TNFSF4 (TNF superfamily member 4) - Rat Genome Database

Send us a Message
Submit Data |  Help |  Video Tutorials |  News |  Publications |  Download |  REST API |  Citing RGD |  Contact   
Search RGD Grant Resources Citing RGD About Us Contact Us
Genes Variants Community Projects QTLs Strains Markers Genome Information Ontologies Cell Lines References Download Submit Data
OntoMate (Literature Search) JBrowse (Genome Browser) Synteny Browser (VCMap) Variant Visualizer Multi-Ontology Enrichment (MOET) Gene-Ortholog Location Finder (GOLF) InterViewer (Protein-Protein Interactions) PhenoMiner (Quatitative Phenotypes) Gene Annotator OLGA (Gene List Generator) AllianceMine GViewer (Genome Viewer)
Aging & Age-Related Disease Behavioral & Substance Use Disorder Cancer & Neoplastic Disease Cardiovascular Disease Coronavirus Disease Developmental Disease Diabetes Hematologic Disease Immune & Inflammatory Disease Infectious Disease Liver Disease Neurological Disease Obesity & Metabolic Syndrome Renal Disease Respiratory Disease Sensory Organ Disease
Find Models Genetic Models Autism Models Rat PhenoMiner (Quantitative Phenotypes) Chinchilla PhenoMiner Expected Ranges (Quantitative Phenotype) PhenoMiner Term Comparison Hybrid Rat Diversity Panel Phenotypes Phenotypes in Other Animal Models Animal Husbandry Strain Medical Records Phylogenetics Strain Availability Calendar Rats 101 Submissions Photo Archive
Pathways
Rat Community Forum Directory of Rat Laboratories Video Tutorials News RGD Publications RGD Presentations Archive Nomenclature Guidelines Resource Links Laboratory Resources Employment Resources
Advanced Search (OLGA)
Gene: TNFSF4 (TNF superfamily member 4) Canis lupus familiaris
Analyze
Symbol: TNFSF4
Name: TNF superfamily member 4
RGD ID: 12312733
Description: ENCODES a protein that exhibits receptor ligand activity (ortholog); tumor necrosis factor receptor superfamily binding (ortholog); INVOLVED IN acute inflammatory response (ortholog); CD4-positive, alpha-beta T cell costimulation (ortholog); cellular response to nitrogen dioxide (ortholog); ASSOCIATED WITH 1q24 Deletion Syndrome (ortholog); antithrombin III deficiency (ortholog); autoimmune lymphoproliferative syndrome (ortholog); FOUND IN cell surface (ortholog)
Type: protein-coding
RefSeq Status: MODEL
Previously known as: TNLG2B; tumor necrosis factor (ligand) superfamily, member 4 (tax-transcriptionally activated glycoprotein 1, 34kDa); tumor necrosis factor ligand 2B; tumor necrosis factor ligand superfamily member 4; tumor necrosis factor superfamily member 4
RGD Orthologs
Human
Mouse
Rat
Chinchilla
Bonobo
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: CanFam3.1 - Dog CanFam3.1 Assembly
Position:
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1725,883,297 - 25,909,608 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl725,883,251 - 25,906,892 (+)EnsemblcanFam3CanFam3.1
Dog10K_Boxer_Tasha725,415,436 - 25,441,738 (+)NCBIDog10K_Boxer_TashaDog10K_Boxer_Tasha
ROS_Cfam_1.0725,634,585 - 25,660,879 (+)NCBIROS_Cfam_1.0ROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl725,634,528 - 25,660,603 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1725,553,133 - 25,579,437 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0725,626,526 - 25,652,838 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0725,780,205 - 25,806,523 (+)NCBIUU_Cfam_GSD_1.0UU_Cfam_GSD_1.0
JBrowse:




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  (IEA)
cellular response to nitrogen dioxide  (ISO)
cellular response to prostaglandin E stimulus  (IEA)
cholesterol metabolic process  (ISO)
cytokine production  (ISO)
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 interleukin-17 production  (IEA)
negative regulation of regulatory T cell differentiation  (ISO)
negative regulation of T-helper 1 cell differentiation  (ISO)
negative regulation of transcription by RNA polymerase II  (ISO)
negative regulation of type II interferon production  (ISO)
positive regulation of activated T cell proliferation  (ISO)
positive regulation of alpha-beta T cell proliferation  (ISO)
positive regulation of B cell activation  (ISO)
positive regulation of B cell proliferation  (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  (IEA)
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  (ISO)
positive regulation of interleukin-4 production  (IEA)
positive regulation of interleukin-4-dependent isotype switching to IgE isotypes  (ISO)
positive regulation of interleukin-6 production  (IEA)
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  (IEA)
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  (ISO)
T-helper 2 cell activation  (ISO)

Cellular Component
cell surface  (IEA,ISO)
extracellular space  (IBA,IEA)
membrane  (IEA)

Molecular Function

References
Additional References at PubMed
PMID:22301074   PMID:26646413   PMID:30032202  


Genomics

Comparative Map Data
TNFSF4
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1725,883,297 - 25,909,608 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl725,883,251 - 25,906,892 (+)EnsemblcanFam3CanFam3.1
Dog10K_Boxer_Tasha725,415,436 - 25,441,738 (+)NCBIDog10K_Boxer_TashaDog10K_Boxer_Tasha
ROS_Cfam_1.0725,634,585 - 25,660,879 (+)NCBIROS_Cfam_1.0ROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl725,634,528 - 25,660,603 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1725,553,133 - 25,579,437 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0725,626,526 - 25,652,838 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0725,780,205 - 25,806,523 (+)NCBIUU_Cfam_GSD_1.0UU_Cfam_GSD_1.0
TNFSF4
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381173,172,870 - 173,450,733 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1173,162,645 - 173,477,583 (-)Ensemblhg38GRCh38
GRCh371173,152,870 - 173,176,470 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361171,419,493 - 171,443,094 (-)NCBIBuild 36Build 36hg18NCBI36
Build 341169,884,527 - 169,908,128NCBI
Celera1146,262,332 - 146,285,933 (-)NCBICelera
Cytogenetic Map1q25.1NCBI
HuRef1144,377,608 - 144,401,209 (-)NCBIHuRef
CHM1_11174,575,344 - 174,598,945 (-)NCBICHM1_1
T2T-CHM13v2.01172,541,831 - 172,768,144 (-)NCBIT2T-CHM13v2.0
Tnfsf4
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391161,223,009 - 161,245,777 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1161,222,980 - 161,245,981 (+)EnsemblGRCm39 EnsemblGRCm39
GRCm381161,395,438 - 161,418,206 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1161,395,409 - 161,418,410 (+)Ensemblmm10GRCm38
MGSCv371163,325,569 - 163,348,337 (+)NCBIMGSCv37MGSCv37mm9NCBIm37
MGSCv361163,232,135 - 163,254,883 (+)NCBIMGSCv36mm8
Celera1163,843,815 - 163,866,564 (+)NCBICelera
Cytogenetic Map1H2.1NCBI
cM Map169.75NCBI
Tnfsf4
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81376,256,654 - 76,280,133 (+)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl1376,256,654 - 76,280,133 (+)EnsemblGRCr8
mRatBN7.21373,723,329 - 73,746,809 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1373,723,329 - 73,746,788 (+)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx1376,302,498 - 76,326,020 (+)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01377,600,036 - 77,623,530 (+)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01374,859,914 - 74,883,412 (+)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.01379,269,973 - 79,293,775 (+)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1379,269,973 - 79,293,778 (+)Ensemblrn6Rnor6.0
Rnor_5.01384,166,838 - 84,190,566 (+)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.41377,026,337 - 77,050,223 (+)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera1373,499,753 - 73,523,609 (+)NCBICelera
RGSC_v3.11377,040,524 - 77,064,407 (+)NCBI
Cytogenetic Map13q22NCBI
Tnfsf4
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495540613,477,077 - 13,493,309 (-)Ensembl
ChiLan1.0NW_00495540613,477,077 - 13,493,309 (-)NCBIChiLan1.0ChiLan1.0
TNFSF4
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v2176,255,433 - 76,559,453 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan1175,929,208 - 76,396,416 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v01148,684,689 - 148,989,775 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.11152,391,450 - 152,699,026 (-)NCBIPanPan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1152,251,683 - 152,262,668 (-)EnsemblpanPan2panpan1.1
PanPan1.1 Ensembl1152,391,450 - 152,415,845 (-)EnsemblpanPan2panpan1.1
Tnfsf4
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440934496,542,360 - 96,562,833 (+)NCBIHiC_Itri_2
SpeTri2.0NW_00493648114,391,359 - 14,409,514 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
TNFSF4
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl9115,550,569 - 115,659,263 (-)EnsemblsusScr11Sscrofa11.1
Sscrofa11.19115,535,185 - 115,857,457 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.29127,042,208 - 127,049,271 (+)NCBISscrofa10.2Sscrofa10.2susScr3
LOC103230569
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.12555,714,291 - 55,998,009 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl2555,974,691 - 55,997,374 (+)EnsemblChlSab1.1 EnsemblchlSab2Vervet-AGM
Vero_WHO_p1.0NW_02366605557,291,046 - 57,591,856 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Tnfsf4
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046247718,580,489 - 8,599,735 (+)NCBIHetGla 1.0HetGla 1.0hetGla2

Variants

.
Variants in TNFSF4
320 total Variants

Expression

RNA-SEQ Expression

adipose tissue
circulatory system
ectoderm
endocrine system
endoderm
hemolymphoid system
integumental system
mesenchyme
mesoderm
nervous system
reproductive system
respiratory system
3 1 3 2 4 3 1 5 5 2 3 4

Sequence


Ensembl Acc Id: ENSCAFT00000023152   ⟹   ENSCAFP00000021496
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
CanFam3.1 Ensembl725,883,251 - 25,906,892 (+)Ensembl
Ensembl Acc Id: ENSCAFT00845021648   ⟹   ENSCAFP00845017016
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
ROS_Cfam_1.0 Ensembl725,634,528 - 25,660,603 (+)Ensembl
RefSeq Acc Id: XM_003639167   ⟹   XP_003639215
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
CanFam3.1725,883,297 - 25,909,608 (+)NCBI
Dog10K_Boxer_Tasha725,415,436 - 25,441,738 (+)NCBI
Sequence:
RefSeq Acc Id: XM_038482615   ⟹   XP_038338543
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
UMICH_Zoey_3.1725,553,133 - 25,579,437 (+)NCBI
RefSeq Acc Id: XM_038541770   ⟹   XP_038397698
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
UU_Cfam_GSD_1.0725,780,205 - 25,806,523 (+)NCBI
RefSeq Acc Id: XM_038605895   ⟹   XP_038461823
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
UNSW_CanFamBas_1.0725,626,526 - 25,652,838 (+)NCBI
RefSeq Acc Id: XM_038670605   ⟹   XP_038526533
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
ROS_Cfam_1.0725,634,585 - 25,660,879 (+)NCBI
RefSeq Acc Id: XP_003639215   ⟸   XM_003639167
- UniProtKB: E2RP79 (UniProtKB/TrEMBL),   A0A8C0SEP3 (UniProtKB/TrEMBL)
- Sequence:
Ensembl Acc Id: ENSCAFP00000021496   ⟸   ENSCAFT00000023152
RefSeq Acc Id: XP_038338543   ⟸   XM_038482615
RefSeq Acc Id: XP_038461823   ⟸   XM_038605895
RefSeq Acc Id: XP_038526533   ⟸   XM_038670605
- UniProtKB: A0A8C0SEP3 (UniProtKB/TrEMBL),   E2RP79 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_038397698   ⟸   XM_038541770
- UniProtKB: A0A8C0SEP3 (UniProtKB/TrEMBL),   E2RP79 (UniProtKB/TrEMBL)
Ensembl Acc Id: ENSCAFP00845017016   ⟸   ENSCAFT00845021648
Protein Domains
THD


Additional Information

Database Acc Id Source(s)
Ensembl Genes ENSCAFG00000014587 Ensembl
  ENSCAFG00000057149 UniProtKB/TrEMBL
  ENSCAFG00030001399 UniProtKB/TrEMBL
  ENSCAFG00040012577 UniProtKB/TrEMBL
  ENSCAFG00845012176 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSCAFT00000109702.1 UniProtKB/TrEMBL
  ENSCAFT00030002475.1 UniProtKB/TrEMBL
  ENSCAFT00040023183.1 UniProtKB/TrEMBL
  ENSCAFT00845021648 ENTREZGENE
  ENSCAFT00845021648.1 UniProtKB/TrEMBL
Gene3D-CATH 2.60.120.40 UniProtKB/TrEMBL
InterPro TNF_dom UniProtKB/TrEMBL
  TNFSF4 UniProtKB/TrEMBL
  Tumour_necrosis_fac-like_dom UniProtKB/TrEMBL
KEGG Report cfa:100855878 UniProtKB/TrEMBL
NCBI Gene TNFSF4 ENTREZGENE
PANTHER PTHR17534 UniProtKB/TrEMBL
  TUMOR NECROSIS FACTOR LIGAND SUPERFAMILY MEMBER 4 UniProtKB/TrEMBL
PROSITE THD_2 UniProtKB/TrEMBL
SMART TNF UniProtKB/TrEMBL
Superfamily-SCOP SSF49842 UniProtKB/TrEMBL
UniProt A0A8C0SEP3 ENTREZGENE, UniProtKB/TrEMBL
  E2RP79 ENTREZGENE, UniProtKB/TrEMBL
VGNC ID VGNC:47672 ENTREZGENE


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2017-03-08 TNFSF4  TNF superfamily member 4    tumor necrosis factor superfamily member 4  Symbol and/or name change 5135510 APPROVED