Table 2.
Commonly used RNA binding proteins (RBPs). Abbreviations: H = A, C, or U; N = A or U; Y = U or C.
| RBP | RNA Sequence/ Motif |
Interacting RNA | Method | References |
|---|---|---|---|---|
| λN | Box B loop | any fused with Box B loop | Gal4-λN/BoxB reporter system | [90,91] |
| MCP | MS2 loop | any fused with MS2 loop | RNA-tethering | [92] |
| IGF2BP1,2,3 | CAUH | mostly exons, i.e., eEF2 | PAR-CLIP | [84] |
| PUM2 | UGUANAUA | 3′ untranslated region (UTR) | PAR-CLIP | [84] |
| QKI | ACUAAY | mostly introns | PAR-CLIP | [84] |
| AGO (most enriched 7 nucleotide- mers) |
AUGCUGC | miR-103,-107 | PAR-CLIP | [84] |
| GCUGCUA | miR-15a/b,-16,196a | PAR-CLIP | [84] | |
| UUUGCAC | miR-19a/b | PAR-CLIP | [84] | |
| UGCACUU | miR-130a/b,-148a/b,-301a/b | PAR-CLIP | [84] | |
| CACUUUA | miR-106a/b,-20a/b | PAR-CLIP | [84] | |
| UUGCUGC | miR-424 | PAR-CLIP | [84] | |
| UUGCACU | miR-130a/b,181a,-301a/b,-454 | PAR-CLIP | [84] | |
| GCACUUU | miR-17,-20a/b,-93,-106a/b | PAR-CLIP | [84] | |
| UGCUGCU | miR-15a/b,-16,196a,-103,107,-424 | PAR-CLIP | [84] | |
| STAU1 | 3′ UTRs (Alu, 858 nt duplex) | XBP1 | hiCLIP | [87] |