Tnfsf4 (TNF superfamily member 4)

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Gene: Tnfsf4 (TNF superfamily member 4) Rattus norvegicus

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Symbol:

Tnfsf4

Name:

TNF superfamily member 4

RGD ID:

619816

Description:

Enables 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. Located in 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

Previously 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

Alliance Orthologs

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)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
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 (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\|SonicParanoid)
Homo sapiens (human):	TNFSF4 (TNF superfamily member 4)	Alliance	DIOPT (Ensembl Compara\|HGNC\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)

Latest Assembly:

mRatBN7.2 - mRatBN7.2 Assembly

Position:

Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCr8	13	76,256,654 - 76,280,133 (+)	NCBI		GRCr8
mRatBN7.2	13	73,723,329 - 73,746,809 (+)	NCBI	mRatBN7.2	mRatBN7.2
mRatBN7.2 Ensembl	13	73,723,329 - 73,746,788 (+)	Ensembl		mRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx	13	76,302,498 - 76,326,020 (+)	NCBI	Rnor_SHR	UTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0	13	77,600,036 - 77,623,530 (+)	NCBI	Rnor_SHRSP	UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0	13	74,859,914 - 74,883,412 (+)	NCBI	Rnor_WKY	UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0	13	79,269,973 - 79,293,775 (+)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_6.0 Ensembl	13	79,269,973 - 79,293,778 (+)	Ensembl	Rnor6.0		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	RGSC_v3.4	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)

antithrombin III deficiency (ISO)

autoimmune lymphoproliferative syndrome (ISO)

cervical squamous cell carcinoma (ISO)

dilated cardiomyopathy (ISO)

gastrointestinal stromal tumor (ISO)

leishmaniasis (ISO)

myocardial infarction (ISO)

myocarditis (ISO)

parathyroid carcinoma (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)

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

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

2,4,6-trinitrobenzenesulfonic acid (EXP)

2-palmitoylglycerol (ISO)

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

6-propyl-2-thiouracil (EXP)

8-Br-cAMP (ISO)

aflatoxin B1 (ISO)

all-trans-retinoic acid (ISO)

alpha-amanitin (ISO)

aluminium hydroxide (ISO)

ammonium chloride (EXP)

amphotericin B (ISO)

benzo[a]pyrene (ISO)

benzo[b]fluoranthene (ISO)

bis(2-chloroethyl) sulfide (ISO)

bisphenol A (EXP,ISO)

Bisphenol B (ISO)

bleomycin A2 (ISO)

butanal (ISO)

C60 fullerene (EXP)

cadmium dichloride (ISO)

caffeine (ISO)

calcipotriol (ISO)

carbamazepine (ISO)

carbon monoxide (ISO)

carbon nanotube (EXP)

ceric oxide (EXP)

CGP 52608 (ISO)

cobalt dichloride (ISO)

copper(II) sulfate (ISO)

cyclosporin A (ISO)

dexamethasone (ISO)

Dibutyl phosphate (ISO)

disodium selenite (ISO)

dorsomorphin (ISO)

epoxiconazole (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)

mevalonic acid (ISO)

N,N-diethyl-m-toluamide (EXP)

N-acetyl-L-cysteine (ISO)

nickel atom (ISO)

niclosamide (ISO)

Nonylphenol (ISO)

O-methyleugenol (ISO)

p-menthan-3-ol (ISO)

paraquat (ISO)

pentobarbital (EXP)

perfluorooctanoic acid (ISO)

permethrin (EXP)

quercetin (ISO)

SB 431542 (ISO)

simvastatin (ISO)

sodium arsenite (ISO)

sulfur dioxide (ISO)

tacrine (EXP)

testosterone (EXP)

thapsigargin (ISO)

trichloroethene (EXP)

triphenyl phosphate (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 DNA-templated transcription (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 type II interferon production (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 (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 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)

positive regulation of type II interferon production (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)

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

#	Reference Title	Reference Citation
1.	Identification of rat OX40 ligand by molecular cloning.	Akiba H, etal., Biochem Biophys Res Commun 1998 Oct 9;251(1):131-6.
2.	Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium.	Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
3.	Revenue sharing: source of more program funds for the disabled and others.	Hammer P and Uhlman TM, Soc Rehabil Rec 1975 Jul-Aug;2(6):28-32.
4.	Rat ISS GO annotations from MGI mouse gene data--August 2006	MGD data from the GO Consortium
5.	Electronic Transfer of LocusLink and RefSeq Data	NCBI rat LocusLink and RefSeq merged data July 26, 2002
6.	OMIM Disease Annotation Pipeline	OMIM Disease Annotation Pipeline
7.	KEGG Annotation Import Pipeline	Pipeline to import KEGG annotations from KEGG into RGD
8.	GOA pipeline	RGD automated data pipeline
9.	Data Import for Chemical-Gene Interactions	RGD automated import pipeline for gene-chemical interactions
10.	Characterization of rat OX40 ligand by monoclonal antibody.	Satake Y, etal., Biochem Biophys Res Commun. 2000 Apr 21;270(3):1041-8.
11.	Positional identification of TNFSF4, encoding OX40 ligand, as a gene that influences atherosclerosis susceptibility.	Wang X, etal., Nat Genet. 2005 Apr;37(4):365-72. Epub 2005 Mar 6.
12.	The role of the CD134-CD134 ligand costimulatory pathway in alloimmune responses in vivo.	Yuan X, etal., J Immunol. 2003 Mar 15;170(6):2949-55.
13.	Negative immune factors might predominate local tumor immune status and promote carcinogenesis in cervical carcinoma.	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
GRCr8	13	76,256,654 - 76,280,133 (+)	NCBI		GRCr8
mRatBN7.2	13	73,723,329 - 73,746,809 (+)	NCBI	mRatBN7.2	mRatBN7.2
mRatBN7.2 Ensembl	13	73,723,329 - 73,746,788 (+)	Ensembl		mRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx	13	76,302,498 - 76,326,020 (+)	NCBI	Rnor_SHR	UTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0	13	77,600,036 - 77,623,530 (+)	NCBI	Rnor_SHRSP	UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0	13	74,859,914 - 74,883,412 (+)	NCBI	Rnor_WKY	UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0	13	79,269,973 - 79,293,775 (+)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_6.0 Ensembl	13	79,269,973 - 79,293,778 (+)	Ensembl	Rnor6.0		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	RGSC_v3.4	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	1	173,172,870 - 173,450,733 (-)	NCBI	GRCh38	GRCh38	hg38	GRCh38
GRCh38.p14 Ensembl	1	173,162,645 - 173,477,583 (-)	Ensembl	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	Build 36	hg18	NCBI36
Build 34	1	169,884,527 - 169,908,128	NCBI
Celera	1	146,262,332 - 146,285,933 (-)	NCBI		Celera
Cytogenetic Map	1	q25.1	NCBI
HuRef	1	144,377,608 - 144,401,209 (-)	NCBI		HuRef
CHM1_1	1	174,575,344 - 174,598,945 (-)	NCBI		CHM1_1
T2T-CHM13v2.0	1	172,541,831 - 172,768,144 (-)	NCBI		T2T-CHM13v2.0

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	GRCm39	mm39
GRCm39 Ensembl	1	161,222,980 - 161,245,981 (+)	Ensembl		GRCm39 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	MGSCv37	mm9	NCBIm37
MGSCv36	1	163,232,135 - 163,254,883 (+)	NCBI		MGSCv36	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
NHGRI_mPanPan1-v2	1	76,255,433 - 76,559,453 (+)	NCBI		NHGRI_mPanPan1-v2
NHGRI_mPanPan1	1	75,929,208 - 76,396,416 (+)	NCBI		NHGRI_mPanPan1
Mhudiblu_PPA_v0	1	148,684,689 - 148,989,775 (-)	NCBI	Mhudiblu_PPA_v0	Mhudiblu_PPA_v0	panPan3
PanPan1.1	1	152,391,450 - 152,699,026 (-)	NCBI	panpan1.1	PanPan1.1	panPan2
PanPan1.1 Ensembl	1	152,251,683 - 152,262,668 (-)	Ensembl	panpan1.1		panPan2
PanPan1.1 Ensembl	1	152,391,450 - 152,415,845 (-)	Ensembl	panpan1.1		panPan2

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	7	25,883,297 - 25,909,608 (+)	NCBI	CanFam3.1	CanFam3.1	canFam3	CanFam3.1
CanFam3.1 Ensembl	7	25,883,251 - 25,906,892 (+)	Ensembl	CanFam3.1		canFam3	CanFam3.1
Dog10K_Boxer_Tasha	7	25,415,436 - 25,441,738 (+)	NCBI		Dog10K_Boxer_Tasha
ROS_Cfam_1.0	7	25,634,585 - 25,660,879 (+)	NCBI		ROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl	7	25,634,528 - 25,660,603 (+)	Ensembl		ROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1	7	25,553,133 - 25,579,437 (+)	NCBI		UMICH_Zoey_3.1
UNSW_CanFamBas_1.0	7	25,626,526 - 25,652,838 (+)	NCBI		UNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0	7	25,780,205 - 25,806,523 (+)	NCBI		UU_Cfam_GSD_1.0

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
HiC_Itri_2	NW_024409344	96,542,360 - 96,562,833 (+)	NCBI		HiC_Itri_2
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	115,550,569 - 115,659,263 (-)	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 - green monkey)

Green Monkey Assembly	Chr	Position (strand)	Source	Genome Browsers
Green Monkey Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
ChlSab1.1	25	55,714,291 - 55,998,009 (+)	NCBI	ChlSab1.1	ChlSab1.1	chlSab2
ChlSab1.1 Ensembl	25	55,974,691 - 55,997,374 (+)	Ensembl	ChlSab1.1	ChlSab1.1 Ensembl	chlSab2
Vero_WHO_p1.0	NW_023666055	57,291,046 - 57,591,856 (+)	NCBI	Vero_WHO_p1.0	Vero_WHO_p1.0

Tnfsf4
(Heterocephalus glaber - naked mole-rat)

Naked Mole-Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Naked Mole-Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
HetGla 1.0	NW_004624771	8,580,489 - 8,599,735 (+)	NCBI	HetGla_female_1.0	HetGla 1.0	hetGla2

Variants

Variants in Tnfsf4
142 total Variants

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.

QTLs in Region (mRatBN7.2)

The following QTLs overlap with this region.

RGD ID	Symbol	Name	LOD	P Value	Trait	Sub Trait	Chr	Start	Stop	Species
1298066	Bp159	Blood pressure QTL 159		0.004	arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	13	46088046	91088046	Rat
10755495	Bp387	Blood pressure QTL 387	3.78		arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	13	34663461	87525369	Rat
1354655	Bp241	Blood pressure QTL 241	3.9		arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	13	56056920	101056920	Rat
8655951	Rf63	Renal function QTL 63	12.2		blood urea nitrogen amount (VT:0005265)	plasma urea nitrogen level (CMO:0000586)	13	69060519	77046890	Rat
70220	Bp55	Blood pressure QTL 55	5.75		arterial blood pressure trait (VT:2000000)	blood pressure measurement (CMO:0000003)	13	37374509	82374509	Rat
8655945	Rf61	Renal function QTL 61	3.6		blood creatinine amount (VT:0005328)	creatinine clearance (CMO:0000765)	13	69060519	86800898	Rat
71119	Thym2	Thymus enlargement QTL 2	3.8		thymus mass (VT:0004954)	thymus weight to body weight ratio (CMO:0000612)	13	46197976	84753113	Rat
4889861	Pur29	Proteinuria QTL 29	13.8	0.005	urine total protein amount (VT:0000032)	urine total protein excretion rate (CMO:0000756)	13	37415584	80753406	Rat
1331783	Bp221	Blood pressure QTL 221	3.72886		arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	13	69060519	86800898	Rat
12879441	Bp396	Blood pressure QTL 396			arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	13	45699983	90699983	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	65103704	106807694	Rat
1300166	Kidm6	Kidney mass QTL 6	3.93		kidney mass (VT:0002707)	single kidney wet weight to body weight ratio (CMO:0000622)	13	69060519	86800898	Rat
619615	Bp80	Blood pressure QTL 80		0.0354	arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	13	39754544	84754544	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	8897350	101631289	Rat
61340	Bp25	Blood pressure QTL 25	4.2	0.004	arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	13	34535218	79535218	Rat
1581573	Uae36	Urinary albumin excretion QTL 36			urine albumin amount (VT:0002871)	urine albumin excretion rate (CMO:0000757)	13	5994833	77046787	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	38433408	83433408	Rat
724564	Uae11	Urinary albumin excretion QTL 11	5.7		urine albumin amount (VT:0002871)	urine albumin level (CMO:0000130)	13	59492522	77046890	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	20605871	101339738	Rat
7387280	Uae43	Urinary albumin excretion QTL 43	5.69	0.4174	urine albumin amount (VT:0002871)	urine albumin excretion rate (CMO:0000757)	13	66451204	106807694	Rat
738026	Lnnr5	Liver neoplastic nodule remodeling QTL 5	3.29		liver integrity trait (VT:0010547)	liver remodeling tumorous lesion number (CMO:0001461)	13	59874408	85581182	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	31241331	93395974	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	65103704	106807694	Rat
61349	Bp31	Blood pressure QTL 31	5.75		arterial blood pressure trait (VT:2000000)	blood pressure measurement (CMO:0000003)	13	37374509	82374509	Rat
2303563	Bw89	Body weight QTL 89	6		body mass (VT:0001259)	body weight (CMO:0000012)	13	32284471	77284471	Rat
1354621	Rf47	Renal function QTL 47	3.7		kidney renin amount (VT:0010559)	kidney renin level (CMO:0002166)	13	30395351	101056920	Rat
1581554	Pur11	Proteinuria QTL 11			urine albumin amount (VT:0002871)	urine albumin excretion rate (CMO:0000757)	13	5994833	77046787	Rat
12879477	Bp401	Blood pressure QTL 401			arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	13	37262092	82262092	Rat
1331750	Bp220	Blood pressure QTL 220	2.98		arterial blood pressure trait (VT:2000000)	diastolic blood pressure (CMO:0000005)	13	37415584	82415584	Rat
1641901	Alcrsp6	Alcohol response QTL 6			response to alcohol trait (VT:0010489)	duration of loss of righting reflex (CMO:0002289)	13	52362171	97362171	Rat
12879475	Bp400	Blood pressure QTL 400			arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	13	61825626	106807694	Rat
1354666	Bp244	Blood pressure QTL 244	4.9		arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	13	1	101056920	Rat

Expression

RNA-SEQ Expression

Click on a value in the shaded box below the category label to view a detailed expression data table for that system.

Download All Expressed Objects for this Gene

alimentary part of gastrointestinal system	appendage	circulatory system	ectoderm	endocrine system	endoderm	exocrine system	hemolymphoid system	hepatobiliary system	integumental system	mesenchyme	mesoderm	nervous system	renal system	reproductive system	respiratory system
8	6	16	93	37	46	19	25	19	4	116	47	85	36	45	27

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
	JAXUCZ010000013	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	LN874409	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles

Ensembl Acc Id:

ENSRNOT00000003969 ⟹ ENSRNOP00000003969

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2 Ensembl	13	73,723,329 - 73,746,788 (+)	Ensembl
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
GRCr8	13	76,256,654 - 76,280,133 (+)	NCBI
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
Ensembl Protein	ENSRNOP00000003969.3
	ENSRNOP00055024025
	ENSRNOP00060010961
	ENSRNOP00065026563
GenBank Protein	Q9Z2P3	(Get FASTA)	NCBI Sequence Viewer

RefSeq Acc Id:

NP_446004 ⟸ NM_053552

- UniProtKB:

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

- Sequence:

show sequence

MEGEGVQPPDENLENGSRPRFKWKKVLRLVVSGIKAAGLLLCVVYVCLQFSSSPAKDSPIQRLR
APVTGCEGGRLFIGTSKNEYETMEVQNNSVIINCDGLYLIHLKGSFFQEVKINLHFRKDRSPIF
VPMLNNGQRVVFTVVTSLAFKDEVYLTVNASDTLCEHLQINDGELIIVQLTPNGYCAPERPYSS
TVNQVPL

hide sequence

Ensembl Acc Id:

ENSRNOP00000003969 ⟸ ENSRNOT00000003969

Protein Domains

THD

Protein Structures

Name	Modeler	Protein Id	AA Range	Protein Structure
AF-Q9Z2P3-F1-model_v2	AlphaFold	Q9Z2P3	1-199	view protein structure

Transcriptome

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

Additional Information

External Database Links

Database	Acc Id	Source(s)
AGR Gene	RGD:619816	AgrOrtholog
BioCyc Gene	G2FUF-17714	BioCyc
Ensembl Genes	ENSRNOG00000002968	Ensembl, UniProtKB/Swiss-Prot
	ENSRNOG00055017668	UniProtKB/Swiss-Prot
	ENSRNOG00060008558	UniProtKB/Swiss-Prot
	ENSRNOG00065019706	UniProtKB/Swiss-Prot
Ensembl Transcript	ENSRNOT00000003969.6	UniProtKB/Swiss-Prot
	ENSRNOT00055029902	UniProtKB/Swiss-Prot
	ENSRNOT00060014273	UniProtKB/Swiss-Prot
	ENSRNOT00065033199	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
	TUMOR NECROSIS FACTOR LIGAND SUPERFAMILY MEMBER 4	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen	Tnfsf4	PhenoGen
PROSITE	THD_2	UniProtKB/Swiss-Prot
	TNF_1	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
RatGTEx	ENSRNOG00000002968	RatGTEx
	ENSRNOG00055017668	RatGTEx
	ENSRNOG00060008558	RatGTEx
	ENSRNOG00065019706	RatGTEx
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)

Mammalian Phenotype

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Imported Disease Annotations - ClinVar

Imported Disease Annotations - CTD

Imported Disease Annotations - MGI

Imported Disease Annotations - OMIM

Imported Annotations - KEGG (archival)

Mammalian Phenotype