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    TNFSF13 TNF superfamily member 13 [ Homo sapiens (human) ]

    Gene ID: 8741, updated on 12-Mar-2019

    Summary

    Official Symbol
    TNFSF13provided by HGNC
    Official Full Name
    TNF superfamily member 13provided by HGNC
    Primary source
    HGNC:HGNC:11928
    See related
    Ensembl:ENSG00000161955 MIM:604472
    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
    APRIL; CD256; TALL2; ZTNF2; TALL-2; TNLG7B; TRDL-1; UNQ383/PRO715
    Summary
    The protein encoded by this gene is a member of the tumor necrosis factor (TNF) ligand family. This protein is a ligand for TNFRSF17/BCMA, a member of the TNF receptor family. This protein and its receptor are both found to be important for B cell development. In vitro experiments suggested that this protein may be able to induce apoptosis through its interaction with other TNF receptor family proteins such as TNFRSF6/FAS and TNFRSF14/HVEM. Alternative splicing results in multiple transcript variants. Some transcripts that skip the last exon of the upstream gene (TNFSF12) and continue into the second exon of this gene have been identified; such read-through transcripts are contained in GeneID 407977, TNFSF12-TNFSF13. [provided by RefSeq, Oct 2010]
    Expression
    Ubiquitous expression in lung (RPKM 37.5), gall bladder (RPKM 25.6) and 25 other tissues See more
    Orthologs

    Genomic context

    See TNFSF13 in Genome Data Viewer
    Location:
    17p13.1
    Exon count:
    6
    Annotation release Status Assembly Chr Location
    109 current GRCh38.p12 (GCF_000001405.38) 17 NC_000017.11 (7558292..7561608)
    105 previous assembly GRCh37.p13 (GCF_000001405.25) 17 NC_000017.10 (7461609..7464925)

    Chromosome 17 - NC_000017.11Genomic Context describing neighboring genes Neighboring gene RNA polymerase II subunit A Neighboring gene TNFSF12-TNFSF13 readthrough Neighboring gene TNF superfamily member 12 Neighboring gene SENP3-EIF4A1 readthrough (NMD candidate) Neighboring gene SUMO specific peptidase 3 Neighboring gene eukaryotic translation initiation factor 4A1 Neighboring gene small nucleolar RNA, H/ACA box 48

    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 FunctionsWhat's a GeneRIF?

    Phenotypes

    NHGRI GWAS Catalog

    Description
    A genome-wide association study in Han Chinese identifies multiple susceptibility loci for IgA nephropathy.
    NHGRI GWA Catalog
    Association of common variants in TNFRSF13B, TNFSF13, and ANXA3 with serum levels of non-albumin protein and immunoglobulin isotypes in Japanese.
    NHGRI GWA Catalog
    Genome-wide association study identifies TNFSF13 as a susceptibility gene for IgA in a South Chinese population in smokers.
    NHGRI GWA Catalog
    Genome-wide scan identifies variant in TNFSF13 associated with serum IgM in a healthy Chinese male population.
    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 ...
    • Gene Expression, organism-specific biosystem (from REACTOME)
      Gene Expression, organism-specific biosystemGene Expression covers the pathways by which genomic DNA is transcribed to yield RNA, the regulation of these transcription processes, and the pathways by which newly-made RNA Transcripts are process...
    • HuR (ELAVL1) binds and stabilizes mRNA, organism-specific biosystem (from REACTOME)
      HuR (ELAVL1) binds and stabilizes mRNA, organism-specific biosystemHuR (ELAVL1) is a ubiquitous protein that binds AU-rich elements in mRNAs and acts to stabilize the mRNAs. HuR activity is controlled by phosphorylation, with PKC alpha and PCK delta enhancing the ab...
    • 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...
    • Intestinal immune network for IgA production, organism-specific biosystem (from KEGG)
      Intestinal immune network for IgA production, organism-specific biosystemThe intestine is the largest lymphoid tissue in the body. One striking feature of intestinal immunity is its ability to generate great amounts of noninflammatory immunoglobulin A (IgA) antibodies tha...
    • Intestinal immune network for IgA production, conserved biosystem (from KEGG)
      Intestinal immune network for IgA production, conserved biosystemThe intestine is the largest lymphoid tissue in the body. One striking feature of intestinal immunity is its ability to generate great amounts of noninflammatory immunoglobulin A (IgA) antibodies tha...
    • Regulation of mRNA stability by proteins that bind AU-rich elements, organism-specific biosystem (from REACTOME)
      Regulation of mRNA stability by proteins that bind AU-rich elements, organism-specific biosystemRNA elements rich in adenine and uracil residues (AU-rich elements) bind specific proteins which either target the RNA for degradation or, more rarely, stabilize the RNA. The activity of the AU-eleme...
    • Rheumatoid arthritis, organism-specific biosystem (from KEGG)
      Rheumatoid arthritis, organism-specific biosystemRheumatoid arthritis (RA) is a chronic autoimmune joint disease where persistent inflammation affects bone remodeling leading to progressive bone destruction. In RA, abnormal activation of the immune...
    • Rheumatoid arthritis, conserved biosystem (from KEGG)
      Rheumatoid arthritis, conserved biosystemRheumatoid arthritis (RA) is a chronic autoimmune joint disease where persistent inflammation affects bone remodeling leading to progressive bone destruction. In RA, abnormal activation of the immune...
    • Spinal Cord Injury, organism-specific biosystem (from WikiPathways)
      Spinal Cord Injury, organism-specific biosystemThis pathway provides an overview of cell types, therapeutic targets, drugs, new proposed targets and pathways implicated in spinal cord injury. Spinal cord injury is a complex multistep process that...
    • 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...

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Readthrough TNFSF12-TNFSF13

    Readthrough gene: TNFSF12-TNFSF13, Included gene: TNFSF12

    Homology

    Clone Names

    • FLJ57090

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    cytokine activity IEA
    Inferred from Electronic Annotation
    more info
     
    signaling receptor binding TAS
    Traceable Author Statement
    more info
    PubMed 
    tumor necrosis factor receptor binding IEA
    Inferred from Electronic Annotation
    more info
     
    Process Evidence Code Pubs
    immune response IEA
    Inferred from Electronic Annotation
    more info
     
    positive regulation of cell proliferation TAS
    Traceable Author Statement
    more info
    PubMed 
    positive regulation of isotype switching to IgA isotypes IDA
    Inferred from Direct Assay
    more info
    PubMed 
    regulation of mRNA stability TAS
    Traceable Author Statement
    more info
     
    regulation of signaling receptor activity IEA
    Inferred from Electronic Annotation
    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
    cytoplasm IDA
    Inferred from Direct Assay
    more info
    PubMed 
    cytosol TAS
    Traceable Author Statement
    more info
     
    extracellular exosome HDA PubMed 
    extracellular region TAS
    Traceable Author Statement
    more info
     
    membrane IEA
    Inferred from Electronic Annotation
    more info
     
    nucleoplasm TAS
    Traceable Author Statement
    more info
     

    General protein information

    Preferred Names
    tumor necrosis factor ligand superfamily member 13
    Names
    TNF- and APOL-related leukocyte expressed ligand 2
    a proliferation-inducing ligand
    tumor necrosis factor (ligand) superfamily, member 13
    tumor necrosis factor ligand 7B
    tumor necrosis factor superfamily member 13
    tumor necrosis factor-like protein ZTNF2
    tumor necrosis factor-related death ligand-1

    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_029949.1 RefSeqGene

      Range
      5001..8317
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001198622.1NP_001185551.1  tumor necrosis factor ligand superfamily member 13 isoform delta

      See identical proteins and their annotated locations for NP_001185551.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (delta) lacks an alternate in-frame segment in the 5' coding region, compared to variant alpha, resulting in an isoform (delta) that is shorter than isoform alpha. It is not known whether this isoform (delta) is proteolytically processed in the same manner as isoforms alpha and beta.
      Source sequence(s)
      AI828515, AK225556, BI764562, DQ149579
      Consensus CDS
      CCDS73957.1
      UniProtKB/TrEMBL
      Q2QBA2
      Related
      ENSP00000369908.5, ENST00000380535.8
      Conserved Domains (1) summary
      cd00184
      Location:90221
      TNF; Tumor Necrosis Factor; TNF superfamily members include the cytokines: TNF (TNF-alpha), LT (lymphotoxin-alpha, TNF-beta), CD40 ligand, Apo2L (TRAIL), Fas ligand, and osteoprotegerin (OPG) ligand. These proteins generally have an intracellular N-terminal ...
    2. NM_001198623.1NP_001185552.1  tumor necrosis factor ligand superfamily member 13 isoform zeta

      See identical proteins and their annotated locations for NP_001185552.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (zeta) lacks an alternate in-frame segment in the 5' coding region, compared to variant alpha, resulting in an isoform (zeta) that is shorter than isoform alpha. It is not known whether this isoform (zeta) is proteolytically processed in the same manner as isoforms alpha and beta.
      Source sequence(s)
      AI828515, AK225556, AK301221, BI764562
      Consensus CDS
      CCDS56018.1
      UniProtKB/Swiss-Prot
      O75888
      Related
      ENSP00000486052.1, ENST00000625791.2
      Conserved Domains (1) summary
      cd00184
      Location:89220
      TNF; Tumor Necrosis Factor; TNF superfamily members include the cytokines: TNF (TNF-alpha), LT (lymphotoxin-alpha, TNF-beta), CD40 ligand, Apo2L (TRAIL), Fas ligand, and osteoprotegerin (OPG) ligand. These proteins generally have an intracellular N-terminal ...
    3. NM_001198624.1NP_001185553.1  tumor necrosis factor ligand superfamily member 13 isoform eta

      Status: REVIEWED

      Description
      Transcript Variant: This variant (eta) differs in the 5' UTR, uses a downstream start codon, and lacks an alternate in-frame segment in the 5' coding region, compared to variant alpha, resulting in an isoform (eta) that is shorter than isoform alpha. It is not known whether this isoform (eta) is proteolytically processed in the same manner as isoforms alpha and beta.
      Source sequence(s)
      AC016876, AI828515, AK225556, BF793371, BI764562
      Consensus CDS
      CCDS56019.1
      UniProtKB/Swiss-Prot
      O75888
      Related
      ENSP00000379792.1, ENST00000396542.5
      Conserved Domains (1) summary
      cd00184
      Location:72203
      TNF; Tumor Necrosis Factor; TNF superfamily members include the cytokines: TNF (TNF-alpha), LT (lymphotoxin-alpha, TNF-beta), CD40 ligand, Apo2L (TRAIL), Fas ligand, and osteoprotegerin (OPG) ligand. These proteins generally have an intracellular N-terminal ...
    4. NM_003808.3NP_003799.1  tumor necrosis factor ligand superfamily member 13 isoform alpha precursor

      See identical proteins and their annotated locations for NP_003799.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (alpha) represents the longest transcript and encodes the longest isoform (alpha).
      Source sequence(s)
      AF046888, AI828515, AK225556, BI764562
      Consensus CDS
      CCDS11111.1
      UniProtKB/Swiss-Prot
      O75888
      Related
      ENSP00000343505.4, ENST00000338784.8
      Conserved Domains (1) summary
      cd00184
      Location:117248
      TNF; Tumor Necrosis Factor; TNF superfamily members include the cytokines: TNF (TNF-alpha), LT (lymphotoxin-alpha, TNF-beta), CD40 ligand, Apo2L (TRAIL), Fas ligand, and osteoprotegerin (OPG) ligand. These proteins generally have an intracellular N-terminal ...
    5. NM_172087.2NP_742084.1  tumor necrosis factor ligand superfamily member 13 isoform beta precursor

      See identical proteins and their annotated locations for NP_742084.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (beta) lacks an alternate in-frame exon in the central coding region, compared to variant alpha, resulting in an isoform (beta) that is shorter than isoform alpha.
      Source sequence(s)
      AF114012, AI828515, AK090698, BI764562
      Consensus CDS
      CCDS11112.1
      UniProtKB/Swiss-Prot
      O75888
      UniProtKB/TrEMBL
      B3KR02
      Related
      ENSP00000314455.6, ENST00000349228.8
      Conserved Domains (1) summary
      cd00184
      Location:115232
      TNF; Tumor Necrosis Factor; TNF superfamily members include the cytokines: TNF (TNF-alpha), LT (lymphotoxin-alpha, TNF-beta), CD40 ligand, Apo2L (TRAIL), Fas ligand, and osteoprotegerin (OPG) ligand. These proteins generally have an intracellular N-terminal ...
    6. NM_172088.2NP_742085.1  tumor necrosis factor ligand superfamily member 13 isoform gamma

      See identical proteins and their annotated locations for NP_742085.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (gamma) lacks an alternate segment in the 3' coding region and 3' UTR, compared to variant alpha, resulting in an isoform (gamma) that has a distinct and shorter C-terminus, compared to isoform alpha. It is not known whether this isoform (gamma) is proteolytically processed in the same manner as isoforms alpha and beta.
      Source sequence(s)
      AF114013, AI828515, BC008042, BI764562
      Consensus CDS
      CCDS42256.1
      UniProtKB/Swiss-Prot
      O75888
      Related
      ENSP00000379794.4, ENST00000396545.4
      Conserved Domains (1) summary
      cd00184
      Location:117247
      TNF; Tumor Necrosis Factor; TNF superfamily members include the cytokines: TNF (TNF-alpha), LT (lymphotoxin-alpha, TNF-beta), CD40 ligand, Apo2L (TRAIL), Fas ligand, and osteoprotegerin (OPG) ligand. These proteins generally have an intracellular N-terminal ...

    RNA

    1. NR_073490.2 RNA Sequence

      Status: REVIEWED

      Description
      Transcript Variant: This variant (episilon) lacks two internal exons in the 5' region, compared to variant alpha. This variant is represented as non-coding because the use of the 5'-most expected translational start codon, as used in variant alpha, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
      Source sequence(s)
      AI828515, AK090698, BI764562, EF211088

    RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109

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

    Reference GRCh38.p12 Primary Assembly

    Genomic

    1. NC_000017.11 Reference GRCh38.p12 Primary Assembly

      Range
      7558292..7561608
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
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