Aptamer-target interaction descriptor
Aptamer-target interaction information
Interaction ID: 472
Aptamer sequence: GGGAGGACGAUGCGGCAGUGCCCAACCGGAACAACAACCACCGGCGGCUCCUGCUCAGACGACUCGCUGAGGAUCCGAGA
Target unique ID: Q61656
Aptamer ID Aptamer descriptor Target chemistry Target name Affinity Binding Conditions/Buffer PubMed ID
Apta_467 14-16 Protein DDX5_MOUSE 30.8 nM 5 nmol of aptamer pool in 200 μl of PBS, injected systemically and allowed to circulate for 20 minutes 19946274
Structure information of aptamer
Aptamer Sequence: GGGAGGACGAUGCGGCAGUGCCCAACCGGAACAACAACCACCGGCGGCUCCUGCUCAGACGACUCGCUGAGGAUCCGAGA
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_467 Description 14-16
Aptamer chemistry RNA Length 80 nt
GC content 65.0% Molecular weight 25,881.54 Da
Molarity of 1 μg/μl solution 38.64 μM Number of G-quadruplexes No QGRS found
G-Score N/A Function Targeted therapy
Sequence GGGAGGACGAUGCGGCAGUGCCCAACCGGAACAACAACCACCGGCGGCUCCUGCUCAGACGACUCGCUGAGGAUCCGAGA
Applications Binding to p68
Target information
Type Detail Type Detail
Uniprot ID Q61656 Protein name Probable ATP-dependent RNA helicase DDX5 (EC 3.6.4.13) (DEAD box RNA helicase DEAD1) (mDEAD1) (DEAD box protein 5) (RNA helicase p68)
Gene name(s) Ddx5 Tnz2 Organism Probable ATP-dependent RNA helicase DDX5 (EC 3.6.4.13) (DEAD box RNA helicase DEAD1) (mDEAD1) (DEAD box protein 5) (RNA helicase p68)
Status reviewed in uniprot database Length 614
Mass 69,290 Activity regulation N/A
Involvement in disease N/A Catalytic activity Reaction=ATP + H2O = ADP + H(+) + phosphate
PDB ID(s)
N/A
Function Involved in the alternative regulation of pre-mRNA splicing; its RNA helicase activity is necessary for increasing tau exon 10 inclusion and occurs in a RBM4-dependent manner.
Activity data
Interaction ID 472
Target type Protein
Target unique ID Q61656
Activity 30.8 nM
Binding Conditions/Buffer

5 nmol of aptamer pool in 200 μl of PBS, injected systemically and allowed to circulate for 20 minutes
Assay

The representative RNA molecules 14-16 and 14-8 were assayed for binding in vitro to tumor extracted protein
PubMed ID 19946274
Similar aptamers
Aptamer ID Aptamer chemistry Sequence Similarity
Apta_396 RNA GGGAGGACGAUGCGGCAGUCUGCAUCGUAGGAAUCGCCACCGUAUACUUUCCCACCAGACGACUCGCUGAGGAUCCGAGA 75.00%
Apta_397 RNA GGGAGGACGAUGCGGAUACCAGGAUCACAUCCUGAGGAACCCCGGCUCCCAACCUCAGACGACUCGCUGAGGAUCCGAGA 72.50%
Apta_399 RNA GGGAGGACGAUGCGGCAAACCAGCUAUUUCCUGAGGUACCCCGGCUCUCCAUGGCAGACGACUCGCUGAGGAUCCGAGA 72.50%
Apta_400 RNA GGGAGGACGAUGCGGAUACCAGCGAAUAACUCGCUGAGGAACCCGACUCACAAACAGACGACUCGCUGAGGAUCCGAGA 70.00%
Apta_414 RNA GGGAGGACGAUGCGGCCGAUUAGAACUGGGCUGAGGCGUUCUGCAUUUCGGUGAUCAGACGACUCGCUGAGGAUCCGAGA 70.00%
Apta_415 RNA GGGAGGACGAUGCGGAAACUCAUCGGUAGCCUUCCUGCGGUCAGUCUAUUAGGACCAGACGACUCGCUGAGGAUCCGAGA 70.00%
Apta_398 RNA GGGAGGACGAUGCGGCUUUAAUCCUCGCACUCAGCGCGCAUCACCCUUGACAUCACAGACGACUCGCUGAGGAUCCGAGA 68.75%
Apta_352 RNA GGGAGGACGAUGCGGUGGUCUCCCAAUUCUAAACUUUCUCCAUCGUAUCUGGGCAGACGACUCGCCCGA 62.50%
Apta_305 RNA GGGAGGACGAUGCGGAUCGCCCUGAACCGGCCCAGCAGACUGCUGACGGCACGAUCCGCAUCGUCCUCCC 61.25%
Apta_984 RNA GGGAGGACGAUGCGGCGUAUUGCGCGAGGAUUAUCCGCUCAUCGUUGUUGUUGUGCAGACGACUCGCCCGA 61.25%
Apta_130 RNA GGGAGGACGAUGCGGUGGUAGCGCGAUAUAGCGCUGGUAGGGUUGCCGGUGAUCAGACGACUCGCCCGA 58.75%
Apta_129 RNA GGGAGGACGAUGCGGACACCGUUAAUCUGAGGCCCUGUCCUAUUCCUUCACGCCUCAGA 56.25%
Apta_132 RNA GGGAGGACGAUGCGGCGUUUCCUCUGGUUCGUCCCCAGACGACUCGCCCGA 56.25%
Apta_133 RNA GGGAGGACGAUGCGGUGAGUCGUUCCCUUCGUCCCCAGACGACUCGCCCGA 56.25%
Apta_135 RNA GGGAGGACGAUGCGGAUUCUGGUUACUGGCCGCCCCAGACGACUCGCCCGA 56.25%
Apta_315 RNA GGGAGGACGAUGCGGUCGUAUUAUCCGCUGCACGCCAGACGACUCGCCCGA 56.25%
Apta_131 RNA GGGAGGACGAUGCGGUCCUGUCGUCUGUUCGUCCCCAGACGACUCGCCCGA 53.75%
Apta_687 DNA GGGACAGCGGAGGTCTCCCACCCACCGGCCCCTGCGGCACACCAACCTGTATGGATGCG 53.75%
Apta_885 RNA GGGAGAGCGGAAGCGUGCUGGGCCUGGUUGCUGUAAAAAUAGACACGAAUCUGCCGACCAUAACCCAGAGGUCGAUGGAUCCCCCC 53.49%
Apta_43 RNA GGGAGAGCGGAAGCGUGCUGGGCCACCAUCCGUAACUAGCUAAUACUUGUUAUCUUUUUAUUUUCAUAACCCAGAGGUCGAUGGAUCCCCCC 53.26%

ABOUT

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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