Traf6 (TNF receptor associated factor 6)

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Gene: Traf6 (TNF receptor associated factor 6) Rattus norvegicus

Analyze

Symbol:

Traf6

Name:

TNF receptor associated factor 6

RGD ID:

1306853

Description:

Predicted to have several functions, including enzyme binding activity; tumor necrosis factor receptor binding activity; and ubiquitin protein ligase activity. Involved in JNK cascade; interleukin-1-mediated signaling pathway; and positive regulation of smooth muscle cell proliferation. Localizes to protein-containing complex. Orthologous to human TRAF6 (TNF receptor associated factor 6); PARTICIPATES IN interleukin-1 signaling pathway; nuclear factor kappa B signaling pathway; p38 MAPK signaling pathway; INTERACTS WITH 17beta-estradiol; 2,6-dinitrotoluene; bisphenol A.

Type:

protein-coding

RefSeq Status:

PROVISIONAL

Also known as:

E3 ubiquitin-protein ligase TRAF6; LOC311245; RING-type E3 ubiquitin transferase TRAF6; TNF receptor-associated factor 6; TNF receptor-associated factor 6, E3 ubiquitin protein ligase

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):	TRAF6 (TNF receptor associated factor 6)	HGNC	EggNOG, Ensembl, HomoloGene, Inparanoid, NCBI, OMA, OrthoDB, Panther, PhylomeDB, Treefam
Mus musculus (house mouse):	Traf6 (TNF receptor-associated factor 6)	HGNC	Treefam, EggNOG, NCBI, OMA, HomoloGene, Inparanoid, Panther, PhylomeDB, OrthoDB, Ensembl
Chinchilla lanigera (long-tailed chinchilla):	Traf6 (TNF receptor associated factor 6)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Pan paniscus (bonobo/pygmy chimpanzee):	TRAF6 (TNF receptor associated factor 6)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Canis lupus familiaris (dog):	TRAF6 (TNF receptor associated factor 6)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Ictidomys tridecemlineatus (thirteen-lined ground squirrel):	Traf6 (TNF receptor associated factor 6)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Sus scrofa (pig):	TRAF6 (TNF receptor associated factor 6)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Chlorocebus sabaeus (African green monkey):	TRAF6 (TNF receptor associated factor 6)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Heterocephalus glaber (naked mole-rat):	Traf6 (TNF receptor associated factor 6)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Alliance orthologs ³
Homo sapiens (human):	TRAF6 (TNF receptor associated factor 6)	Alliance	DIOPT (Ensembl Compara\|HGNC\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|TreeFam)
Mus musculus (house mouse):	Traf6 (TNF receptor-associated factor 6)	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|TreeFam)
Danio rerio (zebrafish):	traf6 (TNF receptor-associated factor 6)	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|TreeFam)
Caenorhabditis elegans (roundworm):	trf-2	Alliance	DIOPT (PhylomeDB\|TreeFam)
Drosophila melanogaster (fruit fly):	Traf6	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|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	3	87,963,517 - 87,988,316 (+)	NCBI
Rnor_6.0 Ensembl	3	91,252,829 - 91,271,607 (+)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_6.0	3	91,252,829 - 91,271,607 (+)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_5.0	3	97,912,482 - 97,935,027 (+)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	3	86,827,582 - 86,847,408 (+)	NCBI	RGSC3.4		rn4	RGSC3.4
RGSC_v3.1	3	86,728,165 - 86,742,912 (+)	NCBI
Celera	3	87,069,225 - 87,089,051 (+)	NCBI		Celera
Cytogenetic Map	3	q31	NCBI

JBrowse:

View Region in Genome Browser (JBrowse)

Model

Annotation Click to see Annotation Detail View

Disease Annotations Click to see Annotation Detail View

coronary artery disease (ISO)

hypohidrotic ectodermal dysplasia (ISS)

intellectual disability (ISO)

rheumatoid arthritis (ISO)

Gene-Chemical Interaction Annotations Click to see Annotation Detail View

(-)-epigallocatechin 3-gallate (ISO)

1,2-dichloroethane (ISO)

1,2-dimethylhydrazine (ISO)

17beta-estradiol (EXP,ISO)

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

2,6-dinitrotoluene (EXP)

2-amino-2-deoxy-D-galactopyranose (ISO)

2-amino-2-deoxy-D-glucopyranose (ISO)

3-phenylprop-2-enal (ISO)

4,4'-diaminodiphenylmethane (ISO)

acetic acid (ISO)

acetylsalicylic acid (ISO)

aldehydo-D-glucosamine (ISO)

anthra[1,9-cd]pyrazol-6(2H)-one (ISO)

arsane (ISO)

arsenic atom (ISO)

arsenous acid (ISO)

atorvastatin calcium (ISO)

benzo[a]pyrene (ISO)

beta-D-glucosamine (ISO)

bisphenol A (EXP)

C60 fullerene (EXP)

cadmium dichloride (ISO)

cadmium selenide (ISO)

camptothecin (ISO)

clofibrate (ISO)

clothianidin (ISO)

copper atom (ISO)

copper(0) (ISO)

corticosterone (EXP,ISO)

crocin-1 (ISO)

curcumin (ISO)

cyclosporin A (ISO)

DAPT (EXP,ISO)

deoxynivalenol (ISO)

dexamethasone (ISO)

dextran sulfate (ISO)

diarsenic trioxide (ISO)

diethylstilbestrol (ISO)

dioxygen (EXP,ISO)

doxorubicin (ISO)

enalapril (ISO)

erlotinib hydrochloride (ISO)

ethanol (EXP,ISO)

flutamide (EXP)

folic acid (ISO)

formaldehyde (ISO)

fructose (ISO)

furosemide (EXP)

Fusarenone X (ISO)

Fusaric acid (ISO)

glycyrrhetinate (ISO)

glycyrrhetinic acid (ISO)

glyphosate (ISO)

hydrogen peroxide (ISO)

hydroxychloroquine (ISO)

kaempferol (ISO)

lactulose (EXP)

lipoarabinomannan (ISO)

lipopolysaccharide (EXP,ISO)

maneb (ISO)

mangiferin (ISO)

melittin (ISO)

methamphetamine (EXP)

methylglyoxal (ISO)

methylmercury chloride (ISO)

nickel dichloride (ISO)

niclosamide (ISO)

Nonylphenol (EXP)

ochratoxin A (ISO)

p-menthan-3-ol (ISO)

paracetamol (ISO)

paraquat (ISO)

pentachlorophenol (ISO)

pirinixic acid (ISO)

platycodin D (EXP)

poly(I:C) (ISO)

potassium dichromate (ISO)

progesterone (EXP,ISO)

quercetin (ISO)

resveratrol (ISO)

silver atom (ISO)

silver(0) (ISO)

sodium arsenite (ISO)

sulfasalazine (ISO)

telmisartan (ISO)

testosterone (EXP,ISO)

titanium atom (EXP)

titanium dioxide (ISO)

urethane (ISO)

xanthohumol (ISO)

zinc atom (ISO)

zinc oxide (ISO)

zinc protoporphyrin (EXP)

zinc(0) (ISO)

Gene Ontology Annotations Click to see Annotation Detail View

Biological Process

activation of NF-kappaB-inducing kinase activity (ISO)

activation of protein kinase activity (ISO)

animal organ morphogenesis (ISO)

antigen processing and presentation of exogenous peptide antigen via MHC class II (ISO)

bone remodeling (ISO)

bone resorption (ISO)

cell development (ISO)

cellular response to cytokine stimulus (ISO)

cellular response to DNA damage stimulus (IEA)

cytokine-mediated signaling pathway (IMP)

I-kappaB kinase/NF-kappaB signaling (ISO)

immune response (ISO)

in utero embryonic development (ISO)

interleukin-1-mediated signaling pathway (IBA,IMP,ISO)

interleukin-17-mediated signaling pathway (IEA,ISO)

JNK cascade (IMP)

myeloid dendritic cell differentiation (ISO)

negative regulation of transcription by RNA polymerase II (ISO)

negative regulation of transcription, DNA-templated (ISO)

neural tube closure (ISO)

odontogenesis of dentin-containing tooth (ISO)

ossification (ISO)

osteoclast differentiation (ISO)

positive regulation of DNA-binding transcription factor activity (ISO)

positive regulation of I-kappaB kinase/NF-kappaB signaling (ISO,ISS)

positive regulation of interleukin-12 production (ISO)

positive regulation of interleukin-2 production (ISO)

positive regulation of interleukin-6 production (ISO)

positive regulation of JNK cascade (IBA)

positive regulation of JUN kinase activity (ISO)

positive regulation of leukocyte adhesion to vascular endothelial cell (ISO)

positive regulation of lipopolysaccharide-mediated signaling pathway (ISO)

positive regulation of NF-kappaB transcription factor activity (IBA,ISO,ISS)

positive regulation of NIK/NF-kappaB signaling (ISO)

positive regulation of osteoclast differentiation (ISO)

positive regulation of smooth muscle cell proliferation (IMP)

positive regulation of T cell cytokine production (ISO)

positive regulation of T cell proliferation (ISO)

positive regulation of transcription by RNA polymerase II (ISO)

positive regulation of transcription regulatory region DNA binding (ISO)

protein autoubiquitination (ISO)

protein K63-linked ubiquitination (IBA,ISO,ISS)

protein polyubiquitination (ISO)

protein ubiquitination (ISO)

regulation of apoptotic process (IEA)

regulation of I-kappaB kinase/NF-kappaB signaling (IBA)

regulation of immunoglobulin production (ISO)

response to interleukin-1 (ISO)

signal transduction (ISO)

T cell receptor signaling pathway (ISO)

T-helper 1 type immune response (ISO)

tumor necrosis factor-mediated signaling pathway (IBA)

Cellular Component

CD40 receptor complex (ISO)

cell cortex (IEA)

cytoplasm (ISO)

cytoplasmic side of plasma membrane (ISO)

cytosol (ISO)

lipid droplet (ISO,ISS)

nucleus (ISO)

perinuclear region of cytoplasm (ISO)

plasma membrane (ISO)

protein-containing complex (IDA)

Molecular Function

histone deacetylase binding (ISO)

identical protein binding (ISO)

mitogen-activated protein kinase kinase kinase binding (ISO)

protein binding (ISO)

protein kinase B binding (ISO)

protein kinase binding (ISO)

protein N-terminus binding (ISO)

thioesterase binding (ISO)

tumor necrosis factor receptor binding (IBA,ISO)

tumor necrosis factor receptor superfamily binding (IBA)

ubiquitin protein ligase activity (ISO)

ubiquitin protein ligase binding (ISO)

ubiquitin-protein transferase activity (IBA,ISO,ISS)

zinc ion binding (IEA)

Molecular Pathway Annotations Click to see Annotation Detail View

Chagas disease pathway (IEA)

endocytosis pathway (IEA)

hepatitis C pathway (IEA)

interleukin-1 signaling pathway (IMP,ISO)

Leishmaniasis pathway (IEA)

measles pathway (IEA)

mitogen activated protein kinase signaling pathway (IEA)

neurotrophic factor signaling pathway (IEA)

NOD-like receptor signaling pathway (IEA)

nuclear factor kappa B signaling pathway (ISO)

p38 MAPK signaling pathway (ISO)

Retinoic acid-inducible gene (RIG) I-like receptor signaling pathway (IEA)

small cell lung carcinoma pathway (IEA)

Toll-like receptor signaling pathway (IEA,ISO)

toxoplasmosis pathway (IEA)

tuberculosis pathway (IEA)

ubiquitin/proteasome degradation pathway (IEA)

References

References - curated


1.	Chandrasekar B, etal., J Biol Chem. 2005 Jul 15;280(28):26263-77. Epub 2005 May 11.
2.	Cuadrado A and Nebreda AR, Biochem J. 2010 Aug 1;429(3):403-17. doi: 10.1042/BJ20100323.
3.	Fernandes A, etal., Glia. 2011 Jan;59(1):14-25. doi: 10.1002/glia.21072. Epub 2010 Oct 21.
4.	Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
5.	GOA data from the GO Consortium
6.	Kumar H, etal., Int Rev Immunol. 2011 Feb;30(1):16-34.
7.	MGD data from the GO Consortium
8.	Pipeline to import KEGG annotations from KEGG into RGD
9.	Pipeline to import Pathway Interaction Database annotations from NCI into RGD
10.	RGD automated import pipeline for gene-chemical interactions
11.	Verstrepen L, etal., Cell Mol Life Sci. 2008 Oct;65(19):2964-78.
12.	Weber A, etal., Sci Signal. 2010 Jan 19;3(105):cm1. doi: 10.1126/scisignal.3105cm1.

Additional References at PubMed

PMID:10094049	PMID:10215628	PMID:10421844	PMID:11007897	PMID:11279055	PMID:11728344	PMID:11751921	PMID:12296995	PMID:12477932	PMID:12958312	PMID:14499111	PMID:14530355
PMID:14699584	PMID:15125833	PMID:15322147	PMID:15361868	PMID:15705807	PMID:16079148	PMID:16246731	PMID:16252010	PMID:16378096	PMID:16831874	PMID:17135271	PMID:17633018
PMID:18093978	PMID:18996842	PMID:19465916	PMID:19482181	PMID:19675569	PMID:19713527	PMID:20079715	PMID:20136795	PMID:20345905	PMID:20614026	PMID:20659889	PMID:21068390
PMID:21072581	PMID:21435586	PMID:21984198	PMID:21988832	PMID:22095711	PMID:22493164	PMID:22521762	PMID:22829592	PMID:22863753	PMID:23001490	PMID:23042151	PMID:23776175
PMID:25416956	PMID:25515214	PMID:25708205	PMID:26291555	PMID:26895894	PMID:26925748	PMID:27107012	PMID:27494324	PMID:27538408	PMID:27813153	PMID:27830143	PMID:27889748
PMID:27996060	PMID:28543180	PMID:28771774	PMID:29304519	PMID:29745371	PMID:31177708	PMID:32029478	PMID:32299285

Genomics

Comparative Map Data

Traf6
(Rattus norvegicus - Norway rat)

Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
mRatBN7.2	3	87,963,517 - 87,988,316 (+)	NCBI
Rnor_6.0 Ensembl	3	91,252,829 - 91,271,607 (+)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_6.0	3	91,252,829 - 91,271,607 (+)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_5.0	3	97,912,482 - 97,935,027 (+)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	3	86,827,582 - 86,847,408 (+)	NCBI	RGSC3.4		rn4	RGSC3.4
RGSC_v3.1	3	86,728,165 - 86,742,912 (+)	NCBI
Celera	3	87,069,225 - 87,089,051 (+)	NCBI		Celera
Cytogenetic Map	3	q31	NCBI

TRAF6
(Homo sapiens - human)

Human Assembly	Chr	Position (strand)	Source	Genome Browsers
Human Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCh38.p13 Ensembl	11	36,483,769 - 36,510,272 (-)	Ensembl	GRCh38		hg38	GRCh38
GRCh38	11	36,483,769 - 36,510,313 (-)	NCBI	GRCh38	GRCh38	hg38	GRCh38
GRCh37	11	36,505,319 - 36,531,822 (-)	NCBI	GRCh37	GRCh37	hg19	GRCh37
Build 36	11	36,467,302 - 36,488,398 (-)	NCBI	NCBI36		hg18	NCBI36
Build 34	11	36,467,298 - 36,488,398	NCBI
Celera	11	36,661,891 - 36,684,256 (-)	NCBI
Cytogenetic Map	11	p12	NCBI
HuRef	11	36,207,402 - 36,234,755 (-)	NCBI		HuRef
CHM1_1	11	36,504,096 - 36,530,410 (-)	NCBI		CHM1_1

Traf6
(Mus musculus - house mouse)

Mouse Assembly	Chr	Position (strand)	Source	Genome Browsers
Mouse Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCm39	2	101,508,765 - 101,532,013 (+)	NCBI	GRCm39		mm39
GRCm39 Ensembl	2	101,508,774 - 101,532,014 (+)	Ensembl
GRCm38	2	101,678,420 - 101,701,668 (+)	NCBI	GRCm38	GRCm38	mm10	GRCm38
GRCm38.p6 Ensembl	2	101,678,429 - 101,701,669 (+)	Ensembl	GRCm38		mm10	GRCm38
MGSCv37	2	101,518,597 - 101,541,133 (+)	NCBI	GRCm37		mm9	NCBIm37
MGSCv36	2	101,479,279 - 101,501,815 (+)	NCBI			mm8
Celera	2	102,903,294 - 102,925,894 (+)	NCBI		Celera
Cytogenetic Map	2	E2	NCBI

