Table 1 Predominant RNA element for each eCLIP dataset
From: Principles of RNA processing from analysis of enhanced CLIP maps for 150 RNA binding proteins
| Â | RNA element class | Number of RBPs | RBPs (eCLIP cell type) |
|---|---|---|---|
Uniquely mapped to genome (exonic) | 5′UTR | 1 | DDX3X(K) |
CDS | 42 | AQR(H) BCLAF1(H) BUD13(K) EIF3H(H) FMR1(K) FXR1(K) FXR2(K) G3BP1(H) GRWD1(H,K) HLTF(H,K) IGF2BP1(H,K) IGF2BP2(K) IGF2BP3(H) LARP4(H) LIN28B(H,K) LSM11(H) METAP2(K) PABPC4(K) PABPN1(H) PPIG(H) PRPF4(H) PRPF8(H) PUM1(K) RBM15(H,K) SND1(H) SRSF1(H,K) SRSF7(H,K) SRSF9(H) SUB1(H) UCHL5(H,K) YBX3(H,K) ZNF622(K) ZNF800(H) | |
3′UTR | 24 | AGGF1(H) AKAP1(H) FAM120A(H,K) FUBP3(H) IGF2BP1(H,K) IGF2BP2(K) IGF2BP3(H) LARP4(H) LIN28B(K) LSM11(H) PABPC4(K) PCBP2(H) PUM2(K) SUB1(H) TIA1(H,K) TIAL1(H) UPF1(H,K) YBX3(H,K) ZC3H11A(K) | |
Uniquely mapped to genome (intronic) | Distal intronic | 40 | BCCIP(H) CSTF2(H) CSTF2T(H,K) EWSR1(K) FAM120A(H) FUBP3(H) FUS(H,K) HNRNPA1(H,K) HNRNPC(K) HNRNPK(H) HNRNPL(H,K) HNRNPM(H,K) HNRNPU(H,K) HNRNPUL1(H,K) KHDRBS1(K) KHSRP(H,K) MATR3(H) NCBP2(H) NONO(K) PCBP2(H) QKI(H) RBFOX2(H) SAFB(H,K) SAFB2(K) SFPQ(H) SUGP2(H) TAF15(H,K) TIA1(H,K) TIAL1(H) |
Proximal intronic | 23 | AQR(H,K) BUD13(K) CSTF2T(K) EFTUD2(H,K) EWSR1(K) FAM120A(H) KHSRP(K) PRPF4(H) PRPF8(H,K) RBFOX2(H) RBM22(H,K) SF3B4(H,K) TIA1(H,K) TIAL1(H) U2AF1(H) U2AF2(H,K) | |
Spliceosomal small nuclear RNAs | RNU1 | 1 | GEMIN5(K) |
RNU2 | 6 | SF3A3(H) SF3B1(K) SF3B4(H,K) SMNDC1(H,K) | |
RNU6 | 1 | QKI(K) | |
Ribosomal RNA function and processing | RNA28S | 24 | AATF(K) ABCF1(K) BUD13(H) DDX24(K) DDX51(K) DKC1(H) EXOSC5(H) FTO(H) GEMIN5(K) NIP7(H) NIPBL(K) NKRF(H) NOL12(H) NOLC1(H) PCBP1(H) PHF6(K) SDAD1(H,K) SERBP1(K) TROVE2(H) WRN(K) XRCC6(K) ZNF800(H,K) |
RNA18S | 15 | APOBEC3C(K) DDX21(K) DDX52(H,K) DKC1(H) EIF3G(K) METAP2(K) NOLC1(H) RPS11(K) RPS3(H,K) SBDS(K) WDR43(K) XRCC6(K) ZC3H8(K) | |
rRNA_extra | 12 | AATF(K) LIN28B(H) NIPBL(K) NPM1(K) SSB(H,K) UTP18(H,K) WDR3(K) WDR43(H,K) XRN2(H) | |
SNORD | 3 | UTP18(H,K) WDR3(K) | |
Retrotransposable elements | L1 | 3 | HLTF(K) KHDRBS1(K) SAFB2(K) |
antisense_L1 | 9 | EXOSC5(K) HNRNPC(K) HNRNPM(H,K) KHSRP(K) MATR3(H,K) SUGP2(H) TIA1(H) | |
Alu | 1 | ILF3(H) | |
antisense_Alu | 2 | HNRNPC(H,K) | |
Mitochondrial RNAs | H (+) strand | 7 | BCLAF1(H) DHX30(H) FASTKD2(H,K) QKI(H,K) TBRG4(H) |
L (−) strand | 7 | DHX30(H,K) FASTKD2(H,K) GRSF1(H) SUPV3L1(H,K) | |
Other unique regulatory RNA classes | tRNA | 2 | NSUN2(K) WRN(K) |
RN7SK | 2 | LARP7(H,K) | |
RNU7 | 1 | LSM11(K) | |
H1RNA | 1 | SSB(K) | |
SNORA | 1 | DKC1(H) | |
YRNA | 1 | TROVE2(K) | |
miRNA | 1 | DGCR8(K) | |
Other | Simple_repeat | 5 | AGGF1(H,K) AQR(H) HNRNPL(H) TARDBP(K) |