AptaDB: Result

Interaction ID: 1039

Aptamer sequence: ACGUUUCCCUUUUCGCGUA

Target unique ID: P16422

Aptamer ID	Aptamer descriptor	Target chemistry	Target name	Affinity	Binding Conditions/Buffer	PubMed ID
Apta_956	A5U	Protein	EPCAM_HUMAN	10.78 nM	PBS containing 5 mM MgCl2	32234785

Aptamer Sequence:	ACGUUUCCCUUUUCGCGUA
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

Type	Detail	Type	Detail
Aptamer ID	Apta_956	Description	A5U
Aptamer chemistry	RNA	Length	19 nt
GC content	47.4%	Molecular weight	5,912.48 Da
Molarity of 1 μg/μl solution	169.13 μM	Number of G-quadruplexes	No QGRS found
G-Score	N/A	Function	Targeted binding
Sequence	ACGUUUCCCUUUUCGCGUA
Applications	Binding to target proteins

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.

	Interaction ID	1039
	Target type	Protein
	Target unique ID	P16422
	Activity	10.78 nM
	Binding Conditions/Buffer	PBS containing 5 mM MgCl2
	Assay	Isothermal titration calorimetric analysis of the interaction of the 50-μM aptamer solutions from EP23, A5U, or G15U, with EpCAM protein (5 μM) in ITC buffer at 25 °C. (Top and Bottom) Raw data and binding isotherm obtained over a series of injections of aptamer into EpCAM protein. (Top) Differential power (μcal/sec) versus time is presented in the form of integrated heat values. The data were fitted using a one binding site model
	PubMed ID	32234785

Aptamer ID	Aptamer chemistry	Sequence	Similarity
Apta_955	RNA	ACGUAUCCCUUUUCGCGUA	94.74%
Apta_957	RNA	ACGUAUCCCUUUUCUCGUA	89.47%
Apta_1292	RNA	GGCACGUGUAUUACCCUAGUGGUCGACGUGCC	53.12%
Apta_1	RNA	ACGAAGCUUGAUCCCGUUUGCCGGUCGAUCGCUUCGA	51.35%
Apta_855	RNA	UCACUGUUAUCCGAUAGCAGCGCGGGAUGA	50.00%
Apta_384	RNA	AUGAUCAAUCGCCUCAAUUCGACAGGAGGCUCAC	47.06%
Apta_97	RNA	UUGUCGUCUUCUCCAGUUAGUCAACGAACUUGUGU	45.71%
Apta_634	RNA	GGUCUUACGUCGUUCGCGACUAUUGGGAGACC	43.75%
Apta_85	RNA	UGCGACUGUUAUAACCUAACAGCGACGUAAAGAUA	42.86%
Apta_87	RNA	UACCGACUAGCAAAACCUGCUGGCGACGUUUAGAU	42.86%
Apta_89	RNA	AAUAACCUUAAUGCGACGUUGGUUCGUCAACAUGG	42.86%
Apta_94	RNA	AUGACAGGAUGCAGAGCUCCACUGUCUAGUGUUUA	42.86%
Apta_345	DNA	ACAGTAACCGCGTGAGGTCGA	42.86%
Apta_1211	RNA	ACUAGCCUCAUCAGCUCAUGUGCCCCUCCGCCUGGAUCAC	42.50%
Apta_714	RNA	GGCGGUUCCUGCCGAAAGGCUCGUGGCAACGUC	42.42%
Apta_716	RNA	GGCGCUUCAUGCCGAAAGGCCCGUUGUAACGUC	42.42%
Apta_237	RNA	UUCAACGCUGUGAAGGGCUUAUACGAGCGGAUUACCC	40.54%
Apta_86	RNA	GAAACGACUCGACAACCUCGAGCGACGUGAAUCAU	40.00%
Apta_88	RNA	AAUAACCUUAAUGCGACGUUGGUUUGUCAACAACG	40.00%
Apta_90	RNA	ACAACCUAAAUGCGACGUUGGGUCAAAAACGUGAA	40.00%

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