Traf6
(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_004955422	9,932,680 - 9,949,100 (+)	Ensembl	ChiLan1.0
ChiLan1.0	NW_004955422	9,925,765 - 9,950,354 (+)	NCBI	ChiLan1.0	ChiLan1.0

TRAF6
(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	11	36,330,336 - 36,356,334 (-)	NCBI	panpan1.1	PanPan1.1	panPan2
PanPan1.1 Ensembl	11	36,335,609 - 36,356,334 (-)	Ensembl	panpan1.1		panPan2
Mhudiblu_PPA_v0	11	36,457,633 - 36,483,616 (-)	NCBI	Mhudiblu_PPA_v0		panPan3

TRAF6
(Canis lupus familiaris - dog)

Dog Assembly	Chr	Position (strand)	Source	Genome Browsers
Dog Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
CanFam3.1	18	31,674,242 - 31,689,160 (+)	NCBI	CanFam3.1	CanFam3.1	canFam3	CanFam3.1
CanFam3.1 Ensembl	18	31,675,391 - 31,688,641 (+)	Ensembl	CanFam3.1		canFam3	CanFam3.1
Dog10K_Boxer_Tasha	18	31,278,398 - 31,300,151 (+)	NCBI
ROS_Cfam_1.0	18	32,281,552 - 32,303,317 (+)	NCBI
UMICH_Zoey_3.1	18	31,851,198 - 31,872,911 (+)	NCBI
UNSW_CanFamBas_1.0	18	31,435,636 - 31,457,386 (+)	NCBI
UU_Cfam_GSD_1.0	18	32,072,955 - 32,094,690 (+)	NCBI

Traf6
(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_024404947	28,732,923 - 28,750,178 (+)	NCBI
SpeTri2.0	NW_004936533	1,857,685 - 1,874,973 (+)	NCBI	SpeTri2.0	SpeTri2.0		SpeTri2.0

TRAF6
(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	24,602,783 - 24,626,072 (+)	Ensembl	Sscrofa11.1		susScr11	Sscrofa11.1
Sscrofa11.1	2	24,602,749 - 24,628,263 (+)	NCBI	Sscrofa11.1	Sscrofa11.1	susScr11	Sscrofa11.1
Sscrofa10.2	2	26,767,127 - 26,786,940 (+)	NCBI	Sscrofa10.2	Sscrofa10.2	susScr3

TRAF6
(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	1	28,726,357 - 28,752,389 (+)	NCBI
ChlSab1.1 Ensembl	1	28,734,380 - 28,747,092 (+)	Ensembl

Traf6
(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_004624767	10,729,766 - 10,803,253 (+)	NCBI

Position Markers

AW530200

Rat Assembly	Chr	Position (strand)	Source	JBrowse
Rnor_6.0	3	91,268,264 - 91,268,430	NCBI	Rnor6.0
Rnor_5.0	3	97,927,918 - 97,928,084	UniSTS	Rnor5.0
RGSC_v3.4	3	86,844,065 - 86,844,231	UniSTS	RGSC3.4
Celera	3	87,085,708 - 87,085,874	UniSTS
RH 3.4 Map	3	713.0	UniSTS
Cytogenetic Map	3	q31	UniSTS

BE115919

Rat Assembly	Chr	Position (strand)	Source	JBrowse
Rnor_6.0	3	91,270,789 - 91,270,944	NCBI	Rnor6.0
Rnor_5.0	3	97,930,443 - 97,930,598	UniSTS	Rnor5.0
RGSC_v3.4	3	86,846,590 - 86,846,745	UniSTS	RGSC3.4
Celera	3	87,088,233 - 87,088,388	UniSTS
RH 3.4 Map	3	711.8	UniSTS
Cytogenetic Map	3	q31	UniSTS

Traf6

Rat Assembly	Chr	Position (strand)	Source	JBrowse
Rnor_6.0	3	91,270,538 - 91,270,948	NCBI	Rnor6.0
Rnor_5.0	3	97,930,192 - 97,930,602	UniSTS	Rnor5.0
RGSC_v3.4	3	86,846,339 - 86,846,749	UniSTS	RGSC3.4
Celera	3	87,087,982 - 87,088,392	UniSTS
Cytogenetic Map	3	q31	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
2290452	Scl56	Serum cholesterol level QTL 56	2.26		blood cholesterol amount (VT:0000180)	plasma total cholesterol level (CMO:0000585)	3	1	95176874	Rat
1358905	Hrtrt17	Heart rate QTL 17	5.9	0.000014	heart pumping trait (VT:2000009)	heart rate (CMO:0000002)	3	10094081	93415837	Rat
1358885	Bp251	Blood pressure QTL 251	3.8		arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	3	10639528	127023997	Rat
1358888	Bp264	Blood pressure QTL 264	4.43		arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	3	10639528	127023997	Rat
737818	Hcar12	Hepatocarcinoma resistance QTL 12	2.6		liver integrity trait (VT:0010547)	volume of individual liver tumorous lesion (CMO:0001078)	3	30114912	123700444	Rat
70216	Cm14	Cardiac mass QTL 14	2.1		heart mass (VT:0007028)	heart wet weight (CMO:0000069)	3	30846101	172879276	Rat
1354604	Bw36	Body weight QTL 36	2.9		body mass (VT:0001259)	body weight (CMO:0000012)	3	33477354	108914061	Rat
61419	Cia11	Collagen induced arthritis QTL 11	5.6		joint integrity trait (VT:0010548)	joint inflammation composite score (CMO:0000919)	3	34394121	103141944	Rat
1358362	Srcrt2	Stress Responsive Cort QTL 2	2.78		blood corticosterone amount (VT:0005345)	plasma corticosterone level (CMO:0001173)	3	39248391	140271184	Rat
1331777	Bw24	Body weight QTL 24	3.503		body mass (VT:0001259)	body weight (CMO:0000012)	3	40523593	92654473	Rat
1331795	Rf30	Renal function QTL 30	3.708		urine potassium amount (VT:0010539)	urine potassium level (CMO:0000128)	3	40523593	92654473	Rat
1354597	Kidm13	Kidney mass QTL 13	2.9		kidney mass (VT:0002707)	right kidney wet weight (CMO:0000082)	3	43295930	108914061	Rat
2301970	Bw81	Body weight QTL 81	5.19		body mass (VT:0001259)	body weight (CMO:0000012)	3	43295930	163640485	Rat
2301971	Cm71	Cardiac mass QTL 71	4.63		heart left ventricle mass (VT:0007031)	heart left ventricle weight (CMO:0000776)	3	43295930	163640485	Rat
1300178	Hrtrt4	Heart rate QTL 4	3.74		heart pumping trait (VT:2000009)	heart rate (CMO:0000002)	3	45406058	94467785	Rat
1581503	Cm58	Cardiac mass QTL 58	2.7	0.05	heart left ventricle mass (VT:0007031)	heart left ventricle weight to body weight ratio (CMO:0000530)	3	45406058	127023997	Rat
1559282	Emca5	Estrogen-induced mammary cancer QTL 5	3.9		mammary gland integrity trait (VT:0010552)	percentage of study population developing mammary tumors during a period of time (CMO:0000948)	3	45406058	177699992	Rat
2292591	Esta4	Estrogen-induced thymic atrophy QTL 4			thymus mass (VT:0004954)	thymus wet weight (CMO:0000855)	3	48561928	155263151	Rat
1358186	Ept2	Estrogen-induced pituitary tumorigenesis QTL 2	8.3		pituitary gland mass (VT:0010496)	pituitary gland wet weight (CMO:0000853)	3	48562146	115249962	Rat
2292613	Ept16	Estrogen-induced pituitary tumorigenesis QTL 16	8.3		pituitary gland mass (VT:0010496)	pituitary gland wet weight (CMO:0000853)	3	48562146	115249962	Rat
631665	Bw8	Body weight QTL 8	5.5		body mass (VT:0001259)	body weight (CMO:0000012)	3	51821836	124513579	Rat
724523	Tsu1	Thymus enlargement suppressive QTL 1	3.84		thymus mass (VT:0004954)	thymus weight to body weight ratio (CMO:0000612)	3	51822008	120917851	Rat
1582218	Bw74	Body weight QTL 74	3.9	0.0021	body mass (VT:0001259)	body weight (CMO:0000012)	3	54630948	119830094	Rat
1582238	Bw68	Body weight QTL 68	3.2	0.0064	body mass (VT:0001259)	body weight (CMO:0000012)	3	54630948	119830094	Rat
1582239	Epfw1	Epididymal fat weight QTL 1	4.5	0.0006	epididymal fat pad mass (VT:0010421)	epididymal fat pad weight to body weight ratio (CMO:0000658)	3	54630948	119830094	Rat
61377	Edpm3	Estrogen-dependent pituitary mass QTL 3	7.05	0.038	pituitary gland mass (VT:0010496)	pituitary gland wet weight (CMO:0000853)	3	54631046	93415673	Rat
731180	Bp152	Blood pressure QTL 152		0.03	arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	3	55245276	95176874	Rat
731180	Bp152	Blood pressure QTL 152		0.03	arterial blood pressure trait (VT:2000000)	diastolic blood pressure (CMO:0000005)	3	55245276	95176874	Rat
731180	Bp152	Blood pressure QTL 152		0.03	arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	3	55245276	95176874	Rat
1358293	Bw38	Body weight QTL 38	6	0.0000031	body mass (VT:0001259)	body weight (CMO:0000012)	3	56735995	101735995	Rat
1581568	Rf53	Renal function QTL 53			total urine protein amount (VT:0000032)	urine protein excretion rate to body weight ratio (CMO:0001099)	3	58204463	170534769	Rat
8662816	Vetf4	Vascular elastic tissue fragility QTL 4	4		renal artery integrity trait (VT:0010642)	number of ruptures of the internal elastic lamina of the renal arteries (CMO:0002563)	3	61241033	165369047	Rat
1300111	Rf12	Renal function QTL 12	3.78		renal blood flow trait (VT:2000006)	absolute change in renal blood flow rate (CMO:0001168)	3	62922868	127023997	Rat
631200	Cm25	Cardiac mass QTL 25	4.8	0.0001	heart left ventricle mass (VT:0007031)	heart left ventricle wet weight (CMO:0000071)	3	63049050	92654302	Rat
1582221	Kidm30	Kidney mass QTL 30	3.5	0.0008	kidney mass (VT:0002707)	both kidneys wet weight (CMO:0000085)	3	66711607	119830094	Rat
1582210	Bw71	Body weight QTL 71	3.3	0.0012	body mass (VT:0001259)	body weight (CMO:0000012)	3	66711607	119830094	Rat
12879848	Bw181	Body weght QTL 181		0.015	body mass (VT:0001259)	body weight (CMO:0000012)	3	72672290	127023997	Rat
2301414	Kidm37	Kidney mass QTL 37		0.001	kidney mass (VT:0002707)	both kidneys wet weight to body weight ratio (CMO:0000340)	3	72973445	127023997	Rat
1600376	Arunc5	Aerobic running capacity QTL 5		0.21	exercise endurance trait (VT:0002332)	maximum distance run on treadmill (CMO:0001406)	3	78700444	123700444	Rat
1581546	Pur13	Proteinuria QTL 13	2.93	0.0335	total urine protein amount (VT:0000032)	urine protein excretion rate (CMO:0000759)	3	81136227	154416635	Rat
2302273	Gluco35	Glucose level QTL 35	5.3	0.001	blood glucose amount (VT:0000188)	blood glucose level (CMO:0000046)	3	83817637	119509260	Rat
7387306	Bw124	Body weight QTL 124	3.2	0.0003	body mass (VT:0001259)	body weight (CMO:0000012)	3	88910015	133910015	Rat

miRNA Target Status

Predicted Target Of

	Summary Value
Count of predictions:	470
Count of miRNA genes:	242
Interacting mature miRNAs:	283
Transcripts:	ENSRNOT00000006148
Prediction methods:	Microtar, Miranda, Targetscan
Result types:	miRGate_prediction

The detailed report is available here: Full Report CSV TAB Printer

miRNA Target Status data imported from miRGate (http://mirgate.bioinfo.cnio.es/).
For more information about miRGate, see PMID:25858286 or access the full paper here.

Expression

RNA-SEQ Expression

High: > 1000 TPM value Medium: Between 11 and 1000 TPM
Low: Between 0.5 and 10 TPM Below Cutoff: < 0.5 TPM

	alimentary part of gastrointestinal system	circulatory system	endocrine system	exocrine system	hemolymphoid system	hepatobiliary system	integumental system	musculoskeletal system	nervous system	renal system	reproductive system	respiratory system	appendage
High
Medium	2		16		19				23	27	19	11
Low	1	43	41	41		41	8	11	51	8	22		8
Below cutoff

View RNA-SEQ Expression Data

Sequence

Nucleotide Sequences


RefSeq Transcripts	NM_001107754	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_039104924	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_039104925	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
GenBank Nucleotide	BC168921	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	CH473949	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	FQ209645	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	JACYVU010000118	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles

Reference Sequences

RefSeq Acc Id:

ENSRNOT00000006148 ⟹ ENSRNOP00000006148

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
Rnor_6.0 Ensembl	3	91,252,829 - 91,271,607 (+)	Ensembl

RefSeq Acc Id:

NM_001107754 ⟹ NP_001101224

RefSeq Status:

PROVISIONAL

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2	3	87,963,517 - 87,983,350 (+)	NCBI
Rnor_6.0	3	91,252,829 - 91,271,607 (+)	NCBI
Rnor_5.0	3	97,912,482 - 97,935,027 (+)	NCBI
RGSC_v3.4	3	86,827,582 - 86,847,408 (+)	RGD
Celera	3	87,069,225 - 87,089,051 (+)	RGD

Sequence:

