Fgfr4 (fibroblast growth factor receptor 4)

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Gene: Fgfr4 (fibroblast growth factor receptor 4) Rattus norvegicus

Analyze

Symbol:

Fgfr4

Name:

fibroblast growth factor receptor 4

RGD ID:

2612

Description:

Predicted to have fibroblast growth factor binding activity; fibroblast growth factor-activated receptor activity; and heparin binding activity. Involved in fibroblast growth factor receptor signaling pathway. Predicted to colocalize with cell-cell junction. Orthologous to human FGFR4 (fibroblast growth factor receptor 4); PARTICIPATES IN fibroblast growth factor signaling pathway; endocytosis pathway; mitogen activated protein kinase signaling pathway; INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; 2,4-dinitrotoluene; 3H-1,2-dithiole-3-thione.

Type:

protein-coding

RefSeq Status:

VALIDATED

Also known as:

FGFR-4; MGC116290

RGD Orthologs

Human

Mouse

Chinchilla

Bonobo

Dog

Squirrel

Pig

Green Monkey

Naked Mole-Rat

Alliance Genes

More Info

more info ...

More Info

Species	Gene symbol and name	Data Source	Assertion derived from	less info ...
Orthologs ¹				less info ...
Homo sapiens (human):	FGFR4 (fibroblast growth factor receptor 4)	HGNC	EggNOG, Ensembl, HomoloGene, Inparanoid, NCBI, OMA, OrthoDB, Panther, PhylomeDB, Treefam
Mus musculus (house mouse):	Fgfr4 (fibroblast growth factor receptor 4)	HGNC	Treefam, EggNOG, NCBI, OMA, HomoloGene, Inparanoid, Panther, OrthoDB, Ensembl
Chinchilla lanigera (long-tailed chinchilla):	Fgfr4 (fibroblast growth factor receptor 4)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Pan paniscus (bonobo/pygmy chimpanzee):	FGFR4 (fibroblast growth factor receptor 4)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Canis lupus familiaris (dog):	FGFR4 (fibroblast growth factor receptor 4)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Ictidomys tridecemlineatus (thirteen-lined ground squirrel):	Fgfr4 (fibroblast growth factor receptor 4)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Sus scrofa (pig):	FGFR4 (fibroblast growth factor receptor 4)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Chlorocebus sabaeus (African green monkey):	FGFR4 (fibroblast growth factor receptor 4)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Heterocephalus glaber (naked mole-rat):	Fgfr4 (fibroblast growth factor receptor 4)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Alliance orthologs ³
Homo sapiens (human):	FGFR4 (fibroblast growth factor receptor 4)	Alliance	DIOPT (Ensembl Compara\|HGNC\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|TreeFam)
Mus musculus (house mouse):	Fgfr4 (fibroblast growth factor receptor 4)	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|TreeFam)
Danio rerio (zebrafish):	fgfr4 (fibroblast growth factor receptor 4)	Alliance	DIOPT (Ensembl Compara\|OMA\|OrthoFinder\|PANTHER\|PhylomeDB\|TreeFam)
Drosophila melanogaster (fruit fly):	btl	Alliance	DIOPT (Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PhylomeDB\|TreeFam)
Caenorhabditis elegans (roundworm):	egl-15	Alliance	DIOPT (Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PhylomeDB\|TreeFam)
Drosophila melanogaster (fruit fly):	htl	Alliance	DIOPT (Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PhylomeDB\|TreeFam)

Latest Assembly:

Rnor_6.0 - RGSC Genome Assembly v6.0

Position:

Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
mRatBN7.2	17	9,461,541 - 9,476,268 (-)	NCBI
Rnor_6.0 Ensembl	17	9,990,078 - 10,004,321 (-)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_6.0	17	9,990,072 - 10,004,339 (-)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_5.0	17	12,099,383 - 12,113,637 (-)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	17	15,512,144 - 15,527,348 (-)	NCBI	RGSC3.4		rn4	RGSC3.4
RGSC_v3.1	17	15,512,146 - 15,523,432 (-)	NCBI
Celera	17	9,540,006 - 9,554,750 (-)	NCBI		Celera
Cytogenetic Map	17	p14	NCBI

JBrowse:

View Region in Genome Browser (JBrowse)

Model

Annotation Click to see Annotation Detail View

Disease Annotations Click to see Annotation Detail View

adenoid cystic carcinoma (ISO)

adult respiratory distress syndrome (ISO)

Breast Neoplasms (ISO)

Chromosome 5, Trisomy 5q (ISO)

Marfanoid Mental Retardation Syndrome, Autosomal (ISO)

Neoplasm Invasiveness (ISO)

Prostatic Neoplasms (ISO)

rhabdomyosarcoma (ISO)

Gene-Chemical Interaction Annotations Click to see Annotation Detail View

(+)-catechin (ISO)

1,2-dimethylhydrazine (ISO)

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

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

2,4-dinitrotoluene (EXP)

3-isobutyl-1-methyl-7H-xanthine (ISO)

3H-1,2-dithiole-3-thione (EXP)

4-hydroxyphenyl retinamide (ISO)

acrylamide (ISO)

aflatoxin B1 (ISO)

all-trans-retinoic acid (ISO)

arsane (ISO)

arsenic atom (ISO)

benomyl (EXP)

benzo[a]pyrene (ISO)

bis(2-ethylhexyl) phthalate (ISO)

bisphenol A (EXP,ISO)

buta-1,3-diene (ISO)

C60 fullerene (EXP)

cannabidiol (EXP)

carbon nanotube (ISO)

chloroprene (ISO)

chlorpyrifos (EXP)

cholesterol (ISO)

chromium(6+) (ISO)

cisplatin (ISO)

clofibrate (ISO)

clofibric acid (EXP)

cobalt dichloride (EXP)

copper atom (EXP,ISO)

copper(0) (EXP,ISO)

copper(II) sulfate (ISO)

crocidolite asbestos (ISO)

cyclosporin A (EXP,ISO)

DDE (EXP)

dexamethasone (ISO)

dextran sulfate (ISO)

diazinon (EXP)

dibutyl phthalate (EXP)

dieldrin (EXP)

dioxygen (ISO)

dorsomorphin (ISO)

endosulfan (EXP)

ethanol (EXP)

flusilazole (EXP)

flutamide (EXP)

furosemide (EXP)

GW 4064 (ISO)

heparan sulfate (ISO)

heparin (EXP,ISO)

hydrogen peroxide (ISO)

lead diacetate (ISO)

mono(2-ethylhexyl) phthalate (ISO)

N-methyl-N-nitrosourea (EXP)

N-nitrosodiethylamine (EXP,ISO)

N-nitrosodimethylamine (EXP)

nickel atom (EXP)

nitrofen (EXP)

obeticholic acid (ISO)

okadaic acid (ISO)

p-toluidine (EXP)

paracetamol (ISO)

