>Fnta|NM_008033|3'UTR
   1 CAGCGAGGGCATCCGGAAGAAGTGGACGATGCTTTCTAAGGCCTCTTATGCAGGAGCGTAGAGTGGTTAGAGCGGTCATC
  81 TCTTGCCTGTGCGCTAAAGCTGTCCAGGTGCTGCTTTTAACAAGAACTAAGTATGACTCCTGTGTGCTGACGCTGTTCAG
 161 ACGAGCTCTAAGAATCCATTTTCTAAAGCAAAGTCATTGGAGGGGAGGGTGAGGAAAGTTTCCCATAAAGGAACTACTGC
 241 TTTTGTAGTCTTCCCAACATTTAGTCCAGTCCTGTAGAATCCGCTCCTCCTGAAAGATGTGTATGCAAGGCTGTGCGCTG
 321 GGAGTGACGATTGATTTGCAGTAACCTGAATCTCGGTGCATTATGCGGCAACTGCGCCTGTTGGTTAGAGCTGCTGTGCG
 401 CACTCACAGGATCTTGCTATCACTGTAACCAACTAATGCCAAAAGAAAGGTTTTATAATAAAGTCACATTATCTATAAAC
 481 AATTCCATAGTGTTTGATGTTTAACAGTATATAAGGGACAAACAAGAAGCCCAGTGCTTGGGAGGCTGAGACAGGAGGAT
 561 TGCTGCAAGTTTGAGCCAGTCTGGACTACATAGAGAGGTTTGGGCCAGTTCAGAATATAGAGGGTAGCCTTCTTTGAAAA
 641 AAAAAAAAAAAAGTCAAAAACTTAAAAAGAAAATATTACTATACATTTTGTGATTATGGGAGGGAAATGTGAATTTATTA
 721 AAAATG

ID	Duplex structure	Position	Score	MFE
1	miRNA 3' aaaccaacaCUCGGAUCGGAAa 5' ||| ||||||| Target 5' cagaatataGAGGGTAGCCTTc 3'	611 - 632	149.00	-11.60
2	miRNA 3' aaACCAA------CACUCG-GAUCGGAaa 5' ||||| || | | || |||| Target 5' agTGGTTAGAGCGGTCATCTCTTGCCTgt 3'	62 - 90	106.00	-11.50
3	miRNA 3' aaaCCAACAC--UCGGAUCGGAaa 5' | ||| | ||:||:| || Target 5' caaGTTTGAGCCAGTCTGGACTac 3'	566 - 589	97.00	-13.89

- Molecular cell, 2012

MicroRNAs (miRNAs) are essential components of gene regulation, but identification of miRNA targets remains a major challenge. Most target prediction and discovery relies on perfect complementarity of the miRNA seed to the 3' untranslated region (UTR). However, it is unclear to what extent miRNAs target sites without seed matches. Here, we performed a transcriptome-wide identification of the endogenous targets of a single miRNA-miR-155-in a genetically controlled manner. We found that approximately 40% of miR-155-dependent Argonaute binding occurs at sites without perfect seed matches. The majority of these noncanonical sites feature extensive complementarity to the miRNA seed with one mismatch. These noncanonical sites confer regulation of gene expression, albeit less potently than canonical sites. Thus, noncanonical miRNA binding sites are widespread, often contain seed-like motifs, and can regulate gene expression, generating a continuum of targeting and regulation.