Tnfrsf4 (TNF receptor superfamily member 4) - Rat Genome Database

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Gene: Tnfrsf4 (TNF receptor superfamily member 4) Rattus norvegicus
Analyze
Symbol: Tnfrsf4
Name: TNF receptor superfamily member 4
RGD ID: 3920
Description: Predicted to enable tumor necrosis factor receptor activity. Involved in T cell proliferation. Located in cell surface. Human ortholog(s) of this gene implicated in immunodeficiency 16. Orthologous to human TNFRSF4 (TNF receptor superfamily member 4); PARTICIPATES IN cytokine mediated signaling pathway; INTERACTS WITH alpha-Zearalanol; ammonium chloride; bisphenol A.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: MRC OX40; Ox40; OX40 antigen; OX40L receptor; Tax-transcriptionally activated glycoprotein 1; tumor necrosis factor (ligand) superfamily member 4; tumor necrosis factor (ligand) superfamily, member 4; tumor necrosis factor receptor superfamily member 4; tumor necrosis factor receptor superfamily, member 4; tumor necrosis factor superfamily member 4; tumor necrosis factor superfamily, member 4; Txgp1
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr85171,889,134 - 171,891,824 (+)NCBIGRCr8
mRatBN7.25166,606,909 - 166,609,599 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl5166,606,909 - 166,609,599 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx5169,310,441 - 169,313,132 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.05171,131,863 - 171,134,554 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.05171,094,395 - 171,097,086 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.05173,447,784 - 173,450,474 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl5173,447,784 - 173,450,474 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.05176,921,804 - 176,924,494 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.45172,856,351 - 172,859,041 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.15172,866,845 - 172,869,536 (+)NCBI
Celera5164,807,766 - 164,810,456 (+)NCBICelera
Cytogenetic Map5q36NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Molecular Pathway Annotations     Click to see Annotation Detail View
References

References - curated
# Reference Title Reference Citation
1. 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.
2. Rat ISS GO annotations from GOA human gene data--August 2006 GOA data from the GO Consortium
3. Characterization of the MRC OX40 antigen of activated CD4 positive T lymphocytes--a molecule related to nerve growth factor receptor. Mallett S, etal., EMBO J 1990 Apr;9(4):1063-8.
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. Antigens of activated rat T lymphocytes including a molecule of 50,000 Mr detected only on CD4 positive T blasts. Paterson DJ, etal., Mol Immunol 1987 Dec;24(12):1281-90.
8. KEGG Annotation Import Pipeline Pipeline to import KEGG annotations from KEGG into RGD
9. GOA pipeline RGD automated data pipeline
10. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
11. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
12. 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:7749983   PMID:8765008   PMID:10586044   PMID:11567634   PMID:12626546   PMID:14635034   PMID:14730361   PMID:16301745   PMID:19008373   PMID:20871162  


Genomics

Comparative Map Data
Tnfrsf4
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr85171,889,134 - 171,891,824 (+)NCBIGRCr8
mRatBN7.25166,606,909 - 166,609,599 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl5166,606,909 - 166,609,599 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx5169,310,441 - 169,313,132 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.05171,131,863 - 171,134,554 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.05171,094,395 - 171,097,086 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.05173,447,784 - 173,450,474 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl5173,447,784 - 173,450,474 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.05176,921,804 - 176,924,494 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.45172,856,351 - 172,859,041 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.15172,866,845 - 172,869,536 (+)NCBI
Celera5164,807,766 - 164,810,456 (+)NCBICelera
Cytogenetic Map5q36NCBI
TNFRSF4
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh3811,211,340 - 1,214,153 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl11,211,326 - 1,214,153 (-)EnsemblGRCh38hg38GRCh38
GRCh3711,146,720 - 1,149,533 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 3611,136,569 - 1,139,375 (-)NCBINCBI36Build 36hg18NCBI36
Build 3411,186,629 - 1,189,435NCBI
Celera11,434,142 - 1,436,950 (+)NCBICelera
Cytogenetic Map1p36.33NCBI
HuRef1418,421 - 421,246 (-)NCBIHuRef
CHM1_111,133,180 - 1,136,022 (-)NCBICHM1_1
T2T-CHM13v2.01639,783 - 642,610 (-)NCBIT2T-CHM13v2.0
Tnfrsf4
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm394156,098,049 - 156,101,070 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl4156,098,300 - 156,101,069 (+)EnsemblGRCm39 Ensembl
GRCm384156,013,595 - 156,016,613 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl4156,013,843 - 156,016,612 (+)EnsemblGRCm38mm10GRCm38
MGSCv374155,387,804 - 155,390,698 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv364154,857,495 - 154,860,389 (+)NCBIMGSCv36mm8
Celera4158,276,449 - 158,279,355 (+)NCBICelera
Cytogenetic Map4E2NCBI
cM Map487.68NCBI
Tnfrsf4
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554869,567,220 - 9,569,676 (+)EnsemblChiLan1.0
ChiLan1.0NW_0049554869,565,424 - 9,569,836 (+)NCBIChiLan1.0ChiLan1.0
TNFRSF4
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v21227,011,897 - 227,014,893 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan11225,707,527 - 225,711,573 (+)NCBINHGRI_mPanPan1
PanPan1.111,168,706 - 1,171,341 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl11,168,935 - 1,171,337 (-)Ensemblpanpan1.1panPan2
TNFRSF4
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1556,401,410 - 56,404,410 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl556,401,384 - 56,404,761 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha556,478,386 - 56,481,328 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0556,604,302 - 56,607,244 (-)NCBIROS_Cfam_1.0
UMICH_Zoey_3.1556,595,039 - 56,597,980 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0556,487,321 - 56,490,255 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0556,877,316 - 56,880,258 (-)NCBIUU_Cfam_GSD_1.0
Tnfrsf4
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440505827,561,562 - 27,567,137 (-)NCBIHiC_Itri_2
SpeTri2.0NW_0049367371,901,749 - 1,904,382 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
TNFRSF4
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl663,523,804 - 63,526,666 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1663,523,850 - 63,526,672 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2658,011,607 - 58,014,420 (+)NCBISscrofa10.2Sscrofa10.2susScr3
TNFRSF4
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.120130,231,064 - 130,234,525 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl20130,231,584 - 130,234,313 (+)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366605434,799,764 - 34,803,311 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Tnfrsf4
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046248188,373,810 - 8,376,204 (+)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_0046248188,372,092 - 8,376,108 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Tnfrsf4
1 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:58
Count of miRNA genes:50
Interacting mature miRNAs:56
Transcripts:ENSRNOT00000027251
Prediction methods:Miranda, Rnahybrid, 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.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1576314Eutr1Estrogen induced uterine response QTL 1uterus integrity trait (VT:0010575)pyometritis severity score (CMO:0002009)52138965166875058Rat
1302790Scl20Serum cholesterol level QTL 206.40.0001blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)582394392166664054Rat
1641920Colcs1Colorectal carcinoma susceptibility QTL 12.990.0055intestine integrity trait (VT:0010554)benign colorectal tumor surface area measurement (CMO:0001799)5121846814166846814Rat
10053720Scort26Serum corticosterone level QTL 262.060.0147blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)5124965598166875058Rat
724525Bp147Blood pressure QTL 1474.30.0001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)5126424772166875058Rat
1598819Bp292Blood pressure QTL 2924.3arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)5127798274166875058Rat
1598861Cm64Cardiac mass QTL 642.9heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)5127798274166875058Rat
8552908Pigfal4Plasma insulin-like growth factor 1 level QTL 46.6blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)5128506074166875058Rat
8694169Bw148Body weight QTL 14850.001body mass (VT:0001259)body weight gain (CMO:0000420)5128506074166875058Rat
634349Bp139Blood pressure QTL 1390.001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)5128924607166875058Rat
738018Anxrr4Anxiety related response QTL 45.1exploratory behavior trait (VT:0010471)percentage of entries into a discrete space in an experimental apparatus (CMO:0000961)5130130159166875058Rat
7794791Mcs33Mammary carcinoma susceptibility QTL 331.93mammary gland integrity trait (VT:0010552)mammary tumor incidence/prevalence measurement (CMO:0000946)5131345754166875058Rat
631562Apr2Acute phase response QTL 23.7blood murinoglobulin 1 amount (VT:0010597)plasma murinoglobulin 1 level (CMO:0001931)5135927956166875058Rat
61444Strs2Sensitivity to stroke QTL 24.7cerebrum integrity trait (VT:0010549)post-insult time to onset of cerebrovascular lesion (CMO:0002343)5135929696166875058Rat
1331721Bp210Blood pressure QTL 2103.413arterial blood pressure trait (VT:2000000)blood pressure time series experimental set point of the baroreceptor response (CMO:0002593)5143069996166846814Rat
631272Lanf1Left ventricular atrial natriuretic factor QTL 112heart left ventricle natriuretic peptide A amount (VT:0010596)heart left ventricle natriuretic peptide A level (CMO:0002165)5151113452166875058Rat
1549904Neuinf1Neuroinflammation QTL 130nervous system integrity trait (VT:0010566)blood T lymphocyte count (CMO:0000110)5154828214166875058Rat

Markers in Region
RH136773  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.25166,606,111 - 166,606,287 (+)MAPPERmRatBN7.2
Rnor_6.05173,446,987 - 173,447,162NCBIRnor6.0
Rnor_5.05176,921,007 - 176,921,182UniSTSRnor5.0
RGSC_v3.45172,855,554 - 172,855,729UniSTSRGSC3.4
Celera5164,806,969 - 164,807,144UniSTS
RH 3.4 Map51174.5UniSTS
Cytogenetic Map5q36UniSTS


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 6 8 1
Low 1 39 49 39 11 39 8 11 74 34 39 10 8
Below cutoff 4 2 2 2 1 2

Sequence


RefSeq Acc Id: ENSRNOT00000027251   ⟹   ENSRNOP00000027251
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl5166,606,909 - 166,609,599 (+)Ensembl
Rnor_6.0 Ensembl5173,447,784 - 173,450,474 (+)Ensembl
RefSeq Acc Id: NM_013049   ⟹   NP_037181
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr85171,889,134 - 171,891,824 (+)NCBI
mRatBN7.25166,606,909 - 166,609,599 (+)NCBI
Rnor_6.05173,447,784 - 173,450,474 (+)NCBI
Rnor_5.05176,921,804 - 176,924,494 (+)NCBI
RGSC_v3.45172,856,351 - 172,859,041 (+)RGD
Celera5164,807,766 - 164,810,456 (+)RGD
Sequence:
Protein Sequences
Protein RefSeqs NP_037181 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein CAA34897 (Get FASTA)   NCBI Sequence Viewer  
  EDL81353 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000027251
  ENSRNOP00000027251.3
  ENSRNOP00055020004
  ENSRNOP00060005958
  ENSRNOP00065012767
GenBank Protein P15725 (Get FASTA)   NCBI Sequence Viewer  
RefSeq Acc Id: NP_037181   ⟸   NM_013049
- Peptide Label: precursor
- UniProtKB: P15725 (UniProtKB/Swiss-Prot),   A6IUV2 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000027251   ⟸   ENSRNOT00000027251
Protein Domains
TNFR-Cys

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-P15725-F1-model_v2 AlphaFold P15725 1-271 view protein structure

Transcriptome

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

Promoters
RGD ID:13694342
Promoter ID:EPDNEW_R4866
Type:single initiation site
Name:Tnfrsf4_1
Description:TNF receptor superfamily member 4
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_6.05173,447,767 - 173,447,827EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:3920 AgrOrtholog
BioCyc Gene G2FUF-38878 BioCyc
Ensembl Genes ENSRNOG00000020106 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
  ENSRNOG00055014258 UniProtKB/Swiss-Prot
  ENSRNOG00060004741 UniProtKB/Swiss-Prot
  ENSRNOG00065010350 UniProtKB/Swiss-Prot
Ensembl Transcript ENSRNOT00000027251 ENTREZGENE
  ENSRNOT00000027251.5 UniProtKB/Swiss-Prot
  ENSRNOT00055024482 UniProtKB/Swiss-Prot
  ENSRNOT00060007931 UniProtKB/Swiss-Prot
  ENSRNOT00065016725 UniProtKB/Swiss-Prot
Gene3D-CATH Tumor Necrosis Factor Receptor, subunit A, domain 2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
InterPro TNFR/NGFR_Cys_rich_reg UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  TNFR_4 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  TNFRSF4_N UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:25572 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
NCBI Gene 25572 ENTREZGENE
PANTHER PTHR47881 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  TUMOR NECROSIS FACTOR RECEPTOR SUPERFAMILY MEMBER 4 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam TNFR_c6 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Tnfrsf4 PhenoGen
PRINTS TNFACTORR4 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PROSITE TNFR_NGFR_1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  TNFR_NGFR_2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
RatGTEx ENSRNOG00000020106 RatGTEx
  ENSRNOG00055014258 RatGTEx
  ENSRNOG00060004741 RatGTEx
  ENSRNOG00065010350 RatGTEx
SMART TNFR UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP TNF receptor-like UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt A6IUV2 ENTREZGENE, UniProtKB/TrEMBL
  P15725 ENTREZGENE, UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2016-07-05 Tnfrsf4  TNF receptor superfamily member 4  Tnfrsf4  tumor necrosis factor receptor superfamily, member 4  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2004-09-10 Tnfrsf4  tumor necrosis factor receptor superfamily, member 4    tumor necrosis factor superfamily, member 4  Name updated 1299863 APPROVED
2002-06-10 Tnfrsf4  tumor necrosis factor superfamily, member 4      Name updated 70585 PROVISIONAL
2001-12-10 Tnfrsf4  tumor necrosis factor (ligand) superfamily, member 4      Symbol and Name updated to reflect Human and Mouse nomenclature 69665 APPROVED

RGD Curation Notes
Note Type Note Reference
gene_product member of the tumor necrosis factor (TNF)-receptor superfamily 70044