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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagttgagttccccccacgtcctagttgatgcacctcaattcacgaacaactggccaacttcattgcagtatctgttcttattgtgcacaaaatttaagtcttaaacaattcataacattgtgattttatttttagTGTTCAAGGGAGGATCATGCAAAGAGTGTTGATGTTGCAGTTCTTTTTCTTGGCTCGAAG

Basic information

species Oryza sativa
transcript LOC_Os11g03380.1
intron # 3
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|4715628|gb|AU056744.1|AU056744
EST:     AGAGCTTAGTGAAATCTGTTCTTGAAGAAGGTGGTTGGTCAAACTTGGTG                         TGTTCAAGGGAGGATCATGCAAAGAGTGTTGATGTTGCAGTTCTTTTTCTT
genomic: AGAGCTTAGTGAAATCTGTTCTTGAAGAAGGTGGTTGGTCAAACTTGGTGgtgagttgag ... ttatttttagTGTTCAAGGGAGGATCATGCAAAGAGTGTTGATGTTGCAGTTCTTTTTCTT
EST: gi|33658304|gb|CF280918.1|CF280918
EST:     GAGCTTAGTGAAATCTGTTCTTGAAGAAGGGTGGTTGGTCAAACTTGGTG                         TGTTCAAGGGAGGATCATGCAAAGAG-GTTTGATGTTTGCAGTTCTTTTTC
genomic: GAGCTTAGTGAAATCTGTTCTTGAAGAAGG-TGGTTGGTCAAACTTGGTGgtgagttgag ... ttatttttagTGTTCAAGGGAGGATCATGCAAAGAGTGTT-GATGTT-GCAGTTCTTTTTC
EST: gi|33658126|gb|CF280740.1|CF280740
EST:     AGAGCTTAGTGAAATCTGTTCTTGAAGAAGGTGGTTGGTCAAACTTGGTG                         TGTTCAAGGGAGGATCATGCAAAGAGTGTTGATGTTGCAGTTCTTTTTCTT
genomic: AGAGCTTAGTGAAATCTGTTCTTGAAGAAGGTGGTTGGTCAAACTTGGTGgtgagttgag ... ttatttttagTGTTCAAGGGAGGATCATGCAAAGAGTGTTGATGTTGCAGTTCTTTTTCTT
EST: gi|33690612|gb|CF318851.1|CF318851
EST:     AGAGCTTAGTGAAATCTGTTCTTGAAGAAGGTGGTTGGTCAAACTTGGTG                         TGTTCAAGGGAGGATCATGCAAAGAGTGTTGATGTTGCAGTTCTTTTTCTT
genomic: AGAGCTTAGTGAAATCTGTTCTTGAAGAAGGTGGTTGGTCAAACTTGGTGgtgagttgag ... ttatttttagTGTTCAAGGGAGGATCATGCAAAGAGTGTTGATGTTGCAGTTCTTTTTCTT
EST: gi|14714076|gb|AU198016.1|AU198016
EST:     AGAGCTTAGTGAAATCTGTTCTTGAAGAAGGTGGTTGGTCAAACTTGGTG                         TGTTCAAGGGAGGATCATGCAAAGAGTGTTGATGTTGCAGTTCTTTTTCTT
genomic: AGAGCTTAGTGAAATCTGTTCTTGAAGAAGGTGGTTGGTCAAACTTGGTGgtgagttgag ... ttatttttagTGTTCAAGGGAGGATCATGCAAAGAGTGTTGATGTTGCAGTTCTTTTTCTT
EST: gi|88312635|gb|CI587543.1|CI587543
EST:     AGAGCTTAGTGAAATCTGTTCTTGAAGAAGGTGGTTGGTCAAACTTGGTG                         TGTTCAAGGGAGGATCATGCAAAGAGTGTTGATGTTGCAGTTCTTTTTCTT
genomic: AGAGCTTAGTGAAATCTGTTCTTGAAGAAGGTGGTTGGTCAAACTTGGTGgtgagttgag ... ttatttttagTGTTCAAGGGAGGATCATGCAAAGAGTGTTGATGTTGCAGTTCTTTTTCTT
EST: gi|29663528|gb|CB659803.1|CB659803
EST:     AGAGCTTAGTGAAATCTGTTCTTGAAGAAGGTGGTTGGTCAAACTTGGTG                         TGTTCAAGGGAGGATCATGCAAAGAGTGTTGATGTTGCAGTTCTTTTTCTT
genomic: AGAGCTTAGTGAAATCTGTTCTTGAAGAAGGTGGTTGGTCAAACTTGGTGgtgagttgag ... ttatttttagTGTTCAAGGGAGGATCATGCAAAGAGTGTTGATGTTGCAGTTCTTTTTCTT
EST: gi|33679537|gb|CF307776.1|CF307776
EST:     GAGCTTAGTGAAATCTGTTCTTGAAGAAGGGTGGTTGGTCAAACTTGGTG                         TGTTCAAGGGAGGATCATGCAAAGAGGGTTGATGTTGCAGTTCTTTTTCTT
genomic: GAGCTTAGTGAAATCTGTTCTTGAAGAAGG-TGGTTGGTCAAACTTGGTGgtgagttgag ... ttatttttagTGTTCAAGGGAGGATCATGCAAAGAGTGTTGATGTTGCAGTTCTTTTTCTT
EST: gi|29658170|gb|CB654445.1|CB654445
EST:     AGAGCTTAGTGAAATCTGTTCTTGAAGAAGGTGGTTGGTCAAACTTGGTG                         TGTTCAAGGGAGGATCATGCAAAGAGTGTTGATGTTGCAGTTCTTTTTCTT
genomic: AGAGCTTAGTGAAATCTGTTCTTGAAGAAGGTGGTTGGTCAAACTTGGTGgtgagttgag ... ttatttttagTGTTCAAGGGAGGATCATGCAAAGAGTGTTGATGTTGCAGTTCTTTTTCTT
EST: gi|88316617|gb|CI622863.1|CI622863
EST:     AGAGCTTAGTGAAATCTGTTCTTGAAGAAGGTGGTTGGTCAAACTTGGTG                         TGTTCAAGGGAGGATCATGCAAAGAGTGTTGATGTTGCAGTTCTTTTTCTT
genomic: AGAGCTTAGTGAAATCTGTTCTTGAAGAAGGTGGTTGGTCAAACTTGGTGgtgagttgag ... ttatttttagTGTTCAAGGGAGGATCATGCAAAGAGTGTTGATGTTGCAGTTCTTTTTCTT
EST: gi|58664366|gb|CK053052.1|CK053052
EST:     AGAGCTTAGTGAAATCTGTTCTTGAAGACGGTGGTTGGTCAAACTTGGTG                         TGTTCAAGGGAGGATCATGCAAAGAGTGTTGATGTTGCAGTTCTTTTTCTT
genomic: AGAGCTTAGTGAAATCTGTTCTTGAAGAAGGTGGTTGGTCAAACTTGGTGgtgagttgag ... ttatttttagTGTTCAAGGGAGGATCATGCAAAGAGTGTTGATGTTGCAGTTCTTTTTCTT
EST: gi|58677950|gb|CK066637.1|CK066637
EST:     AGAGCTTAGTGAAATCTGTTCTTGAAGAAGGTGGTTGGTCAAACTTGGTG                         TGTTCAAGGGAGGATCATGCAAAGAGTGTTGATGTTGCAGTTCTTTTTCTT
genomic: AGAGCTTAGTGAAATCTGTTCTTGAAGAAGGTGGTTGGTCAAACTTGGTGgtgagttgag ... ttatttttagTGTTCAAGGGAGGATCATGCAAAGAGTGTTGATGTTGCAGTTCTTTTTCTT
EST: gi|88332593|gb|CI651753.1|CI651753
EST:     AGAGCTTAGTGAAATCTGTTCTTGAAGAAGGTGGTTGGTCAAACTTGGTG                         TGTTCAAGGGAGGATCATGCAAAGAGTGTTGATGTTGCAGTTCTTTTTCTT
genomic: AGAGCTTAGTGAAATCTGTTCTTGAAGAAGGTGGTTGGTCAAACTTGGTGgtgagttgag ... ttatttttagTGTTCAAGGGAGGATCATGCAAAGAGTGTTGATGTTGCAGTTCTTTTTCTT
EST: gi|29678424|gb|CB674699.1|CB674699
EST:     AGAGCTTAGTGAAATCTGTTCTTGAAGAAGGTGGTTGGTCAAACTTGGTG                         TGTTCAAGGGAGGATCATGCAAAGAGTGTTGATGTTGCAGTTCTTTTTCTT
genomic: AGAGCTTAGTGAAATCTGTTCTTGAAGAAGGTGGTTGGTCAAACTTGGTGgtgagttgag ... ttatttttagTGTTCAAGGGAGGATCATGCAAAGAGTGTTGATGTTGCAGTTCTTTTTCTT
EST: gi|33822526|gb|CF337070.1|CF337070
EST:     AGAGCTTAGTGAAATCTGTTCTTGAAGAAGGTGGTTGGTCAAACTTGGTG                         TGTTCAAGGGAGGATCATGCAAAGAGTGTTGATGTTGCAGTTCTTTTTCTT
genomic: AGAGCTTAGTGAAATCTGTTCTTGAAGAAGGTGGTTGGTCAAACTTGGTGgtgagttgag ... ttatttttagTGTTCAAGGGAGGATCATGCAAAGAGTGTTGATGTTGCAGTTCTTTTTCTT
EST: gi|86906721|gb|CI291169.1|CI291169
EST:     AGAGCTTAGTGAAATCTGTTCTTGAAGAAGGTGGTTGGTCAAACTTGGTG                         TGTTCAAGGGAGGATCATGCAAAGAGTGTTGATGTTGCAGTTCTTTTTCTT
genomic: AGAGCTTAGTGAAATCTGTTCTTGAAGAAGGTGGTTGGTCAAACTTGGTGgtgagttgag ... ttatttttagTGTTCAAGGGAGGATCATGCAAAGAGTGTTGATGTTGCAGTTCTTTTTCTT
EST: gi|33658022|gb|CF280636.1|CF280636
EST:     AGAGCTTAGTGAAATCTGTTCTTGAAGAAGGTGGTTGGTCAAACTTGGTG                         TGTTCAAGGGAGGATCATGCAAAGAGTGTNTGATGTTGCAGTTCTTTTTCT
genomic: AGAGCTTAGTGAAATCTGTTCTTGAAGAAGGTGGTTGGTCAAACTTGGTGgtgagttgag ... ttatttttagTGTTCAAGGGAGGATCATGCAAAGAGTGT-TGATGTTGCAGTTCTTTTTCT
EST: gi|58598104|gb|CK008632.1|CK008632
EST:     AGAGCTTAGTGAAATCTGTTCTTGAAGAAGGTGGTTGGTCAAACTTGGTG                         TGTTCAAGGGAGGATCATGCAAAGAGTGTTGATGTTGCAGTTCTTTTTCTT
genomic: AGAGCTTAGTGAAATCTGTTCTTGAAGAAGGTGGTTGGTCAAACTTGGTGgtgagttgag ... ttatttttagTGTTCAAGGGAGGATCATGCAAAGAGTGTTGATGTTGCAGTTCTTTTTCTT
EST: gi|88728556|gb|CI752066.1|CI752066
EST:     AGAGCTTAGTGAAATCTGTTCTTGAAGAAGGTGGTTGGTCAAACTTGGTG                         TGTTCAAGGGAGGATCATGCAAAGAGTGTTGATGTTGCAGTTCTTTTTCTT
genomic: AGAGCTTAGTGAAATCTGTTCTTGAAGAAGGTGGTTGGTCAAACTTGGTGgtgagttgag ... ttatttttagTGTTCAAGGGAGGATCATGCAAAGAGTGTTGATGTTGCAGTTCTTTTTCTT
EST: gi|88445308|gb|CI587202.1|CI587202
EST:     AGAGCTTAGTGAAATCTGTTCTTGAAGAAGGTGGTTGGTCAAACTTGGTG                         TGTTCAAGGGAGGATCATGCAAAGAGTGTTGATGTTGCAGTTCTTTTTCTT
genomic: AGAGCTTAGTGAAATCTGTTCTTGAAGAAGGTGGTTGGTCAAACTTGGTGgtgagttgag ... ttatttttagTGTTCAAGGGAGGATCATGCAAAGAGTGTTGATGTTGCAGTTCTTTTTCTT
EST: gi|88696206|gb|CI739781.1|CI739781
EST:     AGAGCTTAGTGAAATCTGTTCTTGAAGAAGGTGGTTGGTCAAACTTGGTG                         TGTCCAAGGGAGGATCATGCAAAGAGTGTTGATGTTGCAGTTCT
genomic: AGAGCTTAGTGAAATCTGTTCTTGAAGAAGGTGGTTGGTCAAACTTGGTGgtgagttgag ... ttatttttagTGTTCAAGGGAGGATCATGCAAAGAGTGTTGATGTTGCAGTTCT
EST: gi|29624905|gb|CB629916.1|CB629916
EST:     AGAGCTTAGTGAAATCTGTTCTTGAAGAAGGTGGTTGGTCAAACTTGGTG                         TGTTCAAGGGAGGATCATGCAAAGAGTGTTGATGTTGCAGTTCTTTTTCTT
genomic: AGAGCTTAGTGAAATCTGTTCTTGAAGAAGGTGGTTGGTCAAACTTGGTGgtgagttgag ... ttatttttagTGTTCAAGGGAGGATCATGCAAAGAGTGTTGATGTTGCAGTTCTTTTTCTT
EST: gi|2428191|gb|C72654.1|C72654
EST:     AGAGCTTAGTGAAATCTGTTCTTGAAGAAGGTGGTTGGTCAAACTTGGTG                         TGTTCAAGGGAGGATCATGCAAAGAGTGTTGATGTTGCAGTTCTTTTTCTT
genomic: AGAGCTTAGTGAAATCTGTTCTTGAAGAAGGTGGTTGGTCAAACTTGGTGgtgagttgag ... ttatttttagTGTTCAAGGGAGGATCATGCAAAGAGTGTTGATGTTGCAGTTCTTTTTCTT
EST: gi|58694105|gb|CK082792.1|CK082792
EST:     AGAGCTTAGTGAAATCTGTTCTTGAAGAAGGTGGTTGGTCAAACTTGGTG                         TGTTCAAGGGAGGATCATGCAAAGAGTGTTGATGTTGCAGTTCTTTTTCTT
genomic: AGAGCTTAGTGAAATCTGTTCTTGAAGAAGGTGGTTGGTCAAACTTGGTGgtgagttgag ... ttatttttagTGTTCAAGGGAGGATCATGCAAAGAGTGTTGATGTTGCAGTTCTTTTTCTT

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: 71 (upstream exon), 75 (downstream exon)
Score: 60

CTCTTCTGATGAGGCTAAAGAAATAGTCCATTATCAGACAGTATCCCCGAAGAGCTTAGTGAAATCTGTTCTTGAAGAAGGTGGTTGGTCAAACTTGGTGgtgagttgag ... ttatttttagTGTTCAAGGGAGGATCATGCAAAGAGTGTTGATGTTGCAGTTCTTTTTCTTGGCTCGAAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgtgcacaaaatttaagtcttaaacaattcataacattgtgattttatttttagTGTTCAAGGGAGGATCATGCAAAGAGTGTTGATGTTGCAGTTCTTTTTCTTGGCTCGAAG
                             tcataac  putative branch site (score: 60)
                                           ttttattttt  putative PPT
                    ttaaacaattcataac  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagttgagttccccccacgtcctagttgatgcacctcaattcacgaacaactggccaacttcattgcagtatctgttcttattgtgcacaaaatttaagtcttaaacaattcataacattgtgattttatttttagTGTTCAAGGGAGGATCATGCAAAGAGTGTTGATGTTGCAGTTCTTTTTCTTGGCTCGAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG