AptaDB: Result

Interaction ID: 349

Aptamer sequence: AACAGAGGGACAAACGGGGGAAGATTTGACGTCGACGAC

Target unique ID: P16422

Aptamer ID	Aptamer descriptor	Target chemistry	Target name	Affinity	Binding Conditions/Buffer	PubMed ID
Apta_343	EP166	Protein	EPCAM_HUMAN	5.48 μM	4.5 g/L glucose, 5 mM MgCl2 and 10% FBS in Dulbecco's PBS (Sigma); Bovine Serum Albumin (1 mg/ml; Thermo Inc., USA)	25266702

Aptamer Sequence:	AACAGAGGGACAAACGGGGGAAGATTTGACGTCGACGAC
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_343	Description	EP166
Aptamer chemistry	DNA	Length	39 nt
GC content	53.8%	Molecular weight	12,412.80 Da
Molarity of 1 μg/μl solution	80.56 μM	Number of G-quadruplexes	No QGRS found
G-Score	N/A	Function	Targeted binding
Sequence	AACAGAGGGACAAACGGGGGAAGATTTGACGTCGACGAC
Applications	Stem cell marker or in other applications in both stem cell and cancer studies

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	349
	Target type	Protein
	Target unique ID	P16422
	Activity	5.48 μM
	Binding Conditions/Buffer	4.5 g/L glucose, 5 mM MgCl2 and 10% FBS in Dulbecco's PBS (Sigma); Bovine Serum Albumin (1 mg/ml; Thermo Inc., USA)
	Assay	Along with rising aptamer concentration, the binding affinity of EP166 towards HepG2 cells expressing EpCAM was examined by FACS
	PubMed ID	25266702

Aptamer ID	Aptamer chemistry	Sequence	Similarity
Apta_579	DNA	ACTGAGGGCACGGACAGGAGGGGGAGAGATGGCGTGAGGT	60.00%
Apta_813	DNA	TAGAGATATGACAGCGGGGAAGGTTAAGAGGCGCTAGGAG	57.50%
Apta_419	DNA	ATCAGGGCTAAAGAGTGCAGAGTTACTTAG	56.41%
Apta_630	DNA	GACCAGGGCAAACGGTAGGGAGTGGTC	56.41%
Apta_968	DNA	TAACACGACAGACGTTCGGAGGTCGAACCCTGACAGCGTGGGC	55.81%
Apta_484	DNA	CAGGGAGGGACAGGGCGGGAATTTGTATGATGGTTCGTTTGCTCG	55.56%
Apta_639	DNA	CTAAGCACAGGGAAACCAGCTAATGAGTTAGGCCTGTCCCCCACG	55.56%
Apta_258	DNA	CACTGCGGGGGTCTATACGTGAGGAAGAAGTGGGCAGGTC	55.00%
Apta_262	DNA	ACGGACTCGCAAAAGGTGGAACAGGAGTGGGCCCCGCGGC	55.00%
Apta_960	DNA	CCCGAGGCACGAGGGGGAACGTATCGTCATGTGCCGGCCA	55.00%
Apta_795	DNA	CGCAGCAAGGAGATTCGAGGGGGAAGGTTTGTTATAGGGGTTAATGGA	54.17%
Apta_700	DNA	GCAGGGGCGTTCGGGGGGTACCGCTGC	53.85%
Apta_47	DNA	GACCTAGCAGTGGACATGTGGCAGGGTGAAGTGGCATCGTC	53.66%
Apta_988	DNA	AAGGATGACTGACGACGATGGGAATGGAGAGGAAGGGGATATAGGTATGTTGGATGTAG	52.54%
Apta_385	DNA	ACAGATACGGAACTACAGAGGTCAATTACGGTGGCCACGC	52.50%
Apta_915	DNA	ACTTCGGCTAGTTAGGGGGTAGTTTAGATCGTCTCTACAT	52.50%
Apta_1190	DNA	TTCAGGGCGGGGTAAACGGGAGGTGGGGGGGGCTTGGGAC	52.50%
Apta_1043	DNA	TTCAAGGCGGCGAGATTTAGTGGTTGGGAGGCTGTACGCCCTACGTGAAC	52.00%
Apta_1045	DNA	GGTGCTCAGGGAACTGTCTGAGGGATCAGGCTTAAGCCTGTCGAGCAGTT	52.00%
Apta_1047	DNA	TAGTCCCAAGGCACATAAGGGCCGGAGGTCTAGCGTCAGGGATACAGAGA	52.00%

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