PD173074 (ISO)

perfluorooctane-1-sulfonic acid (ISO)

perfluorooctanoic acid (EXP,ISO)

phenylmercury acetate (ISO)

phosgene (ISO)

pirinixic acid (EXP,ISO)

ponatinib (ISO)

pregnenolone 16alpha-carbonitrile (ISO)

quercetin (ISO)

SB 431542 (ISO)

silicon dioxide (ISO)

sodium arsenite (ISO)

sulindac sulfide (ISO)

taurocholic acid (ISO)

tetrachloromethane (EXP,ISO)

thioacetamide (EXP)

titanium dioxide (ISO)

triptonide (ISO)

valproic acid (ISO)

zoledronic acid (ISO)

Gene Ontology Annotations Click to see Annotation Detail View

Biological Process

alveolar secondary septum development (ISO)

cell migration (ISO,ISS)

cholesterol homeostasis (ISO,ISS)

fibroblast growth factor receptor signaling pathway (ISO)

glucose homeostasis (ISO,ISS)

lung development (ISO)

multicellular organism development (IBA)

negative regulation of fibroblast growth factor production (ISO)

negative regulation of gene expression (ISO)

organ induction (ISO)

peptidyl-tyrosine phosphorylation (ISO,ISS)

phosphate ion homeostasis (ISO,ISS)

positive regulation of catalytic activity (ISO,ISS)

positive regulation of cell population proliferation (ISO,ISS)

positive regulation of DNA biosynthetic process (ISO,ISS)

positive regulation of ERK1 and ERK2 cascade (IBA,ISO,ISS)

positive regulation of gene expression (ISO)

positive regulation of kinase activity (IBA)

positive regulation of parathyroid hormone secretion (ISO)

positive regulation of proteolysis (ISO,ISS)

protein autophosphorylation (ISO,ISS)

regulation of bile acid biosynthetic process (IBA,ISO,ISS)

regulation of extracellular matrix disassembly (ISO,ISS)

regulation of lipid metabolic process (ISO,ISS)

regulation of phosphate transport (ISO)

regulation of phosphorus metabolic process (ISO)

response to bile acid (ISO)

transmembrane receptor protein tyrosine kinase signaling pathway (IBA)

vitamin D3 metabolic process (ISO)

Cellular Component

cell-cell junction (ISO,ISS)

endoplasmic reticulum (ISO,ISS)

endosome (IEA)

Golgi apparatus (ISO)

integral component of plasma membrane (IBA,ISO,ISS)

plasma membrane (ISO)

receptor complex (IBA)

transport vesicle (ISO)

Molecular Function

ATP binding (IEA)

fibroblast growth factor binding (IBA,ISO,ISS)

fibroblast growth factor-activated receptor activity (IBA,ISO)

heparin binding (ISO,ISS)

protein binding (ISO)

transmembrane receptor protein tyrosine kinase activity (IBA)

Molecular Pathway Annotations Click to see Annotation Detail View

endocytosis pathway (IEA)

fibroblast growth factor signaling pathway (ISO)

mitogen activated protein kinase signaling pathway (IEA)

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.	Horlick RA, etal., Gene 1992 Oct 21;120(2):291-5.
4.	Konishi M, etal., J Biol Chem. 2000 Apr 21;275(16):12119-22.
5.	MGD data from the GO Consortium
6.	NCBI rat LocusLink and RefSeq merged data July 26, 2002
7.	Pipeline to import KEGG annotations from KEGG into RGD
8.	Pipeline to import Pathway Interaction Database annotations from NCI into RGD
9.	RGD automated data pipeline
10.	RGD automated import pipeline for gene-chemical interactions
11.	Szpirer C, etal., Mamm Genome 1998 Sep;9(9):721-34

Additional References at PubMed

PMID:8663044	PMID:9716527	PMID:10525310	PMID:10809780	PMID:12477932	PMID:15489334	PMID:15576401	PMID:17623664	PMID:17627937	PMID:17664243	PMID:18061161	PMID:18187602
PMID:18480409	PMID:19085950	PMID:20683963	PMID:20798051	PMID:20876804	PMID:21561999	PMID:21653700	PMID:24259513	PMID:28339837

Genomics

Comparative Map Data

Fgfr4
(Rattus norvegicus - Norway rat)

Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
mRatBN7.2	17	9,461,541 - 9,476,268 (-)	NCBI
Rnor_6.0 Ensembl	17	9,990,078 - 10,004,321 (-)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_6.0	17	9,990,072 - 10,004,339 (-)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_5.0	17	12,099,383 - 12,113,637 (-)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	17	15,512,144 - 15,527,348 (-)	NCBI	RGSC3.4		rn4	RGSC3.4
RGSC_v3.1	17	15,512,146 - 15,523,432 (-)	NCBI
Celera	17	9,540,006 - 9,554,750 (-)	NCBI		Celera
Cytogenetic Map	17	p14	NCBI

FGFR4
(Homo sapiens - human)

Human Assembly	Chr	Position (strand)	Source	Genome Browsers
Human Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCh38.p13 Ensembl	5	177,086,905 - 177,098,144 (+)	Ensembl	GRCh38		hg38	GRCh38
GRCh38	5	177,086,915 - 177,098,144 (+)	NCBI	GRCh38	GRCh38	hg38	GRCh38
GRCh37	5	176,513,916 - 176,525,145 (+)	NCBI	GRCh37	GRCh37	hg19	GRCh37
Build 36	5	176,446,527 - 176,457,733 (+)	NCBI	NCBI36		hg18	NCBI36
Build 34	5	176,446,526 - 176,457,730	NCBI
Celera	5	171,976,184 - 171,987,401 (-)	NCBI
Cytogenetic Map	5	q35.2	NCBI
HuRef	5	171,435,609 - 171,446,679 (+)	NCBI		HuRef
CHM1_1	5	175,946,705 - 175,957,908 (+)	NCBI		CHM1_1

Fgfr4
(Mus musculus - house mouse)

Mouse Assembly	Chr	Position (strand)	Source	Genome Browsers
Mouse Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCm39	13	55,300,631 - 55,316,572 (+)	NCBI	GRCm39		mm39
GRCm39 Ensembl	13	55,300,453 - 55,316,572 (+)	Ensembl
GRCm38	13	55,152,818 - 55,168,759 (+)	NCBI	GRCm38	GRCm38	mm10	GRCm38
GRCm38.p6 Ensembl	13	55,152,640 - 55,168,759 (+)	Ensembl	GRCm38		mm10	GRCm38
MGSCv37	13	55,254,179 - 55,270,120 (+)	NCBI	GRCm37		mm9	NCBIm37
MGSCv36	13	55,162,497 - 55,178,362 (+)	NCBI			mm8
Celera	13	56,213,486 - 56,229,296 (+)	NCBI		Celera
Cytogenetic Map	13	B1	NCBI
cM Map	13	29.8	NCBI

Fgfr4
(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_004955408	29,370,468 - 29,383,971 (+)	Ensembl	ChiLan1.0
ChiLan1.0	NW_004955408	29,370,480 - 29,383,531 (+)	NCBI	ChiLan1.0	ChiLan1.0

FGFR4
(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	5	179,454,995 - 179,466,114 (+)	NCBI	panpan1.1	PanPan1.1	panPan2
PanPan1.1 Ensembl	5	179,454,995 - 179,467,605 (+)	Ensembl	panpan1.1		panPan2
Mhudiblu_PPA_v0	5	172,386,443 - 172,400,271 (+)	NCBI	Mhudiblu_PPA_v0		panPan3

FGFR4
(Canis lupus familiaris - dog)

Dog Assembly	Chr	Position (strand)	Source	Genome Browsers
Dog Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
CanFam3.1	4	36,243,689 - 36,254,636 (-)	NCBI	CanFam3.1	CanFam3.1	canFam3	CanFam3.1
CanFam3.1 Ensembl	4	36,244,220 - 36,252,035 (-)	Ensembl	CanFam3.1		canFam3	CanFam3.1
Dog10K_Boxer_Tasha	4	36,209,722 - 36,220,671 (-)	NCBI
ROS_Cfam_1.0	4	36,607,886 - 36,618,835 (-)	NCBI
UMICH_Zoey_3.1	4	36,434,871 - 36,445,815 (-)	NCBI
UNSW_CanFamBas_1.0	4	36,622,022 - 36,632,969 (-)	NCBI
UU_Cfam_GSD_1.0	4	37,130,265 - 37,141,210 (-)	NCBI

Fgfr4
(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_024407213	122,360,727 - 122,372,869 (+)	NCBI
SpeTri2.0	NW_004936597	1,388,394 - 1,397,731 (+)	NCBI	SpeTri2.0	SpeTri2.0		SpeTri2.0

FGFR4
(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	80,841,536 - 80,853,796 (-)	Ensembl	Sscrofa11.1		susScr11	Sscrofa11.1
Sscrofa11.1	2	80,841,536 - 80,853,791 (-)	NCBI	Sscrofa11.1	Sscrofa11.1	susScr11	Sscrofa11.1
Sscrofa10.2	2	82,414,997 - 82,427,239 (-)	NCBI	Sscrofa10.2	Sscrofa10.2	susScr3

FGFR4
(Chlorocebus sabaeus - African green monkey)

Vervet Assembly	Chr	Position (strand)	Source	Genome Browsers
Vervet Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
ChlSab1.1	23	79,095,031 - 79,106,018 (+)	NCBI
ChlSab1.1 Ensembl	23	79,097,429 - 79,105,456 (+)	Ensembl
Vero_WHO_p1.0	NW_023666075	10,259,717 - 10,291,447 (+)	NCBI

Fgfr4
(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_004624733	12,964,893 - 12,979,198 (-)	NCBI

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
9590316	Scort21	Serum corticosterone level QTL 21	4.75	0.001	blood corticosterone amount (VT:0005345)	plasma corticosterone level (CMO:0001173)	17	1	24787908	Rat
10401807	Kidm52	Kidney mass QTL 52			kidney mass (VT:0002707)	both kidneys wet weight (CMO:0000085)	17	1	32230361	Rat
70184	BpQTLcluster14	Blood pressure QTL cluster 14	3.38		arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	17	1	33303755	Rat
631207	Niddm41	Non-insulin dependent diabetes mellitus QTL 41			blood glucose amount (VT:0000188)	plasma glucose level (CMO:0000042)	17	1	38243814	Rat
1354658	Spl8	Serum phospholipid level QTL 8	3.8		blood VLDL phospholipid amount (VT:0010507)	blood very low density lipoprotein phospholipid level (CMO:0001571)	17	1	63676140	Rat
1354662	Rf49	Renal function QTL 49	2.9		blood creatinine amount (VT:0005328)	plasma creatinine level (CMO:0000537)	17	1	73413148	Rat
1354581	Bp247	Blood pressure QTL 247	4.5		arterial blood pressure trait (VT:2000000)	pulse pressure (CMO:0000292)	17	1	73413148	Rat
1641902	Colcr7	Colorectal carcinoma resistance QTL 7	3.35	0.0044	intestine integrity trait (VT:0010554)	benign colorectal tumor surface area measurement (CMO:0001799)	17	519770	23422380	Rat
1300123	Bp194	Blood pressure QTL 194	2.82		arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	17	519770	36283402	Rat
2324619	Coatc4	Coat color QTL 4		0.001	coat/hair pigmentation trait (VT:0010463)	pigmented coat/hair area to total coat/hair area ratio (CMO:0001810)	17	3336972	24030841	Rat
2324619	Coatc4	Coat color QTL 4		0.001	coat/hair pigmentation trait (VT:0010463)	pigmented dorsal coat/hair area to total dorsal coat/hair area ratio (CMO:0001811)	17	3336972	24030841	Rat
1354613	Kidm14	Kidney mass QTL 14	6.2		kidney mass (VT:0002707)	left kidney wet weight (CMO:0000083)	17	3336972	37790462	Rat
1354596	Bw32	Body weight QTL 32	4.5		body mass (VT:0001259)	body weight (CMO:0000012)	17	3336972	63676140	Rat
1354638	Insul1	Insulin level QTL 1	4.8		blood insulin amount (VT:0001560)	plasma insulin level (CMO:0000342)	17	3336972	73413148	Rat
1354651	Lmblg2	Limb length QTL 2	6		tibia length (VT:0004357)	tibia length (CMO:0000450)	17	3336972	73413148	Rat
1354630	Cm34	Cardiac mass QTL 34	8.7		heart left ventricle mass (VT:0007031)	heart left ventricle wet weight (CMO:0000071)	17	3336972	73413148	Rat
631499	Stl1	Serum triglyceride level QTL 1	3.6		blood triglyceride amount (VT:0002644)	blood triglyceride level (CMO:0000118)	17	3414039	28073589	Rat
2293648	Bmd31	Bone mineral density QTL 31	4.5	0.0001	femur size trait (VT:1000369)	femoral neck cortical cross-sectional area (CMO:0001702)	17	4716067	27691136	Rat
2293664	Bmd28	Bone mineral density QTL 28	5.1	0.0001	femur mineral mass (VT:0010011)	trabecular volumetric bone mineral density (CMO:0001729)	17	4716067	27691136	Rat
2303627	Vencon8	Ventilatory control QTL 8		0.001	respiration trait (VT:0001943)	tidal volume (CMO:0000222)	17	5191047	50191047	Rat
10054088	Scort28	Serum corticosterone level QTL 28	2.04	0.0102	blood corticosterone amount (VT:0005345)	plasma corticosterone level (CMO:0001173)	17	5191047	50191047	Rat
1581553	Pur14	Proteinuria QTL 14	5.3	0.0001	total urine protein amount (VT:0000032)	urine protein excretion rate (CMO:0000759)	17	8424467	16620067	Rat
1582224	Epfw4	Epididymal fat weight QTL 4	3.5	0.0058	epididymal fat pad mass (VT:0010421)	epididymal fat pad weight to body weight ratio (CMO:0000658)	17	9730263	21491085	Rat
1582225	Bw67	Body weight QTL 67	6.2	0.0001	body mass (VT:0001259)	body weight (CMO:0000012)	17	9730263	21491085	Rat
1582226	Bw64	Body weight QTL 64	4.2	0.0017	body mass (VT:0001259)	body weight (CMO:0000012)	17	9730263	21491085	Rat
1582241	Bw70	Body weight QTL 70	4.6	0.0003	body mass (VT:0001259)	body weight (CMO:0000012)	17	9730263	21491085	Rat
1582245	Bw73	Body weight QTL 73	4.6	0.0004	body mass (VT:0001259)	body weight (CMO:0000012)	17	9730263	21491085	Rat
1582258	Bw76	Body weight QTL 76	4.6	0.0005	body mass (VT:0001259)	body weight (CMO:0000012)	17	9730263	21491085	Rat
1582199	Insul5	Insulin level QTL 5	3.4	0.0119	blood insulin amount (VT:0001560)	calculated serum insulin level (CMO:0000359)	17	9730263	21491085	Rat
1582208	Kidm32	Kidney mass QTL 32	3.9	0.0018	kidney mass (VT:0002707)	both kidneys wet weight (CMO:0000085)	17	9730263	21491085	Rat
2303561	Bw91	Body weight QTL 91	2		body mass (VT:0001259)	body weight (CMO:0000012)	17	9827304	54827304	Rat

