TNFSF15 TNF superfamily member 15 [Homo sapiens (human)] - Gene

Summary

Official Symbol: TNFSF15provided by HGNC
Official Full Name: TNF superfamily member 15provided by HGNC
Primary source: HGNC:HGNC:11931
See related: Ensembl:ENSG00000181634 MIM:604052; AllianceGenome:HGNC:11931
Gene type: protein coding
RefSeq status: REVIEWED
Organism: Homo sapiens
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as: TL1; TL1A; VEGI; TNLG1B; VEGI192A
Summary: The protein encoded by this gene is a cytokine that belongs to the tumor necrosis factor (TNF) ligand family. This protein is abundantly expressed in endothelial cells, but is not expressed in either B or T cells. The expression of this protein is inducible by TNF and IL-1 alpha. This cytokine is a ligand for receptor TNFRSF25 and decoy receptor TNFRSF21/DR6. It can activate NF-kappaB and MAP kinases, and acts as an autocrine factor to induce apoptosis in endothelial cells. This cytokine is also found to inhibit endothelial cell proliferation, and thus may function as an angiogenesis inhibitor. Two transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Feb 2011]
Expression: Broad expression in duodenum (RPKM 4.3), urinary bladder (RPKM 3.6) and 17 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 9q32

Exon count:: 4

Annotation release	Status	Assembly	Chr	Location
RS_2023_10	current	GRCh38.p14 (GCF_000001405.40)	9	NC_000009.12 (114784635..114806039, complement)
RS_2023_10	current	T2T-CHM13v2.0 (GCF_009914755.1)	9	NC_060933.1 (126977075..126998476, complement)
105.20220307	previous assembly	GRCh37.p13 (GCF_000001405.25)	9	NC_000009.11 (117546915..117568319, complement)

Chromosome 9 - NC_000009.12 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: HPA RNA-seq normal tissues
Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
BioProject: PRJEB4337
Publication: PMID 24309898
Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

TL1A is an epithelial alarmin that cooperates with IL-33 for initiation of allergic airway inflammation.
Title: TL1A is an epithelial alarmin that cooperates with IL-33 for initiation of allergic airway inflammation.
The Relation of VEGFA, VEGFR2, VEGI, and HIF1A Genetic Variants and Their Serum Protein Levels with Breast Cancer in Egyptian Patients.
Title: The Relation of VEGFA, VEGFR2, VEGI, and HIF1A Genetic Variants and Their Serum Protein Levels with Breast Cancer in Egyptian Patients.
Genetic architecture of the inflammatory bowel diseases across East Asian and European ancestries.
Title: Genetic architecture of the inflammatory bowel diseases across East Asian and European ancestries.
Increased Serum Levels of Tumor Necrosis Factor-like Ligand 1A in Atopic Dermatitis.
Title: Increased Serum Levels of Tumor Necrosis Factor-like Ligand 1A in Atopic Dermatitis.
Immune Checkpoint Inhibitor (ICI) Genes and Aging in Clear Cell Renal Cell Carcinoma (ccRCC): Clinical and Genomic Study.
Title: Immune Checkpoint Inhibitor (ICI) Genes and Aging in Clear Cell Renal Cell Carcinoma (ccRCC): Clinical and Genomic Study.
Role of TNFSF15 variants in oral cancer development and clinicopathologic characteristics.
Title: Role of TNFSF15 variants in oral cancer development and clinicopathologic characteristics.
Genome-wide association study identifies TNFSF15 associated with childhood asthma.
Title: Genome-wide association study identifies TNFSF15 associated with childhood asthma.
Nonylphenol regulates TL1A through the AhR/HDAC2/HNF4alpha pathway in endothelial cells to promote the angiogenesis of colorectal cancer.
Title: Nonylphenol regulates TL1A through the AhR/HDAC2/HNF4α pathway in endothelial cells to promote the angiogenesis of colorectal cancer.
The relationship between TNF-like protein 1A and coronary artery aneurysms in children with Kawasaki disease.
Title: The relationship between TNF-like protein 1A and coronary artery aneurysms in children with Kawasaki disease.
Effect and Mechanism of TL1A Expression on Epithelial-Mesenchymal Transition during Chronic Colitis-Related Intestinal Fibrosis.
Title: Effect and Mechanism of TL1A Expression on Epithelial-Mesenchymal Transition during Chronic Colitis-Related Intestinal Fibrosis.

Submit: New GeneRIF Correction See all GeneRIFs (149)

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

EBI GWAS Catalog

Description
A genome-wide association study identifies 2 susceptibility Loci for Crohn's disease in a Japanese population. EBI GWAS Catalog EBI GWAS CatalogPubMed
Discovery of six new susceptibility loci and analysis of pleiotropic effects in leprosy. EBI GWAS Catalog EBI GWAS CatalogPubMed
Genetic predictors of medically refractory ulcerative colitis. EBI GWAS Catalog EBI GWAS CatalogPubMed
Genome-wide association defines more than 30 distinct susceptibility loci for Crohn's disease. EBI GWAS Catalog EBI GWAS CatalogPubMed
Genome-wide association study identifies TNFSF15 and POU2AF1 as susceptibility loci for primary biliary cirrhosis in the Japanese population. EBI GWAS Catalog EBI GWAS CatalogPubMed
Genome-wide meta-analysis increases to 71 the number of confirmed Crohn's disease susceptibility loci. EBI GWAS Catalog EBI GWAS CatalogPubMed
Genomewide association study of leprosy. EBI GWAS Catalog EBI GWAS CatalogPubMed
HLA-Cw1202-B5201-DRB1*1502 haplotype increases risk for ulcerative colitis but reduces risk for Crohn's disease. EBI GWAS Catalog EBI GWAS CatalogPubMed
Host-microbe interactions have shaped the genetic architecture of inflammatory bowel disease. EBI GWAS Catalog EBI GWAS CatalogPubMed
IgA measurements in over 12 000 Swedish twins reveal sex differential heritability and regulatory locus near CD30L. EBI GWAS Catalog EBI GWAS CatalogPubMed
Loci on 20q13 and 21q22 are associated with pediatric-onset inflammatory bowel disease. EBI GWAS Catalog EBI GWAS CatalogPubMed
Meta-analysis identifies 29 additional ulcerative colitis risk loci, increasing the number of confirmed associations to 47. EBI GWAS Catalog EBI GWAS CatalogPubMed

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

HIV-1 interactions

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Protein interactions

Protein	Gene	Interaction	Pubs
Vif	vif	HIV-1 Vif upregulates the expression of tumor necrosis factor ligand superfamily, member 15 (TNFSF15) in Vif-expression T cells	PubMed
Vpr	vpr	HIV-1 Vpr upregulates the gene expression of TNFSF15 in human monocyte-derived dendritic cells	PubMed

Go to the HIV-1, Human Interaction Database

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

NoName (e-PCR)
- UniSTS:486934

NoName (e-PCR)
- UniSTS:480791

NoName (e-PCR)
- UniSTS:482098

D8S2279 (e-PCR)
- UniSTS:473907

TNFSF15_410 (e-PCR)
- UniSTS:277835

D1S1423 (e-PCR)
- UniSTS:149619

D9S2088 (e-PCR)
- UniSTS:53939

RH120641 (e-PCR)
- UniSTS:132582

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables cytokine activity	IEA Inferred from Electronic Annotation more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables signaling receptor binding	TAS Traceable Author Statement more info	PubMed
enables tumor necrosis factor receptor binding	IEA Inferred from Electronic Annotation more info

Process	Evidence Code	Pubs
acts_upstream_of_or_within activation of NF-kappaB-inducing kinase activity	IDA Inferred from Direct Assay more info	PubMed
involved_in activation of cysteine-type endopeptidase activity involved in apoptotic process	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within activation of cysteine-type endopeptidase activity involved in apoptotic process	IDA Inferred from Direct Assay more info	PubMed
involved_in immune response	IEA Inferred from Electronic Annotation more info
involved_in signal transduction	NAS Non-traceable Author Statement more info	PubMed

Component	Evidence Code	Pubs
located_in extracellular space	IEA Inferred from Electronic Annotation more info
located_in membrane	NAS Non-traceable Author Statement more info	PubMed
located_in plasma membrane	IDA Inferred from Direct Assay more info	PubMed
located_in plasma membrane	TAS Traceable Author Statement more info

General protein information

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Preferred Names: tumor necrosis factor ligand superfamily member 15

Names: TNF ligand-related molecule 1; TNF superfamily ligand TL1A; tumor necrosis factor (ligand) superfamily, member 15; tumor necrosis factor ligand 1B; tumor necrosis factor superfamily member 15; vascular endothelial cell growth inhibitor; vascular endothelial growth inhibitor-192A

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

Genomic

NG_011488.2 RefSeqGene

Range

5090..26477

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_001204344.1 → NP_001191273.1 tumor necrosis factor ligand superfamily member 15 isoform VEGI-192

See identical proteins and their annotated locations for NP_001191273.1

Status: REVIEWED

Description

Transcript Variant: This variant (2) differs in the 5' UTR and coding sequence compared to variant 1. The resulting isoform (VEGI-192) has a shorter and distinct N-terminus compared to isoform VEGI-251.

Source sequence(s)

AL390240, AW014795, AY434464

UniProtKB/Swiss-Prot

O95150

Conserved Domains (1) summary

pfam00229
Location:58 → 192

TNF; TNF(Tumour Necrosis Factor) family
NM_005118.4 → NP_005109.2 tumor necrosis factor ligand superfamily member 15 isoform VEGI-251 precursor

See identical proteins and their annotated locations for NP_005109.2

Status: REVIEWED

Description

Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (VEGI-251).

Source sequence(s)

AL390240, BC104463

Consensus CDS

CCDS6809.1

UniProtKB/Swiss-Prot

O95150, Q3SX69, Q5VJK8, Q5VWH1, Q8NFE9

UniProtKB/TrEMBL

A0A0U5JA19

Related

ENSP00000363157.3, ENST00000374045.5

Conserved Domains (1) summary

pfam00229
Location:117 → 251

TNF; TNF(Tumour Necrosis Factor) family