Tnfsf9 (TNF superfamily member 9) - Rat Genome Database

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Gene: Tnfsf9 (TNF superfamily member 9) Rattus norvegicus
Analyze
Symbol: Tnfsf9
Name: TNF superfamily member 9
RGD ID: 727974
Description: Predicted to enable tumor necrosis factor receptor superfamily binding activity. Involved in myeloid dendritic cell differentiation; positive regulation of T cell activation; and positive regulation of cytokine production. Predicted to be located in extracellular space. Predicted to be active in plasma membrane. Orthologous to human TNFSF9 (TNF superfamily member 9); PARTICIPATES IN cytokine mediated signaling pathway; INTERACTS WITH 17beta-estradiol; 17beta-estradiol 3-benzoate; 1H-pyrazole.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: costimulatory molecule; Tnlg5a; tumor necrosis factor (ligand) superfamily, member 9; tumor necrosis factor ligand 5a; tumor necrosis factor ligand superfamily member 9; tumor necrosis factor superfamily member 9
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.291,944,017 - 1,946,351 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl91,944,017 - 1,946,345 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx92,378,289 - 2,380,620 (+)NCBIRnor_SHR
UTH_Rnor_SHRSP_BbbUtx_1.0960,384 - 62,715 (+)NCBIRnor_SHRSP
UTH_Rnor_WKY_Bbb_1.096,683,512 - 6,685,843 (+)NCBIRnor_WKY
Rnor_6.099,909,942 - 9,912,276 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl99,909,948 - 9,912,276 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.098,913,004 - 8,915,338 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
Celera96,571,461 - 6,573,795 (-)NCBICelera
Cytogenetic Map9q12NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
(-)-anisomycin  (ISO)
(S)-colchicine  (ISO)
17beta-estradiol  (EXP)
17beta-estradiol 3-benzoate  (EXP)
1H-pyrazole  (EXP)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,ISO)
5-aza-2'-deoxycytidine  (ISO)
6-propyl-2-thiouracil  (EXP)
7,12-dimethyltetraphene  (ISO)
acrylamide  (EXP,ISO)
actinomycin D  (ISO)
adefovir pivoxil  (ISO)
adenine  (ISO)
aflatoxin B1  (ISO)
all-trans-retinoic acid  (ISO)
amphetamine  (EXP)
aristolochic acid A  (ISO)
arsane  (ISO)
arsenic atom  (ISO)
arsenous acid  (ISO)
avobenzone  (ISO)
benzo[a]pyrene  (ISO)
benzo[a]pyrene diol epoxide I  (ISO)
bisphenol A  (EXP)
butanal  (ISO)
cadmium atom  (ISO)
cadmium dichloride  (ISO)
calciol  (ISO)
camptothecin  (ISO)
carbon nanotube  (ISO)
chloroacetaldehyde  (ISO)
chloroprene  (ISO)
cidofovir anhydrous  (ISO)
cisplatin  (ISO)
cobalt atom  (ISO)
cobalt dichloride  (ISO)
copper atom  (ISO)
copper(0)  (ISO)
copper(II) sulfate  (ISO)
cyclophosphamide  (ISO)
cyclosporin A  (ISO)
daunorubicin  (ISO)
deoxynivalenol  (ISO)
dexamethasone  (ISO)
dextran sulfate  (ISO)
diarsenic trioxide  (ISO)
dieldrin  (ISO)
diethylstilbestrol  (ISO)
dioxygen  (ISO)
dorsomorphin  (ISO)
endosulfan  (EXP,ISO)
entinostat  (ISO)
ethanol  (EXP,ISO)
etoposide  (ISO)
formaldehyde  (ISO)
furosemide  (EXP)
genistein  (ISO)
gentamycin  (EXP)
ifosfamide  (ISO)
ionomycin  (ISO)
isoflurane  (EXP)
lead(0)  (ISO)
lead(2+)  (ISO)
Licochalcone B  (ISO)
lipopolysaccharide  (ISO)
MeIQx  (ISO)
mercury dibromide  (ISO)
methotrexate  (ISO)
methyl methanesulfonate  (ISO)
methylmercury chloride  (ISO)
nickel sulfate  (ISO)
ochratoxin A  (ISO)
ozone  (ISO)
p-chloromercuribenzoic acid  (ISO)
p-menthan-3-ol  (ISO)
panobinostat  (ISO)
paracetamol  (ISO)
paraquat  (EXP,ISO)
pentanal  (ISO)
phenylmercury acetate  (ISO)
potassium bromate  (ISO)
propanal  (ISO)
S-(1,2-dichlorovinyl)-L-cysteine  (ISO)
SB 431542  (ISO)
silicon dioxide  (ISO)
silver atom  (ISO)
silver(0)  (ISO)
sodium arsenite  (ISO)
Soman  (EXP)
temozolomide  (ISO)
testosterone  (EXP)
tetrachloromethane  (EXP)
thapsigargin  (ISO)
titanium dioxide  (EXP,ISO)
Tributyltin oxide  (ISO)
trichostatin A  (ISO)
troglitazone  (EXP)
urethane  (ISO)
valproic acid  (ISO)
vincristine  (ISO)
vorinostat  (ISO)
XL147  (ISO)
zinc atom  (ISO)
zinc(0)  (ISO)
zoledronic acid  (ISO)

Molecular Pathway Annotations     Click to see Annotation Detail View
References

References - curated
# Reference Title Reference Citation
1. Expression of CD137 and CD137 ligand in colorectal cancer patients. Dimberg J, etal., Oncol Rep. 2006 May;15(5):1197-200.
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. 4-1BBL cooperates with B7-1 and B7-2 in converting a B cell lymphoma cell line into a long-lasting antitumor vaccine. Guinn BA, etal., J Immunol. 1999 Apr 15;162(8):5003-10.
4. Increased soluble 4-1BB ligand (4-1BBL) levels in peripheral blood of patients with multiple sclerosis. Liu GZ, etal., Scand J Immunol. 2006 Oct;64(4):412-9.
5. NCBI rat LocusLink and RefSeq merged data October 15, 2003 NCBI rat LocusLink and RefSeq merged data October 15, 2003
6. KEGG Annotation Import Pipeline Pipeline to import KEGG annotations from KEGG into RGD
7. GOA pipeline RGD automated data pipeline
8. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
9. Comprehensive gene review and curation RGD comprehensive gene curation
10. Soluble CD137 (4-1BB) ligand is released following leukocyte activation and is found in sera of patients with hematological malignancies. Salih HR, etal., J Immunol. 2001 Oct 1;167(7):4059-66.
11. [The change of immunoactivity of dendritic cells induced by recombinant rat 4-1BBL] Tan JX, etal., Xi Bao Yu Fen Zi Mian Yi Xue Za Zhi. 2008 Aug;24(8):764-6.
12. Soluble PD-1 facilitates 4-1BBL-triggered antitumor immunity against murine H22 hepatocarcinoma in vivo. Xiao H, etal., Clin Cancer Res. 2007 Mar 15;13(6):1823-30. Epub 2007 Feb 26.
13. Recombinant attenuated Salmonella harboring 4-1BB ligand gene enhances cellular immunity. Ye JX, etal., Vaccine. 2009 Mar 10;27(11):1717-23. Epub 2009 Jan 31.
14. Targeted and untargeted CD137L fusion proteins for the immunotherapy of experimental solid tumors. Zhang N, etal., Clin Cancer Res. 2007 May 1;13(9):2758-67. Epub 2007 Apr 25.
Additional References at PubMed
PMID:8405064   PMID:16215637   PMID:18640726   PMID:26646413  


Genomics

Comparative Map Data
Tnfsf9
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.291,944,017 - 1,946,351 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl91,944,017 - 1,946,345 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx92,378,289 - 2,380,620 (+)NCBIRnor_SHR
UTH_Rnor_SHRSP_BbbUtx_1.0960,384 - 62,715 (+)NCBIRnor_SHRSP
UTH_Rnor_WKY_Bbb_1.096,683,512 - 6,685,843 (+)NCBIRnor_WKY
Rnor_6.099,909,942 - 9,912,276 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl99,909,948 - 9,912,276 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.098,913,004 - 8,915,338 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
Celera96,571,461 - 6,573,795 (-)NCBICelera
Cytogenetic Map9q12NCBI
TNFSF9
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38196,531,026 - 6,535,924 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p13 Ensembl196,531,026 - 6,535,924 (+)EnsemblGRCh38hg38GRCh38
GRCh37196,531,037 - 6,535,935 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36196,482,037 - 6,486,933 (+)NCBINCBI36Build 36hg18NCBI36
Build 34196,482,036 - 6,486,933NCBI
Celera196,470,827 - 6,475,769 (+)NCBICelera
Cytogenetic Map19p13.3NCBI
HuRef196,293,216 - 6,297,937 (+)NCBIHuRef
CHM1_1196,530,958 - 6,535,882 (+)NCBICHM1_1
T2T-CHM13v2.0196,520,520 - 6,525,499 (+)NCBIT2T-CHM13v2.0
Tnfsf9
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391757,412,113 - 57,414,757 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1757,412,325 - 57,414,757 (+)EnsemblGRCm39 Ensembl
GRCm381757,105,287 - 57,107,758 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1757,105,325 - 57,107,757 (+)EnsemblGRCm38mm10GRCm38
MGSCv371757,244,808 - 57,247,180 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv361756,790,776 - 56,792,848 (+)NCBIMGSCv36mm8
Celera1761,453,915 - 61,456,287 (+)NCBICelera
Cytogenetic Map17DNCBI
Tnfsf9
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0NW_0049554953,101,965 - 3,107,552 (-)NCBIChiLan1.0ChiLan1.0
TNFSF9
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.1196,476,941 - 6,483,352 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl196,476,941 - 6,483,352 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v0195,558,021 - 5,562,901 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
TNFSF9
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.12053,680,882 - 53,682,521 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl2053,679,880 - 53,682,706 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha2053,426,553 - 53,439,382 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.02054,333,423 - 54,336,590 (-)NCBIROS_Cfam_1.0
UMICH_Zoey_3.12053,400,156 - 53,403,326 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.02053,848,757 - 53,851,741 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.02054,077,742 - 54,080,911 (-)NCBIUU_Cfam_GSD_1.0
Tnfsf9
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024405118213,987,493 - 213,989,882 (-)NCBIHiC_Itri_2
SpeTri2.0NW_0049365883,844,924 - 3,847,218 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
TNFSF9
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl272,578,821 - 72,582,745 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1272,578,811 - 72,582,834 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2273,102,064 - 73,106,173 (+)NCBISscrofa10.2Sscrofa10.2susScr3
TNFSF9
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.166,131,157 - 6,136,345 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl66,131,571 - 6,135,463 (+)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_0236660811,866,430 - 1,872,328 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Tnfsf9
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046248283,615,860 - 3,623,377 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Tnfsf9
1 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:165
Count of miRNA genes:116
Interacting mature miRNAs:124
Transcripts:ENSRNOT00000071515
Prediction methods:Microtar, Miranda, Rnahybrid
Result types:miRGate_prediction

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

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


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1298088Edpm11Estrogen-dependent pituitary mass QTL 112.5pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)9143718459Rat
9589055Scfw5Subcutaneous fat weight QTL 55.550.001subcutaneous adipose mass (VT:1000472)abdominal subcutaneous fat pad weight (CMO:0002069)9137999212Rat
7411592Foco8Food consumption QTL 87.40.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)9137999212Rat
1300124Cm4Cardiac mass QTL 43.55heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)9140594091Rat
10054125Srcrt7Stress Responsive Cort QTL 73.330.0011blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)9187073594Rat
10054141Gmadr4Adrenal mass QTL 42.450.0074adrenal gland mass (VT:0010420)both adrenal glands wet weight (CMO:0000164)9114209783Rat
1354650Despr5Despair related QTL 54.010.0017locomotor behavior trait (VT:0001392)amount of time spent in voluntary immobility (CMO:0001043)9125408446254084Rat
70226Eae4Experimental allergic encephalomyelitis QTL 4nervous system integrity trait (VT:0010566)experimental autoimmune encephalomyelitis incidence/prevalence measurement (CMO:0001046)9125661317Rat
2303559Gluco54Glucose level QTL 542blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)9125408446254084Rat
9589158Gluco65Glucose level QTL 656.820.001blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)9137999212Rat
1331757Cdexp1CD45RC expression in CD8 T cells QTL 14.3CD8-positive T cell quantity (VT:0008077)blood CD45RC(high) CD8 T cell count to CD45RC(low) CD8 T cell count ratio (CMO:0001990)9102453767509080Rat
1641911Alcrsp13Alcohol response QTL 13response to alcohol trait (VT:0010489)brain neurotensin receptor 1 density (CMO:0002068)9143718459Rat


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
Low 3 35 14 6 19 6 1 3 61 19 33 11 1
Below cutoff 8 34 28 28 6 7 13 16 7 6

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000071515   ⟹   ENSRNOP00000066298
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl91,944,017 - 1,946,345 (+)Ensembl
Rnor_6.0 Ensembl99,909,948 - 9,912,276 (-)Ensembl
RefSeq Acc Id: NM_181384   ⟹   NP_852049
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.291,944,017 - 1,946,351 (+)NCBI
Rnor_6.099,909,942 - 9,912,276 (-)NCBI
Rnor_5.098,913,004 - 8,915,338 (-)NCBI
Celera96,571,461 - 6,573,795 (-)RGD
Sequence:
Protein Sequences
Protein RefSeqs NP_852049 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAP13993 (Get FASTA)   NCBI Sequence Viewer  
  AAQ01228 (Get FASTA)   NCBI Sequence Viewer  
  CTQ86177 (Get FASTA)   NCBI Sequence Viewer  
  EDL83575 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: NP_852049   ⟸   NM_181384
- UniProtKB: Q80WE6 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000066298   ⟸   ENSRNOT00000071515
Protein Domains
TNF_2

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-Q80WE6-F1-model_v2 AlphaFold Q80WE6 1-308 view protein structure

Transcriptome

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

Promoters
RGD ID:13696437
Promoter ID:EPDNEW_R6961
Type:single initiation site
Name:Tnfsf9_1
Description:TNF superfamily member 9
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Single-end sequencing.
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.099,912,198 - 9,912,258EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:727974 AgrOrtholog
BioCyc Gene G2FUF-28487 BioCyc
Ensembl Genes ENSRNOG00000045595 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000066298 ENTREZGENE
  ENSRNOP00000066298.1 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000071515 ENTREZGENE
  ENSRNOT00000071515.2 UniProtKB/TrEMBL
Gene3D-CATH 2.60.120.40 UniProtKB/TrEMBL
InterPro TNF_CS UniProtKB/TrEMBL
  TNF_family UniProtKB/TrEMBL
  TNFSF9 UniProtKB/TrEMBL
  Tumour_necrosis_fac-like UniProtKB/TrEMBL
KEGG Report rno:353218 UniProtKB/TrEMBL
NCBI Gene 353218 ENTREZGENE
PANTHER PTHR15153 UniProtKB/TrEMBL
Pfam TNF UniProtKB/TrEMBL
PharmGKB TNFSF9 RGD
PhenoGen Tnfsf9 PhenoGen
PROSITE TNF_1 UniProtKB/TrEMBL
  TNF_2 UniProtKB/TrEMBL
SMART TNF UniProtKB/TrEMBL
Superfamily-SCOP TNF_like UniProtKB/TrEMBL
UniProt Q80WE6 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2017-03-21 Tnfsf9  TNF superfamily member 9  Tnfsf9  tumor necrosis factor superfamily member 9  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2015-11-25 Tnfsf9  tumor necrosis factor superfamily member 9  Tnfsf9  tumor necrosis factor (ligand) superfamily, member 9  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2005-07-08 Tnfsf9  tumor necrosis factor (ligand) superfamily, member 9      Symbol and Name status set to approved 1299863 APPROVED