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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

 RNA element classNumber of RBPsRBPs (eCLIP cell type)
Uniquely mapped to genome (exonic)5′UTR1DDX3X(K)
CDS42AQR(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′UTR24AGGF1(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 intronic40BCCIP(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 intronic23AQR(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 RNAsRNU11GEMIN5(K)
RNU26SF3A3(H) SF3B1(K) SF3B4(H,K) SMNDC1(H,K)
RNU61QKI(K)
Ribosomal RNA function and processingRNA28S24AATF(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)
RNA18S15APOBEC3C(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_extra12AATF(K) LIN28B(H) NIPBL(K) NPM1(K) SSB(H,K) UTP18(H,K) WDR3(K) WDR43(H,K) XRN2(H)
SNORD3UTP18(H,K) WDR3(K)
Retrotransposable elementsL13HLTF(K) KHDRBS1(K) SAFB2(K)
antisense_L19EXOSC5(K) HNRNPC(K) HNRNPM(H,K) KHSRP(K) MATR3(H,K) SUGP2(H) TIA1(H)
Alu1ILF3(H)
antisense_Alu2HNRNPC(H,K)
Mitochondrial RNAsH (+) strand7BCLAF1(H) DHX30(H) FASTKD2(H,K) QKI(H,K) TBRG4(H)
L (−) strand7DHX30(H,K) FASTKD2(H,K) GRSF1(H) SUPV3L1(H,K)
Other unique regulatory RNA classestRNA2NSUN2(K) WRN(K)
RN7SK2LARP7(H,K)
RNU71LSM11(K)
H1RNA1SSB(K)
SNORA1DKC1(H)
YRNA1TROVE2(K)
miRNA1DGCR8(K)
OtherSimple_repeat5AGGF1(H,K) AQR(H) HNRNPL(H) TARDBP(K)