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PMC:1853120 / 44219-45181 JSONTXT

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craft-sa-dev

Id Subject Object Predicate Lexical cue
T23872 415-416 . denotes .
T23873 416-582 sentence denotes 3′ to Pgk-neo and the loxP site, we inserted, as a XmaI/XmaI DNA fragment, the third intron of Dmrt7 (from 366 bp to 2,773 bp downstream of exon 3) generated by PCR.
T23874 417-418 CD denotes 3
T23875 453-461 VBD denotes inserted
T23797 0-1 DT denotes A
T23798 19-27 NN denotes fragment
T23799 2-7 NN denotes mouse
T23800 8-13 NN denotes Dmrt7
T23801 14-18 NN denotes cDNA
T23802 65-69 VBN denotes used
T23803 28-38 VBG denotes containing
T23804 39-48 NNS denotes sequences
T23805 49-53 IN denotes from
T23806 54-58 NN denotes exon
T23807 59-60 CD denotes 8
T23808 61-64 VBD denotes was
T23809 70-72 TO denotes to
T23810 73-79 VB denotes screen
T23811 80-81 DT denotes a
T23812 92-99 NN denotes library
T23813 82-87 NN denotes mouse
T23814 88-91 NN denotes BAC
T23815 100-104 IN denotes from
T23816 105-108 DT denotes the
T23817 117-123 NN denotes strain
T23818 109-112 CD denotes 129
T23819 113-116 NN denotes SvJ
T23820 112-113 HYPH denotes /
T23821 124-125 -LRB- denotes (
T23822 125-135 NN denotes Stratagene
T23823 135-137 , denotes ,
T23824 137-162 NN denotes http://www.stratagene.com
T23825 162-163 -RRB- denotes )
T23826 163-165 , denotes ,
T23827 165-168 CC denotes and
T23828 169-175 NNS denotes clones
T23829 211-219 VBN denotes isolated
T23830 176-186 VBG denotes containing
T23831 187-195 NN denotes promoter
T23832 196-205 NNS denotes sequences
T23833 206-210 VBD denotes were
T23834 220-223 CC denotes and
T23835 224-233 VBN denotes sequenced
T23836 234-236 TO denotes to
T23837 237-243 VB denotes obtain
T23838 244-249 NN denotes Dmrt7
T23839 258-266 NN denotes sequence
T23840 250-257 JJ denotes genomic
T23841 266-267 . denotes .
T23842 267-416 sentence denotes The targeting vector pDZ169 (diagrammed in Figure S2) was constructed by the following scheme: The vector pDZ157 was used as a backbone vector [31].
T23843 268-271 DT denotes The
T23844 282-288 NN denotes vector
T23845 272-281 NN denotes targeting
T23846 326-337 VBN denotes constructed
T23847 289-295 NN denotes pDZ169
T23848 296-297 -LRB- denotes (
T23849 297-307 VBN denotes diagrammed
T23850 308-310 IN denotes in
T23851 311-317 NN denotes Figure
T23852 318-320 NN denotes S2
T23853 320-321 -RRB- denotes )
T23854 322-325 VBD denotes was
T23855 385-389 VBN denotes used
T23856 338-340 IN denotes by
T23857 341-344 DT denotes the
T23858 355-361 NN denotes scheme
T23859 345-354 VBG denotes following
T23860 361-363 : denotes :
T23861 363-366 DT denotes The
T23862 374-380 NN denotes pDZ157
T23863 367-373 NN denotes vector
T23864 381-384 VBD denotes was
T23865 390-392 IN denotes as
T23866 393-394 DT denotes a
T23867 404-410 NN denotes vector
T23868 395-403 NN denotes backbone
T23869 411-412 -LRB- denotes [
T23870 412-414 CD denotes 31
T23871 414-415 -RRB- denotes ]
T23876 418-419 SYM denotes ′
T23877 420-422 IN denotes to
T23878 423-426 NN denotes Pgk
T23879 427-430 NN denotes neo
T23880 426-427 HYPH denotes -
T23881 431-434 CC denotes and
T23882 435-438 DT denotes the
T23883 444-448 NN denotes site
T23884 439-443 NN denotes loxP
T23885 448-450 , denotes ,
T23886 450-452 PRP denotes we
T23887 461-463 , denotes ,
T23888 463-465 IN denotes as
T23889 466-467 DT denotes a
T23890 482-490 NN denotes fragment
T23891 468-472 NN denotes XmaI
T23892 473-477 NN denotes XmaI
T23893 472-473 HYPH denotes /
T23894 478-481 NN denotes DNA
T23895 490-492 , denotes ,
T23896 492-495 DT denotes the
T23897 502-508 NN denotes intron
T23898 496-501 JJ denotes third
T23899 509-511 IN denotes of
T23900 512-517 NN denotes Dmrt7
T23901 518-519 -LRB- denotes (
T23902 543-553 RB denotes downstream
T23903 519-523 IN denotes from
T23904 524-527 CD denotes 366
T23905 528-530 NNS denotes bp
T23906 531-533 IN denotes to
T23907 534-539 CD denotes 2,773
T23908 540-542 NNS denotes bp
T23909 554-556 IN denotes of
T23910 557-561 NN denotes exon
T23911 562-563 CD denotes 3
T23912 563-564 -RRB- denotes )
T23913 565-574 VBN denotes generated
T23914 575-577 IN denotes by
T23915 578-581 NN denotes PCR
T23916 581-582 . denotes .
T23917 582-707 sentence denotes 5′ to Pgk-neo, we inserted an EcoRI/NotI PCR fragment extending from 4,107 bp to 336 bp 5′ of the Dmrt7 translational start.
T23918 583-584 CD denotes 5
T23919 601-609 VBD denotes inserted
T23920 584-585 SYM denotes ′
T23921 586-588 IN denotes to
T23922 589-592 NN denotes Pgk
T23923 593-596 NN denotes neo
T23924 592-593 HYPH denotes -
T23925 596-598 , denotes ,
T23926 598-600 PRP denotes we
T23927 610-612 DT denotes an
T23928 628-636 NN denotes fragment
T23929 613-618 NN denotes EcoRI
T23930 619-623 NN denotes NotI
T23931 618-619 HYPH denotes /
T23932 624-627 NN denotes PCR
T23933 637-646 VBG denotes extending
T23934 647-651 IN denotes from
T23935 652-657 CD denotes 4,107
T23936 658-660 NNS denotes bp
T23937 661-663 IN denotes to
T23938 664-667 CD denotes 336
T23939 668-670 NNS denotes bp
T23940 671-672 CD denotes 5
T23941 672-673 SYM denotes ′
T23942 674-676 IN denotes of
T23943 677-680 DT denotes the
T23944 701-706 NN denotes start
T23945 681-686 NN denotes Dmrt7
T23946 687-700 JJ denotes translational
T23947 706-707 . denotes .
T23948 707-798 sentence denotes Finally, we inserted a loxP site and NotI site 336 bp 5′ of the Dmrt7 translational start.
T23949 708-715 RB denotes Finally
T23950 720-728 VBD denotes inserted
T23951 715-717 , denotes ,
T23952 717-719 PRP denotes we
T23953 729-730 DT denotes a
T23954 736-740 NN denotes site
T23955 731-735 NN denotes loxP
T23956 741-744 CC denotes and
T23957 745-749 NN denotes NotI
T23958 750-754 NN denotes site
T23959 755-758 CD denotes 336
T23960 759-761 NNS denotes bp
T23961 762-763 CD denotes 5
T23962 763-764 SYM denotes ′
T23963 765-767 IN denotes of
T23964 768-771 DT denotes the
T23965 792-797 NN denotes start
T23966 772-777 NN denotes Dmrt7
T23967 778-791 JJ denotes translational
T23968 797-798 . denotes .
T23969 798-895 sentence denotes In the resulting vector, the second and third exons of Dmrt7 are flanked by loxP sites (floxed).
