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TNFSF4 TNF superfamily member 4 [ Homo sapiens (human) ]

Gene ID: 7292, updated on 11-Sep-2019

Summary

Official Symbol
TNFSF4provided by HGNC
Official Full Name
TNF superfamily member 4provided by HGNC
Primary source
HGNC:HGNC:11934
See related
Ensembl:ENSG00000117586 MIM:603594
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
GP34; CD252; OX4OL; TXGP1; CD134L; OX-40L; TNLG2B
Summary
This gene encodes a cytokine of the tumor necrosis factor (TNF) ligand family. The encoded protein functions in T cell antigen-presenting cell (APC) interactions and mediates adhesion of activated T cells to endothelial cells. Polymorphisms in this gene have been associated with Sjogren's syndrome and systemic lupus erythematosus. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jul 2014]
Expression
Low expression observed in reference dataset See more
Orthologs

Genomic context

See TNFSF4 in Genome Data Viewer
Location:
1q25.1
Exon count:
13
Annotation release Status Assembly Chr Location
109.20190905 current GRCh38.p13 (GCF_000001405.39) 1 NC_000001.11 (173183729..173462208, complement)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (173152870..173176471, complement)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene TNF superfamily member 18 Neighboring gene glutamic-oxaloacetic transaminase 2 pseudogene 2 Neighboring gene uncharacterized LOC100506023 Neighboring gene ribosomal protein L26 pseudogene 11 Neighboring gene centrosomal protein 57kDa pseudogene Neighboring gene uncharacterized LOC107985227 Neighboring gene uncharacterized LOC101928673 Neighboring gene peroxiredoxin 6 Neighboring gene solute carrier family 9 member C2 (putative) Neighboring gene testis expressed 50

Genomic regions, transcripts, and products

Expression

  • 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

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Phenotypes

Associated conditions

Description Tests
Myocardial infarction 1
MedGen: C1832662 OMIM: 608446 GeneReviews: Not available
Compare labs

NHGRI GWAS Catalog

Description
A systemic sclerosis and systemic lupus erythematosus pan-meta-GWAS reveals new shared susceptibility loci.
NHGRI GWA Catalog
Genome-wide association study in a Chinese Han population identifies nine new susceptibility loci for systemic lupus erythematosus.
NHGRI GWA Catalog
Genome-wide association study of celiac disease in North America confirms FRMD4B as new celiac locus.
NHGRI GWA Catalog
Genome-wide meta-analysis for severe diabetic retinopathy.
NHGRI GWA Catalog
Genome-wide meta-analysis increases to 71 the number of confirmed Crohn's disease susceptibility loci.
NHGRI GWA Catalog
Meta-analysis followed by replication identifies loci in or near CDKN1B, TET3, CD80, DRAM1, and ARID5B as associated with systemic lupus erythematosus in Asians.
NHGRI GWA Catalog
Multiple common variants for celiac disease influencing immune gene expression.
NHGRI GWA Catalog

Pathways from BioSystems

  • Cytokine Signaling in Immune system, organism-specific biosystem (from REACTOME)
    Cytokine Signaling in Immune system, organism-specific biosystemCytokines are small proteins that regulate and mediate immunity, inflammation, and hematopoiesis. They are secreted in response to immune stimuli, and usually act briefly, locally, at very low concen...
  • Cytokine-cytokine receptor interaction, organism-specific biosystem (from KEGG)
    Cytokine-cytokine receptor interaction, organism-specific biosystemCytokines are soluble extracellular proteins or glycoproteins that are crucial intercellular regulators and mobilizers of cells engaged in innate as well as adaptive inflammatory host defenses, cell ...
  • Cytokine-cytokine receptor interaction, conserved biosystem (from KEGG)
    Cytokine-cytokine receptor interaction, conserved biosystemCytokines are soluble extracellular proteins or glycoproteins that are crucial intercellular regulators and mobilizers of cells engaged in innate as well as adaptive inflammatory host defenses, cell ...
  • Immune System, organism-specific biosystem (from REACTOME)
    Immune System, organism-specific biosystemHumans are exposed to millions of potential pathogens daily, through contact, ingestion, and inhalation. Our ability to avoid infection depends on the adaptive immune system and during the first crit...
  • TNFR2 non-canonical NF-kB pathway, organism-specific biosystem (from REACTOME)
    TNFR2 non-canonical NF-kB pathway, organism-specific biosystemTumor necrosis factor-alpha (TNFA) exerts a wide range of biological effects through TNF receptor 1 (TNFR1) and TNF receptor 2 (TNFR2). Under normal physiological conditions TNFR2 exhibits more restr...
  • TNFs bind their physiological receptors, organism-specific biosystem (from REACTOME)
    TNFs bind their physiological receptors, organism-specific biosystemMembers of the tumour necrosis factor superfamily (TNFSF) and TNF receptor superfamily (TNFRSF) have crucial roles in both innate and adaptive immunity. These members are implicated in various acquir...
  • Thymic Stromal LymphoPoietin (TSLP) Signaling Pathway, organism-specific biosystem (from WikiPathways)
    Thymic Stromal LymphoPoietin (TSLP) Signaling Pathway, organism-specific biosystem
    Thymic Stromal LymphoPoietin (TSLP) Signaling Pathway

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
cytokine activity IEA
Inferred from Electronic Annotation
more info
 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
signaling receptor binding TAS
Traceable Author Statement
more info
PubMed 
tumor necrosis factor receptor binding IEA
Inferred from Electronic Annotation
more info
 
tumor necrosis factor receptor superfamily binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
tumor necrosis factor receptor superfamily binding ISS
Inferred from Sequence or Structural Similarity
more info
 
Process Evidence Code Pubs
T-helper 2 cell activation ISS
Inferred from Sequence or Structural Similarity
more info
 
acute inflammatory response ISS
Inferred from Sequence or Structural Similarity
more info
 
cellular response to lipopolysaccharide IDA
Inferred from Direct Assay
more info
PubMed 
cellular response to prostaglandin E stimulus IDA
Inferred from Direct Assay
more info
PubMed 
chemokine (C-C motif) ligand 11 production ISS
Inferred from Sequence or Structural Similarity
more info
 
defense response to nematode ISS
Inferred from Sequence or Structural Similarity
more info
 
immune response IEA
Inferred from Electronic Annotation
more info
 
inflammatory response IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
memory T cell activation ISS
Inferred from Sequence or Structural Similarity
more info
 
negative regulation of DNA-binding transcription factor activity ISS
Inferred from Sequence or Structural Similarity
more info
 
negative regulation of T-helper 1 cell differentiation ISS
Inferred from Sequence or Structural Similarity
more info
 
negative regulation of interferon-gamma production ISS
Inferred from Sequence or Structural Similarity
more info
 
negative regulation of interleukin-17 production IDA
Inferred from Direct Assay
more info
PubMed 
negative regulation of regulatory T cell differentiation ISS
Inferred from Sequence or Structural Similarity
more info
 
negative regulation of transcription, DNA-templated ISS
Inferred from Sequence or Structural Similarity
more info
 
positive regulation of B cell activation ISS
Inferred from Sequence or Structural Similarity
more info
 
positive regulation of CD4-positive, alpha-beta T cell costimulation ISS
Inferred from Sequence or Structural Similarity
more info
 
positive regulation of CD4-positive, alpha-beta T cell differentiation ISS
Inferred from Sequence or Structural Similarity
more info
 
positive regulation of T cell cytokine production ISS
Inferred from Sequence or Structural Similarity
more info
 
positive regulation of T-helper 2 cell differentiation ISS
Inferred from Sequence or Structural Similarity
more info
 
positive regulation of alpha-beta T cell proliferation ISS
Inferred from Sequence or Structural Similarity
more info
 
positive regulation of cell proliferation TAS
Traceable Author Statement
more info
PubMed 
positive regulation of immunoglobulin mediated immune response ISS
Inferred from Sequence or Structural Similarity
more info
 
positive regulation of immunoglobulin secretion ISS
Inferred from Sequence or Structural Similarity
more info
 
positive regulation of inflammatory response IDA
Inferred from Direct Assay
more info
PubMed 
positive regulation of interferon-gamma production IDA
Inferred from Direct Assay
more info
PubMed 
positive regulation of interleukin-10 production ISS
Inferred from Sequence or Structural Similarity
more info
 
positive regulation of interleukin-12 production ISS
Inferred from Sequence or Structural Similarity
more info
 
positive regulation of interleukin-13 production ISS
Inferred from Sequence or Structural Similarity
more info
 
positive regulation of interleukin-4 production IDA
Inferred from Direct Assay
more info
PubMed 
positive regulation of interleukin-4-dependent isotype switching to IgE isotypes ISS
Inferred from Sequence or Structural Similarity
more info
 
positive regulation of interleukin-6 production IDA
Inferred from Direct Assay
more info
PubMed 
positive regulation of memory T cell differentiation ISS
Inferred from Sequence or Structural Similarity
more info
 
positive regulation of type 2 immune response ISS
Inferred from Sequence or Structural Similarity
more info
 
regulation of adaptive immune response ISS
Inferred from Sequence or Structural Similarity
more info
 
regulation of inflammatory response ISS
Inferred from Sequence or Structural Similarity
more info
 
response to nitrogen dioxide ISS
Inferred from Sequence or Structural Similarity
more info
 
response to virus ISS
Inferred from Sequence or Structural Similarity
more info
 
signal transduction TAS
Traceable Author Statement
more info
PubMed 
tumor necrosis factor-mediated signaling pathway TAS
Traceable Author Statement
more info
 
Component Evidence Code Pubs
cell surface IDA
Inferred from Direct Assay
more info
PubMed 
extracellular space IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
extracellular space IDA
Inferred from Direct Assay
more info
PubMed 
integral component of plasma membrane NAS
Non-traceable Author Statement
more info
PubMed 
plasma membrane TAS
Traceable Author Statement
more info
 

General protein information

Preferred Names
tumor necrosis factor ligand superfamily member 4
Names
CD134 ligand
OX40 antigen ligand
glycoprotein Gp34
tax-transcriptionally activated glycoprotein 1 (34kD)
tumor necrosis factor (ligand) superfamily member 4
tumor necrosis factor ligand 2B
tumor necrosis factor superfamily member 4

NCBI Reference Sequences (RefSeq)

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

  1. NG_011477.1 RefSeqGene

    Range
    5002..28602
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001297562.2NP_001284491.1  tumor necrosis factor ligand superfamily member 4 isoform 2

    See identical proteins and their annotated locations for NP_001284491.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) differs in the 5' UTR, lacks a portion of the 5' coding region, and initiates translation at an alternate start codon, compared to variant 1. The encoded isoform (2) has a distinct N-terminus and is shorter than isoform 1.
    Source sequence(s)
    BC041663, R45433
    Consensus CDS
    CCDS72985.1
    UniProtKB/Swiss-Prot
    P23510
    Related
    ENSP00000356691.1, ENST00000367718.5
    Conserved Domains (1) summary
    smart00207
    Location:24133
    TNF; Tumour necrosis factor family
  2. NM_003326.5NP_003317.1  tumor necrosis factor ligand superfamily member 4 isoform 1

    See identical proteins and their annotated locations for NP_003317.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).
    Source sequence(s)
    AL022310, BC041663, R45433, X79929
    Consensus CDS
    CCDS1306.1
    UniProtKB/Swiss-Prot
    P23510
    UniProtKB/TrEMBL
    A0A024R937
    Related
    ENSP00000281834.3, ENST00000281834.4
    Conserved Domains (1) summary
    smart00207
    Location:74183
    TNF; Tumour necrosis factor family

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109 details...Open this link in a new tab

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000001.11 Reference GRCh38.p13 Primary Assembly

    Range
    173183729..173462208 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_017002228.1XP_016857717.1  tumor necrosis factor ligand superfamily member 4 isoform X2

  2. XM_017002229.1XP_016857718.1  tumor necrosis factor ligand superfamily member 4 isoform X3

  3. XM_017002230.1XP_016857719.1  tumor necrosis factor ligand superfamily member 4 isoform X4

  4. XM_011509964.2XP_011508266.2  tumor necrosis factor ligand superfamily member 4 isoform X1

RNA

  1. XR_002957545.1 RNA Sequence

  2. XR_001737393.2 RNA Sequence

  3. XR_001737394.2 RNA Sequence

  4. XR_001737395.2 RNA Sequence

  5. XR_002957543.1 RNA Sequence

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