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1.0alpha7.train.800
19980256
[ { "id": "1.0alpha7.train.800.sent", "type": "sentence", "text": [ "Several consensus sites for common transcription regulators including Oct-1 (consensus binding motif NNGAATATKCANNNN), NF1 (core string TGGC), AP2 (MKCCCSCNGGCG), AP4 (WGARYCAGCTGYGGNCNK), CREB (NNGNTGACGYNN), Sp1 (KRGGCGKRRY), Nkx2.5 (TYAAGTG), and MyoD (NNCANTGNY) (Quandt et al., 1995) were mapped to the promoter region." ], "offsets": [ [ 0, 324 ] ] } ]
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[]
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[]
1.0alpha7.train.801
1002538
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[]
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1.0alpha7.train.802
1986897
[ { "id": "1.0alpha7.train.802.sent", "type": "sentence", "text": [ "TnI, the inhibitory subunit, inhibits the actomyosin ATPase and binds actin, while TnT binds tropomyosin." ], "offsets": [ [ 0, 108 ] ] } ]
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[]
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1.0alpha7.train.803
4500339
[ { "id": "1.0alpha7.train.803.sent", "type": "sentence", "text": [ "Paradoxically, however, we detected similar quantitative binding between STK15 and PP1 at 8, 9, and 12 h post-thymidine release, despite the fact that STK15 was predominantly seen in active hyperphosphorylated form at 8 and 9 h post-release unlike the hypophosphorylated form detected at 12 h post-release (Fig. 2 A)." ], "offsets": [ [ 0, 317 ] ] } ]
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[]
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1.0alpha7.train.804
6619102
[ { "id": "1.0alpha7.train.804.sent", "type": "sentence", "text": [ "Because Src does not bind to Abl (not shown), its binding to Cbl in the presence of Abl could be explained by a modification of Cbl conformation induced by its binding to Abl." ], "offsets": [ [ 0, 181 ] ] } ]
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[]
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1.0alpha7.train.805
3743398
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[]
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1.0alpha7.train.806
15100988
[ { "id": "1.0alpha7.train.806.sent", "type": "sentence", "text": [ "The conserved sequences corresponding to 3′HS1, 5′HS5 of the LCR, the HS located at kb −62.5 in mice and kb −111 in humans, and the HS at kb −85.5 in mice resemble the CTCF binding sites from previously characterized enhancer-blocking elements (Fig. 2A)." ], "offsets": [ [ 0, 254 ] ] } ]
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[]
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[]
1.0alpha7.train.807
13396369
[ { "id": "1.0alpha7.train.807.sent", "type": "sentence", "text": [ "Pseudomonas aeruginosa and Pseudomonas cepacia isolated from cystic fibrosis patients bind specifically to gangliotetraosylceramide ( Asialo GM1) and gangliotriaosylceramide ( Asialo GM2)." ], "offsets": [ [ 0, 191 ] ] } ]
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[]
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[]
1.0alpha7.train.808
2064044
[ { "id": "1.0alpha7.train.808.sent", "type": "sentence", "text": [ "B, binding of recombinant EGR-1 and NFATc to a 33P-labeled oligonucleotide that represents the ZIP and the NFAT site of the human IL-2 gene promoter (ZN)." ], "offsets": [ [ 0, 159 ] ] } ]
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[]
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1.0alpha7.train.809
11930070
[ { "id": "1.0alpha7.train.809.sent", "type": "sentence", "text": [ "Altogether, these observations suggest that binding of DDP1 to the dodeca-satellite C-strand is largely conformational dependent and support the hypothesis that DDP1 could also bind ssDNA fragments other that the dodeca-satellite C-strand." ], "offsets": [ [ 0, 243 ] ] } ]
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[]
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1.0alpha7.train.810
17781167
[ { "id": "1.0alpha7.train.810.sent", "type": "sentence", "text": [ "From the earliest demonstrations that CRP binds to microbes and mediates their killing in vitro, to more recent observations of protection against Gram-positive and Gram-negative bacteria in CRPtg mice, the evidence has overwhelmingly supported the notion that CRP plays an important role in host defense." ], "offsets": [ [ 0, 305 ] ] } ]
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[]
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[]
1.0alpha7.train.811
22709392
[ { "id": "1.0alpha7.train.811.sent", "type": "sentence", "text": [ "A prediction from the hypothesis that Wnt signaling might use Brg to activate Myc is that Brg binds the Myc promoter, a direct target of Wnt signaling (He et al., 1998)." ], "offsets": [ [ 0, 169 ] ] } ]
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[]
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1.0alpha7.train.812
24544891
[ { "id": "1.0alpha7.train.812.sent", "type": "sentence", "text": [ "Our results support the former kinetic model where eIF4G binds to eIF4E independently of an interaction with eIF3 ( Figure 3)." ], "offsets": [ [ 0, 130 ] ] } ]
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[]
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1.0alpha7.train.813
8939567
[ { "id": "1.0alpha7.train.813.sent", "type": "sentence", "text": [ "For most actin-binding proteins this would require that domains 1 and 3 of actin be exposed in the BAF complex, which is the case since both profilin and cofilin bind to actin within the complex." ], "offsets": [ [ 0, 204 ] ] } ]
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[]
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1.0alpha7.train.814
9021608
[ { "id": "1.0alpha7.train.814.sent", "type": "sentence", "text": [ "Binding of p23 to Hsp90 is promoted by ATP or ATPγS but inhibited by ADP (Sullivan et al. 1997) and thus appears to be dependant on the presence of the γ phosphate. " ], "offsets": [ [ 0, 165 ] ] } ]
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[]
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1.0alpha7.train.815
9432298
[ { "id": "1.0alpha7.train.815.sent", "type": "sentence", "text": [ "Mutation of this Arg (Arg25) Cys in the Akt1 PH domain or Arg28 Cys in Btk abrogates the binding of these PH domains to PI(3,4,5)P3." ], "offsets": [ [ 0, 137 ] ] } ]
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[]
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1.0alpha7.train.816
9029915
[ { "id": "1.0alpha7.train.816.sent", "type": "sentence", "text": [ "SXL Can Directly Bind both UTRs of msl-2" ], "offsets": [ [ 0, 40 ] ] } ]
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[]
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1.0alpha7.train.817
2888049
[ { "id": "1.0alpha7.train.817.sent", "type": "sentence", "text": [ "PS1 preferentially binds immature APP and Notch within the ER/Golgi in transfected mammalian cells ( 21, 22)." ], "offsets": [ [ 0, 113 ] ] } ]
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[]
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1.0alpha7.train.818
15573464
[ { "id": "1.0alpha7.train.818.sent", "type": "sentence", "text": [ "Furthermore, the binding of Abi-1 to Sos alone is apparently not sufficient to block all signaling to Erks; for example, overexpression of Abi-1 fails to abolish v-Src-induced Erk activation." ], "offsets": [ [ 0, 197 ] ] } ]
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[]
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1.0alpha7.train.819
15642357
[ { "id": "1.0alpha7.train.819.sent", "type": "sentence", "text": [ "The fact that CKI binding of dPER and mPER1 has been preserved while the location and sequence of the binding site may have been shuffled suggests there is strong selective pressure to maintain the interaction of the two proteins." ], "offsets": [ [ 0, 233 ] ] } ]
[ { "id": "1.0alpha7.train.819.ent0_0", "type": "protein", "text": [ "mPER1" ], "offsets": [ [ 41, 46 ] ], "normalized": [ { "db_name": "NCBI gene", "db_id": "5187" }, { "db_name": "hgnc", "db_id": "PER1" }, { "db_name": "uniprot", "db_id": "O15534" } ] }, { "id": "1.0alpha7.train.819.ent1_0", "type": "protein-family", "text": [ "CKI" ], "offsets": [ [ 15, 18 ] ], "normalized": [] }, { "id": "1.0alpha7.train.819.ent2_0", "type": "protein", "text": [ "dPER" ], "offsets": [ [ 31, 35 ] ], "normalized": [ { "db_name": "uniprot", "db_id": "B4GYL6" } ] } ]
[]
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1.0alpha7.train.820
5053447
[ { "id": "1.0alpha7.train.820.sent", "type": "sentence", "text": [ "EBP50/NHERF through an ERM-binding domain binds to the cortical actin cytoskeleton." ], "offsets": [ [ 0, 85 ] ] } ]
[ { "id": "1.0alpha7.train.820.ent0_0", "type": "protein", "text": [ "NHERF" ], "offsets": [ [ 6, 11 ] ], "normalized": [ { "db_name": "NCBI gene", "db_id": "9368" }, { "db_name": "hgnc", "db_id": "SLC9A3R1" }, { "db_name": "uniprot", "db_id": "O14745" } ] }, { "id": "1.0alpha7.train.820.ent1_0", "type": "protein", "text": [ "EBP50" ], "offsets": [ [ 0, 5 ] ], "normalized": [ { "db_name": "NCBI gene", "db_id": "9368" }, { "db_name": "hgnc", "db_id": "SLC9A3R1" }, { "db_name": "uniprot", "db_id": "O14745" } ] }, { "id": "1.0alpha7.train.820.ent2_0", "type": "protein-domain", "text": [ "ERM-binding domain" ], "offsets": [ [ 24, 42 ] ], "normalized": [] }, { "id": "1.0alpha7.train.820.ent3_0", "type": "protein", "text": [ "actin" ], "offsets": [ [ 66, 71 ] ], "normalized": [ { "db_name": "NCBI gene", "db_id": "58" }, { "db_name": "hgnc", "db_id": "ACTA1" }, { "db_name": "uniprot", "db_id": "P68133" } ] }, { "id": "1.0alpha7.train.820.ent4_0", "type": "protein-family", "text": [ "ERM" ], "offsets": [ [ 24, 27 ] ], "normalized": [ { "db_name": "interpro", "db_id": "IPR000798" } ] }, { "id": "1.0alpha7.train.820.ent5_0", "type": "organelle", "text": [ "actin cytoskeleton" ], "offsets": [ [ 66, 84 ] ], "normalized": [] } ]
[]
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1.0alpha7.train.821
12892976
[ { "id": "1.0alpha7.train.821.sent", "type": "sentence", "text": [ "If transcription of a target gene is not initiated in a cell, PcG proteins bound to the gene's PRE chromatin form a silencing structure that supersedes colocalized TRX ( P OUX et al. 1996 )." ], "offsets": [ [ 0, 190 ] ] } ]
[ { "id": "1.0alpha7.train.821.ent0_0", "type": "DNA", "text": [ "PRE" ], "offsets": [ [ 95, 98 ] ], "normalized": [] }, { "id": "1.0alpha7.train.821.ent1_0", "type": "protein", "text": [ "TRX" ], "offsets": [ [ 164, 167 ] ], "normalized": [ { "db_name": "NCBI gene", "db_id": "7295" }, { "db_name": "hgnc", "db_id": "TXN" }, { "db_name": "uniprot", "db_id": "P10599" } ] }, { "id": "1.0alpha7.train.821.ent2_0", "type": "protein-family", "text": [ "PcG" ], "offsets": [ [ 62, 65 ] ], "normalized": [] } ]
[]
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1.0alpha7.train.822
22615505
[ { "id": "1.0alpha7.train.822.sent", "type": "sentence", "text": [ "Thus, we propose that the mutations define the site at which DM binds DR during peptide exchange." ], "offsets": [ [ 0, 99 ] ] } ]
[ { "id": "1.0alpha7.train.822.ent0_0", "type": "protein-family", "text": [ "DM" ], "offsets": [ [ 62, 64 ] ], "normalized": [ { "db_name": "interpro", "db_id": "IPR036407" } ] }, { "id": "1.0alpha7.train.822.ent1_0", "type": "protein-family", "text": [ "DR" ], "offsets": [ [ 72, 74 ] ], "normalized": [ { "db_name": "interpro", "db_id": "IPR037028" } ] } ]
[]
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1.0alpha7.train.823
4976826
[ { "id": "1.0alpha7.train.823.sent", "type": "sentence", "text": [ "Synaptotagmin I also binds to polymerized tubulin." ], "offsets": [ [ 0, 50 ] ] } ]
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[]
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1.0alpha7.train.824
19857601
[ { "id": "1.0alpha7.train.824.sent", "type": "sentence", "text": [ "The involvement of CBP/ p300 binding with E2F transactivation indicates that recruitment of these acetylases following release of E2F-1 from pRB may represent an important mechanism in the relief of pRB-mediated transcriptional repression." ], "offsets": [ [ 0, 244 ] ] } ]
[ { "id": "1.0alpha7.train.824.ent0_0", "type": "protein", "text": [ "CBP/ p300" ], "offsets": [ [ 20, 29 ] ], "normalized": [ { "db_name": "NCBI gene", "db_id": "2033" }, { "db_name": "hgnc", "db_id": "EP300" }, { "db_name": "uniprot", "db_id": "Q09472" } ] }, { "id": "1.0alpha7.train.824.ent1_0", "type": "protein", "text": [ "pRB" ], "offsets": [ [ 145, 148 ] ], "normalized": [ { "db_name": "NCBI gene", "db_id": "5925" }, { "db_name": "hgnc", "db_id": "RB1" }, { "db_name": "uniprot", "db_id": "P06400" } ] }, { "id": "1.0alpha7.train.824.ent2_1", "type": "protein", "text": [ "pRB" ], "offsets": [ [ 204, 207 ] ], "normalized": [ { "db_name": "NCBI gene", "db_id": "5925" }, { "db_name": "hgnc", "db_id": "RB1" }, { "db_name": "uniprot", "db_id": "P06400" } ] }, { "id": "1.0alpha7.train.824.ent3_0", "type": "protein-complex", "text": [ "E2F" ], "offsets": [ [ 44, 47 ] ], "normalized": [] }, { "id": "1.0alpha7.train.824.ent4_1", "type": "protein-complex", "text": [ "E2F" ], "offsets": [ [ 133, 136 ] ], "normalized": [] }, { "id": "1.0alpha7.train.824.ent5_0", "type": "protein", "text": [ "E2F-1" ], "offsets": [ [ 133, 138 ] ], "normalized": [ { "db_name": "NCBI gene", "db_id": "1869" }, { "db_name": "hgnc", "db_id": "E2F1" }, { "db_name": "uniprot", "db_id": "Q01094" } ] }, { "id": "1.0alpha7.train.824.ent6_0", "type": "protein", "text": [ "CBP" ], "offsets": [ [ 20, 23 ] ], "normalized": [ { "db_name": "NCBI gene", "db_id": "1387" }, { "db_name": "hgnc", "db_id": "CREBBP" }, { "db_name": "uniprot", "db_id": "Q92793" } ] }, { "id": "1.0alpha7.train.824.ent7_0", "type": "protein", "text": [ "p300" ], "offsets": [ [ 25, 29 ] ], "normalized": [ { "db_name": "NCBI gene", "db_id": "2033" }, { "db_name": "hgnc", "db_id": "EP300" }, { "db_name": "uniprot", "db_id": "Q09472" } ] } ]
[]
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1.0alpha7.train.825
9738446
[ { "id": "1.0alpha7.train.825.sent", "type": "sentence", "text": [ "Together, these results support the notion that Crk binding to CAS is critical for the migratory properties of these cells and that the substrate domain of CAS as well as the SH2 domain of Crk contribute to this response." ], "offsets": [ [ 0, 228 ] ] } ]
[ { "id": "1.0alpha7.train.825.ent0_0", "type": "protein-family", "text": [ "CAS" ], "offsets": [ [ 66, 69 ] ], "normalized": [ { "db_name": "interpro", "db_id": "IPR037362" } ] }, { "id": "1.0alpha7.train.825.ent1_1", "type": "protein-family", "text": [ "CAS" ], "offsets": [ [ 160, 163 ] ], "normalized": [ { "db_name": "interpro", "db_id": "IPR037362" } ] }, { "id": "1.0alpha7.train.825.ent2_0", "type": "protein", "text": [ "Crk" ], "offsets": [ [ 50, 53 ] ], "normalized": [ { "db_name": "NCBI gene", "db_id": "1398" }, { "db_name": "hgnc", "db_id": "CRK" }, { "db_name": "uniprot", "db_id": "P46108" } ] }, { "id": "1.0alpha7.train.825.ent3_1", "type": "protein", "text": [ "Crk" ], "offsets": [ [ 195, 198 ] ], "normalized": [ { "db_name": "NCBI gene", "db_id": "1398" }, { "db_name": "hgnc", "db_id": "CRK" }, { "db_name": "uniprot", "db_id": "P46108" } ] }, { "id": "1.0alpha7.train.825.ent4_0", "type": "protein-domain", "text": [ "SH2 domain" ], "offsets": [ [ 180, 190 ] ], "normalized": [ { "db_name": "interpro", "db_id": "IPR000980" } ] } ]
[]
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1.0alpha7.train.826
8922434
[ { "id": "1.0alpha7.train.826.sent", "type": "sentence", "text": [ "We found that both the wild-type and the triple mutant form of FKHRL1 bound to the IRS of the IGFBP1 gene, leading to a shift in the mobility of the IRS DNA element on a nondenaturing polyacrylamide gel ( Figure 5B, lanes 1, 2, and 3)." ], "offsets": [ [ 0, 244 ] ] } ]
[ { "id": "1.0alpha7.train.826.ent0_0", "type": "protein", "text": [ "FKHRL1" ], "offsets": [ [ 64, 70 ] ], "normalized": [ { "db_name": "NCBI gene", "db_id": "2309" }, { "db_name": "hgnc", "db_id": "FOXO3" }, { "db_name": "uniprot", "db_id": "O43524" } ] }, { "id": "1.0alpha7.train.826.ent1_0", "type": "DNA", "text": [ "IGFBP1 gene" ], "offsets": [ [ 98, 109 ] ], "normalized": [] }, { "id": "1.0alpha7.train.826.ent2_0", "type": "protein", "text": [ "triple mutant form of FKHRL1" ], "offsets": [ [ 42, 70 ] ], "normalized": [] }, { "id": "1.0alpha7.train.826.ent3_0", "type": "DNA", "text": [ "IRS" ], "offsets": [ [ 86, 89 ] ], "normalized": [] }, { "id": "1.0alpha7.train.826.ent4_1", "type": "DNA", "text": [ "IRS" ], "offsets": [ [ 155, 158 ] ], "normalized": [] }, { "id": "1.0alpha7.train.826.ent5_0", "type": "DNA", "text": [ "IRS DNA element" ], "offsets": [ [ 155, 170 ] ], "normalized": [] } ]
[]
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1.0alpha7.train.827
4166010
[ { "id": "1.0alpha7.train.827.sent", "type": "sentence", "text": [ "However, the 131-1-1 chimera containing the Na region of Smad1 could weakly induce transcription of 3GC2-Lux, but the 13-1-1 and 133-1-1 chimeras failed to do so,2 suggesting that Smad1 may bind to GC-rich sequences in a fashion different from that of Smad3 and that both the Na and the C regions of MH1 may play a role in the direct DNA binding of Smad1." ], "offsets": [ [ 0, 355 ] ] } ]
[ { "id": "1.0alpha7.train.827.ent0_0", "type": "DNA", "text": [ "GC-rich sequences" ], "offsets": [ [ 198, 215 ] ], "normalized": [] }, { "id": "1.0alpha7.train.827.ent1_0", "type": "DNA", "text": [ "DNA" ], "offsets": [ [ 334, 337 ] ], "normalized": [ { "db_name": "NCBI gene", "db_id": "25782" }, { "db_name": "hgnc", "db_id": "RAB3GAP2" }, { "db_name": "uniprot", "db_id": "Q9H2M9" } ] }, { "id": "1.0alpha7.train.827.ent2_0", "type": "experimental-construct", "text": [ "131-1-1 chimera" ], "offsets": [ [ 13, 28 ] ], "normalized": [] }, { "id": "1.0alpha7.train.827.ent3_0", "type": "protein", "text": [ "Smad1" ], "offsets": [ [ 57, 62 ] ], "normalized": [ { "db_name": "NCBI gene", "db_id": "4086" }, { "db_name": "hgnc", "db_id": "SMAD1" }, { "db_name": "uniprot", "db_id": "Q15797" } ] }, { "id": "1.0alpha7.train.827.ent4_1", "type": "protein", "text": [ "Smad1" ], "offsets": [ [ 180, 185 ] ], "normalized": [ { "db_name": "NCBI gene", "db_id": "4086" }, { "db_name": "hgnc", "db_id": "SMAD1" }, { "db_name": "uniprot", "db_id": "Q15797" } ] }, { "id": "1.0alpha7.train.827.ent5_2", "type": "protein", "text": [ "Smad1" ], "offsets": [ [ 349, 354 ] ], "normalized": [ { "db_name": "NCBI gene", "db_id": "4086" }, { "db_name": "hgnc", "db_id": "SMAD1" }, { "db_name": "uniprot", "db_id": "Q15797" } ] }, { "id": "1.0alpha7.train.827.ent6_0", "type": "protein", "text": [ "Smad3" ], "offsets": [ [ 252, 257 ] ], "normalized": [ { "db_name": "NCBI gene", "db_id": "4088" }, { "db_name": "hgnc", "db_id": "SMAD3" }, { "db_name": "uniprot", "db_id": "P84022" } ] }, { "id": "1.0alpha7.train.827.ent7_0", "type": "protein-region", "text": [ "Na region" ], "offsets": [ [ 44, 53 ] ], "normalized": [] }, { "id": "1.0alpha7.train.827.ent8_0", "type": "experimental-construct", "text": [ "13-1-1" ], "offsets": [ [ 118, 124 ] ], "normalized": [] }, { "id": "1.0alpha7.train.827.ent9_0", "type": "experiment-tag", "text": [ "3GC2-Lux" ], "offsets": [ [ 100, 108 ] ], "normalized": [] }, { "id": "1.0alpha7.train.827.ent10_0", "type": "protein-domain", "text": [ "MH1" ], "offsets": [ [ 300, 303 ] ], "normalized": [ { "db_name": "interpro", "db_id": "IPR013019" } ] } ]
[]
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1.0alpha7.train.828
12683865
[ { "id": "1.0alpha7.train.828.sent", "type": "sentence", "text": [ "This agrees with our previous finding that the Q domain is required for efficient binding between Gro and Rpd3 (Fig. ​(Fig.4D)4D) and with our previously published results showing that efficient repression by Gro requires a functional tetramerization domain (Chen et al. 1998)." ], "offsets": [ [ 0, 277 ] ] } ]
[ { "id": "1.0alpha7.train.828.ent0_0", "type": "protein", "text": [ "Gro" ], "offsets": [ [ 98, 101 ] ], "normalized": [ { "db_name": "NCBI gene", "db_id": "2919" }, { "db_name": "hgnc", "db_id": "CXCL1" }, { "db_name": "uniprot", "db_id": "P09341" } ] }, { "id": "1.0alpha7.train.828.ent1_1", "type": "protein", "text": [ "Gro" ], "offsets": [ [ 209, 212 ] ], "normalized": [ { "db_name": "NCBI gene", "db_id": "2919" }, { "db_name": "hgnc", "db_id": "CXCL1" }, { "db_name": "uniprot", "db_id": "P09341" } ] }, { "id": "1.0alpha7.train.828.ent2_0", "type": "protein", "text": [ "Rpd3" ], "offsets": [ [ 106, 110 ] ], "normalized": [ { "db_name": "uniprot", "db_id": "Q94517" } ] }, { "id": "1.0alpha7.train.828.ent3_0", "type": "protein-domain", "text": [ "Q domain" ], "offsets": [ [ 47, 55 ] ], "normalized": [] } ]
[]
[ { "id": "1.0alpha7.train.828.coref0", "entity_ids": [ "1.0alpha7.train.828.ent0_0", "1.0alpha7.train.828.ent1_1" ] }, { "id": "1.0alpha7.train.828.coref1", "entity_ids": [ "1.0alpha7.train.828.ent2_0" ] }, { "id": "1.0alpha7.train.828.coref2", "entity_ids": [ "1.0alpha7.train.828.ent3_0" ] } ]
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1.0alpha7.train.829
9396327
[ { "id": "1.0alpha7.train.829.sent", "type": "sentence", "text": [ "Myopodin can directly bind to actin and contains a novel actin binding site in the center of the protein." ], "offsets": [ [ 0, 107 ] ] } ]
[ { "id": "1.0alpha7.train.829.ent0_0", "type": "protein", "text": [ "Myopodin" ], "offsets": [ [ 0, 8 ] ], "normalized": [ { "db_name": "NCBI gene", "db_id": "171024" }, { "db_name": "hgnc", "db_id": "SYNPO2" }, { "db_name": "uniprot", "db_id": "Q9UMS6" } ] }, { "id": "1.0alpha7.train.829.ent1_0", "type": "protein", "text": [ "actin" ], "offsets": [ [ 31, 36 ] ], "normalized": [ { "db_name": "NCBI gene", "db_id": "58" }, { "db_name": "hgnc", "db_id": "ACTA1" }, { "db_name": "uniprot", "db_id": "P68133" } ] }, { "id": "1.0alpha7.train.829.ent2_1", "type": "protein", "text": [ "actin" ], "offsets": [ [ 59, 64 ] ], "normalized": [ { "db_name": "NCBI gene", "db_id": "58" }, { "db_name": "hgnc", "db_id": "ACTA1" }, { "db_name": "uniprot", "db_id": "P68133" } ] } ]
[]
[ { "id": "1.0alpha7.train.829.coref0", "entity_ids": [ "1.0alpha7.train.829.ent0_0" ] }, { "id": "1.0alpha7.train.829.coref1", "entity_ids": [ "1.0alpha7.train.829.ent1_0", "1.0alpha7.train.829.ent2_1" ] } ]
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1.0alpha7.train.830
12658363
[ { "id": "1.0alpha7.train.830.sent", "type": "sentence", "text": [ "Deletion analysis confirmed that U2AF65 bound to the Py tract (data not shown)." ], "offsets": [ [ 0, 81 ] ] } ]
[ { "id": "1.0alpha7.train.830.ent0_0", "type": "protein", "text": [ "U2AF65" ], "offsets": [ [ 34, 40 ] ], "normalized": [ { "db_name": "NCBI gene", "db_id": "11338" }, { "db_name": "hgnc", "db_id": "U2AF2" }, { "db_name": "uniprot", "db_id": "P26368" } ] }, { "id": "1.0alpha7.train.830.ent1_0", "type": "DNA", "text": [ "Py tract" ], "offsets": [ [ 55, 63 ] ], "normalized": [] } ]
[]
[ { "id": "1.0alpha7.train.830.coref0", "entity_ids": [ "1.0alpha7.train.830.ent0_0" ] }, { "id": "1.0alpha7.train.830.coref1", "entity_ids": [ "1.0alpha7.train.830.ent1_0" ] } ]
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1.0alpha7.train.831
9469058
[ { "id": "1.0alpha7.train.831.sent", "type": "sentence", "text": [ "However, it did so with lower efficiency than the COOH-terminal portion of Eps15 itself, suggesting that, in vivo, Eps15 binds to AP2 with higher affinity than with Numb ( Fig 4 D)." ], "offsets": [ [ 0, 185 ] ] } ]
[ { "id": "1.0alpha7.train.831.ent0_0", "type": "protein-complex", "text": [ "AP2" ], "offsets": [ [ 134, 137 ] ], "normalized": [] }, { "id": "1.0alpha7.train.831.ent1_0", "type": "protein", "text": [ "Eps15" ], "offsets": [ [ 77, 82 ] ], "normalized": [ { "db_name": "NCBI gene", "db_id": "2060" }, { "db_name": "hgnc", "db_id": "EPS15" }, { "db_name": "uniprot", "db_id": "P42566" } ] }, { "id": "1.0alpha7.train.831.ent2_1", "type": "protein", "text": [ "Eps15" ], "offsets": [ [ 118, 123 ] ], "normalized": [ { "db_name": "NCBI gene", "db_id": "2060" }, { "db_name": "hgnc", "db_id": "EPS15" }, { "db_name": "uniprot", "db_id": "P42566" } ] }, { "id": "1.0alpha7.train.831.ent3_0", "type": "protein", "text": [ "Numb" ], "offsets": [ [ 169, 173 ] ], "normalized": [ { "db_name": "NCBI gene", "db_id": "8650" }, { "db_name": "hgnc", "db_id": "NUMB" }, { "db_name": "uniprot", "db_id": "P49757" } ] } ]
[]
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1.0alpha7.train.832
9508895
[ { "id": "1.0alpha7.train.832.sent", "type": "sentence", "text": [ "Biochemical analyses show that the Tiam1 fragment (amino acids 393 - 738) contains an ankyrin-binding site and competes for Tiam1 binding to ankyrin." ], "offsets": [ [ 0, 153 ] ] } ]
[ { "id": "1.0alpha7.train.832.ent0_0", "type": "protein", "text": [ "Tiam1" ], "offsets": [ [ 36, 41 ] ], "normalized": [ { "db_name": "NCBI gene", "db_id": "7074" }, { "db_name": "hgnc", "db_id": "TIAM1" }, { "db_name": "uniprot", "db_id": "Q13009" } ] }, { "id": "1.0alpha7.train.832.ent1_1", "type": "protein", "text": [ "Tiam1" ], "offsets": [ [ 127, 132 ] ], "normalized": [ { "db_name": "NCBI gene", "db_id": "7074" }, { "db_name": "hgnc", "db_id": "TIAM1" }, { "db_name": "uniprot", "db_id": "Q13009" } ] }, { "id": "1.0alpha7.train.832.ent2_0", "type": "protein-family", "text": [ "ankyrin" ], "offsets": [ [ 88, 95 ] ], "normalized": [ { "db_name": "interpro", "db_id": "IPR036770" } ] }, { "id": "1.0alpha7.train.832.ent3_1", "type": "protein-family", "text": [ "ankyrin" ], "offsets": [ [ 145, 152 ] ], "normalized": [ { "db_name": "interpro", "db_id": "IPR036770" } ] } ]
[]
[ { "id": "1.0alpha7.train.832.coref0", "entity_ids": [ "1.0alpha7.train.832.ent0_0", "1.0alpha7.train.832.ent1_1" ] }, { "id": "1.0alpha7.train.832.coref1", "entity_ids": [ "1.0alpha7.train.832.ent2_0", "1.0alpha7.train.832.ent3_1" ] } ]
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1.0alpha7.train.833
5301509
[ { "id": "1.0alpha7.train.833.sent", "type": "sentence", "text": [ "We next examined whether the binding of menin to GTP is affected by the concentration of Mg2+, as observed with many GTPases ( 28, 29)." ], "offsets": [ [ 0, 138 ] ] } ]
[ { "id": "1.0alpha7.train.833.ent0_0", "type": "protein", "text": [ "menin" ], "offsets": [ [ 41, 46 ] ], "normalized": [ { "db_name": "NCBI gene", "db_id": "4221" }, { "db_name": "hgnc", "db_id": "MEN1" }, { "db_name": "uniprot", "db_id": "O00255" } ] }, { "id": "1.0alpha7.train.833.ent1_0", "type": "chemical", "text": [ "GTP" ], "offsets": [ [ 51, 54 ] ], "normalized": [ { "db_name": "pubchem:compound", "db_id": "135398633" } ] }, { "id": "1.0alpha7.train.833.ent2_0", "type": "protein-family", "text": [ "GTPases" ], "offsets": [ [ 119, 126 ] ], "normalized": [] }, { "id": "1.0alpha7.train.833.ent3_0", "type": "chemical", "text": [ "Mg2+" ], "offsets": [ [ 91, 95 ] ], "normalized": [ { "db_name": "pubchem:compound", "db_id": "5462224" } ] } ]
[]
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1.0alpha7.train.834
19342959
[ { "id": "1.0alpha7.train.834.sent", "type": "sentence", "text": [ "As the Dlt-binding site in Crb differs from these motifs, the first PDZ domain of Dlt, which binds to Crb in vitro [23] , may belong to a different class." ], "offsets": [ [ 0, 161 ] ] } ]
[ { "id": "1.0alpha7.train.834.ent0_0", "type": "protein", "text": [ "Crb" ], "offsets": [ [ 29, 32 ] ], "normalized": [ { "db_name": "uniprot", "db_id": "P10040" } ] }, { "id": "1.0alpha7.train.834.ent1_1", "type": "protein", "text": [ "Crb" ], "offsets": [ [ 107, 110 ] ], "normalized": [ { "db_name": "uniprot", "db_id": "P10040" } ] }, { "id": "1.0alpha7.train.834.ent2_0", "type": "protein-family", "text": [ "PDZ domain" ], "offsets": [ [ 71, 81 ] ], "normalized": [ { "db_name": "interpro", "db_id": "IPR001478" } ] }, { "id": "1.0alpha7.train.834.ent3_0", "type": "protein", "text": [ "Dlt" ], "offsets": [ [ 8, 11 ] ], "normalized": [ { "db_name": "uniprot", "db_id": "Q8T626" } ] }, { "id": "1.0alpha7.train.834.ent4_1", "type": "protein", "text": [ "Dlt" ], "offsets": [ [ 86, 89 ] ], "normalized": [ { "db_name": "uniprot", "db_id": "Q8T626" } ] } ]
[]
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1.0alpha7.train.835
19349311
[ { "id": "1.0alpha7.train.835.sent", "type": "sentence", "text": [ "The cNMP-BD of CNrasGEF is similar to the cAMP-binding region of PKA and cAMP GEFs 2, 3 and to the cGMP-binding region of PKG and cyclic-nucleotide-gated K+ channels, although it lacks conservation of the AA or TA within the R(A/T)A motif found in PKA (and Epac) or in PKG, respectively (see Supplementary material). " ], "offsets": [ [ 0, 317 ] ] } ]
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[]
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1.0alpha7.train.836
5252345
[ { "id": "1.0alpha7.train.836.sent", "type": "sentence", "text": [ "Abeta1-42 has such high affinity for Cu2+ (attomolar) ( 8) that it is likely to be metallated in vivo, and indeed we found that Abeta purified from AD plaque is mainly bound to Zn (1.7 eq per mol of Abeta) and Cu (0.4 eq)." ], "offsets": [ [ 0, 229 ] ] } ]
[ { "id": "1.0alpha7.train.836.ent0_0", "type": "chemical", "text": [ "Zn" ], "offsets": [ [ 180, 182 ] ], "normalized": [ { "db_name": "pubchem:compound", "db_id": "23994" } ] }, { "id": "1.0alpha7.train.836.ent1_0", "type": "peptide", "text": [ "Abeta1-42" ], "offsets": [ [ 0, 9 ] ], "normalized": [] }, { "id": "1.0alpha7.train.836.ent2_0", "type": "peptide", "text": [ "Abeta" ], "offsets": [ [ 131, 136 ] ], "normalized": [] }, { "id": "1.0alpha7.train.836.ent3_1", "type": "peptide", "text": [ "Abeta" ], "offsets": [ [ 204, 209 ] ], "normalized": [] }, { "id": "1.0alpha7.train.836.ent4_0", "type": "tissue", "text": [ "AD plaque" ], "offsets": [ [ 151, 160 ] ], "normalized": [] }, { "id": "1.0alpha7.train.836.ent5_0", "type": "chemical", "text": [ "Cu2+" ], "offsets": [ [ 38, 42 ] ], "normalized": [ { "db_name": "pubchem:compound", "db_id": "27099" } ] }, { "id": "1.0alpha7.train.836.ent6_0", "type": "chemical", "text": [ "Cu" ], "offsets": [ [ 216, 218 ] ], "normalized": [ { "db_name": "pubchem:compound", "db_id": "23978" } ] } ]
[]
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1.0alpha7.train.837
4311874
[ { "id": "1.0alpha7.train.837.sent", "type": "sentence", "text": [ "However, our recent observation that TDP-43 can efficiently bind to (UG)m sequences (1) is consistent with the presence of two putative full-length RRM domains (Fig. 1 A) located between residues 106 and 175 (RRM1) and 193 and 257 (RRM2) of its coding sequence according to the output of the Pfam program (available at www.sanger.ac.uk)." ], "offsets": [ [ 0, 337 ] ] } ]
[ { "id": "1.0alpha7.train.837.ent0_0", "type": "assay", "text": [ "Pfam" ], "offsets": [ [ 292, 296 ] ], "normalized": [] }, { "id": "1.0alpha7.train.837.ent1_0", "type": "protein", "text": [ "TDP-43" ], "offsets": [ [ 37, 43 ] ], "normalized": [ { "db_name": "NCBI gene", "db_id": "23435" }, { "db_name": "hgnc", "db_id": "TARDBP" }, { "db_name": "uniprot", "db_id": "Q13148" } ] }, { "id": "1.0alpha7.train.837.ent2_0", "type": "RNA", "text": [ "(UG)m sequences" ], "offsets": [ [ 68, 83 ] ], "normalized": [] }, { "id": "1.0alpha7.train.837.ent3_0", "type": "protein-domain", "text": [ "RRM2" ], "offsets": [ [ 232, 236 ] ], "normalized": [] }, { "id": "1.0alpha7.train.837.ent4_0", "type": "protein-domain", "text": [ "RRM domains" ], "offsets": [ [ 148, 159 ] ], "normalized": [] }, { "id": "1.0alpha7.train.837.ent5_0", "type": "protein-domain", "text": [ "RRM domains" ], "offsets": [ [ 148, 159 ] ], "normalized": [] }, { "id": "1.0alpha7.train.837.ent6_0", "type": "protein-domain", "text": [ "RRM1" ], "offsets": [ [ 209, 213 ] ], "normalized": [] } ]
[]
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1.0alpha7.train.838
7534342
[ { "id": "1.0alpha7.train.838.sent", "type": "sentence", "text": [ "The other peptide motifs that inhibit angiogenesis might enhance the binding of TSP-1 to CD36, for example through ligation of proteoglycan coreceptors, or could have indirect effects such as sequestration of proangiogenic morphoregulatory factors (Guo et al. 1997, Iruela-Arispe et al. 1999)." ], "offsets": [ [ 0, 293 ] ] } ]
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[]
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1.0alpha7.train.839
5043113
[ { "id": "1.0alpha7.train.839.sent", "type": "sentence", "text": [ "Co-expression of deltaN, which binds APP but not JNK, affects the amount of immature APP as much as does the co-expression of JIP1b." ], "offsets": [ [ 0, 137 ] ] } ]
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[]
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1.0alpha7.train.840
3875356
[ { "id": "1.0alpha7.train.840.sent", "type": "sentence", "text": [ "Binding of mdm2 to p53 also targets p53 for degradation through ubiquitin-mediated pathways ( 19, 20)." ], "offsets": [ [ 0, 107 ] ] } ]
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[]
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1.0alpha7.train.841
19616503
[ { "id": "1.0alpha7.train.841.sent", "type": "sentence", "text": [ "In particular, Pbx binds to Hox proteins from paralog group 1-10 (Shen et al., 1997b ) and Meis binds to Hox proteins from paralog group 9-13 (Shen et al., 1997a )." ], "offsets": [ [ 0, 171 ] ] } ]
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[]
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1.0alpha7.train.842
2450041
[ { "id": "1.0alpha7.train.842.sent", "type": "sentence", "text": [ "Recent evidence also suggested that Crk binding to paxillin might play an important role in signaling by IGF-1 and growth hormone receptors ( 43, 44)." ], "offsets": [ [ 0, 155 ] ] } ]
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[]
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1.0alpha7.train.843
15384233
[ { "id": "1.0alpha7.train.843.sent", "type": "sentence", "text": [ "Since the HOX proteins exhibit binding to CBP and p300, one possible mechanism by which CBP might prevent HOX protein DNA binding might be by direct acetylation of the HD." ], "offsets": [ [ 0, 177 ] ] } ]
[ { "id": "1.0alpha7.train.843.ent0_0", "type": "protein", "text": [ "CBP" ], "offsets": [ [ 44, 47 ] ], "normalized": [ { "db_name": "NCBI gene", "db_id": "1387" }, { "db_name": "hgnc", "db_id": "CREBBP" }, { "db_name": "uniprot", "db_id": "Q92793" } ] }, { "id": "1.0alpha7.train.843.ent1_1", "type": "protein", "text": [ "CBP" ], "offsets": [ [ 92, 95 ] ], "normalized": [ { "db_name": "NCBI gene", "db_id": "1387" }, { "db_name": "hgnc", "db_id": "CREBBP" }, { "db_name": "uniprot", "db_id": "Q92793" } ] }, { "id": "1.0alpha7.train.843.ent2_0", "type": "protein", "text": [ "p300" ], "offsets": [ [ 53, 57 ] ], "normalized": [ { "db_name": "NCBI gene", "db_id": "2033" }, { "db_name": "hgnc", "db_id": "EP300" }, { "db_name": "uniprot", "db_id": "Q09472" } ] }, { "id": "1.0alpha7.train.843.ent3_0", "type": "DNA", "text": [ "DNA" ], "offsets": [ [ 123, 126 ] ], "normalized": [ { "db_name": "NCBI gene", "db_id": "25782" }, { "db_name": "hgnc", "db_id": "RAB3GAP2" }, { "db_name": "uniprot", "db_id": "Q9H2M9" } ] }, { "id": "1.0alpha7.train.843.ent4_0", "type": "protein-domain", "text": [ "HD" ], "offsets": [ [ 174, 176 ] ], "normalized": [ { "db_name": "interpro", "db_id": "IPR006674" } ] }, { "id": "1.0alpha7.train.843.ent5_0", "type": "protein-family", "text": [ "HOX proteins" ], "offsets": [ [ 11, 23 ] ], "normalized": [] } ]
[]
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1.0alpha7.train.844
3807002
[ { "id": "1.0alpha7.train.844.sent", "type": "sentence", "text": [ "To further narrow down the TEF-1-binding region of SRF, we analyzed an additional SRF mutant containing amino acids 1-204." ], "offsets": [ [ 0, 125 ] ] } ]
[ { "id": "1.0alpha7.train.844.ent0_0", "type": "protein", "text": [ "TEF-1" ], "offsets": [ [ 28, 33 ] ], "normalized": [ { "db_name": "NCBI gene", "db_id": "7003" }, { "db_name": "hgnc", "db_id": "TEAD1" }, { "db_name": "uniprot", "db_id": "P28347" } ] }, { "id": "1.0alpha7.train.844.ent1_0", "type": "protein", "text": [ "SRF" ], "offsets": [ [ 53, 56 ] ], "normalized": [ { "db_name": "NCBI gene", "db_id": "6722" }, { "db_name": "hgnc", "db_id": "SRF" }, { "db_name": "uniprot", "db_id": "P11831" } ] }, { "id": "1.0alpha7.train.844.ent2_1", "type": "protein", "text": [ "SRF" ], "offsets": [ [ 85, 88 ] ], "normalized": [ { "db_name": "NCBI gene", "db_id": "6722" }, { "db_name": "hgnc", "db_id": "SRF" }, { "db_name": "uniprot", "db_id": "P11831" } ] } ]
[]
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1.0alpha7.train.845
12014121
[ { "id": "1.0alpha7.train.845.sent", "type": "sentence", "text": [ "The results showed that ATP bound only to Orc1, Orc4 and Orc5 (Figure 1), consistent with the presence of Walker A and B amino acid sequence motifs in these proteins." ], "offsets": [ [ 0, 171 ] ] } ]
[ { "id": "1.0alpha7.train.845.ent0_0", "type": "protein-motif", "text": [ "B" ], "offsets": [ [ 124, 125 ] ], "normalized": [] }, { "id": "1.0alpha7.train.845.ent1_0", "type": "protein-motif", "text": [ "Walker A" ], "offsets": [ [ 111, 119 ] ], "normalized": [] }, { "id": "1.0alpha7.train.845.ent2_0", "type": "protein", "text": [ "Orc4" ], "offsets": [ [ 51, 55 ] ], "normalized": [ { "db_name": "NCBI gene", "db_id": "5000" }, { "db_name": "hgnc", "db_id": "ORC4" }, { "db_name": "uniprot", "db_id": "O43929" } ] }, { "id": "1.0alpha7.train.845.ent3_0", "type": "protein", "text": [ "Orc5" ], "offsets": [ [ 61, 65 ] ], "normalized": [ { "db_name": "NCBI gene", "db_id": "5001" }, { "db_name": "hgnc", "db_id": "ORC5" }, { "db_name": "uniprot", "db_id": "A4D0P7" } ] }, { "id": "1.0alpha7.train.845.ent4_0", "type": "protein", "text": [ "Orc1" ], "offsets": [ [ 44, 48 ] ], "normalized": [ { "db_name": "NCBI gene", "db_id": "4998" }, { "db_name": "hgnc", "db_id": "ORC1" }, { "db_name": "uniprot", "db_id": "Q13415" } ] }, { "id": "1.0alpha7.train.845.ent5_0", "type": "chemical", "text": [ "ATP" ], "offsets": [ [ 25, 28 ] ], "normalized": [ { "db_name": "pubchem:compound", "db_id": "5957" } ] } ]
[]
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1.0alpha7.train.846
11966813
[ { "id": "1.0alpha7.train.846.sent", "type": "sentence", "text": [ "More binding of PR and better synergism in the presence of H1 he results of the ChIP experiments with anti-PR antibodies show that PR binding to the MMTV promoter nucleosome is enhanced in minichromosomes containing histone H1." ], "offsets": [ [ 0, 235 ] ] } ]
[ { "id": "1.0alpha7.train.846.ent0_0", "type": "protein", "text": [ "PR" ], "offsets": [ [ 17, 19 ] ], "normalized": [ { "db_name": "NCBI gene", "db_id": "5241" }, { "db_name": "hgnc", "db_id": "PGR" }, { "db_name": "uniprot", "db_id": "P06401" } ] }, { "id": "1.0alpha7.train.846.ent1_1", "type": "protein", "text": [ "PR" ], "offsets": [ [ 112, 114 ] ], "normalized": [ { "db_name": "NCBI gene", "db_id": "5241" }, { "db_name": "hgnc", "db_id": "PGR" }, { "db_name": "uniprot", "db_id": "P06401" } ] }, { "id": "1.0alpha7.train.846.ent2_2", "type": "protein", "text": [ "PR" ], "offsets": [ [ 137, 139 ] ], "normalized": [ { "db_name": "NCBI gene", "db_id": "5241" }, { "db_name": "hgnc", "db_id": "PGR" }, { "db_name": "uniprot", "db_id": "P06401" } ] }, { "id": "1.0alpha7.train.846.ent3_0", "type": "DNA", "text": [ "MMTV promoter" ], "offsets": [ [ 156, 169 ] ], "normalized": [] }, { "id": "1.0alpha7.train.846.ent4_0", "type": "reagent", "text": [ "anti-PR antibodies" ], "offsets": [ [ 107, 125 ] ], "normalized": [] }, { "id": "1.0alpha7.train.846.ent5_0", "type": "assay", "text": [ "ChIP" ], "offsets": [ [ 84, 88 ] ], "normalized": [] }, { "id": "1.0alpha7.train.846.ent6_0", "type": "protein-family", "text": [ "H1" ], "offsets": [ [ 61, 63 ] ], "normalized": [] }, { "id": "1.0alpha7.train.846.ent7_1", "type": "protein-family", "text": [ "H1" ], "offsets": [ [ 232, 234 ] ], "normalized": [] }, { "id": "1.0alpha7.train.846.ent8_0", "type": "protein-family", "text": [ "histone H1" ], "offsets": [ [ 224, 234 ] ], "normalized": [] }, { "id": "1.0alpha7.train.846.ent9_0", "type": "cell", "text": [ "MMTV" ], "offsets": [ [ 156, 160 ] ], "normalized": [] } ]
[]
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1.0alpha7.train.847
4399572
[ { "id": "1.0alpha7.train.847.sent", "type": "sentence", "text": [ "The binding of HSC nuclear extracts to a Sp1 cognate oligonucleotide was low in control cells but increased significantly following an NAC treatment of HSC with optimal activation at around 6 h (Fig. 5 A)." ], "offsets": [ [ 0, 211 ] ] } ]
[ { "id": "1.0alpha7.train.847.ent0_0", "type": "cell", "text": [ "HSC" ], "offsets": [ [ 16, 19 ] ], "normalized": [] }, { "id": "1.0alpha7.train.847.ent1_1", "type": "cell", "text": [ "HSC" ], "offsets": [ [ 157, 160 ] ], "normalized": [] }, { "id": "1.0alpha7.train.847.ent2_0", "type": "chemical", "text": [ "NAC" ], "offsets": [ [ 139, 142 ] ], "normalized": [] }, { "id": "1.0alpha7.train.847.ent3_0", "type": "protein", "text": [ "Sp1" ], "offsets": [ [ 43, 46 ] ], "normalized": [ { "db_name": "NCBI gene", "db_id": "6667" }, { "db_name": "hgnc", "db_id": "SP1" }, { "db_name": "uniprot", "db_id": "P08047" } ] } ]
[]
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[]
1.0alpha7.train.848
413223
[ { "id": "1.0alpha7.train.848.sent", "type": "sentence", "text": [ "The observation that the binding of cytoplasmic dynein to p150 is mediated by DIC is interesting in view of the functional homology of this polypeptide to the 70-kDa intermediate chain of flagellar outer arm dynein from Chlamydomonas." ], "offsets": [ [ 0, 245 ] ] } ]
[ { "id": "1.0alpha7.train.848.ent0_0", "type": "protein-family", "text": [ "dynein" ], "offsets": [ [ 50, 56 ] ], "normalized": [ { "db_name": "interpro", "db_id": "IPR037177" } ] }, { "id": "1.0alpha7.train.848.ent1_1", "type": "protein-family", "text": [ "dynein" ], "offsets": [ [ 217, 223 ] ], "normalized": [ { "db_name": "interpro", "db_id": "IPR037177" } ] }, { "id": "1.0alpha7.train.848.ent2_0", "type": "protein", "text": [ "p150" ], "offsets": [ [ 61, 65 ] ], "normalized": [ { "db_name": "NCBI gene", "db_id": "10036" }, { "db_name": "hgnc", "db_id": "CHAF1A" }, { "db_name": "uniprot", "db_id": "Q13111" } ] }, { "id": "1.0alpha7.train.848.ent3_0", "type": "protein", "text": [ "DIC" ], "offsets": [ [ 84, 87 ] ], "normalized": [ { "db_name": "NCBI gene", "db_id": "1468" }, { "db_name": "hgnc", "db_id": "SLC25A10" }, { "db_name": "uniprot", "db_id": "Q9UBX3" } ] } ]
[]
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1.0alpha7.train.849
9737434
[ { "id": "1.0alpha7.train.849.sent", "type": "sentence", "text": [ "In CD44, a.a.1-19 and a.a.1-31 (thick lines, bottom, a) bound to moesin with similar affinity to the whole cytoplasmic domain of CD44 at 40 mM KCl, whereas a.a.19-70 as well as a.a.1-70 showed very low affinity to moesin (broken lines, bottom, a), indicating that a.a.1-19 are responsible for moesin binding of CD44 (Fig. 2) and that a.a.19-70 are inhibitory for moesin binding of CD44." ], "offsets": [ [ 0, 386 ] ] } ]
[ { "id": "1.0alpha7.train.849.ent0_0", "type": "protein", "text": [ "CD44" ], "offsets": [ [ 3, 7 ] ], "normalized": [ { "db_name": "NCBI gene", "db_id": "960" }, { "db_name": "hgnc", "db_id": "CD44" }, { "db_name": "uniprot", "db_id": "P16070" } ] }, { "id": "1.0alpha7.train.849.ent1_1", "type": "protein", "text": [ "CD44" ], "offsets": [ [ 129, 133 ] ], "normalized": [ { "db_name": "NCBI gene", "db_id": "960" }, { "db_name": "hgnc", "db_id": "CD44" }, { "db_name": "uniprot", "db_id": "P16070" } ] }, { "id": "1.0alpha7.train.849.ent2_2", "type": "protein", "text": [ "CD44" ], "offsets": [ [ 311, 315 ] ], "normalized": [ { "db_name": "NCBI gene", "db_id": "960" }, { "db_name": "hgnc", "db_id": "CD44" }, { "db_name": "uniprot", "db_id": "P16070" } ] }, { "id": "1.0alpha7.train.849.ent3_3", "type": "protein", "text": [ "CD44" ], "offsets": [ [ 381, 385 ] ], "normalized": [ { "db_name": "NCBI gene", "db_id": "960" }, { "db_name": "hgnc", "db_id": "CD44" }, { "db_name": "uniprot", "db_id": "P16070" } ] }, { "id": "1.0alpha7.train.849.ent4_0", "type": "protein-domain", "text": [ "cytoplasmic domain of CD44" ], "offsets": [ [ 107, 133 ] ], "normalized": [] }, { "id": "1.0alpha7.train.849.ent5_0", "type": "chemical", "text": [ "KCl" ], "offsets": [ [ 143, 146 ] ], "normalized": [ { "db_name": "pubchem:compound", "db_id": "4873" } ] }, { "id": "1.0alpha7.train.849.ent6_0", "type": "protein", "text": [ "moesin" ], "offsets": [ [ 65, 71 ] ], "normalized": [ { "db_name": "NCBI gene", "db_id": "4478" }, { "db_name": "hgnc", "db_id": "MSN" }, { "db_name": "uniprot", "db_id": "P26038" } ] }, { "id": "1.0alpha7.train.849.ent7_1", "type": "protein", "text": [ "moesin" ], "offsets": [ [ 214, 220 ] ], "normalized": [ { "db_name": "NCBI gene", "db_id": "4478" }, { "db_name": "hgnc", "db_id": "MSN" }, { "db_name": "uniprot", "db_id": "P26038" } ] }, { "id": "1.0alpha7.train.849.ent8_2", "type": "protein", "text": [ "moesin" ], "offsets": [ [ 293, 299 ] ], "normalized": [ { "db_name": "NCBI gene", "db_id": "4478" }, { "db_name": "hgnc", "db_id": "MSN" }, { "db_name": "uniprot", "db_id": "P26038" } ] }, { "id": "1.0alpha7.train.849.ent9_3", "type": "protein", "text": [ "moesin" ], "offsets": [ [ 363, 369 ] ], "normalized": [ { "db_name": "NCBI gene", "db_id": "4478" }, { "db_name": "hgnc", "db_id": "MSN" }, { "db_name": "uniprot", "db_id": "P26038" } ] } ]
[]
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1.0alpha7.train.850
15502676
[ { "id": "1.0alpha7.train.850.sent", "type": "sentence", "text": [ "GAGA factor, which binds the GAGA element, has been shown to remodel chromatin and may be involved in rendering the DNA in chromatin accessible to the transcriptional machinery ( 41, 45, 46)." ], "offsets": [ [ 0, 194 ] ] } ]
[ { "id": "1.0alpha7.train.850.ent0_0", "type": "DNA", "text": [ "DNA" ], "offsets": [ [ 117, 120 ] ], "normalized": [ { "db_name": "NCBI gene", "db_id": "25782" }, { "db_name": "hgnc", "db_id": "RAB3GAP2" }, { "db_name": "uniprot", "db_id": "Q9H2M9" } ] }, { "id": "1.0alpha7.train.850.ent1_0", "type": "protein", "text": [ "GAGA factor" ], "offsets": [ [ 0, 11 ] ], "normalized": [ { "db_name": "uniprot", "db_id": "Q08605" } ] }, { "id": "1.0alpha7.train.850.ent2_0", "type": "DNA", "text": [ "GAGA element" ], "offsets": [ [ 30, 42 ] ], "normalized": [] } ]
[]
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[ { "id": "1.0alpha7.train.850.rel0s1.0alpha7.train.850.ent1_0.o1.0alpha7.train.850.ent2_0", "type": "bind", "arg1_id": "1.0alpha7.train.850.ent1_0", "arg2_id": "1.0alpha7.train.850.ent2_0", "normalized": [] } ]
1.0alpha7.train.851
872897
[ { "id": "1.0alpha7.train.851.sent", "type": "sentence", "text": [ "It has been proposed that Rb binds to the E2F activation domain and blocks its function as a transcription factor." ], "offsets": [ [ 0, 117 ] ] } ]
[ { "id": "1.0alpha7.train.851.ent0_0", "type": "protein-domain", "text": [ "E2F activation domain" ], "offsets": [ [ 44, 65 ] ], "normalized": [] }, { "id": "1.0alpha7.train.851.ent1_0", "type": "protein-complex", "text": [ "E2F" ], "offsets": [ [ 44, 47 ] ], "normalized": [] }, { "id": "1.0alpha7.train.851.ent2_0", "type": "protein", "text": [ "Rb" ], "offsets": [ [ 27, 29 ] ], "normalized": [ { "db_name": "NCBI gene", "db_id": "5925" }, { "db_name": "hgnc", "db_id": "RB1" }, { "db_name": "uniprot", "db_id": "P06400" } ] } ]
[]
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1.0alpha7.train.852
7508384
[ { "id": "1.0alpha7.train.852.sent", "type": "sentence", "text": [ "Precisely how Wnt binding to Fz causes inhibition of GSK-3beta is still not clear, but we now know that it involves two members of the LDL receptor gene family, LRP5 and LRP6." ], "offsets": [ [ 0, 181 ] ] } ]
[ { "id": "1.0alpha7.train.852.ent0_0", "type": "protein", "text": [ "LRP6" ], "offsets": [ [ 176, 180 ] ], "normalized": [ { "db_name": "NCBI gene", "db_id": "4040" }, { "db_name": "hgnc", "db_id": "LRP6" } ] }, { "id": "1.0alpha7.train.852.ent1_0", "type": "protein", "text": [ "LRP5" ], "offsets": [ [ 166, 170 ] ], "normalized": [ { "db_name": "NCBI gene", "db_id": "4041" }, { "db_name": "hgnc", "db_id": "LRP5" }, { "db_name": "uniprot", "db_id": "E9PHY1" } ] }, { "id": "1.0alpha7.train.852.ent2_0", "type": "protein-family", "text": [ "Fz" ], "offsets": [ [ 31, 33 ] ], "normalized": [ { "db_name": "interpro", "db_id": "IPR036790" } ] }, { "id": "1.0alpha7.train.852.ent3_0", "type": "protein-family", "text": [ "Wnt" ], "offsets": [ [ 15, 18 ] ], "normalized": [ { "db_name": "interpro", "db_id": "IPR005817" } ] }, { "id": "1.0alpha7.train.852.ent4_0", "type": "protein", "text": [ "GSK-3beta" ], "offsets": [ [ 56, 65 ] ], "normalized": [ { "db_name": "NCBI gene", "db_id": "2932" }, { "db_name": "hgnc", "db_id": "GSK3B" }, { "db_name": "uniprot", "db_id": "P49841" } ] }, { "id": "1.0alpha7.train.852.ent5_0", "type": "protein-family", "text": [ "LDL receptor gene family" ], "offsets": [ [ 139, 163 ] ], "normalized": [] } ]
[]
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1.0alpha7.train.853
6203039
[ { "id": "1.0alpha7.train.853.sent", "type": "sentence", "text": [ "Here we have shown that myozenin also binds alpha-actinin in this region, likely somewhere within residues 606-757." ], "offsets": [ [ 0, 117 ] ] } ]
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[]
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1.0alpha7.train.854
4276629
[ { "id": "1.0alpha7.train.854.sent", "type": "sentence", "text": [ "A, TFIID binds more efficiently than TBP to immobilized pol II." ], "offsets": [ [ 0, 66 ] ] } ]
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[]
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1.0alpha7.train.855
11416856
[ { "id": "1.0alpha7.train.855.sent", "type": "sentence", "text": [ "Although stable binding of MDH to HSP18.1 was not detected below 40°C by SEC (Figure 2), substantial bis-ANS labeling of MDH at 38°C suggested that, at this temperature, MDH was partially unfolded and may have bound HSP18.1 reversibly, thereby limiting bis-ANS binding." ], "offsets": [ [ 0, 269 ] ] } ]
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[]
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1.0alpha7.train.856
11251562
[ { "id": "1.0alpha7.train.856.sent", "type": "sentence", "text": [ "To search for proteins interacting with the GTP-bound form of Rab5, we have previously screened a HeLa expression cDNA library and identified Rabaptin-5 (Stenmark et al., 1995a )." ], "offsets": [ [ 0, 185 ] ] } ]
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[]
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1.0alpha7.train.857
7317936
[ { "id": "1.0alpha7.train.857.sent", "type": "sentence", "text": [ "We have confirmed the fact that Gro can strongly bind Hairy and the E (spl) bHLH proteins regardless of fusion orientation." ], "offsets": [ [ 0, 125 ] ] } ]
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[]
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1.0alpha7.train.858
5428092
[ { "id": "1.0alpha7.train.858.sent", "type": "sentence", "text": [ "Thus, we infer that the conditional growth phenotype of the E83A cells was likely not caused by a defect in the interaction of SpCdk9 with Pch1, but rather a conditional defect in kinase activity resulting from loss of the ion pair to the essential lysine that binds ATP." ], "offsets": [ [ 0, 271 ] ] } ]
[ { "id": "1.0alpha7.train.858.ent0_0", "type": "amino-acid", "text": [ "lysine" ], "offsets": [ [ 249, 255 ] ], "normalized": [ { "db_name": "pubchem:compound", "db_id": "5962" } ] }, { "id": "1.0alpha7.train.858.ent1_0", "type": "chemical", "text": [ "ATP" ], "offsets": [ [ 267, 270 ] ], "normalized": [ { "db_name": "pubchem:compound", "db_id": "5957" } ] }, { "id": "1.0alpha7.train.858.ent2_0", "type": "protein", "text": [ "SpCdk9" ], "offsets": [ [ 127, 133 ] ], "normalized": [] }, { "id": "1.0alpha7.train.858.ent3_0", "type": "protein", "text": [ "Pch1" ], "offsets": [ [ 139, 143 ] ], "normalized": [ { "db_name": "uniprot", "db_id": "O74627" } ] }, { "id": "1.0alpha7.train.858.ent4_0", "type": "cell", "text": [ "E83A cells" ], "offsets": [ [ 60, 70 ] ], "normalized": [] } ]
[]
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1.0alpha7.train.859
9686904
[ { "id": "1.0alpha7.train.859.sent", "type": "sentence", "text": [ "The cytoplasmic domain of cadherin binds to catenins, which are required for binding the cadherin/ catenin complex to the actin cytoskeleton." ], "offsets": [ [ 0, 147 ] ] } ]
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[]
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1.0alpha7.train.860
9793148
[ { "id": "1.0alpha7.train.860.sent", "type": "sentence", "text": [ "The p120cas protein associates also directly with the cytoplasmic domain of E-cadherin, but is not binding to α-catenin (Daniel and Reynolds, 1995)." ], "offsets": [ [ 0, 148 ] ] } ]
[ { "id": "1.0alpha7.train.860.ent0_0", "type": "protein", "text": [ "p120cas" ], "offsets": [ [ 4, 11 ] ], "normalized": [ { "db_name": "NCBI gene", "db_id": "1500" }, { "db_name": "hgnc", "db_id": "CTNND1" }, { "db_name": "uniprot", "db_id": "O60716" } ] }, { "id": "1.0alpha7.train.860.ent1_0", "type": "protein-family", "text": [ "α-catenin" ], "offsets": [ [ 110, 119 ] ], "normalized": [ { "db_name": "interpro", "db_id": "IPR001033" } ] }, { "id": "1.0alpha7.train.860.ent2_0", "type": "protein", "text": [ "E-cadherin" ], "offsets": [ [ 76, 86 ] ], "normalized": [ { "db_name": "NCBI gene", "db_id": "999" }, { "db_name": "hgnc", "db_id": "CDH1" }, { "db_name": "uniprot", "db_id": "P12830" } ] }, { "id": "1.0alpha7.train.860.ent3_0", "type": "protein-domain", "text": [ "cytoplasmic domain of E-cadherin" ], "offsets": [ [ 54, 86 ] ], "normalized": [] } ]
[]
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1.0alpha7.train.861
4671054
[ { "id": "1.0alpha7.train.861.sent", "type": "sentence", "text": [ "ELP70 binds to MTs in vitro." ], "offsets": [ [ 0, 31 ] ] } ]
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[]
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1.0alpha7.train.862
15950424
[ { "id": "1.0alpha7.train.862.sent", "type": "sentence", "text": [ "Fractionation of splicing extracts showed that two fractions associated with U2 snRNP, SF3a and SF3b, are required for the binding of U2 snRNP to pre-mRNAs ( 10, 31)." ], "offsets": [ [ 0, 172 ] ] } ]
[ { "id": "1.0alpha7.train.862.ent0_0", "type": "RNA", "text": [ "pre-mRNAs" ], "offsets": [ [ 151, 160 ] ], "normalized": [] }, { "id": "1.0alpha7.train.862.ent1_0", "type": "protein-complex", "text": [ "SF3b" ], "offsets": [ [ 99, 103 ] ], "normalized": [] }, { "id": "1.0alpha7.train.862.ent2_0", "type": "RNA", "text": [ "U2 snRNP" ], "offsets": [ [ 78, 86 ] ], "normalized": [] }, { "id": "1.0alpha7.train.862.ent3_1", "type": "RNA", "text": [ "U2 snRNP" ], "offsets": [ [ 138, 146 ] ], "normalized": [] }, { "id": "1.0alpha7.train.862.ent4_0", "type": "protein-complex", "text": [ "SF3a" ], "offsets": [ [ 89, 93 ] ], "normalized": [] } ]
[]
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1.0alpha7.train.863
17016955
[ { "id": "1.0alpha7.train.863.sent", "type": "sentence", "text": [ "The observations that substitution of serine 195 with both cysteine and alanine inhibit cleavage, and that the mutant ETs still specifically bind Dsg1 (see below), demonstrate that serine 195 is necessary for efficient catalytic cleavage of Dsg1." ], "offsets": [ [ 0, 246 ] ] } ]
[ { "id": "1.0alpha7.train.863.ent0_0", "type": "protein-family", "text": [ "ETs" ], "offsets": [ [ 118, 121 ] ], "normalized": [ { "db_name": "interpro", "db_id": "IPR002603" } ] }, { "id": "1.0alpha7.train.863.ent1_0", "type": "amino-acid", "text": [ "alanine" ], "offsets": [ [ 72, 79 ] ], "normalized": [ { "db_name": "pubchem:compound", "db_id": "5950" } ] }, { "id": "1.0alpha7.train.863.ent2_0", "type": "amino-acid", "text": [ "cysteine" ], "offsets": [ [ 59, 67 ] ], "normalized": [ { "db_name": "pubchem:compound", "db_id": "5862" } ] }, { "id": "1.0alpha7.train.863.ent3_0", "type": "amino-acid", "text": [ "serine 195" ], "offsets": [ [ 38, 48 ] ], "normalized": [] }, { "id": "1.0alpha7.train.863.ent4_1", "type": "amino-acid", "text": [ "serine 195" ], "offsets": [ [ 181, 191 ] ], "normalized": [] }, { "id": "1.0alpha7.train.863.ent5_0", "type": "protein", "text": [ "Dsg1" ], "offsets": [ [ 146, 150 ] ], "normalized": [ { "db_name": "NCBI gene", "db_id": "1828" }, { "db_name": "hgnc", "db_id": "DSG1" }, { "db_name": "uniprot", "db_id": "Q02413" } ] }, { "id": "1.0alpha7.train.863.ent6_1", "type": "protein", "text": [ "Dsg1" ], "offsets": [ [ 241, 245 ] ], "normalized": [ { "db_name": "NCBI gene", "db_id": "1828" }, { "db_name": "hgnc", "db_id": "DSG1" }, { "db_name": "uniprot", "db_id": "Q02413" } ] }, { "id": "1.0alpha7.train.863.ent7_0", "type": "protein", "text": [ "mutant ETs" ], "offsets": [ [ 111, 121 ] ], "normalized": [] } ]
[]
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1.0alpha7.train.864
1266390
[ { "id": "1.0alpha7.train.864.sent", "type": "sentence", "text": [ "In this report, we used far Western analysis, fluorescence titration, and RNA mobility shift assays to demonstrate that PABP does bind eIF-4F, eIF-iso4F, and eIF-4B either in the presence or absence of poly(A) and that their interaction increases PABP RNA binding activity." ], "offsets": [ [ 0, 273 ] ] } ]
[ { "id": "1.0alpha7.train.864.ent0_0", "type": "protein", "text": [ "PABP" ], "offsets": [ [ 120, 124 ] ], "normalized": [ { "db_name": "NCBI gene", "db_id": "26986" }, { "db_name": "hgnc", "db_id": "PABPC1" }, { "db_name": "uniprot", "db_id": "P11940" } ] }, { "id": "1.0alpha7.train.864.ent1_1", "type": "protein", "text": [ "PABP" ], "offsets": [ [ 247, 251 ] ], "normalized": [ { "db_name": "NCBI gene", "db_id": "26986" }, { "db_name": "hgnc", "db_id": "PABPC1" }, { "db_name": "uniprot", "db_id": "P11940" } ] }, { "id": "1.0alpha7.train.864.ent2_0", "type": "RNA", "text": [ "RNA" ], "offsets": [ [ 74, 77 ] ], "normalized": [] }, { "id": "1.0alpha7.train.864.ent3_1", "type": "RNA", "text": [ "RNA" ], "offsets": [ [ 252, 255 ] ], "normalized": [] }, { "id": "1.0alpha7.train.864.ent4_0", "type": "RNA", "text": [ "poly(A)" ], "offsets": [ [ 202, 209 ] ], "normalized": [] }, { "id": "1.0alpha7.train.864.ent5_0", "type": "assay", "text": [ "RNA mobility shift" ], "offsets": [ [ 74, 92 ] ], "normalized": [] }, { "id": "1.0alpha7.train.864.ent6_0", "type": "protein", "text": [ "eIF-4B" ], "offsets": [ [ 158, 164 ] ], "normalized": [ { "db_name": "NCBI gene", "db_id": "1975" }, { "db_name": "hgnc", "db_id": "EIF4B" }, { "db_name": "uniprot", "db_id": "P23588" } ] }, { "id": "1.0alpha7.train.864.ent7_0", "type": "protein-complex", "text": [ "eIF-4F" ], "offsets": [ [ 135, 141 ] ], "normalized": [] }, { "id": "1.0alpha7.train.864.ent8_0", "type": "protein-complex", "text": [ "eIF-iso4F" ], "offsets": [ [ 143, 152 ] ], "normalized": [] } ]
[]
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1.0alpha7.train.865
4786661
[ { "id": "1.0alpha7.train.865.sent", "type": "sentence", "text": [ "Fig. 1 C shows that p53 binds comparably to the CR2 regions from both CBP and p300 (lanes 3 and 4)." ], "offsets": [ [ 0, 99 ] ] } ]
[ { "id": "1.0alpha7.train.865.ent0_0", "type": "protein", "text": [ "CBP" ], "offsets": [ [ 70, 73 ] ], "normalized": [ { "db_name": "NCBI gene", "db_id": "1387" }, { "db_name": "hgnc", "db_id": "CREBBP" }, { "db_name": "uniprot", "db_id": "Q92793" } ] }, { "id": "1.0alpha7.train.865.ent1_0", "type": "protein-region", "text": [ "CR2 regions" ], "offsets": [ [ 48, 59 ] ], "normalized": [] }, { "id": "1.0alpha7.train.865.ent2_0", "type": "protein", "text": [ "p300" ], "offsets": [ [ 78, 82 ] ], "normalized": [ { "db_name": "NCBI gene", "db_id": "2033" }, { "db_name": "hgnc", "db_id": "EP300" }, { "db_name": "uniprot", "db_id": "Q09472" } ] }, { "id": "1.0alpha7.train.865.ent3_0", "type": "protein", "text": [ "p53" ], "offsets": [ [ 20, 23 ] ], "normalized": [ { "db_name": "NCBI gene", "db_id": "7157" }, { "db_name": "hgnc", "db_id": "TP53" }, { "db_name": "uniprot", "db_id": "P04637" } ] } ]
[]
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1.0alpha7.train.866
9245689
[ { "id": "1.0alpha7.train.866.sent", "type": "sentence", "text": [ "To ask whether MICAL binds FAD, we made a bacterial fusion protein containing the MICAL flavoprotein monooxygenase domain (MICAL-FM)." ], "offsets": [ [ 0, 136 ] ] } ]
[ { "id": "1.0alpha7.train.866.ent0_0", "type": "protein-domain", "text": [ "MICAL-FM" ], "offsets": [ [ 126, 134 ] ], "normalized": [] }, { "id": "1.0alpha7.train.866.ent1_0", "type": "protein-domain", "text": [ "MICAL flavoprotein monooxygenase domain" ], "offsets": [ [ 85, 124 ] ], "normalized": [] }, { "id": "1.0alpha7.train.866.ent2_0", "type": "chemical", "text": [ "FAD" ], "offsets": [ [ 28, 31 ] ], "normalized": [ { "db_name": "pubchem:compound", "db_id": "643975" } ] }, { "id": "1.0alpha7.train.866.ent3_0", "type": "protein-family", "text": [ "MICAL" ], "offsets": [ [ 16, 21 ] ], "normalized": [ { "db_name": "interpro", "db_id": "IPR028563" } ] }, { "id": "1.0alpha7.train.866.ent4_1", "type": "protein-family", "text": [ "MICAL" ], "offsets": [ [ 85, 90 ] ], "normalized": [ { "db_name": "interpro", "db_id": "IPR028563" } ] }, { "id": "1.0alpha7.train.866.ent5_2", "type": "protein-family", "text": [ "MICAL" ], "offsets": [ [ 126, 131 ] ], "normalized": [ { "db_name": "interpro", "db_id": "IPR028563" } ] } ]
[]
[ { "id": "1.0alpha7.train.866.coref0", "entity_ids": [ "1.0alpha7.train.866.ent0_0", "1.0alpha7.train.866.ent1_0" ] }, { "id": "1.0alpha7.train.866.coref1", "entity_ids": [ "1.0alpha7.train.866.ent2_0" ] }, { "id": "1.0alpha7.train.866.coref2", "entity_ids": [ "1.0alpha7.train.866.ent3_0", "1.0alpha7.train.866.ent4_1", "1.0alpha7.train.866.ent5_2" ] } ]
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1.0alpha7.train.867
12455154
[ { "id": "1.0alpha7.train.867.sent", "type": "sentence", "text": [ "( A) Effect of rapamycin on phosphorylation of eIF2alpha is strongly dependent on dephosphorylation of Ser 577 and the tRNA binding activity of GCN2." ], "offsets": [ [ 0, 153 ] ] } ]
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[]
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1.0alpha7.train.868
18095761
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[]
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1.0alpha7.train.869
3654328
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[]
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1.0alpha7.train.870
15054675
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[]
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[]
1.0alpha7.train.871
24684556
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[]
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1.0alpha7.train.872
15576869
[ { "id": "1.0alpha7.train.872.sent", "type": "sentence", "text": [ "The requirement for the MADS box for both DNA binding and interaction with GATA-4 when SRF is bound to SREs may impose structural constraints that are not present when the MADS box is tethered to DNA." ], "offsets": [ [ 0, 205 ] ] } ]
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[]
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1.0alpha7.train.873
1984160
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[]
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1.0alpha7.train.874
9539450
[ { "id": "1.0alpha7.train.874.sent", "type": "sentence", "text": [ "Crk Binding to Paxillin Is Impaired in F31/118-expressing Cells Tyrosine residues 31 and 118 of paxillin reside within a YXXP motif that corresponds to an optimal Crk-SH2-binding sequence ( Birge et al. 1993 )." ], "offsets": [ [ 0, 218 ] ] } ]
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[]
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1.0alpha7.train.875
22370330
[ { "id": "1.0alpha7.train.875.sent", "type": "sentence", "text": [ "At present, the significance of binding of EB1 and Pin2/TRF1 is unclear, and we can only speculate how expression of the mutant Pin21-316 is able to restore the mitotic spindle checkpoint defect in A-T cells and how Pin2/TRF1 is normally involved in the mitotic spindle checkpoint." ], "offsets": [ [ 0, 281 ] ] } ]
[ { "id": "1.0alpha7.train.875.ent0_0", "type": "protein", "text": [ "Pin2" ], "offsets": [ [ 51, 55 ] ], "normalized": [ { "db_name": "NCBI gene", "db_id": "7013" }, { "db_name": "hgnc", "db_id": "TERF1" }, { "db_name": "uniprot", "db_id": "P54274" } ] }, { "id": "1.0alpha7.train.875.ent1_1", "type": "protein", "text": [ "Pin2" ], "offsets": [ [ 216, 220 ] ], "normalized": [ { "db_name": "NCBI gene", "db_id": "7013" }, { "db_name": "hgnc", "db_id": "TERF1" }, { "db_name": "uniprot", "db_id": "P54274" } ] }, { "id": "1.0alpha7.train.875.ent2_0", "type": "protein", "text": [ "TRF1" ], "offsets": [ [ 56, 60 ] ], "normalized": [ { "db_name": "NCBI gene", "db_id": "7013" }, { "db_name": "hgnc", "db_id": "TERF1" }, { "db_name": "uniprot", "db_id": "P54274" } ] }, { "id": "1.0alpha7.train.875.ent3_1", "type": "protein", "text": [ "TRF1" ], "offsets": [ [ 221, 225 ] ], "normalized": [ { "db_name": "NCBI gene", "db_id": "7013" }, { "db_name": "hgnc", "db_id": "TERF1" }, { "db_name": "uniprot", "db_id": "P54274" } ] }, { "id": "1.0alpha7.train.875.ent4_0", "type": "cell", "text": [ "A-T cells" ], "offsets": [ [ 198, 207 ] ], "normalized": [] }, { "id": "1.0alpha7.train.875.ent5_0", "type": "protein", "text": [ "EB1" ], "offsets": [ [ 43, 46 ] ], "normalized": [ { "db_name": "NCBI gene", "db_id": "22919" }, { "db_name": "hgnc", "db_id": "MAPRE1" }, { "db_name": "uniprot", "db_id": "Q15691" } ] }, { "id": "1.0alpha7.train.875.ent6_0", "type": "protein", "text": [ "Pin21-316" ], "offsets": [ [ 128, 137 ] ], "normalized": [] } ]
[]
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[]
1.0alpha7.train.876
1689218
[ { "id": "1.0alpha7.train.876.sent", "type": "sentence", "text": [ "Pbx Homologs Extradenticle and ceh-20 Interact with Meis1 to Cooperatively Bind CRS1" ], "offsets": [ [ 0, 84 ] ] } ]
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[]
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1.0alpha7.train.877
1689218
[ { "id": "1.0alpha7.train.877.sent", "type": "sentence", "text": [ "To determine whether the interaction of Pbx and Meis1 families extends beyond mammalian isoforms, the Pbx homologs from Drosophila and C. elegans were tested for cooperative CRS1 binding with Meis1." ], "offsets": [ [ 0, 198 ] ] } ]
[ { "id": "1.0alpha7.train.877.ent0_0", "type": "protein", "text": [ "CRS1" ], "offsets": [ [ 174, 178 ] ], "normalized": [ { "db_name": "NCBI gene", "db_id": "7291" }, { "db_name": "hgnc", "db_id": "TWIST1" }, { "db_name": "uniprot", "db_id": "Q15672" } ] }, { "id": "1.0alpha7.train.877.ent1_0", "type": "protein-family", "text": [ "Pbx" ], "offsets": [ [ 40, 43 ] ], "normalized": [ { "db_name": "interpro", "db_id": "IPR005542" } ] }, { "id": "1.0alpha7.train.877.ent2_1", "type": "protein-family", "text": [ "Pbx" ], "offsets": [ [ 102, 105 ] ], "normalized": [ { "db_name": "interpro", "db_id": "IPR005542" } ] }, { "id": "1.0alpha7.train.877.ent3_0", "type": "protein", "text": [ "Meis1" ], "offsets": [ [ 48, 53 ] ], "normalized": [ { "db_name": "NCBI gene", "db_id": "4211" }, { "db_name": "hgnc", "db_id": "MEIS1" }, { "db_name": "uniprot", "db_id": "O00470" } ] }, { "id": "1.0alpha7.train.877.ent4_1", "type": "protein", "text": [ "Meis1" ], "offsets": [ [ 192, 197 ] ], "normalized": [ { "db_name": "NCBI gene", "db_id": "4211" }, { "db_name": "hgnc", "db_id": "MEIS1" }, { "db_name": "uniprot", "db_id": "O00470" } ] } ]
[]
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1.0alpha7.train.878
11678312
[ { "id": "1.0alpha7.train.878.sent", "type": "sentence", "text": [ "The crystal structure of REGα reveals a 20–30 Å-wide aqueous channel through a donut-shaped heptamer (Knowlton et al., 1997), and electron microscopic images suggest that REG heptamers bind the proteasome with their aqueous channels normal to and centered over the proteasome α subunit ring (Gray et al., 1994)." ], "offsets": [ [ 0, 311 ] ] } ]
[ { "id": "1.0alpha7.train.878.ent0_0", "type": "protein-complex", "text": [ "REG heptamers" ], "offsets": [ [ 171, 184 ] ], "normalized": [] }, { "id": "1.0alpha7.train.878.ent1_0", "type": "organelle", "text": [ "proteasome" ], "offsets": [ [ 194, 204 ] ], "normalized": [] }, { "id": "1.0alpha7.train.878.ent2_1", "type": "organelle", "text": [ "proteasome" ], "offsets": [ [ 265, 275 ] ], "normalized": [] }, { "id": "1.0alpha7.train.878.ent3_0", "type": "protein", "text": [ "proteasome α subunit" ], "offsets": [ [ 265, 285 ] ], "normalized": [] }, { "id": "1.0alpha7.train.878.ent4_0", "type": "protein", "text": [ "REGα" ], "offsets": [ [ 25, 29 ] ], "normalized": [ { "db_name": "NCBI gene", "db_id": "5967" }, { "db_name": "hgnc", "db_id": "REG1A" }, { "db_name": "uniprot", "db_id": "P05451" } ] } ]
[]
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1.0alpha7.train.879
18871208
[ { "id": "1.0alpha7.train.879.sent", "type": "sentence", "text": [ "The effect is thought to arise through the non-specific binding of transcription factors with the PS backbone [ 2." ], "offsets": [ [ 0, 116 ] ] } ]
[ { "id": "1.0alpha7.train.879.ent0_0", "type": "chemical", "text": [ "PS" ], "offsets": [ [ 100, 102 ] ], "normalized": [ { "db_name": "pubchem:compound", "db_id": "52925988" } ] } ]
[]
[ { "id": "1.0alpha7.train.879.coref0", "entity_ids": [ "1.0alpha7.train.879.ent0_0" ] } ]
[]
1.0alpha7.train.880
3617423
[ { "id": "1.0alpha7.train.880.sent", "type": "sentence", "text": [ "Sp1 and Sp3 bind to the AR1 sequence." ], "offsets": [ [ 0, 41 ] ] } ]
[ { "id": "1.0alpha7.train.880.ent0_0", "type": "DNA", "text": [ "AR1 sequence" ], "offsets": [ [ 27, 40 ] ], "normalized": [] }, { "id": "1.0alpha7.train.880.ent1_0", "type": "protein", "text": [ "Sp1" ], "offsets": [ [ 0, 3 ] ], "normalized": [ { "db_name": "NCBI gene", "db_id": "6667" }, { "db_name": "hgnc", "db_id": "SP1" }, { "db_name": "uniprot", "db_id": "P08047" } ] }, { "id": "1.0alpha7.train.880.ent2_0", "type": "protein", "text": [ "Sp3" ], "offsets": [ [ 9, 12 ] ], "normalized": [ { "db_name": "NCBI gene", "db_id": "6670" }, { "db_name": "hgnc", "db_id": "SP3" }, { "db_name": "uniprot", "db_id": "Q02447" } ] } ]
[]
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1.0alpha7.train.881
9264463
[ { "id": "1.0alpha7.train.881.sent", "type": "sentence", "text": [ "The structure of the HP1 chromodomain bound to histone H3 di- or trimethylated at lysine 9 shows that either peptide fits in a groove and lodges the methyllysine in a hydrophobic pocket (Nielsen et al., 2002 ; Jacobs and Khorasanizadeh, 2002 )." ], "offsets": [ [ 0, 251 ] ] } ]
[ { "id": "1.0alpha7.train.881.ent0_0", "type": "amino-acid", "text": [ "methyllysine" ], "offsets": [ [ 152, 164 ] ], "normalized": [ { "db_name": "pubchem:compound", "db_id": "7010497" } ] }, { "id": "1.0alpha7.train.881.ent1_0", "type": "protein-family", "text": [ "histone H3" ], "offsets": [ [ 48, 58 ] ], "normalized": [ { "db_name": "interpro", "db_id": "IPR007125" } ] }, { "id": "1.0alpha7.train.881.ent2_0", "type": "protein", "text": [ "HP1" ], "offsets": [ [ 22, 25 ] ], "normalized": [ { "db_name": "NCBI gene", "db_id": "23468" }, { "db_name": "hgnc", "db_id": "CBX5" }, { "db_name": "uniprot", "db_id": "P45973" } ] }, { "id": "1.0alpha7.train.881.ent3_0", "type": "protein-domain", "text": [ "HP1 chromodomain" ], "offsets": [ [ 22, 38 ] ], "normalized": [] }, { "id": "1.0alpha7.train.881.ent4_0", "type": "amino-acid", "text": [ "lysine 9" ], "offsets": [ [ 85, 93 ] ], "normalized": [] } ]
[]
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1.0alpha7.train.882
11693154
[ { "id": "1.0alpha7.train.882.sent", "type": "sentence", "text": [ "This interaction seems to be mediated through Polalpha as MBP alone did not bind to Swi6." ], "offsets": [ [ 0, 92 ] ] } ]
[ { "id": "1.0alpha7.train.882.ent0_0", "type": "protein", "text": [ "Swi6" ], "offsets": [ [ 87, 91 ] ], "normalized": [ { "db_name": "uniprot", "db_id": "P09959" } ] }, { "id": "1.0alpha7.train.882.ent1_0", "type": "protein", "text": [ "MBP" ], "offsets": [ [ 60, 63 ] ], "normalized": [ { "db_name": "NCBI gene", "db_id": "4153" }, { "db_name": "hgnc", "db_id": "MBL2" }, { "db_name": "uniprot", "db_id": "P11226" } ] }, { "id": "1.0alpha7.train.882.ent2_0", "type": "protein-complex", "text": [ "Polalpha" ], "offsets": [ [ 47, 55 ] ], "normalized": [] } ]
[]
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1.0alpha7.train.883
1845588
[ { "id": "1.0alpha7.train.883.sent", "type": "sentence", "text": [ "It is also possible that both PR and the carboxyl-terminal PR binding motif of RIZ1 may interact with other as yet unidentified proteins." ], "offsets": [ [ 0, 141 ] ] } ]
[ { "id": "1.0alpha7.train.883.ent0_0", "type": "protein", "text": [ "PR" ], "offsets": [ [ 31, 33 ] ], "normalized": [ { "db_name": "NCBI gene", "db_id": "5241" }, { "db_name": "hgnc", "db_id": "PGR" }, { "db_name": "uniprot", "db_id": "P06401" } ] }, { "id": "1.0alpha7.train.883.ent1_1", "type": "protein", "text": [ "PR" ], "offsets": [ [ 61, 63 ] ], "normalized": [ { "db_name": "NCBI gene", "db_id": "5241" }, { "db_name": "hgnc", "db_id": "PGR" }, { "db_name": "uniprot", "db_id": "P06401" } ] }, { "id": "1.0alpha7.train.883.ent2_0", "type": "protein-motif", "text": [ "PR binding motif" ], "offsets": [ [ 61, 77 ] ], "normalized": [] }, { "id": "1.0alpha7.train.883.ent3_0", "type": "protein", "text": [ "RIZ1" ], "offsets": [ [ 82, 86 ] ], "normalized": [ { "db_name": "NCBI gene", "db_id": "7799" }, { "db_name": "hgnc", "db_id": "PRDM2" }, { "db_name": "uniprot", "db_id": "Q13029" } ] } ]
[]
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1.0alpha7.train.884
15126017
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1.0alpha7.train.885
23170514
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1.0alpha7.train.886
18085747
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1.0alpha7.train.887
19629330
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[]
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1.0alpha7.train.888
8921054
[ { "id": "1.0alpha7.train.888.sent", "type": "sentence", "text": [ "As shown in Figure 7B, the extracellular domain, but not the intracellular domain, of Kek1 can bind to the EGFR." ], "offsets": [ [ 0, 118 ] ] } ]
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1.0alpha7.train.889
12692855
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[]
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1.0alpha7.train.890
23643757
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1.0alpha7.train.891
2841835
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[]
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1.0alpha7.train.892
4906765
[ { "id": "1.0alpha7.train.892.sent", "type": "sentence", "text": [ "These results suggest that at least mammalian JIP1b and JIP2 could bind the cytoplasmic domain of APP, whereas the preferences of JIP1b and JIP2 to bind APP are a little different." ], "offsets": [ [ 0, 186 ] ] } ]
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[]
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1.0alpha7.train.893
20170452
[ { "id": "1.0alpha7.train.893.sent", "type": "sentence", "text": [ "Despite this fact, WIF-1 binds to Xwnt-8 and is able to block the late ventralizing Xwnt-8 pathway." ], "offsets": [ [ 0, 102 ] ] } ]
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[]
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1.0alpha7.train.894
3617484
[ { "id": "1.0alpha7.train.894.sent", "type": "sentence", "text": [ "Zic2 efficiently blocked Sp1 and Sp3 binding to the AR1 probe (Fig. 7 C, lane 3), whereas control lysate did not (Fig. 7 C, lane 2)." ], "offsets": [ [ 0, 137 ] ] } ]
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[]
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1.0alpha7.train.895
18222004
[ { "id": "1.0alpha7.train.895.sent", "type": "sentence", "text": [ "As shown in Figure 2A, APC11 binds tightly to APC2 and weakly to APC6." ], "offsets": [ [ 0, 74 ] ] } ]
[ { "id": "1.0alpha7.train.895.ent0_0", "type": "protein", "text": [ "APC2" ], "offsets": [ [ 49, 53 ] ], "normalized": [ { "db_name": "NCBI gene", "db_id": "10297" }, { "db_name": "hgnc", "db_id": "APC2" } ] }, { "id": "1.0alpha7.train.895.ent1_0", "type": "protein", "text": [ "APC11" ], "offsets": [ [ 25, 30 ] ], "normalized": [ { "db_name": "NCBI gene", "db_id": "51529" }, { "db_name": "hgnc", "db_id": "ANAPC11" }, { "db_name": "uniprot", "db_id": "Q9NYG5" } ] }, { "id": "1.0alpha7.train.895.ent2_0", "type": "protein", "text": [ "APC6" ], "offsets": [ [ 69, 73 ] ], "normalized": [ { "db_name": "NCBI gene", "db_id": "8881" }, { "db_name": "hgnc", "db_id": "CDC16" }, { "db_name": "uniprot", "db_id": "Q13042" } ] } ]
[]
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1.0alpha7.train.896
891052
[ { "id": "1.0alpha7.train.896.sent", "type": "sentence", "text": [ "The data presented indicate that 1) Sp1 or a related protein recognizes and binds a GC-rich site located between the two regions where the retinoid receptors bind, and 2) site-directed mutagenesis of this sequence abrogates the binding." ], "offsets": [ [ 0, 238 ] ] } ]
[ { "id": "1.0alpha7.train.896.ent0_0", "type": "protein", "text": [ "Sp1" ], "offsets": [ [ 37, 40 ] ], "normalized": [ { "db_name": "NCBI gene", "db_id": "6667" }, { "db_name": "hgnc", "db_id": "SP1" }, { "db_name": "uniprot", "db_id": "P08047" } ] }, { "id": "1.0alpha7.train.896.ent1_0", "type": "DNA", "text": [ "GC-rich site" ], "offsets": [ [ 86, 98 ] ], "normalized": [] }, { "id": "1.0alpha7.train.896.ent2_0", "type": "protein-family", "text": [ "retinoid receptors" ], "offsets": [ [ 141, 159 ] ], "normalized": [ { "db_name": "interpro", "db_id": "IPR003078" } ] } ]
[]
[ { "id": "1.0alpha7.train.896.coref0", "entity_ids": [ "1.0alpha7.train.896.ent0_0" ] }, { "id": "1.0alpha7.train.896.coref1", "entity_ids": [ "1.0alpha7.train.896.ent1_0" ] }, { "id": "1.0alpha7.train.896.coref2", "entity_ids": [ "1.0alpha7.train.896.ent2_0" ] } ]
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1.0alpha7.train.897
6321317
[ { "id": "1.0alpha7.train.897.sent", "type": "sentence", "text": [ "Because Sec15p also binds to activated Sec4p, the exocyst might be an effector for this Rab-like GTPase that is necessary for the targeting or tethering of secretory vesicles to sites of secretion." ], "offsets": [ [ 0, 200 ] ] } ]
[ { "id": "1.0alpha7.train.897.ent0_0", "type": "protein-family", "text": [ "Rab-like GTPase" ], "offsets": [ [ 91, 106 ] ], "normalized": [] }, { "id": "1.0alpha7.train.897.ent1_0", "type": "protein", "text": [ "Sec15p" ], "offsets": [ [ 9, 15 ] ], "normalized": [ { "db_name": "uniprot", "db_id": "P22224" } ] }, { "id": "1.0alpha7.train.897.ent2_0", "type": "protein", "text": [ "Sec4p" ], "offsets": [ [ 41, 46 ] ], "normalized": [ { "db_name": "uniprot", "db_id": "P07560" } ] } ]
[]
[ { "id": "1.0alpha7.train.897.coref0", "entity_ids": [ "1.0alpha7.train.897.ent0_0" ] }, { "id": "1.0alpha7.train.897.coref1", "entity_ids": [ "1.0alpha7.train.897.ent1_0" ] }, { "id": "1.0alpha7.train.897.coref2", "entity_ids": [ "1.0alpha7.train.897.ent2_0" ] } ]
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1.0alpha7.train.898
5499988
[ { "id": "1.0alpha7.train.898.sent", "type": "sentence", "text": [ "Therefore, we conclude that phosphorylation of the CTD is sufficient to determine the binding of Set2 to RNA polymerase II in vitro." ], "offsets": [ [ 0, 136 ] ] } ]
[ { "id": "1.0alpha7.train.898.ent0_0", "type": "protein-domain", "text": [ "CTD" ], "offsets": [ [ 52, 55 ] ], "normalized": [] }, { "id": "1.0alpha7.train.898.ent1_0", "type": "protein-complex", "text": [ "RNA polymerase II" ], "offsets": [ [ 108, 125 ] ], "normalized": [] }, { "id": "1.0alpha7.train.898.ent2_0", "type": "protein", "text": [ "Set2" ], "offsets": [ [ 99, 103 ] ], "normalized": [ { "db_name": "uniprot", "db_id": "Q9VYD1" } ] } ]
[]
[ { "id": "1.0alpha7.train.898.coref0", "entity_ids": [ "1.0alpha7.train.898.ent0_0" ] }, { "id": "1.0alpha7.train.898.coref1", "entity_ids": [ "1.0alpha7.train.898.ent1_0" ] }, { "id": "1.0alpha7.train.898.coref2", "entity_ids": [ "1.0alpha7.train.898.ent2_0" ] } ]
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1.0alpha7.train.899
3169293
[ { "id": "1.0alpha7.train.899.sent", "type": "sentence", "text": [ "To verify whether gamma1- and gamma2-syntrophins can also bind dystrophin or related proteins, assays of protein-protein interaction were used." ], "offsets": [ [ 0, 147 ] ] } ]
[ { "id": "1.0alpha7.train.899.ent0_0", "type": "protein", "text": [ "gamma1-" ], "offsets": [ [ 19, 26 ] ], "normalized": [] }, { "id": "1.0alpha7.train.899.ent1_0", "type": "protein", "text": [ "gamma2-syntrophins" ], "offsets": [ [ 32, 50 ] ], "normalized": [ { "db_name": "NCBI gene", "db_id": "54221" }, { "db_name": "hgnc", "db_id": "SNTG2" }, { "db_name": "uniprot", "db_id": "Q9NY99" } ] }, { "id": "1.0alpha7.train.899.ent2_0", "type": "protein", "text": [ "dystrophin" ], "offsets": [ [ 66, 76 ] ], "normalized": [] } ]
[]
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