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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagccccccaatggatggatttgcaatgtcgtttgtggtttgtggtatgatttcagaggactgaattttggacctgtttgatgtgtgttcagGACTTGACAAAGCGCCCTCGTCGCAACCGCAGGTCGCCTGCTCTTAGGGCCGCATTCCAGGAGACCACCATCTCACCTGCCAATTTGGTGCTCCCGCTGT

Basic information

species Oryza sativa
transcript LOC_Os06g49110.2
intron # 1
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|58606899|gb|CK034932.1|CK034932
EST:     CGTTGGTCAGACCCAAGGCTCCCGAAGGAACACCTCAGATCAGGCCTCTT                         GACATGACAAAGCGCCCTCGTCGCAACCGCAGGTCGCCTGCTCTTAGGGCC
genomic: CGTTGGTCAGACCCAAGGCTCCCGAAGGAACACCTCAGATCAGGCCTCTTgtaagccccc ... gtgtgttcagGACTTGACAAAGCGCCCTCGTCGCAACCGCAGGTCGCCTGCTCTTAGGGCC
EST: gi|29681115|gb|CB677390.1|CB677390
EST:     CGTTGGTCAGACCCAAGGCTCCCGAAGGAACACCTCAGATCAGGCCTCTT                         GACTTGACAAAGCGCCCTCGTCGCAACCGCAGGTCGCCTGCTCTTAGGGCC
genomic: CGTTGGTCAGACCCAAGGCTCCCGAAGGAACACCTCAGATCAGGCCTCTTgtaagccccc ... gtgtgttcagGACTTGACAAAGCGCCCTCGTCGCAACCGCAGGTCGCCTGCTCTTAGGGCC
EST: gi|29644874|gb|CB649881.1|CB649881
EST:     CGTTGGTCAGACCCAAGGCTCCCGAAGGAACACCTCAGATCAGGCCTCTT                         GACTTGACAAAGCGCCCTCGTCGCAACCGCAGGTCGCCTGCTCTTAGGGCC
genomic: CGTTGGTCAGACCCAAGGCTCCCGAAGGAACACCTCAGATCAGGCCTCTTgtaagccccc ... gtgtgttcagGACTTGACAAAGCGCCCTCGTCGCAACCGCAGGTCGCCTGCTCTTAGGGCC
EST: gi|29616370|gb|CB621382.1|CB621382
EST:     CGTTGGTCAGACCCAAGGCTCCCGAAGGAACACCTCAGATCAGGCCTCTT                         GACATGACAAAGCGCCCTCGTCGCAACCGCAGGTCGCCTGCTCTTAGGGCC
genomic: CGTTGGTCAGACCCAAGGCTCCCGAAGGAACACCTCAGATCAGGCCTCTTgtaagccccc ... gtgtgttcagGACTTGACAAAGCGCCCTCGTCGCAACCGCAGGTCGCCTGCTCTTAGGGCC
EST: gi|29619108|gb|CB624120.1|CB624120
EST:     CGTTGGTCAGACCCAAGGCTCCCGAAGGAACACCTCAGATCAGGCCTCTT                         GACATGACAAAGCGCCCTCGTCGCAACCGCAGGTCGCCTGCTCTTAGGGCC
genomic: CGTTGGTCAGACCCAAGGCTCCCGAAGGAACACCTCAGATCAGGCCTCTTgtaagccccc ... gtgtgttcagGACTTGACAAAGCGCCCTCGTCGCAACCGCAGGTCGCCTGCTCTTAGGGCC
EST: gi|29613357|gb|CB618370.1|CB618370
EST:     CGTTGGTCAGACCCAAGGCTCCCGAAGGAACACCTCAGATCAGGCCTCTT                         GACATGACAAAGCGCCCTCGTCGCAACCGCAGGTCGCCTGCTCTTAGGGCC
genomic: CGTTGGTCAGACCCAAGGCTCCCGAAGGAACACCTCAGATCAGGCCTCTTgtaagccccc ... gtgtgttcagGACTTGACAAAGCGCCCTCGTCGCAACCGCAGGTCGCCTGCTCTTAGGGCC
EST: gi|58605499|gb|CK033532.1|CK033532
EST:     CGTTGGTCAGACCCAAGGCTCCCGAAGGAACACCTCAGATCAGGCCTCTT                         GACATGACAAAGCGCCCTCGTCGCAACCGCAGGTCGCCTGCTCTTAGGGCC
genomic: CGTTGGTCAGACCCAAGGCTCCCGAAGGAACACCTCAGATCAGGCCTCTTgtaagccccc ... gtgtgttcagGACTTGACAAAGCGCCCTCGTCGCAACCGCAGGTCGCCTGCTCTTAGGGCC
EST: gi|29666981|gb|CB663256.1|CB663256
EST:     CGTTGGTCAGACCCAAGGCTCCCGAAGGAACACCTCAGATCAGGCCTCTT                         GACTTGACAAAGCGCCCTCGTCGCAACCGCAGGTCGCCTGCTCTTAGGGCC
genomic: CGTTGGTCAGACCCAAGGCTCCCGAAGGAACACCTCAGATCAGGCCTCTTgtaagccccc ... gtgtgttcagGACTTGACAAAGCGCCCTCGTCGCAACCGCAGGTCGCCTGCTCTTAGGGCC
EST: gi|29660427|gb|CB656702.1|CB656702
EST:     CGTTGGTCAGACCCAAGGCTCCCGAAGGAACACCTCAGATCAGGCCTCTT                         GACTTGACAAAGCGCCCTCGTCGCAACCGCAGGTCGCCTGCTCTTAGGGCC
genomic: CGTTGGTCAGACCCAAGGCTCCCGAAGGAACACCTCAGATCAGGCCTCTTgtaagccccc ... gtgtgttcagGACTTGACAAAGCGCCCTCGTCGCAACCGCAGGTCGCCTGCTCTTAGGGCC
EST: gi|700999|gb|D47290.1|D47290
EST:     CGTTGGTCAGACCCAAGGCTCCCGAAG-AACAACTCAGATCAGGCCTCTT                         GACTTGACAAAGCGCCCTCGTCGCAACCGNAG-TCGCCTGCTTCTTAGGGC
genomic: CGTTGGTCAGACCCAAGGCTCCCGAAGGAACACCTCAGATCAGGCCTCTTgtaagccccc ... gtgtgttcagGACTTGACAAAGCGCCCTCGTCGCAACCGCAGGTCGCCTGCT-CTTAGGGC
EST: gi|29617546|gb|CB622558.1|CB622558
EST:     CGTTGGTCAGACCCAAGGCTCCCGAAGGAACACCTCAGATCAGGCCTCTT                         GACATGACAAAGCGCCCTCGTCGCAACCGCAGGTCGCCTGCTCTTAGGGCC
genomic: CGTTGGTCAGACCCAAGGCTCCCGAAGGAACACCTCAGATCAGGCCTCTTgtaagccccc ... gtgtgttcagGACTTGACAAAGCGCCCTCGTCGCAACCGCAGGTCGCCTGCTCTTAGGGCC
EST: gi|29621569|gb|CB626580.1|CB626580
EST:     GGTCAGACCCAAGGCTCCCGAAGGAACACCTCAGATCAGGCCTCTT                         GACATGACAAAGCGCCCTCGTCGCAACCGCAGGTCGCCTGCTCTTAGGGCC
genomic: GGTCAGACCCAAGGCTCCCGAAGGAACACCTCAGATCAGGCCTCTTgtaagccccc ... gtgtgttcagGACTTGACAAAGCGCCCTCGTCGCAACCGCAGGTCGCCTGCTCTTAGGGCC
EST: gi|29673911|gb|CB670186.1|CB670186
EST:     CGTTGGTCAGACCCAAGGCTCCCGAAGGAACACCTCAGATCAGGCCTCTT                         GACTTGACAAAGCGCCCTCGTCGCAACCGCAGGTCGCCTGCTCTTAGGGCC
genomic: CGTTGGTCAGACCCAAGGCTCCCGAAGGAACACCTCAGATCAGGCCTCTTgtaagccccc ... gtgtgttcagGACTTGACAAAGCGCCCTCGTCGCAACCGCAGGTCGCCTGCTCTTAGGGCC
EST: gi|29641824|gb|CB646831.1|CB646831
EST:     CGTTGGTCAGACCCAAGGCTCCCGAAGGAACACCTCAGATCAGGCCTCTT                         GACTTGACAAAGCGCCCTCGTCGCAACCGCAGGTCGCCTGCTCTTAGGGCC
genomic: CGTTGGTCAGACCCAAGGCTCCCGAAGGAACACCTCAGATCAGGCCTCTTgtaagccccc ... gtgtgttcagGACTTGACAAAGCGCCCTCGTCGCAACCGCAGGTCGCCTGCTCTTAGGGCC
EST: gi|29687455|gb|CB683730.1|CB683730
EST:     CGTTGGTCAGACCCAAGGCTCCCGAAGGAACACCTCAGATCAGGCCTCTT                         GACTTGACAAAGCGCCCTCGTCGCAACCGCAGGTCGCCTGCTCTTAGGGCC
genomic: CGTTGGTCAGACCCAAGGCTCCCGAAGGAACACCTCAGATCAGGCCTCTTgtaagccccc ... gtgtgttcagGACTTGACAAAGCGCCCTCGTCGCAACCGCAGGTCGCCTGCTCTTAGGGCC
EST: gi|88426580|gb|CI579409.1|CI579409
EST:     CGTTGGTCATACCCAAGGCTCCCGAAGGAACACCTCAGATCAGGCCTCTT                         GACTTGACAAAGCGCCCTCGTCGCAACCGCAGGTCGCCTGCTCTTAGGGCC
genomic: CGTTGGTCAGACCCAAGGCTCCCGAAGGAACACCTCAGATCAGGCCTCTTgtaagccccc ... gtgtgttcagGACTTGACAAAGCGCCCTCGTCGCAACCGCAGGTCGCCTGCTCTTAGGGCC
EST: gi|29672090|gb|CB668365.1|CB668365
EST:     CGTTGGTCAGACCCAAGGCTCCCGAAGGAACACCTCAGATCAGGCCTCTT                         GACTTGACAAAGCGCCCTCGTCGCAACCGCAGGTCGCCTGCTCTTAGGGCC
genomic: CGTTGGTCAGACCCAAGGCTCCCGAAGGAACACCTCAGATCAGGCCTCTTgtaagccccc ... gtgtgttcagGACTTGACAAAGCGCCCTCGTCGCAACCGCAGGTCGCCTGCTCTTAGGGCC
EST: gi|29661434|gb|CB657709.1|CB657709
EST:     CGTTGGTCAGACCCAAGGCTCCCGAAGGAACACCTCAGATCAGGCCTCTT                         GACTTGACAAAGCGCCCTCGTCGCAACCGCAGGTCGCCTGCTCTTAGGGCC
genomic: CGTTGGTCAGACCCAAGGCTCCCGAAGGAACACCTCAGATCAGGCCTCTTgtaagccccc ... gtgtgttcagGACTTGACAAAGCGCCCTCGTCGCAACCGCAGGTCGCCTGCTCTTAGGGCC
EST: gi|29645158|gb|CB650165.1|CB650165
EST:     CGTTGGTCAGACCCAAGGCTCCCGAAGGAACACCTCAGATCAGGCCTCTT                         GACTTGACAAAGCGCCCTCGTCGCAACCGCAGGTCGCCTGCTCTTAGGGCC
genomic: CGTTGGTCAGACCCAAGGCTCCCGAAGGAACACCTCAGATCAGGCCTCTTgtaagccccc ... gtgtgttcagGACTTGACAAAGCGCCCTCGTCGCAACCGCAGGTCGCCTGCTCTTAGGGCC
EST: gi|29641133|gb|CB646140.1|CB646140
EST:     CGTTGGTCAGACCCAAGGCTCCCGAAGGAACACCTCAGATCAGGCCTCTT                         GACTTGACAAAGCGCCCTCGTCGCAACCGCAGGTCGCCTGCTCTTAGGGCC
genomic: CGTTGGTCAGACCCAAGGCTCCCGAAGGAACACCTCAGATCAGGCCTCTTgtaagccccc ... gtgtgttcagGACTTGACAAAGCGCCCTCGTCGCAACCGCAGGTCGCCTGCTCTTAGGGCC
EST: gi|29679002|gb|CB675277.1|CB675277
EST:     CGTTGGTCAGACCCAAGGCTCCCGAAGGAACACCTCAGATCAGGCCTCTT                         GACTTGACAAAGCGCCCTCGTCGCAACCGCAGGTCGCCTGCTCTTAGGGCC
genomic: CGTTGGTCAGACCCAAGGCTCCCGAAGGAACACCTCAGATCAGGCCTCTTgtaagccccc ... gtgtgttcagGACTTGACAAAGCGCCCTCGTCGCAACCGCAGGTCGCCTGCTCTTAGGGCC
EST: gi|29619411|gb|CB624423.1|CB624423
EST:     CGTTGGTCAGACCCAAGGCTCCCGAAGGAACACCTCAGATCAGGCCTCTT                         GACATGACAAAGCGCCCTCGTCGCAACCGCAGGTCGCCTGCTCTTAGGGCC
genomic: CGTTGGTCAGACCCAAGGCTCCCGAAGGAACACCTCAGATCAGGCCTCTTgtaagccccc ... gtgtgttcagGACTTGACAAAGCGCCCTCGTCGCAACCGCAGGTCGCCTGCTCTTAGGGCC
EST: gi|29667711|gb|CB663986.1|CB663986
EST:     CGTTGGTCAGACCCAAGGCTCCCGAAGGAACACCTCAGATCAGGCCTCTT                         GACTTGACAAAGCGCCCTCGTCGCAACCGCAGGTCGCCTGCTCTTAGGGCC
genomic: CGTTGGTCAGACCCAAGGCTCCCGAAGGAACACCTCAGATCAGGCCTCTTgtaagccccc ... gtgtgttcagGACTTGACAAAGCGCCCTCGTCGCAACCGCAGGTCGCCTGCTCTTAGGGCC
EST: gi|29615586|gb|CB620598.1|CB620598
EST:     CGTTGGTCAGACCCAAGGCTCCCGAATGAACTCCTCAAATCAGGCCTCTT                         GACATGACAAAGCGCCCTCGTCGCAACCGCAGGTCGCCTGCTCTTAGGGCC
genomic: CGTTGGTCAGACCCAAGGCTCCCGAAGGAACACCTCAGATCAGGCCTCTTgtaagccccc ... gtgtgttcagGACTTGACAAAGCGCCCTCGTCGCAACCGCAGGTCGCCTGCTCTTAGGGCC
EST: gi|29637162|gb|CB642171.1|CB642171
EST:     CGTTGGTCAGACCCAAGGCTCCCGAAGGAACACCTCAGATCAGGCCTCTT                         GACTTGACAAAGCGCCCTCGTCGCAACCGCAGGTCGCCTGCTCTTAGGGCC
genomic: CGTTGGTCAGACCCAAGGCTCCCGAAGGAACACCTCAGATCAGGCCTCTTgtaagccccc ... gtgtgttcagGACTTGACAAAGCGCCCTCGTCGCAACCGCAGGTCGCCTGCTCTTAGGGCC
EST: gi|29682583|gb|CB678858.1|CB678858
EST:     CGTTGGTCAGACCCAAGGCTCCCGAAGGAACACCTCAGATCAGGCCTCTT                         GACTTGACAAAGCGCCCTCGTCGCAACCGCAGGTCGCCTGCTCTTAGGGCC
genomic: CGTTGGTCAGACCCAAGGCTCCCGAAGGAACACCTCAGATCAGGCCTCTTgtaagccccc ... gtgtgttcagGACTTGACAAAGCGCCCTCGTCGCAACCGCAGGTCGCCTGCTCTTAGGGCC
EST: gi|29619315|gb|CB624327.1|CB624327
EST:     CGTTGGTCAGACCCAAGGCTCCCGAAGGAACACCTCAGATCAGGCCTCTT                         GACATGACAAAGCGCCCTCGTCGCAACCGCAGGTCGCCTGCTCTTAGGGCC
genomic: CGTTGGTCAGACCCAAGGCTCCCGAAGGAACACCTCAGATCAGGCCTCTTgtaagccccc ... gtgtgttcagGACTTGACAAAGCGCCCTCGTCGCAACCGCAGGTCGCCTGCTCTTAGGGCC
EST: gi|58612032|gb|CK039744.1|CK039744
EST:     CGTTGGTCAGACCCAAGGCTCCCGAAGGAACACCTCAGATCAGGCCTCTT                         GACATGACAAAGCGCCCTCGTCGCAACCGCAGGTCGCCTGCTCTTAGGGCC
genomic: CGTTGGTCAGACCCAAGGCTCCCGAAGGAACACCTCAGATCAGGCCTCTTgtaagccccc ... gtgtgttcagGACTTGACAAAGCGCCCTCGTCGCAACCGCAGGTCGCCTGCTCTTAGGGCC
EST: gi|29643724|gb|CB648731.1|CB648731
EST:     CGTTGGTCAGACCCAAGGCTCCCGAAGGAACACCTCAGATCAGGCCTCTT                         GACTTGACAAAGCGCCCTCGTCGCAACCGCAGGTCGCCTGCTCTTAGGGCC
genomic: CGTTGGTCAGACCCAAGGCTCCCGAAGGAACACCTCAGATCAGGCCTCTTgtaagccccc ... gtgtgttcagGACTTGACAAAGCGCCCTCGTCGCAACCGCAGGTCGCCTGCTCTTAGGGCC
EST: gi|29655802|gb|CB652077.1|CB652077
EST:     CGTTGGTCAGACCCAAGGCTCCCGAAGGAACACCTCAGATCAGGCCTCTT                         GACTTGACAAAGCGCCCTCGTCGCAACCGCAGGTCGCCTGCTCTTAGGGCC
genomic: CGTTGGTCAGACCCAAGGCTCCCGAAGGAACACCTCAGATCAGGCCTCTTgtaagccccc ... gtgtgttcagGACTTGACAAAGCGCCCTCGTCGCAACCGCAGGTCGCCTGCTCTTAGGGCC
EST: gi|29637541|gb|CB642550.1|CB642550
EST:     CGTTGGTCAGACCCAAGGCTCCCGAAGGAACACCTCAGATCAGGCCTCTT                         GACTTGACAAAGCGCCCTCGTCGCAACCGCAGGTCGCCTGCTCTTAGGGCC
genomic: CGTTGGTCAGACCCAAGGCTCCCGAAGGAACACCTCAGATCAGGCCTCTTgtaagccccc ... gtgtgttcagGACTTGACAAAGCGCCCTCGTCGCAACCGCAGGTCGCCTGCTCTTAGGGCC
EST: gi|88422647|gb|CI573809.1|CI573809
EST:     CGTTGGTCAGACCCAAGGCTCCCGAAGGAACACCTCAGATCAGGCCTCTT                         GACTTGACAAAGCGCCCTCGTCGCAACCGCAGGTCGCCTGCTCTTAGGGC-
genomic: CGTTGGTCAGACCCAAGGCTCCCGAAGGAACACCTCAGATCAGGCCTCTTgtaagccccc ... gtgtgttcagGACTTGACAAAGCGCCCTCGTCGCAACCGCAGGTCGCCTGCTCTTAGGGCC
EST: gi|29681299|gb|CB677574.1|CB677574
EST:     CGTTGGTCAGACCCAAGGCTCCCGAAGGAACACCTCAGATCAGGCCTCTT                         GACTTGACAAAGCGCCCTCGTCGCAACCGCAGGTCGCCTGCTCTTAGGGCC
genomic: CGTTGGTCAGACCCAAGGCTCCCGAAGGAACACCTCAGATCAGGCCTCTTgtaagccccc ... gtgtgttcagGACTTGACAAAGCGCCCTCGTCGCAACCGCAGGTCGCCTGCTCTTAGGGCC
EST: gi|88411271|gb|CI564392.1|CI564392
EST:     CGTTGGTCAGACCCAAGGCTCCCGAAGGAACACCTCAGATCAGGCCTCTT                         GACTTGACAAAGCGCCCTCGTCGCAACCGCAGGTCGCCTGCTCTTAGGGCC
genomic: CGTTGGTCAGACCCAAGGCTCCCGAAGGAACACCTCAGATCAGGCCTCTTgtaagccccc ... gtgtgttcagGACTTGACAAAGCGCCCTCGTCGCAACCGCAGGTCGCCTGCTCTTAGGGCC
EST: gi|29688148|gb|CB684423.1|CB684423
EST:     CGTTGGTCAGACCCAAGGCTCCCGAAGGAACACCTCAGATCAGGCCTCTT                         GACTTGACAAAGCGCCCTCGTCGCAACCGCAGGTCGCCTGCTCTTAGGGCC
genomic: CGTTGGTCAGACCCAAGGCTCCCGAAGGAACACCTCAGATCAGGCCTCTTgtaagccccc ... gtgtgttcagGACTTGACAAAGCGCCCTCGTCGCAACCGCAGGTCGCCTGCTCTTAGGGCC
EST: gi|29660273|gb|CB656548.1|CB656548
EST:     CGTTGGTCAGACCCAAGGCTCCCGAAGGAACACCTCAGATCAGGCCTCTT                         GACTTGACAAAGCGCCCTCGTCGCAACCGCAGGTCGCCTGCTCTTAGGGCC
genomic: CGTTGGTCAGACCCAAGGCTCCCGAAGGAACACCTCAGATCAGGCCTCTTgtaagccccc ... gtgtgttcagGACTTGACAAAGCGCCCTCGTCGCAACCGCAGGTCGCCTGCTCTTAGGGCC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtttgtggtatgatttcagaggactgaattttggacctgtttgatgtgtgttcagGACTTGACAAAGCGCCCTCGTCGCAACCGCAGGTCGCCTGCTCTTAGGGCCGCATTCCAGGAGACCACCATCTCACCTGCCAATTTGGTGCTCCCGCTGT
                                      gtttgat  putative branch site (score: 5)
        tatgattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagccccccaatggatggatttgcaatgtcgtttgtggtttgtggtatgatttcagaggactgaattttggacctgtttgatgtgtgttcagGACTTGACAAAGCGCCCTCGTCGCAACCGCAGGTCGCCTGCTCTTAGGGCCGCATTCCAGGAGACCACCATCTCACCTGCCAATTTGGTGCTCCCGCTGT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA