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PR01972

Identifier
TNFACTORR25  [View Relations]  [View Alignment]  
Accession
PR01972
No. of Motifs
6
Creation Date
24-JUN-2009
Title
Tumour necrosis factor receptor 25 signature
Database References

MIM; 603366
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. GRENET, J., VALENTINE, V., KITSON, J., LI, H., FARROW, S. AND KIDD, V.
Duplication of the DR3 gene on human chromosome 1p36 and its deletion in 
human neuroblastoma.
GENOMICS 49 385-393 (1998).
 
8. WANG, E., THERN, A., DENZEL, A., KITSON, J., FARROW, S. AND OWEN, M.
DR3 regulates negative selection during thymocyte development.
MOL.CELL.BIOL. 21 3451-3461 (2001).

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 25 (alternatively known as death receptor 3 (DR3) and 
lymphocyte-associated receptor of death (LARD)) is expressed primarily on 
the surface of thymocytes and lymphocytes [7]. The receptor contains a death
domain in its C-terminal region, and acts as a key regulator of life/death 
decisions during thymocyte development [8].
 
TNFACTORR25 is a 6-element fingerprint that provides a signature for tumour
necrosis factor receptor 25. The fingerprint was derived from an initial
alignment of 2 sequences: the motifs were drawn from conserved regions
spanning virtually the full alignment length, focusing on those sections
that characterise TNF receptor 25 but distinguish it from other TNF receptor
subtypes - motifs 1 and 2 lie in the extracellular N-terminal region; motifs
3 and 4 reside within the intracellular C-terminal region; and motif 5 lies
within the death domain in the intracellular C-terminal region. Two 
iterations on SPTR57_40f were required to reach convergence, at which point
a true set comprising 5 sequences was identified. Two partial matches were 
also found, Q8VD70_MOUSE and B3KSV7_HUMAN, which are translated cDNA 
sequences from mouse and human that fail to make significant matches with 
motif 2, and with motifs 1 and 2, respectively.
Summary Information
   5 codes involving  6 elements
1 codes involving 5 elements
1 codes involving 4 elements
0 codes involving 3 elements
0 codes involving 2 elements
Composite Feature Index
6555555
5101111
4001111
3000000
2000000
123456
True Positives
B1AWN9_MOUSE  B7ZLL7_HUMAN  Q17RU4_HUMAN  Q99MM1_MOUSE  
TNR25_HUMAN
True Positive Partials
Codes involving 5 elements
Q8VD70_MOUSE
Codes involving 4 elements
B3KSV7_HUMAN
Sequence Titles
B1AWN9_MOUSE Tumor necrosis factor receptor superfamily, member 25 - Mus musculus (Mouse). 
B7ZLL7_HUMAN Tumor necrosis factor receptor superfamily, member 25 - Homo sapiens (Human).
Q17RU4_HUMAN Tumor necrosis factor receptor superfamily, member 25 - Homo sapiens (Human).
Q99MM1_MOUSE WSL-1-like protein - Mus musculus (Mouse).
TNR25_HUMAN Tumor necrosis factor receptor superfamily member 25 - Homo sapiens (Human).

Q8VD70_MOUSE Tumor necrosis factor receptor superfamily, member 25 - Mus musculus (Mouse).

B3KSV7_HUMAN cDNA FLJ37144 fis, clone BRACE2024610, highly similar to Tumor necrosis factor receptor superfamily member 25 - Homo sapiens (Human).
Scan History
SPTR57_40f 2  300  NSINGLE    
Initial Motifs
Motif 1  width=17
Element Seqn Id St Int Rpt
CDCAGDFHKKIGLFCCR TNR25_HUMAN 33 33 -
CDCASESQKRYGPFCCR Q99MM1_MOUSE 40 40 -

Motif 2 width=18
Element Seqn Id St Int Rpt
CPTSTLGSCPERCAAVCG TNR25_HUMAN 179 129 -
CPTGFSSVCPKACTAVCG Q99MM1_MOUSE 177 120 -

Motif 3 width=14
Element Seqn Id St Int Rpt
HLSPLDSAHTLLAP TNR25_HUMAN 251 54 -
HLSASDSAHTLLAP Q99MM1_MOUSE 246 51 -

Motif 4 width=17
Element Seqn Id St Int Rpt
EALCPQVTWSWDQLPSR TNR25_HUMAN 290 25 -
EVVCGQASQPWDQLPNR Q99MM1_MOUSE 286 26 -

Motif 5 width=13
Element Seqn Id St Int Rpt
IGRFRDQQYEMLK TNR25_HUMAN 368 61 -
ICRFRDQQYEMLK Q99MM1_MOUSE 364 61 -

Motif 6 width=13
Element Seqn Id St Int Rpt
CVEDLRSRLQRGP TNR25_HUMAN 405 24 -
CAEDLRSRLQRGP Q99MM1_MOUSE 401 24 -
Final Motifs
Motif 1  width=17
Element Seqn Id St Int Rpt
CDCAGDFHKKIGLFCCR B7ZLL7_HUMAN 33 33 -
CDCAGDFHKKIGLFCCR TNR25_HUMAN 33 33 -
CDCAGDFHKKIGLFCCR Q17RU4_HUMAN 33 33 -
CDCASESQKRYGPFCCR B1AWN9_MOUSE 38 38 -
CDCASESQKRYGPFCCR Q99MM1_MOUSE 40 40 -

Motif 2 width=18
Element Seqn Id St Int Rpt
CPTSTLGSCPERCAAVCG B7ZLL7_HUMAN 179 129 -
CPTSTLGSCPERCAAVCG TNR25_HUMAN 179 129 -
CPTSTLGSCPERCAAVCG Q17RU4_HUMAN 179 129 -
CPTGFSSVCPKACTAVCG B1AWN9_MOUSE 175 120 -
CPTGFSSVCPKACTAVCG Q99MM1_MOUSE 177 120 -

Motif 3 width=14
Element Seqn Id St Int Rpt
HLSPLDSAHTLLAP B7ZLL7_HUMAN 214 17 -
HLSPLDSAHTLLAP TNR25_HUMAN 251 54 -
HLSPLDSAHTLLAP Q17RU4_HUMAN 251 54 -
HLSASDSAHTLLAP B1AWN9_MOUSE 244 51 -
HLSASDSAHTLLAP Q99MM1_MOUSE 246 51 -

Motif 4 width=17
Element Seqn Id St Int Rpt
EALCPQVTWSWDQLPSR B7ZLL7_HUMAN 253 25 -
EALCPQVTWSWDQLPSR TNR25_HUMAN 290 25 -
EALCPQVTWSWDQLPSR Q17RU4_HUMAN 290 25 -
EVVCGQASQPWDQLPNR B1AWN9_MOUSE 284 26 -
EVVCGQASQPWDQLPNR Q99MM1_MOUSE 286 26 -

Motif 5 width=13
Element Seqn Id St Int Rpt
IGRFRDQQYEMLK B7ZLL7_HUMAN 331 61 -
IGRFRDQQYEMLK TNR25_HUMAN 368 61 -
IGRFRDQQYEMLK Q17RU4_HUMAN 368 61 -
ICRFRDQQYEMLK B1AWN9_MOUSE 362 61 -
ICRFRDQQYEMLK Q99MM1_MOUSE 364 61 -

Motif 6 width=13
Element Seqn Id St Int Rpt
CVEDLRSRLQRGP B7ZLL7_HUMAN 368 24 -
CVEDLRSRLQRGP TNR25_HUMAN 405 24 -
CVEDLRSRLQRGP Q17RU4_HUMAN 405 24 -
CAEDLRSRLQRGP B1AWN9_MOUSE 399 24 -
CAEDLRSRLQRGP Q99MM1_MOUSE 401 24 -