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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtccgtgacaacccccttcacgccgtcctttgatttctttcgctggtggtttttttgttcgatttgatcgcgaattgatgtgtgtgtgtgtgtgtgtttttttttttttttggtttggttttgcatgcagATTGTGACGCTGTTGCTGGAGAAGGGCGCGGATGTGAACGTACGGAACTACTGCGGGCAG

Basic information

species Oryza sativa
transcript LOC_Os10g37730.3
intron # 1
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|88424672|gb|CI606471.1|CI606471
EST:     GCGGCCTCAACTCCCCGCTCCACTTCGCCGCCGCTAAGGGCCACCTCGAC                         ATTGTGACGCTGTTGGTGGAGAAGGGCGCGGATGTGAACGTACGGAACTAC
genomic: GCGGCCTCAACTCCCCGCTCCACTTCGCCGCCGCTAAGGGCCACCTCGACgtccgtgaca ... ttgcatgcagATTGTGACGCTGTTGCTGGAGAAGGGCGCGGATGTGAACGTACGGAACTAC
EST: gi|29682101|gb|CB678376.1|CB678376
EST:     GCGGCCTCAACTCCCCGCTCCACTTCGCCGCCGCTAAGGGCCACCTCGAC                         ATTGTGACGCTGTTGCTGGAGAAGGGCGCGGATGTGAACGTACGGAACTAC
genomic: GCGGCCTCAACTCCCCGCTCCACTTCGCCGCCGCTAAGGGCCACCTCGACgtccgtgaca ... ttgcatgcagATTGTGACGCTGTTGCTGGAGAAGGGCGCGGATGTGAACGTACGGAACTAC
EST: gi|29631918|gb|CB636927.1|CB636927
EST:     GCGGCCTCAACTCCCCGCTCCACTTCGCCGCCGCTAAGGGCCACCTCGAC                         ATTGTGACGCTGTTGCTGGAGAAGGGCGCGGATGTGAACGTACGGAACTAC
genomic: GCGGCCTCAACTCCCCGCTCCACTTCGCCGCCGCTAAGGGCCACCTCGACgtccgtgaca ... ttgcatgcagATTGTGACGCTGTTGCTGGAGAAGGGCGCGGATGTGAACGTACGGAACTAC
EST: gi|88394904|gb|CI607631.1|CI607631
EST:     GCGGCCTCAACTCCCCGCTCCAATTCGCCGCCGCTAAGGGCCACCTCGAC                         ATTGTGACGCTGTTGCTGGAGAAGGG-GCGGATGTGAAGGTACGGAA
genomic: GCGGCCTCAACTCCCCGCTCCACTTCGCCGCCGCTAAGGGCCACCTCGACgtccgtgaca ... ttgcatgcagATTGTGACGCTGTTGCTGGAGAAGGGCGCGGATGTGAACGTACGGAA
EST: gi|88385475|gb|CI564135.1|CI564135
EST:     GCGGCCTCAACTCCCCGCTCCACTTCGCCGCCGCTAAGGGCCACCTCGAC                         ATTGTGACGCTGTTGCTGGAGAAGGGCGCGGATGTGAACGTACGGAACTAC
genomic: GCGGCCTCAACTCCCCGCTCCACTTCGCCGCCGCTAAGGGCCACCTCGACgtccgtgaca ... ttgcatgcagATTGTGACGCTGTTGCTGGAGAAGGGCGCGGATGTGAACGTACGGAACTAC
EST: gi|88310409|gb|CI659199.1|CI659199
EST:     GCGGCCTCAACTCCCCGCTCCACTTCGCCGCCGCTAAGGGCCANCTCGAC                         ATTGTGACGCTGTTGCTG
genomic: GCGGCCTCAACTCCCCGCTCCACTTCGCCGCCGCTAAGGGCCACCTCGACgtccgtgaca ... ttgcatgcagATTGTGACGCTGTTGCTG
EST: gi|29645490|gb|CB650497.1|CB650497
EST:     GCGGCCTCAACTCCCCGCTCCACTTCGCCGCCGCTAAGGGCCACCTCGAC                         ATTGTGACGCTGTTGCTGGAGAAGGGCGCGGATGTGAACGTACGGAACTAC
genomic: GCGGCCTCAACTCCCCGCTCCACTTCGCCGCCGCTAAGGGCCACCTCGACgtccgtgaca ... ttgcatgcagATTGTGACGCTGTTGCTGGAGAAGGGCGCGGATGTGAACGTACGGAACTAC
EST: gi|88299379|gb|CI572331.1|CI572331
EST:     GCGGCCTCAACTCCCCGCTCCACTTCGCCGCCGCTAAGGGCCACCTCGAC                         ATTGTGACGCTGTTGCTGGAGAAGGGCGCGGATGTGAACGTACGGAACTAC
genomic: GCGGCCTCAACTCCCCGCTCCACTTCGCCGCCGCTAAGGGCCACCTCGACgtccgtgaca ... ttgcatgcagATTGTGACGCTGTTGCTGGAGAAGGGCGCGGATGTGAACGTACGGAACTAC
EST: gi|86909776|gb|CI304752.1|CI304752
EST:     GCGGCCTCAACTCCCCGCTCCACTTCGCCGCCGCTAAGGGCCACCTCGAC                         ATTGTGACGCTGTTGCTGGAGAAGGGCGCGGATGTGAACGTACGGAACTAC
genomic: GCGGCCTCAACTCCCCGCTCCACTTCGCCGCCGCTAAGGGCCACCTCGACgtccgtgaca ... ttgcatgcagATTGTGACGCTGTTGCTGGAGAAGGGCGCGGATGTGAACGTACGGAACTAC
EST: gi|88314988|gb|CI610047.1|CI610047
EST:     GCGGCCTCAACTCCCCGCTCCACTTCGCCGCCGCTAAGGGCCACCTCGAC                         ATTGTGACGCTGTTGCTGGAGAAGGGCGCGGATGTGAACGTACGGAACTAC
genomic: GCGGCCTCAACTCCCCGCTCCACTTCGCCGCCGCTAAGGGCCACCTCGACgtccgtgaca ... ttgcatgcagATTGTGACGCTGTTGCTGGAGAAGGGCGCGGATGTGAACGTACGGAACTAC
EST: gi|29673129|gb|CB669404.1|CB669404
EST:     GCGGCCTCAACTCCCCGCTCCACTTCGCCGCCGCTAAGGGCCACCTCGAC                         ATTGTGACGCTGTTGCTGGAGAAGGGCGCGGATGTGAACGTACGGAACTAC
genomic: GCGGCCTCAACTCCCCGCTCCACTTCGCCGCCGCTAAGGGCCACCTCGACgtccgtgaca ... ttgcatgcagATTGTGACGCTGTTGCTGGAGAAGGGCGCGGATGTGAACGTACGGAACTAC
EST: gi|29632141|gb|CB637150.1|CB637150
EST:     GCCACCTCGAC                         ATTGTGACGCTGTTGCTGGAGAAGGGCGCGGATGTGAACGTACGGAACTAC
genomic: GCCACCTCGACgtccgtgaca ... ttgcatgcagATTGTGACGCTGTTGCTGGAGAAGGGCGCGGATGTGAACGTACGGAACTAC
EST: gi|88424663|gb|CI606462.1|CI606462
EST:     GCGGCCTCAACTCCCCGCTCCACTTCGCCGCCGCTAAGGGCCACCTCGAA                         ATTGTGACGCTGTTGCTGGAGAAGGGCGCGGATGTGAAAGTACGGAACTAC
genomic: GCGGCCTCAACTCCCCGCTCCACTTCGCCGCCGCTAAGGGCCACCTCGACgtccgtgaca ... ttgcatgcagATTGTGACGCTGTTGCTGGAGAAGGGCGCGGATGTGAACGTACGGAACTAC
EST: gi|88351478|gb|CI627494.1|CI627494
EST:     GCGGCCTCAACTCCCCGCTC-ACTTCGCCGCCGCTAAGGGCCACCTCGAC                         ATTGTGACGCTGTTGCTGGAGAAGGG
genomic: GCGGCCTCAACTCCCCGCTCCACTTCGCCGCCGCTAAGGGCCACCTCGACgtccgtgaca ... ttgcatgcagATTGTGACGCTGTTGCTGGAGAAGGG
EST: gi|29641797|gb|CB646804.1|CB646804
EST:     GCGGCCTCAACTCCCCGCTCCACTTCGCCGCCGCTAAGGGCCACCTCGAC                         ATTGTGACGCTGTTGCTGGAGAAGGGCGCGGATGTGAACGTACGGAACTAC
genomic: GCGGCCTCAACTCCCCGCTCCACTTCGCCGCCGCTAAGGGCCACCTCGACgtccgtgaca ... ttgcatgcagATTGTGACGCTGTTGCTGGAGAAGGGCGCGGATGTGAACGTACGGAACTAC
EST: gi|88426126|gb|CI574009.1|CI574009
EST:     GCGGCCTCAACTCCCCGCTCCACTTCGCCGCCGCTAAGGGCCACCTCGAC                         ATTGTGACGCTGTTGCTGGAGAAGGGCGCGGATGTGAACGTACGGAACTAC
genomic: GCGGCCTCAACTCCCCGCTCCACTTCGCCGCCGCTAAGGGCCACCTCGACgtccgtgaca ... ttgcatgcagATTGTGACGCTGTTGCTGGAGAAGGGCGCGGATGTGAACGTACGGAACTAC
EST: gi|88299309|gb|CI572261.1|CI572261
EST:     GCGGCCTCAACTCCCCGCTCCACTTCGCCGCCGCTAAGGGCCACCTCGAC                         ATTGTGACGCTGTTGCTGGAGAAGGGCGCGGATGTGAACGTACGGAACTAC
genomic: GCGGCCTCAACTCCCCGCTCCACTTCGCCGCCGCTAAGGGCCACCTCGACgtccgtgaca ... ttgcatgcagATTGTGACGCTGTTGCTGGAGAAGGGCGCGGATGTGAACGTACGGAACTAC
EST: gi|29628246|gb|CB633257.1|CB633257
EST:     GCGGCCTCAACTCCCCGCTCCACTTCGCCGCCGCTAAGGGCCACCTCGAC                         ATTGTGACGCTGTTGCTGGAGAAGGGCGCGGATGTGAACGTACGGAACTAC
genomic: GCGGCCTCAACTCCCCGCTCCACTTCGCCGCCGCTAAGGGCCACCTCGACgtccgtgaca ... ttgcatgcagATTGTGACGCTGTTGCTGGAGAAGGGCGCGGATGTGAACGTACGGAACTAC
EST: gi|88352087|gb|CI626087.1|CI626087
EST:     CGGCCTCAACTCCCCGCCTCCACTTCGCCGCCGCTAAGGGCCACCTCGAC                         ATTGTGACGCTGTTGCTGGAGAAGGGCGCGGATGTGAACGTACGGAACTAC
genomic: CGGCCTCAACTCCCCGC-TCCACTTCGCCGCCGCTAAGGGCCACCTCGACgtccgtgaca ... ttgcatgcagATTGTGACGCTGTTGCTGGAGAAGGGCGCGGATGTGAACGTACGGAACTAC
EST: gi|29673087|gb|CB669362.1|CB669362
EST:     GCGGCCTCAACTCCCCGCTCCACTTCGCCGCCGCTAAGGGCCACCTCGAC                         ATTGTGACGCTGTTGCTGGAGAAGGGCGCGGATGTGAACGTACGGAACTAC
genomic: GCGGCCTCAACTCCCCGCTCCACTTCGCCGCCGCTAAGGGCCACCTCGACgtccgtgaca ... ttgcatgcagATTGTGACGCTGTTGCTGGAGAAGGGCGCGGATGTGAACGTACGGAACTAC
EST: gi|29644924|gb|CB649931.1|CB649931
EST:     GCGGCCTCAACTCCCCGCTCCACTTCGCCGCCGCTAAGGGCCACCTCGAC                         ATTGTGACGCTGTTGCTGGAGAAGGGCGCGGATGTGAACGTACGGAACTAC
genomic: GCGGCCTCAACTCCCCGCTCCACTTCGCCGCCGCTAAGGGCCACCTCGACgtccgtgaca ... ttgcatgcagATTGTGACGCTGTTGCTGGAGAAGGGCGCGGATGTGAACGTACGGAACTAC
EST: gi|88569846|gb|CI661021.1|CI661021
EST:     GCGGCCTCAACTCCCCGCTCCACTTCGCCGCCGCTAAGGGCCACCTCGAC                         ATTGTGACGCTGTTGCTGGAGAAGGGC
genomic: GCGGCCTCAACTCCCCGCTCCACTTCGCCGCCGCTAAGGGCCACCTCGACgtccgtgaca ... ttgcatgcagATTGTGACGCTGTTGCTGGAGAAGGGC
EST: gi|29631475|gb|CB636484.1|CB636484
EST:     GCGGCCTCAACTCCCCGCTCCACTTCGCCGCCGGTAAGGGCCACCTCGAC                         ATTGTGACGCTGTTGCTGGAGAAGGGCGCGGATGTGAACGTACGGAACTAC
genomic: GCGGCCTCAACTCCCCGCTCCACTTCGCCGCCGCTAAGGGCCACCTCGACgtccgtgaca ... ttgcatgcagATTGTGACGCTGTTGCTGGAGAAGGGCGCGGATGTGAACGTACGGAACTAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgatgtgtgtgtgtgtgtgtgtttttttttttttttggtttggttttgcatgcagATTGTGACGCTGTTGCTGGAGAAGGGCGCGGATGTGAACGTACGGAACTACTGCGGGCAG
 aattgat  putative branch site (score: 4)
                   tgtttttttttttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtccgtgacaacccccttcacgccgtcctttgatttctttcgctggtggtttttttgttcgatttgatcgcgaattgatgtgtgtgtgtgtgtgtgtttttttttttttttggtttggttttgcatgcagATTGTGACGCTGTTGCTGGAGAAGGGCGCGGATGTGAACGTACGGAACTACTGCGGGCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA
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- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAA