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Gene: Hoxd1 (homeo box D1) Rattus norvegicus

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Symbol:

Hoxd1

Name:

homeo box D1

RGD ID:

1309179

Description:

Predicted to enable DNA-binding transcription factor activity, RNA polymerase II-specific and RNA polymerase II cis-regulatory region sequence-specific DNA binding activity. Predicted to be involved in regulation of transcription by RNA polymerase II. Predicted to act upstream of or within embryonic skeletal system development; neuron differentiation; and sensory perception of pain. Predicted to be located in nucleoplasm. Predicted to be active in nucleus. Orthologous to human HOXD1 (homeobox D1); INTERACTS WITH amitriptyline; bisphenol A; copper atom.

Type:

protein-coding

RefSeq Status:

PROVISIONAL

Previously known as:

homeobox protein Hox-D1; LOC288151

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):	HOXD1 (homeobox D1)	HGNC	EggNOG, Ensembl, HomoloGene, Inparanoid, NCBI, OMA, OrthoDB, OrthoMCL, Panther, PhylomeDB, Treefam
Mus musculus (house mouse):	Hoxd1 (homeobox D1)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Chinchilla lanigera (long-tailed chinchilla):	Hoxd1 (homeobox D1)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Pan paniscus (bonobo/pygmy chimpanzee):	HOXD1 (homeobox D1)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Canis lupus familiaris (dog):	HOXD1 (homeobox D1)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Ictidomys tridecemlineatus (thirteen-lined ground squirrel):	Hoxd1 (homeobox D1)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Sus scrofa (pig):	HOXD1 (homeobox D1)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Chlorocebus sabaeus (green monkey):	HOXD1 (homeobox D1)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Heterocephalus glaber (naked mole-rat):	Hoxd1 (homeobox D1)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Rattus rattus (black rat):	Hoxd1 (homeobox D1)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Other homologs ²
Homo sapiens (human):	HOXB1 (homeobox B1)	HGNC	PhylomeDB
Alliance orthologs ³
Homo sapiens (human):	HOXD1 (homeobox D1)	Alliance	DIOPT (Ensembl Compara\|HGNC\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Mus musculus (house mouse):	Hoxd1 (homeobox D1)	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Danio rerio (zebrafish):	hoxc1a (homeobox C1a)	Alliance	DIOPT (Ensembl Compara\|PANTHER)
Caenorhabditis elegans (roundworm):	ceh-13	Alliance	DIOPT (Ensembl Compara\|InParanoid\|OrthoFinder\|OrthoInspector\|PhylomeDB\|SonicParanoid)
Drosophila melanogaster (fruit fly):	lab	Alliance	DIOPT (Ensembl Compara\|OrthoFinder\|OrthoInspector\|PANTHER)
Xenopus tropicalis (tropical clawed frog):	hoxd1	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)

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	80,073,041 - 80,075,180 (+)	NCBI	GRCr8	GRCr8		GRCr8
GRCr8 Ensembl	3	80,073,041 - 80,075,180 (+)	Ensembl				GRCr8
mRatBN7.2	3	59,665,629 - 59,667,769 (+)	NCBI	mRatBN7.2	mRatBN7.2
mRatBN7.2 Ensembl	3	59,665,629 - 59,667,769 (+)	Ensembl				mRatBN7.2
UTH_Rnor_SHR_Utx	3	63,052,804 - 63,054,943 (+)	NCBI	UTH_Rnor_SHR_Utx	UTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0	3	71,636,445 - 71,638,584 (+)	NCBI	UTH_Rnor_SHRSP_BbbUtx_1.0	UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0	3	69,401,510 - 69,403,649 (+)	NCBI	UTH_Rnor_WKY_Bbb_1.0	UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0	3	61,685,619 - 61,687,758 (+)	NCBI	Rnor_6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_6.0 Ensembl	3	61,685,619 - 61,687,758 (+)	Ensembl			rn6	Rnor6.0
Rnor_5.0	3	68,151,156 - 68,153,295 (+)	NCBI	Rnor_5.0	Rnor_5.0	rn5
RGSC_v3.4	3	57,377,839 - 57,379,978 (+)	NCBI	RGSC_v3.4	RGSC_v3.4	rn4
Celera	3	59,186,877 - 59,189,016 (+)	NCBI		Celera
RGSC_v3.1	3	57,274,308 - 57,275,611 (+)	NCBI
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)

Hyperalgesia (ISO)

Ovarian Neoplasms (ISO)

Pain (ISO)

Gene-Chemical Interaction Annotations Click to see Annotation Detail View

1,2,4-trichloro-5-(2,5-dichlorophenyl)benzene (ISO)

2,2',4,4',5,5'-hexachlorobiphenyl (ISO)

2,2',5,5'-tetrachlorobiphenyl (ISO)

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

2,4,4'-trichlorobiphenyl (ISO)

3,3',5,5'-tetrabromobisphenol A (ISO)

5-fluorouracil (ISO)

aflatoxin B1 (ISO)

all-trans-retinoic acid (ISO)

amitriptyline (EXP)

ampicillin (ISO)

arsane (ISO)

arsenic atom (ISO)

arsenite(3-) (ISO)

azathioprine (ISO)

benzo[a]pyrene (ISO)

benzo[a]pyrene diol epoxide I (ISO)

bisphenol A (EXP,ISO)

butanal (ISO)

CGP 52608 (ISO)

copper atom (EXP,ISO)

copper(0) (EXP,ISO)

copper(II) sulfate (ISO)

cyclosporin A (ISO)

dicrotophos (ISO)

disulfiram (ISO)

entinostat (ISO)

ethanol (ISO)

FR900359 (ISO)

gentamycin (EXP)

hydrogen peroxide (ISO)

indometacin (ISO)

iron dichloride (ISO)

leflunomide (ISO)

melphalan (ISO)

menadione (ISO)

methylmercury chloride (ISO)

nickel atom (ISO)

okadaic acid (ISO)

paracetamol (EXP)

PCB138 (ISO)

pentanal (ISO)

propanal (ISO)

quercetin (ISO)

resorcinol (ISO)

resveratrol (ISO)

silicon dioxide (ISO)

tert-butyl hydroperoxide (ISO)

titanium dioxide (ISO)

trichloroethene (EXP)

trichostatin A (ISO)

tunicamycin (ISO)

valproic acid (ISO)

zinc sulfate (ISO)

Gene Ontology Annotations Click to see Annotation Detail View

Biological Process

embryonic skeletal system development (ISO)

neuron differentiation (ISO)

regulation of DNA-templated transcription (IEA)

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

sensory perception of pain (ISO)

Cellular Component

nucleoplasm (IEA,ISO)

nucleus (IBA,IEA,ISO)

Molecular Function

DNA binding (IEA)

DNA-binding transcription factor activity (IEA)

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

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

sequence-specific DNA binding (IEA)

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:11209945	PMID:11511348	PMID:21151121

Genomics

Comparative Map Data

Hoxd1
(Rattus norvegicus - Norway rat)

Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCr8	3	80,073,041 - 80,075,180 (+)	NCBI	GRCr8	GRCr8		GRCr8
GRCr8 Ensembl	3	80,073,041 - 80,075,180 (+)	Ensembl				GRCr8
mRatBN7.2	3	59,665,629 - 59,667,769 (+)	NCBI	mRatBN7.2	mRatBN7.2
mRatBN7.2 Ensembl	3	59,665,629 - 59,667,769 (+)	Ensembl				mRatBN7.2
UTH_Rnor_SHR_Utx	3	63,052,804 - 63,054,943 (+)	NCBI	UTH_Rnor_SHR_Utx	UTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0	3	71,636,445 - 71,638,584 (+)	NCBI	UTH_Rnor_SHRSP_BbbUtx_1.0	UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0	3	69,401,510 - 69,403,649 (+)	NCBI	UTH_Rnor_WKY_Bbb_1.0	UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0	3	61,685,619 - 61,687,758 (+)	NCBI	Rnor_6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_6.0 Ensembl	3	61,685,619 - 61,687,758 (+)	Ensembl			rn6	Rnor6.0
Rnor_5.0	3	68,151,156 - 68,153,295 (+)	NCBI	Rnor_5.0	Rnor_5.0	rn5
RGSC_v3.4	3	57,377,839 - 57,379,978 (+)	NCBI	RGSC_v3.4	RGSC_v3.4	rn4
Celera	3	59,186,877 - 59,189,016 (+)	NCBI		Celera
RGSC_v3.1	3	57,274,308 - 57,275,611 (+)	NCBI
Cytogenetic Map	3	q23	NCBI

HOXD1
(Homo sapiens - human)

Human Assembly	Chr	Position (strand)	Source	Genome Browsers
Human Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCh38	2	176,188,668 - 176,190,907 (+)	NCBI	GRCh38	GRCh38	hg38	GRCh38
GRCh38.p14 Ensembl	2	176,188,667 - 176,190,907 (+)	Ensembl			hg38	GRCh38
GRCh37	2	177,053,396 - 177,055,635 (+)	NCBI	GRCh37	GRCh37	hg19	GRCh37
Build 36	2	176,761,553 - 176,763,881 (+)	NCBI	Build 36	Build 36	hg18	NCBI36
Build 34	2	176,878,813 - 176,881,142	NCBI
Celera	2	170,662,486 - 170,664,814 (+)	NCBI		Celera
Cytogenetic Map	2	q31.1	NCBI
HuRef	2	168,930,260 - 168,932,588 (+)	NCBI		HuRef
CHM1_1	2	177,059,181 - 177,061,509 (+)	NCBI		CHM1_1
T2T-CHM13v2.0	2	176,676,799 - 176,679,038 (+)	NCBI		T2T-CHM13v2.0

Hoxd1
(Mus musculus - house mouse)

Mouse Assembly	Chr	Position (strand)	Source	Genome Browsers
Mouse Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCm39	2	74,593,324 - 74,595,486 (+)	NCBI	GRCm39	GRCm39	mm39
GRCm39 Ensembl	2	74,593,324 - 74,595,486 (+)	Ensembl		GRCm39 Ensembl		GRCm39
GRCm38	2	74,762,980 - 74,765,142 (+)	NCBI	GRCm38	GRCm38	mm10	GRCm38
GRCm38.p6 Ensembl	2	74,762,980 - 74,765,142 (+)	Ensembl			mm10	GRCm38
MGSCv37	2	74,601,037 - 74,603,199 (+)	NCBI	MGSCv37	MGSCv37	mm9	NCBIm37
MGSCv36	2	74,563,819 - 74,565,982 (+)	NCBI		MGSCv36	mm8
Celera	2	76,433,115 - 76,435,276 (+)	NCBI		Celera
Cytogenetic Map	2	C3	NCBI
cM Map	2	44.13	NCBI

Hoxd1
(Chinchilla lanigera - long-tailed chinchilla)

Chinchilla Assembly	Chr	Position (strand)	Source	Genome Browsers
Chinchilla Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
ChiLan1.0 Ensembl	NW_004955403	20,476,645 - 20,478,604 (-)	Ensembl
ChiLan1.0	NW_004955403	20,476,813 - 20,478,604 (-)	NCBI	ChiLan1.0	ChiLan1.0

HOXD1
(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	78,856,146 - 78,858,397 (+)	NCBI		NHGRI_mPanPan1-v2
NHGRI_mPanPan1	2B	78,871,121 - 78,873,372 (+)	NCBI		NHGRI_mPanPan1
Mhudiblu_PPA_v0	2B	63,468,317 - 63,470,658 (+)	NCBI	Mhudiblu_PPA_v0	Mhudiblu_PPA_v0	panPan3
PanPan1.1	2B	181,176,789 - 181,179,105 (+)	NCBI	PanPan1.1	PanPan1.1	panPan2

HOXD1
(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	19,995,326 - 19,997,059 (+)	NCBI	CanFam3.1	CanFam3.1	canFam3	CanFam3.1
CanFam3.1 Ensembl	36	19,995,323 - 19,997,072 (+)	Ensembl			canFam3	CanFam3.1
Dog10K_Boxer_Tasha	36	20,004,663 - 20,006,594 (+)	NCBI	Dog10K_Boxer_Tasha	Dog10K_Boxer_Tasha
ROS_Cfam_1.0	36	20,136,108 - 20,138,025 (+)	NCBI	ROS_Cfam_1.0	ROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl	36	20,136,051 - 20,138,025 (+)	Ensembl				ROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1	36	20,210,053 - 20,211,984 (+)	NCBI		UMICH_Zoey_3.1
UNSW_CanFamBas_1.0	36	20,210,733 - 20,212,644 (+)	NCBI		UNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0	36	20,322,637 - 20,324,574 (+)	NCBI	UU_Cfam_GSD_1.0	UU_Cfam_GSD_1.0

Hoxd1
(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	137,119,139 - 137,121,389 (+)	NCBI		HiC_Itri_2
SpeTri2.0 Ensembl	NW_004936509	5,673,184 - 5,674,521 (+)	Ensembl		SpeTri2.0 Ensembl
SpeTri2.0	NW_004936509	5,673,184 - 5,674,636 (+)	NCBI	SpeTri2.0	SpeTri2.0		SpeTri2.0

HOXD1
(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	81,987,769 - 81,990,134 (+)	Ensembl			susScr11	Sscrofa11.1
Sscrofa11.1	15	81,987,618 - 81,990,026 (+)	NCBI	Sscrofa11.1	Sscrofa11.1	susScr11	Sscrofa11.1
Sscrofa10.2	15	91,455,233 - 91,457,417 (+)	NCBI	Sscrofa10.2	Sscrofa10.2	susScr3

HOXD1
(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	61,764,519 - 61,766,846 (+)	NCBI	ChlSab1.1	ChlSab1.1	chlSab2
ChlSab1.1 Ensembl	10	61,764,741 - 61,766,081 (+)	Ensembl		ChlSab1.1 Ensembl	chlSab2	Vervet-AGM
Vero_WHO_p1.0	NW_023666040	137,843,997 - 137,846,232 (-)	NCBI	Vero_WHO_p1.0	Vero_WHO_p1.0

Hoxd1
(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	13,325,276 - 13,326,824 (+)	Ensembl		HetGla_female_1.0 Ensembl	hetGla2	HetGla_female_1.0 Ensembl
HetGla 1.0	NW_004624787	13,325,232 - 13,327,400 (+)	NCBI	HetGla 1.0	HetGla 1.0	hetGla2

Hoxd1
(Rattus rattus - black rat)

Black Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Black Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
Rrattus_CSIRO_v1	5	52,104,661 - 52,106,820 (+)	NCBI		Rrattus_CSIRO_v1

Variants

Variants in Hoxd1
19 total Variants

miRNA Target Status (No longer updated)

Predicted Target Of

	Summary Value
Count of predictions:	73
Count of miRNA genes:	66
Interacting mature miRNAs:	69
Transcripts:	ENSRNOT00000002140
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.

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
1300178	Hrtrt4	Heart rate QTL 4	3.74		heart pumping trait (VT:2000009)	heart rate (CMO:0000002)	3	51490129	111359995	Rat
1358293	Bw38	Body weight QTL 38	6	0.0000031	body mass (VT:0001259)	body weight (CMO:0000012)	3	74364268	119364268	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	73592611	110333156	Rat
1582238	Bw68	Body weight QTL 68	3.2	0.0064	body mass (VT:0001259)	body weight (CMO:0000012)	3	73592512	136118980	Rat
1331795	Rf30	Renal function QTL 30	3.708		urine potassium amount (VT:0010539)	urine potassium level (CMO:0000128)	3	59863663	87321459	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	73592512	136118980	Rat
70216	Cm14	Cardiac mass QTL 14	2.1		heart mass (VT:0007028)	heart wet weight (CMO:0000069)	3	51581665	184004958	Rat
1354589	Bw31	Body weight QTL 31	3.3		body mass (VT:0001259)	body weight (CMO:0000012)	3	53651826	98651826	Rat
2303593	Gluco46	Glucose level QTL 46	3		blood glucose amount (VT:0000188)	blood glucose level (CMO:0000046)	3	48876619	93876619	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	48876619	93876619	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	35403199	97383526	Rat
2292591	Esta4	Estrogen-induced thymic atrophy QTL 4			thymus mass (VT:0004954)	thymus wet weight (CMO:0000855)	3	67641776	167835660	Rat
1358362	Srcrt2	Stress Responsive Cort QTL 2	2.78		blood corticosterone amount (VT:0005345)	plasma corticosterone level (CMO:0001173)	3	58601291	153936591	Rat
737818	Hcar12	Hepatocarcinoma resistance QTL 12	2.6		liver integrity trait (VT:0010547)	volume of individual liver tumorous lesion (CMO:0001078)	3	49872657	138829559	Rat
631832	Sach1	Saccharin preference QTL 1	2.7	0.02	consumption behavior trait (VT:0002069)	calculated saccharin drink intake volume (CMO:0001600)	3	47904172	92904172	Rat
1582218	Bw74	Body weight QTL 74	3.9	0.0021	body mass (VT:0001259)	body weight (CMO:0000012)	3	73592512	136118980	Rat
1331777	Bw24	Body weight QTL 24	3.503		body mass (VT:0001259)	body weight (CMO:0000012)	3	59863663	87321459	Rat
631647	Bp122	Blood pressure QTL 122	6.2		arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	3	51092561	96092561	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	36425116	81425116	Rat
9590286	Uminl1	Urine mineral level QTL 1	3.5	0.001	urine mineral amount (VT:0015086)	urine electrolyte level (CMO:0000593)	3	48657744	93657744	Rat
724523	Tsu1	Thymus enlargement suppressive QTL 1	3.84		thymus mass (VT:0004954)	thymus weight to body weight ratio (CMO:0000612)	3	70845569	136091483	Rat
4889966	Bss95	Bone structure and strength QTL 95	4.4		tibia area (VT:1000281)	tibia-fibula cross-sectional area (CMO:0001718)	3	37796919	82796919	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	79649560	177741895	Rat
2302276	Bw82	Body weight QTL 82	4.32		body mass (VT:0001259)	body weight (CMO:0000012)	3	59863663	83358329	Rat
2292613	Ept16	Estrogen-induced pituitary tumorigenesis QTL 16	8.3		pituitary gland mass (VT:0010496)	pituitary gland wet weight (CMO:0000853)	3	67641995	130815812	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	58925062	103925062	Rat
631841	Niddm39	Non-insulin dependent diabetes mellitus QTL 39	3.36		blood glucose amount (VT:0000188)	blood glucose level (CMO:0000046)	3	70311536	115311536	Rat
9590136	Scort3	Serum corticosterone level QTL 3	23.37	0.001	blood corticosterone amount (VT:0005345)	plasma corticosterone level (CMO:0001173)	3	48657744	93657744	Rat
61419	Cia11	Collagen induced arthritis QTL 11	5.6		joint integrity trait (VT:0010548)	joint inflammation composite score (CMO:0000919)	3	50766145	95766145	Rat
61356	Bp37	Blood pressure QTL 37	3		blood pressure trait (VT:0000183)	systolic blood pressure (CMO:0000004)	3	51092561	96092561	Rat
1558650	Cm48	Cardiac mass QTL 48	4	0.0001	heart mass (VT:0007028)	heart weight to body weight ratio (CMO:0000074)	3	50766145	95766145	Rat
1358905	Hrtrt17	Heart rate QTL 17	5.9	0.000014	heart pumping trait (VT:2000009)	heart rate (CMO:0000002)	3	36721849	110333156	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	48657744	93657744	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	73592512	85062403	Rat
1354597	Kidm13	Kidney mass QTL 13	2.9		kidney mass (VT:0002707)	right kidney wet weight (CMO:0000082)	3	42158111	124558371	Rat
1358885	Bp251	Blood pressure QTL 251	3.8		arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	3	1	141509147	Rat
2325840	Bp345	Blood pressure QTL 345		0.001	arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	3	38708931	83708931	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	48657744	93657744	Rat
631676	Cm8	Cardiac mass QTL 8	7.03	0.0001	aorta mass (VT:0002845)	aorta weight (CMO:0000076)	3	37363734	82363734	Rat
2290452	Scl56	Serum cholesterol level QTL 56	2.26		blood cholesterol amount (VT:0000180)	plasma total cholesterol level (CMO:0000585)	3	36101403	81101403	Rat
8694386	Bw159	Body weight QTL 159	4.52	0.001	body lean mass (VT:0010483)	lean tissue morphological measurement (CMO:0002184)	3	48657744	93657744	Rat
1354604	Bw36	Body weight QTL 36	2.9		body mass (VT:0001259)	body weight (CMO:0000012)	3	42158111	124558371	Rat
1358888	Bp264	Blood pressure QTL 264	4.43		arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	3	5675975	141509147	Rat
1358186	Ept2	Estrogen-induced pituitary tumorigenesis QTL 2	8.3		pituitary gland mass (VT:0010496)	pituitary gland wet weight (CMO:0000853)	3	67641995	130815812	Rat

Markers in Region

Hoxd1

Rat Assembly	Chr	Position (strand)	Source	JBrowse
mRatBN7.2	3	59,666,331 - 59,666,725 (+)	MAPPER	mRatBN7.2
Rnor_6.0	3	61,686,322 - 61,686,715	NCBI	Rnor6.0
Rnor_5.0	3	68,151,859 - 68,152,252	UniSTS	Rnor5.0
Celera	3	59,187,580 - 59,187,973	UniSTS
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	hepatobiliary system	mesenchyme	mesoderm	nervous system	renal system	reproductive system	respiratory system	sensory system	visual system
9	1	11	50	12	10	8	8	81	15	54	48	44	2	3	3

Sequence

Nucleotide Sequences


RefSeq Transcripts	NM_001105884	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
GenBank Nucleotide	CH473949	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	JAXUCZ010000003	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles

Ensembl Acc Id:

ENSRNOT00000002140 ⟹ ENSRNOP00000002140

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
GRCr8 Ensembl	3	80,073,041 - 80,075,180 (+)	Ensembl
mRatBN7.2 Ensembl	3	59,665,629 - 59,667,769 (+)	Ensembl
Rnor_6.0 Ensembl	3	61,685,619 - 61,687,758 (+)	Ensembl

RefSeq Acc Id:

NM_001105884 ⟹ NP_001099354

RefSeq Status:

PROVISIONAL

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
GRCr8	3	80,073,041 - 80,075,180 (+)	NCBI
mRatBN7.2	3	59,665,629 - 59,667,769 (+)	NCBI
Rnor_6.0	3	61,685,619 - 61,687,758 (+)	NCBI
Rnor_5.0	3	68,151,156 - 68,153,295 (+)	NCBI
RGSC_v3.4	3	57,377,839 - 57,379,978 (+)	RGD
Celera	3	59,186,877 - 59,189,016 (+)	RGD

Sequence:

show sequence

ATATGAGGCCACTATTTACCTCGGGCTCGCTCGCCATGGCTCGGCGAGGGCAGCGGGGGTAGCG
GACCGGCAGGGTGCGGCGCCTGGGTCTCGCGGATCGAGCCATGAGCTCCTACCTGGAGTACGTA
TCGTGCGCTGCGGGCGGAGGCAGCGGAGGGGTAGGCGGCGACGTGCTGGGCTTCGCACCCAAGT
TCTGCCGCGCCGACGCGCGCCCAGTGGCCCTGCAGCCCGCCTTCCCCCTGGGCAGCGGCGACGG
CGCCTTCGTGAGCTGCCTGCCCCTGGCCGCTGCCCGGCCCACGCCTTCACCTCCCGTAGCCCCC
GCGCAGCCCCCGGGCCCGCAGCCGGCCGCGTCCCGGTACGCGCCCTGTACCCTGGAAGGCGCCT
ACGAACGGGGCGCCGCACCTGCCTCTGCCGCCGAGTATGGTTTCTTGGGGTCCGGGCCGGCATT
CGACTTTCCGGGCGCGCTTGGGAGAGCAGCGGACGACAGCGGCCCGCACGTCCACTATGCCACC
TCGGCGGTCTTTTCCAGCGGAGGATCATTCCTGCTCAGCGGCCAGGTGGACTTCGCTGCCTTTG
CCGAGCCTGGCCCCTTTCCCGCTTGTCTCAAGGAACCCGCAGACGGCCACCCCGGGCCCTTTCA
GACTGTGTCCCCGGCCCCCGGAGCCTGCCCCAAGCCCGCCTCGCCCACCTCCGGCCTCCCGGCC
GCCCACAGCACTTTCGAGTGGATGAAAGTGAAGAGGAACGCCCCCAAGAAAAGCAAACTGTCCG
AATATGGAGCCACAAGCCCCTCCAGTGCCATCCGCACGAATTTCAGCACCAAGCAACTGACAGA
ACTCGAGAAAGAGTTTCATTTCAATAAGTACCTAACTAGAGCCCGACGCATGGAGATAGCCAAC
TGTTTACAGCTGAATGACACCCAGGTCAAAATCTGGTTCCAGAACCGGAGGATGAAACAGAAGA
AAAGGGAACGAGAGGGGCTTCTGGCCACAGCTGCCTCTGTGGCCTCGCTTCAACTTCCCGGGTC
AGAAACAAGTCCCATCAAATCTGGCCGGAATCTAGGAAGCCCTTCTCAGGCTCAAGAGCCTTCC
TGAGGCCCACTCTTAAGGCTGAGGACCTTTGGATTATACAGAAGTCACAGACTGCCCCCAGCCA
CCTTTGTATAGACTTAAAAGCTTAGTCTAGGCTGGAGACGGGCGTGGGTAGAAGTTAATACGGA
TTTTACTTGGCAAAGGAATTGTCTATACTGGCTTCTGAGGCCCAGAGGCTATGTATAGAGATAT
ATATTTGATACCTTTTATTTGCATATTATTTTTGCCTCATCAGGGGAAAGCTGTCTAGCTACCA
GCCTAAACGCTGCTATGTTAGTCATGAACAATTCTTGGGTACGGAATGGCAGGCCTTCTTAGTC
TGATGTGGTCAAAACGTACCTCTCTGAAGTCATTTCAGTTTTAAGTTCCTGGACAGACTACATA
TATTCAGCTTCCTGAAATGACCAAAGCTAGCCAGGGTTCCCTCAATGGAGCTAAGCTGCTTCAA
TGATGTTCATATTGTACTCCAGTTTTATTTAAAGTCGTTCCTACCTCTTCTTGTGCCTGAGTGA
AGATACACAATCGCTCTTTAGTTGGTACCGGAATAAATCCATTGGGTAGATAAGGATTAGAATC
TAATTATACCTTGACATCAGTTACTCAAACTTGAAGTATAAATATATACAGTATGTATATTTTT
TAAAGATTTGCTTGCAGTGAACCCTATATATGACATTTAATGTCATGCATAGCATGTAAAGATT
TTGACCGTTTTTTTGGTAATAAAAGTTACAGAATCTAC

hide sequence

Protein Sequences


Protein RefSeqs	NP_001099354	(Get FASTA)	NCBI Sequence Viewer
GenBank Protein	EDL79191	(Get FASTA)	NCBI Sequence Viewer
Ensembl Protein	ENSRNOP00000002140
	ENSRNOP00000002140.4

RefSeq Acc Id:

NP_001099354 ⟸ NM_001105884

- UniProtKB:

D4ACE4 (UniProtKB/TrEMBL), A6HME0 (UniProtKB/TrEMBL)

- Sequence:

show sequence

MSSYLEYVSCAAGGGSGGVGGDVLGFAPKFCRADARPVALQPAFPLGSGDGAFVSCLPLAAARP
TPSPPVAPAQPPGPQPAASRYAPCTLEGAYERGAAPASAAEYGFLGSGPAFDFPGALGRAADDS
GPHVHYATSAVFSSGGSFLLSGQVDFAAFAEPGPFPACLKEPADGHPGPFQTVSPAPGACPKPA
SPTSGLPAAHSTFEWMKVKRNAPKKSKLSEYGATSPSSAIRTNFSTKQLTELEKEFHFNKYLTR
ARRMEIANCLQLNDTQVKIWFQNRRMKQKKREREGLLATAASVASLQLPGSETSPIKSGRNLGS
PSQAQEPS

hide sequence

Ensembl Acc Id:

ENSRNOP00000002140 ⟸ ENSRNOT00000002140

Protein Domains

Homeobox

Protein Structures

Name	Modeler	Protein Id	AA Range	Protein Structure
AF-D4ACE4-F1-model_v2	AlphaFold	D4ACE4	1-328	view protein structure

Transcriptome

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

Additional Information

External Database Links

Database	Acc Id	Source(s)
AGR Gene	RGD:1309179	AgrOrtholog
BioCyc Gene	G2FUF-49320	BioCyc
Ensembl Genes	ENSRNOG00000001572	Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript	ENSRNOT00000002140	ENTREZGENE
	ENSRNOT00000002140.6	UniProtKB/TrEMBL
Gene3D-CATH	Homeodomain-like	UniProtKB/TrEMBL
InterPro	Homeobox	UniProtKB/TrEMBL
	Homeobox_CS	UniProtKB/TrEMBL
	Homeobox_region	UniProtKB/TrEMBL
	Homeodomain-like	UniProtKB/TrEMBL
	HXA1/B1/D1	UniProtKB/TrEMBL
KEGG Report	rno:288151	UniProtKB/TrEMBL
NCBI Gene	288151	ENTREZGENE
PANTHER	HOMEOBOX PROTEIN HOX-D1	UniProtKB/TrEMBL
	PTHR45946	UniProtKB/TrEMBL
Pfam	Homeobox	UniProtKB/TrEMBL
PhenoGen	Hoxd1	PhenoGen
PRINTS	HOMEOBOX	UniProtKB/TrEMBL
PROSITE	HOMEOBOX_1	UniProtKB/TrEMBL
	HOMEOBOX_2	UniProtKB/TrEMBL
RatGTEx	ENSRNOG00000001572	RatGTEx
SMART	HOX	UniProtKB/TrEMBL
Superfamily-SCOP	Homeodomain_like	UniProtKB/TrEMBL
UniProt	A6HME0	ENTREZGENE, UniProtKB/TrEMBL
	D4ACE4	ENTREZGENE, UniProtKB/TrEMBL

Nomenclature History

Date	Current Symbol	Current Name	Previous Symbol	Previous Name	Description	Reference	Status
2008-04-30	Hoxd1	homeo box D1	Hoxd1_predicted	homeo box D1 (predicted)	'predicted' is removed	2292626	APPROVED
2005-01-12	Hoxd1_predicted	homeo box D1 (predicted)			Symbol and Name status set to approved	70820	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