Foxg1 (forkhead box G1) - Rat Genome Database

Name: Foxg1
Creator: Rat Genome Database
License: Creative Commons CC BY 4.0
Keywords: Rat Gene RGD Genome

	Submit Data \| Help \| Video Tutorials \| News \| Publications \| FTP Download \| REST API \| Citing RGD \| Contact
	Search RGD Grant Resources Citing RGD About Us Contact Us Genes QTLs Strains Markers Genome Information Ontologies Cell Lines References FTP Download Submit Data OntoMate (Literature Search) JBrowse (Genome Browser) Variant Visualizer Multi-Ontology Enrichment (MOET) Gene-Ortholog Location Finder (GOLF) InterViewer (Protein-Protein Interactions) PhenoMiner (Quatitative Phenotypes) Gene Annotator OLGA (Gene List Generator) RatMine GViewer (Genome Viewer) Overgo Probe Designer ACP Haplotyper Genome Scanner Aging & Age-Related Disease Cancer Cardiovascular Disease COVID-19 Developmental Disease Diabetes Hematologic Disease Immune & Inflammatory Disease Liver Disease Neurological Disease Obesity & Metabolic Syndrome Renal Disease Respiratory Disease Sensory Organ Disease Find Models new Genetic Models PhenoMiner (Quantitative Phenotypes) Expected Ranges (Quantitative Phenotype) PhenoMiner Term Comparison Hybrid Rat Diversity Panel Phenotypes GERRC (Gene Editing Rat Resource Center) Phenotypes in Other Animal Models Animal Husbandry Strain Medical Records Phylogenetics Strain Availability Calendar Rats 101 Submissions Photo Archive Pathways Rat Community Forum Directory of Rat Laboratories Video Tutorials News RGD Publications RGD Poster Archive Nomenclature Guidelines Resource Links Laboratory Resources Employment Resources
	Advanced Search (OLGA)

Gene: Foxg1 (forkhead box G1) Rattus norvegicus

Analyze

Symbol:

Foxg1

Name:

forkhead box G1

RGD ID:

2619

Description:

Predicted to have sequence-specific double-stranded DNA binding activity. Involved in aging and brain development. Predicted to localize to nucleus. Orthologous to human FOXG1 (forkhead box G1); INTERACTS WITH dexamethasone; flavonoids; N-Vinyl-2-pyrrolidone.

Type:

protein-coding

RefSeq Status:

VALIDATED

Also known as:

BF-1; BF1; BF1A; brain factor 1; Fkhl1; Fkhr; forkhead box O1; forkhead box protein G1; Forkhead-like transcription factor BF-1; forkhead-related protein FKHL1; Foxo1; RATBF1A; transcription factor BF-1

RGD Orthologs

Human

Mouse

Chinchilla

Bonobo

Dog

Squirrel

Pig

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):	FOXG1 (forkhead box G1)	HGNC	EggNOG, Ensembl, HomoloGene, Inparanoid, NCBI, OMA, OrthoDB, Panther, PhylomeDB
Mus musculus (house mouse):	Foxg1 (forkhead box G1)	HGNC	EggNOG, NCBI, OMA, HomoloGene, Inparanoid, Panther, PhylomeDB, OrthoDB, Ensembl
Chinchilla lanigera (long-tailed chinchilla):	Foxg1 (forkhead box G1)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Pan paniscus (bonobo/pygmy chimpanzee):	FOXG1 (forkhead box G1)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Canis lupus familiaris (dog):	FOXG1 (forkhead box G1)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Ictidomys tridecemlineatus (thirteen-lined ground squirrel):	Foxg1 (forkhead box G1)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Sus scrofa (pig):	FOXG1 (forkhead box G1)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Heterocephalus glaber (naked mole-rat):	Foxg1 (forkhead box G1)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Alliance orthologs ³
Mus musculus (house mouse):	Foxg1 (forkhead box G1)	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB)
Homo sapiens (human):	FOXG1 (forkhead box G1)	Alliance	DIOPT (Ensembl Compara\|HGNC\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB)
Danio rerio (zebrafish):	foxg1a (forkhead box G1a)	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoInspector\|PANTHER\|PhylomeDB)
Caenorhabditis elegans (roundworm):	fkh-2	Alliance	DIOPT (Hieranoid\|OrthoFinder\|OrthoInspector)
Drosophila melanogaster (fruit fly):	slp1	Alliance	DIOPT (Hieranoid\|OrthoFinder\|OrthoInspector)
Drosophila melanogaster (fruit fly):	slp2	Alliance	DIOPT (Hieranoid\|InParanoid\|OrthoFinder\|OrthoInspector\|PANTHER)

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
Rnor_6.0	6	69,971,227 - 69,974,037 (+)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_6.0 Ensembl	6	69,971,227 - 69,974,037 (+)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_5.0	6	79,532,855 - 79,535,665 (+)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	6	69,217,672 - 69,220,482 (+)	NCBI	RGSC3.4		rn4	RGSC3.4
RGSC_v3.1	6	69,220,797 - 69,223,608 (+)	NCBI
Celera	6	65,602,643 - 65,605,453 (+)	NCBI		Celera
Cytogenetic Map	6	q22	NCBI

JBrowse:

View Region in Genome Browser (JBrowse)

Model

Annotation Click to see Annotation Detail View

Disease Annotations Click to see Annotation Detail View

acrocallosal syndrome (ISO)

Arthrogryposis (ISO)

Developmental Disabilities (ISO)

epilepsy (ISO)

genetic disease (ISO)

intellectual disability (ISO)

microcephaly (ISO)

nervous system disease (ISO)

Neurodevelopmental Disorders (ISO)

Rett syndrome (ISS)

Rett Syndrome, Congenital Variant (ISO)

visual epilepsy (ISO)

Gene-Chemical Interaction Annotations Click to see Annotation Detail View

(S)-amphetamine (ISO)

17beta-hydroxy-5alpha-androstan-3-one (ISO)

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

4,4'-sulfonyldiphenol (ISO)

5-fluorouracil (ISO)

acetaldehyde (ISO)

aflatoxin B1 (ISO)

all-trans-retinoic acid (ISO)

atrazine (ISO)

benzo[a]pyrene (ISO)

bis(2-chloroethyl) sulfide (ISO)

bis(2-ethylhexyl) phthalate (ISO)

bisphenol A (ISO)

bisphenol F (ISO)

butanal (ISO)

chlorpyrifos (ISO)

cyproconazole (ISO)

dexamethasone (EXP)

dorsomorphin (ISO)

entinostat (ISO)

enzyme inhibitor (ISO)

erlotinib hydrochloride (ISO)

ethanol (ISO)

flavonoids (EXP)

flusilazole (ISO)

hexaconazole (ISO)

lipopolysaccharide (ISO)

LY294002 (ISO)

methotrexate (ISO)

methylisothiazolinone (ISO)

N-Vinyl-2-pyrrolidone (EXP)

PD 0325901 (ISO)

phenylmercury acetate (ISO)

poly(ethylene) (ISO)

potassium chromate (ISO)

retinyl acetate (ISO)

SB 431542 (ISO)

testosterone (EXP)

titanium dioxide (ISO)

torin 1 (ISO)

trichostatin A (ISO)

valproic acid (ISO)

Gene Ontology Annotations Click to see Annotation Detail View

Biological Process

aging (IEP)

axon midline choice point recognition (ISO)

brain development (IEP)

cell morphogenesis involved in neuron differentiation (ISO)

central nervous system neuron development (ISO)

cerebral cortex development (ISO)

dorsal/ventral pattern formation (ISO)

forebrain development (ISO)

inner ear morphogenesis (ISO)

negative regulation of neuron differentiation (ISO)

negative regulation of transcription by RNA polymerase II (ISO)

negative regulation of transcription, DNA-templated (ISO)

neurogenesis (ISO)

neuron fate determination (ISO)

positive regulation of cell cycle (ISO)

positive regulation of neuroblast proliferation (ISO)

positive regulation of neuron differentiation (ISO)

pyramidal neuron migration (ISO)

regulation of cell cycle (ISO)

regulation of gene expression (ISO)

regulation of mitotic cell cycle (ISO)

regulation of neural precursor cell proliferation (ISO)

regulation of transcription by RNA polymerase II (IBA)

Cellular Component

cellular_component (ND)

nucleus (IBA,ISO)

Molecular Function

DNA-binding transcription factor activity (IEA)

molecular_function (ND)

protein binding (ISO)

sequence-specific DNA binding (ISO)

sequence-specific double-stranded DNA binding (IBA,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.	GOA data from the GO Consortium
3.	MGD data from the GO Consortium
4.	NCBI rat LocusLink and RefSeq merged data July 26, 2002
5.	Obendorf M, etal., J Steroid Biochem Mol Biol. 2007 May;104(3-5):195-207. Epub 2007 Mar 23.
6.	OMIM Disease Annotation Pipeline
7.	Online Mendelian Inheritance in Man, OMIM (TM).
8.	RGD automated data pipeline
9.	RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
10.	RGD automated import pipeline for gene-chemical interactions
11.	RGD comprehensive gene curation
12.	Richards JS, etal., Mol Endocrinol 2002 Mar;16(3):580-99.
13.	Rout UK and Clausen P, Neurosci Res. 2009 Jun;64(2):162-9. Epub 2009 Mar 6.
14.	Tao W and Lai E, Neuron 1992 May;8(5):957-66.
15.	Tentative Sequence Data IDs. TIGR Gene Index, Rat Data
16.	Wang X, etal., J Biol Chem 2004 Jan 2;279(1):133-41. Epub 2003 Oct 16.

Additional References at PubMed

PMID:7605629	PMID:12151532	PMID:12657635	PMID:14566948	PMID:14704420	PMID:15240555	PMID:15893304	PMID:16314515	PMID:16680166	PMID:16691564	PMID:17916612	PMID:18184563
PMID:18842901	PMID:22354967	PMID:22516202	PMID:22726835	PMID:23332764	PMID:31731101

Genomics

Comparative Map Data

Foxg1
(Rattus norvegicus - Norway rat)

Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
Rnor_6.0	6	69,971,227 - 69,974,037 (+)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_6.0 Ensembl	6	69,971,227 - 69,974,037 (+)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_5.0	6	79,532,855 - 79,535,665 (+)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	6	69,217,672 - 69,220,482 (+)	NCBI	RGSC3.4		rn4	RGSC3.4
RGSC_v3.1	6	69,220,797 - 69,223,608 (+)	NCBI
Celera	6	65,602,643 - 65,605,453 (+)	NCBI		Celera
Cytogenetic Map	6	q22	NCBI

FOXG1
(Homo sapiens - human)

Human Assembly	Chr	Position (strand)	Source	Genome Browsers
Human Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCh38.p13 Ensembl	14	28,766,787 - 28,770,277 (+)	Ensembl	GRCh38		hg38	GRCh38
GRCh38.p13 Ensembl	14	28,760,330 - 28,770,277 (+)	Ensembl	GRCh38		hg38	GRCh38
GRCh38	14	28,766,787 - 28,770,277 (+)	NCBI	GRCh38	GRCh38	hg38	GRCh38
GRCh37	14	29,236,278 - 29,239,483 (+)	NCBI	GRCh37	GRCh37	hg19	GRCh37
Build 36	14	28,306,038 - 28,308,622 (+)	NCBI	NCBI36		hg18	NCBI36
Build 34	14	28,306,037 - 28,308,621	NCBI
Celera	14	9,101,781 - 9,104,365 (+)	NCBI
Cytogenetic Map	14	q12	NCBI
HuRef	14	9,354,165 - 9,356,212 (+)	NCBI		HuRef
CHM1_1	14	29,235,018 - 29,238,135 (+)	NCBI		CHM1_1

Foxg1
(Mus musculus - house mouse)

Mouse Assembly	Chr	Position (strand)	Source	Genome Browsers
Mouse Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCm39	12	49,429,666 - 49,433,650 (+)	NCBI	GRCm39		mm39
GRCm38	12	49,382,883 - 49,386,867 (+)	NCBI	GRCm38	GRCm38	mm10	GRCm38
GRCm38.p6 Ensembl	12	49,382,660 - 49,386,861 (+)	Ensembl	GRCm38		mm10	GRCm38
MGSCv37	12	50,483,870 - 50,487,854 (+)	NCBI	GRCm37		mm9	NCBIm37
MGSCv36	12	50,259,134 - 50,262,983 (+)	NCBI			mm8
Celera	12	50,702,987 - 50,706,779 (+)	NCBI		Celera
Cytogenetic Map	12	B3	NCBI
cM Map	12	21.78	NCBI

Foxg1
(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_004955409	31,672,960 - 31,674,970 (-)	NCBI	ChiLan1.0	ChiLan1.0

FOXG1
(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	14	27,702,232 - 27,723,324 (+)	NCBI	panpan1.1	PanPan1.1	panPan2
Mhudiblu_PPA_v0	14	9,545,147 - 9,572,309 (+)	NCBI	Mhudiblu_PPA_v0		panPan3

FOXG1
(Canis lupus familiaris - dog)

Dog Assembly	Chr	Position (strand)	Source	Genome Browsers
Dog Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
CanFam3.1	8	8,276,300 - 8,279,785 (+)	NCBI	CanFam3.1	CanFam3.1	canFam3	CanFam3.1

Foxg1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)

Squirrel Assembly	Chr	Position (strand)	Source	Genome Browsers
Squirrel Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
SpeTri2.0	NW_004936494	3,738,419 - 3,740,419 (+)	NCBI	SpeTri2.0	SpeTri2.0		SpeTri2.0

FOXG1
(Sus scrofa - pig)

Pig Assembly	Chr	Position (strand)	Source	Genome Browsers
Pig Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
Sscrofa11.1 Ensembl	7	70,658,685 - 70,660,145 (-)	Ensembl	Sscrofa11.1		susScr11	Sscrofa11.1
Sscrofa11.1	7	70,656,603 - 70,660,236 (-)	NCBI	Sscrofa11.1	Sscrofa11.1	susScr11	Sscrofa11.1

Foxg1
(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_004624820	3,542,767 - 3,547,180 (-)	NCBI

Position Markers

D6Arb13

No map positions available.

Foxg1

Rat Assembly	Chr	Position (strand)	Source	JBrowse
Rnor_6.0	6	69,972,913 - 69,973,916	NCBI	Rnor6.0
Rnor_5.0	6	79,534,541 - 79,535,544	UniSTS	Rnor5.0
RGSC_v3.4	6	69,219,358 - 69,220,361	UniSTS	RGSC3.4
Celera	6	65,604,329 - 65,605,332	UniSTS
Cytogenetic Map	6	q22	UniSTS

UniSTS:225243

Rat Assembly	Chr	Position (strand)	Source	JBrowse
Rnor_6.0	6	69,973,256 - 69,973,424	NCBI	Rnor6.0
Rnor_5.0	6	79,534,884 - 79,535,052	UniSTS	Rnor5.0
RGSC_v3.4	6	69,219,701 - 69,219,869	UniSTS	RGSC3.4
Celera	6	65,604,672 - 65,604,840	UniSTS
Cytogenetic Map	6	q22	UniSTS

Foxg1

Rat Assembly	Chr	Position (strand)	Source	JBrowse
Rnor_6.0	6	69,973,277 - 69,973,731	NCBI	Rnor6.0
Rnor_5.0	6	79,534,905 - 79,535,359	UniSTS	Rnor5.0
RGSC_v3.4	6	69,219,722 - 69,220,176	UniSTS	RGSC3.4
Celera	6	65,604,693 - 65,605,147	UniSTS
Cytogenetic Map	6	q22	UniSTS

Foxg1

Rat Assembly	Chr	Position (strand)	Source	JBrowse
Rnor_6.0	6	69,972,690 - 69,973,085	NCBI	Rnor6.0
Rnor_5.0	6	79,534,318 - 79,534,713	UniSTS	Rnor5.0
RGSC_v3.4	6	69,219,135 - 69,219,530	UniSTS	RGSC3.4
Celera	6	65,604,106 - 65,604,501	UniSTS
Cytogenetic Map	6	q22	UniSTS

Foxg1

Rat Assembly	Chr	Position (strand)	Source	JBrowse
Rnor_6.0	6	69,970,151 - 69,971,510	NCBI	Rnor6.0
Rnor_5.0	6	79,531,779 - 79,533,138	UniSTS	Rnor5.0
Celera	6	65,601,865 - 65,602,926	UniSTS
Cytogenetic Map	6	q22	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
2301972	Bp325	Blood pressure QTL 325	4.8		arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	6	1	75623393	Rat
1354664	Slep2	Serum leptin concentration QTL 2	4.49		blood leptin amount (VT:0005667)	serum leptin level (CMO:0000780)	6	1120393	75023446	Rat
1576309	Emca7	Estrogen-induced mammary cancer QTL 7	4		mammary gland integrity trait (VT:0010552)	mammary tumor number (CMO:0000343)	6	2537030	111715717	Rat
1578665	Bss16	Bone structure and strength QTL 16	4.4		femur morphology trait (VT:0000559)	bone trabecular cross-sectional area (CMO:0002311)	6	6161722	76002731	Rat
1578668	Bmd14	Bone mineral density QTL 14	3.8		femur mineral mass (VT:0010011)	total volumetric bone mineral density (CMO:0001728)	6	6161722	76002731	Rat
4145119	Mcs25	Mammary carcinoma susceptibility QTL 25		0.0001	mammary gland integrity trait (VT:0010552)	ratio of deaths to total study population during a period of time (CMO:0001023)	6	7009971	115379601	Rat
2293839	Kiddil2	Kidney dilation QTL 2	4.8		kidney pelvis morphology trait (VT:0004194)	hydronephrosis severity score (CMO:0001208)	6	22042854	84763421	Rat
2293841	Kiddil4	Kidney dilation QTL 4	4.4		kidney pelvis morphology trait (VT:0004194)	hydronephrosis severity score (CMO:0001208)	6	22042854	84763421	Rat
1300143	Rf14	Renal function QTL 14	2.92		renal blood flow trait (VT:2000006)	absolute change in renal blood flow rate (CMO:0001168)	6	34367436	80490628	Rat
1331779	Rf38	Renal function QTL 38	2.876		kidney blood vessel physiology trait (VT:0100012)	absolute change in renal vascular resistance (CMO:0001900)	6	34995656	75623393	Rat
6893340	Cm77	Cardiac mass QTL 77	0.26	0.57	heart mass (VT:0007028)	heart weight to body weight ratio (CMO:0000074)	6	36260288	84763275	Rat
1354632	Scl29	Serum cholesterol level QTL 29	3.74		blood cholesterol amount (VT:0000180)	serum total cholesterol level (CMO:0000363)	6	37608980	75023446	Rat
634307	Bp141	Blood pressure QTL 141	4		arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	6	38106308	83106308	Rat
9590290	Uminl2	Urine mineral level QTL 2	3.96	0.001	urine mineral amount (VT:0015086)	urine electrolyte level (CMO:0000593)	6	41679046	86679046	Rat
9590306	Scort18	Serum corticosterone level QTL 18	2.88	0.001	blood corticosterone amount (VT:0005345)	plasma corticosterone level (CMO:0001173)	6	41679046	86679046	Rat
9590140	Scort4	Serum corticosterone level QTL 4	14.49	0.001	blood corticosterone amount (VT:0005345)	plasma corticosterone level (CMO:0001173)	6	41679046	86679046	Rat
634330	Pia16	Pristane induced arthritis QTL 16	3.9		joint integrity trait (VT:0010548)	arthritic paw count (CMO:0001460)	6	48432758	108268790	Rat
4889848	Pur25	Proteinuria QTL 25	14	0.003	total urine protein amount (VT:0000032)	urine total protein excretion rate (CMO:0000756)	6	59803065	94001333	Rat
1558641	Cm47	Cardiac mass QTL 47	2.9	0.001	heart mass (VT:0007028)	heart wet weight (CMO:0000069)	6	60606431	108154445	Rat
6893332	Cm74	Cardiac mass QTL 74	0.4	0.64	heart mass (VT:0007028)	heart weight to body weight ratio (CMO:0000074)	6	60606431	108154445	Rat
70176	Mcsm1	Mammary carcinoma susceptibility modifier QTL 1			mammary gland integrity trait (VT:0010552)	mammary tumor number (CMO:0000343)	6	62263348	107263348	Rat
12801471	Schws9	Schwannoma susceptibility QTL 9			nervous system integrity trait (VT:0010566)	percentage of study population developing trigeminal nerve neurilemmomas during a period of time (CMO:0002017)	6	66129520	111129520	Rat
2293088	Iddm28	Insulin dependent diabetes mellitus QTL 28	5.21		blood glucose amount (VT:0000188)	blood glucose level (CMO:0000046)	6	66222612	75023308	Rat
731173	Uae22	Urinary albumin excretion QTL 22	10.1		urine albumin amount (VT:0002871)	urine albumin excretion rate (CMO:0000757)	6	68781170	147991367	Rat
2290393	Uae37	Urinary albumin excretion QTL 37		0.0001	urine albumin amount (VT:0002871)	urine albumin excretion rate (CMO:0000757)	6	68781170	147991367	Rat

miRNA Target Status

Predicted Target Of

	Summary Value
Count of predictions:	665
Count of miRNA genes:	280
Interacting mature miRNAs:	369
Transcripts:	ENSRNOT00000075349
Prediction methods:	Microtar, Miranda, 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									42
Low		2	10	2	8	2			14		6	1
Below cutoff	1	19	17	10	8	10	5	5	16	11	30	8	5

View RNA-SEQ Expression Data

Sequence

Nucleotide Sequences


RefSeq Transcripts	NM_012560	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
GenBank Nucleotide	AABR07064224	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	AAHX01044001	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	CH473947	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	M87634	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles

Reference Sequences

RefSeq Acc Id:

ENSRNOT00000075349 ⟹ ENSRNOP00000067118

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
Rnor_6.0 Ensembl	6	69,971,227 - 69,974,037 (+)	Ensembl

RefSeq Acc Id:

NM_012560 ⟹ NP_036692

RefSeq Status:

VALIDATED

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
Rnor_6.0	6	69,971,227 - 69,974,037 (+)	NCBI
Rnor_5.0	6	79,532,855 - 79,535,665 (+)	NCBI
RGSC_v3.4	6	69,217,672 - 69,220,482 (+)	RGD
Celera	6	65,602,643 - 65,605,453 (+)	RGD

Sequence:

show sequence

GCGGCCGCTCCGGGACGCGCCCGCCCGCTGCCCGGCTCTCCCCCCCTTCGGGCTGCCGCTGCTG
CTGCTGTGACTGCTGCGGCGCGAGGAGGAGGAGGCAGCGGGGGAGGGGGAGGCCGGGCGCGGAA
CGGAGCGGGGCGCTGCACCCCGGGCGACGGGTTGCTTCTGCCTCTAGCTTCTCTCTCTCTCTCT
CTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTAATTCTTGAGGGGTGG
TTGCAGCTTTTGCTACATGCCTTGCCAGCGCCGGAGCCTGCGGTCCAACTGCGCTGCTGCCGGA
GCGCTCAGTGCCGCCGCCGCTGCCCGCTCCCCCCGCTCCCCACTCCGAACCCGCCGGTCGCTCG
CCGCGCTGCTGCTCGGCTCCTGCGCCGCCGCCGTCGCCGCCCCCCGACGCCTGGGTGATGCTGG
ACATGGGAGATAGGAAAGAGGTGAAAATGATTCCCAAGTCCTCGTTCAGCATCAACAGCCTGGT
CCCTGAGGCCGTCCAGAACGACAACCACCACGCGAGCCACGGTCACCACAACAGCCACCACCCC
CAGCATCACCATCATCATCACCACCACCACCACCCGCCGCCGCCCGCGCCTCAGCCGCCGCCAC
CGCCGCCCCAGCAGCAGCAGCAGCCGCCCCCGGCCCCGCAGCCCCCGCAGGCGCGCGGCGCCCC
AGCAGCGGACGACGACAAGGGCCCCCAGCCGCTTCTGCTCCCGCCGTCCGCCGCCCTGGACGGG
GCCAAGGCTGACGCACTTGGAGCCAAAGGCGAGCCAGGCGGCGGGCCTGCGGAGCTGGCGCCCG
TCGGGCCGGACGAGAAGGAGAAGGGCGCGGGCGCTGGGGGGGAGGAGAAGAAGGGGGCGGGCGA
GGGCGGCAAGGACGGGGAGGGGGGCAAGGAGGGCGACAAGAAGAACGGCAAGTACGAGAAGCCG
CCGTTCAGCTACAACGCGCTCATCATGATGGCCATCAGGCAGAGTCCCGAGAAGCGCCTGACGC
TCAACGGCATCTACGAGTTCATCATGAAGAACTTCCCTTACTACCGCGAGAACAAGCAGGGCTG
GCAGAACTCCATCCGCCACAACCTGTCCCTCAACAAGTGCTTCGTGAAGGTACCGCGCCACTAC
GACGACCCGGGCAAGGGCAACTACTGGATGCTGGACCCGTCGAGCGACGACGTGTTCATCGGCG
GCACGACCGGCAAGCTGCGGCGCCGCTCCACCACGTCTCGGGCCAAGCTAGCCTTTAAGCGCGG
GGCACGGCTCACCTCCACCGGCCTCACCTTCATGGACCGCGCCGGCTCCCTCTACTGGCCCATG
TCGCCCTTCCTGTCCCTGCACCACCCTCGCGCCAGCAGCACTTTGAGTTACAACGGGACCACGT
CGGCCTACCCCAGCCACCCCATGCCCTACAGCTCCGTGTTGACTCAAAACTCGCTGGGCAACAA
CCACTCCTTCTCCACCGCCAACGGGCTGAGCGTGGACCGGCTGGTCAACGGGGAGATCCCGTAC
GCCACGCACCACCTCACGGCCGCTGCGCTCGCCGCCTCCGTGCCCTGCGGCCTGTCGGTGCCCT
GCTCCGGGACCTACTCCCTCAACCCCTGCTCCGTCAACCTGCTCGCGGGCCAGACCAGTTACTT
TTTCCCCCACGTCCCGCACCCGTCAATGACTTCGCAGACCAGCACGTCCATGAGCGCCCGGGCC
GCGTCCTCCTCTACGTCGCCGCAGGCCCCCTCGACCCTGCCCTGTGAGTCTTTAAGACCCTCTT
TGCCAAGTTTTACGACAGGACTGTCCGGGGGACTGTCTGATTATTTCACACATCAAAATCAGGG
GTCTTCTTCCAACCCTTTAATACATTAACATCCCGGGGACCAGACTGTAAGTGAACGTTTTACA
CACATTTGCATTGTAAATGATAATTAAAAAATAAGTCCAGGTATTTTTTATTAAGCCCTTCCCC
CCATTTCTGTACGTTTGTTCAGTCTTTAGGGTTGTTTACTATTCTAACACGGTGTGGAGTGTCA
GCGAGGTGCAATGTGGGAGAATACATTGTAGAATATAAGGTTTGGACGTCAAATTATAGTAGAA
TGTGTATCTAAATAGTGACTGCTTTGCCATTTCATTCAAACCTGACAAGTCTATCTCTAAAGGC
TGCCAGATTTCCATGTGTGCAGTATTATAAGTTATCATGGATCTATCTGGTGGACGCAGGCCTT
GAAGAACAACCTAAATTATGAAGAGAGTTTTAAAATGTTAAACTGTAATTTGTATTTAAGAATT
TGTAGTAAAGGTGCCCAAGAAATTATATTGGCCATTTATTGTTTTGTCCTTTTCTTTAAAGAAC
TGTTTTTTTCTTTTGTTTACTTTTAGACCAAAGATTGGATTCTAGCAAATGCACTTGGTATACT
AAGTATTAAAACAAGCAAACAAACAAACAAAAAAGGAAGGTTGTTTAGTTTGGCAACACTGCCC
ATTCAATTGAATCCGAAGGAGACAAAATTAAGGATTGCCTTCAGTTTGTGTTGTGTATATTTCG
ATGTATGTGGTCACTAACAGGTCACTTTTATTTTTTCTAAATGTAGTGAAATGTTAATACCTAT
TGTACTTATAGGTAAACCTTGCAAATATGTAACCTGTGTTGCGCAAATGCCGCATCAATTTGAG
TGATTGTTAATGTTGTCTTAAAATTTCTTGATTGTGATACTGTGGTCATATGCCCGTGTTTGTC
ACTTACAAAAATGTTTACTATGAACACACAGAAATAAAAAATAGGCTAAATTCATATAT

hide sequence

Protein Sequences


Protein RefSeqs	NP_036692	(Get FASTA)	NCBI Sequence Viewer
GenBank Protein	AAA40812	(Get FASTA)	NCBI Sequence Viewer
	EDM03366	(Get FASTA)	NCBI Sequence Viewer
	Q00939	(Get FASTA)	NCBI Sequence Viewer

Reference Sequences

RefSeq Acc Id:

NP_036692 ⟸ NM_012560

- UniProtKB:

Q00939 (UniProtKB/Swiss-Prot)

- Sequence:

show sequence

MLDMGDRKEVKMIPKSSFSINSLVPEAVQNDNHHASHGHHNSHHPQHHHHHHHHHHPPPPAPQP
PPPPPQQQQQPPPAPQPPQARGAPAADDDKGPQPLLLPPSAALDGAKADALGAKGEPGGGPAEL
APVGPDEKEKGAGAGGEEKKGAGEGGKDGEGGKEGDKKNGKYEKPPFSYNALIMMAIRQSPEKR
LTLNGIYEFIMKNFPYYRENKQGWQNSIRHNLSLNKCFVKVPRHYDDPGKGNYWMLDPSSDDVF
IGGTTGKLRRRSTTSRAKLAFKRGARLTSTGLTFMDRAGSLYWPMSPFLSLHHPRASSTLSYNG
TTSAYPSHPMPYSSVLTQNSLGNNHSFSTANGLSVDRLVNGEIPYATHHLTAAALAASVPCGLS
VPCSGTYSLNPCSVNLLAGQTSYFFPHVPHPSMTSQTSTSMSARAASSSTSPQAPSTLPCESLR
PSLPSFTTGLSGGLSDYFTHQNQGSSSNPLIH

hide sequence

RefSeq Acc Id:

ENSRNOP00000067118 ⟸ ENSRNOT00000075349

Transcriptome

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

Promoters

RGD ID:

13694580

Promoter ID:

EPDNEW_R5105

Type:

single initiation site

Name:

Foxg1_1

Description:

forkhead box G1

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	6	69,971,157 - 69,971,217	EPDNEW

Strain Variation

Strain Sequence Variants (Rnor 6.0)

ACI/EurMcwi (MCW)

Visual

CSV

TAB

Printer

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)

Visual

CSV

TAB

Printer

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)

Visual

CSV

TAB

Printer

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)

Visual

CSV

TAB

Printer

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)

Visual

CSV

TAB

Printer

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)

Visual

CSV

TAB

Printer

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)

Visual

CSV

TAB

Printer

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)

Visual

CSV

TAB

Printer

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)

Visual

CSV

TAB

Printer

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)

Visual

CSV

TAB

Printer

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)

Visual

CSV

TAB

Printer

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)

Visual

CSV

TAB

Printer

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)

Visual

CSV

TAB

Printer

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)

Visual

CSV

TAB

Printer

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)

Visual

CSV

TAB

Printer

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)

Visual

CSV

TAB

Printer

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)

Visual

CSV

TAB

Printer

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)

Visual

CSV

TAB

Printer

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)

Visual

CSV

TAB

Printer

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)

Visual

CSV

TAB

Printer

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)

Visual

CSV

TAB

Printer

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)

Visual

CSV

TAB

Printer

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)

Visual

CSV

TAB

Printer

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)

Visual

CSV

TAB

Printer

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)

Visual

CSV

TAB

Printer

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)

Visual

CSV

TAB

Printer

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)

Visual

CSV

TAB

Printer

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)

Visual

CSV

TAB

Printer

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)

Visual

CSV

TAB

Printer

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)

Visual

CSV

TAB

Printer

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)

Visual

CSV

TAB

Printer

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)

Visual

CSV

TAB

Printer

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)

Visual

CSV

TAB

Printer

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)

Visual

CSV

TAB

Printer

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)

Visual

CSV

TAB

Printer

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)

Visual

CSV

TAB

Printer

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)

Visual

CSV

TAB

Printer

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)

Visual

CSV

TAB

Printer

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)

Visual

CSV

TAB

Printer

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)

Visual

CSV

TAB

Printer

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)

Visual

CSV

TAB

Printer

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)

Visual

CSV

TAB

Printer

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

Damaging Variants

Assembly: Rnor_5.0

Chromosome	Start Pos	End Pos	Reference Nucleotide	Variant Nucleotide	Variant Type	Strain
6	79534371	79534372	T	G	snv	SR/JrHsd (MCW), ACI/EurMcwi (MCW)

Assembly: RGSC_v3.4

Chromosome	Start Pos	End Pos	Reference Nucleotide	Variant Nucleotide	Variant Type	Strain
6	69219188	69219189	T	G	snv	SR/JrHsd (MCW), ACI/EurMcwi (MCW)

Additional Information

External Database Links

Database	Acc Id	Source(s)
AGR Gene	RGD:2619	AgrOrtholog
Ensembl Genes	ENSRNOG00000047891	Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Protein	ENSRNOP00000067118	ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript	ENSRNOT00000075349	ENTREZGENE, UniProtKB/Swiss-Prot
Gene3D-CATH	1.10.10.10	UniProtKB/Swiss-Prot
InterPro	Fork_head_dom	UniProtKB/Swiss-Prot
	TF_fork_head_CS_1	UniProtKB/Swiss-Prot
	TF_fork_head_CS_2	UniProtKB/Swiss-Prot
	WH-like_DNA-bd_sf	UniProtKB/Swiss-Prot
	WH_DNA-bd_sf	UniProtKB/Swiss-Prot
KEGG Report	rno:24370	UniProtKB/Swiss-Prot
NCBI Gene	24370	ENTREZGENE
Pfam	Forkhead	UniProtKB/Swiss-Prot
PhenoGen	Foxg1	PhenoGen
PRINTS	FORKHEAD	UniProtKB/Swiss-Prot
PROSITE	FORK_HEAD_1	UniProtKB/Swiss-Prot
	FORK_HEAD_2	UniProtKB/Swiss-Prot
	FORK_HEAD_3	UniProtKB/Swiss-Prot
SMART	SM00339	UniProtKB/Swiss-Prot
Superfamily-SCOP	SSF46785	UniProtKB/Swiss-Prot
TIGR	TC226558
UniGene	Rn.9864	ENTREZGENE
UniProt	FOXG1_RAT	UniProtKB/Swiss-Prot, ENTREZGENE

Nomenclature History

Date	Current Symbol	Current Name	Previous Symbol	Previous Name	Description	Reference	Status
2004-12-14	Foxg1	forkhead box G1	Foxo1	forkhead box O1	Symbol and Name updated	1299863	APPROVED
2003-03-04	Foxo1	CCR4 carbon catabolite repression 4-like (S. cerevisiae)	Foxg1	forkhead box O1	Symbol updated to reflect Human and Mouse nomenclature	61478	PROVISIONAL
2002-11-06	Foxg1	forkhead box O1	Fkhr	Forkhead-like transcription factor BF-1	Symbol and Name updated	625702	APPROVED
2002-06-10	Fkhr	Forkhead-like transcription factor BF-1			Symbol and Name status set to approved	70586	APPROVED

RGD Curation Notes

Note Type	Note	Reference
gene_expression	expressed in the granulosa cells of growing follicles	632665
gene_process	may be responsible for proliferation of granulosa cells and their phosphorylation by FSH	632665

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)

Imported Disease Annotations - ClinVar

Imported Disease Annotations - CTD

Imported Disease Annotations - MGI

Imported Disease Annotations - OMIM