Aptamer-target interaction descriptor
Aptamer-target interaction information
Interaction ID: 1274
Aptamer sequence: CTGTTCTCGGTCGCGACCTATCTGGTCGTCGCCGCGCTCGTGTTCGGAACGCTCATCGCGTTCGGGCTCGGCG
Target unique ID: P16422
Aptamer ID Aptamer descriptor Target chemistry Target name Affinity Binding Conditions/Buffer PubMed ID
Apta_1212 Eppc6 Protein EPCAM_HUMAN 41.74 nM 0.1 M Hepes, 0.75 M NaCl, 0.025 M KCl, 0.01 M CaCl2, 0.01 M MgCl2·6H2O in double distilled water, pH 7.4 34584404
Structure information of aptamer
Aptamer Sequence: CTGTTCTCGGTCGCGACCTATCTGGTCGTCGCCGCGCTCGTGTTCGGAACGCTCATCGCGTTCGGGCTCGGCG
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_1212 Description Eppc6
Aptamer chemistry DNA Length 73 nt
GC content 67.1% Molecular weight 22,414.23 Da
Molarity of 1 μg/μl solution 44.61 μM Number of G-quadruplexes No QGRS found
G-Score N/A Function Target detection
Sequence CTGTTCTCGGTCGCGACCTATCTGGTCGTCGCCGCGCTCGTGTTCGGAACGCTCATCGCGTTCGGGCTCGGCG
Applications Recognize prostate cancer cells and tissues
Target information
Type Detail Type Detail
Uniprot ID P16422 Protein name Epithelial cell adhesion molecule (Ep-CAM) (Adenocarcinoma-associated antigen) (Cell surface glycoprotein Trop-1) (Epithelial cell surface antigen) (Epithelial glycoprotein) (EGP) (Epithelial glycoprotein 314) (EGP314) (hEGP314) (KS 1/4 antigen) (KSA) (Major gastrointestinal tumor-associated protein GA733-2) (Tumor-associated calcium signal transducer 1) (CD antigen CD326)
Gene name(s) EPCAM GA733-2 M1S2 M4S1 MIC18 TACSTD1 TROP1 Organism Epithelial cell adhesion molecule (Ep-CAM) (Adenocarcinoma-associated antigen) (Cell surface glycoprotein Trop-1) (Epithelial cell surface antigen) (Epithelial glycoprotein) (EGP) (Epithelial glycoprotein 314) (EGP314) (hEGP314) (KS 1/4 antigen) (KSA) (Major gastrointestinal tumor-associated protein GA733-2) (Tumor-associated calcium signal transducer 1) (CD antigen CD326)
Status reviewed in uniprot database Length 314
Mass 34,932 Activity regulation N/A
Involvement in disease Diarrhea 5, with tufting enteropathy, congenital (DIAR5) Catalytic activity N/A
PDB ID(s)
4MZV;6I07;
Function May act as a physical homophilic interaction molecule between intestinal epithelial cells (IECs) and intraepithelial lymphocytes (IELs) at the mucosal epithelium for providing immunological barrier as a first line of defense against mucosal infection.
Activity data
Interaction ID 1274
Target type Protein
Target unique ID P16422
Activity 41.74 nM
Binding Conditions/Buffer

0.1 M Hepes, 0.75 M NaCl, 0.025 M KCl, 0.01 M CaCl2, 0.01 M MgCl2·6H2O in double distilled water, pH 7.4
Assay

binding curves
PubMed ID 34584404
Similar aptamers
Aptamer ID Aptamer chemistry Sequence Similarity
Apta_891 DNA GGAGACCGTACCATCTGTTCGTGGAAGCGCTTTGCTCGTCCATTAGCCTTGTGCTCGTGC 56.16%
Apta_653 DNA CCTGCACCTCGTCCAGCATCCGATGGCGGTCCTGTTTTACGGTAGCTTATATGCAGGGGGGTG 54.79%
Apta_1183 DNA GAATTCAGTCGGACAGCGGCGTGAGTCTTTTGCGGTGGCTCGGGTTCGAATATCTACGACCTTGATGGACGAATATCGTCTCCC 53.57%
Apta_335 DNA ACCGGGCGTACACCGTCGCGGCACATGTCTGAATGCGTTTAGTCTCTGTG 53.42%
Apta_1180 DNA GAATTCAGTCGGACAGCGCAATTGTGGTTCTTACCCTATCCCTTGTGTTTGGCGTTCGTTGCGATGGACGAATATCGTCTCCC 53.01%
Apta_589 DNA GGGAATTCGAGCTCGGTACCATCTGTGTAAGGGGTAAGGGGTGGGGGTGGGTACGTCTAGCTGCAGGCATGCAAGCTTGG 52.50%
Apta_1028 DNA CTTCTGCCCGCCTCCTTCCGGCGTCCCTGCGCACTGTATAACGTACACACGATACGTGGGAGACGAGATAGGCGGACACT 52.50%
Apta_589 DNA GGGAATTCGAGCTCGGTACCATCTGTGTAAGGGGTAAGGGGTGGGGGTGGGTACGTCTAGCTGCAGGCATGCAAGCTTGG 52.50%
Apta_223 DNA CATTGAGATAGCTAGTTGTAGCTGCGTCATAGGCTGGGTTGGGTCTAGTGGTTGGGTGTG 52.05%
Apta_558 DNA CCGGTGGGTGGTCAGGTGGGATAGCGTTCCGCGTATGGCCCAGCGCATCACGGGTTCGCACCA 52.05%
Apta_591 DNA CTCTCGGGACGACGGCTGGCACGTTTGGTTCAAGAATGTGGGTGTCGTCCC 52.05%
Apta_592 DNA CTCTCGGGACGACCACTACGCATAGTTTCTATCGCCAGGAAGGGTCGTCCC 52.05%
Apta_721 DNA CTCTCGGGACGACCGCGGTAGTCTTAACCTAAAGCGGTGTCAGGTCGTCCC 52.05%
Apta_1229 DNA CACGGGCAGAGGGATAGGTTGTTGACGGGGCTGGTGGGTGGGTGCGCTCGCGCTATCGTGG 52.05%
Apta_736 DNA ATCGTCTGCTCCGTCCAATATGATGACACCTGCATAATTTATAGTGAGTCTTGATTCACGCTGCATTTGGTGTGAGGTCGTGC 51.81%
Apta_741 DNA ATCGTCTGCTCCGTCCAATAGCCTCACCCTGCATAATTTATAGACTACACTTAGGAATCGCTGCATTTGGTGTGAGGTCGTGC 51.81%
Apta_461 DNA CGCTCGGCTTCACGAGATTCGTGTCGTTGTGTCCTGTACCCGCCTTGACCAGTCACTCTAGAGCATCCGGACTG 51.35%
Apta_1108 DNA GTGCTTAGGTGCAGAACGCACACACGCTCGGTATGACGTGTTCGCTACGGTATAATTGCAGGCGCGAGCACAACAG 51.32%
Apta_1291 DNA CGTACGGAATTCGCTAGCCCCCCGGCAGGCCACGGCTTGGGTTGGTCCCACTGCGCGTGGATCCGAGCTCCACGTG 51.32%
Apta_127 DNA GGTATTGAGGGTCGCATCCACTGGTCGTTGTTGTCTGTTGTCTGTTATGTTGTTTCGTGATGGCTCTAACTCTCCTCT 51.28%

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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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