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PMC:1140370 / 10978-12745 JSONTXT

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Id Subject Object Predicate Lexical cue
T3477 219-228 VBD denotes conducted
T3444 0-4 NN denotes Mcm4
T3445 9-14 VBZ denotes binds
T3446 4-5 HYPH denotes /
T3447 5-6 CD denotes 6
T3448 6-7 HYPH denotes /
T3449 7-8 CD denotes 7
T3450 15-17 IN denotes to
T3451 18-19 `` denotes ‘
T3452 31-41 NNS denotes substrates
T3453 19-25 NN denotes bubble
T3454 25-26 '' denotes ’
T3455 27-30 NN denotes DNA
T3456 42-45 CC denotes and
T3457 46-53 VBZ denotes unwinds
T3458 54-57 DT denotes the
T3459 65-73 NNS denotes segments
T3460 58-64 NN denotes duplex
T3461 74-78 WRB denotes when
T3462 115-123 VBZ denotes contains
T3463 79-82 DT denotes the
T3464 107-114 NN denotes segment
T3465 83-90 JJ denotes central
T3466 91-97 JJ denotes single
T3467 98-106 VBN denotes stranded
T3468 97-98 HYPH denotes -
T3469 124-131 NN denotes thymine
T3470 132-141 NNS denotes stretches
T3471 142-143 -LRB- denotes (
T3472 143-145 CD denotes 13
T3473 145-146 -RRB- denotes )
T3474 146-147 . denotes .
T3475 147-406 sentence denotes In order to examine the mode of binding of Mcm4/6/7 on bubble DNAs, we conducted nuclease protection assays using labeled bubble substrate DNAs and Mcm4/6/7 in the presence of ATP-γ-S which permits binding to substrate DNA but does not mobilize the helicase.
T3476 148-150 IN denotes In
T3478 151-156 NN denotes order
T3479 157-159 TO denotes to
T3480 160-167 VB denotes examine
T3481 168-171 DT denotes the
T3482 172-176 NN denotes mode
T3483 177-179 IN denotes of
T3484 180-187 NN denotes binding
T3485 188-190 IN denotes of
T3486 191-195 NN denotes Mcm4
T3487 195-196 HYPH denotes /
T3488 196-197 CD denotes 6
T3489 197-198 HYPH denotes /
T3490 198-199 CD denotes 7
T3491 200-202 IN denotes on
T3492 203-209 NN denotes bubble
T3493 210-214 NNS denotes DNAs
T3494 214-216 , denotes ,
T3495 216-218 PRP denotes we
T3496 229-237 NN denotes nuclease
T3497 249-255 NNS denotes assays
T3498 238-248 NN denotes protection
T3499 256-261 VBG denotes using
T3500 262-269 VBN denotes labeled
T3501 287-291 NNS denotes DNAs
T3502 270-276 NN denotes bubble
T3503 277-286 NN denotes substrate
T3504 292-295 CC denotes and
T3505 296-300 NN denotes Mcm4
T3506 300-301 HYPH denotes /
T3507 301-302 CD denotes 6
T3508 302-303 HYPH denotes /
T3509 303-304 CD denotes 7
T3510 305-307 IN denotes in
T3511 308-311 DT denotes the
T3512 312-320 NN denotes presence
T3513 321-323 IN denotes of
T3514 324-327 NN denotes ATP
T3515 330-331 NN denotes S
T3516 327-328 HYPH denotes -
T3517 328-329 SYM denotes γ
T3518 329-330 HYPH denotes -
T3519 332-337 WDT denotes which
T3520 338-345 VBZ denotes permits
T3521 346-353 NN denotes binding
T3522 354-356 IN denotes to
T3523 357-366 NN denotes substrate
T3524 367-370 NN denotes DNA
T3525 371-374 CC denotes but
T3526 375-379 VBZ denotes does
T3527 384-392 VB denotes mobilize
T3528 380-383 RB denotes not
T3529 393-396 DT denotes the
T3530 397-405 NN denotes helicase
T3531 405-406 . denotes .
T3532 406-677 sentence denotes At an optimum concentration of DNase I, strong cleavages were detected on the 21 bp duplex regions at both ends of the substrates, whereas weaker cleavages were detected on the central single-stranded region, consistent with preference of DNase I to double-stranded DNA.
T3533 407-409 IN denotes At
T3534 469-477 VBN denotes detected
T3535 410-412 DT denotes an
T3536 421-434 NN denotes concentration
T3537 413-420 JJ denotes optimum
T3538 435-437 IN denotes of
T3539 438-443 NN denotes DNase
T3540 444-445 CD denotes I
T3541 445-447 , denotes ,
T3542 447-453 JJ denotes strong
T3543 454-463 NNS denotes cleavages
T3544 464-468 VBD denotes were
T3545 478-480 IN denotes on
T3546 481-484 DT denotes the
T3547 498-505 NNS denotes regions
T3548 485-487 CD denotes 21
T3549 488-490 NN denotes bp
T3550 491-497 NN denotes duplex
T3551 506-508 IN denotes at
T3552 509-513 DT denotes both
T3553 514-518 NNS denotes ends
T3554 519-521 IN denotes of
T3555 522-525 DT denotes the
T3556 526-536 NNS denotes substrates
T3557 536-538 , denotes ,
T3558 538-545 IN denotes whereas
T3559 568-576 VBN denotes detected
T3560 546-552 JJR denotes weaker
T3561 553-562 NNS denotes cleavages
T3562 563-567 VBD denotes were
T3563 577-579 IN denotes on
T3564 580-583 DT denotes the
T3565 608-614 NN denotes region
T3566 584-591 JJ denotes central
T3567 592-598 JJ denotes single
T3568 599-607 VBN denotes stranded
T3569 598-599 HYPH denotes -
T3570 614-616 , denotes ,
T3571 616-626 JJ denotes consistent
T3572 627-631 IN denotes with
T3573 632-642 NN denotes preference
T3574 643-645 IN denotes of
T3575 646-651 NN denotes DNase
T3576 652-653 CD denotes I
T3577 654-656 IN denotes to
T3578 657-663 JJ denotes double
T3579 664-672 VBN denotes stranded
T3580 663-664 HYPH denotes -
T3581 673-676 NN denotes DNA
T3582 676-677 . denotes .
T3583 677-935 sentence denotes With the Bub66/T-rich substrate, strong protection was detected on the entire single-stranded regions of both top and bottom strands with increasing concentration of Mcm4/6/7, consistent with high affinity of Mcm4/6/7 to T-rich bubble sequences (Figure 1A).
T3584 678-682 IN denotes With
T3585 733-741 VBN denotes detected
T3586 683-686 DT denotes the
T3587 700-709 NN denotes substrate
T3588 687-692 NN denotes Bub66
T3589 692-693 HYPH denotes /
T3590 693-694 NN denotes T
T3591 694-695 HYPH denotes -
T3592 695-699 JJ denotes rich
T3593 709-711 , denotes ,
T3594 711-717 JJ denotes strong
T3595 718-728 NN denotes protection
T3596 729-732 VBD denotes was
T3597 742-744 IN denotes on
T3598 745-748 DT denotes the
T3599 772-779 NNS denotes regions
T3600 749-755 JJ denotes entire
T3601 756-762 JJ denotes single
T3602 763-771 VBN denotes stranded
T3603 762-763 HYPH denotes -
T3604 780-782 IN denotes of
T3605 783-787 CC denotes both
T3606 788-791 JJ denotes top
T3607 803-810 NNS denotes strands
T3608 792-795 CC denotes and
T3609 796-802 JJ denotes bottom
T3610 811-815 IN denotes with
T3611 816-826 VBG denotes increasing
T3612 827-840 NN denotes concentration
T3613 841-843 IN denotes of
T3614 844-848 NN denotes Mcm4
T3615 848-849 HYPH denotes /
T3616 849-850 CD denotes 6
T3617 850-851 HYPH denotes /
T3618 851-852 CD denotes 7
T3619 852-854 , denotes ,
T3620 854-864 JJ denotes consistent
T3621 865-869 IN denotes with
T3622 870-874 JJ denotes high
T3623 875-883 NN denotes affinity
T3624 884-886 IN denotes of
T3625 887-891 NN denotes Mcm4
T3626 891-892 HYPH denotes /
T3627 892-893 CD denotes 6
T3628 893-894 HYPH denotes /
T3629 894-895 CD denotes 7
T3630 896-898 IN denotes to
T3631 899-900 NN denotes T
T3632 913-922 NNS denotes sequences
T3633 900-901 HYPH denotes -
T3634 901-905 JJ denotes rich
T3635 906-912 NN denotes bubble
T3636 923-924 -LRB- denotes (
T3637 931-933 NN denotes 1A
T3638 924-930 NN denotes Figure
T3639 933-934 -RRB- denotes )
T3640 934-935 . denotes .
T3641 935-1097 sentence denotes Similar, but less significant protection was detected on the single-stranded DNA segment with P1 nucleases (Figure 1A), which is specific to single-stranded DNA.
T3642 936-943 JJ denotes Similar
T3643 966-976 NN denotes protection
T3644 943-945 , denotes ,
T3645 945-948 CC denotes but
T3646 949-953 RBR denotes less
T3647 954-965 JJ denotes significant
T3648 981-989 VBN denotes detected
T3649 977-980 VBD denotes was
T3650 990-992 IN denotes on
T3651 993-996 DT denotes the
T3652 1017-1024 NN denotes segment
T3653 997-1003 JJ denotes single
T3654 1004-1012 VBN denotes stranded
T3655 1003-1004 HYPH denotes -
T3656 1013-1016 NN denotes DNA
T3657 1025-1029 IN denotes with
T3658 1030-1032 NN denotes P1
T3659 1033-1042 NNS denotes nucleases
T3660 1043-1044 -LRB- denotes (
T3661 1051-1053 NN denotes 1A
T3662 1044-1050 NN denotes Figure
T3663 1053-1054 -RRB- denotes )
T3664 1054-1056 , denotes ,
T3665 1056-1061 WDT denotes which
T3666 1062-1064 VBZ denotes is
T3667 1065-1073 JJ denotes specific
T3668 1074-1076 IN denotes to
T3669 1077-1083 JJ denotes single
T3670 1084-1092 VBN denotes stranded
T3671 1083-1084 HYPH denotes -
T3672 1093-1096 NN denotes DNA
T3673 1096-1097 . denotes .
T3674 1097-1228 sentence denotes The results indicate that the Mcm complex is loaded onto bubble DNA through binding to both strands of the single-stranded region.
T3675 1098-1101 DT denotes The
T3676 1102-1109 NNS denotes results
T3677 1110-1118 VBP denotes indicate
T3678 1119-1123 IN denotes that
T3679 1143-1149 VBN denotes loaded
T3680 1124-1127 DT denotes the
T3681 1132-1139 NN denotes complex
T3682 1128-1131 NN denotes Mcm
T3683 1140-1142 VBZ denotes is
T3684 1150-1154 IN denotes onto
T3685 1155-1161 NN denotes bubble
T3686 1162-1165 NN denotes DNA
T3687 1166-1173 IN denotes through
T3688 1174-1181 NN denotes binding
T3689 1182-1184 IN denotes to
T3690 1185-1189 DT denotes both
T3691 1190-1197 NNS denotes strands
T3692 1198-1200 IN denotes of
T3693 1201-1204 DT denotes the
T3694 1221-1227 NN denotes region
T3695 1205-1211 JJ denotes single
T3696 1212-1220 VBN denotes stranded
T3697 1211-1212 HYPH denotes -
T3698 1227-1228 . denotes .
T3699 1228-1502 sentence denotes Careful examination of Mcm4/6/7 footprints on a bubble indicated strong protection on the 5′-half of the top strand and moderate protection on the remaining 3′-half, as well as on several base-pair duplex segment adjacent to the branch point (Figure 1A and data not shown).
T3700 1229-1236 JJ denotes Careful
T3701 1237-1248 NN denotes examination
T3702 1284-1293 VBD denotes indicated
T3703 1249-1251 IN denotes of
T3704 1252-1256 NN denotes Mcm4
T3705 1261-1271 NNS denotes footprints
T3706 1256-1257 HYPH denotes /
T3707 1257-1258 CD denotes 6
T3708 1258-1259 HYPH denotes /
T3709 1259-1260 CD denotes 7
T3710 1272-1274 IN denotes on
T3711 1275-1276 DT denotes a
T3712 1277-1283 NN denotes bubble
T3713 1294-1300 JJ denotes strong
T3714 1301-1311 NN denotes protection
T3715 1312-1314 IN denotes on
T3716 1315-1318 DT denotes the
T3717 1322-1326 NN denotes half
T3718 1319-1320 CD denotes 5
T3719 1320-1321 SYM denotes ′
T3720 1321-1322 HYPH denotes -
T3721 1327-1329 IN denotes of
T3722 1330-1333 DT denotes the
T3723 1338-1344 NN denotes strand
T3724 1334-1337 JJ denotes top
T3725 1345-1348 CC denotes and
T3726 1349-1357 JJ denotes moderate
T3727 1358-1368 NN denotes protection
T3728 1369-1371 IN denotes on
T3729 1372-1375 DT denotes the
T3730 1389-1393 NN denotes half
T3731 1376-1385 VBG denotes remaining
T3732 1386-1387 CD denotes 3
T3733 1387-1388 SYM denotes ′
T3734 1388-1389 HYPH denotes -
T3735 1393-1395 , denotes ,
T3736 1395-1397 RB denotes as
T3737 1403-1405 IN denotes as
T3738 1398-1402 RB denotes well
T3739 1406-1408 IN denotes on
T3740 1409-1416 JJ denotes several
T3741 1434-1441 NN denotes segment
T3742 1417-1421 NN denotes base
T3743 1422-1426 NN denotes pair
T3744 1421-1422 HYPH denotes -
T3745 1427-1433 NN denotes duplex
T3746 1442-1450 JJ denotes adjacent
T3747 1451-1453 IN denotes to
T3748 1454-1457 DT denotes the
T3749 1465-1470 NN denotes point
T3750 1458-1464 NN denotes branch
T3751 1471-1472 -LRB- denotes (
T3752 1479-1481 NN denotes 1A
T3753 1472-1478 NN denotes Figure
T3754 1482-1485 CC denotes and
T3755 1486-1490 NNS denotes data
T3756 1491-1494 RB denotes not
T3757 1495-1500 VBN denotes shown
T3758 1500-1501 -RRB- denotes )
T3759 1501-1502 . denotes .
T3760 1502-1574 sentence denotes A similar pattern of protection was observed also on the bottom strand.
T3761 1503-1504 DT denotes A
T3762 1513-1520 NN denotes pattern
T3763 1505-1512 JJ denotes similar
T3764 1539-1547 VBN denotes observed
T3765 1521-1523 IN denotes of
T3766 1524-1534 NN denotes protection
T3767 1535-1538 VBD denotes was
T3768 1548-1552 RB denotes also
T3769 1553-1555 IN denotes on
T3770 1556-1559 DT denotes the
T3771 1567-1573 NN denotes strand
T3772 1560-1566 JJ denotes bottom
T3773 1573-1574 . denotes .
T3774 1574-1767 sentence denotes This suggests that Mcm4/6/7 may bind to a replication bubble substrate with a 2-fold symmetry as a double hexamer (Figure 1A, see the lower scheme), in a manner similar to SV40 T-antigen (21).
T3775 1575-1579 DT denotes This
T3776 1580-1588 VBZ denotes suggests
T3777 1589-1593 IN denotes that
T3778 1607-1611 VB denotes bind
T3779 1594-1598 NN denotes Mcm4
T3780 1598-1599 HYPH denotes /
T3781 1599-1600 CD denotes 6
T3782 1600-1601 HYPH denotes /
T3783 1601-1602 CD denotes 7
T3784 1603-1606 MD denotes may
T3785 1612-1614 IN denotes to
T3786 1615-1616 DT denotes a
T3787 1636-1645 NN denotes substrate
T3788 1617-1628 NN denotes replication
T3789 1629-1635 NN denotes bubble
T3790 1646-1650 IN denotes with
T3791 1651-1652 DT denotes a
T3792 1660-1668 NN denotes symmetry
T3793 1653-1659 CD denotes 2-fold
T3794 1669-1671 IN denotes as
T3795 1672-1673 DT denotes a
T3796 1681-1688 NN denotes hexamer
T3797 1674-1680 JJ denotes double
T3798 1689-1690 -LRB- denotes (
T3799 1697-1699 NN denotes 1A
T3800 1690-1696 NN denotes Figure
T3801 1699-1701 , denotes ,
T3802 1701-1704 VBP denotes see
T3803 1705-1708 DT denotes the
T3804 1715-1721 NN denotes scheme
T3805 1709-1714 JJ denotes lower
T3806 1721-1722 -RRB- denotes )
T3807 1722-1724 , denotes ,
T3808 1724-1726 IN denotes in
T3809 1727-1728 DT denotes a
T3810 1729-1735 NN denotes manner
T3811 1736-1743 JJ denotes similar
T3812 1744-1746 IN denotes to
T3813 1747-1751 NN denotes SV40
T3814 1754-1761 NN denotes antigen
T3815 1752-1753 NN denotes T
T3816 1753-1754 HYPH denotes -
T3817 1762-1763 -LRB- denotes (
T3818 1763-1765 CD denotes 21
T3819 1765-1766 -RRB- denotes )
T3820 1766-1767 . denotes .
R2167 T3444 T3445 nsubj Mcm4,binds
R2168 T3446 T3444 punct /,Mcm4
R2169 T3447 T3444 nummod 6,Mcm4
R2170 T3448 T3444 punct /,Mcm4
R2171 T3449 T3444 nummod 7,Mcm4
R2172 T3450 T3445 prep to,binds
R2173 T3451 T3452 punct ‘,substrates
R2174 T3452 T3450 pobj substrates,to
R2175 T3453 T3452 nmod bubble,substrates
R2176 T3454 T3452 punct ’,substrates
R2177 T3455 T3452 compound DNA,substrates
R2178 T3456 T3445 cc and,binds
R2179 T3457 T3445 conj unwinds,binds
R2180 T3458 T3459 det the,segments
R2181 T3459 T3457 dobj segments,unwinds
R2182 T3460 T3459 compound duplex,segments
R2183 T3461 T3462 advmod when,contains
R2184 T3462 T3457 advcl contains,unwinds
R2185 T3463 T3464 det the,segment
R2186 T3464 T3462 nsubj segment,contains
R2187 T3465 T3464 amod central,segment
R2188 T3466 T3467 amod single,stranded
R2189 T3467 T3464 amod stranded,segment
R2190 T3468 T3467 punct -,stranded
R2191 T3469 T3470 compound thymine,stretches
R2192 T3470 T3462 dobj stretches,contains
R2193 T3471 T3472 punct (,13
R2194 T3472 T3462 parataxis 13,contains
R2195 T3473 T3472 punct ),13
R2196 T3474 T3445 punct .,binds
R2197 T3476 T3477 prep In,conducted
R2198 T3478 T3476 pobj order,In
R2199 T3479 T3480 aux to,examine
R2200 T3480 T3478 acl examine,order
R2201 T3481 T3482 det the,mode
R2202 T3482 T3480 dobj mode,examine
R2203 T3483 T3482 prep of,mode
R2204 T3484 T3483 pobj binding,of
R2205 T3485 T3484 prep of,binding
R2206 T3486 T3485 pobj Mcm4,of
R2207 T3487 T3486 punct /,Mcm4
R2208 T3488 T3486 nummod 6,Mcm4
R2209 T3489 T3486 punct /,Mcm4
R2210 T3490 T3486 nummod 7,Mcm4
R2211 T3491 T3484 prep on,binding
R2212 T3492 T3493 compound bubble,DNAs
R2213 T3493 T3491 pobj DNAs,on
R2214 T3494 T3477 punct ", ",conducted
R2215 T3495 T3477 nsubj we,conducted
R2216 T3496 T3497 compound nuclease,assays
R2217 T3497 T3477 dobj assays,conducted
R2218 T3498 T3497 compound protection,assays
R2219 T3499 T3477 advcl using,conducted
R2220 T3500 T3501 amod labeled,DNAs
R2221 T3501 T3499 dobj DNAs,using
R2222 T3502 T3503 compound bubble,substrate
R2223 T3503 T3501 compound substrate,DNAs
R2224 T3504 T3501 cc and,DNAs
R2225 T3505 T3501 conj Mcm4,DNAs
R2226 T3506 T3505 punct /,Mcm4
R2227 T3507 T3505 nummod 6,Mcm4
R2228 T3508 T3505 punct /,Mcm4
R2229 T3509 T3505 nummod 7,Mcm4
R2230 T3510 T3477 prep in,conducted
R2231 T3511 T3512 det the,presence
R2232 T3512 T3510 pobj presence,in
R2233 T3513 T3512 prep of,presence
R2234 T3514 T3515 nmod ATP,S
R2235 T3515 T3513 pobj S,of
R2236 T3516 T3515 punct -,S
R2237 T3517 T3515 punct γ,S
R2238 T3518 T3515 punct -,S
R2239 T3519 T3520 dep which,permits
R2240 T3520 T3515 relcl permits,S
R2241 T3521 T3520 dobj binding,permits
R2242 T3522 T3521 prep to,binding
R2243 T3523 T3524 compound substrate,DNA
R2244 T3524 T3522 pobj DNA,to
R2245 T3525 T3520 cc but,permits
R2246 T3526 T3527 aux does,mobilize
R2247 T3527 T3520 conj mobilize,permits
R2248 T3528 T3527 neg not,mobilize
R2249 T3529 T3530 det the,helicase
R2250 T3530 T3527 dobj helicase,mobilize
R2251 T3531 T3477 punct .,conducted
R2252 T3533 T3534 prep At,detected
R2253 T3535 T3536 det an,concentration
R2254 T3536 T3533 pobj concentration,At
R2255 T3537 T3536 amod optimum,concentration
R2256 T3538 T3536 prep of,concentration
R2257 T3539 T3538 pobj DNase,of
R2258 T3540 T3539 nummod I,DNase
R2259 T3541 T3534 punct ", ",detected
R2260 T3542 T3543 amod strong,cleavages
R2261 T3543 T3534 nsubjpass cleavages,detected
R2262 T3544 T3534 auxpass were,detected
R2263 T3545 T3534 prep on,detected
R2264 T3546 T3547 det the,regions
R2265 T3547 T3545 pobj regions,on
R2266 T3548 T3549 nummod 21,bp
R2267 T3549 T3547 compound bp,regions
R2268 T3550 T3547 compound duplex,regions
R2269 T3551 T3534 prep at,detected
R2270 T3552 T3553 det both,ends
R2271 T3553 T3551 pobj ends,at
R2272 T3554 T3553 prep of,ends
R2273 T3555 T3556 det the,substrates
R2274 T3556 T3554 pobj substrates,of
R2275 T3557 T3534 punct ", ",detected
R2276 T3558 T3559 mark whereas,detected
R2277 T3559 T3534 advcl detected,detected
R2278 T3560 T3561 amod weaker,cleavages
R2279 T3561 T3559 nsubjpass cleavages,detected
R2280 T3562 T3559 auxpass were,detected
R2281 T3563 T3559 prep on,detected
R2282 T3564 T3565 det the,region
R2283 T3565 T3563 pobj region,on
R2284 T3566 T3565 amod central,region
R2285 T3567 T3568 amod single,stranded
R2286 T3568 T3565 amod stranded,region
R2287 T3569 T3568 punct -,stranded
R2288 T3570 T3559 punct ", ",detected
R2289 T3571 T3559 advcl consistent,detected
R2290 T3572 T3571 prep with,consistent
R2291 T3573 T3572 pobj preference,with
R2292 T3574 T3573 prep of,preference
R2293 T3575 T3574 pobj DNase,of
R2294 T3576 T3575 nummod I,DNase
R2295 T3577 T3573 prep to,preference
R2296 T3578 T3579 amod double,stranded
R2297 T3579 T3581 amod stranded,DNA
R2298 T3580 T3579 punct -,stranded
R2299 T3581 T3577 pobj DNA,to
R2300 T3582 T3534 punct .,detected
R2301 T3584 T3585 prep With,detected
R2302 T3586 T3587 det the,substrate
R2303 T3587 T3584 pobj substrate,With
R2304 T3588 T3587 nmod Bub66,substrate
R2305 T3589 T3588 punct /,Bub66
R2306 T3590 T3588 appos T,Bub66
R2307 T3591 T3590 punct -,T
R2308 T3592 T3590 amod rich,T
R2309 T3593 T3585 punct ", ",detected
R2310 T3594 T3595 amod strong,protection
R2311 T3595 T3585 nsubjpass protection,detected
R2312 T3596 T3585 auxpass was,detected
R2313 T3597 T3585 prep on,detected
R2314 T3598 T3599 det the,regions
R2315 T3599 T3597 pobj regions,on
R2316 T3600 T3599 amod entire,regions
R2317 T3601 T3602 amod single,stranded
R2318 T3602 T3599 amod stranded,regions
R2319 T3603 T3602 punct -,stranded
R2320 T3604 T3599 prep of,regions
R2321 T3605 T3606 preconj both,top
R2322 T3606 T3607 amod top,strands
R2323 T3607 T3604 pobj strands,of
R2324 T3608 T3606 cc and,top
R2325 T3609 T3606 conj bottom,top
R2326 T3610 T3585 prep with,detected
R2327 T3611 T3612 amod increasing,concentration
R2328 T3612 T3610 pobj concentration,with
R2329 T3613 T3612 prep of,concentration
R2330 T3614 T3613 pobj Mcm4,of
R2331 T3615 T3614 punct /,Mcm4
R2332 T3616 T3614 nummod 6,Mcm4
R2333 T3617 T3614 punct /,Mcm4
R2334 T3618 T3614 nummod 7,Mcm4
R2335 T3619 T3585 punct ", ",detected
R2336 T3620 T3585 advcl consistent,detected
R2337 T3621 T3620 prep with,consistent
R2338 T3622 T3623 amod high,affinity
R2339 T3623 T3621 pobj affinity,with
R2340 T3624 T3623 prep of,affinity
R2341 T3625 T3624 pobj Mcm4,of
R2342 T3626 T3625 punct /,Mcm4
R2343 T3627 T3625 nummod 6,Mcm4
R2344 T3628 T3625 punct /,Mcm4
R2345 T3629 T3625 nummod 7,Mcm4
R2346 T3630 T3623 prep to,affinity
R2347 T3631 T3632 nmod T,sequences
R2348 T3632 T3630 pobj sequences,to
R2349 T3633 T3631 punct -,T
R2350 T3634 T3631 amod rich,T
R2351 T3635 T3632 compound bubble,sequences
R2352 T3636 T3637 punct (,1A
R2353 T3637 T3585 parataxis 1A,detected
R2354 T3638 T3637 compound Figure,1A
R2355 T3639 T3637 punct ),1A
R2356 T3640 T3585 punct .,detected
R2357 T3642 T3643 amod Similar,protection
R2358 T3643 T3648 nsubjpass protection,detected
R2359 T3644 T3642 punct ", ",Similar
R2360 T3645 T3642 cc but,Similar
R2361 T3646 T3647 advmod less,significant
R2362 T3647 T3642 conj significant,Similar
R2363 T3649 T3648 auxpass was,detected
R2364 T3650 T3648 prep on,detected
R2365 T3651 T3652 det the,segment
R2366 T3652 T3650 pobj segment,on
R2367 T3653 T3654 amod single,stranded
R2368 T3654 T3652 amod stranded,segment
R2369 T3655 T3654 punct -,stranded
R2370 T3656 T3652 compound DNA,segment
R2371 T3657 T3652 prep with,segment
R2372 T3658 T3659 compound P1,nucleases
R2373 T3659 T3657 pobj nucleases,with
R2374 T3660 T3661 punct (,1A
R2375 T3661 T3652 parataxis 1A,segment
R2376 T3662 T3661 compound Figure,1A
R2377 T3663 T3661 punct ),1A
R2378 T3664 T3652 punct ", ",segment
R2379 T3665 T3666 dep which,is
R2380 T3666 T3652 relcl is,segment
R2381 T3667 T3666 acomp specific,is
R2382 T3668 T3667 prep to,specific
R2383 T3669 T3670 amod single,stranded
R2384 T3670 T3672 amod stranded,DNA
R2385 T3671 T3670 punct -,stranded
R2386 T3672 T3668 pobj DNA,to
R2387 T3673 T3648 punct .,detected
R2388 T3675 T3676 det The,results
R2389 T3676 T3677 nsubj results,indicate
R2390 T3678 T3679 mark that,loaded
R2391 T3679 T3677 ccomp loaded,indicate
R2392 T3680 T3681 det the,complex
R2393 T3681 T3679 nsubjpass complex,loaded
R2394 T3682 T3681 compound Mcm,complex
R2395 T3683 T3679 auxpass is,loaded
R2396 T3684 T3679 prep onto,loaded
R2397 T3685 T3686 compound bubble,DNA
R2398 T3686 T3684 pobj DNA,onto
R2399 T3687 T3679 prep through,loaded
R2400 T3688 T3687 pobj binding,through
R2401 T3689 T3688 prep to,binding
R2402 T3690 T3691 det both,strands
R2403 T3691 T3689 pobj strands,to
R2404 T3692 T3691 prep of,strands
R2405 T3693 T3694 det the,region
R2406 T3694 T3692 pobj region,of
R2407 T3695 T3696 amod single,stranded
R2408 T3696 T3694 amod stranded,region
R2409 T3697 T3696 punct -,stranded
R2410 T3698 T3677 punct .,indicate
R2411 T3700 T3701 amod Careful,examination
R2412 T3701 T3702 nsubj examination,indicated
R2413 T3703 T3701 prep of,examination
R2414 T3704 T3705 nmod Mcm4,footprints
R2415 T3705 T3703 pobj footprints,of
R2416 T3706 T3704 punct /,Mcm4
R2417 T3707 T3704 nummod 6,Mcm4
R2418 T3708 T3704 punct /,Mcm4
R2419 T3709 T3704 nummod 7,Mcm4
R2420 T3710 T3705 prep on,footprints
R2421 T3711 T3712 det a,bubble
R2422 T3712 T3710 pobj bubble,on
R2423 T3713 T3714 amod strong,protection
R2424 T3714 T3702 dobj protection,indicated
R2425 T3715 T3714 prep on,protection
R2426 T3716 T3717 det the,half
R2427 T3717 T3715 pobj half,on
R2428 T3718 T3717 nummod 5,half
R2429 T3719 T3718 punct ′,5
R2430 T3720 T3717 punct -,half
R2431 T3721 T3717 prep of,half
R2432 T3722 T3723 det the,strand
R2433 T3723 T3721 pobj strand,of
R2434 T3724 T3723 amod top,strand
R2435 T3725 T3714 cc and,protection
R2436 T3726 T3727 amod moderate,protection
R2437 T3727 T3714 conj protection,protection
R2438 T3728 T3727 prep on,protection
R2439 T3729 T3730 det the,half
R2440 T3730 T3728 pobj half,on
R2441 T3731 T3730 amod remaining,half
R2442 T3732 T3730 nummod 3,half
R2443 T3733 T3732 punct ′,3
R2444 T3734 T3730 punct -,half
R2445 T3735 T3728 punct ", ",on
R2446 T3736 T3737 advmod as,as
R2447 T3737 T3728 cc as,on
R2448 T3738 T3737 advmod well,as
R2449 T3739 T3728 conj on,on
R2450 T3740 T3741 amod several,segment
R2451 T3741 T3739 pobj segment,on
R2452 T3742 T3743 compound base,pair
R2453 T3743 T3741 compound pair,segment
R2454 T3744 T3743 punct -,pair
R2455 T3745 T3741 compound duplex,segment
R2456 T3746 T3741 amod adjacent,segment
R2457 T3747 T3746 prep to,adjacent
R2458 T3748 T3749 det the,point
R2459 T3749 T3747 pobj point,to
R2460 T3750 T3749 compound branch,point
R2461 T3751 T3752 punct (,1A
R2462 T3752 T3739 parataxis 1A,on
R2463 T3753 T3752 compound Figure,1A
R2464 T3754 T3752 cc and,1A
R2465 T3755 T3752 conj data,1A
R2466 T3756 T3757 neg not,shown
R2467 T3757 T3755 acl shown,data
R2468 T3758 T3752 punct ),1A
R2469 T3759 T3702 punct .,indicated
R2470 T3761 T3762 det A,pattern
R2471 T3762 T3764 nsubjpass pattern,observed
R2472 T3763 T3762 amod similar,pattern
R2473 T3765 T3762 prep of,pattern
R2474 T3766 T3765 pobj protection,of
R2475 T3767 T3764 auxpass was,observed
R2476 T3768 T3764 advmod also,observed
R2477 T3769 T3764 prep on,observed
R2478 T3770 T3771 det the,strand
R2479 T3771 T3769 pobj strand,on
R2480 T3772 T3771 amod bottom,strand
R2481 T3773 T3764 punct .,observed
R2482 T3775 T3776 nsubj This,suggests
R2483 T3777 T3778 mark that,bind
R2484 T3778 T3776 ccomp bind,suggests
R2485 T3779 T3778 nsubj Mcm4,bind
R2486 T3780 T3779 punct /,Mcm4
R2487 T3781 T3779 nummod 6,Mcm4
R2488 T3782 T3779 punct /,Mcm4
R2489 T3783 T3779 nummod 7,Mcm4
R2490 T3784 T3778 aux may,bind
R2491 T3785 T3778 prep to,bind
R2492 T3786 T3787 det a,substrate
R2493 T3787 T3785 pobj substrate,to
R2494 T3788 T3787 compound replication,substrate
R2495 T3789 T3787 compound bubble,substrate
R2496 T3790 T3787 prep with,substrate
R2497 T3791 T3792 det a,symmetry
R2498 T3792 T3790 pobj symmetry,with
R2499 T3793 T3792 nummod 2-fold,symmetry
R2500 T3794 T3778 prep as,bind
R2501 T3795 T3796 det a,hexamer
R2502 T3796 T3794 pobj hexamer,as
R2503 T3797 T3796 amod double,hexamer
R2504 T3798 T3799 punct (,1A
R2505 T3799 T3796 parataxis 1A,hexamer
R2506 T3800 T3799 compound Figure,1A
R2507 T3801 T3799 punct ", ",1A
R2508 T3802 T3799 advcl see,1A
R2509 T3803 T3804 det the,scheme
R2510 T3804 T3802 dobj scheme,see
R2511 T3805 T3804 amod lower,scheme
R2512 T3806 T3799 punct ),1A
R2513 T3807 T3778 punct ", ",bind
R2514 T3808 T3778 prep in,bind
R2515 T3809 T3810 det a,manner
R2516 T3810 T3808 pobj manner,in
R2517 T3811 T3810 amod similar,manner
R2518 T3812 T3811 prep to,similar
R2519 T3813 T3814 compound SV40,antigen
R2520 T3814 T3812 pobj antigen,to
R2521 T3815 T3814 compound T,antigen
R2522 T3816 T3814 punct -,antigen
R2523 T3817 T3818 punct (,21
R2524 T3818 T3778 parataxis 21,bind
R2525 T3819 T3818 punct ),21
R2526 T3820 T3776 punct .,suggests

craft-ca-core-ex-dev

Below, discontinuous spans are shown in the chain model. You can change it to the bag model.

Id Subject Object Predicate Lexical cue
T3355 0-4 PR_EXT:000010246 denotes Mcm4
T3356 0-8 GO:0097373 denotes Mcm4/6/7
T3357 9-14 CHEMINF_GO_EXT:chemical_binding_or_bond_formation denotes binds
T3358 27-30 CHEBI_SO_EXT:DNA denotes DNA
T3359 58-64 SO:0000985 denotes duplex
T3360 91-106 SO:0000984 denotes single-stranded
T3361 124-131 CHEBI_EXT:thymine_nucleobase_or_nucleoside_or_nucleotide_molecular_entity_or_group denotes thymine
T3362 180-187 CHEMINF_GO_EXT:chemical_binding_or_bond_formation denotes binding
T3363 191-195 PR_EXT:000010246 denotes Mcm4
T3364 191-199 GO:0097373 denotes Mcm4/6/7
T3365 210-214 CHEBI_SO_EXT:DNA denotes DNAs
T3366 229-237 GO_EXT:0004518 denotes nuclease
T3367 262-269 CHEBI_SO_EXT:molecular_label_or_mark_or_tag_process denotes labeled
T3368 287-291 CHEBI_SO_EXT:DNA denotes DNAs
T3369 296-300 PR_EXT:000010246 denotes Mcm4
T3370 296-304 GO:0097373 denotes Mcm4/6/7
T3371 324-331 CHEBI:27575 denotes ATP-γ-S
T3372 346-353 CHEMINF_GO_EXT:chemical_binding_or_bond_formation denotes binding
T3373 367-370 CHEBI_SO_EXT:DNA denotes DNA
T3374 384-392 GO_EXT:biological_recruitment denotes mobilize
T3375 397-405 GO_EXT:0004386 denotes helicase
T3376 438-445 GO_PR_EXT:deoxyribonuclease_I denotes DNase I
T3377 454-463 MOP:0000780 denotes cleavages
T3378 488-490 SO_EXT:0000028 denotes bp
T3379 491-497 SO:0000985 denotes duplex
T3380 553-562 MOP:0000780 denotes cleavages
T3381 592-607 SO:0000984 denotes single-stranded
T3382 646-653 GO_PR_EXT:deoxyribonuclease_I denotes DNase I
T3383 657-676 CHEBI_SO_EXT:double_stranded_DNA denotes double-stranded DNA
T3384 693-694 CHEBI_EXT:thymine_nucleobase_or_nucleoside_or_nucleotide_molecular_entity_or_group denotes T
T3385 756-771 SO:0000984 denotes single-stranded
T3386 844-848 PR_EXT:000010246 denotes Mcm4
T3387 844-852 GO:0097373 denotes Mcm4/6/7
T3388 887-891 PR_EXT:000010246 denotes Mcm4
T3389 887-895 GO:0097373 denotes Mcm4/6/7
T3390 899-900 CHEBI_EXT:thymine_nucleobase_or_nucleoside_or_nucleotide_molecular_entity_or_group denotes T
T3391 913-922 SO_EXT:biological_sequence denotes sequences
T3392 997-1016 CHEBI_SO_EXT:single_stranded_DNA denotes single-stranded DNA
T3393 1033-1042 GO_EXT:0004518 denotes nucleases
T3394 1077-1096 CHEBI_SO_EXT:single_stranded_DNA denotes single-stranded DNA
T3395 1128-1139 GO:0042555 denotes Mcm complex
T3396 1162-1165 CHEBI_SO_EXT:DNA denotes DNA
T3397 1174-1181 CHEMINF_GO_EXT:chemical_binding_or_bond_formation denotes binding
T3398 1205-1220 SO:0000984 denotes single-stranded
T3399 1252-1256 PR_EXT:000010246 denotes Mcm4
T3400 1252-1260 GO:0097373 denotes Mcm4/6/7
T3401 1417-1421 CHEBI_SO_EXT:base denotes base
T3402 1417-1426 SO_EXT:0000028 denotes base-pair
T3403 1427-1433 SO:0000985 denotes duplex
T3404 1594-1598 PR_EXT:000010246 denotes Mcm4
T3405 1594-1602 GO:0097373 denotes Mcm4/6/7
T3406 1607-1611 CHEMINF_GO_EXT:chemical_binding_or_bond_formation denotes bind
T3407 1617-1628 GO:0006260 denotes replication
T3408 1674-1688 GO_EXT:double_hexameric_macromolecular_complex denotes double hexamer
T3409 1747-1751 NCBITaxon:10633 denotes SV40
T3410 1754-1761 CHEBI_EXT:59132 denotes antigen

craft-ca-core-dev

Below, discontinuous spans are shown in the chain model. You can change it to the bag model.

Id Subject Object Predicate Lexical cue
T3306 0-4 PR:000010246 denotes Mcm4
T3307 0-8 GO:0097373 denotes Mcm4/6/7
T3308 58-64 SO:0000985 denotes duplex
T3309 91-106 SO:0000984 denotes single-stranded
T3310 191-195 PR:000010246 denotes Mcm4
T3311 191-199 GO:0097373 denotes Mcm4/6/7
T3312 296-300 PR:000010246 denotes Mcm4
T3313 296-304 GO:0097373 denotes Mcm4/6/7
T3314 324-331 CHEBI:27575 denotes ATP-γ-S
T3315 454-463 MOP:0000780 denotes cleavages
T3316 488-490 SO:0000028 denotes bp
T3317 491-497 SO:0000985 denotes duplex
T3318 553-562 MOP:0000780 denotes cleavages
T3319 592-607 SO:0000984 denotes single-stranded
T3320 657-672 SO:0000985 denotes double-stranded
T3321 756-771 SO:0000984 denotes single-stranded
T3322 844-848 PR:000010246 denotes Mcm4
T3323 844-852 GO:0097373 denotes Mcm4/6/7
T3324 887-891 PR:000010246 denotes Mcm4
T3325 887-895 GO:0097373 denotes Mcm4/6/7
T3326 997-1012 SO:0000984 denotes single-stranded
T3327 1077-1092 SO:0000984 denotes single-stranded
T3328 1128-1139 GO:0042555 denotes Mcm complex
T3329 1205-1220 SO:0000984 denotes single-stranded
T3330 1252-1256 PR:000010246 denotes Mcm4
T3331 1252-1260 GO:0097373 denotes Mcm4/6/7
T3332 1417-1426 SO:0000028 denotes base-pair
T3333 1427-1433 SO:0000985 denotes duplex
T3334 1594-1598 PR:000010246 denotes Mcm4
T3335 1594-1602 GO:0097373 denotes Mcm4/6/7
T3336 1617-1628 GO:0006260 denotes replication
T3337 1747-1751 NCBITaxon:10633 denotes SV40
T3338 1754-1761 CHEBI:59132 denotes antigen

2_test

Id Subject Object Predicate Lexical cue
15917436-14609960-76775508 143-145 14609960 denotes 13
15917436-9765408-76775509 1763-1765 9765408 denotes 21