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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgatgttaaattgttaacatgacattggactcgttattttcttcagaacatcatggatagtcttattgaagcaccaaaatatttgttccagGCTGAGTGTGAAGAGCTTTCTGTACGCGCTGACAATTTAAGGGCAGAAAACTCCTCTCTTAGGGCTGAGCTTGAACGGATCAAAAAGGAGTACGAGGCAC

Basic information

species Oryza sativa
transcript LOC_Os02g03580.3
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g03580.1 (Oryza sativa), 3'ss of exon 12
lower sequence: GRMZM2G153144_T01 (Zea mays), 3'ss of exon 12
-----gtatgatgttaaattgttaacatgacattggactcgttattt--tcttcagaacatcatggatagtcttattgaagcac-caaaatatt-------tgttccagGCTGAGTGTGAAGAGCTTTCTGTACGCGCTGACAATTTAAGGGCAGAAAACTCCTCTCTTAGGGCTGAGCTTGAACGGATCAAAAAGGAGTACGAGGCAC
     ||   |   |||  || ||||||    |||    |   | |   |||||  |   ||| |   | | |  |    ||   |   || ||       | ||| ||||||||||||| ||||||     ||| ||||| | | | ||| | |||||||| ||||| ||||| |||||||||||||||| ||||||||||||    |
gtgttgtgcaacactaa--tgctaacatcgtcttgcttcctgaactccatcttctaagtttcaagaggattttgttcagtgctttcgtgatcttattcgattattctagGCTGAGTGTGAGGAGCTTGGGCAACGTGCTGAAACTCTGAGGTCGGAAAACTCGTCTCTCAGGGCCGAGCTTGAACGGATCAGAAAGGAGTACGAACAGC
















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:     GGAAGCAGTCTAATCGGGAATCAGCACGTAGATCCCGGCTGCGCAAGCAG                         GCTGAGTGTGAAGAGCTTTCTGTACGCGCTGACAATTTAAGGGCAGAAAAC
genomic: GGAAGCAGTCTAATCGGGAATCAGCACGTAGATCCCGGCTGCGCAAGCAGgtatgatgtt ... tttgttccagGCTGAGTGTGAAGAGCTTTCTGTACGCGCTGACAATTTAAGGGCAGAAAAC
EST: gi|88903327|gb|CI088865.1|CI088865
EST:     GGAAGCAGTCTAATCGGGAATCAGCACGTAGATCCCGGCTGCGCAAGCAG                         GCTGAGTGTGAAGAGCTTTCTGTACGCGCTGACAATTTAAGGGCAGAAAAC
genomic: GGAAGCAGTCTAATCGGGAATCAGCACGTAGATCCCGGCTGCGCAAGCAGgtatgatgtt ... tttgttccagGCTGAGTGTGAAGAGCTTTCTGTACGCGCTGACAATTTAAGGGCAGAAAAC
EST: gi|113931076|gb|DQ883825.1|DQ883825
EST:     GGAAGCAGTCTAATCGGGAATCAGCACGTAGATCCCGGCTGCGCAAGCAG                         GCTGAGTGTGAAGAGCTTTCTGTACGCGCTGACA
genomic: GGAAGCAGTCTAATCGGGAATCAGCACGTAGATCCCGGCTGCGCAAGCAGgtatgatgtt ... tttgttccagGCTGAGTGTGAAGAGCTTTCTGTACGCGCTGACA
EST: gi|29670500|gb|CB666775.1|CB666775
EST:     GGAAGCAGTCTAATCGGGAATCAGCACGTAGATCCCGGCTGCGCAAGCAG                         GCTGAGTGTGAAGAGCTTTCTGTACGCGCTGACAATTTAAGGGCAGAAAAC
genomic: GGAAGCAGTCTAATCGGGAATCAGCACGTAGATCCCGGCTGCGCAAGCAGgtatgatgtt ... tttgttccagGCTGAGTGTGAAGAGCTTTCTGTACGCGCTGACAATTTAAGGGCAGAAAAC
EST: gi|86497997|gb|CI140630.1|CI140630
EST:     GGAAGCAGTCTAATCGGGAATCAGCACGTAGATCCCGGCTGCGCAAGCAG                         GCTGAGTGTGAAGAGCTTTCTGTACGCGCTGACAATTTAAGGGCAGAAAAC
genomic: GGAAGCAGTCTAATCGGGAATCAGCACGTAGATCCCGGCTGCGCAAGCAGgtatgatgtt ... tttgttccagGCTGAGTGTGAAGAGCTTTCTGTACGCGCTGACAATTTAAGGGCAGAAAAC
EST: gi|86505811|gb|CI148444.1|CI148444
EST:     GGAAGCAGTCTAATCGGGAATCAGCACGTAGATCCCGGCTGCGCAAGCAG                         GCTGAGTGTGAAGAGCTTTCTGTACGCGCTGACAATTTAAGGGCAGAAAAC
genomic: GGAAGCAGTCTAATCGGGAATCAGCACGTAGATCCCGGCTGCGCAAGCAGgtatgatgtt ... tttgttccagGCTGAGTGTGAAGAGCTTTCTGTACGCGCTGACAATTTAAGGGCAGAAAAC
EST: gi|88850496|gb|CI093177.1|CI093177
EST:     AGTCTAATCGGGAATCAGCACGTAGATCCCGGCTGCGCAAGCAG                         GCTGAGTGTGAAGAGCTTTCTGTACGCGCTGACAATTTAAGGGCAGAAAAC
genomic: AGTCTAATCGGGAATCAGCACGTAGATCCCGGCTGCGCAAGCAGgtatgatgtt ... tttgttccagGCTGAGTGTGAAGAGCTTTCTGTACGCGCTGACAATTTAAGGGCAGAAAAC
EST: gi|86879457|gb|CI327145.1|CI327145
EST:     GGGAATCAGCACGTAGATCCCGGCTGGGCAAGCAG                         GCTGAGTGT-AAGAGCTTTGTGTACGCGCTGACAATTTAAGGGCAGAAAAC
genomic: GGGAATCAGCACGTAGATCCCGGCTGCGCAAGCAGgtatgatgtt ... tttgttccagGCTGAGTGTGAAGAGCTTTCTGTACGCGCTGACAATTTAAGGGCAGAAAAC
EST: gi|29670501|gb|CB666776.1|CB666776
EST:     GGAAGCAGTCTAATCGGGAATCAGCACGTAGATCCCGGCTGCGCAAGCAG                         GCTGAGTGTGAAGAGCTTTCTGTACGCGCTGACAATTTAAGGGCAGAAAAC
genomic: GGAAGCAGTCTAATCGGGAATCAGCACGTAGATCCCGGCTGCGCAAGCAGgtatgatgtt ... tttgttccagGCTGAGTGTGAAGAGCTTTCTGTACGCGCTGACAATTTAAGGGCAGAAAAC
EST: gi|88829448|gb|CI074318.1|CI074318
EST:     GGAAGCAGTCTAATCGGGAATCAGCACGTAGATCCCGGCTGCGCAAGCAG                         GCTGAGTGTGAAGAGCTTTCTGCACGCGCTGACAATTTAAGGGCAGAAAAC
genomic: GGAAGCAGTCTAATCGGGAATCAGCACGTAGATCCCGGCTGCGCAAGCAGgtatgatgtt ... tttgttccagGCTGAGTGTGAAGAGCTTTCTGTACGCGCTGACAATTTAAGGGCAGAAAAC
EST: gi|88965389|gb|CI011640.1|CI011640
EST:     GGAAGCAGTCTAATCGGGAATCAGCACGTAGATCCCGGCTGCGCAAGCAG                         GCTGAGTGTGAAGAGCTTTCTGTACGCGCTGACAATTTAAGGGCAGAAAAC
genomic: GGAAGCAGTCTAATCGGGAATCAGCACGTAGATCCCGGCTGCGCAAGCAGgtatgatgtt ... tttgttccagGCTGAGTGTGAAGAGCTTTCTGTACGCGCTGACAATTTAAGGGCAGAAAAC
EST: gi|29665043|gb|CB661318.1|CB661318
EST:     GGAAGCAGTCTAATCGGGAATCAGCACGTAGATCCCGGCTGCGCAAGCAG                         GCTGAGTGTGAAGAGCTTTCTGTACGCGCTGACAATTTAAGGGCAGAAAAC
genomic: GGAAGCAGTCTAATCGGGAATCAGCACGTAGATCCCGGCTGCGCAAGCAGgtatgatgtt ... tttgttccagGCTGAGTGTGAAGAGCTTTCTGTACGCGCTGACAATTTAAGGGCAGAAAAC
EST: gi|88517412|gb|CI445066.1|CI445066
EST:     GAATCAGCACGTAGATCCCGGCTGCGCAAGCAG                         GCTGAGTGTGAAGAGCTTTCTGTACGCGCTGACAATTTAAGGGCAGAAAAC
genomic: GAATCAGCACGTAGATCCCGGCTGCGCAAGCAGgtatgatgtt ... tttgttccagGCTGAGTGTGAAGAGCTTTCTGTACGCGCTGACAATTTAAGGGCAGAAAAC
EST: gi|32948093|gb|BP184665.1|BP184665
EST:     GGAAGCAGTCTAATCGGGAATCAGCACGTAGATCCCGGCTGCGCAAGCAG                         GCTGAGTGTGAAGAGCTTTCTGTACGCGCTGACA
genomic: GGAAGCAGTCTAATCGGGAATCAGCACGTAGATCCCGGCTGCGCAAGCAGgtatgatgtt ... tttgttccagGCTGAGTGTGAAGAGCTTTCTGTACGCGCTGACA
EST: gi|86488210|gb|CI130843.1|CI130843
EST:     GGAAGCAGTCTAATCGGGAATCAGCACGTAGATCCCGGCTGCGCAAGCAG                         GCTGAGTGTGAAGAGCTTTCTGTACGCGCTGACAATTTAAGGGCAGAAAAC
genomic: GGAAGCAGTCTAATCGGGAATCAGCACGTAGATCCCGGCTGCGCAAGCAGgtatgatgtt ... tttgttccagGCTGAGTGTGAAGAGCTTTCTGTACGCGCTGACAATTTAAGGGCAGAAAAC
EST: gi|86252236|gb|CI055973.1|CI055973
EST:     GGAAGCAGTCTAATCGGGAATCAGCACGTAGATCCCGGCTGCGCAAGCAG                         GCTGAGTGTGAAGAGCTTTCTGTACGCGCTGACCATTTAAGGGCAGAAAAC
genomic: GGAAGCAGTCTAATCGGGAATCAGCACGTAGATCCCGGCTGCGCAAGCAGgtatgatgtt ... tttgttccagGCTGAGTGTGAAGAGCTTTCTGTACGCGCTGACAATTTAAGGGCAGAAAAC
EST: gi|88958454|gb|CI095970.1|CI095970
EST:     GGAAGCAGTCTAATCGGGAATCAGCACGTAGATCCCGGCTGCGCAAGCAG                         GCTGAGTGTGAAGAGCTTTCTGTACGCGCTGACAATTTAAGGGCAGAAAAC
genomic: GGAAGCAGTCTAATCGGGAATCAGCACGTAGATCCCGGCTGCGCAAGCAGgtatgatgtt ... tttgttccagGCTGAGTGTGAAGAGCTTTCTGTACGCGCTGACAATTTAAGGGCAGAAAAC
EST: gi|89172965|gb|CI040858.1|CI040858
EST:     GGAAGCAGTCTAATCGGGAATCAGCACGTAGATCCCGGCTGCGCAAGCAG                         GCTGAGTGTGAAGAGCTTTCTGTACGCGCTGACAATTTAAGGGCAGAAAAC
genomic: GGAAGCAGTCTAATCGGGAATCAGCACGTAGATCCCGGCTGCGCAAGCAGgtatgatgtt ... tttgttccagGCTGAGTGTGAAGAGCTTTCTGTACGCGCTGACAATTTAAGGGCAGAAAAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttttcttcagaacatcatggatagtcttattgaagcaccaaaatatttgttccagGCTGAGTGTGAAGAGCTTTCTGTACGCGCTGACAATTTAAGGGCAGAAAACTCCTCTCTTAGGGCTGAGCTTGAACGGATCAAAAAGGAGTACGAGGCAC
                                             tttgttcc  CT-rich tract
                                       aaaatatttgtt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgatgttaaattgttaacatgacattggactcgttattttcttcagaacatcatggatagtcttattgaagcaccaaaatatttgttccagGCTGAGTGTGAAGAGCTTTCTGTACGCGCTGACAATTTAAGGGCAGAAAACTCCTCTCTTAGGGCTGAGCTTGAACGGATCAAAAAGGAGTACGAGGCAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTCCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG