Human Gene TNFSF9 (ENST00000245817.5_4) from GENCODE V47lift37
  Description: TNF superfamily member 9 (from RefSeq NM_003811.4)
Gencode Transcript: ENST00000245817.5_4
Gencode Gene: ENSG00000125657.5_7
Transcript (Including UTRs)
   Position: hg19 chr19:6,531,037-6,535,935 Size: 4,899 Total Exon Count: 3 Strand: +
Coding Region
   Position: hg19 chr19:6,531,048-6,535,077 Size: 4,030 Coding Exon Count: 3 

Page IndexSequence and LinksUniProtKB CommentsPrimersCTDGene Alleles
RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesGO Annotations
mRNA DescriptionsPathwaysOther NamesModel InformationMethods
Data last updated at UCSC: 2024-08-22 23:36:26

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr19:6,531,037-6,535,935)mRNA (may differ from genome)Protein (254 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
HGNCMGIOMIMPubMedReactomeUniProtKB
BioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: TNFL9_HUMAN
DESCRIPTION: RecName: Full=Tumor necrosis factor ligand superfamily member 9; AltName: Full=4-1BB ligand; Short=4-1BBL;
FUNCTION: Cytokine that binds to TNFRSF9. Induces the proliferation of activated peripheral blood T-cells. May have a role in activation-induced cell death (AICD). May play a role in cognate interactions between T-cells and B-cells/macrophages.
SUBUNIT: Homotrimer.
SUBCELLULAR LOCATION: Membrane; Single-pass type II membrane protein.
TISSUE SPECIFICITY: Expressed in brain, placenta, lung, skeletal muscle and kidney.
SIMILARITY: Belongs to the tumor necrosis factor family.

-  Primer design for this transcript
 

Primer3Plus can design qPCR Primers that straddle exon-exon-junctions, which amplify only cDNA, not genomic DNA.
Click here to load the transcript sequence and exon structure into Primer3Plus

Exonprimer can design one pair of Sanger sequencing primers around every exon, located in non-genic sequence.
Click here to open Exonprimer with this transcript

To design primers for a non-coding sequence, zoom to a region of interest and select from the drop-down menu: View > In External Tools > Primer3


-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene           more ... click here to view the complete list

+  Common Gene Haplotype Alleles
  Press "+" in the title bar above to open this section.

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 55.44 RPKM in Cells - EBV-transformed lymphocytes
Total median expression: 101.41 RPKM



View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
  Press "+" in the title bar above to open this section.

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
3' UTR -280.30858-0.327 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  InterPro Domains: Graphical view of domain structure
IPR006052 - TNF
IPR021184 - TNF_CS
IPR008983 - Tumour_necrosis_fac-like

Pfam Domains:
PF00229 - TNF(Tumour Necrosis Factor) family

SCOP Domains:
49842 - TNF-like

Protein Data Bank (PDB) 3-D Structure
MuPIT help
2X29 - X-ray MuPIT


ModBase Predicted Comparative 3D Structure on P41273
FrontTopSide
The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
No orthologNo orthologNo orthologNo orthologNo orthologNo ortholog
Gene DetailsGene Details    
Gene SorterGene Sorter    
 RGD    
      
      

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0005102 receptor binding
GO:0005125 cytokine activity
GO:0005164 tumor necrosis factor receptor binding
GO:0032813 tumor necrosis factor receptor superfamily binding

Biological Process:
GO:0006915 apoptotic process
GO:0006955 immune response
GO:0007165 signal transduction
GO:0007267 cell-cell signaling
GO:0008283 cell proliferation
GO:0010469 regulation of receptor activity
GO:0033209 tumor necrosis factor-mediated signaling pathway
GO:0042104 positive regulation of activated T cell proliferation
GO:0045585 positive regulation of cytotoxic T cell differentiation

Cellular Component:
GO:0005615 extracellular space
GO:0005886 plasma membrane
GO:0016020 membrane
GO:0016021 integral component of membrane


-  Descriptions from all associated GenBank mRNAs
  BC104805 - Homo sapiens tumor necrosis factor (ligand) superfamily, member 9, mRNA (cDNA clone MGC:132465 IMAGE:8143808), complete cds.
BC104807 - Homo sapiens tumor necrosis factor (ligand) superfamily, member 9, mRNA (cDNA clone MGC:132467 IMAGE:8143810), complete cds.
AK313999 - Homo sapiens cDNA, FLJ94653, highly similar to Homo sapiens tumor necrosis factor (ligand) superfamily, member 9 (TNFSF9), mRNA.
AB590869 - Synthetic construct DNA, clone: pFN21AE1751, Homo sapiens TNFSF9 gene for tumor necrosis factor (ligand) superfamily, member 9, without stop codon, in Flexi system.
U03398 - Human receptor 4-1BB ligand mRNA, complete cds.
KJ892610 - Synthetic construct Homo sapiens clone ccsbBroadEn_02004 TNFSF9 gene, encodes complete protein.
LF210898 - JP 2014500723-A/18401: Polycomb-Associated Non-Coding RNAs.
JD539678 - Sequence 520702 from Patent EP1572962.
JD520191 - Sequence 501215 from Patent EP1572962.
JD329401 - Sequence 310425 from Patent EP1572962.
JD054935 - Sequence 35959 from Patent EP1572962.
JD400180 - Sequence 381204 from Patent EP1572962.
JD400171 - Sequence 381195 from Patent EP1572962.
JD391357 - Sequence 372381 from Patent EP1572962.
JD342422 - Sequence 323446 from Patent EP1572962.
JD480557 - Sequence 461581 from Patent EP1572962.
JD435498 - Sequence 416522 from Patent EP1572962.
JD308227 - Sequence 289251 from Patent EP1572962.
JD157832 - Sequence 138856 from Patent EP1572962.
JD105093 - Sequence 86117 from Patent EP1572962.
JD283664 - Sequence 264688 from Patent EP1572962.
JD377035 - Sequence 358059 from Patent EP1572962.
JD190251 - Sequence 171275 from Patent EP1572962.
JD188370 - Sequence 169394 from Patent EP1572962.
JD388725 - Sequence 369749 from Patent EP1572962.
JD509475 - Sequence 490499 from Patent EP1572962.
JD172383 - Sequence 153407 from Patent EP1572962.
JD037976 - Sequence 19000 from Patent EP1572962.
JD148078 - Sequence 129102 from Patent EP1572962.
JD182834 - Sequence 163858 from Patent EP1572962.
JD500917 - Sequence 481941 from Patent EP1572962.
JD409594 - Sequence 390618 from Patent EP1572962.
JD377578 - Sequence 358602 from Patent EP1572962.
JD187278 - Sequence 168302 from Patent EP1572962.
JD070729 - Sequence 51753 from Patent EP1572962.
JD071891 - Sequence 52915 from Patent EP1572962.
JD235137 - Sequence 216161 from Patent EP1572962.
MA446475 - JP 2018138019-A/18401: Polycomb-Associated Non-Coding RNAs.

-  Biochemical and Signaling Pathways
  BioCarta from NCI Cancer Genome Anatomy Project
h_41bbPathway - The 4-1BB-dependent immune response

Reactome (by CSHL, EBI, and GO)

Protein P41273 (Reactome details) participates in the following event(s):

R-HSA-8858475 TNFSF9 binds TNFRSF9
R-HSA-5669034 TNFs bind their physiological receptors
R-HSA-5668541 TNFR2 non-canonical NF-kB pathway
R-HSA-1280215 Cytokine Signaling in Immune system
R-HSA-168256 Immune System

-  Other Names for This Gene
  Alternate Gene Symbols: ENST00000245817.1, ENST00000245817.2, ENST00000245817.3, ENST00000245817.4, NM_003811, P41273, Q2M3S2, TNFL9_HUMAN, uc317ern.1, uc317ern.2
UCSC ID: ENST00000245817.5_4
RefSeq Accession: NM_003811.4
Protein: P41273 (aka TNFL9_HUMAN or TNF9_HUMAN)

-  Gene Model Information
  Click here for a detailed description of the fields of the table above.

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.