314,481	UniSTS	RGSC3.4
Celera	3	59,124,347 - 59,124,537	UniSTS
Cytogenetic Map	3	q23	UniSTS

RH139211

Rat Assembly	Chr	Position (strand)	Source	JBrowse
mRatBN7.2	3	59,605,793 - 59,605,944 (+)	MAPPER
Rnor_6.0	3	61,625,403 - 61,625,553	NCBI	Rnor6.0
Rnor_5.0	3	68,091,271 - 68,091,421	UniSTS	Rnor5.0
RGSC_v3.4	3	57,317,629 - 57,317,779	UniSTS	RGSC3.4
Celera	3	59,127,605 - 59,127,755	UniSTS
Cytogenetic Map	3	q23	UniSTS

Hoxd9

Rat Assembly	Chr	Position (strand)	Source	JBrowse
RGSC_v3.4	3	57,313,126 - 57,313,573	UniSTS	RGSC3.4
Cytogenetic Map	3	q23	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
2290452	Scl56	Serum cholesterol level QTL 56	2.26		blood cholesterol amount (VT:0000180)	plasma total cholesterol level (CMO:0000585)	3	1	95176874	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
631676	Cm8	Cardiac mass QTL 8	7.03	0.0001	aorta mass (VT:0002845)	aorta weight (CMO:0000076)	3	18023664	63023664	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	21223803	66223803	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	21223803	66223803	Rat
631685	Bp118	Blood pressure QTL 118	3.2		arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	3	24655225	69655225	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	29321714	74321714	Rat
9590286	Uminl1	Urine mineral level QTL 1	3.5	0.001	urine mineral amount (VT:0015086)	urine electrolyte level (CMO:0000593)	3	29682732	74682732	Rat
9590136	Scort3	Serum corticosterone level QTL 3	23.37	0.001	blood corticosterone amount (VT:0005345)	plasma corticosterone level (CMO:0001173)	3	29682732	74682732	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	29682732	74682732	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	29682732	74682732	Rat
8694386	Bw159	Body weight QTL 159	4.52	0.001	body lean mass (VT:0010483)	lean tissue morphological measurement (CMO:0002184)	3	29682732	74682732	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	29908255	74908255	Rat
2303593	Gluco46	Glucose level QTL 46	3		blood glucose amount (VT:0000188)	blood glucose level (CMO:0000046)	3	29908255	74908255	Rat
737818	Hcar12	Hepatocarcinoma resistance QTL 12	2.6		liver integrity trait (VT:0010547)	volume of individual liver tumorous lesion (CMO:0001078)	3	30114912	123700444	Rat
70216	Cm14	Cardiac mass QTL 14	2.1		heart mass (VT:0007028)	heart wet weight (CMO:0000069)	3	30846101	172879276	Rat
2301400	Cm68	Cardiac mass QTL 68		0.001	heart mass (VT:0007028)	heart wet weight to body weight ratio (CMO:0002408)	3	31103589	72989078	Rat
11565451	Bw177	Body weight QTL 177		0.002	body mass (VT:0001259)	body weight (CMO:0000012)	3	31103589	72989078	Rat
11565452	Kidm57	Kidney mass QTL 57		0.001	kidney mass (VT:0002707)	both kidneys wet weight to body weight ratio (CMO:0000340)	3	31103589	72989078	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	31103589	72989078	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	31103589	72989078	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	31103589	72989078	Rat
61356	Bp37	Blood pressure QTL 37	3		blood pressure trait (VT:0000183)	systolic blood pressure (CMO:0000004)	3	32130997	77130997	Rat
631647	Bp122	Blood pressure QTL 122	6.2		arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	3	32130997	77130997	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	33477354	62922975	Rat
1354589	Bw31	Body weight QTL 31	3.3		body mass (VT:0001259)	body weight (CMO:0000012)	3	33477354	81136227	Rat
1354604	Bw36	Body weight QTL 36	2.9		body mass (VT:0001259)	body weight (CMO:0000012)	3	33477354	108914061	Rat
61419	Cia11	Collagen induced arthritis QTL 11	5.6		joint integrity trait (VT:0010548)	joint inflammation composite score (CMO:0000919)	3	34394121	103141944	Rat
1358362	Srcrt2	Stress Responsive Cort QTL 2	2.78		blood corticosterone amount (VT:0005345)	plasma corticosterone level (CMO:0001173)	3	39248391	140271184	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	40422921	85422921	Rat
2302276	Bw82	Body weight QTL 82	4.32		body mass (VT:0001259)	body weight (CMO:0000012)	3	40523593	64880586	Rat
1331777	Bw24	Body weight QTL 24	3.503		body mass (VT:0001259)	body weight (CMO:0000012)	3	40523593	92654473	Rat
1331795	Rf30	Renal function QTL 30	3.708		urine potassium amount (VT:0010539)	urine potassium level (CMO:0000128)	3	40523593	92654473	Rat
1354597	Kidm13	Kidney mass QTL 13	2.9		kidney mass (VT:0002707)	right kidney wet weight (CMO:0000082)	3	43295930	108914061	Rat
2301970	Bw81	Body weight QTL 81	5.19		body mass (VT:0001259)	body weight (CMO:0000012)	3	43295930	163640485	Rat
2301971	Cm71	Cardiac mass QTL 71	4.63		heart left ventricle mass (VT:0007031)	heart left ventricle weight (CMO:0000776)	3	43295930	163640485	Rat
1300178	Hrtrt4	Heart rate QTL 4	3.74		heart pumping trait (VT:2000009)	heart rate (CMO:0000002)	3	45406058	94467785	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	45406058	127023997	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	45406058	177699992	Rat
2292591	Esta4	Estrogen-induced thymic atrophy QTL 4			thymus mass (VT:0004954)	thymus wet weight (CMO:0000855)	3	48561928	155263151	Rat
1358186	Ept2	Estrogen-induced pituitary tumorigenesis QTL 2	8.3		pituitary gland mass (VT:0010496)	pituitary gland wet weight (CMO:0000853)	3	48562146	115249962	Rat
2292613	Ept16	Estrogen-induced pituitary tumorigenesis QTL 16	8.3		pituitary gland mass (VT:0010496)	pituitary gland wet weight (CMO:0000853)	3	48562146	115249962	Rat
631665	Bw8	Body weight QTL 8	5.5		body mass (VT:0001259)	body weight (CMO:0000012)	3	51821836	124513579	Rat
724523	Tsu1	Thymus enlargement suppressive QTL 1	3.84		thymus mass (VT:0004954)	thymus weight to body weight ratio (CMO:0000612)	3	51822008	120917851	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	54630948	66711785	Rat
1582218	Bw74	Body weight QTL 74	3.9	0.0021	body mass (VT:0001259)	body weight (CMO:0000012)	3	54630948	119830094	Rat
1582238	Bw68	Body weight QTL 68	3.2	0.0064	body mass (VT:0001259)	body weight (CMO:0000012)	3	54630948	119830094	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	54630948	119830094	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	54631046	93415673	Rat
731180	Bp152	Blood pressure QTL 152		0.03	arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	3	55245276	95176874	Rat
731180	Bp152	Blood pressure QTL 152		0.03	arterial blood pressure trait (VT:2000000)	diastolic blood pressure (CMO:0000005)	3	55245276	95176874	Rat
731180	Bp152	Blood pressure QTL 152		0.03	arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	3	55245276	95176874	Rat
1358293	Bw38	Body weight QTL 38	6	0.0000031	body mass (VT:0001259)	body weight (CMO:0000012)	3	56735995	101735995	Rat
1581568	Rf53	Renal function QTL 53			total urine protein amount (VT:0000032)	urine protein excretion rate to body weight ratio (CMO:0001099)	3	58204463	170534769	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	61241033	165369047	Rat

miRNA Target Status

Predicted Target Of

	Summary Value
Count of predictions:	388
Count of miRNA genes:	232
Interacting mature miRNAs:	267
Transcripts:	ENSRNOT00000065426
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	1									32	31
Low	1		10		3		8	11	2	3	10		8
Below cutoff	1	23	12	6	14	6			5			8

View RNA-SEQ Expression Data

Sequence

Nucleotide Sequences


RefSeq Transcripts	NM_001173469	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
GenBank Nucleotide	BC169092	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	JACYVU010000115	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles

Reference Sequences

RefSeq Acc Id:

ENSRNOT00000065426 ⟹ ENSRNOP00000059218

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
Rnor_6.0 Ensembl	3	61,620,192 - 61,622,359 (+)	Ensembl

RefSeq Acc Id:

NM_001173469 ⟹ NP_001166940

RefSeq Status:

PROVISIONAL

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2	3	59,600,575 - 59,602,755 (+)	NCBI
Rnor_6.0	3	61,620,192 - 61,622,360 (+)	NCBI
Rnor_5.0	3	68,086,528 - 68,088,228 (+)	NCBI
Celera	3	59,122,389 - 59,124,566 (+)	NCBI

Sequence:

show sequence

CGGGCGCCGGCGAGGAGCCGCTCGGCGGTGGGCAGTGTAACCTTGGGTGGGAGCGCGCGGTGCC
TCAACATGTCGTCCAGTGGCACCCTCAGCAACTACTACGTGGACTCGCTCATAGGCCATGAGGG
CGACGAGGTGTTCGCCGCGCGCTTTGGGCCACCGGGGCCGGGGACACAGGGTCGGCCCGCAGGT
GTGGCCGATGGCCCGGCCGCCGCCGCCGAGTTCGCCTCGTGTAGTTTTGCCCCCAAATCGTCCG
TGTTCTCCGCCTCGTGGTCCGCGGTGGCCGCCCAGCCCCCGGCGGCGGCGACGATGAGCGGCCT
GTACCACCCGTACGTGTCCCCGCCGCCCCTGGCCGCCGCCGAGCCGGGCCGCTACGTACGCTCC
TGGATGGAGCCGCTGCCCGGCTTCCCCGGCGGCGCGGGCGGTGGCGGTGGCAGTGGTGGCGGCG
GTGGCGGAGGTAGCGGAGGCCCGGGTCCCGTTCCCAGCCCCGGCGGTCCAGCCAACGGGCGCCA
CTACGGGATTAAGCCTGAAACCGGAGCAGCCCCGGCCCCCTCTGCAGCCTCCACTTCCTCCTCC
ACCTCCTCGTCCTCCTCCTCCAAAAGGACTGAGTGCTCCGCGGCCCGCGAGTCCCAGGGGAGCG
GCGGCCCAGAATTCCCGTGCAACTCGTTCCTGCGGGACAAGGCGGCAGCGGCGGCGGCGGCGGC
GGCAGGGAACGGGCCCGGGGTGGGAATCGGGACCGGGCCTGGGACGGGAGGCTCGTCCGAGCCC
TCAGCTTGCAGCGATCACCCGAGCCCGGGCTGCCCGCTGAAGGAGGAGGAGAAGCAGCCGCCGC
AGCCGCCGCAGCAGCAACTTGACCCAAACAACCCTGCAGCGAACTGGATCCACGCTCGCTCCAC
CCGGAAAAAGCGCTGTCCCTACACCAAATACCAGACGCTAGAGCTGGAGAAGGAATTCCTCTTC
AACATGTACCTCACCCGGGACCGGCGCTACGAGGTGGCCAGGATTCTGAACCTTACAGAGAGAC
AAGTCAAAATCTGGTTCCAGAACCGTAGGATGAAAATGAAAAAGATGAGCAAGGAGAAATGTCC
TAAAGGAGACTGACCCAGTGCGGGTCAGGCCTGCAGCGCTCAAAAGGCAGCGGGTTTTGGTTTT
TTGTTGTTGATTGTTTTCTTTGTGGGTGCTTGATTCAGAAACTCTGCAGCGATTCGGACATTCT
TCTTTTTTTTTTTTAGGTAGAAGTGACTGTGTGGTTGGTCTCTGTGAGTTATTTGGGGGACGCT
GTATTTGCTCGCATATGTATTGGAGAATCCAAGTGGCTTTGGAGTCTTGTCCTATCTCACTCCC
TCCCTTTCCCACTCCCTTGGTTCCTTAGGAAATGCTTTATTTTGTGAGTGCACGCAGGCTTGAT
GGAGCCCTATCCTGTGTAAATGTTCCTCATGTTTCTGGAAAGTGCTGTAGTGTAGTCTCACCCC
ATCCAGCCTCCCAAACAGGGCCAACTATCTAATTCCGAGAATCTGAAAGAAGAGAAAGACTGTG
GACACACACCCCCTCCCCCAAAAAACCCAGCTCAGCTGCAGGAAAACCCCTATCCTCAGGGAGC
CCGCGGACTGACTTCCAGAGAGGCCTACCAAGAAGCCCTGGGCCCTGGGACACGAGGTTGGGGT
GGGGTTGAGGAGAGGCTTAGTCCTTGGAGCACGGGGAAGCTACTTTCTCCCCAGGAGGGCTGGG
CTCCCTGGGGCGGCCTCGGGAGGTGGCCCTCCATATTCCTGCCTGAGGACCAGTTGTAAATGTT
ACCGCTTCCTACAAATAAATGCTGATCTGAACAAATGGAGCCCAAAAAAAAAAAAAAA

hide sequence

Protein Sequences


Protein RefSeqs	NP_001166940	(Get FASTA)	NCBI Sequence Viewer
GenBank Protein	AAI69092	(Get FASTA)	NCBI Sequence Viewer
	B5DFK3	(Get FASTA)	NCBI Sequence Viewer

Reference Sequences

RefSeq Acc Id:

NP_001166940 ⟸ NM_001173469

- UniProtKB:

B5DFK3 (UniProtKB/Swiss-Prot)

- Sequence:

show sequence

MSSSGTLSNYYVDSLIGHEGDEVFAARFGPPGPGTQGRPAGVADGPAAAAEFASCSFAPKSSVF
SASWSAVAAQPPAAATMSGLYHPYVSPPPLAAAEPGRYVRSWMEPLPGFPGGAGGGGGSGGGGG
GGSGGPGPVPSPGGPANGRHYGIKPETGAAPAPSAASTSSSTSSSSSSKRTECSAARESQGSGG
PEFPCNSFLRDKAAAAAAAAAGNGPGVGIGTGPGTGGSSEPSACSDHPSPGCPLKEEEKQPPQP
PQQQLDPNNPAANWIHARSTRKKRCPYTKYQTLELEKEFLFNMYLTRDRRYEVARILNLTERQV
KIWFQNRRMKMKKMSKEKCPKGD

hide sequence

RefSeq Acc Id:

ENSRNOP00000059218 ⟸ ENSRNOT00000065426

Protein Domains

Homeobox

Transcriptome

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

Promoters

RGD ID:

13692149

Promoter ID:

EPDNEW_R2674

Type:

single initiation site

Name:

Hoxd9_1

Description:

homeo box D9

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	61,620,181 - 61,620,241	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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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

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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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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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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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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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 (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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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

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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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

Additional Information

External Database Links

Database	Acc Id	Source(s)
AGR Gene	RGD:1582908	AgrOrtholog
Ensembl Genes	ENSRNOG00000001580	Ensembl, UniProtKB/TrEMBL
Ensembl Protein	ENSRNOP00000059218	UniProtKB/TrEMBL
Ensembl Transcript	ENSRNOT00000065426	UniProtKB/TrEMBL
InterPro	Homeobox-like_sf	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	Homeobox_CS	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	Homeobox_dom	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	Homeobox_metazoa	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	Hox9_activation_N	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	HXA9/HXB9/HXC9	UniProtKB/TrEMBL
KEGG Report	rno:688999	UniProtKB/Swiss-Prot
NCBI Gene	688999	ENTREZGENE
Pfam	Homeodomain	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	Hox9_act	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen	Hoxd9	PhenoGen
PIRSF	Homeobox_Hox9	UniProtKB/TrEMBL
PRINTS	HOMEOBOX	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PROSITE	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	B5DFK3	ENTREZGENE
	D4A2V8_RAT	UniProtKB/TrEMBL
	HXD9_RAT	UniProtKB/Swiss-Prot

Nomenclature History

Date	Current Symbol	Current Name	Previous Symbol	Previous Name	Description	Reference	Status
2008-03-06	Hoxd9	homeo box D9	LOC688999	similar to Homeobox protein Hox-D8 (Hox-4.3) (Hox-5.4)	Nomenclature updated to reflect human and mouse nomenclature	1299863	APPROVED
2008-01-09	LOC688999	similar to Homeobox protein Hox-D8 (Hox-4.3) (Hox-5.4)	RGD1561879_predicted	similar to Homeobox protein Hox-D8 (Hox-4.3) (Hox-5.4) (predicted)	Data Merged	1643240	APPROVED
2006-11-19	LOC688999	similar to Homeobox protein Hox-D8 (Hox-4.3) (Hox-5.4)			Symbol and Name status set to provisional	70820	PROVISIONAL
2006-03-07	RGD1561879_predicted	similar to Homeobox protein Hox-D8 (Hox-4.3) (Hox-5.4) (predicted)	LOC366083	similar to Homeobox protein Hox-D8 (Hox-4.3) (Hox-5.4)	Symbol and Name status set to approved	1299863	APPROVED
2006-02-09	LOC366083	similar to Homeobox protein Hox-D8 (Hox-4.3) (Hox-5.4)			Symbol and Name status set to provisional	70820	PROVISIONAL

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