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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...attttttcgcagacagggtcaatctcagtgtggcacacgatattctcaggtgttggcgagttcatctaacgtacaagtatcttgtgaacgatggatgcagGTCGTACCGGTTAAAAGCGAGCTGCCAGATGCTTCAGAAGAGATGGAAGCAGCGCTCTCTCCTTATTCATTCACTTCATTTGACCTCGCTCTAGATCAGT

Basic information

species Oryza sativa
transcript LOC_Os11g03780.1
intron # 17
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|88693001|gb|CI736576.1|CI736576
EST:     TCACATCCGGCAATTTGCTGGATGAAAATTCATTTGCTGAACCAAACAAA                         GTCGTACCGGTTAAAAGCGAGCTGCCAGATGCTTCAGAAGAGATGGAAGCA
genomic: TCACATCCGGCAATTTGCTGGATGAAAATTCATTTGCTGAACCAAACAAAgtaagacaac ... atggatgcagGTCGTACCGGTTAAAAGCGAGCTGCCAGATGCTTCAGAAGAGATGGAAGCA
EST: gi|88321281|gb|CI533031.1|CI533031
EST:     TCACATCCGGCAATTTGCTGGATGAAAATTCATTTGCTGAACCAAACAAA                         GTCGTACCGGTTAAAAGCGAGCTGCCAGATGCTTCAGAAGAGATGGAAGCA
genomic: TCACATCCGGCAATTTGCTGGATGAAAATTCATTTGCTGAACCAAACAAAgtaagacaac ... atggatgcagGTCGTACCGGTTAAAAGCGAGCTGCCAGATGCTTCAGAAGAGATGGAAGCA
EST: gi|88264303|gb|CI368077.1|CI368077
EST:     TCACATCCGGCAATTTGCTGGATGAAAATTCATTTGCTGAACCAAACAAA                         GTCGTACCGGTTAAAAGCGAGCTGCCAGATGCTTCAGAAGAGATGGAAGCA
genomic: TCACATCCGGCAATTTGCTGGATGAAAATTCATTTGCTGAACCAAACAAAgtaagacaac ... atggatgcagGTCGTACCGGTTAAAAGCGAGCTGCCAGATGCTTCAGAAGAGATGGAAGCA
EST: gi|88455246|gb|CI519267.1|CI519267
EST:     TCACATCCGGCAATTTGGTGGATGAAAATTCATTTGCTGAACCAAACAAA                         GTCGTACCGGTTAAAAGCGAGCTGCCAGATGCTTCAGAAGAGATGGAAGCA
genomic: TCACATCCGGCAATTTGCTGGATGAAAATTCATTTGCTGAACCAAACAAAgtaagacaac ... atggatgcagGTCGTACCGGTTAAAAGCGAGCTGCCAGATGCTTCAGAAGAGATGGAAGCA
EST: gi|86884439|gb|CI337007.1|CI337007
EST:     TCACATCCGGCAATTTGCTGGATGAAAATTCATTTGCTGAACCAAACAAA                         GTCGTACCGGTTAAAAGCGAGCTGCCAGATGCTTCAGAAGAGATGGAAGCA
genomic: TCACATCCGGCAATTTGCTGGATGAAAATTCATTTGCTGAACCAAACAAAgtaagacaac ... atggatgcagGTCGTACCGGTTAAAAGCGAGCTGCCAGATGCTTCAGAAGAGATGGAAGCA
EST: gi|88843353|gb|CI372253.1|CI372253
EST:     TCACATCCGGCAATTTGCTGGATGAAAATTCATTTGCTGAACCAAACAAA                         GTCGTACCGGTTAAAAGCGAGCTGCCAGATGCTTCAGAAGAGATGGAAGCA
genomic: TCACATCCGGCAATTTGCTGGATGAAAATTCATTTGCTGAACCAAACAAAgtaagacaac ... atggatgcagGTCGTACCGGTTAAAAGCGAGCTGCCAGATGCTTCAGAAGAGATGGAAGCA
EST: gi|86861451|gb|CI328157.1|CI328157
EST:     TCACATCCGGCAATTTGCTGGATGAAAATTCATTTGCTGAACCAAACAAA                         GTCGTACCGGTTAAAAGCGAGCTGCCAGATGCTTCAGAAGAGATGGAAGCA
genomic: TCACATCCGGCAATTTGCTGGATGAAAATTCATTTGCTGAACCAAACAAAgtaagacaac ... atggatgcagGTCGTACCGGTTAAAAGCGAGCTGCCAGATGCTTCAGAAGAGATGGAAGCA
EST: gi|88451203|gb|CI534196.1|CI534196
EST:     TCACATCCGGCAATTTGCTGGATGAAAATTCATTTGCTGAACCAAACAAA                         GTCGTACCGGTTAAAAGCGAGCTGCCAGATGCTTCAGAAGAGATGGAAGCA
genomic: TCACATCCGGCAATTTGCTGGATGAAAATTCATTTGCTGAACCAAACAAAgtaagacaac ... atggatgcagGTCGTACCGGTTAAAAGCGAGCTGCCAGATGCTTCAGAAGAGATGGAAGCA
EST: gi|88253224|gb|CI351850.1|CI351850
EST:     TCACATCCGGCAATTTGCTGGATGAAAATTCATTTGCTGAACCAAACAAA                         GTCGTACCGGTTAAAAGCGAGCTGCCAGATGCTTCAGAAGAGATGGAAGCA
genomic: TCACATCCGGCAATTTGCTGGATGAAAATTCATTTGCTGAACCAAACAAAgtaagacaac ... atggatgcagGTCGTACCGGTTAAAAGCGAGCTGCCAGATGCTTCAGAAGAGATGGAAGCA
EST: gi|33684986|gb|CF313225.1|CF313225
EST:     CACATCCGGCAATTTGCTGGATGAAAATTCATTTGCTGAACCAAANCAAA                         GTCGTACCGGTTAAAAGCGAGCTGCCAGATGCTTCAGAAGAGATGGAAGC
genomic: CACATCCGGCAATTTGCTGGATGAAAATTCATTTGCTGAACCAAA-CAAAgtaagacaac ... atggatgcagGTCGTACCGGTTAAAAGCGAGCTGCCAGATGCTTCAGAAGAGATGGAAGC
EST: gi|14192448|gb|AU184659.1|AU184659
EST:     TCACATCCGGCAATTTGCTGGATGAAAATTCATTTGCTGAACCAAACAAA                         GTCGTACCGGTTAAAAGCGAGCTGCCAGATGCTTCAGAAGAGATGGAAGCA
genomic: TCACATCCGGCAATTTGCTGGATGAAAATTCATTTGCTGAACCAAACAAAgtaagacaac ... atggatgcagGTCGTACCGGTTAAAAGCGAGCTGCCAGATGCTTCAGAAGAGATGGAAGCA
EST: gi|88838794|gb|CI376332.1|CI376332
EST:     TCACATCCGGCAATTTGCTGGATGAAAATTCATTTGCTGAACCAAACAAA                         GTCGTACCGGTTAAAAGCGAGCTGCCAGATGCTTCAGAAGAGATGGAAGCA
genomic: TCACATCCGGCAATTTGCTGGATGAAAATTCATTTGCTGAACCAAACAAAgtaagacaac ... atggatgcagGTCGTACCGGTTAAAAGCGAGCTGCCAGATGCTTCAGAAGAGATGGAAGCA
EST: gi|88261512|gb|CI365088.1|CI365088
EST:     TCACATCCGGCAATTTGCTGGATGAAAATTCATTTGCTGAACCAAACAAA                         GTCGTACCGGTTAAAAGCGAGCTGCCAGATGCTTCAGAAGAGATGGAAGCA
genomic: TCACATCCGGCAATTTGCTGGATGAAAATTCATTTGCTGAACCAAACAAAgtaagacaac ... atggatgcagGTCGTACCGGTTAAAAGCGAGCTGCCAGATGCTTCAGAAGAGATGGAAGCA
EST: gi|88270031|gb|CI381329.1|CI381329
EST:     TCACATCCGGCAATTTGCTGGATGAAAATTCATTTGCTGAACCAAACAAA                         GTCGTACCGGTTAAAAGCGAGGCTGCCAGATGCTTCAGAAGAGATGGAAGC
genomic: TCACATCCGGCAATTTGCTGGATGAAAATTCATTTGCTGAACCAAACAAAgtaagacaac ... atggatgcagGTCGTACCGGTTAAAAGCGA-GCTGCCAGATGCTTCAGAAGAGATGGAAGC
EST: gi|88844891|gb|CI022245.1|CI022245
EST:     TCACATCCGGCAATTTGCTGGATGAAAATTCATTTGCTGAACCAAACAAA                         GTCGTACCGGTTAAAAGCGAGCTGCCAGATGCTTCAGAAGAGATGGAAGCA
genomic: TCACATCCGGCAATTTGCTGGATGAAAATTCATTTGCTGAACCAAACAAAgtaagacaac ... atggatgcagGTCGTACCGGTTAAAAGCGAGCTGCCAGATGCTTCAGAAGAGATGGAAGCA
EST: gi|88906895|gb|CI375967.1|CI375967
EST:     TCACATCCGGCAATTTGCTGGATGAAAATTCATTTGCTGAACCAAACAAA                         GTCGTACCGGTTAAAAGCGAGCTGCCAGATGCTTCAGAAGAGATGGAAGCA
genomic: TCACATCCGGCAATTTGCTGGATGAAAATTCATTTGCTGAACCAAACAAAgtaagacaac ... atggatgcagGTCGTACCGGTTAAAAGCGAGCTGCCAGATGCTTCAGAAGAGATGGAAGCA
EST: gi|86835172|gb|CI346647.1|CI346647
EST:     TCACATCCGGCAATTTGCTGGATGAAAATTCATTTGCTGAACCAAACAAA                         GTCGTACCGGTTAAAAGCGAGCTGCCAGATGCTTCAGAAGAGATGGAAGCA
genomic: TCACATCCGGCAATTTGCTGGATGAAAATTCATTTGCTGAACCAAACAAAgtaagacaac ... atggatgcagGTCGTACCGGTTAAAAGCGAGCTGCCAGATGCTTCAGAAGAGATGGAAGCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcaggtgttggcgagttcatctaacgtacaagtatcttgtgaacgatggatgcagGTCGTACCGGTTAAAAGCGAGCTGCCAGATGCTTCAGAAGAGATGGAAGCAGCGCTCTCTCCTTATTCATTCACTTCATTTGACCTCGCTCTAGATCAGT
                  atctaac  putative branch site (score: 2)
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
attttttcgcagacagggtcaatctcagtgtggcacacgatattctcaggtgttggcgagttcatctaacgtacaagtatcttgtgaacgatggatgcagGTCGTACCGGTTAAAAGCGAGCTGCCAGATGCTTCAGAAGAGATGGAAGCAGCGCTCTCTCCTTATTCATTCACTTCATTTGACCTCGCTCTAGATCAGT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGATCA