Foxd1 (forkhead box D1) - Rat Genome Database

Name: Foxd1
Creator: Rat Genome Database
License: Creative Commons CC BY 4.0
Keywords: Rat Gene RGD Genome

Gene: Foxd1 (forkhead box D1) Rattus norvegicus

Analyze

Symbol:

Foxd1

Name:

forkhead box D1

RGD ID:

621712

Description:

Predicted to enable DNA binding activity, bending; DNA-binding transcription activator activity, RNA polymerase II-specific; and RNA polymerase II cis-regulatory region sequence-specific DNA binding activity. Predicted to be involved in several processes, including kidney development; luteinizing hormone secretion; and regulation of gene expression. Predicted to act upstream of or within axon guidance; branching involved in ureteric bud morphogenesis; and positive regulation of transcription by RNA polymerase II. Predicted to be located in nucleus. Orthologous to human FOXD1 (forkhead box D1); INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; ammonium chloride; bis(2-ethylhexyl) phthalate.

Type:

protein-coding

RefSeq Status:

VALIDATED

Previously known as:

BF-2; brain factor 2; forkhead box protein D1; HFH-BF-2; Hfhbf2

RGD Orthologs

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):	FOXD1 (forkhead box D1)	HGNC	HomoloGene, NCBI, OMA, OrthoDB
Mus musculus (house mouse):	Foxd1 (forkhead box D1)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Chinchilla lanigera (long-tailed chinchilla):	Foxd1 (forkhead box D1)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Pan paniscus (bonobo/pygmy chimpanzee):	FOXD1 (forkhead box D1)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Canis lupus familiaris (dog):	FOXD1 (forkhead box D1)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Sus scrofa (pig):	FOXD1 (forkhead box D1)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Chlorocebus sabaeus (green monkey):	FOXD1 (forkhead box D1)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Heterocephalus glaber (naked mole-rat):	Foxd1 (forkhead box D1)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Alliance orthologs ³
Homo sapiens (human):	FOXD1 (forkhead box D1)	Alliance	DIOPT (HGNC\|OrthoInspector)
Caenorhabditis elegans (roundworm):	unc-130	Alliance	DIOPT (OrthoFinder\|PhylomeDB\|SonicParanoid)
Drosophila melanogaster (fruit fly):	fd59A	Alliance	DIOPT (Ensembl Compara\|OrthoFinder\|PhylomeDB\|SonicParanoid)

Latest Assembly:

mRatBN7.2 - mRatBN7.2 Assembly

Position:

Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCr8	2	31,436,802 - 31,439,222 (+)	NCBI		GRCr8
mRatBN7.2	2	29,702,558 - 29,704,978 (+)	NCBI	mRatBN7.2	mRatBN7.2
mRatBN7.2 Ensembl	2	29,702,558 - 29,704,978 (+)	Ensembl		mRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx	2	36,759,829 - 36,762,247 (+)	NCBI	Rnor_SHR	UTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0	2	34,854,175 - 34,856,593 (+)	NCBI	Rnor_SHRSP	UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0	2	29,672,088 - 29,674,506 (+)	NCBI	Rnor_WKY	UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0	2	28,460,068 - 28,462,488 (+)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_6.0 Ensembl	2	28,460,068 - 28,462,488 (+)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_5.0	2	47,560,939 - 47,563,359 (+)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	2	28,944,067 - 28,945,665 (+)	NCBI	RGSC3.4	RGSC_v3.4	rn4	RGSC3.4
RGSC_v3.1	2	28,864,816 - 28,865,119 (+)	NCBI
Celera	2	25,739,043 - 25,741,152 (+)	NCBI		Celera
Cytogenetic Map	2	q12	NCBI

JBrowse:

View Region in Genome Browser (JBrowse)

Model

Annotation Click to see Annotation Detail View

Disease Annotations Click to see Annotation Detail View

genetic disease (ISO)

hereditary breast ovarian cancer syndrome (ISO)

Neurodevelopmental Disorders (ISO)

Gene-Chemical Interaction Annotations Click to see Annotation Detail View

1,1,1-Trichloro-2-(o-chlorophenyl)-2-(p-chlorophenyl)ethane (ISO)

1,1-dichloroethene (ISO)

17beta-estradiol (ISO)

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

4,4'-sulfonyldiphenol (ISO)

ammonium chloride (EXP)

arsane (ISO)

arsenic atom (ISO)

benzo[a]pyrene (ISO)

benzo[a]pyrene diol epoxide I (ISO)

bis(2-ethylhexyl) phthalate (EXP,ISO)

bisphenol A (ISO)

bisphenol F (ISO)

cannabidiol (ISO)

carbamazepine (ISO)

choline (ISO)

cisplatin (ISO)

cobalt dichloride (ISO)

coumestrol (ISO)

crocidolite asbestos (ISO)

cyclosporin A (ISO)

diallyl trisulfide (ISO)

diethylstilbestrol (ISO)

entinostat (ISO)

folic acid (ISO)

genistein (ISO)

gentamycin (EXP)

hydrazine (ISO)

isotretinoin (ISO)

L-methionine (ISO)

Licochalcone B (ISO)

N-nitrosodiethylamine (EXP)

nickel atom (ISO)

paracetamol (EXP,ISO)

phenethyl caffeate (EXP)

resveratrol (ISO)

rofecoxib (ISO)

silver atom (ISO)

silver(0) (ISO)

sodium arsenate (ISO)

temozolomide (ISO)

tert-butyl hydroperoxide (ISO)

topotecan (ISO)

trichloroethene (EXP)

urethane (ISO)

valproic acid (ISO)

zearalenone (ISO)

zinc atom (ISO)

zinc dichloride (ISO)

zinc(0) (ISO)

Gene Ontology Annotations Click to see Annotation Detail View

Biological Process

axon guidance (IEA,ISO)

branching involved in ureteric bud morphogenesis (ISO)

canonical Wnt signaling pathway (IEA,ISO)

dichotomous subdivision of terminal units involved in ureteric bud branching (IEA,ISO,ISS)

kidney development (ISO)

luteinizing hormone secretion (IEA,ISO)

metanephric capsule development (ISO,ISS)

metanephric capsule specification (IEA,ISO,ISS)

metanephric nephron development (IEA,ISO)

negative regulation of DNA-templated transcription (IEA,ISO,ISS)

nephrogenic mesenchyme development (IEA,ISO)

pattern specification involved in metanephros development (ISO)

positive regulation of BMP signaling pathway (IEA,ISO,ISS)

positive regulation of gene expression (IEA,ISO,ISS)

positive regulation of kidney development (IEA,ISO,ISS)

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

Cellular Component

nucleus (IEA)

Molecular Function

DNA binding (ISO)

DNA binding, bending (IEA,ISO)

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

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

sequence-specific DNA binding (ISO)

References

References - curated

#	Reference Title	Reference Citation
1.	Identification of nine tissue-specific transcription factors of the hepatocyte nuclear factor 3/forkhead DNA-binding-domain family.	Clevidence DE, etal., Proc Natl Acad Sci U S A 1993 May 1;90(9):3948-52.
2.	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.
3.	Rat ISS GO annotations from GOA human gene data--August 2006	GOA data from the GO Consortium
4.	Rat ISS GO annotations from MGI mouse gene data--August 2006	MGD data from the GO Consortium
5.	Electronic Transfer of LocusLink and RefSeq Data	NCBI rat LocusLink and RefSeq merged data July 26, 2002
6.	GOA pipeline	RGD automated data pipeline
7.	Data Import for Chemical-Gene Interactions	RGD automated import pipeline for gene-chemical interactions

Additional References at PubMed

PMID:7957066	PMID:8666231	PMID:11943768	PMID:13678594	PMID:15509772	PMID:15634693	PMID:23284914	PMID:32954854

Genomics

Comparative Map Data

Foxd1
(Rattus norvegicus - Norway rat)

Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCr8	2	31,436,802 - 31,439,222 (+)	NCBI		GRCr8
mRatBN7.2	2	29,702,558 - 29,704,978 (+)	NCBI	mRatBN7.2	mRatBN7.2
mRatBN7.2 Ensembl	2	29,702,558 - 29,704,978 (+)	Ensembl		mRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx	2	36,759,829 - 36,762,247 (+)	NCBI	Rnor_SHR	UTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0	2	34,854,175 - 34,856,593 (+)	NCBI	Rnor_SHRSP	UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0	2	29,672,088 - 29,674,506 (+)	NCBI	Rnor_WKY	UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0	2	28,460,068 - 28,462,488 (+)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_6.0 Ensembl	2	28,460,068 - 28,462,488 (+)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_5.0	2	47,560,939 - 47,563,359 (+)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	2	28,944,067 - 28,945,665 (+)	NCBI	RGSC3.4	RGSC_v3.4	rn4	RGSC3.4
RGSC_v3.1	2	28,864,816 - 28,865,119 (+)	NCBI
Celera	2	25,739,043 - 25,741,152 (+)	NCBI		Celera
Cytogenetic Map	2	q12	NCBI

FOXD1
(Homo sapiens - human)

Human Assembly	Chr	Position (strand)	Source	Genome Browsers
Human Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCh38	5	73,446,266 - 73,448,777 (-)	NCBI	GRCh38	GRCh38	hg38	GRCh38
GRCh38.p14 Ensembl	5	73,444,827 - 73,448,777 (-)	Ensembl	GRCh38		hg38	GRCh38
GRCh37	5	72,742,093 - 72,744,602 (-)	NCBI	GRCh37	GRCh37	hg19	GRCh37
Build 36	5	72,777,839 - 72,780,108 (-)	NCBI	NCBI36	Build 36	hg18	NCBI36
Build 34	5	72,777,870 - 72,780,356	NCBI
Celera	5	68,637,378 - 68,639,649 (-)	NCBI		Celera
Cytogenetic Map	5	q13.2	NCBI
HuRef	5	67,947,569 - 67,949,821 (-)	NCBI		HuRef
CHM1_1	5	72,174,804 - 72,177,081 (-)	NCBI		CHM1_1
T2T-CHM13v2.0	5	73,927,589 - 73,930,100 (-)	NCBI		T2T-CHM13v2.0

Foxd1
(Mus musculus - house mouse)

Mouse Assembly	Chr	Position (strand)	Source	Genome Browsers
Mouse Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCm39	13	98,490,753 - 98,493,213 (+)	NCBI	GRCm39	GRCm39	mm39
GRCm39 Ensembl	13	98,490,750 - 98,495,813 (+)	Ensembl		GRCm39 Ensembl
GRCm38	13	98,354,245 - 98,356,705 (+)	NCBI	GRCm38	GRCm38	mm10	GRCm38
GRCm38.p6 Ensembl	13	98,354,242 - 98,359,305 (+)	Ensembl	GRCm38		mm10	GRCm38
MGSCv37	13	99,124,200 - 99,126,660 (+)	NCBI	GRCm37	MGSCv37	mm9	NCBIm37
MGSCv36	13	99,454,412 - 99,456,849 (+)	NCBI		MGSCv36	mm8
Celera	13	102,010,574 - 102,012,702 (+)	NCBI		Celera
Cytogenetic Map	13	D1	NCBI
cM Map	13	51.96	NCBI

Foxd1
(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_004955425	27,158,601 - 27,159,447 (+)	NCBI	ChiLan1.0	ChiLan1.0

FOXD1
(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	4	41,869,400 - 41,871,933 (+)	NCBI		NHGRI_mPanPan1-v2
NHGRI_mPanPan1	5	40,021,506 - 40,025,581 (+)	NCBI		NHGRI_mPanPan1
Mhudiblu_PPA_v0	5	41,867,118 - 41,870,497 (+)	NCBI	Mhudiblu_PPA_v0	Mhudiblu_PPA_v0	panPan3

FOXD1
(Canis lupus familiaris - dog)

Dog Assembly	Chr	Position (strand)	Source	Genome Browsers
Dog Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
Dog10K_Boxer_Tasha	2	53,266,967 - 53,269,485 (-)	NCBI		Dog10K_Boxer_Tasha
ROS_Cfam_1.0	2	56,812,484 - 56,814,991 (-)	NCBI		ROS_Cfam_1.0
UMICH_Zoey_3.1	2	53,873,429 - 53,875,972 (-)	NCBI		UMICH_Zoey_3.1
UNSW_CanFamBas_1.0	2	54,641,541 - 54,644,071 (-)	NCBI		UNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0	2	55,532,914 - 55,535,465 (-)	NCBI		UU_Cfam_GSD_1.0

FOXD1
(Sus scrofa - pig)

Pig Assembly	Chr	Position (strand)	Source	Genome Browsers
Pig Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
Sscrofa11.1 Ensembl	2	82,607,848 - 82,609,248 (-)	Ensembl	Sscrofa11.1		susScr11	Sscrofa11.1
Sscrofa11.1	2	82,607,113 - 82,612,005 (-)	NCBI	Sscrofa11.1	Sscrofa11.1	susScr11	Sscrofa11.1

FOXD1
(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	4	67,790,423 - 67,796,901 (-)	NCBI	ChlSab1.1	ChlSab1.1	chlSab2
Vero_WHO_p1.0	NW_023666049	16,561,007 - 16,563,829 (-)	NCBI	Vero_WHO_p1.0	Vero_WHO_p1.0

Foxd1
(Heterocephalus glaber - naked mole-rat)

Naked Mole-Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Naked Mole-Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
HetGla 1.0	NW_004624905	2,487,981 - 2,490,068 (-)	NCBI	HetGla_female_1.0	HetGla 1.0	hetGla2

Variants

Variants in Foxd1
12 total Variants

miRNA Target Status

Predicted Target Of

	Summary Value
Count of predictions:	50
Count of miRNA genes:	46
Interacting mature miRNAs:	49
Transcripts:	ENSRNOT00000066819
Prediction methods:	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 (mRatBN7.2)

The following QTLs overlap with this region.

RGD ID	Symbol	Name	LOD	P Value	Trait	Sub Trait	Chr	Start	Stop	Species
631682	Bp115	Blood pressure QTL 115	4.3	0.0001	arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	2	1	37410502	Rat
738010	Lnnr3	Liver neoplastic nodule remodeling QTL 3	2.94		liver integrity trait (VT:0010547)	liver remodeling tumorous lesion number (CMO:0001461)	2	1	41244106	Rat
61355	Bp36	Blood pressure QTL 36	2.9		blood pressure trait (VT:0000183)	systolic blood pressure (CMO:0000004)	2	5873687	102844969	Rat
1600379	Mcs18	Mammary carcinoma susceptibility QTL 18	2.6		mammary gland integrity trait (VT:0010552)	mammary tumor number (CMO:0000343)	2	7887772	42804738	Rat
738012	Anxrr3	Anxiety related response QTL 3	3.8		exploratory behavior trait (VT:0010471)	percentage of entries into a discrete space in an experimental apparatus (CMO:0000961)	2	9023519	54023519	Rat
10755430	Coatc6	Coat color QTL 6		0.02576	coat/hair pigmentation trait (VT:0010463)	pigmented ventral coat/hair area to total ventral coat/hair area ratio (CMO:0001812)	2	11591100	56591100	Rat
1578664	Bmd9	Bone mineral QTL density 9	5		femur mineral mass (VT:0010011)	total volumetric bone mineral density (CMO:0001728)	2	11852062	49003364	Rat
731184	Mamtr4	Mammary tumor resistance QTL 4		0.0003	mammary gland integrity trait (VT:0010552)	mammary tumor number (CMO:0000343)	2	16491740	61491740	Rat
1357990	Ael1	Aortic elastin QTL 1	3.1	0.00091	aorta elastin amount (VT:0003905)	aortic elastin	2	19076825	64076825	Rat
731167	Glom4	Glomerulus QTL 4	2.4	0.0082	kidney glomerulus morphology trait (VT:0005325)	count of superficial glomeruli not directly contacting the kidney surface (CMO:0001002)	2	20304672	65304672	Rat
2300168	Bmd47	Bone mineral density QTL 47	6.6	0.0001	femur mineral mass (VT:0010011)	bone mineral density (CMO:0001226)	2	20662448	65662448	Rat
10402051	Gdil2	Gastrointestinal dilation QTL 2			enteric ganglion morphology trait (VT:0001045)	length of intestine affected by colonic aganglionosis to total length of colon ratio (CMO:0001836)	2	24903853	74786777	Rat
1302794	Stl27	Serum triglyceride level QTL 27	4.4	0.0001	blood triglyceride amount (VT:0002644)	plasma triglyceride level (CMO:0000548)	2	25413423	143657569	Rat
1358894	Kidm24	Kidney mass QTL 24	4.03		kidney mass (VT:0002707)	both kidneys wet weight to body weight ratio (CMO:0000340)	2	25413423	157142209	Rat
1358899	Kidm23	Kidney mass QTL 23	3.88		kidney mass (VT:0002707)	both kidneys wet weight to body weight ratio (CMO:0000340)	2	25413423	157142209	Rat
1358901	Cm38	Cardiac mass QTL 38	2		heart mass (VT:0007028)	heart weight to body weight ratio (CMO:0000074)	2	25413423	157142209	Rat
1358904	Cm39	Cardiac mass QTL 39	2.26		heart mass (VT:0007028)	heart weight to body weight ratio (CMO:0000074)	2	25413423	157142209	Rat
1358910	Kidm27	Kidney mass QTL 27	5.77		kidney mass (VT:0002707)	both kidneys wet weight to body weight ratio (CMO:0000340)	2	25413423	157142209	Rat
1358911	Kidm28	Kidney mass QTL 28	5.42		kidney mass (VT:0002707)	both kidneys wet weight to body weight ratio (CMO:0000340)	2	25413423	157142209	Rat
1358913	Cm41	Cardiac mass QTL 41	2.73		heart mass (VT:0007028)	heart weight to body weight ratio (CMO:0000074)	2	25413423	203928301	Rat
1358917	Cm42	Cardiac mass QTL 42	2.82		heart mass (VT:0007028)	heart weight to body weight ratio (CMO:0000074)	2	25413423	203928301	Rat
1358887	Bw50	Body weight QTL 50	2.39		body mass (VT:0001259)	body weight (CMO:0000012)	2	25413652	157142078	Rat
1358908	Bw49	Body weight QTL 49	3.36		body mass (VT:0001259)	body weight (CMO:0000012)	2	25413652	157142078	Rat
1354617	Bp240	Blood pressure QTL 240	4		arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	2	26917817	81754745	Rat
1354617	Bp240	Blood pressure QTL 240	4		arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	2	26917817	81754745	Rat
1354617	Bp240	Blood pressure QTL 240	4		arterial blood pressure trait (VT:2000000)	diastolic blood pressure (CMO:0000005)	2	26917817	81754745	Rat
1354603	Bp243	Blood pressure QTL 243	3.9		arterial blood pressure trait (VT:2000000)	diastolic blood pressure (CMO:0000005)	2	26917817	127469484	Rat
2290453	Scl55	Serum cholesterol level QTL 55	2.83		blood cholesterol amount (VT:0000180)	plasma total cholesterol level (CMO:0000585)	2	26917817	136917119	Rat
1331764	Bp205	Blood pressure QTL 205	3.476		arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	2	26999571	43154682	Rat
1643006	Pain1	Pain QTL 1	3.63	0.005	mechanical nociception trait (VT:0002734)	self mutilation severity score (CMO:0002145)	2	26999571	48268661	Rat
9590095	Sffal3	Serum free fatty acids level QTL 3	6.78	0.001	blood free fatty acid amount (VT:0001553)	plasma free fatty acids level (CMO:0000546)	2	27157160	72157160	Rat

Markers in Region

AI385632

Rat Assembly	Chr	Position (strand)	Source	JBrowse
mRatBN7.2	2	29,704,415 - 29,704,555 (+)	MAPPER	mRatBN7.2
Rnor_6.0	2	28,461,926 - 28,462,065	NCBI	Rnor6.0
Rnor_5.0	2	47,562,797 - 47,562,936	UniSTS	Rnor5.0
RGSC_v3.4	2	28,945,563 - 28,945,702	UniSTS	RGSC3.4
Cytogenetic Map	2	q12	UniSTS

Foxd1

Rat Assembly	Chr	Position (strand)	Source	JBrowse
mRatBN7.2	2	29,704,007 - 29,704,858 (+)	MAPPER	mRatBN7.2
Rnor_6.0	2	28,461,518 - 28,462,368	NCBI	Rnor6.0
Rnor_5.0	2	47,562,389 - 47,563,239	UniSTS	Rnor5.0
RGSC_v3.4	2	28,945,155 - 28,946,005	UniSTS	RGSC3.4
Cytogenetic Map	2	q12	UniSTS

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									10	18	12
Low			8						61	17	7
Below cutoff	1	6	5	4	1	4	4	5	3		10	4	4

View RNA-SEQ Expression Data

Sequence

Nucleotide Sequences


RefSeq Transcripts	NM_134337	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
GenBank Nucleotide	AC119356	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	JAXUCZ010000002	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	L13192	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles

RefSeq Acc Id:

ENSRNOT00000066819 ⟹ ENSRNOP00000060730

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2 Ensembl	2	29,702,558 - 29,704,978 (+)	Ensembl
Rnor_6.0 Ensembl	2	28,460,068 - 28,462,488 (+)	Ensembl

RefSeq Acc Id:

NM_134337 ⟹ NP_599164

RefSeq Status:

VALIDATED

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
GRCr8	2	31,436,802 - 31,439,222 (+)	NCBI
mRatBN7.2	2	29,702,558 - 29,704,978 (+)	NCBI
Rnor_6.0	2	28,460,068 - 28,462,488 (+)	NCBI
Rnor_5.0	2	47,560,939 - 47,563,359 (+)	NCBI
Celera	2	25,739,043 - 25,741,152 (+)	NCBI

Sequence:

show sequence

ACTCAGCCCTGGCCTTGCCGAGCTCTGTTTCTAGATTCTCACTCGTCTCGCGCCCCTCTGGGCG
CCCGACACCGACTGGCCCGCCAGGGTCCAGCCAACCCCTCCTGGACTGACCGGGCTAGAGGGAC
CGCAGTGGAAAAGGTCAAGTCTAGCACGCCCGCCACCCCGTGCACGCCGAGCCGGGGAGCGCAG
GCACCCCGCGCAGCCCGGCTCGTCAAGTAGCGGCGCGGAGCGGCCCCAGCCGCCCGTCGCAGCG
TGGCGTCCTCGCTCCGGGTCCGCCGCTCCGGGGTCGGCCTGGGGAGGCCAGAGAGCCGGGAGCC
CGGTGCCCCTATGTGCCGCCGCGCCACCGCGCCGCCCCAGCTATGACCCTGAGCACAGAGATGT
CCGATGCCTCCGGCCTCGCCGAGGAGACAGACATCGACGTGGTGGGGGAGGGAGAGGACGAAGA
GGAGGAAGAGGACGATGACGACGAGGGCGGCGGCGGGTCCCAGTTGCCCAGCTCGGCCCAGCGG
CGGCGGCGCTCCTACGCCGGGGAGGACGAGCTCGAGGACCTGGAGGAAGAGGACGACGACGAAG
ACCTGCTGCTGGCCTCGCGGCCTGCCGCGTCCCCCGCGCCTCCGGGTCCTGCGCCCGCCCCAGG
GGCCGGATCGGGCGGCTGCAGCGGCGCGGGAGCGGGAGGCGGCGCGGGAGGTGGCGTGGGCGCG
GGCGCGGGCACGGGTGGGGGCGGGAGCTCCAAGAACCCGCTGGTGAAGCCTCCCTACTCGTACA
TCGCGCTCATCACCATGGCCATCCTGCAGAGCCCCAAGAAGCGCCTGACGCTCAGCGAGATCTG
CGAGTTCATCAGCGGTCGCTTCCCTTACTACCGGGAGAAGTTCCCCGCCTGGCAGAACAGCATC
CGTCACAACCTGTCGCTCAACGACTGCTTCGTCAAGATCCCGCGCGAGCCCGGCAACCCGGGCA
AGGGCAACTACTGGACGCTCGACCCGGAGTCCGCAGACATGTTCGACAACGGCAGCTTCCTGCG
GCGCCGCAAGCGCTTCAAGCGCCAGCCGTTGCTCGCCCCCCACGCGGCGGCCGAGGCGCTGCTG
CTGCGCGGTGCGGGGCCCGCGGCGAGCGCAGGGGACCCGGGCGCCGCGCTCTTCCCGCCGCCGC
CCCCGCCGACCGCCTGCGGCTATGGAGCCTACGGCTGCGCCTACGGCCTGCAGCTGCCGCCCTG
CGCGCCGCCCTCCGCGCTCTTCGCTGCCGCCGCCGCCGCAGCCGCTGCCGCCTTCCACCCGCAC
TCACCCCCGCCACCGCCGCCGCCGCCGCCTCCTCCCGGCGCGGCCGCCGAGCTGGCGCGGACCG
CCTTCGGCTACCGGCCGCATGCGCTGGCCGCCGCCCTGCCCGGCCCGTTGCAGGCGGCCGCAGT
CAAGGCGGGAGGCCCGGGCACCGCAGCGCTCGCACGCTCGCCCTTCTCCATTGAGAGCCTCATC
GGGCGCACTCGGGGTCCCGCGACCGCCGGTGCACACGCCTCGCCTGGGGCCACCAGCGGGACCG
CACCGGGCCCCGGGGGCGGAGGCTGCGCCGTGCAAGCGGCTGCGGGTCCCGCCGTCGCGCTCAC
CCGCTCGCTGGTGGTCGCCGCCGCGGCTGCTGCCTCCTCCGTGTCGTCGTCCGCCGCGCTGGGT
ACTCTGCACCAAGGGACTGCGCTGTCCAGTGTGGAGAACTTTACTGCTAGGATTTCCAATTGTT
AGAAACGCCGTTAGCGCGCGGGAGAGAGTGAAGGTAGGACCCCGGCTCCTTTCTACGGATGGGG
GGTTGGTTTTGTTCGCCCCTCCCGGCCCTCGGCGACCTCGCGCCCCCATTTTCGCCACTTCGGA
ATCTTGGACCAGACCGTGTTGGGCGACAGCGGGGGCGCCGCGCAGTTTGGCTGAGAGGGTCAAT
CTATTTATGCAAAATCGCCCTATGCTGCAACCCTGACTTGGGGTGGGAGAGAGGGGAATCGCCC
TGTCTTGGCACTAGGAGCTTCCTTGACTTTTGAAAAATTGAGAAAAACCAAGCAAAATCATCAA
AACCAAGCCTTTTTGAAGTATAGAGATTCTCAGGTTCAGGCGTTAAAAAAAAAAAATCAGTAAT
GTTTAAATGCAGCTTATGCAAAACCAGTAAAGGTCTCCAAGAAACGCCTTTATTTGTTCACACA
TGTTTGGTATACTTTTTCATGGAAAGGAAAAAATGATTAACATGTTTACACAAGAAACAAGTCG
AGACTTATCATTTCCTATTTTTAACCTGTGTTTTGTATCATAATGGACTTGCGGAATTTTTATT
TTGTACTTACTACGTATTCTTTGCAAGGAGTATTGTAAATTTTACTGGCAATTATTATTGTACT
ATTCTAATGTAAGATTTTTACGCGGTTTTCCAGAAATAAAATGCTTAATTTTC

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Protein Sequences


Protein RefSeqs	NP_599164	(Get FASTA)	NCBI Sequence Viewer
GenBank Protein	AAA41324	(Get FASTA)	NCBI Sequence Viewer
Ensembl Protein	ENSRNOP00000060730
	ENSRNOP00000060730.3
GenBank Protein	Q63251	(Get FASTA)	NCBI Sequence Viewer

RefSeq Acc Id:

NP_599164 ⟸ NM_134337

- UniProtKB:

D3ZP43 (UniProtKB/TrEMBL)

- Sequence:

show sequence

MTLSTEMSDASGLAEETDIDVVGEGEDEEEEEDDDDEGGGGSQLPSSAQRRRRSYAGEDELEDL
EEEDDDEDLLLASRPAASPAPPGPAPAPGAGSGGCSGAGAGGGAGGGVGAGAGTGGGGSSKNPL
VKPPYSYIALITMAILQSPKKRLTLSEICEFISGRFPYYREKFPAWQNSIRHNLSLNDCFVKIP
REPGNPGKGNYWTLDPESADMFDNGSFLRRRKRFKRQPLLAPHAAAEALLLRGAGPAASAGDPG
AALFPPPPPPTACGYGAYGCAYGLQLPPCAPPSALFAAAAAAAAAAFHPHSPPPPPPPPPPPGA
AAELARTAFGYRPHALAAALPGPLQAAAVKAGGPGTAALARSPFSIESLIGRTRGPATAGAHAS
PGATSGTAPGPGGGGCAVQAAAGPAVALTRSLVVAAAAAASSVSSSAALGTLHQGTALSSVENF
TARISNC

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RefSeq Acc Id:

ENSRNOP00000060730 ⟸ ENSRNOT00000066819

Protein Domains

Fork-head

Protein Structures

Name	Modeler	Protein Id	AA Range	Protein Structure
AF-Q63251-F1-model_v2	AlphaFold	Q63251	1-101	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:621712	AgrOrtholog
BioCyc Gene	G2FUF-54725	BioCyc
Ensembl Genes	ENSRNOG00000043332	Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript	ENSRNOT00000066819	ENTREZGENE
	ENSRNOT00000066819.4	UniProtKB/TrEMBL
Gene3D-CATH	1.10.10.10	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
InterPro	Fork_head_dom	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	TF_fork_head_CS_1	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	TF_fork_head_CS_2	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	WH-like_DNA-bd_sf	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	WH_DNA-bd_sf	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
NCBI Gene	171299	ENTREZGENE
PANTHER	FORKHEAD BOX PROTEIN	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	FORKHEAD BOX PROTEIN D1	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam	Forkhead	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen	Foxd1	PhenoGen
PRINTS	FORKHEAD	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PROSITE	FORK_HEAD_1	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	FORK_HEAD_2	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	FORK_HEAD_3	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
RatGTEx	ENSRNOG00000043332	RatGTEx
SMART	SM00339	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP	SSF46785	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt	D3ZP43	ENTREZGENE, UniProtKB/TrEMBL
	FOXD1_RAT	UniProtKB/Swiss-Prot, ENTREZGENE

Nomenclature History

Date	Current Symbol	Current Name	Previous Symbol	Previous Name	Description	Reference	Status
2008-01-09	Foxd1	forkhead box D1	LOC684320	similar to Forkhead box protein D1 (Forkhead-related protein FKHL8) (Forkhead-related transcription factor 4) (FREAC-4)	Data merged from RGD:1591492	1643240	APPROVED
2006-11-20	LOC684320	similar to Forkhead box protein D1 (Forkhead-related protein FKHL8) (Forkhead-related transcription factor 4) (FREAC-4)			Symbol and Name status set to provisional	70820	PROVISIONAL
2004-09-10	Foxd1	forkhead box D1			Symbol and Name status set to approved	1299863	APPROVED
2002-08-07	Foxd1	forkhead box D1			Symbol and Name status set to provisional	70820	PROVISIONAL

RGD Curation Notes

Note Type	Note	Reference
gene_domains	contains domain binding homology with the other hepatocyte nuclear factors and with Drosophila homeotic protein forkhead (fkh)	632667
gene_process	responsible for tissue-specific gene regulation and development	632667

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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