show sequence

CGCGGCTGGGGCTGAGGCTCCGGCCGTCGGCGGACGCAGTAGCCGCGGCCCAGGAACCGGGAGT
TTGGCGTCGGAGACACTTGATCTCGGAGTGCTGCGTGTATAGGCGGCGCGTGGCGGCCCGGGGG
AGCTTTCTAGTCGGTTGTGAAGCCTCTGCGTGTGCGATCGATTGACTGACAACAAAGCTACTAT
GAGTCTCTTAAACTGTGAAAACAGCTGTGCGTCCAGCCAGTCTTCAAGCGACTGCTGTGCTGCC
ATGGCCAACTCCTGCAGTGCTGCCATGAAAGATGACAGTGTGAGTGGCTGTGTCAGCACGGGGA
ACCTGTCCAGCTCCTTCATGGAGGAGATCCAGGGATATGATGTGGAGTTTGACCCACCTTTGGA
AAGCAAGTATGAGTGCCCCATCTGCTTGATGGCTTTACGGGAAGCAGTGCAAACACCATGTGGC
CACAGGTTCTGCAAAGCCTGCATCACCAAGTCCATAAGGGATGCAGGTCACAAGTGCCCAGTTG
ACAATGAAATACTGCTGGAAAATCAACTGTTTCCTGACAATTTTGCAAAGCGAGAGATTCTTTC
CCTGACGGTAAAGTGTCCAAATAAAGGCTGTGTGCAAAAGATGGAGCTGAGACATCTCGAGGAT
CATCAAGTACATTGTGAATTCGCTCTAGTGATTTGTCCCCAATGCCAACGTTTTTTCCAAAAGT
GCCAGATTAATAAACACATTATCGAGGATTGTCCCAGGAGACAGGTTTCTTGTGTAAACTGTGC
TGTGCCCATGCCGTATGAAGAGAAAGAGATCCACGATCAAAGCTGTCCTCTGGCAAATATCATC
TGTGAATACTGTGGTACAATCCTCATAAGAGAACAGATGCCTAATCATTATGATCTAGACTGCC
CAACAGCTCCAGTCCCCTGCACATTCAGTGTGTTTGGCTGTCACGAAAAGATGCAGAGGAATCA
CTTGGCACGGCACTTGCAAGAGAACACCCAGTTGCACATGAGACTGTTGGCCCAGGCTGTTCAT
AATGTTAACCTCTCTTTGCGGCCATGCGATGCCTCCTCTCCATCCCGGGGATGTCGTCCTGAGG
ACCCAAATTATGAGGAAACGGTCAAACAGTTGGAGGGGCGCCTAGTAAGACAGGACCATCAAAT
CCGGGAGCTGACCGCCAAAATGGAAACGCAGAGCATGCATGTGAGCGAGCTCAAGCGGACCATT
CGAAGCCTCGAGGACAAAGTTGCCGAGATGGAAGCACAGCAGTGTAATGGCATTTACATTTGGA
AGATTGGCAACTTTGGGATGCACTTGAAATCCCAAGAAGAGGAAAGACCTGTGGTCATTCATAG
CCCTGGATTCTACACAGGCAGACCTGGGTACAAGCTGTGCATGCGCCTGCACCTCCAGCTACCG
ACGGCTCAGCGCTGTGCAAACTACATTTCCCTCTTTGTCCACACAATGCAAGGAGAGTATGACA
GCCACCTCCCCTGGCCCTTCCAGGGTACAATACGCCTCACGATCCTTGATCAGTCTGAAGCAGT
AATAAGGCAAAACCACGAAGAGGTCATGGATGCTAAGCCAGAACTGCTTGCCTTTCAGCGGCCC
ACCATCCCACGGAACCCCAAAGGTTTTGGCTATGTGACATTCATGCACCTGGAAGCCTTAAGAC
AGGGAACCTTCATCAAGGATGATACGTTATTAGTGCGCTGTGAAGTCTCTACCCGCTTTGACAT
GGGGGGCCTTCGGAAGGAGGGGTTCCAGCCACGGAGTACTGATGCAGGCGTGTAGCCTCCACTT
ACCTGTGTTCAAAAACTAGGAGCCATATGGAAAAACCGTGCCTTCCGCACCTGGTCCAGTAAAC
AAACGGTGGGAGAGGTGTAAGGCCAGCAGCAGATGTCATCAGCGAGGTCACATTACACTTCTTA
CCGTTAACCAATATCTGGGGCAATTCCCATGGGGACCTCCGTGTCCCCTGTGTCTTCAGAACCT
TAACATTTGAAGGGCCAGACGCTCATCAATTTGTCAGGGAACCTCTTCACTGTGCTTCCATGGG
CTTTTTTGTCCATGTACTTTACTGAAAAAAAAAAAGGCCAGAATTAATGTACTGGAGCTCAATC
GTTTAATACTGGTGCCTTAAACACTTAAAGTGCTTTTAGGGCATGTATTAAACGTGAGGATCAC
CATTGCCTGTGCTGCTGCCAGTGGAAAGGTTACTGCTCTGGTGTTGAGTTCTCATTTAGTTGAC
CCCTGTGAATTTCAGAGGCTTTGAACCATGATCCCTGGAAAGCTGAAGTTCTCATGTACTCCCT
CCTCCATTGACCAGGGACTGGTTTAACCCTTACTTATAAATAGCACGAATGTATTGTCCATTGA
ACACCAAGGGTTTCTCCCCTGCCTTCATTGTTGAAATATGCTCTAGGCAGCATCTTCCCGGTTT
GTAAGACTGTGGTCATGTGGTTGCCAACTGTTCAGTGTGACTGTCATGTAACCTTTCTTGTCTG
TTCAGTATAGCTTGGTTTCCACAGCCTGTCGCACATCTTCTGTTGCTTGCAAACACAAAATCGC
CAGCCTAAACAAGTGATCAGCTCACCAGCCATTAAATGGCATCTCATGGATGATGACAGCAATT
CTTATAGCCAGGAAACTTCAGCCCTCTTAACTACCTTCCAATTTAGCTTAGTTGATTGAAATAA
AACTGATTTCCTCAAGGGGAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
A

hide sequence

RefSeq Acc Id:

XM_039104924 ⟹ XP_038960852

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2	3	87,963,786 - 87,988,316 (+)	NCBI

RefSeq Acc Id:

XM_039104925 ⟹ XP_038960853

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2	3	87,963,544 - 87,988,316 (+)	NCBI

Protein Sequences


Protein RefSeqs	NP_001101224	(Get FASTA)	NCBI Sequence Viewer
	XP_038960852	(Get FASTA)	NCBI Sequence Viewer
	XP_038960853	(Get FASTA)	NCBI Sequence Viewer
GenBank Protein	AAI68921	(Get FASTA)	NCBI Sequence Viewer
	B5DF45	(Get FASTA)	NCBI Sequence Viewer
	EDL79625	(Get FASTA)	NCBI Sequence Viewer

Reference Sequences

RefSeq Acc Id:

NP_001101224 ⟸ NM_001107754

- UniProtKB:

B5DF45 (UniProtKB/Swiss-Prot)

- Sequence:

show sequence

MSLLNCENSCASSQSSSDCCAAMANSCSAAMKDDSVSGCVSTGNLSSSFMEEIQGYDVEFDPPL
ESKYECPICLMALREAVQTPCGHRFCKACITKSIRDAGHKCPVDNEILLENQLFPDNFAKREIL
SLTVKCPNKGCVQKMELRHLEDHQVHCEFALVICPQCQRFFQKCQINKHIIEDCPRRQVSCVNC
AVPMPYEEKEIHDQSCPLANIICEYCGTILIREQMPNHYDLDCPTAPVPCTFSVFGCHEKMQRN
HLARHLQENTQLHMRLLAQAVHNVNLSLRPCDASSPSRGCRPEDPNYEETVKQLEGRLVRQDHQ
IRELTAKMETQSMHVSELKRTIRSLEDKVAEMEAQQCNGIYIWKIGNFGMHLKSQEEERPVVIH
SPGFYTGRPGYKLCMRLHLQLPTAQRCANYISLFVHTMQGEYDSHLPWPFQGTIRLTILDQSEA
VIRQNHEEVMDAKPELLAFQRPTIPRNPKGFGYVTFMHLEALRQGTFIKDDTLLVRCEVSTRFD
MGGLRKEGFQPRSTDAGV

hide sequence

RefSeq Acc Id:

ENSRNOP00000006148 ⟸ ENSRNOT00000006148

RefSeq Acc Id:	XP_038960853 ⟸ XM_039104925
- Peptide Label:	isoform X2

RefSeq Acc Id:	XP_038960852 ⟸ XM_039104924
- Peptide Label:	isoform X1

Protein Domains

MATH

Transcriptome

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

Promoters

RGD ID:

13692242

Promoter ID:

EPDNEW_R2767

Type:

multiple initiation site

Name:

Traf6_1

Description:

TNF receptor associated factor 6

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	3	91,252,805 - 91,252,865	EPDNEW

Strain Variation

Strain Sequence Variants (Rnor 6.0)

ACI/EurMcwi (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)

ACI/EurMcwi (RGD)

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CSV

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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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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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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

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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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CSV

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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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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)

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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)

FHH/EurMcwi (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

FHL/EurMcwi (MCW)

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CSV

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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

Printer

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

GH/OmrMcwi (MCW)

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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)

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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/NCrlBR (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

LH/MavRrrc (RGD)

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CSV

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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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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)

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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

M520/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

MHS/Gib (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

MNS/Gib (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

MR/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

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:1306853	AgrOrtholog
Ensembl Genes	ENSRNOG00000004639	Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Protein	ENSRNOP00000006148	ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript	ENSRNOT00000006148	ENTREZGENE, UniProtKB/Swiss-Prot
Gene3D-CATH	2.60.210.10	UniProtKB/Swiss-Prot
	3.30.40.10	UniProtKB/Swiss-Prot
InterPro	MATH/TRAF_dom	UniProtKB/Swiss-Prot
	TNF_rcpt--assoc_TRAF	UniProtKB/Swiss-Prot
	TNF_rcpt-assoc_TRAF	UniProtKB/Swiss-Prot
	TRAF-like	UniProtKB/Swiss-Prot
	TRAF6	UniProtKB/Swiss-Prot
	TRAF6_MATH	UniProtKB/Swiss-Prot
	TRAF6_Z2	UniProtKB/Swiss-Prot
	Znf_RING	UniProtKB/Swiss-Prot
	Znf_RING/FYVE/PHD	UniProtKB/Swiss-Prot
	Znf_RING_CS	UniProtKB/Swiss-Prot
	Znf_TRAF	UniProtKB/Swiss-Prot
KEGG Report	rno:311245	UniProtKB/Swiss-Prot
NCBI Gene	311245	ENTREZGENE
PANTHER	PTHR10131	UniProtKB/Swiss-Prot
	PTHR10131:SF131	UniProtKB/Swiss-Prot
Pfam	TRAF6_Z2	UniProtKB/Swiss-Prot
	zf-TRAF	UniProtKB/Swiss-Prot
PhenoGen	Traf6	PhenoGen
PIRSF	TRAF	UniProtKB/Swiss-Prot
PROSITE	MATH	UniProtKB/Swiss-Prot
	ZF_RING_1	UniProtKB/Swiss-Prot
	ZF_RING_2	UniProtKB/Swiss-Prot
	ZF_TRAF	UniProtKB/Swiss-Prot
SMART	MATH	UniProtKB/Swiss-Prot
	RING	UniProtKB/Swiss-Prot
Superfamily-SCOP	SSF49599	UniProtKB/Swiss-Prot
UniProt	B5DF45	ENTREZGENE, UniProtKB/Swiss-Prot

Nomenclature History

Date	Current Symbol	Current Name	Previous Symbol	Previous Name	Description	Reference	Status
2015-11-25	Traf6	TNF receptor associated factor 6	Traf6	TNF receptor-associated factor 6, E3 ubiquitin protein ligase	Nomenclature updated to reflect human and mouse nomenclature	1299863	APPROVED
2012-10-16	Traf6	TNF receptor-associated factor 6, E3 ubiquitin protein ligase	Traf6	Tnf receptor-associated factor 6	Nomenclature updated to reflect human and mouse nomenclature	1299863	APPROVED
2008-04-30	Traf6	Tnf receptor-associated factor 6	Traf6_predicted	Tnf receptor-associated factor 6 (predicted)	'predicted' is removed	2292626	APPROVED
2005-01-12	Traf6_predicted	Tnf receptor-associated factor 6 (predicted)			Symbol and Name status set to approved	70820	APPROVED

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

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

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

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

Imported Disease Annotations - ClinVar

Imported Disease Annotations - CTD

Imported Disease Annotations - MGI

RGD Manual Annotations

Imported Annotations - KEGG (archival)

Imported Annotations - PID (archival)

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Imported Disease Annotations - ClinVar

Imported Disease Annotations - CTD

Imported Disease Annotations - MGI

RGD Manual Annotations

Imported Annotations - KEGG (archival)

Imported Annotations - PID (archival)