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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tcacttttgaggaaaaagacacttttttcttgctgttgtgcctgactaaggttagcattgaaccggtatctttctgatggctttgtccgcctattttcagGTGCGCTATCAGAGCAGAAAGAGGTTGGCTGAGCAGCGCCCTCGGATCCGCGGGCAATTCGTGCGACAATCTGGACAGGAAGATCAGGCAGGCCAAGACG

Basic information

species Oryza sativa
transcript LOC_Os03g17570.1
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g17570.5 (Oryza sativa), 3'ss of exon 11
lower sequence: GRMZM2G095727_T04 (Zea mays), 3'ss of exon 11
----tcacttttgaggaaaaagacacttttttcttgctgttgtgcctgactaag-gttagcattgaaccggtatctttctgatggctttgtccgcctattttcagGTGCGCTATCAGAGCAGAAAGAGGTTGGCTGAGCAGCGCCCTCGGATCCGCGGGCAATTCGTGCGACAATCTGGACAGGAAGATCAGGCAGGCCAAGACG
     || ||||     | ||||   | |  |||||| | |     |  || |  ||| |||||| |||| || ||| |||||||| |||||||||||||||||||| ||||| || ||||| |||||| | ||||||||||| || ||| |||| || || || |||||||||||||  || ||||||||  |||  ||||   
gactgcagtttt----tacaagattttatggtcttgccgcttcatttttctgactgtttgcattggaccgatacctt-ctgatggccttgtccgcctattttcagGTTCGCTACCAAAGCAGGAAGAGGCTTGCTGAGCAGCGGCCACGGGTCCGAGGACAGTTTGTGCGACAATCTGAGCAAGAAGATCAAACAGCGCAAGGTT
















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|87021094|gb|CI271901.1|CI271901
EST:     CATTGAACAAATTCAGACAGAAACGGAAAGTGAGGAACTTTGGAAAAAAG                         GTGCGCTATCAGAGCAGAAAGAGGTTGGCTGAGCAGCGCCCTCGGATCCGC
genomic: CATTGAACAAATTCAGACAGAAACGGAAAGTGAGGAACTTTGGAAAAAAGgtagcctgtt ... ctattttcagGTGCGCTATCAGAGCAGAAAGAGGTTGGCTGAGCAGCGCCCTCGGATCCGC
EST: gi|29642420|gb|CB647427.1|CB647427
EST:     CATTGAACAAATTCAGACAGAAACGGAAAGTGAGGAACTTTGGAAAAAAG                         GTGCGCTATCAGAGCAGAAAGAGGTTGGCTGAGCAGCGCCCTCGGATCCGC
genomic: CATTGAACAAATTCAGACAGAAACGGAAAGTGAGGAACTTTGGAAAAAAGgtagcctgtt ... ctattttcagGTGCGCTATCAGAGCAGAAAGAGGTTGGCTGAGCAGCGCCCTCGGATCCGC
EST: gi|86479881|gb|CI122514.1|CI122514
EST:     CATTGAACAAATTCAGACAGAAACGGAAAGTGAGGAACTTTGGAAAAAAG                         GTGCGCTATCAGAGCAGAAAGAGGTTGGCTGAGCAGCGCCCTCGGATCCGC
genomic: CATTGAACAAATTCAGACAGAAACGGAAAGTGAGGAACTTTGGAAAAAAGgtagcctgtt ... ctattttcagGTGCGCTATCAGAGCAGAAAGAGGTTGGCTGAGCAGCGCCCTCGGATCCGC
EST: gi|25778066|gb|CA752818.1|CA752818
EST:     CATTGAACAAATTCAGACAGAAACGGAAAGTGAGGAACTTTGGAAAAAAG                         GTGCGCTATCAGAGCAGAAAGAGGTTGGCTGAGCATCTGCCCTCGGATCCG
genomic: CATTGAACAAATTCAGACAGAAACGGAAAGTGAGGAACTTTGGAAAAAAGgtagcctgtt ... ctattttcagGTGCGCTATCAGAGCAGAAAGAGGTTGGCTGAGCAGC-GCCCTCGGATCCG
EST: gi|86482506|gb|CI125139.1|CI125139
EST:     CATTGAACGAATTCAGACAGAAACGGAAAGTGAGGAACTTTGGAAAAAAG                         GTGCGCTATCAGAGCAGAAAGAGGTTGGCTGAGCAGCGCCCTCGGATCCGC
genomic: CATTGAACAAATTCAGACAGAAACGGAAAGTGAGGAACTTTGGAAAAAAGgtagcctgtt ... ctattttcagGTGCGCTATCAGAGCAGAAAGAGGTTGGCTGAGCAGCGCCCTCGGATCCGC
EST: gi|218499020|gb|FG959222.1|FG959222
EST:     CATTGAACAAATTCAGACAGAAACGGCAAGTGAGGAACTTTGGAAAAAAG                         GTGCGCTATCAGAGCAGAAAGAGGTTGGCTGAGCAGCGCCCTCGGATCCGC
genomic: CATTGAACAAATTCAGACAGAAACGGAAAGTGAGGAACTTTGGAAAAAAGgtagcctgtt ... ctattttcagGTGCGCTATCAGAGCAGAAAGAGGTTGGCTGAGCAGCGCCCTCGGATCCGC
EST: gi|29668908|gb|CB665183.1|CB665183
EST:     CATTGAACAAATTCAGACAGAAACGGAAAGTGAGGAACTTTGGAAAAAAG                         GTGCGCTATCAGAGCAGAAAGAGGTTGGTTGAGCAGCGCCCTCGGATCCGC
genomic: CATTGAACAAATTCAGACAGAAACGGAAAGTGAGGAACTTTGGAAAAAAGgtagcctgtt ... ctattttcagGTGCGCTATCAGAGCAGAAAGAGGTTGGCTGAGCAGCGCCCTCGGATCCGC
EST: gi|87029858|gb|CI274539.1|CI274539
EST:     CATTGAACAAATTCAGACAGAAACGGAAAGTGAGGAACTTTGGAAAAAAG                         GTGCGCTATCAGAGCAGAAAGAGGTTGGCTGAGCAGCGCCCTCGGATCCGC
genomic: CATTGAACAAATTCAGACAGAAACGGAAAGTGAGGAACTTTGGAAAAAAGgtagcctgtt ... ctattttcagGTGCGCTATCAGAGCAGAAAGAGGTTGGCTGAGCAGCGCCCTCGGATCCGC
EST: gi|88226911|gb|CI224679.1|CI224679
EST:     CATTGAACAAATTCAGACAGAAACGGAAAGTGAGGAACTTTGGAAAAAAG                         GTGCGCTATCAGAGCAGAAAGAGGTTGGCTGAGCAGCGCCCTCGGATCCGC
genomic: CATTGAACAAATTCAGACAGAAACGGAAAGTGAGGAACTTTGGAAAAAAGgtagcctgtt ... ctattttcagGTGCGCTATCAGAGCAGAAAGAGGTTGGCTGAGCAGCGCCCTCGGATCCGC
EST: gi|29641357|gb|CB646364.1|CB646364
EST:     CATTGAACAAATTCAGACAGAAACGGAAAGTGAGGAACTTTGGAAAAAAG                         GTGCGCTATCAGAGCAGAAAGAGGTTGGCTGAGCAGCGCCCTCGGATCCGC
genomic: CATTGAACAAATTCAGACAGAAACGGAAAGTGAGGAACTTTGGAAAAAAGgtagcctgtt ... ctattttcagGTGCGCTATCAGAGCAGAAAGAGGTTGGCTGAGCAGCGCCCTCGGATCCGC
EST: gi|88198221|gb|CI198071.1|CI198071
EST:     CATTGAACAAATTCAGACAGAAACGGAAAGTGAGGAACTTTGGAAAAAAG                         GTGCGCTATCAGAGCAGAAAGAGGTTGGCTGAGCAGCGCCCTCGGATCCGC
genomic: CATTGAACAAATTCAGACAGAAACGGAAAGTGAGGAACTTTGGAAAAAAGgtagcctgtt ... ctattttcagGTGCGCTATCAGAGCAGAAAGAGGTTGGCTGAGCAGCGCCCTCGGATCCGC
EST: gi|29642422|gb|CB647429.1|CB647429
EST:     CATTGAACAAATTCAGACAGAAACGGAAAGTGAGGAACTTTGGAAAAAAG                         GTGCGCTATCAGAGCAGAAAGAGGTTGGCTGAGCAGCGCCCTCGGATCCGC
genomic: CATTGAACAAATTCAGACAGAAACGGAAAGTGAGGAACTTTGGAAAAAAGgtagcctgtt ... ctattttcagGTGCGCTATCAGAGCAGAAAGAGGTTGGCTGAGCAGCGCCCTCGGATCCGC
EST: gi|29617887|gb|CB622899.1|CB622899
EST:     CATTGAACAAATTCAGACAGAAACGGAAAGTGAGGAACTTCGGAAAAAAG                         GTGCGCTATCAGAGCAGAAAGAGGTTGGCTGAGCAGCGCCCTCGGATCCGC
genomic: CATTGAACAAATTCAGACAGAAACGGAAAGTGAGGAACTTTGGAAAAAAGgtagcctgtt ... ctattttcagGTGCGCTATCAGAGCAGAAAGAGGTTGGCTGAGCAGCGCCCTCGGATCCGC
EST: gi|86833914|gb|CI338285.1|CI338285
EST:     CATTGAACAAATTCAGACAGAAACGGAAAGTGAGGAACTTTGGAAAAAAG                         GTGCGCTATCAGACCAGAAAGAGGTTGGCTGAGCAGCGCCCTCGGATCCGC
genomic: CATTGAACAAATTCAGACAGAAACGGAAAGTGAGGAACTTTGGAAAAAAGgtagcctgtt ... ctattttcagGTGCGCTATCAGAGCAGAAAGAGGTTGGCTGAGCAGCGCCCTCGGATCCGC
EST: gi|86479862|gb|CI122495.1|CI122495
EST:     CATTGAACAAATTCAGACAGAAACGGAAAGTGAGGAACTTTGGAAAAAAG                         GTGCGCTATCAGAGCAGAAAGAGGTTGGCTGAGCAGCGCCCTCGGATCCGC
genomic: CATTGAACAAATTCAGACAGAAACGGAAAGTGAGGAACTTTGGAAAAAAGgtagcctgtt ... ctattttcagGTGCGCTATCAGAGCAGAAAGAGGTTGGCTGAGCAGCGCCCTCGGATCCGC
EST: gi|8856605|gb|AU093923.1|AU093923
EST:     CATTGAACAATTTCAGCCAGAACCGGAAAGTGAGGAACTTTGGAAAAAA-                         GTGCGCTATCAGAGCAGAAAGAGGTTGGCTGAGCAGCGCCCTCGGATCCGC
genomic: CATTGAACAAATTCAGACAGAAACGGAAAGTGAGGAACTTTGGAAAAAAGgtagcctgtt ... ctattttcagGTGCGCTATCAGAGCAGAAAGAGGTTGGCTGAGCAGCGCCCTCGGATCCGC
EST: gi|29661059|gb|CB657334.1|CB657334
EST:     CATTGAACAAATTCAGACAGAAACGGAAAGTGAGGAACTTTGGAAAAAAG                         GTGCGCTATCAGAGCAGAAAGAGGTTGGCTGAGCAGCGCCCTCGGATCCGC
genomic: CATTGAACAAATTCAGACAGAAACGGAAAGTGAGGAACTTTGGAAAAAAGgtagcctgtt ... ctattttcagGTGCGCTATCAGAGCAGAAAGAGGTTGGCTGAGCAGCGCCCTCGGATCCGC
EST: gi|88455358|gb|CI519379.1|CI519379
EST:     CATTGAACAAATTCAGACAGAAACGGAAAGTGAGGAACTTTGGAAAAAAG                         GTGCGCTATCAGAGCAGAAAGAGGTTGGGTGAGCAGCGCCCTCGGATCCGC
genomic: CATTGAACAAATTCAGACAGAAACGGAAAGTGAGGAACTTTGGAAAAAAGgtagcctgtt ... ctattttcagGTGCGCTATCAGAGCAGAAAGAGGTTGGCTGAGCAGCGCCCTCGGATCCGC
EST: gi|86524675|gb|CI164881.1|CI164881
EST:     CATTGAACAAATTCAGACAGAAACGGAAAGTGAGGAACTTTGGAAAAAAG                         GTGCGCTATCAGAGCAGAAAGAGGTTGGCTGAGCAGCGCCCTCGGATCCGC
genomic: CATTGAACAAATTCAGACAGAAACGGAAAGTGAGGAACTTTGGAAAAAAGgtagcctgtt ... ctattttcagGTGCGCTATCAGAGCAGAAAGAGGTTGGCTGAGCAGCGCCCTCGGATCCGC
EST: gi|86836725|gb|CI347351.1|CI347351
EST:     CATTGAACAAATTCAGACAGAAACGGAAAGTGAGGAACTTTGGAAAAAAG                         GTGCGCTATCAGAGCAGAAAGAGGTTGGCTGAGCAGCGCCCTCGGATCCGC
genomic: CATTGAACAAATTCAGACAGAAACGGAAAGTGAGGAACTTTGGAAAAAAGgtagcctgtt ... ctattttcagGTGCGCTATCAGAGCAGAAAGAGGTTGGCTGAGCAGCGCCCTCGGATCCGC
EST: gi|88246442|gb|CI246291.1|CI246291
EST:     CATTGAACAAATTCAGACAGAAACGGAAAGTGAGGAACTTTGGAAAAAAG                         GTGCGCTATCAGAGCAGAAAGAGGTTGGCTGAGCAGCGCCCTCGGATCCGC
genomic: CATTGAACAAATTCAGACAGAAACGGAAAGTGAGGAACTTTGGAAAAAAGgtagcctgtt ... ctattttcagGTGCGCTATCAGAGCAGAAAGAGGTTGGCTGAGCAGCGCCCTCGGATCCGC
EST: gi|84117030|gb|CD150797.1|CD150797
EST:     CATTGAACAAATTCAGACAGAAACGGAAAGTGAGGAACTTTGGAAAAAAG                         GTGCGCTATCAGAGCAGAAAGAGGTTGGCTGAGCAGCGCCCTCGGATCCGC
genomic: CATTGAACAAATTCAGACAGAAACGGAAAGTGAGGAACTTTGGAAAAAAGgtagcctgtt ... ctattttcagGTGCGCTATCAGAGCAGAAAGAGGTTGGCTGAGCAGCGCCCTCGGATCCGC
EST: gi|218484896|gb|FG966546.1|FG966546
EST:     CATTGAACAAATTCAGACAGAAACGGAAAGTGAGGAACTTTGGAAAAAAG                         GTGCGCTATCAGAGCAGAAAGAGGTTGGCTGAGCAGCGCCCTCGGATCCGC
genomic: CATTGAACAAATTCAGACAGAAACGGAAAGTGAGGAACTTTGGAAAAAAGgtagcctgtt ... ctattttcagGTGCGCTATCAGAGCAGAAAGAGGTTGGCTGAGCAGCGCCCTCGGATCCGC
EST: gi|86415638|gb|CI029649.1|CI029649
EST:     CATTGAACAAATTCAGACAGAAACGGAAAGTGAGGAACTTTGGAAAAAAG                         GTGCGCTATCAGAGCAGAAAGAGGTTGGCTGAGCAGCGCCCTCGGATCCGC
genomic: CATTGAACAAATTCAGACAGAAACGGAAAGTGAGGAACTTTGGAAAAAAGgtagcctgtt ... ctattttcagGTGCGCTATCAGAGCAGAAAGAGGTTGGCTGAGCAGCGCCCTCGGATCCGC
EST: gi|29623118|gb|CB628129.1|CB628129
EST:     CATTGAACAAATTCAGACAGAAACGGAAAGTGAGGAACTTTGGAAAAAAG                         GTGCGCTATCAGAGCAGAAAGAGGTTGGCTGAGCAGCGCCCTCGGATCCGC
genomic: CATTGAACAAATTCAGACAGAAACGGAAAGTGAGGAACTTTGGAAAAAAGgtagcctgtt ... ctattttcagGTGCGCTATCAGAGCAGAAAGAGGTTGGCTGAGCAGCGCCCTCGGATCCGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctaaggttagcattgaaccggtatctttctgatggctttgtccgcctattttcagGTGCGCTATCAGAGCAGAAAGAGGTTGGCTGAGCAGCGCCCTCGGATCCGCGGGCAATTCGTGCGACAATCTGGACAGGAAGATCAGGCAGGCCAAGACG
                          ttctgat  putative branch site (score: 3)
                                            cctattttc  putative PPT
                                              tattttca  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tcacttttgaggaaaaagacacttttttcttgctgttgtgcctgactaaggttagcattgaaccggtatctttctgatggctttgtccgcctattttcagGTGCGCTATCAGAGCAGAAAGAGGTTGGCTGAGCAGCGCCCTCGGATCCGCGGGCAATTCGTGCGACAATCTGGACAGGAAGATCAGGCAGGCCAAGACG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGATCA