Fxn (frataxin) - Rat Genome Database

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

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Gene: Fxn (frataxin) Rattus norvegicus

Analyze

Symbol:

Fxn

Name:

frataxin

RGD ID:

1565754

Description:

Exhibits enzyme binding activity. Involved in positive regulation of axon extension; response to drug; and response to organic cyclic compound. Localizes to mitochondrion. Human ortholog(s) of this gene implicated in Friedreich ataxia; Friedreich ataxia 1; and type 2 diabetes mellitus. Orthologous to human FXN (frataxin); PARTICIPATES IN hypoxia inducible factor pathway; INTERACTS WITH 2,4,6-trinitrotoluene; bisphenol A; decabromodiphenyl ether.

Type:

protein-coding

RefSeq Status:

PROVISIONAL

Also known as:

frataxin, mitochondrial; LOC499335; RGD1565754; similar to frataxin

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):	FXN (frataxin)	HGNC	EggNOG, Ensembl, HomoloGene, Inparanoid, NCBI, OMA, OrthoDB, OrthoMCL, Panther, Treefam
Mus musculus (house mouse):	Fxn (frataxin)	HGNC	Treefam, EggNOG, OrthoMCL, NCBI, OMA, HomoloGene, Inparanoid, Panther, OrthoDB, Ensembl
Chinchilla lanigera (long-tailed chinchilla):	Fxn (frataxin)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Pan paniscus (bonobo/pygmy chimpanzee):	FXN (frataxin)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Canis lupus familiaris (dog):	FXN (frataxin)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Ictidomys tridecemlineatus (thirteen-lined ground squirrel):	Fxn (frataxin)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Sus scrofa (pig):	FXN (frataxin)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Chlorocebus sabaeus (African green monkey):	FXN (frataxin)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Heterocephalus glaber (naked mole-rat):	Fxn (frataxin)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Alliance orthologs ³
Mus musculus (house mouse):	Fxn (frataxin)	Alliance	DIOPT (Hieranoid\|InParanoid\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB)
Homo sapiens (human):	FXN (frataxin)	Alliance	DIOPT (HGNC\|Hieranoid\|InParanoid\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB)
Caenorhabditis elegans (roundworm):	frh-1	Alliance	DIOPT (Hieranoid\|InParanoid\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB)
Saccharomyces cerevisiae (baker's yeast):	YFH1	Alliance	DIOPT (Hieranoid\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB)
Drosophila melanogaster (fruit fly):	fh	Alliance	DIOPT (Hieranoid\|InParanoid\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB)

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	1	242,123,975 - 242,152,834 (-)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_6.0 Ensembl	1	242,123,975 - 242,152,834 (-)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_5.0	1	249,419,972 - 249,426,597 (-)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
Rnor_5.0	1	249,400,435 - 249,400,757 (-)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	1	227,647,092 - 227,671,081 (-)	NCBI	RGSC3.4		rn4	RGSC3.4
Celera	1	219,085,510 - 219,108,749 (-)	NCBI		Celera
Cytogenetic Map	1	q51	NCBI

JBrowse:

View Region in Genome Browser (JBrowse)

Model

Annotation Click to see Annotation Detail View

Disease Annotations Click to see Annotation Detail View

diabetes mellitus (ISO)

Friedreich ataxia (ISO)

Friedreich ataxia 1 (ISO)

hypertrophic cardiomyopathy (ISO)

Insulin Resistance (ISO)

Neurobehavioral Manifestations (ISO)

obesity (ISO)

type 2 diabetes mellitus (ISO)

Gene-Chemical Interaction Annotations Click to see Annotation Detail View

(-)-epigallocatechin 3-gallate (ISO)

1,2-dimethylhydrazine (ISO)

2,2',4,4'-Tetrabromodiphenyl ether (ISO)

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

2,4,6-trinitrotoluene (EXP)

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

4,4'-sulfonyldiphenol (ISO)

7,8-dihydro-8-oxoguanine (ISO)

all-trans-retinoic acid (ISO)

Aroclor 1254 (ISO)

benzo[a]pyrene (ISO)

betamethasone (ISO)

bisphenol A (EXP)

bisphenol F (ISO)

cadmium dichloride (ISO)

camptothecin (ISO)

carbon nanotube (ISO)

cisplatin (ISO)

clofibrate (ISO)

cobalt dichloride (ISO)

cyclosporin A (ISO)

decabromodiphenyl ether (EXP)

deferiprone (ISO)

dexamethasone (ISO)

dibutyl phthalate (EXP,ISO)

dioxygen (ISO)

doxorubicin (ISO)

finasteride (EXP)

folic acid (ISO)

hydrogen peroxide (ISO)

indometacin (ISO)

iron atom (ISO)

iron(0) (ISO)

lipopolysaccharide (ISO)

methyl methanesulfonate (ISO)

Molsidomine (ISO)

N-acetyl-L-cysteine (ISO)

nimesulide (EXP)

nimustine (ISO)

oxaliplatin (EXP)

paracetamol (ISO)

pentachlorophenol (ISO)

pirinixic acid (ISO)

potassium chromate (ISO)

resveratrol (ISO)

retinyl acetate (ISO)

silicon dioxide (ISO)

sodium arsenite (ISO)

sulindac (EXP)

thioacetamide (EXP)

toluene (EXP)

topotecan (EXP)

trichostatin A (ISO)

tungsten (ISO)

urethane (ISO)

valproic acid (ISO)

Gene Ontology Annotations Click to see Annotation Detail View

Biological Process

adult walking behavior (IEA,ISO)

aerobic respiration (IEA,ISO)

cellular iron ion homeostasis (IBA,IEA,ISO,NAS)

cellular response to hydrogen peroxide (IEA,ISO)

embryo development ending in birth or egg hatching (IEA,ISO)

heme biosynthetic process (IEA)

ion transport (IEA)

iron incorporation into metallo-sulfur cluster (IBA,IEA,ISO)

iron ion homeostasis (IEA)

iron-sulfur cluster assembly (IEA,ISO)

mitochondrion organization (IEA,ISO)

negative regulation of apoptotic process (ISO)

negative regulation of multicellular organism growth (IEA,ISO)

negative regulation of organ growth (IEA,ISO)

negative regulation of release of cytochrome c from mitochondria (IEA,ISO)

oxidative phosphorylation (IEA,ISO)

positive regulation of aconitate hydratase activity (IEA,ISO)

positive regulation of axon extension (IMP)

positive regulation of catalytic activity (ISO)

positive regulation of cell growth (IEA,ISO)

positive regulation of cell population proliferation (IEA,ISO)

positive regulation of lyase activity (ISO)

positive regulation of succinate dehydrogenase activity (IEA,ISO)

proprioception (IEA,ISO)

protein autoprocessing (IEA,ISO)

regulation of ferrochelatase activity (IEA,ISO)

response to drug (IEP)

response to iron ion (IEA,ISO)

response to organic cyclic compound (IEP)

Cellular Component

cytosol (ISO)

L-cysteine desulfurase complex (IEA,ISO)

mitochondrion (IBA,IDA,IEA,ISO)

Molecular Function

2 iron, 2 sulfur cluster binding (IBA,IEA,ISO)

enzyme binding (IPI)

ferric iron binding (IBA,IEA,ISO)

ferrous iron binding (IBA,IEA,ISO)

ferroxidase activity (IBA,IEA,ISO)

iron chaperone activity (IBA,IEA,ISO)

metallochaperone activity (NAS)

protein binding (ISO)

Molecular Pathway Annotations Click to see Annotation Detail View

hypoxia inducible factor pathway (ISO)

References

References - curated


1.	Bulteau AL, etal., Science 2004 Jul 9;305(5681):242-5.
2.	Campuzano V, etal., Science. 1996 Mar 8;271(5254):1423-7.
3.	Delatycki MB, etal., Hum Genet. 1999 Oct;105(4):343-6.
4.	Durr A, etal., N Engl J Med. 1996 Oct 17;335(16):1169-75.
5.	Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
6.	Hebinck J, etal., Diabetes. 2000 Sep;49(9):1604-7.
7.	Melli G, etal., Exp Neurol. 2008 Dec;214(2):276-84. Epub 2008 Sep 9.
8.	OMIM Disease Annotation Pipeline
9.	Pipeline to import Pathway Interaction Database annotations from NCI into RGD
10.	Pomplun D, etal., Proc Natl Acad Sci U S A. 2007 Apr 10;104(15):6377-81. Epub 2007 Apr 2.
11.	RGD automated data pipeline
12.	RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
13.	RGD automated import pipeline for gene-chemical interactions
14.	Ristow M, etal., Diabetes. 1998 May;47(5):851-4.
15.	Ristow M, etal., J Clin Invest. 2003 Aug;112(4):527-34.
16.	Stehling O, etal., Hum Mol Genet. 2004 Dec 1;13(23):3007-15. Epub 2004 Oct 27.
17.	t Hart LM, etal., Diabetes. 1999 Apr;48(4):924-6.

Additional References at PubMed

PMID:9405681	PMID:10767347	PMID:11175786	PMID:12785837	PMID:14651853	PMID:14985441	PMID:15123683	PMID:15641778	PMID:16278235	PMID:16608849	PMID:17285345	PMID:17468497
PMID:17597094	PMID:18160053	PMID:18424449	PMID:18537827	PMID:18614015	PMID:20053667	PMID:21863062	PMID:24242291	PMID:24751525	PMID:29491838

Genomics

Candidate Gene Status

Fxn is a candidate Gene for QTL Arrd2

Comparative Map Data

Fxn
(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	1	242,123,975 - 242,152,834 (-)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_6.0 Ensembl	1	242,123,975 - 242,152,834 (-)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_5.0	1	249,419,972 - 249,426,597 (-)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
Rnor_5.0	1	249,400,435 - 249,400,757 (-)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	1	227,647,092 - 227,671,081 (-)	NCBI	RGSC3.4		rn4	RGSC3.4
Celera	1	219,085,510 - 219,108,749 (-)	NCBI		Celera
Cytogenetic Map	1	q51	NCBI

FXN
(Homo sapiens - human)

Human Assembly	Chr	Position (strand)	Source	Genome Browsers
Human Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCh38.p13 Ensembl	9	69,035,747 - 69,255,187 (+)	Ensembl	GRCh38		hg38	GRCh38
GRCh38.p13 Ensembl	9	69,035,751 - 69,079,076 (+)	Ensembl	GRCh38		hg38	GRCh38
GRCh38.p13 Ensembl	9	69,035,563 - 69,100,178 (+)	Ensembl	GRCh38		hg38	GRCh38
GRCh38	9	69,035,752 - 69,079,076 (+)	NCBI	GRCh38	GRCh38	hg38	GRCh38
GRCh37	9	71,650,479 - 71,715,094 (+)	NCBI	GRCh37	GRCh37	hg19	GRCh37
Build 36	9	70,840,164 - 70,878,772 (+)	NCBI	NCBI36		hg18	NCBI36
Celera	9	42,245,805 - 42,311,090 (+)	NCBI
Cytogenetic Map	9	q21.11	NCBI
HuRef	9	41,495,732 - 41,559,839 (+)	NCBI		HuRef
CHM1_1	9	71,797,667 - 71,861,767 (+)	NCBI		CHM1_1

Fxn
(Mus musculus - house mouse)

Mouse Assembly	Chr	Position (strand)	Source	Genome Browsers
Mouse Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCm39	19	24,236,909 - 24,257,954 (-)	NCBI	GRCm39		mm39
GRCm38	19	24,259,545 - 24,280,590 (-)	NCBI	GRCm38	GRCm38	mm10	GRCm38
GRCm38.p6 Ensembl	19	24,261,453 - 24,280,605 (-)	Ensembl	GRCm38		mm10	GRCm38
MGSCv37	19	24,335,943 - 24,355,076 (-)	NCBI	GRCm37		mm9	NCBIm37
MGSCv36	19	24,328,550 - 24,347,683 (-)	NCBI			mm8
Celera	19	25,027,779 - 25,046,379 (-)	NCBI		Celera
Cytogenetic Map	19	B	NCBI

Fxn
(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_004955434	3,980,653 - 4,008,761 (-)	Ensembl	ChiLan1.0
ChiLan1.0	NW_004955434	3,983,225 - 4,008,324 (-)	NCBI	ChiLan1.0	ChiLan1.0

FXN
(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	9	67,800,579 - 67,865,945 (+)	NCBI	panpan1.1	PanPan1.1	panPan2
PanPan1.1 Ensembl	9	67,800,579 - 67,866,031 (+)	Ensembl	panpan1.1		panPan2
Mhudiblu_PPA_v0	9	55,690,483 - 55,754,755 (-)	NCBI	Mhudiblu_PPA_v0		panPan3

FXN
(Canis lupus familiaris - dog)

Dog Assembly	Chr	Position (strand)	Source	Genome Browsers
Dog Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
CanFam3.1 Ensembl	1	88,288,566 - 88,311,228 (-)	Ensembl	CanFam3.1		canFam3	CanFam3.1
CanFam3.1	1	88,288,566 - 88,311,228 (-)	NCBI	CanFam3.1	CanFam3.1	canFam3	CanFam3.1

Fxn
(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_004936503	5,323,206 - 5,343,228 (+)	NCBI	SpeTri2.0	SpeTri2.0		SpeTri2.0

FXN
(Sus scrofa - pig)

Pig Assembly	Chr	Position (strand)	Source	Genome Browsers
Pig Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
Sscrofa11.1 Ensembl	1	222,412,500 - 222,461,943 (+)	Ensembl	Sscrofa11.1		susScr11	Sscrofa11.1
Sscrofa11.1	1	222,412,485 - 222,433,224 (+)	NCBI	Sscrofa11.1	Sscrofa11.1	susScr11	Sscrofa11.1

FXN
(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 Ensembl	12	80,134,422 - 80,173,168 (+)	Ensembl
ChlSab1.1	12	80,133,899 - 80,173,950 (+)	NCBI

Fxn
(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_004624736	4,027,054 - 4,047,881 (-)	NCBI

Position Markers

BQ195306

Rat Assembly	Chr	Position (strand)	Source	JBrowse
Rnor_6.0	1	242,124,315 - 242,124,559	NCBI	Rnor6.0
Rnor_5.0	1	249,400,775 - 249,401,019	UniSTS	Rnor5.0
RGSC_v3.4	1	227,647,431 - 227,647,632	UniSTS	RGSC3.4
Celera	1	219,085,850 - 219,086,048	UniSTS
Cytogenetic Map	1	q51	UniSTS
RH 3.4 Map	1	1613.6	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
2292216	Bw80	Body weight QTL 80	3.23	0.0019	body mass (VT:0001259)	body weight (CMO:0000012)	1	233490105	264802994	Rat
2292218	Kidm35	Kidney mass QTL 35			kidney mass (VT:0002707)	both kidneys wet weight to body weight ratio (CMO:0000340)	1	217372257	244992610	Rat
70211	Niddm24	Non-insulin dependent diabetes mellitus QTL 24	3.79		blood glucose amount (VT:0000188)	blood glucose level area under curve (AUC) (CMO:0000350)	1	236795785	281795785	Rat
2302040	Pia35	Pristane induced arthritis QTL 35	3.8	0.001	blood immunoglobulin amount (VT:0002460)	serum immunoglobulin G1 level (CMO:0002115)	1	236265430	281265430	Rat
2302375	Bw83	Body weight QTL 83	4.87	0.0002	body mass (VT:0001259)	body weight (CMO:0000012)	1	215711860	260711860	Rat
2302378	Insul11	Insulin level QTL 11	3.25		blood insulin amount (VT:0001560)	serum insulin level (CMO:0000358)	1	156446196	274977688	Rat
61455	Niddm7	Non-insulin dependent diabetes mellitus QTL 7	5.5		blood glucose amount (VT:0000188)	plasma glucose level (CMO:0000042)	1	236763415	258766873	Rat
724531	Uae5	Urinary albumin excretion QTL 5	4		urine albumin amount (VT:0002871)	urine albumin level (CMO:0000130)	1	161321152	273792054	Rat
724533	Rf51	Renal function QTL 51	5.3	0.0002	kidney plasma flow trait (VT:0005524)	renal plasma flow (CMO:0001914)	1	238830534	278228767	Rat
724538	Kidm1	Kidney mass QTL 1	3.2		kidney mass (VT:0002707)	calculated kidney weight (CMO:0000160)	1	233663100	273792054	Rat
734768	Niddm59	Non-insulin dependent diabetes mellitus QTL 59			body mass (VT:0001259)	body weight (CMO:0000012)	1	235850810	280850810	Rat
737828	Hcas3	Hepatocarcinoma susceptibility QTL 3	4.9		liver integrity trait (VT:0010547)	liver tumorous lesion volume to total liver volume ratio (CMO:0001082)	1	156446196	243311614	Rat
1298084	Thym4	Thymus enlargement QTL 4	10.68		thymus mass (VT:0004954)	thymus weight to body weight ratio (CMO:0000612)	1	215828102	260828102	Rat
631658	Cm7	Cardiac mass QTL 7	5.32	0.0001	aorta mass (VT:0002845)	aorta weight (CMO:0000076)	1	216324817	261324817	Rat
737977	Bp160	Blood pressure QTL 160		0.001	arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	1	197963658	242963658	Rat
1331790	Bp201	Blood pressure QTL 201	3.127		arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	1	216213318	245529710	Rat
1354580	Scort1	Serum corticosterone level QTL 1	3.4		blood corticosterone amount (VT:0005345)	blood corticosterone level (CMO:0001172)	1	167394665	278228889	Rat
1582206	Kidm33	Kidney mass QTL 33	6.9		kidney mass (VT:0002707)	both kidneys wet weight to body weight ratio (CMO:0000340)	1	205603081	244401301	Rat
731175	Uae20	Urinary albumin excretion QTL 20	3.5	0.0018	urine albumin amount (VT:0002871)	urine albumin excretion rate (CMO:0000757)	1	241482188	281795785	Rat
738032	Hcas5	Hepatocarcinoma susceptibility QTL 5	3.12		liver integrity trait (VT:0010547)	liver tumorous lesion number (CMO:0001068)	1	191825895	279986079	Rat
1300168	Bp170	Blood pressure QTL 170	2.76		arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	1	227107736	249206417	Rat
1641926	Teswt2	Testicular weight QTL 2	2.82		testis mass (VT:1000644)	both testes wet weight (CMO:0000175)	1	215711860	258765521	Rat
1598821	Rf55	Renal function QTL 55	6.3		renal blood flow trait (VT:2000006)	ratio of change in renal blood flow to change in renal perfusion pressure (CMO:0001239)	1	238824734	279986079	Rat
2300175	Bmd40	Bone mineral density QTL 40	15.4	0.0001	femur mineral mass (VT:0010011)	bone mineral density (CMO:0001226)	1	221901238	266901238	Rat
2293655	Bss36	Bone structure and strength QTL 36	10.66	0.0001	femur strength trait (VT:0010010)	femur ultimate force (CMO:0001675)	1	221901238	266901238	Rat
2293674	Bss39	Bone structure and strength QTL 39	7.1	0.0001	femur strength trait (VT:0010010)	femur total energy absorbed before break (CMO:0001677)	1	221901238	266901238	Rat
2293694	Bss38	Bone structure and strength QTL 38	7.05	0.0001	femur strength trait (VT:0010010)	femur stiffness (CMO:0001674)	1	221901238	266901238	Rat
631838	Niddm36	Non-insulin dependent diabetes mellitus QTL 36		0.01	insulin secretion trait (VT:0003564)	calculated pancreatic islet insulin release measurement (CMO:0001217)	1	205195290	250195290	Rat
634313	Niddm43	Non-insulin dependent diabetes mellitus QTL 43			blood glucose amount (VT:0000188)	blood glucose level (CMO:0000046)	1	217054291	281795785	Rat
634321	Hc1	Hypercalciuria QTL 1	2.91		urine calcium amount (VT:0002985)	urine calcium excretion rate (CMO:0000763)	1	193968438	261264776	Rat
634340	Hcar5	Hepatocarcinoma resistance QTL 5	8		liver integrity trait (VT:0010547)	liver tumorous lesion number (CMO:0001068)	1	236763415	247065599	Rat
1357335	Bw39	Body weight QTL 39	3.3		body mass (VT:0001259)	body weight (CMO:0000012)	1	215828102	260828102	Rat
1357399	Bw45	Body weight QTL 45	3.05		body mass (VT:0001259)	body mass index (BMI) (CMO:0000105)	1	225689973	270689973	Rat
1357404	Bw42	Body weight QTL 42	4.49	0.0001	body mass (VT:0001259)	body weight (CMO:0000012)	1	225689973	270689973	Rat
1600363	Hc6	Hypercalciuria QTL 6	2.7		urine calcium amount (VT:0002985)	urine calcium excretion rate (CMO:0000763)	1	195598053	265002735	Rat
1600374	Mcs17	Mammary carcinoma susceptibility QTL 17	3		mammary gland integrity trait (VT:0010552)	mammary tumor number (CMO:0000343)	1	215684498	260684498	Rat
1600388	Niddm67	Non-insulin dependent diabetes mellitus QTL 67	5.84	0.000004	blood glucose amount (VT:0000188)	blood glucose level area under curve (AUC) (CMO:0000350)	1	213476630	278978026	Rat
1600395	Niddm69	Non-insulin dependent diabetes mellitus QTL 69	4.14	0.0002	blood insulin amount (VT:0001560)	plasma insulin level (CMO:0000342)	1	213476630	278978026	Rat
1600396	Niddm68	Non-insulin dependent diabetes mellitus QTL 68	4.97	0.0003	blood glucose amount (VT:0000188)	blood glucose level area under curve (AUC) (CMO:0000350)	1	213476630	278978026	Rat
1600397	Edcs4	Endometrial carcinoma susceptibility QTL 4	2.2		uterus morphology trait (VT:0001120)	percentage of study population developing endometrioid carcinoma during a period of time (CMO:0001759)	1	226706329	271706329	Rat
1578759	Uae30	Urinary albumin excretion QTL 30	3.3	0.003	urine albumin amount (VT:0002871)	urine albumin excretion rate (CMO:0000757)	1	161321256	273791893	Rat
1578763	Kidm29	Kidney mass QTL 29	3.3	0.0001	kidney mass (VT:0002707)	both kidneys wet weight (CMO:0000085)	1	196395041	282763074	Rat
1578778	Pur4	Proteinuria QTL 4	3.3	0.003	total urine protein amount (VT:0000032)	urine total protein excretion rate (CMO:0000756)	1	161321256	273791893	Rat
1354610	Bw34	Body weight QTL 34	4.1		body mass (VT:0001259)	body weight (CMO:0000012)	1	161784169	278228889	Rat
1354624	Cm35	Cardiac mass QTL35	5.7		heart left ventricle mass (VT:0007031)	calculated heart weight (CMO:0000073)	1	192639698	278228889	Rat
1354646	Kidm18	Kidney mass QTL 18	5.7		kidney mass (VT:0002707)	calculated kidney weight (CMO:0000160)	1	161784169	278228889	Rat
1354652	Kidm20	Kidney mass QTL 20	4.3		kidney mass (VT:0002707)	calculated kidney weight (CMO:0000160)	1	192639698	278228889	Rat
1354661	Bw33	Body weight QTL 33	5.2		body mass (VT:0001259)	body weight (CMO:0000012)	1	161784169	278228889	Rat
1549910	Bw54	Body weight QTL 54		0.05	body mass (VT:0001259)	body weight (CMO:0000012)	1	236795785	281795785	Rat
1549837	Hcar15	Hepatocarcinoma resistance QTL 15		0.05	liver integrity trait (VT:0010547)	liver tumorous lesion number (CMO:0001068)	1	163796316	282763074	Rat
1358191	Ept10	Estrogen-induced pituitary tumorigenesis QTL 10	3.8		pituitary gland mass (VT:0010496)	pituitary gland wet weight (CMO:0000853)	1	210360774	264802828	Rat
2292220	Bp306	Blood pressure QTL 306	3.47	0.00087	arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	1	174905700	264802994	Rat
2293083	Iddm25	Insulin dependent diabetes mellitus QTL 25	4.18		blood glucose amount (VT:0000188)	blood glucose level (CMO:0000046)	1	198655722	244992610	Rat
2312564	Glom18	Glomerulus QTL 18	2.4	0.003	kidney glomerulus morphology trait (VT:0005325)	index of glomerular damage (CMO:0001135)	1	201358068	252480016	Rat
1358886	Bp260	Blood pressure QTL 260	3.67		arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	1	161784422	246226103	Rat
1358890	Bp259	Blood pressure QTL 259	3.06		arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	1	230420627	282645769	Rat
1358898	Bp255	Blood pressure QTL 255	3.6		arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	1	208517798	266948272	Rat
1358916	Kidm22	Kidney mass QTL 22	3.32		kidney mass (VT:0002707)	both kidneys wet weight to body weight ratio (CMO:0000340)	1	230420627	262031693	Rat
1358292	Cm37	Cardiac mass QTL 37	6.2	0.00000081	heart mass (VT:0007028)	heart weight to body weight ratio (CMO:0000074)	1	216324817	261324817	Rat
61327	Eae7	Experimental allergic encephalomyelitis QTL 7	5.6		body mass (VT:0001259)	change in body weight (CMO:0002045)	1	236265430	281265430	Rat
61376	Bp42	Blood pressure QTL 42	23.4		arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	1	215828102	260828102	Rat
61400	Niddm1	Non-insulin dependent diabetes mellitus QTL 1	11		blood glucose amount (VT:0000188)	blood glucose level (CMO:0000046)	1	238830408	266793958	Rat
61403	Niddm4	Non-insulin dependent diabetes mellitus QTL 4			blood glucose amount (VT:0000188)	plasma glucose level (CMO:0000042)	1	225689973	247836969	Rat
5508828	Leukc3	Leukocyte quantity QTL 3			eosinophil quantity (VT:0002602)	blood eosinophil count (CMO:0000033)	1	238220189	244401301	Rat
8693618	Alc25	Alcohol consumption QTL 25	3	0.28	drinking behavior trait (VT:0001422)	calculated ethanol drink intake rate (CMO:0001615)	1	227509470	249252048	Rat
8693661	Alc34	Alcohol consumption QTL 34	2.2	0.611	drinking behavior trait (VT:0001422)	calculated ethanol drink intake rate (CMO:0001615)	1	227509470	249252048	Rat
8655655	Arrd2	Age-related retinal degeneration QTL 2	7.79		retinal layer morphology trait (VT:0003727)	percentage of study population developing retinopathy during a period of time (CMO:0002453)	1	202571665	264802994	Rat
7794788	Mcs32	Mammary carcinoma susceptibility QTL 32	2.61		mammary gland integrity trait (VT:0010552)	mammary tumor incidence/prevalence measurement (CMO:0000946)	1	122614824	262664716	Rat
8693637	Alc29	Alcohol consumption QTL 29	2.7	0.258	drinking behavior trait (VT:0001422)	calculated ethanol drink intake rate (CMO:0001615)	1	227509470	255131140	Rat
7421630	Bp362	Blood pressure QTL 362		0.001	arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	1	125875758	262433692	Rat
8552891	Epfw5	Epididymal fat weight QTL 5	4.4		epididymal fat pad mass (VT:0010421)	epididymal fat pad weight to body weight ratio (CMO:0000658)	1	210652654	255652654	Rat
7394701	Uae46	Urinary albumin excretion QTL 46	3.6	0.0056	urine albumin amount (VT:0002871)	urine albumin excretion rate (CMO:0000757)	1	221901238	266901238	Rat
8655855	Arrd3	Age-related retinal degeneration QTL 3	3.07		lens clarity trait (VT:0001304)	cataract incidence/prevalence measurement (CMO:0001585)	1	202571665	264802994	Rat
10059587	Bw173	Body weight QTL 173	3.23	0.025	body mass (VT:0001259)	body weight (CMO:0000012)	1	222492538	267492538	Rat
10059590	Kidm44	Kidney mass QTL 44	3.42	0.025	kidney mass (VT:0002707)	both kidneys wet weight to body weight ratio (CMO:0000340)	1	210990171	255990171	Rat

miRNA Target Status

Predicted Target Of

	Summary Value
Count of predictions:	136
Count of miRNA genes:	92
Interacting mature miRNAs:	95
Transcripts:	ENSRNOT00000020412, ENSRNOT00000071614
Prediction methods:	Microtar, 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	3	43	57	41	19	41	8	11	74	35	40	11	8
Low											1
Below cutoff

View RNA-SEQ Expression Data

Sequence

Nucleotide Sequences


RefSeq Transcripts	NM_001191952	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
GenBank Nucleotide	AABR07006601	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	AABR07006602	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	AABR07006603	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	AABR07006604	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	AAHX01010022	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	AAHX01010023	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	CH473953	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles

Reference Sequences

RefSeq Acc Id:

ENSRNOT00000020412 ⟹ ENSRNOP00000020412

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
Rnor_6.0 Ensembl	1	242,124,125 - 242,152,834 (-)	Ensembl

RefSeq Acc Id:

ENSRNOT00000071614 ⟹ ENSRNOP00000066555

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
Rnor_6.0 Ensembl	1	242,123,975 - 242,152,834 (-)	Ensembl

RefSeq Acc Id:

NM_001191952 ⟹ NP_001178881

RefSeq Status:

PROVISIONAL

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
Rnor_6.0	1	242,123,975 - 242,152,834 (-)	NCBI
Rnor_5.0	1	249,400,435 - 249,400,757 (-)	NCBI
Rnor_5.0	1	249,419,972 - 249,426,597 (-)	NCBI
Celera	1	219,085,510 - 219,108,749 (-)	NCBI

Sequence:

show sequence

ATGTGGACGTTCGGACGCCGCGCAGCCGCGGGCTTGCTGCCCCGGACGGCCTCCCGGGCCTCCG
CCTGGGTCCGGAACCCACGCGGGAGGGAACGGATTGGAACCTGCGGCCGCCGAGGCCTACATGT
CACAGCCAACGCCGACGCCATCCGCCACTCTCATTTGAACCTCCACTACCTCGGTCAGATTCTG
AACATCAAAAAGCAGAGTGTCTGCGTGGTGCATTTGAGGAACTCGGGGACGTTGGGCAACCCAA
GCTCTCTAGACGAGACAGCTTATGAAAGACTTGCGGAAGAGACACTGGACGCCCTGGCAGAATT
CTTTGAAGACCTTGCAGACAAGCCCTACACCCTGAAGGACTATGATGTCTCTTTTGGGGATGGC
GTGCTCACCATTAAGCTGGGCGGAGATCTAGGGACCTATGTGATCAACAAGCAGACCCCAAACA
ATGAATTTATTTTGTCCTGCAGTGGCCCCAAGCGCTATGACTGGACCGGGAAGAACTGGGTGTA
CTCCCATGACGGCGTGTCTCTGCATGAGCTGCTGGCCAGGGAGCTGACTGAAGCTTTAAACACC
AAACTGGACTTGTCTTCATTGGCCTATTCTGGAAAGGGCACTTGACTGCTGTCCAGATTCGAAA
ACATTAAAAACTATCAGGCAAAGACCCCAGCCTCCTTCTATAGCTGAATGTCTGGTTTCCCATA
CCTGCTTCCGAAGATAATCACACTGTGTGCAACAACTCTGTGAAAAAAAGTGTGTACCTCCCA

hide sequence

Protein Sequences


Protein RefSeqs	NP_001178881	(Get FASTA)	NCBI Sequence Viewer
GenBank Protein	D3ZYW7	(Get FASTA)	NCBI Sequence Viewer
	EDM13034	(Get FASTA)	NCBI Sequence Viewer

Reference Sequences

RefSeq Acc Id:

NP_001178881 ⟸ NM_001191952

- Sequence:

show sequence

MWTFGRRAAAGLLPRTASRASAWVRNPRGRERIGTCGRRGLHVTANADAIRHSHLNLHYLGQIL
NIKKQSVCVVHLRNSGTLGNPSSLDETAYERLAEETLDALAEFFEDLADKPYTLKDYDVSFGDG
VLTIKLGGDLGTYVINKQTPNNEFILSCSGPKRYDWTGKNWVYSHDGVSLHELLARELTEALNT
KLDLSSLAYSGKGT

hide sequence

RefSeq Acc Id:

ENSRNOP00000020412 ⟸ ENSRNOT00000020412

RefSeq Acc Id:

ENSRNOP00000066555 ⟸ ENSRNOT00000071614

Transcriptome

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

Promoters

RGD ID:

13690835

Promoter ID:

EPDNEW_R1349

Type:

initiation region

Name:

Fxn_1

Description:

frataxin

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	1	242,152,840 - 242,152,900	EPDNEW

Strain Variation

Strain Sequence Variants (Rnor 6.0)

ACI/EurMcwi (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)

ACI/EurMcwi (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

ACI/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

BBDP/Wor (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

BN/SsN (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

Buf/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

COP/CrCrl (MCW & UW)

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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)

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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)

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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)

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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)

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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)

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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)

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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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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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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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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)

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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)

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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)

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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)

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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)

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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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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

Additional Information

External Database Links

Database	Acc Id	Source(s)
AGR Gene	RGD:1565754	AgrOrtholog
Ensembl Genes	ENSRNOG00000015213	Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein	ENSRNOP00000020412	UniProtKB/TrEMBL
	ENSRNOP00000066555	ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript	ENSRNOT00000020412	UniProtKB/TrEMBL
	ENSRNOT00000071614	ENTREZGENE, UniProtKB/TrEMBL
Gene3D-CATH	3.30.920.10	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
InterPro	Frataxin	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	Frataxin/CyaY	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	Frataxin/CyaY_sf	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
NCBI Gene	499335	ENTREZGENE
PANTHER	PTHR16821	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam	Frataxin_Cyay	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen	Fxn	PhenoGen
PRINTS	FRATAXIN	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PROSITE	FRATAXIN_2	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
SMART	Frataxin_Cyay	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP	SSF55387	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
TIGRFAMs	FeS_CyaY	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	mito_frataxin	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniGene	Rn.13133	ENTREZGENE
UniProt	A0A0A0MXX7_RAT	UniProtKB/TrEMBL
	D3ZYW7	ENTREZGENE, UniProtKB/Swiss-Prot
	M0RAK4_RAT	UniProtKB/TrEMBL

Nomenclature History

Date	Current Symbol	Current Name	Previous Symbol	Previous Name	Description	Reference	Status
2008-04-30	Fxn	frataxin	Fxn_predicted	frataxin (predicted)	'predicted' is removed	2292626	APPROVED
2006-11-15	Fxn_predicted	frataxin (predicted)	RGD1565754_predicted	similar to frataxin (predicted)	Symbol and Name updated to reflect Human and Mouse nomenclature	1299863	APPROVED
2006-03-07	RGD1565754_predicted	similar to frataxin (predicted)	LOC499335	similar to frataxin	Symbol and Name status set to approved	1299863	APPROVED
2006-02-09	LOC499335	similar to frataxin			Symbol and Name status set to provisional	70820	PROVISIONAL

Gene Annotator (Functional Annotation) unavailable	Gene Annotator (Annotation Distribution) unavailable	Variant Visualizer (Genomic Variants) unavailble Variant Visualizer (Genomic Variants) unavailable
Gene Annotator (Functional Annotation)	Gene Annotator (Annotation Distribution)	Variant Visualizer (Genomic Variants)

InterViewer (Protein-Protein Interactions) unavailable	Gviewer (Genome Viewer) unavailable	Variant Visualizer (Damaging Variants) unavailble Variant Visualizer (Damaging Variants) unavailable
InterViewer (Protein-Protein Interactions)	GViewer (Genome Viewer)	Variant Visualizer (Damaging Variants)

Gene Annotator (Annotation Comparison) unavailable	OLGA (Gene List Generator) unavailable
Gene Annotator (Annotation Comparison)	OLGA (Gene List Generator)	Excel (Download)

MOET (Multi-Ontology Enrichement) unavailable	GOLF (Gene-Ortholog Location Finder) unavailable
MOET (Multi-Ontology Enrichement)	GOLF (Gene-Ortholog Location Finder)

Imported Disease Annotations - ClinVar

Imported Disease Annotations - CTD

Imported Disease Annotations - OMIM

Imported Annotations - PID (archival)