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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaataattacatctcagctatttttgccataagctaaccatttttagagtgcaaatattgaccctcaatatttccgcgtcatagCGGCAGAGAAATCACACCAAAGCACAGAGGAAGGATCTGACGCTGACTCCGACGATGGCTTGCCACCTCTAGAGGAAAACCTGAACCACCTGAACTTTAA

Basic information

species Oryza sativa
transcript LOC_Os03g09920.2
intron # 9
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|86429295|gb|CI075976.1|CI075976
EST:     GAATTCTTGGTTGTCAAGTAACTCTAATGTTCCAAAGTCACCTGTAAACG                         CGGCAGAGAAATCACACCAAAGCACAGAGGAAGGATCTGACGCTGACTCCG
genomic: GAATTCTTGGTTGTCAAGTAACTCTAATGTTCCAAAGTCACCTGTAAACGgtaataatta ... cgcgtcatagCGGCAGAGAAATCACACCAAAGCACAGAGGAAGGATCTGACGCTGACTCCG
EST: gi|86508759|gb|CI151392.1|CI151392
EST:     CCAAAGTCACCTGTAAACG                         CGGCAGAGAAATCACACCAAAGCACAGAGGAAGGATCTGACGCTGACTCCG
genomic: CCAAAGTCACCTGTAAACGgtaataatta ... cgcgtcatagCGGCAGAGAAATCACACCAAAGCACAGAGGAAGGATCTGACGCTGACTCCG
EST: gi|87007319|gb|CI278990.1|CI278990
EST:     GAATTCTTGGTTGTCAAGTAACTCTAATGTTCCAAAGTCACCTGTAAACG                         CGGCAGAGAAATCACACCAAAGCACAGAGGAAGGATCTGACGCTGACTCCG
genomic: GAATTCTTGGTTGTCAAGTAACTCTAATGTTCCAAAGTCACCTGTAAACGgtaataatta ... cgcgtcatagCGGCAGAGAAATCACACCAAAGCACAGAGGAAGGATCTGACGCTGACTCCG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taagctaaccatttttagagtgcaaatattgaccctcaatatttccgcgtcatagCGGCAGAGAAATCACACCAAAGCACAGAGGAAGGATCTGACGCTGACTCCGACGATGGCTTGCCACCTCTAGAGGAAAACCTGAACCACCTGAACTTTAA
                          tattgac  putative branch site (score: 2)
                                       tatttcc  putative PPT
          atttttaga  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaataattacatctcagctatttttgccataagctaaccatttttagagtgcaaatattgaccctcaatatttccgcgtcatagCGGCAGAGAAATCACACCAAAGCACAGAGGAAGGATCTGACGCTGACTCCGACGATGGCTTGCCACCTCTAGAGGAAAACCTGAACCACCTGAACTTTAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGGA