Aptamer-target interaction descriptor
Aptamer-target interaction information
Interaction ID: 500
Aptamer sequence: GGGAGAUACCAGCUUAUUCAAUUCUGGCAAUGGGCUAUCCCAAGUGCUAGGCUUCAGGGAGCGAGGACCAGACGACGUACCUAACCCUAAGGUGAGAUAGUAAGUGCAAUCU
Target unique ID: Q92729
Aptamer ID Aptamer descriptor Target chemistry Target name Affinity Binding Conditions/Buffer PubMed ID
Apta_494 N71yc16 Protein PTPRU_HUMAN 18 nM 20 mM Tris (pH 7.6), 150 mM NaCl, 5 mM MgCl2, 1 mM dithiothreitol; 100 μL final volume 9603938
Structure information of aptamer
Aptamer Sequence: GGGAGAUACCAGCUUAUUCAAUUCUGGCAAUGGGCUAUCCCAAGUGCUAGGCUUCAGGGAGCGAGGACCAGACGACGUACCUAACCCUAAGGUGAGAUAGUAAGUGCAAUCU
The optimal secondary structure in dot-bracket notation: ...((((....(((((((.....((((((.((((....))))..))))))((((.((((....(((((........)).)))..)))).)))).....)))))))...))))
The centroid secondary structure in dot-bracket notation: ...((((....((((((......((((((.((((....))))..))))))((((.((((....(((((........)).)))..)))).))))......))))))...))))
The MFE structure
The Centroid structure
The mountain plot representation
Aptamer information
Type Detail Type Detail
Aptamer ID Apta_494 Description N71yc16
Aptamer chemistry RNA Length 112 nt
GC content 50.0% Molecular weight 36,151.52 Da
Molarity of 1 μg/μl solution 27.66 μM Number of G-quadruplexes No QGRS found
G-Score N/A Function Targeted binding
Sequence GGGAGAUACCAGCUUAUUCAAUUCUGGCAAUGGGCUAUCCCAAGUGCUAGGCUUCAGGGAGCGAGGACCAGACGACGUACCUAACCCUAAGGUGAGAUAGUAAGUGCAAUCU
Applications Defining the interactions between PTPases and their targets
Target information
Type Detail Type Detail
Uniprot ID Q92729 Protein name Receptor-type tyrosine-protein phosphatase U (R-PTP-U) (EC 3.1.3.48) (Pancreatic carcinoma phosphatase 2) (PCP-2) (Protein-tyrosine phosphatase J) (PTP-J) (hPTP-J) (Protein-tyrosine phosphatase pi) (PTP pi) (Protein-tyrosine phosphatase receptor omicron) (PTP-RO) (Receptor-type protein-tyrosine phosphatase psi) (R-PTP-psi)
Gene name(s) PTPRU FMI PCP2 PTPRO Organism Receptor-type tyrosine-protein phosphatase U (R-PTP-U) (EC 3.1.3.48) (Pancreatic carcinoma phosphatase 2) (PCP-2) (Protein-tyrosine phosphatase J) (PTP-J) (hPTP-J) (Protein-tyrosine phosphatase pi) (PTP pi) (Protein-tyrosine phosphatase receptor omicron) (PTP-RO) (Receptor-type protein-tyrosine phosphatase psi) (R-PTP-psi)
Status reviewed in uniprot database Length 1446
Mass 162,423 Activity regulation N/A
Involvement in disease N/A Catalytic activity Reaction=H2O + O-phospho-L-tyrosyl-[protein] = L-tyrosyl-[protein] + phosphate
PDB ID(s)
6SUB;6SUC;
Function Tyrosine-protein phosphatase which dephosphorylates CTNNB1.
Activity data
Interaction ID 500
Target type Protein
Target unique ID Q92729
Activity 18 nM
Binding Conditions/Buffer

20 mM Tris (pH 7.6), 150 mM NaCl, 5 mM MgCl2, 1 mM dithiothreitol; 100 μL final volume
Assay

Binding curves for anti-Yop51* aptamers with Yop51*D162
PubMed ID 9603938
Similar aptamers
Aptamer ID Aptamer chemistry Sequence Similarity
Apta_296 RNA AUACCAGCUUAUUCAAUUGCCUGAAAACCUGGUCUCUCUGUCAGCAAAGACUAUGTUGAGAUAGUAAGUGCAAUCU 59.82%
Apta_300 RNA AUACCAGCUUAUUCAAUUGCCUGAAACUGCUGCAUCGUCUCCCACGUAUUACACAUGAAGAUAGUAAGUGCAAUCU 59.82%
Apta_294 RNA AUACCAGCUUAUUCAAUUGCCUGAUUAGCGGUAUCACGAUUACUUACCUUCGUUGCUGAGAUAGUAAGUGCAAUCU 58.93%
Apta_297 RNA AUACCAGCUUAUUCAAUUGCCUGAGUAGCUGGGUCCGUCCCCACACAUUACCAUUUGUAGAUAGUAAGUGCAAUCU 58.93%
Apta_295 RNA AUACCAGCUUAUUCAAUUGCCUGAAAAGCUAUCGCCCAAUUCGCAGUGAUAUCCUUUAAGAUAGUAAGUGCAAUCU 57.14%
Apta_299 RNA AUACCAGCUUAUUCAAUUGCCUGAAGACUGGAUAUACUCUUAAGCAUUUCUAUAAUCGAGAUAGUAAGUGCAAUCU 57.14%
Apta_298 RNA AUACCAGCUUAUUCAAUUGCCUGAAAACUGGUGUACCUCUUUGCCCUAUCUUAUCUGGAGAUAGUAAGUGCAAUCU 56.25%
Apta_301 RNA AUACCAGCUUAUUCAAUUGCCUGAAAAGUUGAACUCCAAAUACGCGCUGAGAUAGUAAGUGCAAUCU 55.36%
Apta_1224 RNA GGAGGCGCCAACUGAAUGAAUGUUCUGGAUCUGCUAGAGACUAUCUGCUUCGGCAGCACUCUCCGUUAACAACACGUACAUCCGUAACUAGUCGCGUCAC 53.57%
Apta_380 RNA GGGAUGCUUCGGCAUCCCCGAAGCCGCUAUGGACCAGUGGCGCGGCUUCGGCCCGACGGAGUGGUACCGCUUCGGCGGUACGUAAGCUUGGG 51.79%
Apta_613 RNA GGAUAAUAGCCGUAGGUUGCGAAAGCGACCCUGAUGAGCCUUAGGAUAUGCAUGAUGCAGAAGGACGUCGAAACGGUAGCGAGAGCUC 51.79%
Apta_720 RNA GGGAGAAUUCCGACCAGAAGCUUAGUAUAGCGAGGUUUAGCUACACUCGUGCUGAUCGUUUGGUACGGGACCUGCGUGUAGCCCAUAUGUGCGUCUACAUGGAUCCUCA 51.79%
Apta_885 RNA GGGAGAGCGGAAGCGUGCUGGGCCUGGUUGCUGUAAAAAUAGACACGAAUCUGCCGACCAUAACCCAGAGGUCGAUGGAUCCCCCC 51.79%
Apta_886 RNA GGGAGACGAUAUUCGUCCAUUCGGGUGGCCCGUGUCUGAGCGGGGACGGCCACUUGAGCGCCGCUGUCCGACUGAAUUCUCGACC 51.79%
Apta_1221 RNA GGAGGCGCCAACUGAAUGAACGAGUUGAAAUGCGGAUCAAGUUACUGCUUCGGCAGUACCUAGUGGGAAAAGUUCUUGGGUCCGUAACUAGUCGCGUCAC 51.79%
Apta_1222 RNA GGAGGCGCCAACUGAAUGAAACCGUGCUAAGGAGUUGGACUCCGCUGCUUCGGCAGAGCGAUAUAGUGCCAGCUGAUACAUCCGUAACUAGUCGCGUCAC 51.79%
Apta_123 RNA GGGAGAAAGGGAAGCUUGAGCAGCAGGAGGGCCGGCGUUAGGGUUAGCGAGCCGAUUGAAAGAAGAAGGAACGAGCGUACGGAUCCGAUC 50.89%
Apta_225 RNA GGGGCCACCAACGACAUUUAUCGAAUUGAUAACCUUACGCGAGAGCGUAGUUCGUUGAUAUAAAUAGUGCCCAUGGAUC 50.89%
Apta_382 RNA GGCGUGACCUGAUGAGUCACGCAGACGCUAGCGAAUUGGUUCCUCGAAAGGGGAAAGCGUUAUUAAGAAACCAAAAUGUGUUACGAAACGUUCCC 50.89%
Apta_415 RNA GGGAGGACGAUGCGGAAACUCAUCGGUAGCCUUCCUGCGGUCAGUCUAUUAGGACCAGACGACUCGCUGAGGAUCCGAGA 50.89%

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AptaDB is an online database we developed to integrate comprehensive information about aptamer.
The detail of this database is described here:

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