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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTTATTGGTATTGAGCCTTCTGAGAGTAACATACTCTCTGGTGGAAAACCTGgtatgtttgtgttcttacttccttaaggtttgtcaaatgtctgctctttcccttataattcaccccatttgtttag

Basic information

species Oryza sativa
transcript LOC_Os01g74650.1
intron # 6
splice site 5'
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|58678120|gb|CK066807.1|CK066807
EST:     TATTGGTATTGAGCCTTCTGAGAGTAACATACTCTCTGGTGGAAAACCTG                         GCCCACATAAGATTCAAGGCATTGGGGCAGGATTTGTTCCAAGGAACTTGG
genomic: TATTGGTATTGAGCCTTCTGAGAGTAACATACTCTCTGGTGGAAAACCTGgtatgtttgt ... atttgtttagGCCCACATAAGATTCAAGGCATTGGGGCAGGATTTGTTCCAAGGAACTTGG
EST: gi|701729|gb|D48020.1|D48020
EST:     TATTGGTATTGAGCCTTCTGAGAGTAACATACTCTCTGGTGGAAAACCTG                         GCCCACATAAGATTCAAGGCATTGGGGCAGGATTTGTTCCAAGGAACTTGG
genomic: TATTGGTATTGAGCCTTCTGAGAGTAACATACTCTCTGGTGGAAAACCTGgtatgtttgt ... atttgtttagGCCCACATAAGATTCAAGGCATTGGGGCAGGATTTGTTCCAAGGAACTTGG
EST: gi|86413547|gb|CI019132.1|CI019132
EST:     TATTGGTATTGAGCCTTCTGAGAGTAACATACTCTCTGGTGGAAAACCTG                         GCCCACATAAGATTCAAGGCATTGGGGCAGGATTTGTTCCAAGGAACTTGG
genomic: TATTGGTATTGAGCCTTCTGAGAGTAACATACTCTCTGGTGGAAAACCTGgtatgtttgt ... atttgtttagGCCCACATAAGATTCAAGGCATTGGGGCAGGATTTGTTCCAAGGAACTTGG
EST: gi|29655936|gb|CB652211.1|CB652211
EST:     TATTGGTATTGAGCCTTCTGAGAGTAACATACTCTCTGGTGGAAAACCTG                         GCCCACATAAGATTCAAGGCATTGGGGCAGGATTTGTTCCAAGGAACTTGG
genomic: TATTGGTATTGAGCCTTCTGAGAGTAACATACTCTCTGGTGGAAAACCTGgtatgtttgt ... atttgtttagGCCCACATAAGATTCAAGGCATTGGGGCAGGATTTGTTCCAAGGAACTTGG
EST: gi|55410639|gb|CV723015.1|CV723015
EST:     TATTGGTATTGAGCCTTCTGAGAGTAACATACTCTCTGGTGGAAAACCTG                         GCCCACATAAGATTCAAGGCATTGGGGCAGGATTTGTTCCAAGGAACTTGG
genomic: TATTGGTATTGAGCCTTCTGAGAGTAACATACTCTCTGGTGGAAAACCTGgtatgtttgt ... atttgtttagGCCCACATAAGATTCAAGGCATTGGGGCAGGATTTGTTCCAAGGAACTTGG
EST: gi|58691812|gb|CK080499.1|CK080499
EST:     TATTGGTATTGAGCCTTCTGAGAGTAACATACTCTCTGGTGGAAAACCTG                         GCCCACATAAGATTCAAGGCATTGGGGCAGGATTTGTTCCAAGGAACTTGG
genomic: TATTGGTATTGAGCCTTCTGAGAGTAACATACTCTCTGGTGGAAAACCTGgtatgtttgt ... atttgtttagGCCCACATAAGATTCAAGGCATTGGGGCAGGATTTGTTCCAAGGAACTTGG
EST: gi|29616466|gb|CB621478.1|CB621478
EST:     TATTGGTATTGAGCCTTCTGAGAGTAACATACTCTCTGGTGGAAAACCTG                         GCCCACATAAGATTCAAGGCATTGGGGCAGGATTTGTTCCAAGGAACTTGG
genomic: TATTGGTATTGAGCCTTCTGAGAGTAACATACTCTCTGGTGGAAAACCTGgtatgtttgt ... atttgtttagGCCCACATAAGATTCAAGGCATTGGGGCAGGATTTGTTCCAAGGAACTTGG
EST: gi|28298176|gb|CB238406.1|CB238406
EST:     TATTGGTATTGAGCCTTCTGAGAGTAACATACTCTCTGGTGGAGAACCTG                         GCCCACATAAGATTCAAGGCATTGGG-CAGGATTTGTTCCAAGGAACTTGG
genomic: TATTGGTATTGAGCCTTCTGAGAGTAACATACTCTCTGGTGGAAAACCTGgtatgtttgt ... atttgtttagGCCCACATAAGATTCAAGGCATTGGGGCAGGATTTGTTCCAAGGAACTTGG
EST: gi|29663371|gb|CB659646.1|CB659646
EST:     TATTGGTATTGAGCCTTCTGAGAGTAACATACTCTCTGGTGGAAAACCTG                         GCCCACATAAGATTCAAGGCATTGGGGCAGGATTTGTTCCAAGGAACTTGG
genomic: TATTGGTATTGAGCCTTCTGAGAGTAACATACTCTCTGGTGGAAAACCTGgtatgtttgt ... atttgtttagGCCCACATAAGATTCAAGGCATTGGGGCAGGATTTGTTCCAAGGAACTTGG
EST: gi|29687246|gb|CB683521.1|CB683521
EST:     TATTGGTATTGAGCCTTCTGAGAGTAACATACTCTCTGGTGGAAAACCTG                         GCCCACATAAGATTCAAGGCATTGGGGCAGGATTTGTTCCAAGGAACTTGG
genomic: TATTGGTATTGAGCCTTCTGAGAGTAACATACTCTCTGGTGGAAAACCTGgtatgtttgt ... atttgtttagGCCCACATAAGATTCAAGGCATTGGGGCAGGATTTGTTCCAAGGAACTTGG
EST: gi|163927355|gb|EG710663.1|EG710663
EST:     TATTGGTATTGAGCCTTCTGAGAGTAACATACTCTCTGGTGGAAAACCTG                         GCCCACATAAGATTCAAGGCATTGGGGCAGGATTTGTTCCAAGGAACTTGG
genomic: TATTGGTATTGAGCCTTCTGAGAGTAACATACTCTCTGGTGGAAAACCTGgtatgtttgt ... atttgtttagGCCCACATAAGATTCAAGGCATTGGGGCAGGATTTGTTCCAAGGAACTTGG
EST: gi|84117136|gb|CD150903.1|CD150903
EST:     TATTGGTATTGAGCCTTCTGAGAGTAACATACTCTCTGGTGGAAAACCTG                         GCCCACATAAGATTCAAGGCATTGGGGCAGGATTTGTTCCAAGGAACTTGG
genomic: TATTGGTATTGAGCCTTCTGAGAGTAACATACTCTCTGGTGGAAAACCTGgtatgtttgt ... atttgtttagGCCCACATAAGATTCAAGGCATTGGGGCAGGATTTGTTCCAAGGAACTTGG
EST: gi|33801701|gb|CF326722.1|CF326722
EST:     TATTGGTATTGAGCCTTCTGAGAGTAACATACTCTCTGGTGGAAAACCTG                         GCCCACATAAGATTCAAGTCATTGGGGCAGGATTTGTTCCAAGGAACTTGG
genomic: TATTGGTATTGAGCCTTCTGAGAGTAACATACTCTCTGGTGGAAAACCTGgtatgtttgt ... atttgtttagGCCCACATAAGATTCAAGGCATTGGGGCAGGATTTGTTCCAAGGAACTTGG
EST: gi|38480498|gb|CF964587.1|CF964587
EST:     TATTGGTATTGAGCCTTCTGAGAGTAACATACTCTCTGGTGGAAAACCTG                         GCCCACATAAGATTCAAGGCATTGGGGCAGGATTTGTTCCAAGGAACTTGG
genomic: TATTGGTATTGAGCCTTCTGAGAGTAACATACTCTCTGGTGGAAAACCTGgtatgtttgt ... atttgtttagGCCCACATAAGATTCAAGGCATTGGGGCAGGATTTGTTCCAAGGAACTTGG
EST: gi|29655935|gb|CB652210.1|CB652210
EST:     TATTGGTATTGAGCCTTCTGAGAGTAACATACTCTCTGGTGGAAAACCTG                         GCCCACATAAGATTCAAGGCATTGGGGCAGGATTTGTTCCAAGGAACTTGG
genomic: TATTGGTATTGAGCCTTCTGAGAGTAACATACTCTCTGGTGGAAAACCTGgtatgtttgt ... atttgtttagGCCCACATAAGATTCAAGGCATTGGGGCAGGATTTGTTCCAAGGAACTTGG
EST: gi|88847644|gb|CI018335.1|CI018335
EST:     TCTCTGGTGGAAAACCTG                         GCCCACATAAGATTCAAGGCATTGGGGCAGGATTTGTTCCAAGGAACTTGG
genomic: TCTCTGGTGGAAAACCTGgtatgtttgt ... atttgtttagGCCCACATAAGATTCAAGGCATTGGGGCAGGATTTGTTCCAAGGAACTTGG
EST: gi|29672976|gb|CB669251.1|CB669251
EST:     TATTGGTATTGAGCCTTCTGAGAGTAACATACTCTCTGGTGGAAAACCTG                         GCCCACATAAGATTCAAGGCATTGGGGCAGGATTTGTTCCAAGGAACTTGG
genomic: TATTGGTATTGAGCCTTCTGAGAGTAACATACTCTCTGGTGGAAAACCTGgtatgtttgt ... atttgtttagGCCCACATAAGATTCAAGGCATTGGGGCAGGATTTGTTCCAAGGAACTTGG
EST: gi|29677863|gb|CB674138.1|CB674138
EST:     TATTGGTATTGAGCCTTCTGAGAGTAACATACTCTCTGGTGGAAAACCTG                         GCCCACATAAGATTCAAGGCATTGGGGCAGGATTTGTTCCAAGGAACTTGG
genomic: TATTGGTATTGAGCCTTCTGAGAGTAACATACTCTCTGGTGGAAAACCTGgtatgtttgt ... atttgtttagGCCCACATAAGATTCAAGGCATTGGGGCAGGATTTGTTCCAAGGAACTTGG
EST: gi|87008043|gb|CI297021.1|CI297021
EST:     TATTGGTATTGAGCCTTCTGAGAGTAACATACTCTCTGGTGGAAAACCTG                         GCCCACATAAGATTCAAGGCATTGGGGCAGGATTTGTTCCAAGGAACTTGG
genomic: TATTGGTATTGAGCCTTCTGAGAGTAACATACTCTCTGGTGGAAAACCTGgtatgtttgt ... atttgtttagGCCCACATAAGATTCAAGGCATTGGGGCAGGATTTGTTCCAAGGAACTTGG
EST: gi|58690422|gb|CK079109.1|CK079109
EST:     TATTGGTATTGAGCCTTCTGAGAGTAACATACTCTCTGGTGGAAAACCTG                         GCCCACATAAGATTCAAGGCATTGGGGCAGGATTTGTTCCAAGGAACTTGG
genomic: TATTGGTATTGAGCCTTCTGAGAGTAACATACTCTCTGGTGGAAAACCTGgtatgtttgt ... atttgtttagGCCCACATAAGATTCAAGGCATTGGGGCAGGATTTGTTCCAAGGAACTTGG
EST: gi|29616196|gb|CB621208.1|CB621208
EST:     TATTGGTATTGAGCCTTCTGAGAGTAACATACTCTCTGGTGGAAAACCTG                         GCCCACATAAGATTCAAGGCATTGGGGCAGGATTTGTTCCAAGGAACTTGG
