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The Plant Promoter Database (PPDB) uses word frequency analysis to identify 8 base-pair motifs in promoters. Motifs are categorized as TATA-box, Y-patch (a CT-rich region often found in plant TATA box promoters), the initiator near the transcription start site, and cis-regulatory motifs. The regulatory motifs are a group of 308 8 base-pair sequences which are used to represent regulatory sites.
References (for PPDB):| PPDB_MPSS | The Plant Promoter Database (PPDB) also deposits the data of transcription start sites (TSSs) detected by the CT-MPSS method. The CT-MPSS method is a combination of cap trapper (CT), a reliable method for preparing the 5' end of full-length cDNA, and massively parallel signature sequencing (MPSS), which enables ultra-parallel sequencing in a considerably shorter time and at lower cost than conventional sequencing methods. |
| PPDB_reliable_LDSS | The Plant Promoter Database (PPDB) uses word frequency analysis to identify 8 base-pair motifs in promoters. Motifs are categorized as TATA-box, Y-patch (a CT-rich region often found in plant TATA box promoters), the initiator near the transcription start site, and cis-regulatory motifs. The regulatory motifs are a group of 308 8 base-pair sequences which are used to represent regulatory sites. |
We would like to thank Dr. Yoshiharu Yamamoto for supplying the data of PPDB (Plant Promoter Database) for PromoterCAD & GenoCon2 competition.
License of this work's data is according to the intentions of the PPDB original data source.
http://ppdb.agr.gifu-u.ac.jp/ppdb/cgi-bin/license.cgi
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| #LINK | ||||||||
| #lang | en | |||||||
| #attribution_name | GenoCon | |||||||
| #attribution_url | http://ppdb.agr.gifu-u.ac.jp/ppdb/cgi-bin/index.cgi | |||||||
| #file_name | PPDB_reliable_LDSS | |||||||
| #download_from | http://linkdata.org/work/rdf1s459i | |||||||
| #property | genome version | motif type | start | end | score | strand | phase | attributes |
| #object_type_xsd | string | string | integer | integer | string | string | string | string |
| #property_context | Assertion | Assertion | Assertion | Assertion | Assertion | Assertion | Assertion | Assertion |
| 1 | tair9 | REG | 3455 | 3462 | . | + | . | LDSS_id " At514 " ;LDSS_seq " TAAACCGA " ;Sequence " AT1G01010.1 " |
| 1 | tair9 | REG | 3456 | 3463 | . | + | . | LDSS_id " At519 " ;LDSS_seq " CGGTTTAC " ;Sequence " AT1G01010.1 " |
| 1 | tair9 | REG | 3535 | 3542 | . | + | . | LDSS_id " At473 " ;LDSS_seq " CGGTTTAA " ;Sequence " AT1G01010.1 " |
| 1 | tair9 | REG | 3536 | 3543 | . | + | . | LDSS_id " At412 " ;LDSS_seq " CCGGTTTA " ;Sequence " AT1G01010.1 " |
| 1 | tair9 | REG | 3537 | 3544 | . | + | . | LDSS_id " At521 " ;LDSS_seq " AAACCGGA " ;Sequence " AT1G01010.1 " |
| 1 | tair9 | REG | 3601 | 3608 | . | + | . | LDSS_id " At626 " ;LDSS_seq " AAACGCTG " ;Sequence " AT1G01010.1 " |
| 1 | tair9 | Y | 3619 | 3626 | . | + | . | LDSS_id " At708 " ;LDSS_seq " CTTCCTCC " ;Sequence " AT1G01010.1 " |
| 1 | tair9 | Y | 3622 | 3629 | . | + | . | LDSS_id " At121 " ;LDSS_seq " CCTCCCTC " ;Sequence " AT1G01010.1 " |
| 1 | tair9 | Y | 3623 | 3630 | . | + | . | LDSS_id " At050 " ;LDSS_seq " CTCCCTCC " ;Sequence " AT1G01010.1 " |
| 1 | tair9 | GA | 3697 | 3704 | . | + | . | LDSS_id " At723 " ;LDSS_seq " CGAGAGAG " ;Sequence " AT1G01010.1 " |
| 1 | tair9 | GA | 3698 | 3705 | . | + | . | LDSS_id " At728 " ;LDSS_seq " GAGAGAGA " ;Sequence " AT1G01010.1 " |
| 1 | tair9 | GA | 3699 | 3706 | . | + | . | LDSS_id " At722 " ;LDSS_seq " AGAGAGAT " ;Sequence " AT1G01010.1 " |
| 1 | tair9 | Y | 33100 | 33093 | . | - | . | LDSS_id " At033 " ;LDSS_seq " TCTCTCCC " ;Sequence " AT1G01050.1 " |
| 1 | tair9 | Y | 33101 | 33094 | . | - | . | LDSS_id " At026 " ;LDSS_seq " TTCTCTCC " ;Sequence " AT1G01050.1 " |
| 1 | tair9 | Y | 33102 | 33095 | . | - | . | LDSS_id " At006 " ;LDSS_seq " TTTCTCTC " ;Sequence " AT1G01050.1 " |
| 1 | tair9 | TATA | 33147 | 33140 | . | - | . | LDSS_id " At180 " ;LDSS_seq " TATATACA " ;Sequence " AT1G01050.1 " |
| 1 | tair9 | TATA | 33148 | 33141 | . | - | . | LDSS_id " At207 " ;LDSS_seq " ATATATAC " ;Sequence " AT1G01050.1 " |
| 1 | tair9 | TATA | 33149 | 33142 | . | - | . | LDSS_id " At261 " ;LDSS_seq " CATATATA " ;Sequence " AT1G01050.1 " |
| 1 | tair9 | TATA | 33150 | 33143 | . | - | . | LDSS_id " At290 " ;LDSS_seq " TCATATAT " ;Sequence " AT1G01050.1 " |
| 1 | tair9 | Y | 37743 | 37736 | . | - | . | LDSS_id " At063 " ;LDSS_seq " TCTTCTTC " ;Sequence " AT1G01060.1,AT1G01060.2,AT1G01060.3,AT1G01060.4 " |
| 1 | tair9 | Y | 37744 | 37737 | . | - | . | LDSS_id " At073 " ;LDSS_seq " TTCTTCTT " ;Sequence " AT1G01060.1,AT1G01060.2,AT1G01060.3,AT1G01060.4 " |
| 1 | tair9 | Y | 37745 | 37738 | . | - | . | LDSS_id " At051 " ;LDSS_seq " CTTCTTCT " ;Sequence " AT1G01060.1,AT1G01060.2,AT1G01060.3,AT1G01060.4 " |
| 1 | tair9 | Y | 37746 | 37739 | . | - | . | LDSS_id " At063 " ;LDSS_seq " TCTTCTTC " ;Sequence " AT1G01060.1,AT1G01060.2,AT1G01060.3,AT1G01060.4 " |
| 1 | tair9 | Y | 37747 | 37740 | . | - | . | LDSS_id " At073 " ;LDSS_seq " TTCTTCTT " ;Sequence " AT1G01060.1,AT1G01060.2,AT1G01060.3,AT1G01060.4 " |
| 1 | tair9 | Y | 37748 | 37741 | . | - | . | LDSS_id " At051 " ;LDSS_seq " CTTCTTCT " ;Sequence " AT1G01060.1,AT1G01060.2,AT1G01060.3,AT1G01060.4 " |
| 1 | tair9 | Y | 37749 | 37742 | . | - | . | LDSS_id " At063 " ;LDSS_seq " TCTTCTTC " ;Sequence " AT1G01060.1,AT1G01060.2,AT1G01060.3,AT1G01060.4 " |
| 1 | tair9 | Y | 37750 | 37743 | . | - | . | LDSS_id " At073 " ;LDSS_seq " TTCTTCTT " ;Sequence " AT1G01060.1,AT1G01060.2,AT1G01060.3,AT1G01060.4 " |
| 1 | tair9 | Y | 37751 | 37744 | . | - | . | LDSS_id " At051 " ;LDSS_seq " CTTCTTCT " ;Sequence " AT1G01060.1,AT1G01060.2,AT1G01060.3,AT1G01060.4 " |
| 1 | tair9 | Y | 37752 | 37745 | . | - | . | LDSS_id " At063 " ;LDSS_seq " TCTTCTTC " ;Sequence " AT1G01060.1,AT1G01060.2,AT1G01060.3,AT1G01060.4 " |
| 1 | tair9 | Y | 37753 | 37746 | . | - | . | LDSS_id " At073 " ;LDSS_seq " TTCTTCTT " ;Sequence " AT1G01060.1,AT1G01060.2,AT1G01060.3,AT1G01060.4 " |
| 1 | tair9 | Y | 37754 | 37747 | . | - | . | LDSS_id " At051 " ;LDSS_seq " CTTCTTCT " ;Sequence " AT1G01060.1,AT1G01060.2,AT1G01060.3,AT1G01060.4 " |
| 1 | tair9 | Y | 37755 | 37748 | . | - | . | LDSS_id " At063 " ;LDSS_seq " TCTTCTTC " ;Sequence " AT1G01060.1,AT1G01060.2,AT1G01060.3,AT1G01060.4 " |
| 1 | tair9 | Y | 37756 | 37749 | . | - | . | LDSS_id " At073 " ;LDSS_seq " TTCTTCTT " ;Sequence " AT1G01060.1,AT1G01060.2,AT1G01060.3,AT1G01060.4 " |
| 1 | tair9 | Y | 37757 | 37750 | . | - | . | LDSS_id " At051 " ;LDSS_seq " CTTCTTCT " ;Sequence " AT1G01060.1,AT1G01060.2,AT1G01060.3,AT1G01060.4 " |
| 1 | tair9 | Y | 37758 | 37751 | . | - | . | LDSS_id " At063 " ;LDSS_seq " TCTTCTTC " ;Sequence " AT1G01060.1,AT1G01060.2,AT1G01060.3,AT1G01060.4 " |
| 1 | tair9 | Y | 37759 | 37752 | . | - | . | LDSS_id " At073 " ;LDSS_seq " TTCTTCTT " ;Sequence " AT1G01060.1,AT1G01060.2,AT1G01060.3,AT1G01060.4 " |
| 1 | tair9 | Y | 37760 | 37753 | . | - | . | LDSS_id " At051 " ;LDSS_seq " CTTCTTCT " ;Sequence " AT1G01060.1,AT1G01060.2,AT1G01060.3,AT1G01060.4 " |
| 1 | tair9 | Y | 37761 | 37754 | . | - | . | LDSS_id " At063 " ;LDSS_seq " TCTTCTTC " ;Sequence " AT1G01060.1,AT1G01060.2,AT1G01060.3,AT1G01060.4 " |
| 1 | tair9 | Y | 37762 | 37755 | . | - | . | LDSS_id " At073 " ;LDSS_seq " TTCTTCTT " ;Sequence " AT1G01060.1,AT1G01060.2,AT1G01060.3,AT1G01060.4 " |
| 1 | tair9 | Y | 37763 | 37756 | . | - | . | LDSS_id " At051 " ;LDSS_seq " CTTCTTCT " ;Sequence " AT1G01060.1,AT1G01060.2,AT1G01060.3,AT1G01060.4 " |
| 1 | tair9 | Y | 37764 | 37757 | . | - | . | LDSS_id " At063 " ;LDSS_seq " TCTTCTTC " ;Sequence " AT1G01060.1,AT1G01060.2,AT1G01060.3,AT1G01060.4 " |
| 1 | tair9 | Y | 37765 | 37758 | . | - | . | LDSS_id " At073 " ;LDSS_seq " TTCTTCTT " ;Sequence " AT1G01060.1,AT1G01060.2,AT1G01060.3,AT1G01060.4 " |
| 1 | tair9 | Y | 37766 | 37759 | . | - | . | LDSS_id " At051 " ;LDSS_seq " CTTCTTCT " ;Sequence " AT1G01060.1,AT1G01060.2,AT1G01060.3,AT1G01060.4 " |
| 1 | tair9 | Y | 37767 | 37760 | . | - | . | LDSS_id " At063 " ;LDSS_seq " TCTTCTTC " ;Sequence " AT1G01060.1,AT1G01060.2,AT1G01060.3,AT1G01060.4 " |
| 1 | tair9 | Y | 37768 | 37761 | . | - | . | LDSS_id " At073 " ;LDSS_seq " TTCTTCTT " ;Sequence " AT1G01060.1,AT1G01060.2,AT1G01060.3,AT1G01060.4 " |
| 1 | tair9 | Y | 37769 | 37762 | . | - | . | LDSS_id " At051 " ;LDSS_seq " CTTCTTCT " ;Sequence " AT1G01060.1,AT1G01060.2,AT1G01060.3,AT1G01060.4 " |
| 1 | tair9 | Y | 37770 | 37763 | . | - | . | LDSS_id " At063 " ;LDSS_seq " TCTTCTTC " ;Sequence " AT1G01060.1,AT1G01060.2,AT1G01060.3,AT1G01060.4 " |
| 1 | tair9 | Y | 37771 | 37764 | . | - | . | LDSS_id " At073 " ;LDSS_seq " TTCTTCTT " ;Sequence " AT1G01060.1,AT1G01060.2,AT1G01060.3,AT1G01060.4 " |
| 1 | tair9 | Y | 37772 | 37765 | . | - | . | LDSS_id " At051 " ;LDSS_seq " CTTCTTCT " ;Sequence " AT1G01060.1,AT1G01060.2,AT1G01060.3,AT1G01060.4 " |
| 1 | tair9 | Y | 37773 | 37766 | . | - | . | LDSS_id " At066 " ;LDSS_seq " CCTTCTTC " ;Sequence " AT1G01060.1,AT1G01060.2,AT1G01060.3,AT1G01060.4 " |
| 1 | tair9 | Y | 37774 | 37767 | . | - | . | LDSS_id " At713 " ;LDSS_seq " TCCTTCTT " ;Sequence " AT1G01060.1,AT1G01060.2,AT1G01060.3,AT1G01060.4 " |
| 1 | tair9 | Y | 37775 | 37768 | . | - | . | LDSS_id " At085 " ;LDSS_seq " TTCCTTCT " ;Sequence " AT1G01060.1,AT1G01060.2,AT1G01060.3,AT1G01060.4 " |
| 1 | tair9 | Y | 37776 | 37769 | . | - | . | LDSS_id " At088 " ;LDSS_seq " CTTCCTTC " ;Sequence " AT1G01060.1,AT1G01060.2,AT1G01060.3,AT1G01060.4 " |
| 1 | tair9 | Y | 37777 | 37770 | . | - | . | LDSS_id " At715 " ;LDSS_seq " TCTTCCTT " ;Sequence " AT1G01060.1,AT1G01060.2,AT1G01060.3,AT1G01060.4 " |
| 1 | tair9 | Y | 37797 | 37790 | . | - | . | LDSS_id " At063 " ;LDSS_seq " TCTTCTTC " ;Sequence " AT1G01060.1,AT1G01060.2,AT1G01060.3,AT1G01060.4 " |
| 1 | tair9 | Y | 37807 | 37800 | . | - | . | LDSS_id " At042 " ;LDSS_seq " CTTCTTCC " ;Sequence " AT1G01060.1,AT1G01060.2,AT1G01060.3,AT1G01060.4 " |
| 1 | tair9 | Y | 37808 | 37801 | . | - | . | LDSS_id " At063 " ;LDSS_seq " TCTTCTTC " ;Sequence " AT1G01060.1,AT1G01060.2,AT1G01060.3,AT1G01060.4 " |
| 1 | tair9 | Y | 37809 | 37802 | . | - | . | LDSS_id " At073 " ;LDSS_seq " TTCTTCTT " ;Sequence " AT1G01060.1,AT1G01060.2,AT1G01060.3,AT1G01060.4 " |
| 1 | tair9 | Y | 37810 | 37803 | . | - | . | LDSS_id " At051 " ;LDSS_seq " CTTCTTCT " ;Sequence " AT1G01060.1,AT1G01060.2,AT1G01060.3,AT1G01060.4 " |
| 1 | tair9 | Y | 37811 | 37804 | . | - | . | LDSS_id " At063 " ;LDSS_seq " TCTTCTTC " ;Sequence " AT1G01060.1,AT1G01060.2,AT1G01060.3,AT1G01060.4 " |
| 1 | tair9 | Y | 37812 | 37805 | . | - | . | LDSS_id " At073 " ;LDSS_seq " TTCTTCTT " ;Sequence " AT1G01060.1,AT1G01060.2,AT1G01060.3,AT1G01060.4 " |
| 1 | tair9 | Y | 37813 | 37806 | . | - | . | LDSS_id " At051 " ;LDSS_seq " CTTCTTCT " ;Sequence " AT1G01060.1,AT1G01060.2,AT1G01060.3,AT1G01060.4 " |
| 1 | tair9 | Y | 37814 | 37807 | . | - | . | LDSS_id " At063 " ;LDSS_seq " TCTTCTTC " ;Sequence " AT1G01060.1,AT1G01060.2,AT1G01060.3,AT1G01060.4 " |
| 1 | tair9 | Y | 37815 | 37808 | . | - | . | LDSS_id " At075 " ;LDSS_seq " CTCTTCTT " ;Sequence " AT1G01060.1,AT1G01060.2,AT1G01060.3,AT1G01060.4 " |
| 1 | tair9 | Y | 37816 | 37809 | . | - | . | LDSS_id " At083 " ;LDSS_seq " TCTCTTCT " ;Sequence " AT1G01060.1,AT1G01060.2,AT1G01060.3,AT1G01060.4 " |
| 1 | tair9 | Y | 37817 | 37810 | . | - | . | LDSS_id " At040 " ;LDSS_seq " TTCTCTTC " ;Sequence " AT1G01060.1,AT1G01060.2,AT1G01060.3,AT1G01060.4 " |
| 1 | tair9 | Y | 37818 | 37811 | . | - | . | LDSS_id " At009 " ;LDSS_seq " CTTCTCTT " ;Sequence " AT1G01060.1,AT1G01060.2,AT1G01060.3,AT1G01060.4 " |
| 1 | tair9 | REG | 37913 | 37906 | . | - | . | LDSS_id " At623 " ;LDSS_seq " AAGGGTAT " ;Sequence " AT1G01060.1,AT1G01060.2,AT1G01060.3,AT1G01060.4 " |
| 1 | tair9 | REG | 37950 | 37943 | . | - | . | LDSS_id " At478 " ;LDSS_seq " ACGTGTCG " ;Sequence " AT1G01060.1,AT1G01060.2,AT1G01060.3,AT1G01060.4 " |
| 1 | tair9 | REG | 37951 | 37944 | . | - | . | LDSS_id " At366 " ;LDSS_seq " CACGTGTC " ;Sequence " AT1G01060.1,AT1G01060.2,AT1G01060.3,AT1G01060.4 " |
| 1 | tair9 | REG | 37952 | 37945 | . | - | . | LDSS_id " At382 " ;LDSS_seq " ACACGTGG " ;Sequence " AT1G01060.1,AT1G01060.2,AT1G01060.3,AT1G01060.4 " |
| 1 | tair9 | REG | 37953 | 37946 | . | - | . | LDSS_id " At544 " ;LDSS_seq " ACCACGTG " ;Sequence " AT1G01060.1,AT1G01060.2,AT1G01060.3,AT1G01060.4 " |
| 1 | tair9 | GA | 40884 | 40877 | . | - | . | LDSS_id " At730 " ;LDSS_seq " GAGAGATA " ;Sequence " AT1G01070.2 " |
| 1 | tair9 | GA | 40885 | 40878 | . | - | . | LDSS_id " At722 " ;LDSS_seq " AGAGAGAT " ;Sequence " AT1G01070.2 " |
| 1 | tair9 | GA | 40886 | 40879 | . | - | . | LDSS_id " At728 " ;LDSS_seq " GAGAGAGA " ;Sequence " AT1G01070.2 " |
| 1 | tair9 | GA | 40887 | 40880 | . | - | . | LDSS_id " At721 " ;LDSS_seq " AGAGAGAG " ;Sequence " AT1G01070.2 " |
| 1 | tair9 | GA | 40888 | 40881 | . | - | . | LDSS_id " At731 " ;LDSS_seq " TAGAGAGA " ;Sequence " AT1G01070.2 " |
| 1 | tair9 | TATA | 40891 | 40884 | . | - | . | LDSS_id " At153 " ;LDSS_seq " ATATAGAG " ;Sequence " AT1G01070.2 " |
| 1 | tair9 | REG | 40933 | 40926 | . | - | . | LDSS_id " At462 " ;LDSS_seq " ATAAGCCC " ;Sequence " AT1G01070.2 " |
| 1 | tair9 | Y | 46825 | 46818 | . | - | . | LDSS_id " At005 " ;LDSS_seq " TTCTTCTC " ;Sequence " AT1G01080.1,AT1G01080.2 " |
| 1 | tair9 | REG | 46877 | 46870 | . | - | . | LDSS_id " At375 " ;LDSS_seq " CCGACCCG " ;Sequence " AT1G01080.1,AT1G01080.2 " |
| 1 | tair9 | REG | 46878 | 46871 | . | - | . | LDSS_id " At442 " ;LDSS_seq " CCCGACCC " ;Sequence " AT1G01080.1,AT1G01080.2 " |
| 1 | tair9 | REG | 46879 | 46872 | . | - | . | LDSS_id " At405 " ;LDSS_seq " ACCCGACC " ;Sequence " AT1G01080.1,AT1G01080.2 " |
| 1 | tair9 | REG | 46880 | 46873 | . | - | . | LDSS_id " At390 " ;LDSS_seq " GACCCGAC " ;Sequence " AT1G01080.1,AT1G01080.2 " |
| 1 | tair9 | REG | 46881 | 46874 | . | - | . | LDSS_id " At617 " ;LDSS_seq " TCGGGTCA " ;Sequence " AT1G01080.1,AT1G01080.2 " |
| 1 | tair9 | REG | 46978 | 46971 | . | - | . | LDSS_id " At459 " ;LDSS_seq " AAAAGGCC " ;Sequence " AT1G01080.1,AT1G01080.2 " |
| 1 | tair9 | REG | 46979 | 46972 | . | - | . | LDSS_id " At359 " ;LDSS_seq " AAAGGCCC " ;Sequence " AT1G01080.1,AT1G01080.2 " |
| 1 | tair9 | REG | 46980 | 46973 | . | - | . | LDSS_id " At353 " ;LDSS_seq " AAGGCCCA " ;Sequence " AT1G01080.1,AT1G01080.2 " |
| 1 | tair9 | REG | 46981 | 46974 | . | - | . | LDSS_id " At356 " ;LDSS_seq " AGGCCCAA " ;Sequence " AT1G01080.1,AT1G01080.2 " |
| 1 | tair9 | REG | 46982 | 46975 | . | - | . | LDSS_id " At373 " ;LDSS_seq " GGCCCAAA " ;Sequence " AT1G01080.1,AT1G01080.2 " |
| 1 | tair9 | REG | 47119 | 47112 | . | - | . | LDSS_id " At437 " ;LDSS_seq " ATGGCCCA " ;Sequence " AT1G01080.1,AT1G01080.2 " |
Koro_Nishikata
Robert Cox
