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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gtgaaagatcctctgaaagacaattgaacattaagtttcaatgcaaatataagaatcaataacagggaagcatttcttaccatttttgtgcttcttacagGTGAAAAAGTTGGACTTGTATGCAGCTCTGAAGAATATAACATGCATCTTTGCCAACTATCCACCAAGGACAACTGCAGTTGTAAAATTTTCAGCCAACT

Basic information

species Oryza sativa
transcript LOC_Os02g15970.2
intron # 5
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|30227684|gb|CB965576.1|CB965576
EST:     TCCCCCAAGGTGGTTTGGTGAGGAAGAGCTACCAAAGCAATGACAGCCTG                         GTGAAAAAGTTGGACTTGTATGCAGCTCTGAAGAATATAACATGCATCATT
genomic: TCCCCCAAGGTGGTTTGATGAGGAAGAGCTACCAAAGCAATGACAGCCTGgtaattacta ... cttcttacagGTGAAAAAGTTGGACTTGTATGCAGCTCTGAAGAATATAACATGCATCTTT
EST: gi|88956707|gb|CI092896.1|CI092896
EST:     TCCCCCAAGGTGGTTTGATGAGGAAGAGCTACCAAAGCAATGACAGCCTG                         GTGAAAAAGTTGGACTTGTATGCAGCTCTGAAGAATATAACATGCATCTTT
genomic: TCCCCCAAGGTGGTTTGATGAGGAAGAGCTACCAAAGCAATGACAGCCTGgtaattacta ... cttcttacagGTGAAAAAGTTGGACTTGTATGCAGCTCTGAAGAATATAACATGCATCTTT
EST: gi|86852485|gb|CI320410.1|CI320410
EST:     TCCCCCAAGGTGGTTTGATGAGGAAGAGCTACCAAACCAATGACAGCCTG                         GTGAAAAAGTTGGACTTGTATGCAGCTCTGAAGAATATAACATGCATCTTT
genomic: TCCCCCAAGGTGGTTTGATGAGGAAGAGCTACCAAAGCAATGACAGCCTGgtaattacta ... cttcttacagGTGAAAAAGTTGGACTTGTATGCAGCTCTGAAGAATATAACATGCATCTTT
EST: gi|33687072|gb|CF315311.1|CF315311
EST:     TCCCCCAAGGTGGTTTGATGAGGAAGAGCTACCAAAGCAATGACAGCCTG                         GTGAAAAAGTTGGACTTGTATGCAGCTCTGAAGAATATAACATGCATCTTT
genomic: TCCCCCAAGGTGGTTTGATGAGGAAGAGCTACCAAAGCAATGACAGCCTGgtaattacta ... cttcttacagGTGAAAAAGTTGGACTTGTATGCAGCTCTGAAGAATATAACATGCATCTTT
EST: gi|86499914|gb|CI142547.1|CI142547
EST:     TCCCCCAAGGTGGTTTGATGAGGAAGAGCTACCAAAGCAATGACAGCCTG                         GTGAAAAAGTTGGACTTGTATGCAGCTCTGAAGAATATAACATGCATCTTT
genomic: TCCCCCAAGGTGGTTTGATGAGGAAGAGCTACCAAAGCAATGACAGCCTGgtaattacta ... cttcttacagGTGAAAAAGTTGGACTTGTATGCAGCTCTGAAGAATATAACATGCATCTTT
EST: gi|86842367|gb|CI335266.1|CI335266
EST:     TCCCCCAAGGTGGTTTGATGAGGAAGAGCTACCAAAGCAATGACAGCCTG                         GTGAAAAAGTTGGACTTGTATGCAGCTCTGAAGAATATAACATGCATCTTT
genomic: TCCCCCAAGGTGGTTTGATGAGGAAGAGCTACCAAAGCAATGACAGCCTGgtaattacta ... cttcttacagGTGAAAAAGTTGGACTTGTATGCAGCTCTGAAGAATATAACATGCATCTTT
EST: gi|88971274|gb|CI387197.1|CI387197
EST:     TCCCCCAAGGTGGTTTGATGAGGAAGAGCTACCAAAGCAATGACAGCCTG                         GTGAAAAAGTTGGACTTGTATGCAGCTCTGAAGAATATAACATGCATCTTT
genomic: TCCCCCAAGGTGGTTTGATGAGGAAGAGCTACCAAAGCAATGACAGCCTGgtaattacta ... cttcttacagGTGAAAAAGTTGGACTTGTATGCAGCTCTGAAGAATATAACATGCATCTTT
EST: gi|86511453|gb|CI154086.1|CI154086
EST:     TCCCCCAAGGTGGTTTGATGAGGAAGAGCTACCAAAGCAATGACAGCCTG                         GTGAAAAAGTTGGACTTGTATGCAGCTCTGAAGAATATAACATGCATCTTT
genomic: TCCCCCAAGGTGGTTTGATGAGGAAGAGCTACCAAAGCAATGACAGCCTGgtaattacta ... cttcttacagGTGAAAAAGTTGGACTTGTATGCAGCTCTGAAGAATATAACATGCATCTTT
EST: gi|55413185|gb|CV725561.1|CV725561
EST:     CCCCAAGGTGGTTTGATGAGGAAGAGCTACCAAAGCAATGACAGCCTG                         GTGAAAAAGTTGGACTTGTATGCAGCTCTGAAGAATATAACATGCATCTTT
genomic: CCCCAAGGTGGTTTGATGAGGAAGAGCTACCAAAGCAATGACAGCCTGgtaattacta ... cttcttacagGTGAAAAAGTTGGACTTGTATGCAGCTCTGAAGAATATAACATGCATCTTT
EST: gi|86428139|gb|CI073236.1|CI073236
EST:     TCCCCCAAGGTGGTTTGATGAGGAAGAGCTACCAAAGCAATGACAGCCTG                         GTGAAAAAGTTGGACTTGTATGCAGCTCTGAAGAATATAACATGCATCTTT
genomic: TCCCCCAAGGTGGTTTGATGAGGAAGAGCTACCAAAGCAATGACAGCCTGgtaattacta ... cttcttacagGTGAAAAAGTTGGACTTGTATGCAGCTCTGAAGAATATAACATGCATCTTT
EST: gi|30227453|gb|CB965345.1|CB965345
EST:     TCCCCCAAGGTGGTTTGGTGAGGCAGAGCTACCAAAGCAATGACAGCCTG                         CTGAAAAAGTTGGACTTGTATGCAGCTCTGAAGAATATAACAATGCATCAT
genomic: TCCCCCAAGGTGGTTTGATGAGGAAGAGCTACCAAAGCAATGACAGCCTGgtaattacta ... cttcttacagGTGAAAAAGTTGGACTTGTATGCAGCTCTGAAGAATATAACA-TGCATCTT
EST: gi|3760931|gb|C98185.1|C98185
EST:     NCCCCCAAGGTGGTTTGATGAGGAAGAGCTACCAAAGCAATGACAGCCTG                         GTGAAAAAGTTGGACTTGTATGCAGCTCTGAAGAATATAACATGCATCTTT
genomic: TCCCCCAAGGTGGTTTGATGAGGAAGAGCTACCAAAGCAATGACAGCCTGgtaattacta ... cttcttacagGTGAAAAAGTTGGACTTGTATGCAGCTCTGAAGAATATAACATGCATCTTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aatataagaatcaataacagggaagcatttcttaccatttttgtgcttcttacagGTGAAAAAGTTGGACTTGTATGCAGCTCTGAAGAATATAACATGCATCTTTGCCAACTATCCACCAAGGACAACTGCAGTTGTAAAATTTTCAGCCAACT
                            ttcttac  putative branch site (score: 2)
                                     tttttgtgcttctt  putative PPT
        aatcaataa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgaaagatcctctgaaagacaattgaacattaagtttcaatgcaaatataagaatcaataacagggaagcatttcttaccatttttgtgcttcttacagGTGAAAAAGTTGGACTTGTATGCAGCTCTGAAGAATATAACATGCATCTTTGCCAACTATCCACCAAGGACAACTGCAGTTGTAAAATTTTCAGCCAACT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGCAG