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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGTGACAAAGCTCAAGCAGAAAGGGACTATGTTCTGGCAGAGTTCAAGAGTGGGAAAAGTCCTATAATGGCTGCCACAGATGTAGCGGCACGTGGTCTTGgtatggtgacttgtttgaaaattagaattaggttgtagttccaagtgctcaaggatgataagtcggagggctgtcagctgtttttggttgagtgaactga...

Basic information

species Oryza sativa
transcript LOC_Os01g68320.1
intron # 8
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g68320.2 (Oryza sativa), 5'ss of exon 8
lower sequence: GRMZM2G362850_T01 (Zea mays), 5'ss of exon 9
GGTGACAAAGCTCAAGCAGAAAGGGACTATGTTCTGGCAGAGTTCAAGAGTGGGAAAAGTCCTATAATGGCTGCCACAGATGTAGCGGCACGTGGTCTTGgtatggtgacttgtttgaaaattagaattaggttgtagttccaagtgctcaaggatgataagtcggagggctgtc-agctgtttttggttgagtgaactga
||||| ||||||||||| ||| ||||||||||||| |||||||| ||||| || || || || |||||||||||||||||||| || |||||||||||||||||| ||| || |||||| ||||| ||||||| |||||||||||||||||||| ||||||||||||||| |||  |||||   |||||||||||||||| 
GGTGATAAAGCTCAAGCTGAACGGGACTATGTTCTTGCAGAGTTTAAGAGCGGCAAGAGCCCCATAATGGCTGCCACAGATGTGGCAGCACGTGGTCTTGgtatgatgatttatttgaatattaggattaggtagtagttccaagtgctcaagggtgataagtcggagggttgttgagctgcgattggttgagtgaactg-

upper sequence: LOC_Os01g68320.2 (Oryza sativa), 5'ss of exon 8
lower sequence: AC217043.3_FGT002 (Zea mays), 5'ss of exon 6
GGTGACAAAGCTCAAGCAGAAAGGGACTATGTTCTGGCAGAGTTCAAGAGTGGGAAAAGTCCTATAATGGCTGCCACAGATGTAGCGGCACGTGGTCTTGgtatggtgacttgtttgaaaattagaattaggttgtagttccaagtgctcaaggatgataagtcggagggctgtc-agctgtttttggttgagtgaactga
                                        |||| ||||| || || || ||||||||||||||||||||||| || |||||||||||||||||| ||| || |||||| ||||| ||||||| |||||||||||||||||||||||||||||||||||| |||  |||||   |||||||||||||| | 
----------------------------------------AGTTTAAGAGCGGCAAGAGCCCTATAATGGCTGCCACAGATGTGGCAGCACGTGGTCTTGgtatgatgatttatttgaatattaggattaggtagtagttccaagtgctcaaggatgataagtcggagggttgttgagctgcgattggttgagtgaacag-

upper sequence: LOC_Os01g68320.2 (Oryza sativa), 5'ss of exon 8
lower sequence: AC209019.3_FGT003 (Zea mays), 5'ss of exon 1
GGTGACAAAGCTCAAGCAGAAAGGGACTATGTTCTGGCAGAGTTCAAGAGTGGGAAAAGTCCTATAATGGCTGCCACAGATGTAGCGGCACGTGGTCTTGgtatggtgacttgtttgaaaattagaattaggttgtagttccaagtgctcaaggatgataagtcggagggctgtc-agctgtttttggttgagtgaactga
                                                                  ||||||||||||||||| || |||||||||||||||||| ||| || |||||| ||||| ||||||| |||||||||||||||||||||||||||||||||||| |||  | |||   |||||||||||| ||| 
------------------------------------------------------------------ATGGCTGCCACAGATGTGGCAGCACGTGGTCTTGgtatgatgatttatttgaatattaggattaggtagtagttccaagtgctcaaggatgataagtcggagggttgttgaactgcgattggttgagtgagctg-

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|29643632|gb|CB648639.1|CB648639
EST:     TGGGAAAAGTCCTATAATGGCTGCCACAGATGTAGCGGCACGTGGTCTTG                         ATGTCAAGGATATTAAGTGTGTGATAAATTTTGATTTTCCAACAACTCTTG
genomic: TGGGAAAAGTCCTATAATGGCTGCCACAGATGTAGCGGCACGTGGTCTTGgtatggtgac ... atttttgcagATGTCAAGGATATTAAGTGTGTGATAAATTTTGATTTTCCAACAACTCTTG
EST: gi|29678104|gb|CB674379.1|CB674379
EST:     TGGGAAAAGTCCTATAATGGCTGCCACAGATGTAGCGGCACGTGGTCTTG                         ATGTCAAGGATATTAAGTGTGTGATAAATTTTGATTTTCCAACAACTCTTG
genomic: TGGGAAAAGTCCTATAATGGCTGCCACAGATGTAGCGGCACGTGGTCTTGgtatggtgac ... atttttgcagATGTCAAGGATATTAAGTGTGTGATAAATTTTGATTTTCCAACAACTCTTG
EST: gi|29661778|gb|CB658053.1|CB658053
EST:     TGGGAAAAGTCCTATAATGGCTGCCACAGATGTAGCGGCACGTGGTCTTG                         ATGTCAAGGATATTAAGTGTGTGATAAATTTTGATTTTCCAACAACTCTTG
genomic: TGGGAAAAGTCCTATAATGGCTGCCACAGATGTAGCGGCACGTGGTCTTGgtatggtgac ... atttttgcagATGTCAAGGATATTAAGTGTGTGATAAATTTTGATTTTCCAACAACTCTTG
EST: gi|29664446|gb|CB660721.1|CB660721
EST:     TGGGAAAAGTCCTATAATGGCTGCCACAGATGTAGCGGCACGTGGTCTTG                         ATGTCAAGGATATTAAGTGTGTGATAAATTTTGATTTTCCAA
genomic: TGGGAAAAGTCCTATAATGGCTGCCACAGATGTAGCGGCACGTGGTCTTGgtatggtgac ... atttttgcagATGTCAAGGATATTAAGTGTGTGATAAATTTTGATTTTCCAA
EST: gi|29629642|gb|CB634651.1|CB634651
EST:     TGGGAAAAGTCCTATAATGGCTGCCACAGATGTAGCGGCACGTGGTCTTG                         ATGTCAAGGATATTAAGTGTGTGATAAATTTTGATTTTCCAACAACTCTTG
genomic: TGGGAAAAGTCCTATAATGGCTGCCACAGATGTAGCGGCACGTGGTCTTGgtatggtgac ... atttttgcagATGTCAAGGATATTAAGTGTGTGATAAATTTTGATTTTCCAACAACTCTTG
EST: gi|29643631|gb|CB648638.1|CB648638
EST:     TGGGAAAAGTCCTATAATGGCTGCCACAGATGTAGCGGCACGTGGTCTTG                         ATGTCAAGGATATTAAGTGTGTGATAAATTTTGATTTTCCAACAACTCTTG
genomic: TGGGAAAAGTCCTATAATGGCTGCCACAGATGTAGCGGCACGTGGTCTTGgtatggtgac ... atttttgcagATGTCAAGGATATTAAGTGTGTGATAAATTTTGATTTTCCAACAACTCTTG
EST: gi|88980895|gb|CI021022.1|CI021022
EST:     ATAATGGCTGCCACAGATGTAGCGGCACGTGGTCTTG                         ATGTCAAGGATATTAAGTGTGTGATAAATTTTGATTTTCCAACAACTCTTG
genomic: ATAATGGCTGCCACAGATGTAGCGGCACGTGGTCTTGgtatggtgac ... atttttgcagATGTCAAGGATATTAAGTGTGTGATAAATTTTGATTTTCCAACAACTCTTG
EST: gi|29662446|gb|CB658721.1|CB658721
EST:     TGGGAAAAGTCCTATAATGGCTGCCACAGATGTAGCGGCACGTGGTCTTG                         ATGTCAAGGATATTAAGTGTGTGATAAATTTTGATTTTCCAACAACTCTTG
genomic: TGGGAAAAGTCCTATAATGGCTGCCACAGATGTAGCGGCACGTGGTCTTGgtatggtgac ... atttttgcagATGTCAAGGATATTAAGTGTGTGATAAATTTTGATTTTCCAACAACTCTTG
EST: gi|29669297|gb|CB665572.1|CB665572
EST:     TGGGAAAAGTCCTATAATGGCTGCCACAGATGTAGCGGCACGTGGTCTTG                         ATGTCAAGGATATTAAGTGTGTGATAAATTTTGATTTTCCAACAACTCTTG
genomic: TGGGAAAAGTCCTATAATGGCTGCCACAGATGTAGCGGCACGTGGTCTTGgtatggtgac ... atttttgcagATGTCAAGGATATTAAGTGTGTGATAAATTTTGATTTTCCAACAACTCTTG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGTGACAAAGCTCAAGCAGAAAGGGACTATGTTCTGGCAGAGTTCAAGAGTGGGAAAAGTCCTATAATGGCTGCCACAGATGTAGCGGCACGTGGTCTTGgtatggtgacttgtttgaaaattagaattaggttgtagttccaagtgctcaaggatgataagtcggagggctgtcagctgtttttggttgagtgaactga

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ggagggc