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Table 1 Dataset of thirteen interacting protein-RNA pairs

From: Prediction of protein-RNA residue-base contacts using two-dimensional conditional random field with the lasso

protein sequence A RNA sequence B PDB code # sequences in MSA # contacts
UniProt Pfam chain length GenBank Rfam chain length    3 Å 5 Å
RL18_THETH PF00861 R 110 X01554 RF00001 B 117 2hgu 1543 28 85
RL27_THET8 PF01016 Z 81 X12612 RF01118 A 108 2hgu 1356 20 67
RL27_ECOLI PF01016 W 77 J01695 RF01118 8 108 3kcr 1356 18 69
RL33_THET8 PF00471 5 48 X12612 RF01118 A 108 2hgu 1445 18 40
RL35_ECOLI PF01632 3 61 J01695 RF01118 8 108 3kcr 1337 12 38
RS5_ECOLI PF00333 E 67 J01695 RF00177 A 1530 3kc4 1701 13 57
RS7_ECOLI PF00177 G 147 J01695 RF00177 A 1530 3kc4 1941 25 127
RS8_THET8 PF00410 K 135 M26923 RF00177 A 1515 1yl4 1889 29 93
RS10_THET8 PF00338 M 97 M26923 RF00177 A 1515 1yl4 1711 20 84
RS12_THET8 PF00164 O 122 M26923 RF00177 A 1515 1yl4 1972 45 161
RS15_ECO57 PF00312 O 83 J01695 RF00177 A 1530 3kc4 1821 21 89
RS17_ECOLI PF00366 Q 69 J01695 RF00177 A 1530 3kc4 1690 18 85
RS17_THET8 PF00366 T 69 M26923 RF00177 A 1515 1yl4 1690 29 93
  1. For each protein-RNA pair, the identifiers of UniProt, Pfam, and the chain in PDB, the length of protein sequence A, the identifiers of GenBank, Rfam, and the chain, the length of RNA sequence B, the PDB code, the number of sequences in the multiple sequence alignment (MSA) combined on the basis of the organisms, and the number of contacts within 3 Å and that within 5 Å are shown.