genomic: TATTGGTATTGAGCCTTCTGAGAGTAACATACTCTCTGGTGGAAAACCTGgtatgtttgt ... atttgtttagGCCCACATAAGATTCAAGGCATTGGGGCAGGATTTGTTCCAAGGAACTTGG
EST: gi|29644300|gb|CB649307.1|CB649307
EST:     TATTGGTATTGAGCCTTCTGAGAGTAACATACTCTCTGGTGGAAAACCTG                         GCCCACATAAGATTCAAGGCATTGGGGCAGGATTTGTTCCAAGGAACTTGG
genomic: TATTGGTATTGAGCCTTCTGAGAGTAACATACTCTCTGGTGGAAAACCTGgtatgtttgt ... atttgtttagGCCCACATAAGATTCAAGGCATTGGGGCAGGATTTGTTCCAAGGAACTTGG
EST: gi|13420475|gb|AU174565.1|AU174565
EST:     TATTNGTATTGAGCCTTCTGAGAGTAACATACTCTCTGGTGGAAAACCTG                         GCCCACATAAGATTCAAGGCATTGGGGCAGGATTTGTTCCAAGGAACTTGG
genomic: TATTGGTATTGAGCCTTCTGAGAGTAACATACTCTCTGGTGGAAAACCTGgtatgtttgt ... atttgtttagGCCCACATAAGATTCAAGGCATTGGGGCAGGATTTGTTCCAAGGAACTTGG
EST: gi|300215770|gb|HO088396.1|HO088396
EST:     TATTGGTATTGAGCCTTCTGAGAGTAACATACTCTCTGGTGGAAAACCTG                         GCCCACATAAGATTCAAGGCATTGGGGCAGGATTTGTTCCAAGGAACTTGG
genomic: TATTGGTATTGAGCCTTCTGAGAGTAACATACTCTCTGGTGGAAAACCTGgtatgtttgt ... atttgtttagGCCCACATAAGATTCAAGGCATTGGGGCAGGATTTGTTCCAAGGAACTTGG
EST: gi|29684900|gb|CB681175.1|CB681175
EST:     TATTGGTATTGAGCCTTCTGAGAGTAACATACTCTCTGGTGGAAAACCTG                         GCCCACATAAGATTCAAGGCATTGGGGCAGGATTTGTTCCAAGGAACTTGG
genomic: TATTGGTATTGAGCCTTCTGAGAGTAACATACTCTCTGGTGGAAAACCTGgtatgtttgt ... atttgtttagGCCCACATAAGATTCAAGGCATTGGGGCAGGATTTGTTCCAAGGAACTTGG
EST: gi|38478600|gb|CF962733.1|CF962733
EST:     ATTTGGTATTGAGCCTTCTGAGAGTAACATACTCTCTGGTGGAAAACCTG                         GCCCACATAAGATTCAAGGCATTGGGGCAGGA
genomic: ATT-GGTATTGAGCCTTCTGAGAGTAACATACTCTCTGGTGGAAAACCTGgtatgtttgt ... atttgtttagGCCCACATAAGATTCAAGGCATTGGGGCAGGA

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: 71 (upstream exon), 74 (downstream exon)
Score: 149

GTTATTGGTATTGAGCCTTCTGAGAGTAACATACTCTCTGGTGGAAAACCTGgtatgtttgt ... atttgtttagGCCCACATAAGATTCAAGGCATTGGGGCAGGATTTGTTCCAAGGAACTTGGATAGTGAAGTTCTCGATGAAGTGATTGAG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTTATTGGTATTGAGCCTTCTGAGAGTAACATACTCTCTGGTGGAAAACCTGgtatgtttgtgttcttacttccttaaggtttgtcaaatgtctgctctttcccttataattcaccccatttgtttag

- - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - -  GGTGGA