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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTGCTAGTTCAGACGGTCATGCAGATGACAAAGCGGCACGTGGTGATGAACTTATCGTGTTACCAAAATAGgtaatatattggacgcagatcacttgtttcagtttgctttgatacttttatcttttcccagatgtgcattcatgtgacgttctcatgcggaaagtttggg...

Basic information

species Oryza sativa
transcript LOC_Os01g50340.1
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|88527251|gb|CI455389.1|CI455389
EST:     GAACTTATCGTGTTACCAAAATAG                         TTGAGACTTCTGATTGATGGCTCCTGAGTCCTGAGGAGACCAAGGAGGCGA
genomic: GAACTTATCGTGTTACCAAAATAGgtaatatatt ... ttgtctgcagTTGAGACTTCTGATTGATGGCTCCTGAGTCCTGAGGAGACCAAGGAGGCGA
EST: gi|27548938|gb|CA766971.2|CA766971
EST:     CAGATGACAAAGCGGCACGTGGTGATGAACTTATCGTGTTACCAAAATAG                         TTGAGACTTCTGATTGATGGCTCCTGAGTCCTGAGGAGACCAAGGAGGCGA
genomic: CAGATGACAAAGCGGCACGTGGTGATGAACTTATCGTGTTACCAAAATAGgtaatatatt ... ttgtctgcagTTGAGACTTCTGATTGATGGCTCCTGAGTCCTGAGGAGACCAAGGAGGCGA
EST: gi|86825274|gb|CI359954.1|CI359954
EST:     CAGATGACAAAGCGGCACGTGGTGATGAACTTATCGTGTTACCAAAATAG                         TTGAGACTTCTGATTGATGGCTCCTGAGTCCTGAGGAGACCAAGGAGGCGA
genomic: CAGATGACAAAGCGGCACGTGGTGATGAACTTATCGTGTTACCAAAATAGgtaatatatt ... ttgtctgcagTTGAGACTTCTGATTGATGGCTCCTGAGTCCTGAGGAGACCAAGGAGGCGA
EST: gi|88447148|gb|CI531391.1|CI531391
EST:     CAGATGACAAAGCGGCACGTGGTGATGAACTTATCGTGTTACCAAAATAG                         TTGAGACTTCTGATTGATGGCTCCTGAGTCCTGAGGAGACCAAGGAGGCGA
genomic: CAGATGACAAAGCGGCACGTGGTGATGAACTTATCGTGTTACCAAAATAGgtaatatatt ... ttgtctgcagTTGAGACTTCTGATTGATGGCTCCTGAGTCCTGAGGAGACCAAGGAGGCGA
EST: gi|88544480|gb|CI472582.1|CI472582
EST:     CAGATGACAAAGCGGCACGTGGTGATGAACTTATCGTGTTACCAAAATAG                         TTGAGACTTCTGATTGATGGCTCCTGAGTCCTGAGGAGACCAAGGAGGCGA
genomic: CAGATGACAAAGCGGCACGTGGTGATGAACTTATCGTGTTACCAAAATAGgtaatatatt ... ttgtctgcagTTGAGACTTCTGATTGATGGCTCCTGAGTCCTGAGGAGACCAAGGAGGCGA
EST: gi|87039079|gb|CI193701.1|CI193701
EST:     CAGATGACAAAGCGGCACGTGGTGATGAACTTATCGTGTTACCAAAATAG                         TTGAGACTTCTGATTGATGGCTCCTGAGTCCTGAGGAGACCAAGGAGGCGA
genomic: CAGATGACAAAGCGGCACGTGGTGATGAACTTATCGTGTTACCAAAATAGgtaatatatt ... ttgtctgcagTTGAGACTTCTGATTGATGGCTCCTGAGTCCTGAGGAGACCAAGGAGGCGA
EST: gi|86436890|gb|CI118612.1|CI118612
EST:     CAGATGACAAAGCGGCACGTGGTGATGAACTTATCGTGTTACCAAAATAG                         TTGAGACTTCTGATTGATGGCTCCTGAGTCCTGAGGAGACCAAGGAGGCGA
genomic: CAGATGACAAAGCGGCACGTGGTGATGAACTTATCGTGTTACCAAAATAGgtaatatatt ... ttgtctgcagTTGAGACTTCTGATTGATGGCTCCTGAGTCCTGAGGAGACCAAGGAGGCGA
EST: gi|86873466|gb|CI329844.1|CI329844
EST:     CAGATGACAAAGCGGCACGTGGTGATGAACTTATCGTGTTACCAAAATAG                         TTGAGACTTCTGATTGATGGCTCCTGAGTCCTGAGGAGACCAAGGAGGCGA
genomic: CAGATGACAAAGCGGCACGTGGTGATGAACTTATCGTGTTACCAAAATAGgtaatatatt ... ttgtctgcagTTGAGACTTCTGATTGATGGCTCCTGAGTCCTGAGGAGACCAAGGAGGCGA
EST: gi|88522907|gb|CI450703.1|CI450703
EST:     CAGATGACAAAGCGGCACGTGGTGATGAACTTATCGTGTTACCAAAATAG                         TTGAGACTTCTGATTGATGGCTCCTGAGTCCTGAGGAGACCAAGGAGGCGA
genomic: CAGATGACAAAGCGGCACGTGGTGATGAACTTATCGTGTTACCAAAATAGgtaatatatt ... ttgtctgcagTTGAGACTTCTGATTGATGGCTCCTGAGTCCTGAGGAGACCAAGGAGGCGA
EST: gi|88547260|gb|CI477542.1|CI477542
EST:     CAGATGACAAAGCGGCACGTGGTGATGAACTTATCGTGTTACCAAAATAG                         TTGAGACTTCTGATTGATGGCTCCTGAGTCCTGAGGAGACCAAGGAGGCGA
genomic: CAGATGACAAAGCGGCACGTGGTGATGAACTTATCGTGTTACCAAAATAGgtaatatatt ... ttgtctgcagTTGAGACTTCTGATTGATGGCTCCTGAGTCCTGAGGAGACCAAGGAGGCGA
EST: gi|3760511|gb|C97765.1|C97765
EST:     CAGATGACAAAGCGGCACNTGGTGATGAACTTATCGTGTTACCAAAATAG                         TTGAGACTTCTGATTGATGGCTCCTGAGTCCTGAGGAGACCAAGGAGGCGA
genomic: CAGATGACAAAGCGGCACGTGGTGATGAACTTATCGTGTTACCAAAATAGgtaatatatt ... ttgtctgcagTTGAGACTTCTGATTGATGGCTCCTGAGTCCTGAGGAGACCAAGGAGGCGA
EST: gi|86845050|gb|CI341013.1|CI341013
EST:     CAGATGACAAAGCGGCACGTGGTGATGAACTTATCGTGTTACCAAAATAG                         TTGAGACTTCTGATTGATGGCTCCTGAGTCCTGAGGAGACCAAGGAGGCGA
genomic: CAGATGACAAAGCGGCACGTGGTGATGAACTTATCGTGTTACCAAAATAGgtaatatatt ... ttgtctgcagTTGAGACTTCTGATTGATGGCTCCTGAGTCCTGAGGAGACCAAGGAGGCGA
EST: gi|88466324|gb|CI529733.1|CI529733
EST:     CAGATGACAAAGCGGCACGTGGTGATGAACTTATCGTGTTACCAAAATAG                         TTGAGACTTCTGATTGATGGCTCCTGAGTCCTGAGGAGACCAAGGAGGCGA
genomic: CAGATGACAAAGCGGCACGTGGTGATGAACTTATCGTGTTACCAAAATAGgtaatatatt ... ttgtctgcagTTGAGACTTCTGATTGATGGCTCCTGAGTCCTGAGGAGACCAAGGAGGCGA
EST: gi|88529109|gb|CI456439.1|CI456439
EST:     TGACAAAGCGGCACGTGGTGATGAACTTATCGTGTTACCAAAATAG                         TTGAGACTTCTGATTGATGGCTCCTGAGTCCTGAGGAGACCAAGGAGGCGA
genomic: TGACAAAGCGGCACGTGGTGATGAACTTATCGTGTTACCAAAATAGgtaatatatt ... ttgtctgcagTTGAGACTTCTGATTGATGGCTCCTGAGTCCTGAGGAGACCAAGGAGGCGA
EST: gi|86889733|gb|CI299931.1|CI299931
EST:     CAGATGACAAAGCGGCACGTGGTGATGAACTTATCGTGTTACCAAAATAG                         TTGAGACTTCTGATTGATGGCTCCTGAGTCCTGAGGAGACCAAGGAGGCGA
genomic: CAGATGACAAAGCGGCACGTGGTGATGAACTTATCGTGTTACCAAAATAGgtaatatatt ... ttgtctgcagTTGAGACTTCTGATTGATGGCTCCTGAGTCCTGAGGAGACCAAGGAGGCGA
EST: gi|88465269|gb|CI517438.1|CI517438
EST:     CAGATGACAAAGCGGCACGTGGTGATGAACTTATCGTGTTACCAAAATAG                         TTGAGACTTCTGATTGATGGCTCCTGAGTCCTGAGGAGACCAAGGAGGCGA
genomic: CAGATGACAAAGCGGCACGTGGTGATGAACTTATCGTGTTACCAAAATAGgtaatatatt ... ttgtctgcagTTGAGACTTCTGATTGATGGCTCCTGAGTCCTGAGGAGACCAAGGAGGCGA
EST: gi|88522518|gb|CI450284.1|CI450284
EST:     CAGATGACAAAGCGGCACGTGGTGATGAACTTATCGTGTTACCAAAATAG                         TTGAGACTTCTGATTGATGGCTCCTGAGTCCTGAGGAGACCAAGGAGGCGA
genomic: CAGATGACAAAGCGGCACGTGGTGATGAACTTATCGTGTTACCAAAATAGgtaatatatt ... ttgtctgcagTTGAGACTTCTGATTGATGGCTCCTGAGTCCTGAGGAGACCAAGGAGGCGA
EST: gi|88556406|gb|CI486728.1|CI486728
EST:     GTGATGGACTTATCGTGTTACCAAAATAG                         TTGAGACTTCTGATTGATGGGTCCTGAGTCCTGAGGAGACCAAGGAGGCGA
genomic: GTGATGAACTTATCGTGTTACCAAAATAGgtaatatatt ... ttgtctgcagTTGAGACTTCTGATTGATGGCTCCTGAGTCCTGAGGAGACCAAGGAGGCGA
EST: gi|88532963|gb|CI462298.1|CI462298
EST:     ACGTGGTGATGAACTTATCGTGTTACCAAAATAG                         TTGAGACTTCTGATTGATGGCTCCTGAGTCCTGAGGAGACCAAGGAGGCGA
genomic: ACGTGGTGATGAACTTATCGTGTTACCAAAATAGgtaatatatt ... ttgtctgcagTTGAGACTTCTGATTGATGGCTCCTGAGTCCTGAGGAGACCAAGGAGGCGA
EST: gi|88556982|gb|CI487351.1|CI487351
EST:     GGCACNTGGTGATGAACTTATCGTGTTACCAAAATAG                         TTGAGACTTCTGATTGATGGCTCCTGAGTCCTGAGGAGACCAAGGAGGCGA
genomic: GGCACGTGGTGATGAACTTATCGTGTTACCAAAATAGgtaatatatt ... ttgtctgcagTTGAGACTTCTGATTGATGGCTCCTGAGTCCTGAGGAGACCAAGGAGGCGA
EST: gi|29628885|gb|CB633896.1|CB633896
EST:     CAGATGACAAAGCGGCACGTGGTGATGAACTTATCGTGTTACCAAAATAG                         TTGAGACTTCTGATTGATGGCTCCTGAGTCCTGAGGAGACCAAGGAGGCGA
genomic: CAGATGACAAAGCGGCACGTGGTGATGAACTTATCGTGTTACCAAAATAGgtaatatatt ... ttgtctgcagTTGAGACTTCTGATTGATGGCTCCTGAGTCCTGAGGAGACCAAGGAGGCGA
EST: gi|89174073|gb|CI041966.1|CI041966
EST:     CAGATGACAAAGCGGCACGTGGTGATGAACTTATCGTGTTACCAAAATAG                         TTGAGACTTCTGATTGATGGCTCCTGAGTCCTGAGGAGACCAAGGAGGCGA
genomic: CAGATGACAAAGCGGCACGTGGTGATGAACTTATCGTGTTACCAAAATAGgtaatatatt ... ttgtctgcagTTGAGACTTCTGATTGATGGCTCCTGAGTCCTGAGGAGACCAAGGAGGCGA
EST: gi|86822254|gb|CI357869.1|CI357869
EST:     CAGATGACAAAGCGGCACGTGGTGATGAACTTATCGTGTTACCAAAATAG                         TTGAGACTTCTGATTGATGGCTCCTGAGTCCTGAGGAGACCAAGGAGGCGA
genomic: CAGATGACAAAGCGGCACGTGGTGATGAACTTATCGTGTTACCAAAATAGgtaatatatt ... ttgtctgcagTTGAGACTTCTGATTGATGGCTCCTGAGTCCTGAGGAGACCAAGGAGGCGA
EST: gi|86251728|gb|CI018920.1|CI018920
EST:     CAGATGACAAAGCGGCACGTGGTGATGAACTTATCGTGTTACCAAAATAG                         TTGAGACTTCTGATTGATGGCTCCTGAGTCCTGAGGAGACCAAGGAGGCGA
genomic: CAGATGACAAAGCGGCACGTGGTGATGAACTTATCGTGTTACCAAAATAGgtaatatatt ... ttgtctgcagTTGAGACTTCTGATTGATGGCTCCTGAGTCCTGAGGAGACCAAGGAGGCGA

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), 69 (downstream exon)
Score: 6

TTGCTAGTTCAGACGGTCATGCAGATGACAAAGCGGCACGTGGTGATGAACTTATCGTGTTACCAAAATAGgtaatatatt ... ttgtctgcagTTGAGACTTCTGATTGATGGCTCCTGAGTCCTGAGGAGACCAAGGAGGCGAGGACGCAAGTAACTGCATTATTTATGTTCAACAGTCCAATTTCCAGGCT




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TTGCTAGTTCAGACGGTCATGCAGATGACAAAGCGGCACGTGGTGATGAACTTATCGTGTTACCAAAATAGgtaatatattggacgcagatcacttgtttcagtttgctttgatacttttatcttttcccagatgtgcattcatgtgacgttctcatgcggaaagtttggg

- - - - - - - - - -  CAGATG