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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gcaagaaatgctcattttgattgtttaatatgaaataatttagctgcatgctttgcatagctgtactgactgaacttcatccatgtagGAACTCCATTCGACCCGCCGAGTTTTAGCGGGAGAACAGTCGAGGGCATTCCAGCTCCAG

Basic information

species Oryza sativa
transcript LOC_Os12g35350.1
intron # 15
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|86488227|gb|CI130860.1|CI130860
EST:     GGCCATTACAGATGAGACTCAAAAG                         GAACTCCATTCGACCCGCCGAGTTTTAGCGGGAGAACAGTCGAGGGCATTC
genomic: GGCCATTACAGATGAGACTCAAAAGgcaagaaatg ... atccatgtagGAACTCCATTCGACCCGCCGAGTTTTAGCGGGAGAACAGTCGAGGGCATTC
EST: gi|58612024|gb|CK039736.1|CK039736
EST:     TGGAACGTGAAGTGGCATTCTTGAAGGCCATTACAGATGAGACTCAAAAG                         GAACTCCATTCGACCCGCCGAGTTTTAGCGGGAGAACAGTCGAGGGCATTC
genomic: TGGAACGTGAAGTGGCATTCTTGAAGGCCATTACAGATGAGACTCAAAAGgcaagaaatg ... atccatgtagGAACTCCATTCGACCCGCCGAGTTTTAGCGGGAGAACAGTCGAGGGCATTC
EST: gi|88256246|gb|CI358634.1|CI358634
EST:     TGGAACGTGAAGTGGCATTCTTGAAGGCCATTACAGATGAGACTCAAAAG                         GAACTCCATTCGACCCCCCGAGTTTTAGCGGGAGAACAGTCGAGGGCATTC
genomic: TGGAACGTGAAGTGGCATTCTTGAAGGCCATTACAGATGAGACTCAAAAGgcaagaaatg ... atccatgtagGAACTCCATTCGACCCGCCGAGTTTTAGCGGGAGAACAGTCGAGGGCATTC
EST: gi|86824929|gb|CI358138.1|CI358138
EST:     TGGAACGTGAAGTGGCATTCTTGAAGGCCATTACAGATGAGACTCAAAAG                         GAACTCCATTCGACCCGCCGAGTTTTAGCGGGAGAACAGTCGAGGGCATTC
genomic: TGGAACGTGAAGTGGCATTCTTGAAGGCCATTACAGATGAGACTCAAAAGgcaagaaatg ... atccatgtagGAACTCCATTCGACCCGCCGAGTTTTAGCGGGAGAACAGTCGAGGGCATTC
EST: gi|86257277|gb|CI004095.1|CI004095
EST:     TGGAACGTGAAGTGGCATTCTTGAAGGCCATTACAGATGAGACTCAAAAG                         GAACTCCATTCGACCCGCCGAGTTTTAGCGGGAGAACAGTCGAGGGCATTC
genomic: TGGAACGTGAAGTGGCATTCTTGAAGGCCATTACAGATGAGACTCAAAAGgcaagaaatg ... atccatgtagGAACTCCATTCGACCCGCCGAGTTTTAGCGGGAGAACAGTCGAGGGCATTC
EST: gi|86883096|gb|CI314294.1|CI314294
EST:     TGTAACGTGAAGTGGCATTCTTGAAGGCCATTACAGATGAGACTCAAAAG                         GAACTCCATTCGACCCGCCGAGTTTTAGCGGGAGAACACGTCGAGGGCATT
genomic: TGGAACGTGAAGTGGCATTCTTGAAGGCCATTACAGATGAGACTCAAAAGgcaagaaatg ... atccatgtagGAACTCCATTCGACCCGCCGAGTTTTAGCGGGAGAACA-GTCGAGGGCATT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aataatttagctgcatgctttgcatagctgtactgactgaacttcatccatgtagGAACTCCATTCGACCCGCCGAGTTTTAGCGGGAGAACAGTCGAGGGCATTCCAGCTCCAG
                              tactgac  putative branch site (score: 1)
                                         cttcatcc  putative PPT
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gcaagaaatgctcattttgattgtttaatatgaaataatttagctgcatgctttgcatagctgtactgactgaacttcatccatgtagGAACTCCATTCGACCCGCCGAGTTTTAGCGGGAGAACAGTCGAGGGCATTCCAGCTCCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTC