Tnfsf18 (TNF superfamily member 18) - Rat Genome Database

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Gene: Tnfsf18 (TNF superfamily member 18) Rattus norvegicus
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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 positive regulation of NF-kappaB transcription factor activity; regulation of T cell activation; and regulation of leukocyte chemotaxis. Predicted to be located in 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
Alliance Genes
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21373,833,478 - 73,907,249 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1373,831,252 - 73,843,169 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1376,412,930 - 76,422,686 (+)NCBIRnor_SHR
UTH_Rnor_SHRSP_BbbUtx_1.01377,710,263 - 77,720,018 (+)NCBIRnor_SHRSP
UTH_Rnor_WKY_Bbb_1.01374,970,140 - 74,979,895 (+)NCBIRnor_WKY
Rnor_6.01379,378,412 - 79,388,687 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1379,378,733 - 79,388,498 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01384,270,937 - 84,282,548 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41377,137,045 - 77,145,251 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.11377,151,151 - 77,159,439 (+)NCBI
Celera1373,609,947 - 73,620,222 (+)NCBICelera
Cytogenetic Map13q22NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

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

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
mRatBN7.21373,833,478 - 73,907,249 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1373,831,252 - 73,843,169 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1376,412,930 - 76,422,686 (+)NCBIRnor_SHR
UTH_Rnor_SHRSP_BbbUtx_1.01377,710,263 - 77,720,018 (+)NCBIRnor_SHRSP
UTH_Rnor_WKY_Bbb_1.01374,970,140 - 74,979,895 (+)NCBIRnor_WKY
Rnor_6.01379,378,412 - 79,388,687 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1379,378,733 - 79,388,498 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01384,270,937 - 84,282,548 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41377,137,045 - 77,145,251 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.11377,151,151 - 77,159,439 (+)NCBI
Celera1373,609,947 - 73,620,222 (+)NCBICelera
Cytogenetic Map13q22NCBI
TNFSF18
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381173,039,202 - 173,050,941 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p13 Ensembl1173,039,202 - 173,050,941 (-)EnsemblGRCh38hg38GRCh38
GRCh371173,008,342 - 173,020,081 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361171,276,983 - 171,286,726 (-)NCBINCBI36Build 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
GRCm391161,322,226 - 161,332,859 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1161,322,224 - 161,332,859 (+)EnsemblGRCm39 Ensembl
GRCm381161,494,657 - 161,505,290 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1161,494,655 - 161,505,290 (+)EnsemblGRCm38mm10GRCm38
MGSCv371163,424,788 - 163,435,421 (+)NCBIGRCm37MGSCv37mm9NCBIm37
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
PanPan1.11152,251,683 - 152,262,668 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1152,251,683 - 152,262,668 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v01148,528,535 - 148,662,839 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
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 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha725,514,906 - 25,526,500 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0725,734,171 - 25,745,767 (+)NCBIROS_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_1.0
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
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 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
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 (+)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
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_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_0046247718,711,093 - 8,722,518 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Tnfsf18
978 total Variants
miRNA Target Status

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 (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1354666Bp244Blood pressure QTL 2444.9arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)131101056920Rat
1354666Bp244Blood pressure QTL 2444.9arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)131101056920Rat
1354666Bp244Blood pressure QTL 2444.9arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)131101056920Rat
1581554Pur11Proteinuria QTL 11urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)13599483377046787Rat
1581573Uae36Urinary albumin excretion QTL 36urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)13599483377046787Rat
1581570Eae17Experimental allergic encephalomyelitis QTL 174.1nervous system integrity trait (VT:0010566)experimental autoimmune encephalomyelitis incidence/prevalence measurement (CMO:0001046)138897350101631289Rat
7207885Glom27Glomerulus QTL 273.9kidney glomerulus integrity trait (VT:0010546)kidney crescentic glomeruli count to kidney normal glomeruli count ratio (CMO:0002139)1320605871101339738Rat
1354621Rf47Renal function QTL 473.7kidney renin amount (VT:0010559)kidney renin level (CMO:0002166)1330395351101056920Rat
70181BpQTLcluster11Blood pressure QTL cluster 116.922arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)133124133193395974Rat
70181BpQTLcluster11Blood pressure QTL cluster 116.922arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)133124133193395974Rat
70181BpQTLcluster11Blood pressure QTL cluster 116.922arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)133124133193395974Rat
70181BpQTLcluster11Blood pressure QTL cluster 116.922arterial blood pressure trait (VT:2000000)absolute change in mean arterial blood pressure (CMO:0000533)133124133193395974Rat
2303563Bw89Body weight QTL 896body mass (VT:0001259)body weight (CMO:0000012)133228447177284471Rat
61340Bp25Blood pressure QTL 254.20.004arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)133453521879535218Rat
12879477Bp401Blood pressure QTL 401arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)133726209282262092Rat
61349Bp31Blood pressure QTL 315.75arterial blood pressure trait (VT:2000000)blood pressure measurement (CMO:0000003)133737450982374509Rat
70220Bp55Blood pressure QTL 555.75arterial blood pressure trait (VT:2000000)blood pressure measurement (CMO:0000003)133737450982374509Rat
4889861Pur29Proteinuria QTL 2913.80.005urine total protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)133741558480753406Rat
1331750Bp220Blood pressure QTL 2202.98arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)133741558482415584Rat
1549897Stresp12Stress response QTL 123.35stress-related behavior trait (VT:0010451)number of approaches toward negative stimulus before onset of defensive burying response (CMO:0001960)133843340883433408Rat
619615Bp80Blood pressure QTL 800.0354arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)133975454484754544Rat
12879444Bp397Blood pressure QTL 397arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)134504940490049404Rat
12879471Bp398Blood pressure QTL 398arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)134551471990514719Rat
12879441Bp396Blood pressure QTL 396arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)134569998390699983Rat
1298066Bp159Blood pressure QTL 1590.004arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)134608804691088046Rat
71119Thym2Thymus enlargement QTL 23.8thymus mass (VT:0004954)thymus weight to body weight ratio (CMO:0000612)134619797684753113Rat
1641901Alcrsp6Alcohol response QTL 6response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)135236217197362171Rat
1354655Bp241Blood pressure QTL 2413.9arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)1356056920101056920Rat
724564Uae11Urinary albumin excretion QTL 115.7urine albumin amount (VT:0002871)urine albumin level (CMO:0000130)135949252277046890Rat
738026Lnnr5Liver neoplastic nodule remodeling QTL 53.29liver integrity trait (VT:0010547)liver remodeling tumorous lesion number (CMO:0001461)135987440885581182Rat
12879475Bp400Blood pressure QTL 400arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)1361825626106807694Rat
2293702Bss34Bone structure and strength QTL 344.610.0001femur strength trait (VT:0010010)femur midshaft polar moment of inertia (CMO:0001669)1365103704106807694Rat
2293687Bss26Bone structure and strength QTL 264.60.0001femur morphology trait (VT:0000559)femur cross-sectional area (CMO:0001661)1365103704106807694Rat
8655951Rf63Renal function QTL 6312.2blood urea nitrogen amount (VT:0005265)plasma urea nitrogen level (CMO:0000586)136906051977046890Rat
8655945Rf61Renal function QTL 613.6blood creatinine amount (VT:0005328)creatinine clearance (CMO:0000765)136906051986800898Rat
1331783Bp221Blood pressure QTL 2213.72886arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)136906051986800898Rat
1300166Kidm6Kidney mass QTL 63.93kidney mass (VT:0002707)single kidney wet weight to body weight ratio (CMO:0000622)136906051986800898Rat


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
Low 3 2 5 8 11 16 11
Below cutoff 3 37 37 26 14 26 8 10 57 22 21 8

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000039221   ⟹   ENSRNOP00000035225
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1373,831,252 - 73,843,169 (+)Ensembl
Rnor_6.0 Ensembl1379,378,733 - 79,388,498 (+)Ensembl
RefSeq Acc Id: XM_008769705   ⟹   XP_008767927
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21373,833,502 - 73,843,523 (+)NCBI
Rnor_6.01379,378,412 - 79,388,687 (+)NCBI
Sequence:
RefSeq Acc Id: XM_039091401   ⟹   XP_038947329
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21373,833,478 - 73,907,249 (+)NCBI
Protein Sequences
Protein RefSeqs NP_001385525 (Get FASTA)   NCBI Sequence Viewer  
  XP_008767927 (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  
Reference Sequences
RefSeq Acc Id: XP_008767927   ⟸   XM_008769705
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: ENSRNOP00000035225   ⟸   ENSRNOT00000039221
RefSeq Acc Id: XP_038947329   ⟸   XM_039091401
- Peptide Label: isoform X2

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 Protein ENSRNOP00000035225 ENTREZGENE
  ENSRNOP00000035225.4 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000039221 ENTREZGENE
  ENSRNOT00000039221.6 UniProtKB/TrEMBL
Gene3D-CATH 2.60.120.40 UniProtKB/TrEMBL
InterPro TNFSF18 UniProtKB/TrEMBL
  Tumour_necrosis_fac-like UniProtKB/TrEMBL
NCBI Gene 364031 ENTREZGENE
PANTHER PTHR15267 UniProtKB/TrEMBL
PhenoGen Tnfsf18 PhenoGen
Superfamily-SCOP TNF_like UniProtKB/TrEMBL
UniProt 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