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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ccgggtagtttagtttctgttatgcgtatccttagttttacctttattgttttcgtattttattatgattatacttgctgacattttattacattgccagCTCCTTGAGTACAACGAGTCCAAAGCGGAAGAGGAGGAAGCTTGTGAAGAAGATACAGATAGCAAGCAAAACAAAAAGAAAGAGTAGGGCTCTAACAAGT

Basic information

species Oryza sativa
transcript LOC_Os05g36070.2
intron # 11
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|88838811|gb|CI376349.1|CI376349
EST:     TGATTGGTTTTGTTGCTGTTCACTGTTTGTGGAATGGTGAAGTAAAGCCG                         CTCCTTGAGTACAACGAGTCCAAAGCGGAAGAGGAGGAAGCTTGTGAAGAA
genomic: TGATTGGTTTTGTTGCTGTTCACTGTTTGTGGAATGGTGAAGTAAAGCCGgtaagtttgt ... acattgccagCTCCTTGAGTACAACGAGTCCAAAGCGGAAGAGGAGGAAGCTTGTGAAGAA
EST: gi|86874638|gb|CI318197.1|CI318197
EST:     TGTTGCTGTTCACT-TTTGTGGAATGGTGAAGTAAAGCAG                         CTCCTTGAGTACAACGAGTCCAAAGCGGAAGAGGAGGAAGCTTGTGAAGAA
genomic: TGTTGCTGTTCACTGTTTGTGGAATGGTGAAGTAAAGCCGgtaagtttgt ... acattgccagCTCCTTGAGTACAACGAGTCCAAAGCGGAAGAGGAGGAAGCTTGTGAAGAA
EST: gi|88244093|gb|CI243215.1|CI243215
EST:     TGATTGGTTTTGTTGCTGTTCACTGTTTGTGGAATGGTGAAGTAAAGCCG                         CTCCTTGAGTACAACGAGTCCAAAGCGGAAGAGGAGGAAGCTTGTGAAGAA
genomic: TGATTGGTTTTGTTGCTGTTCACTGTTTGTGGAATGGTGAAGTAAAGCCGgtaagtttgt ... acattgccagCTCCTTGAGTACAACGAGTCCAAAGCGGAAGAGGAGGAAGCTTGTGAAGAA
EST: gi|88249358|gb|CI249207.1|CI249207
EST:     TGATTGGTTTTGTTGCTGTTCACTGTTTGTGGAATGGTGAAGTAAAGCCG                         CTCCTTGAGTACAACGAGTCCAAAGCGGAAGAGGAGGAAGCTTGTGAAGAA
genomic: TGATTGGTTTTGTTGCTGTTCACTGTTTGTGGAATGGTGAAGTAAAGCCGgtaagtttgt ... acattgccagCTCCTTGAGTACAACGAGTCCAAAGCGGAAGAGGAGGAAGCTTGTGAAGAA
EST: gi|86539354|gb|CI179560.1|CI179560
EST:     TGATTGGTTTTGTTGCTGTTCACTGTTTGTGGAATGGTGAAGTAAAGCCG                         CTCCTTGAGTACAACGAGTCCAAAGCGGAAGAGGAGGAAGCTTGTGAAGAA
genomic: TGATTGGTTTTGTTGCTGTTCACTGTTTGTGGAATGGTGAAGTAAAGCCGgtaagtttgt ... acattgccagCTCCTTGAGTACAACGAGTCCAAAGCGGAAGAGGAGGAAGCTTGTGAAGAA
EST: gi|88841700|gb|CI080956.1|CI080956
EST:     TGATTGGTTTTGTTGCTGTTCACTGTTTGTGGAATGGTGAAGTAAAGCCG                         CTCCTTGAGTACAACGAGTCCAAAGCGGAAGAGGAGGAAGCTTGTGAAGAA
genomic: TGATTGGTTTTGTTGCTGTTCACTGTTTGTGGAATGGTGAAGTAAAGCCGgtaagtttgt ... acattgccagCTCCTTGAGTACAACGAGTCCAAAGCGGAAGAGGAGGAAGCTTGTGAAGAA
EST: gi|86538870|gb|CI179076.1|CI179076