T23970 799-801 IN denotes In
T23971 864-871 VBN denotes flanked
T23972 802-805 DT denotes the
T23973 816-822 NN denotes vector
T23974 806-815 VBG denotes resulting
T23975 822-824 , denotes ,
T23976 824-827 DT denotes the
T23977 845-850 NNS denotes exons
T23978 828-834 JJ denotes second
T23979 835-838 CC denotes and
T23980 839-844 JJ denotes third
T23981 851-853 IN denotes of
T23982 854-859 NN denotes Dmrt7
T23983 860-863 VBP denotes are
T23984 872-874 IN denotes by
T23985 875-879 NN denotes loxP
T23986 880-885 NNS denotes sites
T23987 886-887 -LRB- denotes (
T23988 887-893 JJ denotes floxed
T23989 893-894 -RRB- denotes )
T23990 894-895 . denotes .
T23991 895-962 sentence denotes The Dmrt7-containing portions of pDZ169 were completely sequenced.
T23992 896-899 DT denotes The
T23993 917-925 NNS denotes portions
T23994 900-905 NN denotes Dmrt7
T23995 906-916 VBG denotes containing
T23996 905-906 HYPH denotes -
T23997 952-961 VBN denotes sequenced
T23998 926-928 IN denotes of
T23999 929-935 NN denotes pDZ169
T24000 936-940 VBD denotes were
T24001 941-951 RB denotes completely
T24002 961-962 . denotes .
R6386 T23797 T23798 det A,fragment
R6387 T23798 T23802 nsubjpass fragment,used
R6388 T23799 T23798 compound mouse,fragment
R6389 T23800 T23801 compound Dmrt7,cDNA
R6390 T23801 T23798 compound cDNA,fragment
R6391 T23803 T23798 acl containing,fragment
R6392 T23804 T23803 dobj sequences,containing
R6393 T23805 T23804 prep from,sequences
R6394 T23806 T23805 pobj exon,from
R6395 T23807 T23806 nummod 8,exon
R6396 T23808 T23802 auxpass was,used
R6397 T23809 T23810 aux to,screen
R6398 T23810 T23802 advcl screen,used
R6399 T23811 T23812 det a,library
R6400 T23812 T23810 dobj library,screen
R6401 T23813 T23812 compound mouse,library
R6402 T23814 T23812 compound BAC,library
R6403 T23815 T23812 prep from,library
R6404 T23816 T23817 det the,strain
R6405 T23817 T23815 pobj strain,from
R6406 T23818 T23819 nummod 129,SvJ
R6407 T23819 T23817 compound SvJ,strain
R6408 T23820 T23819 punct /,SvJ
R6409 T23821 T23822 punct (,Stratagene
R6410 T23822 T23802 parataxis Stratagene,used
R6411 T23823 T23822 punct ", ",Stratagene
R6412 T23824 T23822 npadvmod http://www.stratagene.com,Stratagene
R6413 T23825 T23822 punct ),Stratagene
R6414 T23826 T23802 punct ", ",used
R6415 T23827 T23802 cc and,used
R6416 T23828 T23829 nsubjpass clones,isolated
R6417 T23829 T23802 conj isolated,used
R6418 T23830 T23828 acl containing,clones
R6419 T23831 T23832 compound promoter,sequences
R6420 T23832 T23830 dobj sequences,containing
R6421 T23833 T23829 auxpass were,isolated
R6422 T23834 T23829 cc and,isolated
R6423 T23835 T23829 conj sequenced,isolated
R6424 T23836 T23837 aux to,obtain
R6425 T23837 T23835 advcl obtain,sequenced
R6426 T23838 T23839 nmod Dmrt7,sequence
R6427 T23839 T23837 dobj sequence,obtain
R6428 T23840 T23839 amod genomic,sequence
R6429 T23841 T23829 punct .,isolated
R6430 T23843 T23844 det The,vector
R6431 T23844 T23846 nsubjpass vector,constructed
R6432 T23845 T23844 compound targeting,vector
R6433 T23846 T23855 ccomp constructed,used
R6434 T23847 T23844 appos pDZ169,vector
R6435 T23848 T23844 punct (,vector
R6436 T23849 T23844 acl diagrammed,vector
R6437 T23850 T23849 prep in,diagrammed
R6438 T23851 T23852 compound Figure,S2
R6439 T23852 T23850 pobj S2,in
R6440 T23853 T23844 punct ),vector
R6441 T23854 T23846 auxpass was,constructed
R6442 T23856 T23846 prep by,constructed
R6443 T23857 T23858 det the,scheme
R6444 T23858 T23856 pobj scheme,by
R6445 T23859 T23858 amod following,scheme
R6446 T23860 T23855 punct : ,used
R6447 T23861 T23862 det The,pDZ157
R6448 T23862 T23855 nsubjpass pDZ157,used
R6449 T23863 T23862 compound vector,pDZ157
R6450 T23864 T23855 auxpass was,used
R6451 T23865 T23855 prep as,used
R6452 T23866 T23867 det a,vector
R6453 T23867 T23865 pobj vector,as
R6454 T23868 T23867 compound backbone,vector
R6455 T23869 T23870 punct [,31
R6456 T23870 T23855 parataxis 31,used
R6457 T23871 T23870 punct ],31
R6458 T23872 T23855 punct .,used
R6459 T23874 T23875 npadvmod 3,inserted
R6460 T23876 T23874 punct ′,3
R6461 T23877 T23874 prep to,3
R6462 T23878 T23879 compound Pgk,neo
R6463 T23879 T23877 pobj neo,to
R6464 T23880 T23879 punct -,neo
R6465 T23881 T23879 cc and,neo
R6466 T23882 T23883 det the,site
R6467 T23883 T23879 conj site,neo
R6468 T23884 T23883 compound loxP,site
R6469 T23885 T23875 punct ", ",inserted
R6470 T23886 T23875 nsubj we,inserted
R6471 T23887 T23875 punct ", ",inserted
R6472 T23888 T23875 prep as,inserted
R6473 T23889 T23890 det a,fragment
R6474 T23890 T23888 pobj fragment,as
R6475 T23891 T23892 compound XmaI,XmaI
R6476 T23892 T23890 compound XmaI,fragment
R6477 T23893 T23892 punct /,XmaI
R6478 T23894 T23890 compound DNA,fragment
R6479 T23895 T23875 punct ", ",inserted
R6480 T23896 T23897 det the,intron
R6481 T23897 T23875 dobj intron,inserted
R6482 T23898 T23897 amod third,intron
R6483 T23899 T23897 prep of,intron
R6484 T23900 T23899 pobj Dmrt7,of
R6485 T23901 T23902 punct (,downstream
R6486 T23902 T23900 parataxis downstream,Dmrt7
R6487 T23903 T23902 prep from,downstream
R6488 T23904 T23905 nummod 366,bp
R6489 T23905 T23903 pobj bp,from
R6490 T23906 T23903 prep to,from
R6491 T23907 T23908 nummod "2,773",bp
R6492 T23908 T23906 pobj bp,to
R6493 T23909 T23902 prep of,downstream
R6494 T23910 T23909 pobj exon,of
R6495 T23911 T23910 nummod 3,exon
R6496 T23912 T23902 punct ),downstream
R6497 T23913 T23897 acl generated,intron
R6498 T23914 T23913 prep by,generated
R6499 T23915 T23914 pobj PCR,by
R6500 T23916 T23875 punct .,inserted
R6501 T23918 T23919 npadvmod 5,inserted
R6502 T23920 T23918 punct ′,5
R6503 T23921 T23918 prep to,5
R6504 T23922 T23923 compound Pgk,neo
R6505 T23923 T23921 pobj neo,to
R6506 T23924 T23923 punct -,neo
R6507 T23925 T23919 punct ", ",inserted
R6508 T23926 T23919 nsubj we,inserted
R6509 T23927 T23928 det an,fragment
R6510 T23928 T23919 dobj fragment,inserted
R6511 T23929 T23930 compound EcoRI,NotI
R6512 T23930 T23928 compound NotI,fragment
R6513 T23931 T23930 punct /,NotI
R6514 T23932 T23928 compound PCR,fragment
R6515 T23933 T23928 acl extending,fragment
R6516 T23934 T23933 prep from,extending
R6517 T23935 T23936 nummod "4,107",bp
R6518 T23936 T23934 pobj bp,from
R6519 T23937 T23934 prep to,from
R6520 T23938 T23939 nummod 336,bp
R6521 T23939 T23937 pobj bp,to
R6522 T23940 T23933 npadvmod 5,extending
R6523 T23941 T23940 punct ′,5
R6524 T23942 T23940 prep of,5
R6525 T23943 T23944 det the,start
R6526 T23944 T23942 pobj start,of
R6527 T23945 T23944 nmod Dmrt7,start
R6528 T23946 T23944 amod translational,start
R6529 T23947 T23919 punct .,inserted
R6530 T23949 T23950 advmod Finally,inserted
R6531 T23951 T23950 punct ", ",inserted
R6532 T23952 T23950 nsubj we,inserted
R6533 T23953 T23954 det a,site
R6534 T23954 T23950 dobj site,inserted
R6535 T23955 T23954 compound loxP,site
R6536 T23956 T23954 cc and,site
R6537 T23957 T23958 compound NotI,site
R6538 T23958 T23954 conj site,site
R6539 T23959 T23960 nummod 336,bp
R6540 T23960 T23950 npadvmod bp,inserted
R6541 T23961 T23960 nummod 5,bp
R6542 T23962 T23960 punct ′,bp
R6543 T23963 T23960 prep of,bp
R6544 T23964 T23965 det the,start
R6545 T23965 T23963 pobj start,of
R6546 T23966 T23965 nmod Dmrt7,start
R6547 T23967 T23965 amod translational,start
R6548 T23968 T23950 punct .,inserted
R6549 T23970 T23971 prep In,flanked
R6550 T23972 T23973 det the,vector
R6551 T23973 T23970 pobj vector,In
R6552 T23974 T23973 amod resulting,vector
R6553 T23975 T23971 punct ", ",flanked
R6554 T23976 T23977 det the,exons
R6555 T23977 T23971 nsubjpass exons,flanked
R6556 T23978 T23977 amod second,exons
R6557 T23979 T23978 cc and,second
R6558 T23980 T23978 conj third,second
R6559 T23981 T23977 prep of,exons
R6560 T23982 T23981 pobj Dmrt7,of
R6561 T23983 T23971 auxpass are,flanked
R6562 T23984 T23971 agent by,flanked
R6563 T23985 T23986 compound loxP,sites
R6564 T23986 T23984 pobj sites,by
R6565 T23987 T23988 punct (,floxed
R6566 T23988 T23986 parataxis floxed,sites
R6567 T23989 T23988 punct ),floxed
R6568 T23990 T23971 punct .,flanked
R6569 T23992 T23993 det The,portions
R6570 T23993 T23997 nsubjpass portions,sequenced
R6571 T23994 T23995 npadvmod Dmrt7,containing
R6572 T23995 T23993 amod containing,portions
R6573 T23996 T23995 punct -,containing
R6574 T23998 T23993 prep of,portions
R6575 T23999 T23998 pobj pDZ169,of
R6576 T24000 T23997 auxpass were,sequenced
R6577 T24001 T23997 advmod completely,sequenced
R6578 T24002 T23997 punct .,sequenced

2_test

Id Subject Object Predicate Lexical cue
17447844-11040213-85805865 412-414 11040213 denotes 31
T5457 412-414 11040213 denotes 31

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
T23632 2-7 NCBITaxon:10088 denotes mouse
T23633 8-13 PR:000006549 denotes Dmrt7
T23634 54-58 SO:0000147 denotes exon
T23635 82-87 NCBITaxon:10088 denotes mouse
T23636 88-91 SO:0000153 denotes BAC
T23637 187-195 SO:0000167 denotes promoter
T23638 244-249 PR:000006549 denotes Dmrt7
T23639 250-257 SO:0001026 denotes genomic
T23640 272-288 SO:0001644 denotes targeting vector
T23641 367-373 SO:0000440 denotes vector
T23642 404-410 SO:0000440 denotes vector
T23643 439-448 SO:0000346 denotes loxP site
T23644 502-508 SO:0000188 denotes intron
T23645 512-517 PR:000006549 denotes Dmrt7
T23646 528-530 SO:0000028 denotes bp
T23647 540-542 SO:0000028 denotes bp
T23648 557-561 SO:0000147 denotes exon
T23649 658-660 SO:0000028 denotes bp
T23650 668-670 SO:0000028 denotes bp
T23651 681-686 PR:000006549 denotes Dmrt7
T23652 687-700 GO:0006412 denotes translational
T23653 731-740 SO:0000346 denotes loxP site
T23654 750-754 SO:0000061 denotes site
T23655 759-761 SO:0000028 denotes bp
T23656 772-777 PR:000006549 denotes Dmrt7
T23657 778-791 GO:0006412 denotes translational
T23658 816-822 SO:0000440 denotes vector
T23659 845-850 SO:0000147 denotes exons
T23660 854-859 PR:000006549 denotes Dmrt7
T23661 864-871 SO:0000357 denotes flanked
T23662 875-885 SO:0000346 denotes loxP sites
T23663 887-893 SO:0000359 denotes floxed
T23664 900-905 PR:000006549 denotes Dmrt7

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
T23703 404-410 SO_EXT:0000440 denotes vector
T23688 2-7 NCBITaxon:10088 denotes mouse
T23689 8-13 PR_EXT:000006549 denotes Dmrt7
T23690 14-18 SO_EXT:cDNA denotes cDNA
T23691 39-48 SO_EXT:biological_sequence denotes sequences
T23692 54-58 SO_EXT:0000147 denotes exon
T23693 82-87 NCBITaxon:10088 denotes mouse
T23694 88-91 SO_EXT:0000153 denotes BAC
T23695 169-175 SO_EXT:sequence_cloned_entity denotes clones
T23696 187-195 SO_EXT:0000167 denotes promoter
T23697 196-205 SO_EXT:biological_sequence denotes sequences
T23698 244-249 PR_EXT:000006549 denotes Dmrt7
T23699 250-257 SO_EXT:0001026 denotes genomic
T23700 258-266 SO_EXT:biological_sequence denotes sequence
T23701 272-288 SO_EXT:0001644 denotes targeting vector
T23702 367-373 SO_EXT:0000440 denotes vector
T23704 423-426 GO_EXT:phosphoglycerate_kinase denotes Pgk
T23705 427-430 CHEBI_GO_EXT:neomycin_or_neomycin_phosphotransferase denotes neo
T23706 439-448 SO_EXT:0000346 denotes loxP site
T23707 453-461 SO_EXT:sequence_insertion_process denotes inserted
T23708 478-481 CHEBI_SO_EXT:DNA denotes DNA
T23709 502-508 SO_EXT:0000188 denotes intron
T23710 512-517 PR_EXT:000006549 denotes Dmrt7
T23711 528-530 SO_EXT:0000028 denotes bp
T23712 540-542 SO_EXT:0000028 denotes bp
T23713 543-553 SO_EXT:sequence_downstreamness denotes downstream
T23714 557-561 SO_EXT:0000147 denotes exon
T23715 589-592 GO_EXT:phosphoglycerate_kinase denotes Pgk
T23716 593-596 CHEBI_GO_EXT:neomycin_or_neomycin_phosphotransferase denotes neo
T23717 601-609 SO_EXT:sequence_insertion_process denotes inserted
T23718 658-660 SO_EXT:0000028 denotes bp
T23719 668-670 SO_EXT:0000028 denotes bp
T23720 681-686 PR_EXT:000006549 denotes Dmrt7
T23721 687-706 GO_SO_EXT:translational_start_entity_or_process denotes translational start
T23722 720-728 SO_EXT:sequence_insertion_process denotes inserted
T23723 731-740 SO_EXT:0000346 denotes loxP site
T23724 750-754 SO_EXT:0000061 denotes site
T23725 759-761 SO_EXT:0000028 denotes bp
T23726 772-777 PR_EXT:000006549 denotes Dmrt7
T23727 778-797 GO_SO_EXT:translational_start_entity_or_process denotes translational start
T23728 816-822 SO_EXT:0000440 denotes vector
T23729 845-850 SO_EXT:0000147 denotes exons
T23730 854-859 PR_EXT:000006549 denotes Dmrt7
T23731 864-871 SO:0000357 denotes flanked
T23732 875-885 SO_EXT:0000346 denotes loxP sites
T23733 887-893 SO:0000359 denotes floxed
T23734 900-905 PR_EXT:000006549 denotes Dmrt7