PlantDeepSEA

Predicting Regulatory Effect of Genomic Variants

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Task ID : 2847_16177604444503944

Mission Info :

Model: trained based on ATAC-seq data from mutiple tissues of the Rice (Oryza sativa L) variety Minghui 63 (with reference genome version RS2)

Input: sequence based on Minghui 63 reference genome version RS2

Task: perform "in silico saturated mutagenesis" analysis for the middle 200-bp of the input sequence

Position :

Chromosome : chr09

Start : 17599129

End : 17599329

Download the predicted results:

chr09_17599129_17599329_16177604444503944.zip

Results:

You can download the predicted results on this page or select one of the sample you would like to display:


The currently selected model was trained using the data "ATAC-seq, flag leaf, rep1". The distribution of the prediction scores for 744 sequences labeled as open chromatin regions (OCRs) in the test set is shown below. The prediction score (0.95) of the submitted sequence "chr09:17599129-17599329" is at the 93.7% quantile of this distribution, as shown by the red line.


Sequence used for prediction

The bases shown in the 'in silico saturation mutagenesis map' section are highlighted (with line width: 100 bp).

ACACAGCTAAAATGAATCGCATATGCAGTGAATGAGACTCTGAGAGCCCAGTTTAAGGTAGGAGTAGCATCAAATTCACTAGTCCTATACACCGGCACGT

CGTCGCAGTGCAATTTTATACGATCTTCATGTGTGCATCAGTGCATGCTGTTTGCAGAAGGGAAGTTGGCCGCCTGCCCGTGCTGAGCTCAACTGAACGC

TGGCTGCCTGCATGGCCAGTTCGTGACTACAGTTACTACGCATACTACCCGGGGTAGCAGCGGCGCGCTATCAGCTCTACCCGGAGTAGGCAGTAGCAGC

AGTGGTGGTAGTAGTAGAAAGCGCGGCAGTGGAAGGGATAGAGGAGTGCCCACATTAATAACTCGTTTCAAATCGGACGGCGTGGCTACTCTAGTACACC

CATTTCAACGGGCCGTTCCACTCCACTCCACCGTAACTGCGCGCGTGGGGCGACCCCATCACGTGCCACGGTACGGGGGCGTCGCTGACCGTCTCTGGCC

CACCGCAACCCTGCTCCCCCAATCCAAACCCCGCGCTGCACGTCTCGCTGGCACTGGCCATTTCGATCCATCGCGGTCGCGGCCGCGGTATCACGACTGA

CGCGCGGGGCCGGCCCGGCACGCGAGACCGATGTAGACGTGTCACCGGGGAAGCTTGTCCGCTCGCGGTTGCCGCTGCGCGGGGGGGAGGGGAGGGCGTC

GAGCCGTACGTCGTCGTCGCATACCTCGGTCGCGTCCCTGTCAAAGCCGGCCATCGCTGCCGGCTGCTCAATTTATTCCCTTGCTGTTTCATTTCGTACG

TAGTCCGCGCTCGGGATGCGGCCATAGCCATATCGCCATATATCTCGGGCAGGCACCGTCACGCTCGCTCGGCAACTGTACGTGCCGTCTCAGGACGCGG

CAGTCAATGCGGAGTTGGTACAAACTTGCGATGAAAGGAGTGGTACTGTGGTACCACCACTGCCCTGTCTTTGCACACATCAGTCTTCCCGGAGTTTAGC


in silico saturated mutagenesis map

In the heatmap, each row represents mutations in the corresponding nucleotide, each column represents a position in the sequence. The color of the heatmap presents the predicted change in probability that an allele belongs to open chromatin. The loss score refers to the maximum decrease in probability that an allele belongs to open chromatin compared to the reference nucleotide in all mutations at each site. And the gain score refers to the maximum increase.

Tip: You can drag the graph to view information about other positions.


Regulatory elements identified by FIMO

Detailed Fimo results and the parameters used can be viewed at fimo.html.

For the motifs identified by FIMO (with the P-value < 1e-4), we calculated the average loss and gain values in the in silico saturated mutagenesis map corresponding to the motif regions, which are listed in the table below as 'Loss value' and 'Gain value', respectively.

Motif IDNameStartEndStrandp-valueq-valueMatched SequenceLoss valueGain value
MP00534 AT5G38860 449 466 + 2.13e-06 5.81e-04 GCGACCCCATCACGTGCC 1.13e-02 3.45e-03
MP00594 AT5G67000 573 587 + 1.04e-05 3.07e-03 CGGTCGCGGCCGCGG 5.76e-03 5.85e-03
MA1261.1 AT5G67000 573 587 + 1.04e-05 3.07e-03 CGGTCGCGGCCGCGG 5.76e-03 5.85e-03
MP00078 AT3G22170 437 448 - 1.16e-05 3.63e-03 CCCACGCGCGCA 9.72e-03 1.16e-03
MA0557.1 FHY3 437 448 - 1.16e-05 3.63e-03 CCCACGCGCGCA 9.72e-03 1.16e-03
MA1011.1 PHYPADRAFT_72483 457 466 + 1.22e-05 2.30e-03 ATCACGTGCC 6.18e-03 2.99e-03
MA1011.1 PHYPADRAFT_72483 457 466 - 1.22e-05 2.30e-03 GGCACGTGAT 6.18e-03 2.99e-03
MP00102 AT4G14410 457 466 + 1.41e-05 2.15e-03 ATCACGTGCC 6.18e-03 2.99e-03
MP00102 AT4G14410 457 466 - 1.41e-05 2.15e-03 GGCACGTGAT 6.18e-03 2.99e-03
MA0960.1 BHLH104 457 466 + 1.41e-05 2.15e-03 ATCACGTGCC 6.18e-03 2.99e-03
MA0960.1 BHLH104 457 466 - 1.41e-05 2.15e-03 GGCACGTGAT 6.18e-03 2.99e-03
MA0966.1 BIM3 457 466 + 1.41e-05 2.67e-03 ATCACGTGCC 6.18e-03 2.99e-03
MA0966.1 BIM3 457 466 - 1.41e-05 2.67e-03 GGCACGTGAT 6.18e-03 2.99e-03
MP00106 AT2G18300 457 468 - 1.41e-05 4.06e-03 GTGGCACGTGAT 6.37e-03 2.65e-03
MA1025.1 HBI1 457 468 - 1.41e-05 4.06e-03 GTGGCACGTGAT 6.37e-03 2.65e-03
MA0965.1 BIM2 457 466 + 1.55e-05 2.95e-03 ATCACGTGCC 6.18e-03 2.99e-03
MA0965.1 BIM2 457 466 - 1.55e-05 2.95e-03 GGCACGTGAT 6.18e-03 2.99e-03
MA0964.1 BIM1 456 465 - 1.91e-05 4.22e-03 GCACGTGATG 8.08e-03 2.72e-03
MA0561.1 PIF4 459 466 + 1.98e-05 5.54e-03 CACGTGCC 5.16e-03 2.22e-03
MP00594 AT5G67000 424 438 - 1.99e-05 3.07e-03 CAGTTACGGTGGAGT 5.45e-03 1.18e-03
MA1261.1 AT5G67000 424 438 - 1.99e-05 3.07e-03 CAGTTACGGTGGAGT 5.45e-03 1.18e-03
MP00660 Pp3c6_9520 458 465 + 2.20e-05 6.80e-03 TCACGTGC 7.93e-03 1.87e-03
MA1021.1 PHYPADRAFT_48267 458 465 + 2.20e-05 6.81e-03 TCACGTGC 7.93e-03 1.87e-03
MP00434 AT4G15090 436 450 - 2.20e-05 6.19e-03 GCCCCACGCGCGCAG 1.01e-02 2.23e-03
MA1382.1 FAR1 436 450 - 2.20e-05 6.19e-03 GCCCCACGCGCGCAG 1.01e-02 2.23e-03
MP00606 AT2G43010 458 466 + 2.25e-05 6.67e-03 TCACGTGCC 6.95e-03 1.94e-03
MP00081 AT1G09530 458 467 - 2.30e-05 7.03e-03 TGGCACGTGA 6.90e-03 1.97e-03
MA0560.1 PIF3 458 467 - 2.30e-05 6.98e-03 TGGCACGTGA 6.90e-03 1.97e-03
MP00082 AT3G59060 458 465 + 2.41e-05 7.42e-03 TCACGTGC 7.93e-03 1.87e-03
MA0562.1 PIF5 458 465 + 2.41e-05 7.42e-03 TCACGTGC 7.93e-03 1.87e-03
MA0964.1 BIM1 458 467 + 2.42e-05 4.22e-03 TCACGTGCCA 6.90e-03 1.97e-03
MA1065.1 TCP20 495 504 + 2.67e-05 6.90e-03 TGGCCCACCG 2.27e-02 0.00e+00
MP00675 GRMZM2G017087 529 548 + 2.84e-05 2.79e-03 CCCGCGCTGCACGTCTCGCT 8.68e-03 2.39e-03
MA0962.1 BHLH34 440 447 + 3.01e-05 8.96e-03 GCGCGTGG 1.18e-02 9.10e-04
MP00542 AT5G44210 424 444 - 3.32e-05 1.08e-02 CGCGCGCAGTTACGGTGGAGT 5.53e-03 1.46e-03
MA1257.1 ERF9 424 444 - 3.32e-05 1.08e-02 CGCGCGCAGTTACGGTGGAGT 5.53e-03 1.46e-03
MP00135 AT1G10120 450 470 + 3.53e-05 9.64e-03 CGACCCCATCACGTGCCACGG 1.12e-02 2.86e-03
MA1360.1 bHLH74 450 470 + 3.53e-05 9.64e-03 CGACCCCATCACGTGCCACGG 1.12e-02 2.86e-03
MP00526 AT5G25190 423 441 - 3.84e-05 1.14e-02 GCGCAGTTACGGTGGAGTG 4.67e-03 1.62e-03
MA1236.1 ESE3 423 441 - 3.84e-05 1.14e-02 GCGCAGTTACGGTGGAGTG 4.67e-03 1.62e-03
MP00073 AT1G19350 439 449 + 3.89e-05 1.01e-02 CGCGCGTGGGG 1.21e-02 2.15e-03
MA0549.1 BZR2 439 449 + 3.89e-05 1.01e-02 CGCGCGTGGGG 1.21e-02 2.15e-03
MP00498 AT5G08130 459 472 + 4.17e-05 1.06e-02 CACGTGCCACGGTA 6.02e-03 1.84e-03
MP00534 AT5G38860 457 474 - 4.24e-05 5.78e-03 CGTACCGTGGCACGTGAT 7.06e-03 2.09e-03
MP00581 AT5G63090 566 586 + 4.26e-05 1.17e-02 TCCATCGCGGTCGCGGCCGCG 7.82e-03 5.36e-03
MP00664 Potri.002G002400 469 475 + 4.39e-05 1.20e-02 GGTACGG 5.56e-03 2.34e-03
MA0955.1 POPTR_0002s00440g 469 475 + 4.39e-05 1.22e-02 GGTACGG 5.56e-03 2.34e-03
MP00034 AT4G00050 458 465 + 4.61e-05 1.32e-02 TCACGTGC 7.93e-03 1.87e-03
MA1074.1 UNE10 458 465 + 4.61e-05 1.36e-02 TCACGTGC 7.93e-03 1.87e-03
MP00219 AT1G69010 450 464 - 4.62e-05 1.25e-02 CACGTGATGGGGTCG 1.34e-02 2.74e-03
MP00584 AT5G64750 425 443 - 4.91e-05 1.23e-02 GCGCGCAGTTACGGTGGAG 4.56e-03 1.62e-03
MA1244.1 ABR1 425 443 - 4.91e-05 1.23e-02 GCGCGCAGTTACGGTGGAG 4.56e-03 1.62e-03
MP00462 AT4G30980 459 473 - 4.96e-05 9.47e-03 GTACCGTGGCACGTG 6.94e-03 1.71e-03
MA1363.1 bHLH69 459 473 - 4.96e-05 9.47e-03 GTACCGTGGCACGTG 6.94e-03 1.71e-03
MA1066.1 TCP23 495 502 + 5.26e-05 1.18e-02 TGGCCCAC 2.71e-02 0.00e+00
MP00618 AT2G44745 481 490 + 5.56e-05 1.92e-02 TCGCTGACCG 1.25e-02 2.57e-03
MA0941.1 ABF2 457 469 - 5.58e-05 2.08e-02 CGTGGCACGTGAT 7.30e-03 2.43e-03
MA0956.1 BEE2 457 466 + 5.59e-05 1.06e-02 ATCACGTGCC 6.18e-03 2.99e-03
MA0956.1 BEE2 457 466 - 5.59e-05 1.06e-02 GGCACGTGAT 6.18e-03 2.99e-03
MP00086 AT4G17880 458 465 + 5.60e-05 2.14e-02 TCACGTGC 7.93e-03 1.87e-03
MA0569.1 MYC4 458 465 + 5.60e-05 2.12e-02 TCACGTGC 7.93e-03 1.87e-03
MP00487 AT5G04390 417 427 - 5.63e-05 2.14e-02 GAGTGGAGTGG 3.45e-03 3.34e-03
MP00062 AT3G15030 495 502 + 6.19e-05 1.69e-02 TGGCCCAC 2.71e-02 0.00e+00
MA1035.1 TCP4 495 502 + 6.19e-05 1.67e-02 TGGCCCAC 2.71e-02 0.00e+00
MP00061 AT4G00270 578 585 + 6.39e-05 7.92e-03 GCGGCCGC 5.00e-03 7.05e-03
MP00061 AT4G00270 578 585 - 6.39e-05 7.92e-03 GCGGCCGC 5.00e-03 7.05e-03
MP00456 AT4G27950 424 444 + 6.42e-05 1.81e-02 ACTCCACCGTAACTGCGCGCG 5.53e-03 1.46e-03
MP00217 AT1G68550 573 587 + 6.64e-05 9.63e-03 CGGTCGCGGCCGCGG 5.76e-03 5.85e-03
MP00135 AT1G10120 453 473 - 6.87e-05 9.64e-03 GTACCGTGGCACGTGATGGGG 1.02e-02 1.76e-03
MA1360.1 bHLH74 453 473 - 6.87e-05 9.64e-03 GTACCGTGGCACGTGATGGGG 1.02e-02 1.76e-03
MP00498 AT5G08130 451 464 - 6.93e-05 1.06e-02 CACGTGATGGGGTC 1.33e-02 2.18e-03
MP00543 AT5G45300 435 449 - 7.00e-05 2.25e-02 CCCCACGCGCGCAGT 1.06e-02 1.80e-03
MP00106 AT2G18300 455 466 + 7.05e-05 1.01e-02 CCATCACGTGCC 8.23e-03 2.45e-03
MA1025.1 HBI1 455 466 + 7.05e-05 1.01e-02 CCATCACGTGCC 8.23e-03 2.45e-03
MP00217 AT1G68550 576 590 - 7.21e-05 9.63e-03 ATACCGCGGCCGCGA 5.26e-03 4.62e-03
MA1075.1 WRKY12 482 489 + 7.54e-05 2.73e-02 CGCTGACC 1.26e-02 3.30e-03
MP00444 AT4G18890 456 466 - 7.63e-05 2.36e-02 GGCACGTGATG 7.28e-03 2.69e-03
MA1333.1 AT4G18890 456 466 - 7.63e-05 2.32e-02 GGCACGTGATG 7.28e-03 2.69e-03
MP00390 AT3G45150 492 502 + 7.64e-05 2.03e-02 CTCTGGCCCAC 2.22e-02 8.65e-04
MP00064 AT5G51910 493 502 + 7.68e-05 1.94e-02 TCTGGCCCAC 2.37e-02 9.61e-04
MP00509 AT5G13910 423 443 + 7.69e-05 2.14e-02 CACTCCACCGTAACTGCGCGC 4.54e-03 1.73e-03
MA1246.1 LEP 423 443 + 7.69e-05 2.12e-02 CACTCCACCGTAACTGCGCGC 4.54e-03 1.73e-03
MP00641 Manes.12G007700 494 503 + 7.70e-05 1.75e-02 CTGGCCCACC 2.30e-02 2.63e-04
MA1062.1 TCP15 495 502 + 7.73e-05 1.72e-02 TGGCCCAC 2.71e-02 0.00e+00
MA0988.1 PHYPADRAFT_143875 457 466 + 7.76e-05 1.47e-02 ATCACGTGCC 6.18e-03 2.99e-03
MA0988.1 PHYPADRAFT_143875 457 466 - 7.76e-05 1.47e-02 GGCACGTGAT 6.18e-03 2.99e-03
MP00659 Pp3c14_15890 457 466 + 7.76e-05 1.47e-02 ATCACGTGCC 6.18e-03 2.99e-03
MP00659 Pp3c14_15890 457 466 - 7.76e-05 1.47e-02 GGCACGTGAT 6.18e-03 2.99e-03
MA1063.1 TCP19 493 502 + 7.77e-05 2.01e-02 TCTGGCCCAC 2.37e-02 9.61e-04
MP00372 AT3G23210 451 473 + 7.91e-05 2.42e-02 GACCCCATCACGTGCCACGGTAC 1.06e-02 2.32e-03
MP00194 AT1G50640 421 435 - 8.06e-05 2.30e-02 TTACGGTGGAGTGGA 4.86e-03 1.89e-03
MP00462 AT4G30980 529 543 + 8.07e-05 9.47e-03 CCCGCGCTGCACGTC 9.34e-03 2.47e-03
MA1363.1 bHLH69 529 543 + 8.07e-05 9.47e-03 CCCGCGCTGCACGTC 9.34e-03 2.47e-03
MP00219 AT1G69010 459 473 + 8.12e-05 1.25e-02 CACGTGCCACGGTAC 6.94e-03 1.71e-03
MP00035 AT4G36930 458 466 - 8.13e-05 2.77e-02 GGCACGTGA 6.95e-03 1.94e-03
MA1061.1 SPT 458 466 - 8.13e-05 3.07e-02 GGCACGTGA 6.95e-03 1.94e-03
MP00376 AT3G23690 457 471 - 8.50e-05 2.64e-02 ACCGTGGCACGTGAT 6.66e-03 2.52e-03
MA1362.1 bHLH77 457 471 - 8.50e-05 2.59e-02 ACCGTGGCACGTGAT 6.66e-03 2.52e-03
MP00227 AT1G71450 565 584 + 8.52e-05 2.86e-02 ATCCATCGCGGTCGCGGCCG 7.75e-03 5.92e-03
MA1233.1 AT1G71450 565 584 + 8.52e-05 2.86e-02 ATCCATCGCGGTCGCGGCCG 7.75e-03 5.92e-03
MA0962.1 BHLH34 458 465 - 8.60e-05 1.28e-02 GCACGTGA 7.93e-03 1.87e-03
MP00667 GSVIVG01027588001 493 502 + 8.70e-05 2.10e-02 TCTGGCCCAC 2.37e-02 9.61e-04
MP00207 AT1G59640 451 471 - 8.86e-05 2.55e-02 ACCGTGGCACGTGATGGGGTC 1.05e-02 2.56e-03
MA1359.1 bHLH31 451 471 - 8.86e-05 2.58e-02 ACCGTGGCACGTGATGGGGTC 1.05e-02 2.56e-03
MP00099 AT4G16430 458 465 + 9.26e-05 1.49e-02 TCACGTGC 7.93e-03 1.87e-03
MP00099 AT4G16430 458 465 - 9.26e-05 1.49e-02 GCACGTGA 7.93e-03 1.87e-03
MA0957.1 BHLH3 458 465 + 9.26e-05 1.49e-02 TCACGTGC 7.93e-03 1.87e-03
MA0957.1 BHLH3 458 465 - 9.26e-05 1.49e-02 GCACGTGA 7.93e-03 1.87e-03
MP00071 AT5G56270 483 490 - 9.27e-05 3.17e-02 CGGTCAGC 1.26e-02 3.30e-03
MA1078.1 WRKY2 483 490 - 9.27e-05 3.12e-02 CGGTCAGC 1.26e-02 3.30e-03
MA1088.1 WRKY48 482 491 - 9.37e-05 3.58e-02 ACGGTCAGCG 1.19e-02 2.57e-03
MP00240 AT1G75490 421 435 + 9.42e-05 2.94e-02 TCCACTCCACCGTAA 4.86e-03 1.89e-03
MA1250.1 AT1G75490 421 435 + 9.42e-05 2.94e-02 TCCACTCCACCGTAA 4.86e-03 1.89e-03
MP00527 AT5G25390 568 588 - 9.53e-05 2.84e-02 ACCGCGGCCGCGACCGCGATG 7.16e-03 5.45e-03
MP00643 BGIOSGA008683 495 502 + 9.53e-05 1.94e-02 TGGCCCAC 2.71e-02 0.00e+00
MA1050.1 OsI_08196 495 502 + 9.53e-05 1.83e-02 TGGCCCAC 2.71e-02 0.00e+00
MP00164 AT1G28370 421 435 + 9.85e-05 2.56e-02 TCCACTCCACCGTAA 4.86e-03 1.89e-03
MA1412.1 TSAR2 439 448 + 9.90e-05 1.58e-02 CGCGCGTGGG 1.08e-02 1.00e-03
MA1412.1 TSAR2 439 448 - 9.90e-05 1.58e-02 CCCACGCGCG 1.08e-02 1.00e-03