miRNA Target Status

Predicted Target Of

	Summary Value
Count of predictions:	56
Count of miRNA genes:	50
Interacting mature miRNAs:	51
Transcripts:	ENSRNOT00000042394
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.

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			31	31	2	31				30	6	11
Low	3	32	17	10	11	10	8	11	44	5	27		8
Below cutoff		11	9		6				30		8

View RNA-SEQ Expression Data

Sequence

Nucleotide Sequences


RefSeq Transcripts	NM_001109904	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_006253606	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_039095374	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
GenBank Nucleotide	BC085772	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	BC100260	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	CB743466	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	CH474032	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	JACYVU010000284	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	M91599	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles

Reference Sequences

RefSeq Acc Id:

ENSRNOT00000042394 ⟹ ENSRNOP00000050988

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
Rnor_6.0 Ensembl	17	9,990,078 - 10,004,321 (-)	Ensembl

RefSeq Acc Id:

ENSRNOT00000082836 ⟹ ENSRNOP00000069871

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
Rnor_6.0 Ensembl	17	9,990,078 - 10,001,901 (-)	Ensembl

RefSeq Acc Id:

NM_001109904 ⟹ NP_001103374

RefSeq Status:

VALIDATED

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2	17	9,461,541 - 9,476,242 (-)	NCBI
Rnor_6.0	17	9,990,072 - 10,004,321 (-)	NCBI
Rnor_5.0	17	12,099,383 - 12,113,637 (-)	NCBI
RGSC_v3.4	17	15,512,144 - 15,527,348 (-)	RGD
Celera	17	9,540,006 - 9,554,750 (-)	RGD

Sequence:

show sequence

CTGTAGTTGCAGGGACATTCCTGGCTCTTCGGCCCGGGGCGGAGGAGCTCCAGGCGGGTGAGTG
TGCCAGCCCTGCCGGGATCGTGACCCCCGAGCACGGGAACCGGGTGGCGGAGGAGCCAGGAAGG
TGGTCAGCGGGAAGTCTGGCCTGGGTCCCGAGAACAGCTGGAAGGAAATGTGGCTGCTGTTGGC
TTTGTTGAGCATCTTTCAGGAGACACCAGCCTTCTCCCTTGAGGCCTCTGAGGAAATGGAACAG
GAGCCCTGCCCAGCCCCAATCTCGGAGCAGCAAGAGCAGGTGTTGACTGTGGCCCTTGGGCAGC
CTGTGCGGCTATGCTGTGGCCGCACTGAGCGTGGTCGTCATTGGTACAAGGAGGGCAGCCGTTT
AGCATCTGCTGGGAGAGTACGGGGCTGGAGAGGCCGCCTGGAGATCGCCAGCTTCCTTCCTGAG
GATGCTGGCCGGTACCTCTGCCTGGCCCGTGGCTCCATGACTGTCGTACACAATCTTACTTTGA
TTATGGATGACTCCTTACCCTCCATCAATAACGAGGACCCCAAGACCCTCAGCAGCTCCTCGAG
TGGGCACTCCTACCTGCAGCAAGCACCTTACTGGACACACCCCCAACGCATGGAGAAGAAACTG
CACGCGGTACCTGCCGGGAACACTGTCAAATTCCGCTGTCCAGCTGCAGGGAACCCCATGCCCA
CCATCCACTGGCTCAAGAACGGACAGGCCTTCCACGGAGAGAATCGTATCGGAGGCATTCGGCT
GCGTCACCAACACTGGAGCCTCGTGATGGAGAGCGTGGTGCCCTCAGACCGTGGCACGTACACG
TGTCTTGTGGAGAACTCTCTGGGTAGCATTCGCTACAGCTATCTGCTGGATGTGCTGGAGCGGT
CCCCGCACCGGCCCATCCTGCAGGCGGGACTCCCAGCCAACACCACGGCTGTGGTTGGCAGCAA
CGTGGAGCTGCTGTGCAAGGTGTACAGTGACGCCCAGCCGCACATCCAGTGGCTGAAGCACATC
GTTATCAACGGCAGCAGTTTCGGCGCTGATGGTTTCCCCTACGTACAAGTCCTGAAGACAACAG
ACATCAATAGCTCAGAGGTGGAGGTGCTGTATCTGAGGAACGTGTCGGCTGAGGATGCAGGGGA
GTACACCTGCCTGGCGGGCAACTCCATCGGCCTCTCCTACCAGTCAGCGTGGCTCACAGTGCTA
CCCGCAGAGGAAGAAGACCTCGCGTGGACAACAGCAACATCGGAGGCCAGATATACAGATATTA
TCCTATATGTATCTGGCTCACTGGCTTTGGTTTTGCTCCTGCTGCTGGCCGGGGTGTATCACCG
ACAAGCAATCCACGGCCACCACTCTCGACAGCCTGTCACTGTACAGAAGCTGTCCCGGTTCCCT
TTGGCCCGGCAGTTCTCCTTGGAGTCGAGGTCCTCTGGCAAGTCAAGTTTGTCCCTGGTGCGAG
GTGTCCGGCTCTCCTCCAGTGGCCCGCCCTTGCTCACGGGCCTTGTGAGTCTAGACCTACCTCT
CGATCCACTTTGGGAGTTCCCCCGGGACAGGCTGGTGCTCGGAAAGCCCCTGGGTGAGGGCTGC
TTTGGGCAAGTGGTTCGTGCAGAAGCCCTTGGCATGGATTCCTCCCGGCCAGACCAAACCAGCA
CCGTGGCTGTGAAGATGCTGAAAGACAATGCCTCCGACAAGGATTTGGCAGACCTGATCTCTGA
GATGGAGATGATGAAGCTAATCGGAAGACACAAGAACATCATTAACCTGCTGGGTGTCTGCACT
CAGGAAGGGCCCCTGTATGTGATTGTGGAATATGCGGCCAAGGGAAACCTTCGGGAATTCCTCC
GTGCCCGGCGTCCCCCAGGCCCTGATCTCAGCCCTGATGGGCCTCGGAGCAGCGAAGGACCGCT
CTCCTTCCCGGCCCTGGTCTCCTGTGCCTACCAGGTGGCCCGAGGCATGCAGTATCTGGAGTCT
CGGAAGTGCATCCACCGGGACCTGGCTGCCCGAAACGTGCTGGTGACCGAGGATGACGTGATGA
AGATCGCTGACTTTGGTCTGGCCCGTGGTGTCCACCACATCGACTACTATAAGAAAACCAGCAA
TGGCCGCCTGCCAGTCAAGTGGATGGCTCCTGAGGCGTTGTTTGACCGTGTATACACACACCAG
AGTGACGTGTGGTCCTTCGGGATCCTGCTGTGGGAAATCTTCACCCTCGGGGGCTCCCCATACC
CCGGCATCCCAGTGGAGGAGCTGTTCTCACTGCTGCGAGAGGGGCACAGGATGGAGCGGCCCCC
AAACTGCCCCTCAGAGCTGTATGGGCTAATGAGGGAGTGTTGGCACGCAGCTCCTTCTCAGAGG
CCGACTTTTAAGCAGCTGGTGGAAGCTCTGGACAAGGTCCTGCTGGCTGTCTCTGAAGAGTACC
TTGACCTCCGCCTGACCTTTGGACCCTATTCCCCCAACAATGGGGATGCCAGCAGCACGTGCTC
CTCCAGCGACTCGGTTTTCAGCCACGACCCTTTGCCCCTCGAGCCAAGCCCCTTCCCATTTCCT
GAGGCGCAGACCACATGAGCCTGGGAACGATGTTGCATGGGCTCGTAGGCCCGTGGCCGTGGGA
CTCCAACCTGTTTCATCAGCATTTGACGTTGGCACTGTCATCAGGCCTCTGACTCGAGGCTACT
GCTGGCCCAGATCCTCTCTCTGGCCCTGTTTTGGGGAGGCCCATTCTTGGTCTTGGGGTTCACA
GTTGAGGCCTTCTGTTCCAAACTTATGTTCCCAGCTCAGAGTTCAACTCCTCGTCTCAAGATCA
TGGTCGTGCCCTTGGACTCATCCTCAAAGGAGCGAAGCATTAAGGCCTTGACACTTAGCCTCCA
CCCCAGGGGCTCTCCGGGCCTGACTGCAAATCTTTGGTCCTAAACATTTCTAGCTCCCCAAACA
ACCTAGAGGCCTCGGGACTTCACTGCACCCCCGCCCCCGCAGCCCACAAGCCTCGCCACCCTGG
TCCCCAACTCCCCACTGCTTGTTCTAGCATCTTGTTGAAGGAGCCTCAGCTCTGGTGTCCTTGA
GAGACGAGAAGCCTGTGGAAAAGACAGAAGAACAAGGCATTTTATAAATTATTATTATTTTTTG
AAATAAAAAAAAAAAAAAAAAAAAAAAA

hide sequence

RefSeq Acc Id:

XM_006253606 ⟹ XP_006253668

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2	17	9,461,541 - 9,476,268 (-)	NCBI
Rnor_6.0	17	9,990,072 - 10,004,339 (-)	NCBI
Rnor_5.0	17	12,099,383 - 12,113,637 (-)	NCBI

Sequence:

show sequence

GGGCAGCCCCCCGCCACGCTGTAGTTGCAGGGACATTCCTGGCTCTTCGGCCCGGGGCGGAGGA
GCTCCAGGCGGGTGAGTGTGCCAGCCCTGCCGGGATCGTGACCCCCGAGCACGGGAACCGGGTG
GCGGAGGAGCCAGGAAGGTGGTCAGCGGGAAGTCTGGCCTGGGTCCCGAGAACAGCTGGAAGGA
AATGTGGCTGCTGTTGGCTTTGTTGAGCATCTTTCAGGAGACACCAGCCTTCTCCCTTGAGGCC
TCTGAGGAAATGGAACAGGAGCCCTGCCCAGCCCCAATCTCGGAGCAGCAAGAGCAGGTGTTGA
CTGTGGCCCTTGGGCAGCCTGTGCGGCTATGCTGTGGCCGCACTGAGCGTGGTCGTCATTGGTA
CAAGGAGGGCAGCCGTTTAGCATCTGCTGGGAGAGTACGGGGCTGGAGAGGCCGCCTGGAGATC
GCCAGCTTCCTTCCTGAGGATGCTGGCCGGTACCTCTGCCTGGCCCGTGGCTCCATGACTGTCG
TACACAATCTTACTTTGATTATGGATGACTCCTTACCCTCCATCAATAACGAGGACCCCAAGAC
CCTCAGCAGCTCCTCGAGTGGGCACTCCTACCTGCAGCAAGCACCTTACTGGACACACCCCCAA
CGCATGGAGAAGAAACTGCACGCGGTACCTGCCGGGAACACTGTCAAATTCCGCTGTCCAGCTG
CAGGGAACCCCATGCCCACCATCCACTGGCTCAAGAACGGACAGGCCTTCCACGGAGAGAATCG
TATCGGAGGCATTCGGCTGCGTCACCAACACTGGAGCCTCGTGATGGAGAGCGTGGTGCCCTCA
GACCGTGGCACGTACACGTGTCTTGTGGAGAACTCTCTGGGTAGCATTCGCTACAGCTATCTGC
TGGATGTGCTGGAGCGGTCCCCGCACCGGCCCATCCTGCAGGCGGGACTCCCAGCCAACACCAC
GGCTGTGGTTGGCAGCAACGTGGAGCTGCTGTGCAAGGTGTACAGTGACGCCCAGCCGCACATC
CAGTGGCTGAAGCACATCGTTATCAACGGCAGCAGTTTCGGCGCTGATGGTTTCCCCTACGTAC
AAGTCCTGAAGACAACAGACATCAATAGCTCAGAGGTGGAGGTGCTGTATCTGAGGAACGTGTC
GGCTGAGGATGCAGGGGAGTACACCTGCCTGGCGGGCAACTCCATCGGCCTCTCCTACCAGTCA
GCGTGGCTCACAGTGCTACCCGAAGCAGAGGAAGAAGACCTCGCGTGGACAACAGCAACATCGG
AGGCCAGATATACAGATATTATCCTATATGTATCTGGCTCACTGGCTTTGGTTTTGCTCCTGCT
GCTGGCCGGGGTGTATCACCGACAAGCAATCCACGGCCACCACTCTCGACAGCCTGTCACTGTA
CAGAAGCTGTCCCGGTTCCCTTTGGCCCGGCAGTTCTCCTTGGAGTCGAGGTCCTCTGGCAAGT
CAAGTTTGTCCCTGGTGCGAGGTGTCCGGCTCTCCTCCAGTGGCCCGCCCTTGCTCACGGGCCT
TGTGAGTCTAGACCTACCTCTCGATCCACTTTGGGAGTTCCCCCGGGACAGGCTGGTGCTCGGA
AAGCCCCTGGGTGAGGGCTGCTTTGGGCAAGTGGTTCGTGCAGAAGCCCTTGGCATGGATTCCT
CCCGGCCAGACCAAACCAGCACCGTGGCTGTGAAGATGCTGAAAGACAATGCCTCCGACAAGGA
TTTGGCAGACCTGATCTCTGAGATGGAGATGATGAAGCTAATCGGAAGACACAAGAACATCATT
AACCTGCTGGGTGTCTGCACTCAGGAAGGGCCCCTGTATGTGATTGTGGAATATGCGGCCAAGG
GAAACCTTCGGGAATTCCTCCGTGCCCGGCGTCCCCCAGGCCCTGATCTCAGCCCTGATGGGCC
TCGGAGCAGCGAAGGACCGCTCTCCTTCCCGGCCCTGGTCTCCTGTGCCTACCAGGTGGCCCGA
GGCATGCAGTATCTGGAGTCTCGGAAGTGCATCCACCGGGACCTGGCTGCCCGAAACGTGCTGG
TGACCGAGGATGACGTGATGAAGATCGCTGACTTTGGTCTGGCCCGTGGTGTCCACCACATCGA
CTACTATAAGAAAACCAGCAATGGCCGCCTGCCAGTCAAGTGGATGGCTCCTGAGGCGTTGTTT
GACCGTGTATACACACACCAGAGTGACGTGTGGTCCTTCGGGATCCTGCTGTGGGAAATCTTCA
CCCTCGGGGGCTCCCCATACCCCGGCATCCCAGTGGAGGAGCTGTTCTCACTGCTGCGAGAGGG
GCACAGGATGGAGCGGCCCCCAAACTGCCCCTCAGAGCTGTATGGGCTAATGAGGGAGTGTTGG
CACGCAGCTCCTTCTCAGAGGCCGACTTTTAAGCAGCTGGTGGAAGCTCTGGACAAGGTCCTGC
TGGCTGTCTCTGAAGAGTACCTTGACCTCCGCCTGACCTTTGGACCCTATTCCCCCAACAATGG
GGATGCCAGCAGCACGTGCTCCTCCAGCGACTCGGTTTTCAGCCACGACCCTTTGCCCCTCGAG
CCAAGCCCCTTCCCATTTCCTGAGGCGCAGACCACATGAGCCTGGGAACGATGTTGCATGGGCT
CGTAGGCCCGTGGCCGTGGGACTCCAACCTGTTTCATCAGCATTTGACGTTGGCACTGTCATCA
GGCCTCTGACTCGAGGCTACTGCTGGCCCAGATCCTCTCTCTGGCCCTGTTTTGGGGAGGCCCA
TTCTTGGTCTTGGGGTTCACAGTTGAGGCCTTCTGTTCCAAACTTATGTTCCCAGCTCAGAGTT
CAACTCCTCGTCTCAAGATCATGGTCGTGCCCTTGGACTCATCCTCAAAGGAGCGAAGCATTAA
GGCCTTGACACTTAGCCTCCACCCCAGGGGCTCTCCGGGCCTGACTGCAAATCTTTGGTCCTAA
ACATTTCTAGCTCCCCAAACAACCTAGAGGCCTCGGGACTTCACTGCACCCCCGCCCCCGCAGC
CCACAAGCCTCGCCACCCTGGTCCCCAACTCCCCACTGCTTGTTCTAGCATCTTGTTGAAGGAG
CCTCAGCTCTGGTGTCCTTGAGAGACGAGAAGCCTGTGGAAAAGACAGAAGAACAAGGCATTTT
ATAAATTATTATTATTTTTTGAAATAA

hide sequence

RefSeq Acc Id:

XM_039095374 ⟹ XP_038951302

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2	17	9,461,541 - 9,470,316 (-)	NCBI

Protein Sequences


Protein RefSeqs	NP_001103374	(Get FASTA)	NCBI Sequence Viewer
	XP_006253668	(Get FASTA)	NCBI Sequence Viewer
	XP_038951302	(Get FASTA)	NCBI Sequence Viewer
GenBank Protein	AAA41157	(Get FASTA)	NCBI Sequence Viewer
	AAI00261	(Get FASTA)	NCBI Sequence Viewer
	EDL94007	(Get FASTA)	NCBI Sequence Viewer
	Q498D6	(Get FASTA)	NCBI Sequence Viewer

Reference Sequences

RefSeq Acc Id:	NP_001103374 ⟸ NM_001109904
- Peptide Label:	precursor
- UniProtKB:	Q498D6 (UniProtKB/Swiss-Prot)
- Sequence:	show sequence MWLLLALLSIFQETPAFSLEASEEMEQEPCPAPISEQQEQVLTVALGQPVRLCCGRTERGRHWY KEGSRLASAGRVRGWRGRLEIASFLPEDAGRYLCLARGSMTVVHNLTLIMDDSLPSINNEDPKT LSSSSSGHSYLQQAPYWTHPQRMEKKLHAVPAGNTVKFRCPAAGNPMPTIHWLKNGQAFHGENR IGGIRLRHQHWSLVMESVVPSDRGTYTCLVENSLGSIRYSYLLDVLERSPHRPILQAGLPANTT AVVGSNVELLCKVYSDAQPHIQWLKHIVINGSSFGADGFPYVQVLKTTDINSSEVEVLYLRNVS AEDAGEYTCLAGNSIGLSYQSAWLTVLPAEEEDLAWTTATSEARYTDIILYVSGSLALVLLLLL AGVYHRQAIHGHHSRQPVTVQKLSRFPLARQFSLESRSSGKSSLSLVRGVRLSSSGPPLLTGLV SLDLPLDPLWEFPRDRLVLGKPLGEGCFGQVVRAEALGMDSSRPDQTSTVAVKMLKDNASDKDL ADLISEMEMMKLIGRHKNIINLLGVCTQEGPLYVIVEYAAKGNLREFLRARRPPGPDLSPDGPR SSEGPLSFPALVSCAYQVARGMQYLESRKCIHRDLAARNVLVTEDDVMKIADFGLARGVHHIDY YKKTSNGRLPVKWMAPEALFDRVYTHQSDVWSFGILLWEIFTLGGSPYPGIPVEELFSLLREGH RMERPPNCPSELYGLMRECWHAAPSQRPTFKQLVEALDKVLLAVSEEYLDLRLTFGPYSPNNGD ASSTCSSSDSVFSHDPLPLEPSPFPFPEAQTT hide sequence

RefSeq Acc Id:

XP_006253668 ⟸ XM_006253606

- Peptide Label:

isoform X1

- Sequence:

show sequence

MWLLLALLSIFQETPAFSLEASEEMEQEPCPAPISEQQEQVLTVALGQPVRLCCGRTERGRHWY
KEGSRLASAGRVRGWRGRLEIASFLPEDAGRYLCLARGSMTVVHNLTLIMDDSLPSINNEDPKT
LSSSSSGHSYLQQAPYWTHPQRMEKKLHAVPAGNTVKFRCPAAGNPMPTIHWLKNGQAFHGENR
IGGIRLRHQHWSLVMESVVPSDRGTYTCLVENSLGSIRYSYLLDVLERSPHRPILQAGLPANTT
AVVGSNVELLCKVYSDAQPHIQWLKHIVINGSSFGADGFPYVQVLKTTDINSSEVEVLYLRNVS
AEDAGEYTCLAGNSIGLSYQSAWLTVLPEAEEEDLAWTTATSEARYTDIILYVSGSLALVLLLL
LAGVYHRQAIHGHHSRQPVTVQKLSRFPLARQFSLESRSSGKSSLSLVRGVRLSSSGPPLLTGL
VSLDLPLDPLWEFPRDRLVLGKPLGEGCFGQVVRAEALGMDSSRPDQTSTVAVKMLKDNASDKD
LADLISEMEMMKLIGRHKNIINLLGVCTQEGPLYVIVEYAAKGNLREFLRARRPPGPDLSPDGP
RSSEGPLSFPALVSCAYQVARGMQYLESRKCIHRDLAARNVLVTEDDVMKIADFGLARGVHHID
YYKKTSNGRLPVKWMAPEALFDRVYTHQSDVWSFGILLWEIFTLGGSPYPGIPVEELFSLLREG
HRMERPPNCPSELYGLMRECWHAAPSQRPTFKQLVEALDKVLLAVSEEYLDLRLTFGPYSPNNG
DASSTCSSSDSVFSHDPLPLEPSPFPFPEAQTT

hide sequence

RefSeq Acc Id:

ENSRNOP00000069871 ⟸ ENSRNOT00000082836

RefSeq Acc Id:

ENSRNOP00000050988 ⟸ ENSRNOT00000042394

RefSeq Acc Id:	XP_038951302 ⟸ XM_039095374
- Peptide Label:	isoform X2

Protein Domains

Ig-like C2-type Protein kinase

Transcriptome

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

Promoters

RGD ID:

13700313

Promoter ID:

EPDNEW_R10837

Type:

multiple initiation site

Name:

Fgfr4_1

Description:

fibroblast growth factor receptor 4

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	17	10,004,305 - 10,004,365	EPDNEW

Strain Variation

Strain Sequence Variants (Rnor 6.0)

ACI/EurMcwi (MCW)

Visual

CSV

TAB

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Sequenced By:	Medical College of Wisconsin (Dr. Howard Jacob)
Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA v0.7.7 and GATK v3.2-2
Breeder:	Medical College of Wisconsin
Description:	Provided by the Medical College of Wisconsin (Dr. Howard Jacob)

ACI/EurMcwi (RGD)

Visual

CSV

TAB

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

ACI/N (MCW)

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CSV

TAB

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Sequenced By:	Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen) Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform:	SOLiD 4 and 5500
Secondary Analysis:	liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder:	National Institutes of Health
Description:	Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin

BBDP/Wor (RGD)

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CSV

TAB

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

BN/SsN (MCW)

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CSV

TAB

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Sequenced By:	Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen) Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform:	SOLiD 4 and 5500
Secondary Analysis:	liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder:	National Institutes of Health
Description:	Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin

Buf/N (MCW)

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CSV

TAB

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Sequenced By:	Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen) Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform:	SOLiD 4 and 5500
Secondary Analysis:	liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder:	National Institutes of Health
Description:	Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin

COP/CrCrl (MCW & UW)

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CSV

TAB

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Sequenced By:	Medical College of Wisconsin (Dr. Howard Jacob) University of Wisconsin (Dr. James Shull)
Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA v0.7.7 and GATK v3.2-2
Breeder:	Charles River Laboratories
Description:	Provided by the Medical College of Wisconsin (Dr. Howard Jacob) and UW Madison (Dr. James Shull)

F344/NCrl (RGD)

Visual

CSV

TAB

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

F344/NRrrc (MCW)

Visual

CSV

TAB

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Sequenced By:	Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen) Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform:	SOLiD 4 and 5500
Secondary Analysis:	liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder:	National Institutes of Health
Description:	Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin

FHH/EurMcwi (MCW)

Visual

CSV

TAB

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Sequenced By:	Medical College of Wisconsin (Dr. Howard Jacob)
Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA v0.7.7 and GATK v3.2-2
Breeder:	Medical College of Wisconsin
Description:	Provided by the Medical College of Wisconsin (Dr. Howard Jacob)

FHH/EurMcwi (RGD)

Visual

CSV

TAB

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

FHL/EurMcwi (MCW)

Visual

CSV

TAB

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Sequenced By:	Medical College of Wisconsin (Dr. Howard Jacob)
Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA v0.7.7 and GATK v3.2-2
Breeder:	Medical College of Wisconsin
Description:	Provided by the Medical College of Wisconsin (Dr. Howard Jacob)

FHL/EurMcwi (RGD)

Visual

CSV

TAB

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

GH/OmrMcwi (MCW)

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CSV

TAB

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Sequenced By:	Medical College of Wisconsin (Dr. Howard Jacob)
Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA v0.7.7 and GATK v3.2-2
Breeder:	Medical College of Wisconsin
Description:	Provided by the Medical College of Wisconsin (Dr. Howard Jacob)

GK/Ox (RGD)

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CSV

TAB

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

LE/Stm (RGD)

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CSV

TAB

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

LEW/Crl (RGD)

Visual

CSV

TAB

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

LEW/NCrlBR (RGD)

Visual

CSV

TAB

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

LH/MavRrrc (RGD)

Visual

CSV

TAB

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

LL/MavRrrc (RGD)

Visual

CSV

TAB

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

LN/MavRrrc (RGD)

Visual

CSV

TAB

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

M520/N (MCW)

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CSV

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Sequenced By:	Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen) Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform:	SOLiD 4 and 5500
Secondary Analysis:	liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder:	National Institutes of Health
Description:	Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin

MHS/Gib (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

MNS/Gib (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

MR/N (MCW)

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Sequenced By:	Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen) Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform:	SOLiD 4 and 5500
Secondary Analysis:	liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder:	National Institutes of Health
Description:	Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin

SBH/Ygl (MCW)

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Sequenced By:	Medical College of Wisconsin (Dr. Howard Jacob)
Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA v0.7.7 and GATK v3.2-2
Breeder:	Medical College of Wisconsin
Description:	SBH/Ygl sequenced by MCW

SBH/Ygl (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

SBN/Ygl (MCW)

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Sequenced By:	Medical College of Wisconsin (Dr. Howard Jacob)
Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA v0.7.7 and GATK v3.2-2
Breeder:	Medical College of Wisconsin
Description:	SBN/Ygl sequenced by MCW

SBN/Ygl (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

SHR/NHsd (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

SHRSP/Gcrc (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

SR/JrHsd (MCW)

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Sequenced By:	Medical College of Wisconsin (Dr. Howard Jacob)
Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA v0.7.7 and GATK v3.2-2
Breeder:	Harlan Laboratories
Description:	Provided by the Medical College of Wisconsin (Dr. Howard Jacob)

SR/JrHsd (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

SS/Jr (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

SS/JrHsdMcwi (MCW)

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Sequenced By:	Medical College of Wisconsin (Dr. Howard Jacob)
Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA v0.7.7 and GATK v3.2-2
Breeder:	Medical College of Wisconsin
Description:	Provided by the Medical College of Wisconsin (Dr. Howard Jacob)

SS/JrHsdMcwi (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

WAG/Rij (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

WKY/Gcrc (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

WKY/N (MCW)

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Sequenced By:	Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen) Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform:	SOLiD 4 and 5500
Secondary Analysis:	liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder:	National Institutes of Health
Description:	Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin

WKY/NCrl (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

WKY/NHsd (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

WN/N (MCW)

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Sequenced By:	Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen) Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform:	SOLiD 4 and 5500
Secondary Analysis:	liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder:	National Institutes of Health
Description:	Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin

Damaging Variants

Assembly: RGSC_v3.4

Chromosome	Start Pos	End Pos	Reference Nucleotide	Variant Nucleotide	Variant Type	Strain
17	15520808	15520809	A	T	snv	SS/JrHsdMcwi (MCW)

Additional Information

External Database Links

Database	Acc Id	Source(s)
AGR Gene	RGD:2612	AgrOrtholog
Ensembl Genes	ENSRNOG00000016763	Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Protein	ENSRNOP00000050988	ENTREZGENE, UniProtKB/Swiss-Prot
	ENSRNOP00000069871	UniProtKB/Swiss-Prot
Ensembl Transcript	ENSRNOT00000042394	ENTREZGENE, UniProtKB/Swiss-Prot
	ENSRNOT00000082836	UniProtKB/Swiss-Prot
Gene3D-CATH	2.60.40.10	UniProtKB/Swiss-Prot
IMAGE_CLONE	IMAGE:7096119	IMAGE-MGC_LOAD
	IMAGE:7100540	IMAGE-MGC_LOAD
InterPro	FGF_rcpt_fam	UniProtKB/Swiss-Prot
	Ig-like_dom	UniProtKB/Swiss-Prot
	Ig-like_dom_sf	UniProtKB/Swiss-Prot
	Ig-like_fold	UniProtKB/Swiss-Prot
	Ig_I-set	UniProtKB/Swiss-Prot
	Ig_sub	UniProtKB/Swiss-Prot
	Ig_sub2	UniProtKB/Swiss-Prot
	Kinase-like_dom_sf	UniProtKB/Swiss-Prot
	Prot_kinase_dom	UniProtKB/Swiss-Prot
	Protein_kinase_ATP_BS	UniProtKB/Swiss-Prot
	Ser-Thr/Tyr_kinase_cat_dom	UniProtKB/Swiss-Prot
	Tyr_kinase_AS	UniProtKB/Swiss-Prot
	Tyr_kinase_cat_dom	UniProtKB/Swiss-Prot
KEGG Report	rno:25114	UniProtKB/Swiss-Prot
MGC_CLONE	MGC:116290	IMAGE-MGC_LOAD
	MGC:93687	IMAGE-MGC_LOAD
NCBI Gene	25114	ENTREZGENE
Pfam	I-set	UniProtKB/Swiss-Prot
	Pkinase_Tyr	UniProtKB/Swiss-Prot
PhenoGen	Fgfr4	PhenoGen
PIRSF	FGFR	UniProtKB/Swiss-Prot
PRINTS	TYRKINASE	UniProtKB/Swiss-Prot
PROSITE	IG_LIKE	UniProtKB/Swiss-Prot
	PROTEIN_KINASE_ATP	UniProtKB/Swiss-Prot
	PROTEIN_KINASE_DOM	UniProtKB/Swiss-Prot
	PROTEIN_KINASE_TYR	UniProtKB/Swiss-Prot
SMART	IGc2	UniProtKB/Swiss-Prot
	SM00409	UniProtKB/Swiss-Prot
	TyrKc	UniProtKB/Swiss-Prot
Superfamily-SCOP	SSF48726	UniProtKB/Swiss-Prot
	SSF56112	UniProtKB/Swiss-Prot
UniProt	FGFR4_RAT	UniProtKB/Swiss-Prot, ENTREZGENE

Nomenclature History

Date	Current Symbol	Current Name	Previous Symbol	Previous Name	Description	Reference	Status
2002-06-10	Fgfr4	fibroblast growth factor receptor 4			Symbol and Name status set to approved	70586	APPROVED

RGD Curation Notes

Note Type	Note	Reference
gene_disease	may have a role in breast and ovarian tumorigenesis	69837
gene_expression	overexpressed in gynecological tumor samples	69837
gene_function	receptor for acidic fibroblast growth factor	69837

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 Annotations - KEGG (archival)

Imported Annotations - PID (archival)

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Imported Disease Annotations - ClinVar

Imported Disease Annotations - CTD

Imported Annotations - KEGG (archival)

Imported Annotations - PID (archival)