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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATATCTAGTGATGAGGCTGTTGAGACAGCAAAGCAATTGGCTCTTCAGGAAGGATTACTGgtattctaatttcatgttgtgatctactcttttaatgcgtcattctttctttggtttgctcttgagttgcaaatttttatattctaatgagaacaggcaa...

Basic information

species Oryza sativa
transcript LOC_Os01g74650.1
intron # 8
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:     ATGAGGCTGTTGAGACAGCAAAGCAATTGGCTCTTCAGGAAGGATTACTG                         GTTGGAATTTCATCTGGGGCAGCAGCAGCAGCTGCCATTAAAGTTGCAAAA
genomic: ATGAGGCTGTTGAGACAGCAAAGCAATTGGCTCTTCAGGAAGGATTACTGgtattctaat ... tgttcttcagGTTGGAATTTCATCTGGGGCAGCAGCAGCAGCTGCCATTAAAGTTGCAAAA
EST: gi|701729|gb|D48020.1|D48020
EST:     ATGAGGCTGTTGAGACAGCAAAGCAATTGGCTCTTCAGGAAGGATTACTG                         GTTGGAATTTCATCTGGGGCAGCAGCAGCAGCTGCCATTAAAGTTGCAAAA
genomic: ATGAGGCTGTTGAGACAGCAAAGCAATTGGCTCTTCAGGAAGGATTACTGgtattctaat ... tgttcttcagGTTGGAATTTCATCTGGGGCAGCAGCAGCAGCTGCCATTAAAGTTGCAAAA
EST: gi|86413547|gb|CI019132.1|CI019132
EST:     ATGAGGCTGTTGAGACAGCAAAGCAATTGGCTCTTCAGGAAGGATTACTG                         GTTGGAATTTCATCTGGGGCAGCAGCAGCAGCTGCCATTAAAGTTGCAAAA
genomic: ATGAGGCTGTTGAGACAGCAAAGCAATTGGCTCTTCAGGAAGGATTACTGgtattctaat ... tgttcttcagGTTGGAATTTCATCTGGGGCAGCAGCAGCAGCTGCCATTAAAGTTGCAAAA
EST: gi|29655936|gb|CB652211.1|CB652211
EST:     ATGAGGCTGTTGAGACAGCAAAGCAATTGGCTCTTCAGGAAGGATTACTG                         GTTGGAATTTCATCTGGGGCAGCAGCAGCAGCTGCCATTAAAGTTGCAAAA
genomic: ATGAGGCTGTTGAGACAGCAAAGCAATTGGCTCTTCAGGAAGGATTACTGgtattctaat ... tgttcttcagGTTGGAATTTCATCTGGGGCAGCAGCAGCAGCTGCCATTAAAGTTGCAAAA
EST: gi|58691812|gb|CK080499.1|CK080499
EST:     ATGAGGCTGTTGAGACAGCAAAGCAATTGGCTCTTCAGGAAGGATTACTG                         GTTGGAATTTCATCTGGGGCAGCAGCAGCAGCTGCCATTAAAGTTGCAAAA
genomic: ATGAGGCTGTTGAGACAGCAAAGCAATTGGCTCTTCAGGAAGGATTACTGgtattctaat ... tgttcttcagGTTGGAATTTCATCTGGGGCAGCAGCAGCAGCTGCCATTAAAGTTGCAAAA
EST: gi|29616466|gb|CB621478.1|CB621478
EST:     ATGAGGCTGTTGAGACAGCAAAGCAATTGGCTCTTCAGGAAGGATTACTG                         GTTGGAATTTCATCTGGGGCAGCAGCAGCAGCTGCCATTAAAGTTGCAAAA
genomic: ATGAGGCTGTTGAGACAGCAAAGCAATTGGCTCTTCAGGAAGGATTACTGgtattctaat ... tgttcttcagGTTGGAATTTCATCTGGGGCAGCAGCAGCAGCTGCCATTAAAGTTGCAAAA
EST: gi|29663371|gb|CB659646.1|CB659646
EST:     ATGAGGCTGTTGAGACAGCAAAGCAATTGGCTCTTCAGGAAGGATTACTG                         GTTGGAATTTCATCTGGGGCAGCAGCAGCAGCTGCCATTAAAGTTGCAAAA
genomic: ATGAGGCTGTTGAGACAGCAAAGCAATTGGCTCTTCAGGAAGGATTACTGgtattctaat ... tgttcttcagGTTGGAATTTCATCTGGGGCAGCAGCAGCAGCTGCCATTAAAGTTGCAAAA
EST: gi|29687246|gb|CB683521.1|CB683521
EST:     ATGAGGCTGTTGAGACAGCAAAGCAATTGGCTCTTCAGGAAGGATTACTG                         GTTGGAATTTCATCTGGGGCAGCAGCAGCAGCTGCCATTAAAGTTGCAAAA
genomic: ATGAGGCTGTTGAGACAGCAAAGCAATTGGCTCTTCAGGAAGGATTACTGgtattctaat ... tgttcttcagGTTGGAATTTCATCTGGGGCAGCAGCAGCAGCTGCCATTAAAGTTGCAAAA
EST: gi|163927355|gb|EG710663.1|EG710663
EST:     ATGAGGCTGTTGAGACAGCAAAGCAATTGGCTCTTCAGGAAGGATTACTG                         GTTGGAATTTCATCTGGGGCAGCAGCAGCAGCTGCCATTAAAGTTGCAAAA
genomic: ATGAGGCTGTTGAGACAGCAAAGCAATTGGCTCTTCAGGAAGGATTACTGgtattctaat ... tgttcttcagGTTGGAATTTCATCTGGGGCAGCAGCAGCAGCTGCCATTAAAGTTGCAAAA
EST: gi|84117136|gb|CD150903.1|CD150903
EST:     ATGAGGCTGTTGAGACAGCAAAGCAATTGGCTCTTCAGGAAGGATTACTG                         GTTGGAATTTCATGTGGGGCAGCAGCAGCAGCTGCCATTAAAGCTGCAAAA
genomic: ATGAGGCTGTTGAGACAGCAAAGCAATTGGCTCTTCAGGAAGGATTACTGgtattctaat ... tgttcttcagGTTGGAATTTCATCTGGGGCAGCAGCAGCAGCTGCCATTAAAGTTGCAAAA
EST: gi|33801701|gb|CF326722.1|CF326722
EST:     ATGAGGCTGTTGAGACAGCAAAGCAATTGGCTCTTCAGGAAGGATTACTG                         GTTGGAATTTCATCTGGGGCAGCAGCAGCAGCTGCCATTAAAGTTGCAAAA
genomic: ATGAGGCTGTTGAGACAGCAAAGCAATTGGCTCTTCAGGAAGGATTACTGgtattctaat ... tgttcttcagGTTGGAATTTCATCTGGGGCAGCAGCAGCAGCTGCCATTAAAGTTGCAAAA
EST: gi|38480498|gb|CF964587.1|CF964587
EST:     ATGAGGCTGTTGAGACAGCAAAGCAATTGGCTCTTCAGGAAGGATTACTG                         GTTGGAATTTCATCTGGGGCAGCAGCAGCAGCTGCCATTAAAGTTGCAAAA
genomic: ATGAGGCTGTTGAGACAGCAAAGCAATTGGCTCTTCAGGAAGGATTACTGgtattctaat ... tgttcttcagGTTGGAATTTCATCTGGGGCAGCAGCAGCAGCTGCCATTAAAGTTGCAAAA
EST: gi|86494722|gb|CI137355.1|CI137355
EST:     ATGAGGCTGTTGAGACAGCAAAGCAATTGGCTCTTCAGGAAGGATTACTG                         GTTGGAATTTCATCTGGGGCAGCAGCAGCAGCTGCCATTAAAGTTGCAAAA
genomic: ATGAGGCTGTTGAGACAGCAAAGCAATTGGCTCTTCAGGAAGGATTACTGgtattctaat ... tgttcttcagGTTGGAATTTCATCTGGGGCAGCAGCAGCAGCTGCCATTAAAGTTGCAAAA
EST: gi|29655935|gb|CB652210.1|CB652210
EST:     ATGAGGCTGTTGAGACAGCAAAGCAATTGGCTCTTCAGGAAGGATTACTG                         GTTGGAATTTCATCTGGGGCAGCAGCAGCAGCTGCCATTAAAGTTGCAAAA
genomic: ATGAGGCTGTTGAGACAGCAAAGCAATTGGCTCTTCAGGAAGGATTACTGgtattctaat ... tgttcttcagGTTGGAATTTCATCTGGGGCAGCAGCAGCAGCTGCCATTAAAGTTGCAAAA
EST: gi|88847644|gb|CI018335.1|CI018335
EST:     ATGAGGCTGTTGAGACAGCAAAGCAATTGGCTCTTCAGGAAGGATTACTG                         GTTGGAATTTCATCTGGGGCAGCAGCAGCAGCTGCCATTAAAGTTGCAAAA
genomic: ATGAGGCTGTTGAGACAGCAAAGCAATTGGCTCTTCAGGAAGGATTACTGgtattctaat ... tgttcttcagGTTGGAATTTCATCTGGGGCAGCAGCAGCAGCTGCCATTAAAGTTGCAAAA
EST: gi|38469869|gb|CF954000.1|CF954000
EST:     ATGAGGCTGTTGAGACAGCAAAGCAATTGGCTCTTCAGGAAGGATTACTG                         GTTGGAATTTCATCTGGGGCAGCAGCAGCAGCTGCCATTAAAGTTGCAAAA
genomic: ATGAGGCTGTTGAGACAGCAAAGCAATTGGCTCTTCAGGAAGGATTACTGgtattctaat ... tgttcttcagGTTGGAATTTCATCTGGGGCAGCAGCAGCAGCTGCCATTAAAGTTGCAAAA
EST: gi|29672976|gb|CB669251.1|CB669251
EST:     ATGAGGCTGTTGAGACAGCAAAGCAATTGGCTCTTCAGGAAGGATTACTG                         GTTGGAATTTCATCTGGGGCAGCAGCAGCAGCTGCCATTAAAGTTGCAAAA
genomic: ATGAGGCTGTTGAGACAGCAAAGCAATTGGCTCTTCAGGAAGGATTACTGgtattctaat ... tgttcttcagGTTGGAATTTCATCTGGGGCAGCAGCAGCAGCTGCCATTAAAGTTGCAAAA
EST: gi|29677863|gb|CB674138.1|CB674138
EST:     ATGAGGCTGTTGAGACAGCAAAGCAATTGGCTCTTCAGGAAGGATTACTG                         GTTGGAATTTCATCTGGGGCAGCAGCAGCAGCTGCCATTAAAGTTGCAAAA
genomic: ATGAGGCTGTTGAGACAGCAAAGCAATTGGCTCTTCAGGAAGGATTACTGgtattctaat ... tgttcttcagGTTGGAATTTCATCTGGGGCAGCAGCAGCAGCTGCCATTAAAGTTGCAAAA
EST: gi|58690422|gb|CK079109.1|CK079109
EST:     ATGAGGCTGTTGAGACAGCAAAGCAATTGGCTCTTCAGGAAGGATTACTG                         GTTGGAATTTCATCTGGGGCAGCAGCAGCAGCTGCCATTAAAGTTGCAAAA
genomic: ATGAGGCTGTTGAGACAGCAAAGCAATTGGCTCTTCAGGAAGGATTACTGgtattctaat ... tgttcttcagGTTGGAATTTCATCTGGGGCAGCAGCAGCAGCTGCCATTAAAGTTGCAAAA
EST: gi|88845335|gb|CI084260.1|CI084260
EST:     ATGAGGCTGTTGAGACAGCAAAGCAATTGGCTCTTCAGGAAGGATTACTG                         GTTGGAATTTCATCTGGGGCAGCAGCAGCAGCTGCCATTAAAGTTGCAAAA
genomic: ATGAGGCTGTTGAGACAGCAAAGCAATTGGCTCTTCAGGAAGGATTACTGgtattctaat ... tgttcttcagGTTGGAATTTCATCTGGGGCAGCAGCAGCAGCTGCCATTAAAGTTGCAAAA
EST: gi|29616196|gb|CB621208.1|CB621208
EST:     ATGAGGCTGTTGAGACAGCAAAGCAATTGGCTCTTCAGGAAGGATTACTG                         GTTGGAATTTCATCTGGGGCAGCAGCAGCAGCTGCCATTAAAGTTGCAAAA
genomic: ATGAGGCTGTTGAGACAGCAAAGCAATTGGCTCTTCAGGAAGGATTACTGgtattctaat ... tgttcttcagGTTGGAATTTCATCTGGGGCAGCAGCAGCAGCTGCCATTAAAGTTGCAAAA
EST: gi|58696201|gb|CK084888.1|CK084888
EST:     ATGAGGCTGTTGAGACAGCAAAGCAATTGGCTCTTCAGGAAGGATTACTG                         GTTGGAATTTCATCTGGGGCAGCAGCAGCAGCTGCCATTAAAGTTGCAAAA
genomic: ATGAGGCTGTTGAGACAGCAAAGCAATTGGCTCTTCAGGAAGGATTACTGgtattctaat ... tgttcttcagGTTGGAATTTCATCTGGGGCAGCAGCAGCAGCTGCCATTAAAGTTGCAAAA
EST: gi|86535476|gb|CI175682.1|CI175682
EST:     ATGAGGCTGTTGAGACAGCAAAGCAATTGGCTCTTCAGGAAGGATTACTG                         GTTGGAATTTCATCTGGGGCAGCAGCAGCAGCTGCCATTAAAGTTGCAAAA
genomic: ATGAGGCTGTTGAGACAGCAAAGCAATTGGCTCTTCAGGAAGGATTACTGgtattctaat ... tgttcttcagGTTGGAATTTCATCTGGGGCAGCAGCAGCAGCTGCCATTAAAGTTGCAAAA
EST: gi|38471318|gb|CF955449.1|CF955449
EST:     TGAGGCTGTTGAGACAGCAAGAGCAATTGGCTCTTCAGGAAGGATTACTG                         GTTGGAATTTCATCTGGGGCAGCAGCAGCAGCTGCCATTAAAGTTGCAATA
genomic: TGAGGCTGTTGAGACAGCAA-AGCAATTGGCTCTTCAGGAAGGATTACTGgtattctaat ... tgttcttcagGTTGGAATTTCATCTGGGGCAGCAGCAGCAGCTGCCATTAAAGTTGCAAAA
EST: gi|88220621|gb|CI220181.1|CI220181
EST:     ATGAGGCTGTTGAGACAGCAAAGCAATTGGCTCTTCAGGAAGGATTACTG                         GTTGGAATTTCATCTGGGGCAGCAGCAGCAGCTGCCATTAAAGTTGCAAAA
genomic: ATGAGGCTGTTGAGACAGCAAAGCAATTGGCTCTTCAGGAAGGATTACTGgtattctaat ... tgttcttcagGTTGGAATTTCATCTGGGGCAGCAGCAGCAGCTGCCATTAAAGTTGCAAAA
EST: gi|29644300|gb|CB649307.1|CB649307
EST:     ATGAGGCTGTTGAGACAGCAAAGCAATTGGCTCTTCAGGAAGGATTACTG                         GTTGGAATTTCATTTGGGGCAGCAGCAGCAGCTGCCATTAAAGTTGCAAAA
genomic: ATGAGGCTGTTGAGACAGCAAAGCAATTGGCTCTTCAGGAAGGATTACTGgtattctaat ... tgttcttcagGTTGGAATTTCATCTGGGGCAGCAGCAGCAGCTGCCATTAAAGTTGCAAAA
EST: gi|13420475|gb|AU174565.1|AU174565
EST:     ATGAGGCTGTTGAGACAGCAAAGCAATTGGCTCTTCAGGAAGGATTACTG                         GTTGGAATTTCATCTGGGGCAGCAGCAGCAGCT-CCATTAAAGTTGCAAAA
genomic: ATGAGGCTGTTGAGACAGCAAAGCAATTGGCTCTTCAGGAAGGATTACTGgtattctaat ... tgttcttcagGTTGGAATTTCATCTGGGGCAGCAGCAGCAGCTGCCATTAAAGTTGCAAAA
EST: gi|300215770|gb|HO088396.1|HO088396
EST:     ATGTGGCTGTTGAGACAGCAAAGCAATTGGCTCTTCAGGAAGGATTACTG                         GTTGGAATTTCATCTGGGGCAGCAGCAGCAGCTGCCATTAAAGTTGCAAAA
genomic: ATGAGGCTGTTGAGACAGCAAAGCAATTGGCTCTTCAGGAAGGATTACTGgtattctaat ... tgttcttcagGTTGGAATTTCATCTGGGGCAGCAGCAGCAGCTGCCATTAAAGTTGCAAAA
EST: gi|29684900|gb|CB681175.1|CB681175
EST:     ATGAGGCTGTTGAGACAGCAAAGCAATTGGCTCTTCAGGAAGGATTACTG                         GTTGGAATTTCATCTGGGGCAGCAGCAGCAGCTGCCATTAAAGTTGCAAAA
genomic: ATGAGGCTGTTGAGACAGCAAAGCAATTGGCTCTTCAGGAAGGATTACTGgtattctaat ... tgttcttcagGTTGGAATTTCATCTGGGGCAGCAGCAGCAGCTGCCATTAAAGTTGCAAAA
EST: gi|86417511|gb|CI031720.1|CI031720
EST:     ATGAGGCTGTTGAGACAGCAAAGCAATTGGCTCTTCAGGAAGGATTACTG                         GTTGGAATTTCATCTGGGGCAGCAGCAGCAGCTGCCATTAAAGTTGCAAAA
genomic: ATGAGGCTGTTGAGACAGCAAAGCAATTGGCTCTTCAGGAAGGATTACTGgtattctaat ... tgttcttcagGTTGGAATTTCATCTGGGGCAGCAGCAGCAGCTGCCATTAAAGTTGCAAAA
EST: gi|88387705|gb|CI585408.1|CI585408
EST:     ATGAGGCTGTTGAGACAGCAAAGCAATTGGCTCTTCAGGAAGGATTACTG                         GTTGGAATTTCATCTGGGGCAGCAGCAGCAGCTGCCATTAAAGTTGCAAAA
genomic: ATGAGGCTGTTGAGACAGCAAAGCAATTGGCTCTTCAGGAAGGATTACTGgtattctaat ... tgttcttcagGTTGGAATTTCATCTGGGGCAGCAGCAGCAGCTGCCATTAAAGTTGCAAAA

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: 58 (upstream exon), 75 (downstream exon)
Score: 126

ATATCTAGTGATGAGGCTGTTGAGACAGCAAAGCAATTGGCTCTTCAGGAAGGATTACTGgtattctaat ... tgttcttcagGTTGGAATTTCATCTGGGGCAGCAGCAGCAGCTGCCATTAAAGTTGCAAAAAGACCAGAAAATGCTGGAAAGTTGGTAGTG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATATCTAGTGATGAGGCTGTTGAGACAGCAAAGCAATTGGCTCTTCAGGAAGGATTACTGgtattctaatttcatgttgtgatctactcttttaatgcgtcattctttctttggtttgctcttgagttgcaaatttttatattctaatgagaacaggcaa

- - - - - - -  GCTGTT
- - - - - - - - - - - - -  GCAAAG
- - - - - - - - - - - - - - - AAGCAA