EST:     TGATTGGTTTTGTTGCTGTTCACTGTTTGTGGAATGGTGAAGTAAAGCCG                         CTCCTTGAGTACAACGAGTCCAAAGCGGAAGAGGAGGAAGCTTGTGAAGAA
genomic: TGATTGGTTTTGTTGCTGTTCACTGTTTGTGGAATGGTGAAGTAAAGCCGgtaagtttgt ... acattgccagCTCCTTGAGTACAACGAGTCCAAAGCGGAAGAGGAGGAAGCTTGTGAAGAA
EST: gi|8859158|gb|AU096476.1|AU096476
EST:     TGATTGGTTTTGTTGCTGTTCNCTGTTTGTGGAATGGTGAAGTAAANCCG                         CTCCTTGAGTACAACGAGTCCAAAGCGGAANAGGACGAAGCTTGTGAAGAA
genomic: TGATTGGTTTTGTTGCTGTTCACTGTTTGTGGAATGGTGAAGTAAAGCCGgtaagtttgt ... acattgccagCTCCTTGAGTACAACGAGTCCAAAGCGGAAGAGGAGGAAGCTTGTGAAGAA
EST: gi|88260561|gb|CI362854.1|CI362854
EST:     GCTGTTCACTGTTTGGTGGAATGGTGAAGTAAAGCCG                         CTCCTTGAGTACAACGAGTCCAAAGCGGAAGAGGAGGAAGCTTGTGAAGAA
genomic: GCTGTTCACTGTTT-GTGGAATGGTGAAGTAAAGCCGgtaagtttgt ... acattgccagCTCCTTGAGTACAACGAGTCCAAAGCGGAAGAGGAGGAAGCTTGTGAAGAA
EST: gi|88487026|gb|CI424297.1|CI424297
EST:     GTTCACTGTTTGTGGAATGGTGAAGTAAAGCCG                         CTCCTTGAGTACAACGAGTCCAAAGCGGAAGAGGAGGAAGCTTGTGAAGAA
genomic: GTTCACTGTTTGTGGAATGGTGAAGTAAAGCCGgtaagtttgt ... acattgccagCTCCTTGAGTACAACGAGTCCAAAGCGGAAGAGGAGGAAGCTTGTGAAGAA
EST: gi|86431507|gb|CI085118.1|CI085118
EST:     TGATTGGTTTTGTTGCTGTTCACTGTTTGTGGAATGGTGAAGTAAAGCCG                         CTCCTTGAGTACAACGAGTCCAAAGCGGAAGAGGAGGAAGCTTGTGAAGAA
genomic: TGATTGGTTTTGTTGCTGTTCACTGTTTGTGGAATGGTGAAGTAAAGCCGgtaagtttgt ... acattgccagCTCCTTGAGTACAACGAGTCCAAAGCGGAAGAGGAGGAAGCTTGTGAAGAA
EST: gi|87028280|gb|CI111974.1|CI111974
EST:     TGATTGGTTTTGTTGCTGTTCACTGTTTGTGGAATGGTGAAGTAAAGCCG                         CTCCTTGAGTACAACGAGTCCAAAGCGGAAGAGGAGGAAGCTTGTGAAGAA
genomic: TGATTGGTTTTGTTGCTGTTCACTGTTTGTGGAATGGTGAAGTAAAGCCGgtaagtttgt ... acattgccagCTCCTTGAGTACAACGAGTCCAAAGCGGAAGAGGAGGAAGCTTGTGAAGAA
EST: gi|86545734|gb|CI185940.1|CI185940
EST:     TGATTGGTTTTGTTGCTGTTCACTGTTTGTGGAATGGTGAAGTAAAGCCG                         CTCCTTGAGTACAACGAGTCCAAAGCGGAAGAGGAGGAAGCTTGTGAAGAA
genomic: TGATTGGTTTTGTTGCTGTTCACTGTTTGTGGAATGGTGAAGTAAAGCCGgtaagtttgt ... acattgccagCTCCTTGAGTACAACGAGTCCAAAGCGGAAGAGGAGGAAGCTTGTGAAGAA
EST: gi|89174130|gb|CI042023.1|CI042023
EST:     TGATTGGTTTTGTTGCTGTTCACTGTTTGTGGAATGGTGAAGTAAAGCCG                         CTCCTTGAGTACAACGAGTCCAAAGCGGAAGAGGAGGAAGCTTGTGAAGAA
genomic: TGATTGGTTTTGTTGCTGTTCACTGTTTGTGGAATGGTGAAGTAAAGCCGgtaagtttgt ... acattgccagCTCCTTGAGTACAACGAGTCCAAAGCGGAAGAGGAGGAAGCTTGTGAAGAA
EST: gi|86893354|gb|CI313446.1|CI313446
EST:     TGATTGGTTTTGTTGCTGTTCACTGTTTGTGGAATGGTGAAGTAAAGCCG                         CTCCTTGAGTACAACGAGTCCAAAGCGGAAGAGGAGGAAGCTTGTGAAGAA
genomic: TGATTGGTTTTGTTGCTGTTCACTGTTTGTGGAATGGTGAAGTAAAGCCGgtaagtttgt ... acattgccagCTCCTTGAGTACAACGAGTCCAAAGCGGAAGAGGAGGAAGCTTGTGAAGAA
EST: gi|29628338|gb|CB633349.1|CB633349
EST:     TGATTGGTTTTGTTGCTGTTCACTGTTTGTGGAATGGTGAAGTAAAGCCG                         CTCCTTGAGTACAACGAGTCCAAAGCGGAAGAGGAGGAAGCTTGTGAAGAA
genomic: TGATTGGTTTTGTTGCTGTTCACTGTTTGTGGAATGGTGAAGTAAAGCCGgtaagtttgt ... acattgccagCTCCTTGAGTACAACGAGTCCAAAGCGGAAGAGGAGGAAGCTTGTGAAGAA
EST: gi|86600029|gb|CI258369.1|CI258369
EST:     TGATTGGTTTTGTTGCTGTTCACTGTTTGTGGAATGGTGAAGTAAAGCCG                         CTCCTTGAGTTACAACGAGTCCAAAGCGGAAGAGGAGGAAGCTTGTGAAGA
genomic: TGATTGGTTTTGTTGCTGTTCACTGTTTGTGGAATGGTGAAGTAAAGCCGgtaagtttgt ... acattgccagCTCCTTGAG-TACAACGAGTCCAAAGCGGAAGAGGAGGAAGCTTGTGAAGA
EST: gi|88845983|gb|CI084713.1|CI084713
EST:     GTTCACTGTTTGTGGAATGGTGAAGTAAAGCCG                         CTCCTTGAGTACAACGAGTCCAAAGCGGAAGAGGAGGAAGCTTGTGAAGAA
genomic: GTTCACTGTTTGTGGAATGGTGAAGTAAAGCCGgtaagtttgt ... acattgccagCTCCTTGAGTACAACGAGTCCAAAGCGGAAGAGGAGGAAGCTTGTGAAGAA
EST: gi|86435528|gb|CI106761.1|CI106761
EST:     TGATTGGTTTTGTTGCTGTTCACTGTTTGTGGAATGGTGAAGTAAAGCCG                         CTCCTTGAGTACAACGAGTCCAAAGCGGAAGAGGAGGAAGCTTGTGAAGAA
genomic: TGATTGGTTTTGTTGCTGTTCACTGTTTGTGGAATGGTGAAGTAAAGCCGgtaagtttgt ... acattgccagCTCCTTGAGTACAACGAGTCCAAAGCGGAAGAGGAGGAAGCTTGTGAAGAA
EST: gi|29628337|gb|CB633348.1|CB633348
EST:     TGATTGGTTTTGTTGCTGTTCACTGTTTGTGGAATGGTGAAGTAAAGCCG                         CTCCTTGAGTACAACGAGTCCAAAGCGGAAGAGGAGGAAGCTTGTGAAGAA
genomic: TGATTGGTTTTGTTGCTGTTCACTGTTTGTGGAATGGTGAAGTAAAGCCGgtaagtttgt ... acattgccagCTCCTTGAGTACAACGAGTCCAAAGCGGAAGAGGAGGAAGCTTGTGAAGAA
EST: gi|88473200|gb|CI410471.1|CI410471
EST:     TTGGTTTTGTTGCTGTTCACTGTTTGTGGAATGGTGAAGTAAAGCCG                         CTCCTTGAGTACAACGAGTCCAAAGCGGAAGAGGAGGAAGCTTGTGAAGAA
genomic: TTGGTTTTGTTGCTGTTCACTGTTTGTGGAATGGTGAAGTAAAGCCGgtaagtttgt ... acattgccagCTCCTTGAGTACAACGAGTCCAAAGCGGAAGAGGAGGAAGCTTGTGAAGAA
EST: gi|86907972|gb|CI298768.1|CI298768
EST:     TGCTGTTCACTGTTTGTGGAATGGTGAAGTAAAGCCG                         CTCCTTGAGTACAACGAGTCCAAAGCGGAAGAGGAGGAAGCTTGTGAAGAA
genomic: TGCTGTTCACTGTTTGTGGAATGGTGAAGTAAAGCCGgtaagtttgt ... acattgccagCTCCTTGAGTACAACGAGTCCAAAGCGGAAGAGGAGGAAGCTTGTGAAGAA
EST: gi|86431057|gb|CI083480.1|CI083480
EST:     TGATCGGTTTTGTTGCTGTTCACTGTTTGTGGAATGGTGAAGTAAAGCCG                         CTCCTTGAGTACAACGAGTCCAAAGCGGAAGAGGAGGAAGCTTGTGAAGAA
genomic: TGATTGGTTTTGTTGCTGTTCACTGTTTGTGGAATGGTGAAGTAAAGCCGgtaagtttgt ... acattgccagCTCCTTGAGTACAACGAGTCCAAAGCGGAAGAGGAGGAAGCTTGTGAAGAA
EST: gi|86880509|gb|CI320999.1|CI320999
EST:     TGATTGGTTTTGTTGCTGTTCACTGTTTGTGGAATGGTGAAGTAAAGCCG                         CTCCTTGAGTACAACGAGTCCAAAGCGGAAGACGAGGAAGCTTGTGAAGAA
genomic: TGATTGGTTTTGTTGCTGTTCACTGTTTGTGGAATGGTGAAGTAAAGCCGgtaagtttgt ... acattgccagCTCCTTGAGTACAACGAGTCCAAAGCGGAAGAGGAGGAAGCTTGTGAAGAA
EST: gi|86413082|gb|CI067487.1|CI067487
EST:     TGATTGGTTTTGTTGCTGTTCACTGTTTGTGGAATGGTGAAGTAAAGCCG                         CTCCTTGAGTACAACGAGTCCAAAGCGGAAGAGGAGGAAGCTTGTGAAGAA
genomic: TGATTGGTTTTGTTGCTGTTCACTGTTTGTGGAATGGTGAAGTAAAGCCGgtaagtttgt ... acattgccagCTCCTTGAGTACAACGAGTCCAAAGCGGAAGAGGAGGAAGCTTGTGAAGAA
EST: gi|88840958|gb|CI000920.1|CI000920
EST:     TGATTGGTTTTGTTGCTGTTCACTGTTTGTGGAATGGTGAAGTAAAGCCG                         CTCCTTGAGTACAACGAGTCCAAAGCGGAAGAGGAGGAAGCTTGTGAAGAA
genomic: TGATTGGTTTTGTTGCTGTTCACTGTTTGTGGAATGGTGAAGTAAAGCCGgtaagtttgt ... acattgccagCTCCTTGAGTACAACGAGTCCAAAGCGGAAGAGGAGGAAGCTTGTGAAGAA

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 1 RNA-Seqlibrary.


Block sizes: 75 (upstream exon), 68 (downstream exon)
Score: 23

CCTGCTCTGTTGTACATTGTTCCTGGTGTGATTGGTTTTGTTGCTGTTCACTGTTTGTGGAATGGTGAAGTAAAGCCGgtaagtttgt ... acattgccagCTCCTTGAGTACAACGAGTCCAAAGCGGAAGAGGAGGAAGCTTGTGAAGAAGATACAGATAGCAAGCAAAACAAAAAGAAAGAGTAGGGCTCTAACAAGT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attgttttcgtattttattatgattatacttgctgacattttattacattgccagCTCCTTGAGTACAACGAGTCCAAAGCGGAAGAGGAGGAAGCTTGTGAAGAAGATACAGATAGCAAGCAAAACAAAAAGAAAGAGTAGGGCTCTAACAAGT
                              tgctgac  putative branch site (score: 23)
     tttcgtattttattat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ccgggtagtttagtttctgttatgcgtatccttagttttacctttattgttttcgtattttattatgattatacttgctgacattttattacattgccagCTCCTTGAGTACAACGAGTCCAAAGCGGAAGAGGAGGAAGCTTGTGAAGAAGATACAGATAGCAAGCAAAACAAAAAGAAAGAGTAGGGCTCTAACAAGT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA