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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gaagttctcctggtttttcttttgcgaagcttaattcattatgcgctccatgtctccatttgtacccgatacactaactcaattcaatttctttcttcagGTTTTCTCAAAATTATCCGAACAGAGATTTCCCAGCGAGTTTGAGCTACGGGAGCTCATTGGCAACAGGTTACCAGATTCTCAATTCGGGAAAAATCTGG

Basic information

species Oryza sativa
transcript LOC_Os01g61580.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g61580.2 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM5G897342_T02 (Zea mays), 3'ss of exon 3
----gaagttctcctg-gtttttcttttgcgaagcttaattcattatgcgctccatgtctccatttgtacccgatacactaactcaattcaatttctttcttcagGTTTTCTCAAAATTATCCGAACAGAGATTTCCCAGCGAGTTTGAGCTACGGGAGCTCATTGGCAACAGGTTACCAGATTCTCAATTCGGGAAAAATCTGG
    |||    |||||  |||  ||||| || | || ||||  ||||||   | |   ||  || ||       ||  ||| |  ||||    | |  | ||||||||||||| ||| | || || ||||| ||||| || ||  ||||||||| ||||||||||||||  ||| |||| ||||||||  | |   |||||||||
gtttgaaccattcctgcatttcccttttccgtaactgaatttcttatgcagccgac--ctggatgtgccttgcttatgctagc--aatttt-ctccacttttcagGTTTTCTCCAAACTGTCTGAGCAGAGGTTTCCTAGTGAACTTGAGCTACAGGAGCTCATTGGCAGTAGGATACCGGATTCTCAGATTGTAGAAAATCTGG
















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|88961030|gb|CI096433.1|CI096433
EST:     CATTTCTACAAAGTTCTGGTGCCTTTGAAGTTTACTGCAATGGACAATTG                         GTTTTCTCAAAATTATCCGAACAGAGATTTCCCAGCGAGTTTGAGCTACGG
genomic: CATTTCTACAAAGTTCTGGTGCCTTTGAAGTTTACTGCAATGGACAATTGgtatgtttgt ... ctttcttcagGTTTTCTCAAAATTATCCGAACAGAGATTTCCCAGCGAGTTTGAGCTACGG
EST: gi|86546432|gb|CI186638.1|CI186638
EST:     CATTTCTACAAAGTTCTGGTGCCTTTGAAGTTTACTGCAATGGACAATTG                         GTTTTCTCAAAATTATCCGAACAGAGATTTCCCAGCGAGTTTGAGCTACGG
genomic: CATTTCTACAAAGTTCTGGTGCCTTTGAAGTTTACTGCAATGGACAATTGgtatgtttgt ... ctttcttcagGTTTTCTCAAAATTATCCGAACAGAGATTTCCCAGCGAGTTTGAGCTACGG
EST: gi|86524805|gb|CI165011.1|CI165011
EST:     CATTTCTACAAAGTTCTGGTGCCTTTGAAGTTTACTGCAATGGACAATTG                         GTTTTCTCAAAATTATCCGAACAGAGATTTCCCAGCGAGTTTGAGCTACGG
genomic: CATTTCTACAAAGTTCTGGTGCCTTTGAAGTTTACTGCAATGGACAATTGgtatgtttgt ... ctttcttcagGTTTTCTCAAAATTATCCGAACAGAGATTTCCCAGCGAGTTTGAGCTACGG
EST: gi|88275678|gb|CI396282.1|CI396282
EST:     TACAAAGTTCTGGTGCCTTTGAAGTTTACTGCAATGGACAATTG                         GTTTTCTCAAAATTATCCGAACAGAGATTTCCCAGCGAGTTTGAGCTACGG
genomic: TACAAAGTTCTGGTGCCTTTGAAGTTTACTGCAATGGACAATTGgtatgtttgt ... ctttcttcagGTTTTCTCAAAATTATCCGAACAGAGATTTCCCAGCGAGTTTGAGCTACGG
EST: gi|4716087|gb|AU057203.1|AU057203
EST:     CAAAGNTCTGGTGCCTTTGAAGTTTACTGCAATGGACAATTG                         GTTTTCTCAAAATTANCCGAACAGAGATTTCCCAGCGAGTTTGAGCTACGG
genomic: CAAAGTTCTGGTGCCTTTGAAGTTTACTGCAATGGACAATTGgtatgtttgt ... ctttcttcagGTTTTCTCAAAATTATCCGAACAGAGATTTCCCAGCGAGTTTGAGCTACGG
EST: gi|86592813|gb|CI268478.1|CI268478
EST:     CATTTCTACAAAGTTCTGGTGCCTTTGAAGTTTACTGCAATGGACAATTG                         GTTTTCTCAAAATTATCCGAACAGAGATTTCCCAGCGAGTTTGAGCTACGG
genomic: CATTTCTACAAAGTTCTGGTGCCTTTGAAGTTTACTGCAATGGACAATTGgtatgtttgt ... ctttcttcagGTTTTCTCAAAATTATCCGAACAGAGATTTCCCAGCGAGTTTGAGCTACGG
EST: gi|38478140|gb|CF962273.1|CF962273
EST:     CATTTCTACAAAGTTCTGGTGCCTTTGAAGTTTACTGCAATGGACAATTG                         GTTTTCTCAAAATTATCCGAACAGAGATTTCCCAGCGAGTTTGAGCTACGG
genomic: CATTTCTACAAAGTTCTGGTGCCTTTGAAGTTTACTGCAATGGACAATTGgtatgtttgt ... ctttcttcagGTTTTCTCAAAATTATCCGAACAGAGATTTCCCAGCGAGTTTGAGCTACGG
EST: gi|86417092|gb|CI031301.1|CI031301
EST:     CATTTCTACAAAGTTCTGGTGCCTTTGAAGTTTACTGCAATGGACAATTG                         GTTTTCTCAAAATTATCCGAACAGAGATTTCCCAGCGAGTTTGAGCTACGG
genomic: CATTTCTACAAAGTTCTGGTGCCTTTGAAGTTTACTGCAATGGACAATTGgtatgtttgt ... ctttcttcagGTTTTCTCAAAATTATCCGAACAGAGATTTCCCAGCGAGTTTGAGCTACGG
EST: gi|88256858|gb|CI354639.1|CI354639
EST:     CATTTCTACAAAGTTCTGGTGCCTTTGAAGTTTACTGCAATGGACAATTG                         GTTTTCTCAAAATTATCCGAACAGAGATTTCCCAGCGAGTTTGAGCTACGG
genomic: CATTTCTACAAAGTTCTGGTGCCTTTGAAGTTTACTGCAATGGACAATTGgtatgtttgt ... ctttcttcagGTTTTCTCAAAATTATCCGAACAGAGATTTCCCAGCGAGTTTGAGCTACGG
EST: gi|117222253|gb|CT845768.1|CT845768
EST:     CATTTCTACAAAGTTCTGGTGCCTTTGAAGTTTACTGCAATGGACAATTG                         GTTTTCTCAAAATTATCCGAACAGAGATTTCCCAGCGAGTTTGAGCTACGG
genomic: CATTTCTACAAAGTTCTGGTGCCTTTGAAGTTTACTGCAATGGACAATTGgtatgtttgt ... ctttcttcagGTTTTCTCAAAATTATCCGAACAGAGATTTCCCAGCGAGTTTGAGCTACGG
EST: gi|86546211|gb|CI186417.1|CI186417
EST:     TCTGGTGCCTTTGAAGTTTACTGCAATGGACAATTG                         GTTTTCTCAAAATTATCCGAACAGAGATTTCCCAGCGAGTTTGAGCTACGG
genomic: TCTGGTGCCTTTGAAGTTTACTGCAATGGACAATTGgtatgtttgt ... ctttcttcagGTTTTCTCAAAATTATCCGAACAGAGATTTCCCAGCGAGTTTGAGCTACGG
EST: gi|27577857|gb|CB000552.1|CB000552
EST:     CATTTCTACAAAGTTCTGGTGCCTTTGAAGTTTACTGCAATGGACAATTG                         GTTTTCTCAAAATTATCCGAACAGAGATTTCCCAGCGAGTTTGAGCTACGG
genomic: CATTTCTACAAAGTTCTGGTGCCTTTGAAGTTTACTGCAATGGACAATTGgtatgtttgt ... ctttcttcagGTTTTCTCAAAATTATCCGAACAGAGATTTCCCAGCGAGTTTGAGCTACGG
EST: gi|86506240|gb|CI148873.1|CI148873
EST:     CATTTCTACAAAGTTCTGGTGCCTTTGAAGTTTACTGCAATGGACATTTG                         GTTTTCTCAAAATTATCCGAACAGAGATTTCCCAGCGAGTTTGAGCTATGG
genomic: CATTTCTACAAAGTTCTGGTGCCTTTGAAGTTTACTGCAATGGACAATTGgtatgtttgt ... ctttcttcagGTTTTCTCAAAATTATCCGAACAGAGATTTCCCAGCGAGTTTGAGCTACGG
EST: gi|86851376|gb|CI313974.1|CI313974
EST:     CATTTCTACAAAGTTCTGGTGCCTTTGAAGTTTACTCCAATGGACAATTG                         GTTTTCTCAAAATTATCCGAACAGAGATTTCCCAGCGATTTTGAGCTACGG
genomic: CATTTCTACAAAGTTCTGGTGCCTTTGAAGTTTACTGCAATGGACAATTGgtatgtttgt ... ctttcttcagGTTTTCTCAAAATTATCCGAACAGAGATTTCCCAGCGAGTTTGAGCTACGG
EST: gi|87014668|gb|CI269375.1|CI269375
EST:     CATTTCTACAAAGTTCTGGTGCCTTTGAAGTTTACTGCAATGGACAATTG                         GTTTTCTCAAAATTATCCGAACAGAGATTTCCCAGCGAGTTTGAGCTACGG
genomic: CATTTCTACAAAGTTCTGGTGCCTTTGAAGTTTACTGCAATGGACAATTGgtatgtttgt ... ctttcttcagGTTTTCTCAAAATTATCCGAACAGAGATTTCCCAGCGAGTTTGAGCTACGG
EST: gi|88829948|gb|CI004986.1|CI004986
EST:     CATTTCTACAAAGTTCTGGTGCCTTTGAAGTTTACTGCAATGGACAATTG                         GTTTTCTCAAAATTATCCGAACAGAGATTTCCCAGCGAGTTTGAGCTACGG
genomic: CATTTCTACAAAGTTCTGGTGCCTTTGAAGTTTACTGCAATGGACAATTGgtatgtttgt ... ctttcttcagGTTTTCTCAAAATTATCCGAACAGAGATTTCCCAGCGAGTTTGAGCTACGG
EST: gi|86593760|gb|CI266440.1|CI266440
EST:     CATTTCTACAAAGTTCTGGTGCCTTTGAAGTTTACTGCAATGGACAATTG                         GTTTTCTCAAAATTATCCGAACAGAGATTTCCCAGCGAGTTTGAGCTACGG
genomic: CATTTCTACAAAGTTCTGGTGCCTTTGAAGTTTACTGCAATGGACAATTGgtatgtttgt ... ctttcttcagGTTTTCTCAAAATTATCCGAACAGAGATTTCCCAGCGAGTTTGAGCTACGG
EST: gi|88200678|gb|CI200528.1|CI200528
EST:     CATTTCTACAAAGTTCTGGTGCCTTTGGAGTTTACTGCAATGGACAATTG                         GTTTTCTCAAAATTATCCGAACAGAGATTTCCCAGCGAGTTTGAGCCACGG
genomic: CATTTCTACAAAGTTCTGGTGCCTTTGAAGTTTACTGCAATGGACAATTGgtatgtttgt ... ctttcttcagGTTTTCTCAAAATTATCCGAACAGAGATTTCCCAGCGAGTTTGAGCTACGG
EST: gi|14192083|gb|AU184294.1|AU184294
EST:     TACTGCAATGGACAATTG                         GTTTTCTCAAAATTATCCGAACAGAGATTTCCCAGCGAGTTTGAGCTACGG
genomic: TACTGCAATGGACAATTGgtatgtttgt ... ctttcttcagGTTTTCTCAAAATTATCCGAACAGAGATTTCCCAGCGAGTTTGAGCTACGG
EST: gi|86502952|gb|CI145585.1|CI145585
EST:     CATTTCTACAAAGTTCTGGTGCCTTTGAAGTTTACTGCAATGGACAATTG                         GTTTTCTCAAAATTATCCGAACAGAGATTTCCCAGCGAGTTTGAGCTACGG
genomic: CATTTCTACAAAGTTCTGGTGCCTTTGAAGTTTACTGCAATGGACAATTGgtatgtttgt ... ctttcttcagGTTTTCTCAAAATTATCCGAACAGAGATTTCCCAGCGAGTTTGAGCTACGG
EST: gi|87034295|gb|CI188919.1|CI188919
EST:     CATTTCTACAAAGTTCTGGTGCCTTTGAAGTTTACTGCAATGGACAATTG                         GTTTTCTCAAAATTATCCGAACAGAGATTTCCCAGCGAGTTTGAGCTACGG
genomic: CATTTCTACAAAGTTCTGGTGCCTTTGAAGTTTACTGCAATGGACAATTGgtatgtttgt ... ctttcttcagGTTTTCTCAAAATTATCCGAACAGAGATTTCCCAGCGAGTTTGAGCTACGG
EST: gi|88382080|gb|CI533284.1|CI533284
EST:     CATTTCTACAAAGTTCTGGTGCCTTTGAAGTTTACTGCAATGGACAATTG                         GTTTTCTCAAAATTATCCGAACAGAGATTTCCCAGCGAGTTTGAGGTACGG
genomic: CATTTCTACAAAGTTCTGGTGCCTTTGAAGTTTACTGCAATGGACAATTGgtatgtttgt ... ctttcttcagGTTTTCTCAAAATTATCCGAACAGAGATTTCCCAGCGAGTTTGAGCTACGG
EST: gi|86839450|gb|CI339379.1|CI339379
EST:     ACAAAGTTCTGGTGTCTTTGAAGTTTACTGCAATGGACAATTG                         GTTTTCTCAAAATTATCCGAACAGAGATTTCCCAGCGAGTTTGAGCTACGG
genomic: ACAAAGTTCTGGTGCCTTTGAAGTTTACTGCAATGGACAATTGgtatgtttgt ... ctttcttcagGTTTTCTCAAAATTATCCGAACAGAGATTTCCCAGCGAGTTTGAGCTACGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctccatgtctccatttgtacccgatacactaactcaattcaatttctttcttcagGTTTTCTCAAAATTATCCGAACAGAGATTTCCCAGCGAGTTTGAGCTACGGGAGCTCATTGGCAACAGGTTACCAGATTCTCAATTCGGGAAAAATCTGG
                          cactaac  putative branch site (score: 1)
                                     ttcaatttctttcttc  putative PPT
                                   aattcaatttcttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gaagttctcctggtttttcttttgcgaagcttaattcattatgcgctccatgtctccatttgtacccgatacactaactcaattcaatttctttcttcagGTTTTCTCAAAATTATCCGAACAGAGATTTCCCAGCGAGTTTGAGCTACGGGAGCTCATTGGCAACAGGTTACCAGATTCTCAATTCGGGAAAAATCTGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTCA