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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgcatatgctcttgttgtgatgtgtttctttcagattgttttaatcttgttttggccacagatattgttgtctgcctcattggtgatttaatatttgcagGAAAAACTAGAGGGGAACAGTGATTCAATACCTTATATGAATGAACAGAACGACACCAATGGCACCCACCAGAAGCAACAGGATTCTGATGCTCAGCCTA

Basic information

species Oryza sativa
transcript LOC_Os02g03580.1
intron # 13
splice site 3'
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|89197742|gb|CI013732.1|CI013732
EST:     GGATCAAAAAGGAGTACGAGGCACTTCTTTCACACAATGCTTCACTCAAG                         GAAAAACTAGAGGGGAACAGTGATTCAATACCTTATATGAATGAACAGAAC
genomic: GGATCAAAAAGGAGTACGAGGCACTTCTTTCACACAATGCTTCACTCAAGgtggctgagc ... atatttgcagGAAAAACTAGAGGGGAACAGTGATTCAATACCTTATATGAATGAACAGAAC
EST: gi|88903327|gb|CI088865.1|CI088865
EST:     GGATCAAAAAGGAGTACGAGGCACTTCTTTCACACAATGCTTCACTCAAG                         GAAAAACTAGAGGGGAACAGTGATTCAATACCTTATATGAATGAACAGAAC
genomic: GGATCAAAAAGGAGTACGAGGCACTTCTTTCACACAATGCTTCACTCAAGgtggctgagc ... atatttgcagGAAAAACTAGAGGGGAACAGTGATTCAATACCTTATATGAATGAACAGAAC
EST: gi|86497997|gb|CI140630.1|CI140630
EST:     GGATCAAAAAGGAGTACGAGGCACTTCTTTCACACAATGCTTCACTCAAG                         GAAAAACTAGAGGGGAACAGTGATTCAATACCTTATATGAATGAACAGAAC
genomic: GGATCAAAAAGGAGTACGAGGCACTTCTTTCACACAATGCTTCACTCAAGgtggctgagc ... atatttgcagGAAAAACTAGAGGGGAACAGTGATTCAATACCTTATATGAATGAACAGAAC
EST: gi|86505811|gb|CI148444.1|CI148444
EST:     GGATCAAAAAGGAGTACGAGGCACTTCTTTCACACAATGCTTCACTCAAG                         GAAAAACTAGAGGGGAACAGTGATTCAATACCTTATATGAATGAACAGAAC
genomic: GGATCAAAAAGGAGTACGAGGCACTTCTTTCACACAATGCTTCACTCAAGgtggctgagc ... atatttgcagGAAAAACTAGAGGGGAACAGTGATTCAATACCTTATATGAATGAACAGAAC
EST: gi|88850496|gb|CI093177.1|CI093177
EST:     GGATCAAAAAGGAGTACGAGGCACTTCTTTCACACAATGCTTCACTCAAG                         GAAAAACTAGAGGGGAACAGTGATTCAATACCTTATATGAATGAACAGAAC
genomic: GGATCAAAAAGGAGTACGAGGCACTTCTTTCACACAATGCTTCACTCAAGgtggctgagc ... atatttgcagGAAAAACTAGAGGGGAACAGTGATTCAATACCTTATATGAATGAACAGAAC
EST: gi|86879457|gb|CI327145.1|CI327145
EST:     GGATCAAAAAGGAGTACGAGGCACTTCTTTCACACAATGCTTCACTCAAG                         GAAAAACTAGAGGGGAACAGTGATTCAATACCTTATATGAATGAACAGAAC
genomic: GGATCAAAAAGGAGTACGAGGCACTTCTTTCACACAATGCTTCACTCAAGgtggctgagc ... atatttgcagGAAAAACTAGAGGGGAACAGTGATTCAATACCTTATATGAATGAACAGAAC
EST: gi|29670501|gb|CB666776.1|CB666776
EST:     GGATCAAAAAGGAGTACGAGGCACTTCTTTCACACAATGCTTCACTCAAG                         GAAAAACTAGAGGGGAACAGTGATTCAATACCTTATATGAATGAACAGAAC
genomic: GGATCAAAAAGGAGTACGAGGCACTTCTTTCACACAATGCTTCACTCAAGgtggctgagc ... atatttgcagGAAAAACTAGAGGGGAACAGTGATTCAATACCTTATATGAATGAACAGAAC
EST: gi|88829448|gb|CI074318.1|CI074318
EST:     GGATCAAAAAGGAGTACGAGGCACTTCTTTCACACAATGCTTCACTCAAG                         G-AAAACTAGAGGGGAACAGTGATTCAATACCTTATATGAATGAACAGAAC
genomic: GGATCAAAAAGGAGTACGAGGCACTTCTTTCACACAATGCTTCACTCAAGgtggctgagc ... atatttgcagGAAAAACTAGAGGGGAACAGTGATTCAATACCTTATATGAATGAACAGAAC
EST: gi|88965389|gb|CI011640.1|CI011640
EST:     GGATCAAAAAGGAGTACGAGGCACTTCTTTCACACAATGCTTCACTCAAG                         GAAAAACTAGAGGGGAACAGTGATTCAATACCTTATATGAATGAACAGAAC
genomic: GGATCAAAAAGGAGTACGAGGCACTTCTTTCACACAATGCTTCACTCAAGgtggctgagc ... atatttgcagGAAAAACTAGAGGGGAACAGTGATTCAATACCTTATATGAATGAACAGAAC
EST: gi|29665043|gb|CB661318.1|CB661318
EST:     GGATCAAAAAGGAGTACGAGGCACTTCTTTCACACAATGCTTCACTCAAG                         GAAAAACTAGAGGGGAACAGTGATTCAATACCTTATATGAATGAACAGAAC
genomic: GGATCAAAAAGGAGTACGAGGCACTTCTTTCACACAATGCTTCACTCAAGgtggctgagc ... atatttgcagGAAAAACTAGAGGGGAACAGTGATTCAATACCTTATATGAATGAACAGAAC
EST: gi|88517412|gb|CI445066.1|CI445066
EST:     GGATCAAAAAGGAGTACGAGGCACTTCTTTCACACAATGCTTCACTCAAG                         GGAAAACTAGAGGGGAACAGTGATTCAATACCTTATATGAATGAACAGAAC
genomic: GGATCAAAAAGGAGTACGAGGCACTTCTTTCACACAATGCTTCACTCAAGgtggctgagc ... atatttgcagGAAAAACTAGAGGGGAACAGTGATTCAATACCTTATATGAATGAACAGAAC
EST: gi|86488210|gb|CI130843.1|CI130843
EST:     GGATCAAAAAGGAGTACGAGGCACTTCTTTCACACAATGCTTCACTCAAG                         GAAAAACTAGAGGGGAACAGTGATTCAATACCTTATATGAATGAACAGAAC
genomic: GGATCAAAAAGGAGTACGAGGCACTTCTTTCACACAATGCTTCACTCAAGgtggctgagc ... atatttgcagGAAAAACTAGAGGGGAACAGTGATTCAATACCTTATATGAATGAACAGAAC
EST: gi|88446664|gb|CI526497.1|CI526497
EST:     GGATCAAAAAGGAGTACGAGGCACTTCTTTCACACAATGCTTCACTCAAG                         GAAAAACTAGAGGGGAACAGTGATTCAATACCTTATATGAATGAACAGAAC
genomic: GGATCAAAAAGGAGTACGAGGCACTTCTTTCACACAATGCTTCACTCAAGgtggctgagc ... atatttgcagGAAAAACTAGAGGGGAACAGTGATTCAATACCTTATATGAATGAACAGAAC
EST: gi|86252236|gb|CI055973.1|CI055973
EST:     GGATCAAAAAGGAGTACGAGGCACTTCTTTCACACAATGCTTCACTCAAG                         GAAAAACTAGAGGGGAACAGTGATTCAATACCTTATATGAATGAACAGAAC
genomic: GGATCAAAAAGGAGTACGAGGCACTTCTTTCACACAATGCTTCACTCAAGgtggctgagc ... atatttgcagGAAAAACTAGAGGGGAACAGTGATTCAATACCTTATATGAATGAACAGAAC
EST: gi|88958454|gb|CI095970.1|CI095970
EST:     GGATCAAAAAGGAGTACGAGGCACTTCTTTCACACAATGCTTCACTCAAG                         GAAAAACTAGAGGGGAACAGTGATTCAATACCTTATATGAATGAACAGAAC
genomic: GGATCAAAAAGGAGTACGAGGCACTTCTTTCACACAATGCTTCACTCAAGgtggctgagc ... atatttgcagGAAAAACTAGAGGGGAACAGTGATTCAATACCTTATATGAATGAACAGAAC
EST: gi|89172965|gb|CI040858.1|CI040858
EST:     GGATCAAAAAGGAGTACGAGGCACTTCTTTCACACAATGCTTCACTCAAG                         GAAAAACTAGAGGGGAACAGTGATTCAATACCTTATATGAATGAACAGAAC
genomic: GGATCAAAAAGGAGTACGAGGCACTTCTTTCACACAATGCTTCACTCAAGgtggctgagc ... atatttgcagGAAAAACTAGAGGGGAACAGTGATTCAATACCTTATATGAATGAACAGAAC

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: 62 (upstream exon), 65 (downstream exon)
Score: 22

CGCTGACAATTTAAGGGCAGAAAACTCCTCTCTTAGGGCTGAGCTTGAACGGATCAAAAAGGAGTACGAGGCACTTCTTTCACACAATGCTTCACTCAAGgtggctgagc ... atatttgcagGAAAAACTAGAGGGGAACAGTGATTCAATACCTTATATGAATGAACAGAACGACACCAATGGCACCCACCAGAAGCAACAGGATTCTGATGCTCAGCCTA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttgttttggccacagatattgttgtctgcctcattggtgatttaatatttgcagGAAAAACTAGAGGGGAACAGTGATTCAATACCTTATATGAATGAACAGAACGACACCAATGGCACCCACCAGAAGCAACAGGATTCTGATGCTCAGCCTA
                                        atttaat  putative branch site (score: 22)
                                      tgatttaatattt  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgcatatgctcttgttgtgatgtgtttctttcagattgttttaatcttgttttggccacagatattgttgtctgcctcattggtgatttaatatttgcagGAAAAACTAGAGGGGAACAGTGATTCAATACCTTATATGAATGAACAGAACGACACCAATGGCACCCACCAGAAGCAACAGGATTCTGATGCTCAGCCTA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
- catatgc
- - - - - cttgttg
- - - - - - - - - - - tgtttct
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgtctgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tggtgat