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PR01968

Identifier
TNFACTORR18  [View Relations]  [View Alignment]  
Accession
PR01968
No. of Motifs
3
Creation Date
14-JUL-2009
Title
Tumour necrosis factor receptor 18 signature
Database References

MIM; 603905
Literature References
1. ARMITAGE, R.
Tumor necrosis factor receptor superfamily members and their ligands.
CURR.OPIN.IMMUNOL. 6 407-413 (1994).
 
2. BANNER D., D'ARCY, A., JAMES, W., GENTZ, R., SCHOENFELD, H., BROGER, C.,
LOETSCHER, H. AND LESSLAUER, W.
Crystal structure of the soluble human 55 kD TNF receptor-human TNF-beta
complex: implications for TNF receptor activation.
CELL 73 431-445 (1993).
 
3. WU, H.
Assembly of post-receptor signaling complexes for the tumor necrosis factor
receptor superfamily.
ADV.PROTEIN CHEM. 68 225-279 (2004).
 
4. LOCKSLEY, R., KILLEEN, N. AND LENARDO, M.
The TNF and TNF Receptor Superfamilies: Integrating Mammalian Biology.
CELL 104 487-501 (2001).
 
5. GRAVESTEIN, L. AND BORST, J.
Tumor necrosis factor receptor family members in the immune system.
SEMIN.IMMUNOL. 10 423-434 (1998).
 
6. LOENEN, W.
D27 and (TNFR) relatives in the immune system: their role in health and
disease.
SEMIN.IMMUNOL. 10 417-422 (1998).
 
7. NOCENTINI, G., GIUNCHI, L., RONCHETTI, S., KRAUSZ, L., BARTOLI, A., 
MORACA, R., MIGLIORATI, G. AND RICCARDI, C.
A new member of the tumor necrosis factor/nerve growth factor receptor 
family inhibits T cell receptor-induced apoptosis.
PROC.NATL.ACAD.SCI.U.S.A. 94 6216-6221 (1997).

Documentation
The tumour necrosis factor (TNF) receptor (TNFR) superfamily comprises more
than 20 type-I transmembrane proteins. Family members are defined based on
similarity in their extracellular domain - a region that contains many
cysteine residues arranged in a specific repetitive pattern [1]. The
cysteines allow formation of an extended rod-like structure, responsible for
ligand binding [2].
 
Upon receptor activation, different intracellular signalling complexes are
assembled for different members of the TNFR superfamily, depending on their
intracellular domains and sequences [3]. Activation of TNFRs can therefore
induce a range of disparate effects, including cell proliferation,
differentiation, survival, or apoptotic cell death, depending upon the
receptor involved [4,5].
 
TNFRs are widely distributed and play important roles in many crucial
biological processes, such as lymphoid and neuronal development, innate and
adaptive immunity, and maintenance of cellular homeostasis [3]. Drugs that
manipulate their signalling have potential roles in the prevention and
treatment of many diseases, such as viral infections, coronary heart
disease, transplant rejection, and immune disease [6].
 
TNF receptor 18 is also known as glucocorticoid-induced TNFR family-related
gene (GITR) and activation-inducible TNFR family member (AITR). Expression
of the receptor by T-lymphocytes has been shown to have an anti-apoptotic 
effect, indicating that it may play a role in the regulation of T-cell 
receptor-mediated cell death [7].
 
TNFACTORR18 is a 3-element fingerprint that provides a signature for tumour
necrosis factor receptor 18. The fingerprint was derived from an initial
alignment of 8 sequences: the motifs were drawn from conserved regions in 
the N-terminal two thirds of the alignment, focusing on those sections that
characterise TNF receptor 18 but distinguish it from other TNF receptor
subtypes - all motifs lie within the extracellular N-terminal region. Two
iterations on SPTR57_40f were required to reach convergence, at which point
a true set comprising 9 sequences was identified. Three partial matches were
also found, all of which fail to match motif 3: B1ASL4_MOUSE and
B1AME1_HUMAN are TNF receptor 18 splice variants from mouse and human,
and Q5M835_RAT is a translated mouse cDNA sequence.
Summary Information
   9 codes involving  3 elements
3 codes involving 2 elements
Composite Feature Index
3999
2330
123
True Positives
A9Y5K8_DANRE  B1AME3_HUMAN  B1ASL6_MOUSE  Q540M6_MOUSE  
Q5U0I4_HUMAN Q5ZMR1_CHICK Q8C4K3_MOUSE TNR18_HUMAN
TNR18_MOUSE
True Positive Partials
Codes involving 2 elements
B1AME1_HUMAN B1ASL4_MOUSE Q5M835_RAT
Sequence Titles
A9Y5K8_DANRE Tumor necrosis factor receptor superfamily member 18 - Danio rerio (Zebrafish) (Brachydanio rerio). 
B1AME3_HUMAN Tumor necrosis factor receptor superfamily, member 18 - Homo sapiens (Human).
B1ASL6_MOUSE Tumor necrosis factor receptor superfamily, member 18 - Mus musculus (Mouse).
Q540M6_MOUSE Tumor necrosis factor receptor superfamily member 18 - Mus musculus (Mouse).
Q5U0I4_HUMAN TNFRSF18 protein - Homo sapiens (Human).
Q5ZMR1_CHICK Putative uncharacterized protein - Gallus gallus (Chicken).
Q8C4K3_MOUSE Putative uncharacterized protein - Mus musculus (Mouse).
TNR18_HUMAN Tumor necrosis factor receptor superfamily member 18 - Homo sapiens (Human).
TNR18_MOUSE Tumor necrosis factor receptor superfamily member 18 - Mus musculus (Mouse).

B1AME1_HUMAN Tumor necrosis factor receptor superfamily, member 18 - Homo sapiens (Human).
B1ASL4_MOUSE Tumor necrosis factor receptor superfamily, member 18 - Mus musculus (Mouse).
Q5M835_RAT Similar to tumor necrosis factor receptor superfamily, member 18 - Rattus norvegicus (Rat).
Scan History
SPTR57_40f 2  300  NSINGLE    
Initial Motifs
Motif 1  width=11
Element Seqn Id St Int Rpt
KHYPCQPGQRV TNR18_MOUSE 78 78 -
KHYPCQPGQRV Q8C4K3_MOUSE 78 78 -
KHYPCQPGQRV Q540M6_MOUSE 78 78 -
RHHPCPPGQGV B1AME3_HUMAN 90 90 -
RHHPCPPGQGV TNR18_HUMAN 90 90 -
RHHPCPPGQGV Q5U0I4_HUMAN 90 90 -
PREKCKPGQQL A9Y5K8_DANRE 96 96 -
KKTECPEGKEL Q5ZMR1_CHICK 89 89 -

Motif 2 width=12
Element Seqn Id St Int Rpt
GDIVFGFRCVAC TNR18_MOUSE 92 3 -
GDIVFGFRCVAC Q8C4K3_MOUSE 92 3 -
GDIVFGFRCVAC Q540M6_MOUSE 92 3 -
GKFSFGFQCIDC B1AME3_HUMAN 104 3 -
GKFSFGFQCIDC TNR18_HUMAN 104 3 -
GKFSFGFQCIDC Q5U0I4_HUMAN 104 3 -
GNFHFSFHCAPC A9Y5K8_DANRE 110 3 -
GIIQYTYSCKPC Q5ZMR1_CHICK 103 3 -

Motif 3 width=14
Element Seqn Id St Int Rpt
GFLTMFPGNKTHNA TNR18_MOUSE 126 22 -
GFLTMFPGNKTHNA Q8C4K3_MOUSE 126 22 -
GFLTMFPGNKTHNA Q540M6_MOUSE 126 22 -
GFLTVFPGNKTHNA B1AME3_HUMAN 138 22 -
GFLTVFPGNKTHNA TNR18_HUMAN 138 22 -
GFLTVFPGNKTHNA Q5U0I4_HUMAN 138 22 -
GVGEFFPGNQTHNA A9Y5K8_DANRE 142 20 -
GLLTIKQGNSTHNS Q5ZMR1_CHICK 137 22 -
Final Motifs
Motif 1  width=11
Element Seqn Id St Int Rpt
KHYPCQPGQRV B1ASL6_MOUSE 78 78 -
KHYPCQPGQRV TNR18_MOUSE 78 78 -
KHYPCQPGQRV Q8C4K3_MOUSE 78 78 -
KHYPCQPGQRV Q540M6_MOUSE 78 78 -
RHHPCPPGQGV B1AME3_HUMAN 90 90 -
RHHPCPPGQGV TNR18_HUMAN 90 90 -
RHHPCPPGQGV Q5U0I4_HUMAN 90 90 -
PREKCKPGQQL A9Y5K8_DANRE 96 96 -
KKTECPEGKEL Q5ZMR1_CHICK 89 89 -

Motif 2 width=12
Element Seqn Id St Int Rpt
GDIVFGFRCVAC B1ASL6_MOUSE 92 3 -
GDIVFGFRCVAC TNR18_MOUSE 92 3 -
GDIVFGFRCVAC Q8C4K3_MOUSE 92 3 -
GDIVFGFRCVAC Q540M6_MOUSE 92 3 -
GKFSFGFQCIDC B1AME3_HUMAN 104 3 -
GKFSFGFQCIDC TNR18_HUMAN 104 3 -
GKFSFGFQCIDC Q5U0I4_HUMAN 104 3 -
GNFHFSFHCAPC A9Y5K8_DANRE 110 3 -
GIIQYTYSCKPC Q5ZMR1_CHICK 103 3 -

Motif 3 width=14
Element Seqn Id St Int Rpt
GFLTMFPGNKTHNA B1ASL6_MOUSE 126 22 -
GFLTMFPGNKTHNA TNR18_MOUSE 126 22 -
GFLTMFPGNKTHNA Q8C4K3_MOUSE 126 22 -
GFLTMFPGNKTHNA Q540M6_MOUSE 126 22 -
GFLTVFPGNKTHNA B1AME3_HUMAN 138 22 -
GFLTVFPGNKTHNA TNR18_HUMAN 138 22 -
GFLTVFPGNKTHNA Q5U0I4_HUMAN 138 22 -
GVGEFFPGNQTHNA A9Y5K8_DANRE 142 20 -
GLLTIKQGNSTHNS Q5ZMR1_CHICK 137 22 -