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Gene-Chemical Interaction Annotations
Gene-Chemical Interaction AnnotationsTerm | Qualifier | Evidence | With | Reference | Notes | Source | Original Reference(s) | (R)-mevalonic acid | multiple interactions | ISO | RGD:1345164 | 6480464 | Mevalonic Acid inhibits the reaction [Simvastatin inhibits the reaction [IFNG results in increased expression of TNFSF4 mRNA]]; more ... | CTD | PMID:19589242 | 1D-myo-inositol 1,4,5-trisphosphate | increases abundance | ISO | RGD:1345164 | 6480464 | TNFSF4 protein results in increased abundance of Inositol 1,4,5-Trisphosphate | CTD | PMID:19416722 | 2,3,7,8-tetrachlorodibenzodioxine | decreases expression | ISO | RGD:1345164 | 6480464 | Tetrachlorodibenzodioxin results in decreased expression of TNFSF4 mRNA | CTD | PMID:20106945 | 2,3,7,8-tetrachlorodibenzodioxine | decreases expression | ISO | RGD:1345164 | 6480464 | Tetrachlorodibenzodioxin results in decreased expression of TNFSF4 mRNA | CTD | PMID:20106945 PMID:21632981 | 2,3,7,8-tetrachlorodibenzodioxine | increases expression | ISO | RGD:733125 | 6480464 | Tetrachlorodibenzodioxin results in increased expression of TNFSF4 mRNA | CTD | PMID:15972635 PMID:14718646 | 2,3,7,8-tetrachlorodibenzodioxine | increases expression | ISO | RGD:733125 | 6480464 | Tetrachlorodibenzodioxin results in increased expression of TNFSF4 mRNA | CTD | PMID:14718646 PMID:15972635 | 2,3,7,8-tetrachlorodibenzodioxine | decreases expression | ISO | RGD:733125 | 6480464 | Tetrachlorodibenzodioxin results in decreased expression of TNFSF4 mRNA | CTD | PMID:18684927 | 3-isobutyl-1-methyl-7H-xanthine | multiple interactions | ISO | RGD:1345164 | 6480464 | [Dexamethasone co-treated with 8-Bromo Cyclic Adenosine Monophosphate co-treated with 1-Methyl-3-isobutylxanthine] results in decreased expression of TNFSF4 mRNA | CTD | PMID:16997883 | 8-bromo-3',5'-cyclic AMP | multiple interactions | ISO | RGD:1345164 | 6480464 | [Dexamethasone co-treated with 8-Bromo Cyclic Adenosine Monophosphate co-treated with 1-Methyl-3-isobutylxanthine] results in decreased expression of TNFSF4 mRNA | CTD | PMID:16997883 | aflatoxin B1 | affects expression | ISO | RGD:1345164 | 6480464 | Aflatoxin B1 affects the expression of TNFSF4 protein | CTD | PMID:20106945 | aflatoxin B1 | increases expression | ISO | RGD:1345164 | 6480464 | Aflatoxin B1 results in increased expression of TNFSF4 mRNA | CTD | PMID:21641981 | ammonium chloride | affects expression | EXP | | 6480464 | Ammonium Chloride affects the expression of TNFSF4 mRNA | CTD | PMID:16483693 | benzo[a]pyrene | decreases expression | ISO | RGD:1345164 | 6480464 | Benzo(a)pyrene results in decreased expression of TNFSF4 mRNA | CTD | PMID:20064835 PMID:20106945 | benzo[a]pyrene | multiple interactions | ISO | RGD:1345164 | 6480464 | [Benzo(a)pyrene co-treated with benzo(b)fluoranthene] affects the expression of TNFSF4 mRNA | CTD | PMID:17690111 | benzo[a]pyrene | decreases expression | ISO | RGD:1345164 | 6480464 | Benzo(a)pyrene results in decreased expression of TNFSF4 mRNA | CTD | PMID:20064835 more ... | benzo[a]pyrene | decreases expression | ISO | RGD:1345164 | 6480464 | Benzo(a)pyrene results in decreased expression of TNFSF4 mRNA | CTD | PMID:20106945 PMID:20064835 | benzo[b]fluoranthene | multiple interactions | ISO | RGD:1345164 | 6480464 | [Benzo(a)pyrene co-treated with benzo(b)fluoranthene] affects the expression of TNFSF4 mRNA | CTD | PMID:17690111 | C60 fullerene | increases expression | EXP | | 6480464 | fullerene C60 results in increased expression of TNFSF4 mRNA | CTD | PMID:20471445 | caffeine | increases expression | ISO | RGD:1345164 | 6480464 | Caffeine results in increased expression of TNFSF4 mRNA | CTD | PMID:18444173 | cobalt dichloride | decreases expression | ISO | RGD:1345164 | 6480464 | cobaltous chloride results in decreased expression of TNFSF4 mRNA | CTD | PMID:19320972 | copper(2+) sulfate | decreases expression | ISO | RGD:1345164 | 6480464 | Copper Sulfate results in decreased expression of TNFSF4 mRNA | CTD | PMID:19549813 | dexamethasone | multiple interactions | ISO | RGD:1345164 | 6480464 | [Dexamethasone co-treated with 8-Bromo Cyclic Adenosine Monophosphate co-treated with 1-Methyl-3-isobutylxanthine] results in decreased expression of TNFSF4 mRNA | CTD | PMID:16997883 | disodium selenite | decreases expression | ISO | RGD:1345164 | 6480464 | Sodium Selenite results in decreased expression of TNFSF4 mRNA | CTD | PMID:18175754 | genistein | decreases expression | ISO | RGD:1345164 | 6480464 | Genistein results in decreased expression of TNFSF4 mRNA | CTD | PMID:18444173 | hydrogen peroxide | increases expression | ISO | RGD:1345164 | 6480464 | Hydrogen Peroxide results in increased expression of TNFSF4 mRNA | CTD | PMID:18951874 | isoflurane | decreases expression | EXP | | 6480464 | Isoflurane results in decreased expression of TNFSF4 mRNA | CTD | PMID:16978161 | methotrexate | increases expression | ISO | RGD:1345164 | 6480464 | Methotrexate results in increased expression of TNFSF4 mRNA | CTD | PMID:17400583 | mevalonic acid | multiple interactions | ISO | RGD:1345164 | 6480464 | Mevalonic Acid inhibits the reaction [Simvastatin inhibits the reaction [IFNG results in increased expression of TNFSF4 mRNA]]; more ... | CTD | PMID:19589242 | paraquat | increases expression | ISO | RGD:733125 | 6480464 | Paraquat results in increased expression of TNFSF4 mRNA | CTD | PMID:22938100 | pentobarbital | decreases expression | EXP | | 6480464 | Pentobarbital results in decreased expression of TNFSF4 mRNA | CTD | PMID:16978161 | quercetin | decreases expression | ISO | RGD:1345164 | 6480464 | Quercetin results in decreased expression of TNFSF4 mRNA | CTD | PMID:21632981 | simvastatin | multiple interactions | ISO | RGD:1345164 | 6480464 | Mevalonic Acid inhibits the reaction [Simvastatin inhibits the reaction [IFNG results in increased expression of TNFSF4 mRNA]]; more ... | CTD | PMID:19589242 | simvastatin | decreases expression | ISO | RGD:1345164 | 6480464 | Simvastatin results in decreased expression of TNFSF4 mRNA; more ... | CTD | PMID:19589242 | tacrine | increases expression | EXP | | 6480464 | Tacrine results in increased expression of TNFSF4 mRNA | CTD | PMID:12832660 | valproic acid | affects expression | ISO | RGD:733125 | 6480464 | Valproic Acid affects the expression of TNFSF4 mRNA | CTD | PMID:17292431 | zinc atom | multiple interactions | ISO | RGD:733125 | 6480464 | [Zinc deficiency promotes the reaction [TRP53 gene mutant form results in increased susceptibility to nitrosobenzylmethylamine]] which results in increased expression of TNFSF4 mRNA | CTD | PMID:12517797 | zinc(0) | multiple interactions | ISO | RGD:733125 | 6480464 | [Zinc deficiency promotes the reaction [TRP53 gene mutant form results in increased susceptibility to nitrosobenzylmethylamine]] which results in increased expression of TNFSF4 mRNA | CTD | PMID:12517797 | | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Gene Ontology Annotations
Molecular Pathway Annotations| External Database Links | |
| KEGG Pathway | Cytokine-cytokine receptor interaction |
Phenotype Annotations
Disease Annotations
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Gene-Chemical Interaction Annotations
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Gene Ontology Annotations
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Molecular Pathway Annotations
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| External Database Links | |
| KEGG Pathway | Cytokine-cytokine receptor interaction |
Phenotype Annotations
References - curated| 1. |
Akiba H, etal., Biochem Biophys Res Commun 1998 Oct 9;251(1):131-6. |
| 2. |
Hammer P and Uhlman TM, Soc Rehabil Rec 1975 Jul-Aug;2(6):28-32. |
| 3. |
MGD data from the GO Consortium |
| 4. |
NCBI rat LocusLink and RefSeq merged data July 26, 2002 |
| 5. |
Pipeline to import KEGG annotations from KEGG into RGD Pathway Ontology |
| 6. |
RGD automated data pipeline |
| 7. |
RGD automated import pipeline for gene-chemical interactions |
| 8. |
RGD Automated Pipelines |
| 9. |
Satake Y, etal., Biochem Biophys Res Commun. 2000 Apr 21;270(3):1041-8. |
| 10. |
Wang X, etal., Nat Genet. 2005 Apr;37(4):365-72. Epub 2005 Mar 6. |
| 11. |
Yuan X, etal., J Immunol. 2003 Mar 15;170(6):2949-55. |
References - uncurated
RGD Disease Portals| Tnfsf4 has been annotated in the following RGD Disease Portals. |
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Comparative Map Data| Tnfsf4 (Rattus norvegicus) |
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| TNFSF4 (Homo sapiens) |
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| Tnfsf4 (Mus musculus) |
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QTLs in Region (RGSC Genome Assembly v3.4)| The following QTLs overlap with this region. | ![]() | Full Report | ![]() | CSV | ![]() | TAB | ![]() | Printer | ![]() | Gviewer |
Nucleotide Sequences| Nucleotide RefSeqs | NM_053552 | (Get FASTA) | Search GEO for Microarray Profiles |
| GenBank Nucleotide | AABR06075787 | (Get FASTA) | Search GEO for Microarray Profiles |
| AABR06075788 | (Get FASTA) | Search GEO for Microarray Profiles | |
| AAHX01076310 | (Get FASTA) | Search GEO for Microarray Profiles | |
| AAHX01076311 | (Get FASTA) | Search GEO for Microarray Profiles | |
| AAHX01076312 | (Get FASTA) | Search GEO for Microarray Profiles | |
| AF037067 | (Get FASTA) | Search GEO for Microarray Profiles | |
| CH473958 | (Get FASTA) | Search GEO for Microarray Profiles |
| RefSeq Acc Id: | NM_053552 | ||||||||||||||||||||
| RefSeq Status: | PROVISIONAL | ||||||||||||||||||||
| Type: | CODING | ||||||||||||||||||||
| Protein Acc Id: | NP_446004 | ||||||||||||||||||||
| Position: |
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Protein Sequences| Protein RefSeqs | NP_446004 | (Get FASTA) |
| GenBank Protein | AAC67236 | (Get FASTA) |
| EDM09415 | (Get FASTA) | |
| Q9Z2P3 | (Get FASTA) |
Strain Sequence Variants
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External Database Links| Database | Acc Id | Source(s) |
| Ensembl Genes | ENSRNOG00000002968 | ENTREZGENE, UniProtKB/Swiss-Prot |
| Ensembl Protein | ENSRNOP00000003969 | ENTREZGENE, UniProtKB/Swiss-Prot |
| Ensembl Transcript | ENSRNOT00000003969 | ENTREZGENE, UniProtKB/Swiss-Prot |
| Entrez Gene | 89814 | ENTREZGENE |
| Germonline | ENSRNOG00000002968 | UniProtKB/Swiss-Prot |
| HomoloGene Group ID | 2495 | ENTREZGENE |
| InterPro | TNF_CS | UniProtKB/Swiss-Prot |
| TNF_family | UniProtKB/Swiss-Prot | |
| Tumour_necrosis_fac-like | UniProtKB/Swiss-Prot | |
| KEGG Report | rno:89814 | ENTREZGENE, UniProtKB/Swiss-Prot |
| Pfam | TNF | UniProtKB/Swiss-Prot |
| PROSITE | TNF_1 | UniProtKB/Swiss-Prot |
| SMART | TNF | UniProtKB/Swiss-Prot |
| Superfamily-SCOP | TNF_like | UniProtKB/Swiss-Prot |
| UniGene | Rn.30043 | ENTREZGENE |
| UniProt | TNFL4_RAT | UniProtKB/Swiss-Prot |
Nomenclature History| Date | Current Symbol | Current Name | Previous Symbol | Previous Name | Description | Reference | Status |
|---|---|---|---|---|---|---|---|
| 2005-01-20 | Tnfsf4 | tumor necrosis factor (ligand) superfamily, member 4 | Symbol and Name status set to approved | 10779 | APPROVED | ||
| 2002-08-07 | Tnfsf4 | tumor necrosis factor (ligand) superfamily, member 4 | Symbol and Name status set to provisional | 1724 | PROVISIONAL |
RGD Curation Notes| Note Type | Note | Reference |
|---|---|---|
| gene_cellular_localization | localized to the cell surface | 634509 |
| gene_protein | 199 amino acids | 634509 |
| More on Tnfsf4 | |
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Entrez Gene |
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Ensembl Gene |
![]() | Genome Browser |
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NCBI Map Viewer |
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Vista |
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Vista + UCSC |
| RGD Object Information | |
| RGD ID: | 619816 |
| Created: | 2002-08-06 |
| Species: | Rattus norvegicus |
| Last Modified: | 2013-05-28 |
| Status: | ACTIVE |
© Bioinformatics Program, HMGC at the Medical College of Wisconsin
RGD is funded by grant HL64541 from the National Heart, Lung, and Blood Institute on behalf of the NIH.




