Tnfsf18 (TNF superfamily member 18) - Rat Genome Database

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Gene: Tnfsf18 (TNF superfamily member 18) Rattus norvegicus
Analyze
Symbol: Tnfsf18
Name: TNF superfamily member 18
RGD ID: 1305066
Description: Predicted to enable identical protein binding activity and tumor necrosis factor receptor superfamily binding activity. Predicted to be involved in several processes, including regulation of T cell activation; regulation of leukocyte chemotaxis; and tumor necrosis factor-mediated signaling pathway. Predicted to be located in extracellular space and plasma membrane. Predicted to be active in cell surface. Orthologous to human TNFSF18 (TNF superfamily member 18); PARTICIPATES IN cytokine mediated signaling pathway; INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; bisphenol A; endosulfan.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: LOC364031; Tnlg2a; tumor necrosis factor (ligand) superfamily, member 18; tumor necrosis factor ligand 2a; tumor necrosis factor ligand superfamily member 18; tumor necrosis factor superfamily member 18
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Black Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: GRCr8 - GRCr8 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81376,366,790 - 76,440,673 (+)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl1376,366,771 - 76,376,608 (+)EnsemblGRCr8
mRatBN7.21373,833,478 - 73,907,249 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1373,831,252 - 73,843,169 (+)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx1376,412,930 - 76,422,686 (+)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01377,710,263 - 77,720,018 (+)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01374,970,140 - 74,979,895 (+)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.01379,378,412 - 79,388,687 (+)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1379,378,733 - 79,388,498 (+)Ensemblrn6Rnor6.0
Rnor_5.01384,270,937 - 84,282,548 (+)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.41377,137,045 - 77,145,251 (+)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera1373,609,947 - 73,620,222 (+)NCBICelera
RGSC_v3.11377,151,151 - 77,159,439 (+)NCBI
Cytogenetic Map13q22NCBI
JBrowse:




Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

Molecular Function

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. KEGG Annotation Import Pipeline Pipeline to import KEGG annotations from KEGG into RGD
4. GOA pipeline RGD automated data pipeline
5. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:14521928   PMID:14608036   PMID:18040044   PMID:18178614   PMID:18182486   PMID:18378892   PMID:23892569   PMID:24107315   PMID:26646413  


Genomics

Comparative Map Data
Tnfsf18
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81376,366,790 - 76,440,673 (+)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl1376,366,771 - 76,376,608 (+)EnsemblGRCr8
mRatBN7.21373,833,478 - 73,907,249 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1373,831,252 - 73,843,169 (+)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx1376,412,930 - 76,422,686 (+)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01377,710,263 - 77,720,018 (+)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01374,970,140 - 74,979,895 (+)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.01379,378,412 - 79,388,687 (+)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1379,378,733 - 79,388,498 (+)Ensemblrn6Rnor6.0
Rnor_5.01384,270,937 - 84,282,548 (+)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.41377,137,045 - 77,145,251 (+)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera1373,609,947 - 73,620,222 (+)NCBICelera
RGSC_v3.11377,151,151 - 77,159,439 (+)NCBI
Cytogenetic Map13q22NCBI
TNFSF18
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381173,039,202 - 173,050,941 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1173,039,202 - 173,050,941 (-)Ensemblhg38GRCh38
GRCh371173,008,342 - 173,020,081 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361171,276,983 - 171,286,726 (-)NCBIBuild 36Build 36hg18NCBI36
Build 341169,742,107 - 169,751,713NCBI
Celera1146,119,822 - 146,129,565 (-)NCBICelera
Cytogenetic Map1q25.1NCBI
HuRef1144,235,111 - 144,244,854 (-)NCBIHuRef
CHM1_11174,432,835 - 174,442,578 (-)NCBICHM1_1
T2T-CHM13v2.01172,397,315 - 172,409,046 (-)NCBIT2T-CHM13v2.0
Tnfsf18
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391161,322,221 - 161,333,903 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1161,322,224 - 161,332,859 (+)EnsemblGRCm39 EnsemblGRCm39
GRCm381161,494,657 - 161,505,290 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1161,494,655 - 161,505,290 (+)Ensemblmm10GRCm38
MGSCv371163,424,788 - 163,435,421 (+)NCBIMGSCv37MGSCv37mm9NCBIm37
MGSCv361163,331,332 - 163,341,967 (+)NCBIMGSCv36mm8
Celera1163,943,104 - 163,953,733 (+)NCBICelera
Cytogenetic Map1H2.1NCBI
cM Map169.75NCBI
Tnfsf18
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0NW_00495540613,391,162 - 13,402,479 (-)NCBIChiLan1.0ChiLan1.0
TNFSF18
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v2176,687,163 - 76,700,053 (+)NCBINHGRI_mPanPan1-v2
TNFSF18
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1725,983,064 - 25,994,605 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl725,963,719 - 25,992,801 (+)EnsemblcanFam3CanFam3.1
Dog10K_Boxer_Tasha725,514,906 - 25,526,500 (+)NCBIDog10K_Boxer_TashaDog10K_Boxer_Tasha
ROS_Cfam_1.0725,734,171 - 25,745,767 (+)NCBIROS_Cfam_1.0ROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl725,734,080 - 25,744,296 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1725,652,719 - 25,664,301 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0725,725,623 - 25,737,220 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0725,879,459 - 25,891,051 (+)NCBIUU_Cfam_GSD_1.0UU_Cfam_GSD_1.0
Tnfsf18
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440934496,652,746 - 96,661,551 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_00493648114,499,577 - 14,508,017 (+)EnsemblSpeTri2.0 Ensembl
SpeTri2.0NW_00493648114,499,495 - 14,508,074 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
TNFSF18
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl9115,448,973 - 115,460,950 (-)EnsemblsusScr11Sscrofa11.1
Sscrofa11.19115,447,438 - 115,460,649 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.29127,140,943 - 127,151,861 (+)NCBISscrofa10.2Sscrofa10.2susScr3
TNFSF18
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.12556,105,757 - 56,118,249 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl2556,106,584 - 56,118,758 (+)EnsemblChlSab1.1 EnsemblchlSab2Vervet-AGM
Vero_WHO_p1.0NW_02366605557,711,144 - 57,721,390 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Tnfsf18
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046247718,711,017 - 8,722,539 (+)EnsemblHetGla_female_1.0 EnsemblhetGla2HetGla_female_1.0 Ensembl
HetGla 1.0NW_0046247718,711,093 - 8,722,518 (+)NCBIHetGla 1.0HetGla 1.0hetGla2
Tnfsf18
(Rattus rattus - black rat)
Black Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rrattus_CSIRO_v11040,799,325 - 40,807,564 (+)NCBIRrattus_CSIRO_v1

Variants

.
Variants in Tnfsf18
678 total Variants
miRNA Target Status (No longer updated)

Predicted Target Of
Summary Value
Count of predictions:148
Count of miRNA genes:128
Interacting mature miRNAs:134
Transcripts:ENSRNOT00000039221
Prediction methods:Microtar, 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 (GRCr8)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1298066Bp159Blood pressure QTL 1590.004arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)134863963493639634Rat
10755495Bp387Blood pressure QTL 3873.78arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)133721624190057603Rat
1354655Bp241Blood pressure QTL 2413.9arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)1338975045103588154Rat
8655951Rf63Renal function QTL 6312.2blood urea nitrogen amount (VT:0005265)plasma urea nitrogen level (CMO:0000586)1371610804109350286Rat
70220Bp55Blood pressure QTL 555.75arterial blood pressure trait (VT:2000000)blood pressure measurement (CMO:0000003)133992469384924693Rat
8655945Rf61Renal function QTL 613.6blood creatinine amount (VT:0005328)creatinine clearance (CMO:0000765)137161080489333251Rat
71119Thym2Thymus enlargement QTL 23.8thymus mass (VT:0004954)thymus weight to body weight ratio (CMO:0000612)134874981487285480Rat
4889861Pur29Proteinuria QTL 2913.80.005urine total protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)133996821183286298Rat
1331783Bp221Blood pressure QTL 2213.72886arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)137161080489333251Rat
8655959Pur32Proteinuria QTL 328.4urine total protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)137298450699745408Rat
1300166Kidm6Kidney mass QTL 63.93kidney mass (VT:0002707)single kidney wet weight to body weight ratio (CMO:0000622)137161080489333251Rat
2293687Bss26Bone structure and strength QTL 264.60.0001femur morphology trait (VT:0000559)femur cross-sectional area (CMO:0001661)1367635937109350286Rat
619615Bp80Blood pressure QTL 800.0354arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)13742179187286911Rat
61340Bp25Blood pressure QTL 254.20.004arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)133708798382087983Rat
1581573Uae36Urinary albumin excretion QTL 36urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)13600200888706694Rat
1549897Stresp12Stress response QTL 123.35stress-related behavior trait (VT:0010451)number of approaches toward negative stimulus before onset of defensive burying response (CMO:0001960)134098358585983585Rat
724564Uae11Urinary albumin excretion QTL 115.7urine albumin amount (VT:0002871)urine albumin level (CMO:0000130)134735425894285672Rat
738027Lnnr6Liver neoplastic nodule remodeling QTL 63.3liver integrity trait (VT:0010547)liver remodeling tumorous lesion number (CMO:0001461)1365613454109350286Rat
7207885Glom27Glomerulus QTL 273.9kidney glomerulus integrity trait (VT:0010546)kidney crescentic glomeruli count to kidney normal glomeruli count ratio (CMO:0002139)1321120177109350286Rat
7387280Uae43Urinary albumin excretion QTL 435.690.4174urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)1368983334109350286Rat
738026Lnnr5Liver neoplastic nodule remodeling QTL 53.29liver integrity trait (VT:0010547)liver remodeling tumorous lesion number (CMO:0001461)136242459288113509Rat
70181BpQTLcluster11Blood pressure QTL cluster 116.922arterial blood pressure trait (VT:2000000)absolute change in mean arterial blood pressure (CMO:0000533)133379409678794096Rat
2293702Bss34Bone structure and strength QTL 344.610.0001femur strength trait (VT:0010010)femur midshaft polar moment of inertia (CMO:0001669)1367635937109350286Rat
61349Bp31Blood pressure QTL 315.75arterial blood pressure trait (VT:2000000)blood pressure measurement (CMO:0000003)133992469384924693Rat
1576318Schws5Schwannoma susceptibility QTL 50.0351nervous system integrity trait (VT:0010566)post-insult time to trigeminal nerve neurilemmoma formation (CMO:0002019)1364497900109350286Rat
2303563Bw89Body weight QTL 896body mass (VT:0001259)body weight (CMO:0000012)133483494779834947Rat
1354621Rf47Renal function QTL 473.7kidney renin amount (VT:0010559)kidney renin level (CMO:0002166)1311081740103588154Rat
1581554Pur11Proteinuria QTL 11urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)13600200888706694Rat
12879477Bp401Blood pressure QTL 401arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)133981472684814726Rat
1331750Bp220Blood pressure QTL 2202.98arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)133996821184968211Rat
12879475Bp400Blood pressure QTL 400arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)1364375743109350286Rat
11530006Niddm72Non-insulin dependent diabetes mellitus QTL 720.001blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)133828629883286298Rat
1354666Bp244Blood pressure QTL 2444.9arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)131103588154Rat
2293341Glom15Glomerulus QTL 159.1kidney glomerulus integrity trait (VT:0010546)kidney sclerotic glomeruli count to total glomeruli count ratio (CMO:0001269)1367635937109350286Rat


Expression

RNA-SEQ Expression

alimentary part of gastrointestinal system
appendage
circulatory system
ectoderm
endocrine system
endoderm
exocrine system
hemolymphoid system
hepatobiliary system
integumental system
mesenchyme
mesoderm
musculoskeletal system
nervous system
renal system
reproductive system
respiratory system
sensory system
visual system
15 10 62 141 66 68 37 45 37 6 253 134 9 123 59 84 31 10 10

Sequence


Ensembl Acc Id: ENSRNOT00000039221   ⟹   ENSRNOP00000035225
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl1376,366,771 - 76,376,608 (+)Ensembl
mRatBN7.2 Ensembl1373,831,252 - 73,843,169 (+)Ensembl
Rnor_6.0 Ensembl1379,378,733 - 79,388,498 (+)Ensembl
RefSeq Acc Id: NM_001398596   ⟹   NP_001385525
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81376,366,853 - 76,376,608 (+)NCBI
mRatBN7.21373,833,534 - 73,843,289 (+)NCBI
RefSeq Acc Id: XM_039091401   ⟹   XP_038947329
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81376,366,790 - 76,440,673 (+)NCBI
mRatBN7.21373,833,478 - 73,907,249 (+)NCBI
Protein Sequences
Protein RefSeqs NP_001385525 (Get FASTA)   NCBI Sequence Viewer  
  XP_038947329 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein CTQ86173 (Get FASTA)   NCBI Sequence Viewer  
  EDM09414 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000035225
  ENSRNOP00000035225.5
Ensembl Acc Id: ENSRNOP00000035225   ⟸   ENSRNOT00000039221
RefSeq Acc Id: XP_038947329   ⟸   XM_039091401
- Peptide Label: isoform X1
RefSeq Acc Id: NP_001385525   ⟸   NM_001398596
- UniProtKB: A6ID83 (UniProtKB/TrEMBL),   D4A3I1 (UniProtKB/TrEMBL)
Protein Domains
THD

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-D4A3I1-F1-model_v2 AlphaFold D4A3I1 1-173 view protein structure

Transcriptome

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

Promoters
RGD ID:13698938
Promoter ID:EPDNEW_R9458
Type:multiple initiation site
Name:Tnfsf18_1
Description:TNF superfamily member 18
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_6.01379,378,733 - 79,378,793EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1305066 AgrOrtholog
BioCyc Gene G2FUF-17709 BioCyc
Ensembl Genes ENSRNOG00000026607 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000039221 ENTREZGENE
  ENSRNOT00000039221.7 UniProtKB/TrEMBL
Gene3D-CATH 2.60.120.40 UniProtKB/TrEMBL
InterPro TNF_dom UniProtKB/TrEMBL
  TNFSF18 UniProtKB/TrEMBL
  Tumour_necrosis_fac-like UniProtKB/TrEMBL
NCBI Gene 364031 ENTREZGENE
PANTHER PTHR15267 UniProtKB/TrEMBL
  TUMOR NECROSIS FACTOR LIGAND SUPERFAMILY MEMBER 18 UniProtKB/TrEMBL
PhenoGen Tnfsf18 PhenoGen
PROSITE THD_2 UniProtKB/TrEMBL
RatGTEx ENSRNOG00000026607 RatGTEx
Superfamily-SCOP TNF_like UniProtKB/TrEMBL
UniProt A6ID83 ENTREZGENE, UniProtKB/TrEMBL
  D4A3I1 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2017-03-21 Tnfsf18  TNF superfamily member 18  Tnfsf18  tumor necrosis factor superfamily member 18  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2015-11-25 Tnfsf18  tumor necrosis factor superfamily member 18  Tnfsf18  tumor necrosis factor (ligand) superfamily, member 18  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-04-30 Tnfsf18  tumor necrosis factor (ligand) superfamily, member 18   Tnfsf18_predicted  tumor necrosis factor (ligand) superfamily, member 18 (predicted)  'predicted' is removed 2292626 APPROVED
2005-01-12 Tnfsf18_predicted  tumor necrosis factor (ligand) superfamily, member 18 (predicted)      Symbol and Name status set to approved 70820 APPROVED