Tnfsf4 (TNF superfamily member 4)

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Gene: Tnfsf4 (TNF superfamily member 4) Rattus norvegicus

Analyze

Symbol:

Tnfsf4

Name:

TNF superfamily member 4

RGD ID:

619816

Description:

Exhibits tumor necrosis factor receptor superfamily binding activity. Involved in T cell proliferation; positive regulation of activated T cell proliferation; and positive regulation of interleukin-2 production. Localizes to cell surface. Human ortholog(s) of this gene implicated in myocardial infarction. Orthologous to human TNFSF4 (TNF superfamily member 4); PARTICIPATES IN cytokine mediated signaling pathway; INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; 2,4,6-trinitrobenzenesulfonic acid; 6-propyl-2-thiouracil.

Type:

protein-coding

RefSeq Status:

PROVISIONAL

Also known as:

OX40 ligand; Ox40l; Tnlg2b; tumor necrosis factor (ligand) superfamily, member 4; tumor necrosis factor ligand 2b; tumor necrosis factor ligand superfamily member 4; tumor necrosis factor superfamily member 4

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):	TNFSF4 (TNF superfamily member 4)	HGNC	EggNOG, Ensembl, HomoloGene, Inparanoid, NCBI, OMA, OrthoDB, OrthoMCL, Panther, PhylomeDB, Treefam
Mus musculus (house mouse):	Tnfsf4 (tumor necrosis factor (ligand) superfamily, member 4)	HGNC	Treefam, EggNOG, OrthoMCL, NCBI, OMA, HomoloGene, Inparanoid, Panther, PhylomeDB, OrthoDB, Ensembl
Chinchilla lanigera (long-tailed chinchilla):	Tnfsf4 (TNF superfamily member 4)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Pan paniscus (bonobo/pygmy chimpanzee):	TNFSF4 (TNF superfamily member 4)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Canis lupus familiaris (dog):	TNFSF4 (TNF superfamily member 4)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Ictidomys tridecemlineatus (thirteen-lined ground squirrel):	Tnfsf4 (TNF superfamily member 4)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Sus scrofa (pig):	TNFSF4 (TNF superfamily member 4)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Chlorocebus sabaeus (African green monkey):	TNFSF4 (TNF superfamily member 4)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Heterocephalus glaber (naked mole-rat):	Tnfsf4 (TNF superfamily member 4)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Alliance orthologs ³
Mus musculus (house mouse):	Tnfsf4 (tumor necrosis factor (ligand) superfamily, member 4)	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|TreeFam)
Homo sapiens (human):	TNFSF4 (TNF superfamily member 4)	Alliance	DIOPT (Ensembl Compara\|HGNC\|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	13	73,723,329 - 73,746,809 (+)	NCBI
Rnor_6.0 Ensembl	13	79,269,973 - 79,293,778 (+)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_6.0	13	79,269,973 - 79,293,775 (+)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_5.0	13	84,166,838 - 84,190,566 (+)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	13	77,026,337 - 77,050,223 (+)	NCBI	RGSC3.4		rn4	RGSC3.4
RGSC_v3.1	13	77,040,524 - 77,064,407 (+)	NCBI
Celera	13	73,499,753 - 73,523,609 (+)	NCBI		Celera
Cytogenetic Map	13	q22	NCBI

JBrowse:

View Region in Genome Browser (JBrowse)

Model

Annotation Click to see Annotation Detail View

Disease Annotations Click to see Annotation Detail View

1q24 Deletion Syndrome (ISO)

cervical squamous cell carcinoma (ISO)

dilated cardiomyopathy (ISO)

leishmaniasis (ISO)

myocardial infarction (ISO)

myocarditis (ISO)

primary pulmonary hypertension (ISS)

systemic lupus erythematosus (ISO)

type 1 diabetes mellitus (ISS)

viral infectious disease (ISO)

Gene-Chemical Interaction Annotations Click to see Annotation Detail View

(-)-demecolcine (ISO)

(R)-mevalonic acid (ISO)

1D-myo-inositol 1,4,5-trisphosphate (ISO)

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

2,4,6-trinitrobenzenesulfonic acid (EXP)

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

6-propyl-2-thiouracil (EXP)

8-Br-cAMP (ISO)

aflatoxin B1 (ISO)

all-trans-retinoic acid (ISO)

ammonium chloride (EXP)

benzo[a]pyrene (ISO)

benzo[b]fluoranthene (ISO)

bisphenol A (EXP,ISO)

Bisphenol B (ISO)

butanal (ISO)

C60 fullerene (EXP)

caffeine (ISO)

calcipotriol (ISO)

carbamazepine (ISO)

carbon monoxide (ISO)

carbon nanotube (EXP)

ceric oxide (EXP)

cobalt dichloride (ISO)

copper(II) sulfate (ISO)

cyclosporin A (ISO)

dexamethasone (ISO)

disodium selenite (ISO)

dorsomorphin (ISO)

ethanol (EXP)

ethyl methanesulfonate (ISO)

flavonoids (EXP)

formaldehyde (ISO)

fragrance (ISO)

genistein (ISO)

graphite (EXP)

hydrogen peroxide (ISO)

isoflurane (EXP)

leflunomide (ISO)

lipopolysaccharide (ISO)

methotrexate (ISO)

methyl methanesulfonate (ISO)

N-acetyl-L-cysteine (ISO)

nickel atom (ISO)

O-methyleugenol (ISO)

p-menthan-3-ol (ISO)

paraquat (ISO)

pentobarbital (EXP)

quercetin (ISO)

SB 431542 (ISO)

simvastatin (ISO)

sodium arsenite (ISO)

sulfur dioxide (ISO)

tacrine (EXP)

testosterone (EXP)

thapsigargin (ISO)

tris(2-butoxyethyl) phosphate (ISO)

tunicamycin (ISO)

urethane (ISO)

valproic acid (ISO)

vinclozolin (EXP)

vincristine (ISO)

zinc atom (ISO)

zinc(0) (ISO)

Gene Ontology Annotations Click to see Annotation Detail View

Biological Process

acute inflammatory response (ISO)

CD4-positive, alpha-beta T cell costimulation (ISO)

cellular response to lipopolysaccharide (ISO)

cellular response to nitrogen dioxide (ISO)

cellular response to prostaglandin E stimulus (ISO)

cholesterol metabolic process (ISO)

cytokine production (IMP)

defense response to nematode (ISO)

immune response (IEA)

inflammatory response (IBA,ISO)

memory T cell activation (ISO)

negative regulation of cytokine production (ISO)

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

negative regulation of interferon-gamma production (ISO)

negative regulation of interleukin-17 production (ISO)

negative regulation of regulatory T cell differentiation (ISO)

negative regulation of T-helper 1 cell differentiation (ISO)

negative regulation of transcription, DNA-templated (ISO)

positive regulation of activated T cell proliferation (IDA)

positive regulation of alpha-beta T cell proliferation (ISO)

positive regulation of B cell activation (ISO)

positive regulation of CD4-positive, alpha-beta T cell costimulation (ISO)

positive regulation of CD4-positive, alpha-beta T cell differentiation (ISO)

positive regulation of chemokine production (IEA,ISO)

positive regulation of cytokine production (IBA)

positive regulation of immunoglobulin mediated immune response (ISO)

positive regulation of immunoglobulin production (ISO)

positive regulation of inflammatory response (ISO)

positive regulation of interferon-gamma production (ISO)

positive regulation of interleukin-10 production (ISO)

positive regulation of interleukin-12 production (ISO)

positive regulation of interleukin-13 production (ISO)

positive regulation of interleukin-2 production (IDA)

positive regulation of interleukin-4 production (ISO)

positive regulation of interleukin-4-dependent isotype switching to IgE isotypes (ISO)

positive regulation of interleukin-6 production (ISO)

positive regulation of memory T cell activation (ISO)

positive regulation of memory T cell differentiation (ISO)

positive regulation of T cell costimulation (ISO)

positive regulation of T cell cytokine production (ISO)

positive regulation of T cell proliferation (IBA)

positive regulation of T-helper 2 cell activation (ISO)

positive regulation of T-helper 2 cell differentiation (ISO)

positive regulation of type 2 immune response (ISO)

regulation of adaptive immune response (ISO)

regulation of inflammatory response (ISO)

response to nitrogen dioxide (ISO)

response to virus (ISO)

signal transduction (IEA)

T cell proliferation (IMP)

T-helper 2 cell activation (ISO)

Cellular Component

cell surface (IDA,ISO)

extracellular space (IBA,ISO)

integral component of membrane (IEA)

Molecular Function

cytokine activity (IEA)

protein binding (ISO)

tumor necrosis factor receptor binding (ISO)

tumor necrosis factor receptor superfamily binding (IBA,IMP,IPI,ISO)

Molecular Pathway Annotations Click to see Annotation Detail View

cytokine mediated signaling pathway (IEA)

Phenotype Annotations Click to see Annotation Detail View

Mammalian Phenotype

abnormal response to transplant (IDA)

References

References - curated


1.	Akiba H, etal., Biochem Biophys Res Commun 1998 Oct 9;251(1):131-6.
2.	Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
3.	Hammer P and Uhlman TM, Soc Rehabil Rec 1975 Jul-Aug;2(6):28-32.
4.	MGD data from the GO Consortium
5.	NCBI rat LocusLink and RefSeq merged data July 26, 2002
6.	OMIM Disease Annotation Pipeline
7.	Pipeline to import KEGG annotations from KEGG into RGD
8.	RGD automated data pipeline
9.	RGD automated import pipeline for gene-chemical interactions
10.	Satake Y, etal., Biochem Biophys Res Commun. 2000 Apr 21;270(3):1041-8.
11.	Wang X, etal., Nat Genet. 2005 Apr;37(4):365-72. Epub 2005 Mar 6.
12.	Yuan X, etal., J Immunol. 2003 Mar 15;170(6):2949-55.
13.	Zhao M, etal., Virol J. 2017 Jan 13;14(1):5. doi: 10.1186/s12985-016-0670-8.

Additional References at PubMed

PMID:3473481	PMID:7749983	PMID:9670042	PMID:12355440	PMID:12496423	PMID:14635034	PMID:15376196	PMID:16670306	PMID:17166734	PMID:17785785	PMID:18354165	PMID:18397322
PMID:18501882	PMID:18713990	PMID:19029446	PMID:20639485	PMID:20659336	PMID:20844189	PMID:20871162	PMID:26646413

Genomics

Comparative Map Data

Tnfsf4
(Rattus norvegicus - Norway rat)

Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
mRatBN7.2	13	73,723,329 - 73,746,809 (+)	NCBI
Rnor_6.0 Ensembl	13	79,269,973 - 79,293,778 (+)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_6.0	13	79,269,973 - 79,293,775 (+)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_5.0	13	84,166,838 - 84,190,566 (+)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	13	77,026,337 - 77,050,223 (+)	NCBI	RGSC3.4		rn4	RGSC3.4
RGSC_v3.1	13	77,040,524 - 77,064,407 (+)	NCBI
Celera	13	73,499,753 - 73,523,609 (+)	NCBI		Celera
Cytogenetic Map	13	q22	NCBI

TNFSF4
(Homo sapiens - human)

Human Assembly	Chr	Position (strand)	Source	Genome Browsers
Human Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCh38.p13 Ensembl	1	173,183,731 - 173,207,331 (-)	Ensembl	GRCh38		hg38	GRCh38
GRCh38	1	173,183,729 - 173,462,208 (-)	NCBI	GRCh38	GRCh38	hg38	GRCh38
GRCh37	1	173,152,870 - 173,176,470 (-)	NCBI	GRCh37	GRCh37	hg19	GRCh37
Build 36	1	171,419,493 - 171,443,094 (-)	NCBI	NCBI36		hg18	NCBI36
Build 34	1	169,884,527 - 169,908,128	NCBI
Celera	1	146,262,332 - 146,285,933 (-)	NCBI
Cytogenetic Map	1	q25.1	NCBI
HuRef	1	144,377,608 - 144,401,209 (-)	NCBI		HuRef
CHM1_1	1	174,575,344 - 174,598,926 (-)	NCBI		CHM1_1

Tnfsf4
(Mus musculus - house mouse)

Mouse Assembly	Chr	Position (strand)	Source	Genome Browsers
Mouse Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCm39	1	161,223,009 - 161,245,777 (+)	NCBI	GRCm39		mm39
GRCm39 Ensembl	1	161,222,980 - 161,245,981 (+)	Ensembl
GRCm38	1	161,395,438 - 161,418,206 (+)	NCBI	GRCm38	GRCm38	mm10	GRCm38
GRCm38.p6 Ensembl	1	161,395,409 - 161,418,410 (+)	Ensembl	GRCm38		mm10	GRCm38
MGSCv37	1	163,325,569 - 163,348,337 (+)	NCBI	GRCm37		mm9	NCBIm37
MGSCv36	1	163,232,135 - 163,254,883 (+)	NCBI			mm8
Celera	1	163,843,815 - 163,866,564 (+)	NCBI		Celera
Cytogenetic Map	1	H2.1	NCBI
cM Map	1	69.75	NCBI

Tnfsf4
(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_004955406	13,477,077 - 13,493,309 (-)	Ensembl	ChiLan1.0
ChiLan1.0	NW_004955406	13,477,077 - 13,493,309 (-)	NCBI	ChiLan1.0	ChiLan1.0

TNFSF4
(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	1	152,391,450 - 152,699,026 (-)	NCBI	panpan1.1	PanPan1.1	panPan2
PanPan1.1 Ensembl	1	152,391,450 - 152,415,845 (-)	Ensembl	panpan1.1		panPan2
Mhudiblu_PPA_v0	1	148,684,689 - 148,989,775 (-)	NCBI	Mhudiblu_PPA_v0		panPan3

TNFSF4
(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	7	25,883,251 - 25,906,892 (+)	Ensembl	CanFam3.1		canFam3	CanFam3.1
CanFam3.1	7	25,883,297 - 25,909,608 (+)	NCBI	CanFam3.1	CanFam3.1	canFam3	CanFam3.1

Tnfsf4
(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_004936481	14,391,359 - 14,409,514 (+)	NCBI	SpeTri2.0	SpeTri2.0		SpeTri2.0

TNFSF4
(Sus scrofa - pig)

Pig Assembly	Chr	Position (strand)	Source	Genome Browsers
Pig Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
Sscrofa11.1 Ensembl	9	115,550,567 - 115,857,448 (-)	Ensembl	Sscrofa11.1		susScr11	Sscrofa11.1
Sscrofa11.1	9	115,535,185 - 115,857,457 (-)	NCBI	Sscrofa11.1	Sscrofa11.1	susScr11	Sscrofa11.1
Sscrofa10.2	9	127,042,208 - 127,049,271 (+)	NCBI	Sscrofa10.2	Sscrofa10.2	susScr3

TNFSF4
(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	25	55,714,291 - 55,998,009 (+)	NCBI
ChlSab1.1 Ensembl	25	55,974,691 - 55,997,374 (+)	Ensembl

Tnfsf4
(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_004624771	8,580,489 - 8,599,735 (+)	NCBI

QTLs in Region (Rnor_6.0)

The following QTLs overlap with this region.

RGD ID	Symbol	Name	LOD	P Value	Trait	Sub Trait	Chr	Start	Stop	Species
1354666	Bp244	Blood pressure QTL 244	4.9		arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	13	1	107975663	Rat
1354666	Bp244	Blood pressure QTL 244	4.9		arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	13	1	107975663	Rat
1354666	Bp244	Blood pressure QTL 244	4.9		arterial blood pressure trait (VT:2000000)	diastolic blood pressure (CMO:0000005)	13	1	107975663	Rat
1581554	Pur11	Proteinuria QTL 11			urine albumin amount (VT:0002871)	urine albumin excretion rate (CMO:0000757)	13	9016906	82995569	Rat
1581573	Uae36	Urinary albumin excretion QTL 36			urine albumin amount (VT:0002871)	urine albumin excretion rate (CMO:0000757)	13	9016906	82995569	Rat
1581570	Eae17	Experimental allergic encephalomyelitis QTL 17	4.1		nervous system integrity trait (VT:0010566)	experimental autoimmune encephalomyelitis incidence/prevalence measurement (CMO:0001046)	13	12193394	108478121	Rat
7207885	Glom27	Glomerulus QTL 27	3.9		kidney glomerulus integrity trait (VT:0010546)	kidney crescentic glomeruli count to kidney normal glomeruli count ratio (CMO:0002139)	13	24502279	108770533	Rat
1354621	Rf47	Renal function QTL 47	3.7		kidney renin amount (VT:0010559)	kidney renin level (CMO:0002166)	13	35301263	107975663	Rat
70181	BpQTLcluster11	Blood pressure QTL cluster 11	6.922		arterial blood pressure trait (VT:2000000)	absolute change in mean arterial blood pressure (CMO:0000533)	13	36147533	99968921	Rat
70181	BpQTLcluster11	Blood pressure QTL cluster 11	6.922		arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	13	36147533	99968921	Rat
70181	BpQTLcluster11	Blood pressure QTL cluster 11	6.922		arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	13	36147533	99968921	Rat
70181	BpQTLcluster11	Blood pressure QTL cluster 11	6.922		arterial blood pressure trait (VT:2000000)	diastolic blood pressure (CMO:0000005)	13	36147533	99968921	Rat
2303563	Bw89	Body weight QTL 89	6		body mass (VT:0001259)	body weight (CMO:0000012)	13	37346348	82346348	Rat
61340	Bp25	Blood pressure QTL 25	4.2	0.004	arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	13	39372927	84372927	Rat
10755495	Bp387	Blood pressure QTL 387	3.78		arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	13	39501300	93652524	Rat
4889861	Pur29	Proteinuria QTL 29	13.8	0.005	total urine protein amount (VT:0000032)	urine total protein excretion rate (CMO:0000756)	13	42310744	86833540	Rat
1331750	Bp220	Blood pressure QTL 220	2.98		arterial blood pressure trait (VT:2000000)	diastolic blood pressure (CMO:0000005)	13	42310744	87310744	Rat
70220	Bp55	Blood pressure QTL 55	5.75		arterial blood pressure trait (VT:2000000)	blood pressure measurement (CMO:0000003)	13	42508345	87508345	Rat
61349	Bp31	Blood pressure QTL 31	5.75		arterial blood pressure trait (VT:2000000)	blood pressure measurement (CMO:0000003)	13	42508345	87508345	Rat
1549897	Stresp12	Stress response QTL 12	3.35		stress-related behavior trait (VT:0010451)	number of approaches toward negative stimulus before onset of defensive burying response (CMO:0001960)	13	43575717	88575717	Rat
619615	Bp80	Blood pressure QTL 80		0.0354	arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	13	45676629	90676629	Rat
12879441	Bp396	Blood pressure QTL 396			arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	13	51080989	96080989	Rat
1298066	Bp159	Blood pressure QTL 159		0.004	arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	13	51569248	96569248	Rat
71119	Thym2	Thymus enlargement QTL 2	3.8		thymus mass (VT:0004954)	thymus weight to body weight ratio (CMO:0000612)	13	51577824	90675199	Rat
1641901	Alcrsp6	Alcohol response QTL 6			response to alcohol trait (VT:0010489)	duration of loss of righting reflex (CMO:0002289)	13	57903612	102903612	Rat
1354655	Bp241	Blood pressure QTL 241	3.9		arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	13	62975663	107975663	Rat
724564	Uae11	Urinary albumin excretion QTL 11	5.7		urine albumin amount (VT:0002871)	urine albumin level (CMO:0000130)	13	64501351	82995671	Rat
738026	Lnnr5	Liver neoplastic nodule remodeling QTL 5	3.29		liver integrity trait (VT:0010547)	liver remodeling tumorous lesion number (CMO:0001461)	13	65008245	91629354	Rat
12879475	Bp400	Blood pressure QTL 400			arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	13	66971778	111971778	Rat
2293687	Bss26	Bone structure and strength QTL 26	4.6	0.0001	femur morphology trait (VT:0000559)	femur cross-sectional area (CMO:0001661)	13	71230858	114033958	Rat
2293702	Bss34	Bone structure and strength QTL 34	4.61	0.0001	femur strength trait (VT:0010010)	femur midshaft polar moment of inertia (CMO:0001669)	13	71230858	114033958	Rat
7387280	Uae43	Urinary albumin excretion QTL 43	5.69	0.4174	urine albumin amount (VT:0002871)	urine albumin excretion rate (CMO:0000757)	13	72583716	114033958	Rat
8655951	Rf63	Renal function QTL 63	12.2		blood urea nitrogen amount (VT:0005265)	plasma urea nitrogen level (CMO:0000586)	13	74568378	82995671	Rat
1300166	Kidm6	Kidney mass QTL 6	3.93		kidney mass (VT:0002707)	single kidney wet weight to body weight ratio (CMO:0000622)	13	74568378	92916783	Rat
1331783	Bp221	Blood pressure QTL 221	3.72886		arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	13	74568378	92916783	Rat
8655945	Rf61	Renal function QTL 61	3.6		blood creatinine amount (VT:0005328)	creatinine clearance (CMO:0000765)	13	74568378	92916783	Rat
10755455	Coatc13	Coat color QTL 13		0	coat/hair pigmentation trait (VT:0010463)	pigmented ventral coat/hair area to total ventral coat/hair area ratio (CMO:0001812)	7	77694986	114033958	Rat

miRNA Target Status

Predicted Target Of

	Summary Value
Count of predictions:	149
Count of miRNA genes:	110
Interacting mature miRNAs:	128
Transcripts:	ENSRNOT00000003969
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											1
Low			6		6				11		4	8
Below cutoff	3	13	15	12	13	12	6	6	55	28	26	3	6

View RNA-SEQ Expression Data

Sequence

Nucleotide Sequences


RefSeq Transcripts	NM_053552	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
GenBank Nucleotide	AF037067	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	CH473958	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	JACYVU010000244	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	LN874409	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles

Reference Sequences

RefSeq Acc Id:

ENSRNOT00000003969 ⟹ ENSRNOP00000003969

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
Rnor_6.0 Ensembl	13	79,269,973 - 79,293,778 (+)	Ensembl

RefSeq Acc Id:

NM_053552 ⟹ NP_446004

RefSeq Status:

PROVISIONAL

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2	13	73,723,329 - 73,746,809 (+)	NCBI
Rnor_6.0	13	79,269,973 - 79,293,775 (+)	NCBI
Rnor_5.0	13	84,166,838 - 84,190,566 (+)	NCBI
RGSC_v3.4	13	77,026,337 - 77,050,223 (+)	RGD
Celera	13	73,499,753 - 73,523,609 (+)	RGD

Sequence:

show sequence

GGCACGAGCTTCAATTGCCTTTTGTCTCCGGTTCTGGGACCTTTGTCTTCTGACCCACAGGCTT
GGCTTCACCCTTGTCTTCTCCTTTGTGGTGAAGAGCAGCCTTCCCCAGGCTCCCCTTTGCCACG
GCTGTGCCTTCTCTGCACCCTGACTTCGAGCATGGAAGGGGAAGGGGTTCAACCCCCGGATGAG
AATCTGGAAAATGGATCAAGGCCAAGGTTCAAGTGGAAGAAGGTGCTAAGGCTGGTGGTCTCTG
GGATTAAGGCAGCAGGGCTGCTCCTGTGCGTCGTCTATGTCTGCCTGCAATTCTCTTCATCTCC
GGCGAAGGACTCTCCAATCCAAAGACTCAGAGCACCAGTTACCGGATGTGAGGGGGGAAGACTA
TTCATTGGCACATCCAAGAATGAGTATGAAACCATGGAGGTGCAGAACAATTCGGTCATCATCA
ACTGCGATGGGCTTTATCTCATCCACCTGAAGGGCTCCTTTTTCCAGGAGGTCAAGATCAACCT
TCATTTCCGGAAGGATCGCAGTCCAATCTTTGTGCCAATGCTGAACAATGGTCAAAGGGTTGTT
TTCACTGTGGTGACCTCTTTGGCTTTTAAAGACGAAGTTTACTTGACTGTAAATGCTTCTGATA
CTCTCTGTGAACACCTCCAGATAAATGATGGGGAACTGATTATTGTCCAGCTAACTCCTAATGG
ATACTGTGCTCCTGAAAGACCTTATAGCAGCACTGTGAACCAAGTACCACTGTGAATTCCACTC
TGAGGGTGGACAGGACACAGGTTCTTTCTTGCGAGAGATGAGTCCATCCTGCTCAACTCCATGA
CATGTGATGGAATGCAGATCCCACCCCACTTCCTCACTCAGGGATATTTAAGTCGTGTCTTACA
TAACAGTTGACCTCTCATTCCCAGGATTGCCTAGAGTCTGCTAAGAGCTCTACAGGGAATGAAA
AAAATAAATGTCTCTTCAAGATGCATTGTTTCAGTTGGTCAGAAGATCATTGTAATAAACATCT
GACACTGAAAATGGGGCTTGATTATTATCTTCTAGAATTTTGACATTGTCAAAAGAAAGAACTA
AGAATGGGACTGTGAGTCTGGAAAGGGTGGTGTCTACCAGCCAGTAGGAGCTGGAGTGCTCTAT
TCAAGGTTAAGGTGATAGACAACTGTTTAGGTGATGAGGTGATGTATACTGTGAGCTTCTCCCA
TTATCTCTCTTCTTTCCTGGCCTCCAAATATACATAATAGAAAACGTCCTTCAAAGAGCTATCT
AGGATGATACCACCGAGTACTGCATCAGTGATGTAAAGAAAACCAGTAGAGCTTTGTTTGTTAT
ACAGAGCATAGGAGAGATTTTACCCCAACAGTTATTTTTATAATCTAGGATAATAGTGAACTGA
ATGTCGCAGGATAAAGGTCAAGAAGGGTTTTGACAGTCTAAGCAAGACTGTTTTCCAAGTTCTC
TTTTCCAATATTTTATGTAAATCTTTGATAATTTAAAAATTTTTAGTATTTTTTGGCCATTTTC
AATAGAAAATATAGCTCAAACTATTTCCAGATGACTTCATATCCCCATAAGGATTATATTGTGT
TACAATACAGTGCGTATGTCTTGAACCTCCAGAAAGTCTGAAGGCTACTAATCCTTATACTAAG
TGAATTCAGTTACATTTGGAATTTTTTGTCTGATAGTATATTTTCTCTTATGCATCTATCTATA
CTTCTATGTACCCTCTGTTTTAATCTGTTATTAAAAGAAGCCAAATAAAAATGCTACATAAAAA
AAAAAAAAAAAA

hide sequence

Protein Sequences


Protein RefSeqs	NP_446004	(Get FASTA)	NCBI Sequence Viewer
GenBank Protein	AAC67236	(Get FASTA)	NCBI Sequence Viewer
	CTQ86174	(Get FASTA)	NCBI Sequence Viewer
	EDM09415	(Get FASTA)	NCBI Sequence Viewer
	Q9Z2P3	(Get FASTA)	NCBI Sequence Viewer

Reference Sequences

RefSeq Acc Id:

NP_446004 ⟸ NM_053552

- UniProtKB:

Q9Z2P3 (UniProtKB/Swiss-Prot), A0A0U5JAD2 (UniProtKB/TrEMBL)

- Sequence:

show sequence

MEGEGVQPPDENLENGSRPRFKWKKVLRLVVSGIKAAGLLLCVVYVCLQFSSSPAKDSPIQRLR
APVTGCEGGRLFIGTSKNEYETMEVQNNSVIINCDGLYLIHLKGSFFQEVKINLHFRKDRSPIF
VPMLNNGQRVVFTVVTSLAFKDEVYLTVNASDTLCEHLQINDGELIIVQLTPNGYCAPERPYSS
TVNQVPL

hide sequence

RefSeq Acc Id:

ENSRNOP00000003969 ⟸ ENSRNOT00000003969

Protein Domains

TNF_2

Transcriptome

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

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:619816	AgrOrtholog
Ensembl Genes	ENSRNOG00000002968	Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Protein	ENSRNOP00000003969	ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript	ENSRNOT00000003969	ENTREZGENE, UniProtKB/Swiss-Prot
Gene3D-CATH	2.60.120.40	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
InterPro	TNF_CS	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	TNF_dom	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	TNFSF4	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	Tumour_necrosis_fac-like_dom	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report	rno:89814	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
NCBI Gene	89814	ENTREZGENE
PANTHER	PTHR17534	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen	Tnfsf4	PhenoGen
PROSITE	TNF_1	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
SMART	TNF	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP	SSF49842	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt	A0A0U5JAD2	ENTREZGENE, UniProtKB/TrEMBL
	Q9Z2P3	ENTREZGENE, UniProtKB/Swiss-Prot

Nomenclature History

Date	Current Symbol	Current Name	Previous Symbol	Previous Name	Description	Reference	Status
2017-03-21	Tnfsf4	TNF superfamily member 4	Tnfsf4	tumor necrosis factor superfamily member 4	Nomenclature updated to reflect human and mouse nomenclature	1299863	APPROVED
2015-11-25	Tnfsf4	tumor necrosis factor superfamily member 4	Tnfsf4	tumor necrosis factor (ligand) superfamily, member 4	Nomenclature updated to reflect human and mouse nomenclature	1299863	APPROVED
2005-01-20	Tnfsf4	tumor necrosis factor (ligand) superfamily, member 4			Symbol and Name status set to approved	1299863	APPROVED
2002-08-07	Tnfsf4	tumor necrosis factor (ligand) superfamily, member 4			Symbol and Name status set to provisional	70820	PROVISIONAL

RGD Curation Notes

Note Type	Note	Reference
gene_cellular_localization	localized to the cell surface	634509
gene_protein	199 amino acids	634509

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

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

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

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

Imported Disease Annotations - ClinVar

Imported Disease Annotations - CTD

Imported Disease Annotations - MGI

Imported Disease Annotations - OMIM

Imported Annotations - KEGG (archival)