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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTGGGCTTAATATAGAGGGAGAGGCAGACAGTTGGGATTTTGGTGTTGgtaaggatttaatctacaatattcaattgttgtgctcttcgcattctataccatataacaacatgttgcatggcctttctttgccataaacaatggacta...

Basic information

species Oryza sativa
transcript LOC_Os01g71300.1
intron # 3
splice site 5'
intron type U2

Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|89172386|gb|CI721445.1|CI721445
EST:     GTGGGCTTAATATAGAGGGAGAGGCAGACAGTTGGGATTTTGGTGTTG                         GTGCTGGATTCTATTTGAATGCAACAAATGAAAAGTGGAAAAATTGGCGCA
genomic: GTGGGCTTAATATAGAGGGAGAGGCAGACAGTTGGGATTTTGGTGTTGgtaaggattt ... caatgagtagGTGCTGGATTCTATTTGAATGCAACAAATGAAAAGTGGAAAAATTGGCGCA
EST: gi|33793936|gb|CF322856.1|CF322856
EST:     GAGG-AGACAGTTGGGATTTTGGTGTTG                         GTGCTGGATTCTATTTGAATGCAACAAATGAAAAGTGGAAAAATTGGCGCA
genomic: GAGGCAGACAGTTGGGATTTTGGTGTTGgtaaggattt ... caatgagtagGTGCTGGATTCTATTTGAATGCAACAAATGAAAAGTGGAAAAATTGGCGCA
EST: gi|88670559|gb|CI724675.1|CI724675
EST:     GTGGGCTTAATATAGAGGGAGAGGCAGACAGTTGGGATTTTGGTGTTG                         GTGCTGGATTCTATTTGAATGCAACAAATGAAAAGTGGAAAAATTGGCGCA
genomic: GTGGGCTTAATATAGAGGGAGAGGCAGACAGTTGGGATTTTGGTGTTGgtaaggattt ... caatgagtagGTGCTGGATTCTATTTGAATGCAACAAATGAAAAGTGGAAAAATTGGCGCA
EST: gi|88673403|gb|CI727516.1|CI727516
EST:     GTGGGCTTAATATAGAGGGAGAGGCAGACAGTTGGGATTTTGGTGTTG                         GTGCTGGATTCTATTTGAATGCAACAAATGAAAAGTGGAAAAATTGGCGCA
genomic: GTGGGCTTAATATAGAGGGAGAGGCAGACAGTTGGGATTTTGGTGTTGgtaaggattt ... caatgagtagGTGCTGGATTCTATTTGAATGCAACAAATGAAAAGTGGAAAAATTGGCGCA
EST: gi|88673631|gb|CI727744.1|CI727744
EST:     GTGGGCTTAATATAGAGGGAGAGGCAGACAGTTGGGATTTTGGTGTTG                         GTGCTGGATTCTATTTGAATGCAACAAATGAAAAGTGGAAAAATTGGCGCA
genomic: GTGGGCTTAATATAGAGGGAGAGGCAGACAGTTGGGATTTTGGTGTTGgtaaggattt ... caatgagtagGTGCTGGATTCTATTTGAATGCAACAAATGAAAAGTGGAAAAATTGGCGCA
EST: gi|88676329|gb|CI730442.1|CI730442
EST:     GTGGGCTTAATATAGAGGGAGAGGCAGACAGTTGGGATTTTGGTGTTG                         GTGCTGGATTCTATTTGAATGCAACAAATGAAAAGTGGAAAAATGGGCGCA
genomic: GTGGGCTTAATATAGAGGGAGAGGCAGACAGTTGGGATTTTGGTGTTGgtaaggattt ... caatgagtagGTGCTGGATTCTATTTGAATGCAACAAATGAAAAGTGGAAAAATTGGCGCA
EST: gi|88676307|gb|CI730420.1|CI730420
EST:     GTGGGCTTAATATAGAGGGAGAGGCAGACAGTTGGGATTTTGGTGTTG                         GTGCTGGATTCTATTTGAATGCAACAAATGAAAAGTGGAAAAATTGGCGCA
genomic: GTGGGCTTAATATAGAGGGAGAGGCAGACAGTTGGGATTTTGGTGTTGgtaaggattt ... caatgagtagGTGCTGGATTCTATTTGAATGCAACAAATGAAAAGTGGAAAAATTGGCGCA
EST: gi|33793279|gb|CF322520.1|CF322520
EST:     GTGGGCTTAATATAGAGGGAGAGGCAGACAGTTGGGATTTTGGTGTTG                         GTGCTGGATTCTATTTGAATGCAACAAATGAAAAGTGGAAAAATTGGCGCA
genomic: GTGGGCTTAATATAGAGGGAGAGGCAGACAGTTGGGATTTTGGTGTTGgtaaggattt ... caatgagtagGTGCTGGATTCTATTTGAATGCAACAAATGAAAAGTGGAAAAATTGGCGCA
EST: gi|29616411|gb|CB621423.1|CB621423
EST:     TAATATAGAGGGAGAGGCAGACAGTTGGGATTTTGGTGTTG                         GTGCTGGATTCTATTTGAATGCAACAAATGAAAAGTGGAAAAATTGGCGCA
genomic: TAATATAGAGGGAGAGGCAGACAGTTGGGATTTTGGTGTTGgtaaggattt ... caatgagtagGTGCTGGATTCTATTTGAATGCAACAAATGAAAAGTGGAAAAATTGGCGCA
EST: gi|88672556|gb|CI726672.1|CI726672
EST:     GTGGGCTTAATATAGAGGGAGAGGCAGACAGTTGGGATTTTGGTGTTG                         GTGCTGGATTCTATTTGAATGCAACAAATGAAAAGTGGAAAAATTGGCGCA
genomic: GTGGGCTTAATATAGAGGGAGAGGCAGACAGTTGGGATTTTGGTGTTGgtaaggattt ... caatgagtagGTGCTGGATTCTATTTGAATGCAACAAATGAAAAGTGGAAAAATTGGCGCA
EST: gi|88667436|gb|CI722175.1|CI722175
EST:     GTGGGCTTAATATAGAGGGAGAGGCAGACAGTTGGGATTTTGGTGTTG                         GTGCTGGATTCTATTTGAATGCAACAAATGAAAAGTGGAAAAATTGGCGCA
genomic: GTGGGCTTAATATAGAGGGAGAGGCAGACAGTTGGGATTTTGGTGTTGgtaaggattt ... caatgagtagGTGCTGGATTCTATTTGAATGCAACAAATGAAAAGTGGAAAAATTGGCGCA
EST: gi|58591479|gb|CF989787.1|CF989787
EST:     GTGGGCTTAATATAGAGGGAGAGGCAGACAGTTGGGATTTTGGTGTTG                         GTGCTGGATTCTATTTGAATGCAACAAATGACACGTGGACAAATTGGCGCA
genomic: GTGGGCTTAATATAGAGGGAGAGGCAGACAGTTGGGATTTTGGTGTTGgtaaggattt ... caatgagtagGTGCTGGATTCTATTTGAATGCAACAAATGAAAAGTGGAAAAATTGGCGCA
EST: gi|58604050|gb|CK014578.1|CK014578
EST:     GTGGGCTTAATATAGAGGGAGAGGCAGACAGTTGGGATTTTGGTGTTG                         GTGCTGGATTCTATTTGAATGCAACAAATGAACAGTGGAAAAATTGGCGCA
genomic: GTGGGCTTAATATAGAGGGAGAGGCAGACAGTTGGGATTTTGGTGTTGgtaaggattt ... caatgagtagGTGCTGGATTCTATTTGAATGCAACAAATGAAAAGTGGAAAAATTGGCGCA
EST: gi|89171382|gb|CI720441.1|CI720441
EST:     GTGGGCTTAATATAGAGGGAGAGGCAGACAGTTGGGATTTTGGTGTTG                         GTGCTGGATTCTATTTGAATGCAACAAATGAAAAGTGGAAAAATTGGCGCA
genomic: GTGGGCTTAATATAGAGGGAGAGGCAGACAGTTGGGATTTTGGTGTTGgtaaggattt ... caatgagtagGTGCTGGATTCTATTTGAATGCAACAAATGAAAAGTGGAAAAATTGGCGCA
EST: gi|88669850|gb|CI723966.1|CI723966
EST:     GTGGGCTTAATATAGAGGGAGAGGCAGACAGTTGGGATTTTGGTGTTG                         GTGCTGGATTCTATTTGAATGCAACAAATGAAAAGTGGAAAAATTGGCGCA
genomic: GTGGGCTTAATATAGAGGGAGAGGCAGACAGTTGGGATTTTGGTGTTGgtaaggattt ... caatgagtagGTGCTGGATTCTATTTGAATGCAACAAATGAAAAGTGGAAAAATTGGCGCA
EST: gi|88675254|gb|CI727369.1|CI727369
EST:     GTGGGCTTAATATAGAGGGAGAGGCAGACAGTTGGGATTTTGGTGTTG                         GTGCTGGATTCTATTTGAATGCAACAAATGAAAAGTGGAAAAATTGGCGCA
genomic: GTGGGCTTAATATAGAGGGAGAGGCAGACAGTTGGGATTTTGGTGTTGgtaaggattt ... caatgagtagGTGCTGGATTCTATTTGAATGCAACAAATGAAAAGTGGAAAAATTGGCGCA
EST: gi|88672977|gb|CI727092.1|CI727092
EST:     GTGGGCTTAATATAGAGGGAGAGGCAGACAGTTGGGATTTTGGTGTTG                         GTGCTGGATTCTATTTGAATGCAACAAATGAAAAGTGGAAAAATTGGCGCA
genomic: GTGGGCTTAATATAGAGGGAGAGGCAGACAGTTGGGATTTTGGTGTTGgtaaggattt ... caatgagtagGTGCTGGATTCTATTTGAATGCAACAAATGAAAAGTGGAAAAATTGGCGCA

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 1 RNA-Seqlibrary.


Block sizes: 48 (upstream exon), 72 (downstream exon)
Score: 50

GTGGGCTTAATATAGAGGGAGAGGCAGACAGTTGGGATTTTGGTGTTGgtaaggattt ... caatgagtagGTGCTGGATTCTATTTGAATGCAACAAATGAAAAGTGGAAAAATTGGCGCATGTATGACTATGTTGTGAAGGAGCTTCCAAAAGTTTTAAGTGACAACTT




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Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTGGGCTTAATATAGAGGGAGAGGCAGACAGTTGGGATTTTGGTGTTGgtaaggatttaatctacaatattcaattgttgtgctcttcgcattctataccatataacaacatgttgcatggcctttctttgccataaacaatggacta

- - - - - - - - - GAGAGG