WORKLIST ENTRIES (1): TNFACTORR9 View alignment Tumour necrosis factor receptor 9 signature Type of fingerprint: COMPOUND with 3 elements Links: PRINTS; PR01918 TNFACTORR1A; PR01919 TNFACTORR1B; PR01920 TNFACTORR3 PRINTS; PR01921 TNFACTORR4; PR01922 TNFACTORR5; PR01680 TNFACTORR6 PRINTS; PR01960 TNFACTORR7; PR01923 TNFACTORR8; PR01956 TNFACTORR10 PRINTS; PR01961 TNFACTORR11; PR01962 TNFACTORR12; PR01963 TNFACTORR13B PRINTS; PR01964 TNFACTORR13C; PR01965 TNFACTORR14; PR01966 TNFACTORR16 PRINTS; PR01967 TNFACTORR17; PR01968 TNFACTORR18; PR01969 TNFACTORR19 PRINTS; PR01970 TNFACTORR19l; PR01971 TNFACTORR21; PR01972 TNFACTORR25 PRINTS; PR01973 TNFACTORR27 PRINTS; PR01974 TNFACTORR11A; PR01975 TNFACTORR11B PDB; 1D0J 3Dinfo SCOP; 1D0J CATH; 1D0J MIM; 602250 Creation date 23-APR-2008 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. SCHWARZ, H., BLANCO, F., VON KEMPIS, J., VALBRACHT, J. AND LOTZ, M. ILA, a member of the human nerve growth factor/tumor necrosis factor receptor family, regulates T-lymphocyte proliferation and survival. BLOOD 87 2839-2845 (1996). 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 . The cysteines allow formation of an extended rod-like structure, responsible for ligand binding . Upon receptor activation, different intracellular signalling complexes are assembled for different members of the TNFR superfamily, depending on their intracellular domains and sequences . 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 . 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 . TNF receptor 9 (also known as ILA and CD137 antigen) is expressed by activated T and B lymphocytes and monocytes. Stimulation of the receptor inhibits proliferation of activated T lymphocytes and induces programmed cell death . TNFACTORR9 is a 3-element fingerprint that provides a signature for tumour necrosis factor receptor 9. The fingerprint was derived from an initial alignment of 2 sequences: the motifs were drawn from conserved regions in the C-terminal half of the alignment, focusing on those sections that characterise TNF receptor 9 but distinguish it from other TNF receptor subtypes - motif 1 lies partially in the transmembrane domain and partially within the C-terminal cytoplasmic region; and motifs 2 and 3 reside within the C-terminal cytoplasmic region. Two iterations on SPTR55_38f were required to reach convergence, at which point a true set comprising 7 sequences was identified. Three partial matches were also found, all of which fail to match motif 1: Q8R037_MOUSE is a translated cDNA from mouse; and A9YYF0_MACFA and A9YYF1_MACFA are receptor variants from crab- eating macaque. SUMMARY INFORMATION 7 codes involving 3 elements 3 codes involving 2 elements COMPOSITE FINGERPRINT INDEX 3| 7 7 7 2| 0 3 3 --+---------------- | 1 2 3 True positives.. Q3U3R1_MOUSE TNR9_MOUSE TNR9_HUMAN A9YYE7_MACFA Q3ZC74_BOVIN Q4V895_RAT Q4W8J3_RAT Subfamily: Codes involving 2 elements Subfamily True positives.. A9YYF0_MACFA A9YYF1_MACFA Q8R037_MOUSE PROTEIN TITLES Q3U3R1_MOUSE NOD-derived CD11c +ve dendritic cells cDNA, RIKEN full-lengt TNR9_MOUSE Tumor necrosis factor receptor superfamily member 9 precurso TNR9_HUMAN Tumor necrosis factor receptor superfamily member 9 precurso A9YYE7_MACFA CD137 - Macaca fascicularis (Crab eating macaque) (Cynomolgu Q3ZC74_BOVIN Similar to tumor necrosis factor receptor superfamily, membe Q4V895_RAT Similar to T-cell antigen 4-1BB-mouse - Rattus norvegicus (R Q4W8J3_RAT 4-1BB homolog - Rattus norvegicus (Rat). A9YYF0_MACFA CD137 variant - Macaca fascicularis (Crab eating macaque) (C A9YYF1_MACFA CD137 variant - Macaca fascicularis (Crab eating macaque) (C Q8R037_MOUSE Tumor necrosis factor receptor superfamily, member 9 (Secret
SCAN HISTORY SPTR55_38f 2 300 NSINGLE INITIAL MOTIF SETS TNFACTORR91 Length of motif = 14 Motif number = 1 Tumour necrosis factor receptor 9 motif I - 1 PCODE ST INT IFITLLFSVLKWIR TNR9_MOUSE 202 202 FFLTLRFSVVKRGR TNR9_HUMAN 204 204 TNFACTORR92 Length of motif = 15 Motif number = 2 Tumour necrosis factor receptor 9 motif II - 1 PCODE ST INT IFKQPFKKTTGAAQE TNR9_MOUSE 221 5 IFKQPFMRPVQTTQE TNR9_HUMAN 223 5 TNFACTORR93 Length of motif = 11 Motif number = 3 Tumour necrosis factor receptor 9 motif III - 1 PCODE ST INT DACSCRCPQEE TNR9_MOUSE 237 1 DGCSCRFPEEE TNR9_HUMAN 239 1 FINAL MOTIF SETS TNFACTORR91 Length of motif = 14 Motif number = 1 Tumour necrosis factor receptor 9 motif I - 2 PCODE ST INT IFITLLFSVLKWIR Q3U3R1_MOUSE 202 202 IFITLLFSVLKWIR TNR9_MOUSE 202 202 FFLTLRFSVVKRGR TNR9_HUMAN 204 204 FFLVLRFSVVKRSR A9YYE7_MACFA 203 203 SFLVLRFSVIKQGR Q3ZC74_BOVIN 203 203 IFIILWFSVPKWLR Q4V895_RAT 204 204 IFIILWFSVPKWLR Q4W8J3_RAT 204 204 TNFACTORR92 Length of motif = 15 Motif number = 2 Tumour necrosis factor receptor 9 motif II - 2 PCODE ST INT IFKQPFKKTTGAAQE Q3U3R1_MOUSE 221 5 IFKQPFKKTTGAAQE TNR9_MOUSE 221 5 IFKQPFMRPVQTTQE TNR9_HUMAN 223 5 IFKQPFMRPVQTTQE A9YYE7_MACFA 222 5 IFKQPFMRPVQTAQE Q3ZC74_BOVIN 222 5 IFKQPFKKAVRTAQE Q4V895_RAT 223 5 IFKQPFKKAVRTAQE Q4W8J3_RAT 223 5 TNFACTORR93 Length of motif = 11 Motif number = 3 Tumour necrosis factor receptor 9 motif III - 2 PCODE ST INT DACSCRCPQEE Q3U3R1_MOUSE 237 1 DACSCRCPQEE TNR9_MOUSE 237 1 DGCSCRFPEEE TNR9_HUMAN 239 1 DGCSCRFPEEE A9YYE7_MACFA 238 1 DACSCRFPEEE Q3ZC74_BOVIN 238 1 DACSCRFPEEE Q4V895_RAT 239 1 DACSCRFPEEE Q4W8J3_RAT 239 1
User query: Display/Full Code "TNFACTORR9"