Schema for CORE Promoters - Promoters Annotated by the CORE Database |
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Database: dm6 Primary Table: coreNechaev Data last updated: 2018-02-19
Big Bed File: /gbdb/dm6/bbi/coreNechaev.bb
Item Count: 7,428
Format description: CORE annotations for RNA-Seq-defined TSSs from Nechaev et al.
| field | example | description |
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| chrom | chr2L | Reference sequence chromosome or scaffold | | chromStart | 15746558 | Start position in chromosome | | chromEnd | 15746659 | End position in chromosome | | name | CG3938-RD_1 | Short Name of item | | score | 0 | Score from 0-1000 | | strand | - | + or - | | BREu | no | BREu motifs | | TATA | no | TATA Box motifs | | BREd | no | BREd motifs | | dInr | -2,0.0172; | Inr motifs | | DPE | -2,0.0160; | DPE motifs | | MTE | no | MTE motifs | | Bridge | -2,0.0134; | BREu motifs | | dTCT | no | TCT motifs |
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Sample Rows
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| chrom | chromStart | chromEnd | name | score | strand | BREu | TATA | BREd | dInr | DPE | MTE | Bridge | dTCT |
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| chr2L | 15746558 | 15746659 | CG3938-RD_1 | 0 | - | no | no | no | -2,0.0172; | -2,0.0160; | no | -2,0.0134; | no |
| chr2L | 15748072 | 15748173 | CG3938-RE_1 | 0 | - | no | no | no | 1,0.0446; | no | no | no | no |
| chr2L | 15751020 | 15751121 | CG13240-RB_1 | 0 | - | no | no | no | no | no | no | no | no |
| chr2L | 15752224 | 15752325 | CG4152-RA_1 | 0 | + | no | no | no | no | no | no | no | no |
| chr2L | 15762704 | 15762805 | CG3903-RA_1 | 0 | - | no | no | no | -2,0.9401; | -2,0.1397; | -2,0.0142; | -2,0.0308; | no |
| chr2L | 15764172 | 15764273 | CG3793-RA_1 | 0 | + | no | no | no | no | no | no | no | no |
| chr2L | 15768237 | 15768338 | CG4148-RA_1 | 0 | - | no | no | no | -2,0.2101; | no | no | no | no |
| chr2L | 15923334 | 15923435 | CG4793-RD_1 | 0 | + | no | no | no | -2,0.0446; | -2,0.0964; | no | -2,0.0135; | no |
| chr2L | 16251722 | 16251823 | CG4993-RA_1 | 0 | - | no | no | no | -2,0.1342; | no | no | no | no |
| chr2L | 16257534 | 16257635 | CG4993-RB_1 | 0 | - | no | -26,0.0204; | no | no | no | no | no | no |
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CORE Promoters (CORE) Track Description
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Description
These tracks show the Drosophila promoter annotations from the CORE database. The TSS annotations in the CORE database were based on CAGE data (Hoskins RA et al., 2011) or RNA-Seq data (Nechaev S et al., 2010). The core promoter motifs associated with each TSS were identified by the ElemeNT program.
For the CAGE TSSs track, the color of the feature corresponds to the shape of the promoter:
| Promoter Shape | Color |
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| Peaked | |
| Broad | |
| Unclassified | |
References
Sloutskin A, Danino YM, Orenstein Y, Zehavi Y, Doniger T, Shamir R, Juven-Gershon T.
ElemeNT: a computational tool for detecting core promoter elements. Transcription. 2015;6(3):41-50.
Hoskins RA, Landolin JM, Brown JB, Sandler JE, Takahashi H, Lassmann T, Yu C, Booth BW, Zhang D, Wan KH, Yang L, Boley N, Andrews J, Kaufman TC, Graveley BR, Bickel PJ, Carninci P, Carlson JW, Celniker SE. Genome-wide analysis of promoter architecture in Drosophila melanogaster. Genome Res. 2011 Feb;21(2):182-92.
Nechaev S, Fargo DC, dos Santos G, Liu L, Gao Y, Adelman K.
Global analysis of short RNAs reveals widespread promoter-proximal stalling and arrest of Pol II in Drosophila. Science. 2010 Jan 15;327(5963):335-8.
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