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Gene: Hoxd9 (homeo box D9) Rattus norvegicus

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Symbol:

Hoxd9

Name:

homeo box D9

RGD ID:

1582908

Description:

Predicted to enable 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 embryonic skeletal system morphogenesis; negative regulation of transcription by RNA polymerase II; and regionalization. Predicted to act upstream of or within several processes, including embryonic skeletal system development; limb morphogenesis; and peripheral nervous system neuron development. Predicted to be located in nucleolus and nucleoplasm. Predicted to be active in nucleus. Orthologous to human HOXD9 (homeobox D9); INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; bisphenol A; dibutyl phthalate.

Type:

protein-coding

RefSeq Status:

PROVISIONAL

Previously 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

Alliance Orthologs

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)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
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 (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\|SonicParanoid)
Mus musculus (house mouse):	Hoxd9 (homeobox D9)	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Danio rerio (zebrafish):	hoxd9a (homeobox D9a)	Alliance	DIOPT (Ensembl Compara\|OMA\|OrthoFinder\|PANTHER)
Xenopus tropicalis (tropical clawed frog):	hoxd9	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|PANTHER\|PhylomeDB\|SonicParanoid)
Xenopus tropicalis (tropical clawed frog):	hoxd9	Alliance	DIOPT (PANTHER\|PhylomeDB)

Latest Assembly:

GRCr8 - GRCr8 Assembly

Position:

Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCr8	3	80,008,006 - 80,010,186 (+)	NCBI	GRCr8	GRCr8		GRCr8
GRCr8 Ensembl	3	80,007,668 - 80,010,171 (+)	Ensembl				GRCr8
mRatBN7.2	3	59,600,575 - 59,602,755 (+)	NCBI	mRatBN7.2	mRatBN7.2
mRatBN7.2 Ensembl	3	59,600,575 - 59,602,754 (+)	Ensembl				mRatBN7.2
UTH_Rnor_SHR_Utx	3	62,987,853 - 62,990,034 (+)	NCBI	UTH_Rnor_SHR_Utx	UTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0	3	71,571,498 - 71,573,679 (+)	NCBI	UTH_Rnor_SHRSP_BbbUtx_1.0	UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0	3	69,336,566 - 69,338,747 (+)	NCBI	UTH_Rnor_WKY_Bbb_1.0	UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0	3	61,620,192 - 61,622,360 (+)	NCBI	Rnor_6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_6.0 Ensembl	3	61,620,192 - 61,622,359 (+)	Ensembl			rn6	Rnor6.0
Rnor_5.0	3	68,086,528 - 68,088,228 (+)	NCBI	Rnor_5.0	Rnor_5.0	rn5
Celera	3	59,122,389 - 59,124,566 (+)	NCBI		Celera
Cytogenetic Map	3	q23	NCBI

JBrowse:

View Region in Genome Browser (JBrowse)

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)

split hand-foot malformation 5 (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 (EXP,ISO)

4-hydroxyphenyl retinamide (ISO)

aflatoxin B1 (ISO)

atrazine (ISO)

benzo[a]pyrene (ISO)

bis(2-ethylhexyl) phthalate (ISO)

bisphenol A (EXP,ISO)

chlordecone (ISO)

chlorpyrifos (ISO)

choline (ISO)

dibutyl phthalate (EXP)

folic acid (ISO)

FR900359 (ISO)

gentamycin (EXP)

L-methionine (ISO)

lead(0) (ISO)

paracetamol (EXP)

potassium dichromate (ISO)

titanium dioxide (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)

DNA-templated transcription (IEA)

embryonic forelimb morphogenesis (IEA,ISO)

embryonic skeletal system development (IEA,ISO)

embryonic skeletal system morphogenesis (IBA,IEA,ISO)

forelimb morphogenesis (IEA,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 DNA-templated transcription (IEA)

regulation of gene expression (IEA,ISO)

regulation of transcription by RNA polymerase II (IBA)

single fertilization (IEA,ISO)

skeletal muscle tissue development (IEA,ISO)

skeletal system development (IEA)

Cellular Component

nucleolus (IEA,ISO)

nucleoplasm (IEA,ISO)

nucleus (IBA,IEA,ISO)

Molecular Function

DNA binding (IEA,ISO)

DNA-binding transcription factor activity (IBA,IEA,ISO)

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

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 (IEA,ISO)

References

References - curated

#	Reference Title	Reference Citation
1.	Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium.	Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
2.	Data Import for Chemical-Gene Interactions	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	PMID:34288810

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
GRCr8	3	80,008,006 - 80,010,186 (+)	NCBI	GRCr8	GRCr8		GRCr8
GRCr8 Ensembl	3	80,007,668 - 80,010,171 (+)	Ensembl				GRCr8
mRatBN7.2	3	59,600,575 - 59,602,755 (+)	NCBI	mRatBN7.2	mRatBN7.2
mRatBN7.2 Ensembl	3	59,600,575 - 59,602,754 (+)	Ensembl				mRatBN7.2
UTH_Rnor_SHR_Utx	3	62,987,853 - 62,990,034 (+)	NCBI	UTH_Rnor_SHR_Utx	UTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0	3	71,571,498 - 71,573,679 (+)	NCBI	UTH_Rnor_SHRSP_BbbUtx_1.0	UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0	3	69,336,566 - 69,338,747 (+)	NCBI	UTH_Rnor_WKY_Bbb_1.0	UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0	3	61,620,192 - 61,622,360 (+)	NCBI	Rnor_6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_6.0 Ensembl	3	61,620,192 - 61,622,359 (+)	Ensembl			rn6	Rnor6.0
Rnor_5.0	3	68,086,528 - 68,088,228 (+)	NCBI	Rnor_5.0	Rnor_5.0	rn5
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	2	176,122,719 - 176,124,937 (+)	NCBI	GRCh38	GRCh38	hg38	GRCh38
GRCh38.p14 Ensembl	2	176,122,719 - 176,124,937 (+)	Ensembl			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	Build 36	Build 36	hg18	NCBI36
Build 34	2	176,812,594 - 176,815,031	NCBI
Celera	2	170,596,564 - 170,598,796 (+)	NCBI		Celera
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
T2T-CHM13v2.0	2	176,610,853 - 176,613,074 (+)	NCBI		T2T-CHM13v2.0

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	GRCm39	mm39
GRCm39 Ensembl	2	74,528,071 - 74,530,552 (+)	Ensembl		GRCm39 Ensembl		GRCm39
GRCm38	2	74,697,763 - 74,700,208 (+)	NCBI	GRCm38	GRCm38	mm10	GRCm38
GRCm38.p6 Ensembl	2	74,697,727 - 74,700,208 (+)	Ensembl			mm10	GRCm38
MGSCv37	2	74,535,820 - 74,538,265 (+)	NCBI	MGSCv37	MGSCv37	mm9	NCBIm37
MGSCv36	2	74,498,602 - 74,501,047 (+)	NCBI		MGSCv36	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
NHGRI_mPanPan1-v2	13	78,789,839 - 78,792,454 (+)	NCBI		NHGRI_mPanPan1-v2
NHGRI_mPanPan1	2B	78,804,897 - 78,807,918 (+)	NCBI		NHGRI_mPanPan1
Mhudiblu_PPA_v0	2B	63,401,813 - 63,404,731 (+)	NCBI	Mhudiblu_PPA_v0	Mhudiblu_PPA_v0	panPan3
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			panPan2	panpan1.1

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	Dog10K_Boxer_Tasha	Dog10K_Boxer_Tasha
ROS_Cfam_1.0	36	20,071,501 - 20,073,894 (+)	NCBI	ROS_Cfam_1.0	ROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl	36	20,057,613 - 20,081,260 (+)	Ensembl				ROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1	36	20,145,703 - 20,148,083 (+)	NCBI		UMICH_Zoey_3.1
UNSW_CanFamBas_1.0	36	20,146,398 - 20,148,785 (+)	NCBI		UNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0	36	20,258,243 - 20,260,602 (+)	NCBI	UU_Cfam_GSD_1.0	UU_Cfam_GSD_1.0

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		HiC_Itri_2
SpeTri2.0 Ensembl	NW_004936509	5,609,744 - 5,611,943 (+)	Ensembl		SpeTri2.0 Ensembl
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			susScr11	Sscrofa11.1
Sscrofa11.1	15	81,910,415 - 81,926,276 (+)	NCBI	Sscrofa11.1	Sscrofa11.1	susScr11	Sscrofa11.1

HOXD9
(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	61,695,065 - 61,699,936 (+)	NCBI	ChlSab1.1	ChlSab1.1	chlSab2
ChlSab1.1 Ensembl	10	61,697,271 - 61,699,933 (+)	Ensembl		ChlSab1.1 Ensembl	chlSab2	Vervet-AGM
Vero_WHO_p1.0	NW_023666040	137,910,535 - 137,913,594 (-)	NCBI	Vero_WHO_p1.0	Vero_WHO_p1.0

Hoxd9
(Heterocephalus glaber - naked mole-rat)

Naked Mole-Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Naked Mole-Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
HetGla_female_1.0 Ensembl	NW_004624787	13,249,946 - 13,265,627 (+)	Ensembl		HetGla_female_1.0 Ensembl	hetGla2	HetGla_female_1.0 Ensembl
HetGla 1.0	NW_004624787	13,263,020 - 13,265,538 (+)	NCBI	HetGla 1.0	HetGla 1.0	hetGla2

Variants

Variants in Hoxd9
12 total Variants

miRNA Target Status (No longer updated)

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.

QTLs in Region (GRCr8)

The following QTLs overlap with this region.

RGD ID	Symbol	Name	LOD	P Value	Trait	Sub Trait	Chr	Start	Stop	Species
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
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
1358362	Srcrt2	Stress Responsive Cort QTL 2	2.78		blood corticosterone amount (VT:0005345)	plasma corticosterone level (CMO:0001173)	3	38192233	133483320	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
1582218	Bw74	Body weight QTL 74	3.9	0.0021	body mass (VT:0001259)	body weight (CMO:0000012)	3	53184593	115665732	Rat
1581568	Rf53	Renal function QTL 53			urine total protein amount (VT:0000032)	urine protein excretion rate to body weight ratio (CMO:0001099)	3	56395968	161299569	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
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
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
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
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
731180	Bp152	Blood pressure QTL 152		0.03	arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	3	53781112	91609953	Rat
61356	Bp37	Blood pressure QTL 37	3		blood pressure trait (VT:0000183)	systolic blood pressure (CMO:0000004)	3	30684642	75684642	Rat
1358905	Hrtrt17	Heart rate QTL 17	5.9	0.000014	heart pumping trait (VT:2000009)	heart rate (CMO:0000002)	3	10861912	89878372	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
2301971	Cm71	Cardiac mass QTL 71	4.63		heart left ventricle mass (VT:0007031)	heart left ventricle weight (CMO:0000776)	3	41874578	155617519	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
2301970	Bw81	Body weight QTL 81	5.19		body mass (VT:0001259)	body weight (CMO:0000012)	3	41874578	155617519	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
2290452	Scl56	Serum cholesterol level QTL 56	2.26		blood cholesterol amount (VT:0000180)	plasma total cholesterol level (CMO:0000585)	3	1	91609953	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
11565451	Bw177	Body weight QTL 177		0.002	body mass (VT:0001259)	body weight (CMO:0000012)	3	31426403	70668733	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
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
1300178	Hrtrt4	Heart rate QTL 4	3.74		heart pumping trait (VT:2000009)	heart rate (CMO:0000002)	3	43827364	90905114	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
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
1331795	Rf30	Renal function QTL 30	3.708		urine potassium amount (VT:0010539)	urine potassium level (CMO:0000128)	3	39454637	89115240	Rat
70216	Cm14	Cardiac mass QTL 14	2.1		heart mass (VT:0007028)	heart wet weight (CMO:0000069)	3	31172320	163586636	Rat
1354589	Bw31	Body weight QTL 31	3.3		body mass (VT:0001259)	body weight (CMO:0000012)	3	33703347	78196190	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
2292591	Esta4	Estrogen-induced thymic atrophy QTL 4			thymus mass (VT:0004954)	thymus wet weight (CMO:0000855)	3	47233211	147415807	Rat
1331777	Bw24	Body weight QTL 24	3.503		body mass (VT:0001259)	body weight (CMO:0000012)	3	39454637	89115240	Rat
631647	Bp122	Blood pressure QTL 122	6.2		arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	3	30684642	75684642	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
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
2302276	Bw82	Body weight QTL 82	4.32		body mass (VT:0001259)	body weight (CMO:0000012)	3	39454637	62951183	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
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
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
61419	Cia11	Collagen induced arthritis QTL 11	5.6		joint integrity trait (VT:0010548)	joint inflammation composite score (CMO:0000919)	3	30356773	98535386	Rat
1354597	Kidm13	Kidney mass QTL 13	2.9		kidney mass (VT:0002707)	right kidney wet weight (CMO:0000082)	3	41874578	104104347	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
631676	Cm8	Cardiac mass QTL 8	7.03	0.0001	aorta mass (VT:0002845)	aorta weight (CMO:0000076)	3	16954708	61954708	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
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
1354604	Bw36	Body weight QTL 36	2.9		body mass (VT:0001259)	body weight (CMO:0000012)	3	33703347	104104347	Rat
631665	Bw8	Body weight QTL 8	5.5		body mass (VT:0001259)	body weight (CMO:0000012)	3	50437042	119183768	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
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

Markers in Region

D2Mit38

Rat Assembly	Chr	Position (strand)	Source	JBrowse
GRCr8	3	80,007,348 - 80,007,520 (+)	Marker Load Pipeline
mRatBN7.2	3	59,599,917 - 59,600,088 (+)	MAPPER	mRatBN7.2
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	mRatBN7.2
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	mRatBN7.2
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
GRCr8	3	80,008,802 - 80,009,249 (+)	Marker Load Pipeline
RGSC_v3.4	3	57,313,126 - 57,313,573	UniSTS	RGSC3.4
Cytogenetic Map	3	q23	UniSTS

Expression

RNA-SEQ Expression

Click on a value in the shaded box below the category label to view a detailed expression data table for that system.

Download All Expressed Objects for this Gene

alimentary part of gastrointestinal system	appendage	circulatory system	ectoderm	endocrine system	endoderm	exocrine system	hemolymphoid system	hepatobiliary system	integumental system	mesenchyme	mesoderm	musculoskeletal system	nervous system	renal system	reproductive system	respiratory system
15	11	39	45	50	49	21	25	21	6	221	96	9	23	81	89	28

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
	JAXUCZ010000003	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles

Ensembl Acc Id:

ENSRNOT00000065426 ⟹ ENSRNOP00000059218

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
GRCr8 Ensembl	3	80,007,668 - 80,010,171 (+)	Ensembl
mRatBN7.2 Ensembl	3	59,600,575 - 59,602,754 (+)	Ensembl
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
GRCr8	3	80,008,006 - 80,010,186 (+)	NCBI
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
Ensembl Protein	ENSRNOP00000059218
	ENSRNOP00000059218.4

RefSeq Acc Id:

NP_001166940 ⟸ NM_001173469

- UniProtKB:

B5DFK3 (UniProtKB/Swiss-Prot), D4A2V8 (UniProtKB/TrEMBL)

- Sequence:

show sequence

MSSSGTLSNYYVDSLIGHEGDEVFAARFGPPGPGTQGRPAGVADGPAAAAEFASCSFAPKSSVF
SASWSAVAAQPPAAATMSGLYHPYVSPPPLAAAEPGRYVRSWMEPLPGFPGGAGGGGGSGGGGG
GGSGGPGPVPSPGGPANGRHYGIKPETGAAPAPSAASTSSSTSSSSSSKRTECSAARESQGSGG
PEFPCNSFLRDKAAAAAAAAAGNGPGVGIGTGPGTGGSSEPSACSDHPSPGCPLKEEEKQPPQP
PQQQLDPNNPAANWIHARSTRKKRCPYTKYQTLELEKEFLFNMYLTRDRRYEVARILNLTERQV
KIWFQNRRMKMKKMSKEKCPKGD

hide sequence

Ensembl Acc Id:

ENSRNOP00000059218 ⟸ ENSRNOT00000065426

Protein Domains

Homeobox

Protein Structures

Name	Modeler	Protein Id	AA Range	Protein Structure
AF-B5DFK3-F1-model_v2	AlphaFold	B5DFK3	1-343	view protein structure

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

Additional Information

External Database Links

Database	Acc Id	Source(s)
AGR Gene	RGD:1582908	AgrOrtholog
BioCyc Gene	G2FUF-49331	BioCyc
Ensembl Genes	ENSRNOG00000001580	Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript	ENSRNOT00000065426	ENTREZGENE
	ENSRNOT00000065426.4	UniProtKB/Swiss-Prot
Gene3D-CATH	Homeodomain-like	UniProtKB/Swiss-Prot
InterPro	Abd-B_homeobox_TF	UniProtKB/Swiss-Prot
	Homeobox-like_sf	UniProtKB/Swiss-Prot
	Homeobox_CS	UniProtKB/Swiss-Prot
	Homeobox_dom	UniProtKB/Swiss-Prot
	Homeobox_metazoa	UniProtKB/Swiss-Prot
	Hox9_activation_N	UniProtKB/Swiss-Prot
KEGG Report	rno:688999	UniProtKB/Swiss-Prot
NCBI Gene	688999	ENTREZGENE
PANTHER	AGAP004664-PA	UniProtKB/Swiss-Prot
	HOMEOBOX PROTEIN HOX-D9	UniProtKB/Swiss-Prot
Pfam	Homeodomain	UniProtKB/Swiss-Prot
	Hox9_act	UniProtKB/Swiss-Prot
PhenoGen	Hoxd9	PhenoGen
PRINTS	HOMEOBOX	UniProtKB/Swiss-Prot
PROSITE	HOMEOBOX_1	UniProtKB/Swiss-Prot
	HOMEOBOX_2	UniProtKB/Swiss-Prot
RatGTEx	ENSRNOG00000001580	RatGTEx
SMART	HOX	UniProtKB/Swiss-Prot
Superfamily-SCOP	SSF46689	UniProtKB/Swiss-Prot
UniProt	B5DFK3	ENTREZGENE
	D4A2V8	ENTREZGENE, 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 from RGD:1561879	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

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Imported Disease Annotations - ClinVar

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