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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTTTGGTTTTCTGAAGTACTGGAAACGTTCTCGATTGGCGAAAAGTTTGTGAGATTTTTGTCTTCTGgtaagtttagggactaaaagctccccttttgccactgagcactgacttagaaatatgtataactgctgcataggaatcatgcttgacaatttggtcatta...

Basic information

species Oryza sativa
transcript LOC_Os12g40490.1
intron # 3
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|29634158|gb|CB639167.1|CB639167
EST:     ACTGGAAACGTTCTCGATTGGCGAAAAGTTTGTGAGATTTTTGTCTTCTG                         GCTACAGAAAATTCGACCCTCAGATAACCTCGAGTCATGGGTTGGTTAAAT
genomic: ACTGGAAACGTTCTCGATTGGCGAAAAGTTTGTGAGATTTTTGTCTTCTGgtaagtttag ... tctgctgcagGCTACAGAAAATTCGACCCTCAGATAACCTCGAGTCATGGGTTGGTTAAAT
EST: gi|88322002|gb|CI673152.1|CI673152
EST:     ACTGGAAACGTTCTCGATTGGCGAAAAGTTTGTGAGATTTTTGTCTTCTG                         GCTACAGAAAATTCGACCCTCAGATAACCTCGAGTCATGGGTTGGTTAAAT
genomic: ACTGGAAACGTTCTCGATTGGCGAAAAGTTTGTGAGATTTTTGTCTTCTGgtaagtttag ... tctgctgcagGCTACAGAAAATTCGACCCTCAGATAACCTCGAGTCATGGGTTGGTTAAAT
EST: gi|88391277|gb|CI595531.1|CI595531
EST:     ACTGGAAACGTTCTCGATTGGCGAAAAGTTTGTGAGATTTTTGTCTTCTG                         GCTACAGAAAATTCGACCCTCAGATAACCTCGAGTCATGGGTTGGTTAAAT
genomic: ACTGGAAACGTTCTCGATTGGCGAAAAGTTTGTGAGATTTTTGTCTTCTGgtaagtttag ... tctgctgcagGCTACAGAAAATTCGACCCTCAGATAACCTCGAGTCATGGGTTGGTTAAAT
EST: gi|29632389|gb|CB637398.1|CB637398
EST:     ACTGGAAACGTTCTCGATTGGCGAAAAGTTTGTGAGATTTTTGTCTTCTG                         GCTACAGAAAATTCGACCCTCAGATAACCTCGAGTCATGGGTTGGTTAAAT
genomic: ACTGGAAACGTTCTCGATTGGCGAAAAGTTTGTGAGATTTTTGTCTTCTGgtaagtttag ... tctgctgcagGCTACAGAAAATTCGACCCTCAGATAACCTCGAGTCATGGGTTGGTTAAAT
EST: gi|88593039|gb|CI711188.1|CI711188
EST:     ACTGGAAACGTTCTCGATTGGCGAAAAGTTTGTGAGATTTTTGTCTTCTG                         GCTACAGAAAATTCGACCCTCAGATAACCTCGAGTCATGGGTTGGTTAAAT
genomic: ACTGGAAACGTTCTCGATTGGCGAAAAGTTTGTGAGATTTTTGTCTTCTGgtaagtttag ... tctgctgcagGCTACAGAAAATTCGACCCTCAGATAACCTCGAGTCATGGGTTGGTTAAAT
EST: gi|88737536|gb|CI759417.1|CI759417
EST:     ACTGGAAACGTTCTCGATTGGCGAAAAGTTTGTGAGATTTTTGTCTTCTG                         GCTACAGAAAATTCGACCCTCAGATAACCTCGAGTCATG
genomic: ACTGGAAACGTTCTCGATTGGCGAAAAGTTTGTGAGATTTTTGTCTTCTGgtaagtttag ... tctgctgcagGCTACAGAAAATTCGACCCTCAGATAACCTCGAGTCATG
EST: gi|88367909|gb|CI572630.1|CI572630
EST:     ACTGGAAACGTTCTCGATTGGCGAAAAGTTTGTGAGATTTTTGTCTTCTG                         GCTACAGAAAATTCGACCCTCAGATAACCTCGAGTCATGGGTTGGTTAAAT
genomic: ACTGGAAACGTTCTCGATTGGCGAAAAGTTTGTGAGATTTTTGTCTTCTGgtaagtttag ... tctgctgcagGCTACAGAAAATTCGACCCTCAGATAACCTCGAGTCATGGGTTGGTTAAAT
EST: gi|88581980|gb|CI699200.1|CI699200
EST:     ACTGGAAACGTTCTCGATTGGCGAAAAGTTTGTGAGATTTTTGTCTTCTG                         GCTACAGAAAATTCGACCCTCAGATAACCTCGAGTCATGGGTTGGTTAAAT
genomic: ACTGGAAACGTTCTCGATTGGCGAAAAGTTTGTGAGATTTTTGTCTTCTGgtaagtttag ... tctgctgcagGCTACAGAAAATTCGACCCTCAGATAACCTCGAGTCATGGGTTGGTTAAAT
EST: gi|33678894|gb|CF307133.1|CF307133
EST:     ACTGGAAACGTTCTCGATTGGCGAAAAGTTTGTGAGATTTTTGTCTTCTG                         GCTACAGAAAATTCGACCCTCAGATAACCTCGAGTCATGGGTTGGTTAAAT
genomic: ACTGGAAACGTTCTCGATTGGCGAAAAGTTTGTGAGATTTTTGTCTTCTGgtaagtttag ... tctgctgcagGCTACAGAAAATTCGACCCTCAGATAACCTCGAGTCATGGGTTGGTTAAAT
EST: gi|88826328|gb|CI776893.1|CI776893
EST:     ACTGGAAACGTTCTCGATTGGCGAAAAGTTTGTGAGATTTTTGTCTTCTG                         GCTACAGAAAATTCGACCCTCAGATAACCTCGAG
genomic: ACTGGAAACGTTCTCGATTGGCGAAAAGTTTGTGAGATTTTTGTCTTCTGgtaagtttag ... tctgctgcagGCTACAGAAAATTCGACCCTCAGATAACCTCGAG
EST: gi|88317739|gb|CI672328.1|CI672328
EST:     ACTGGAAACGTTCTCGATTGGCGAAAAGTTTGTGAGATTTTTGTCTTCTG                         GCTACAGAAAATTCGACCCTCAGATAACCTCGAGTCATGGGTTGGTTAAAT
genomic: ACTGGAAACGTTCTCGATTGGCGAAAAGTTTGTGAGATTTTTGTCTTCTGgtaagtttag ... tctgctgcagGCTACAGAAAATTCGACCCTCAGATAACCTCGAGTCATGGGTTGGTTAAAT
EST: gi|29635157|gb|CB640166.1|CB640166
EST:     ACTGGAAACGTTCTCGATTGGCGAAAAGTTTGTGAGATTTTTGTCTTCTG                         GCTACAGAAAATTCGACCCTCAGATAACCTCGAGTCATGGGTTGGTTAAAT
genomic: ACTGGAAACGTTCTCGATTGGCGAAAAGTTTGTGAGATTTTTGTCTTCTGgtaagtttag ... tctgctgcagGCTACAGAAAATTCGACCCTCAGATAACCTCGAGTCATGGGTTGGTTAAAT
EST: gi|29630464|gb|CB635473.1|CB635473
EST:     ACTGGAAACGTTCTCGATTGGCGAAAAGTTTATGAGATTTTTGTCTTCTG                         GCTACAGAAAATTCGACCCTCAGATAACCTCGAGTCATGGGTTGGTTAAAT
genomic: ACTGGAAACGTTCTCGATTGGCGAAAAGTTTGTGAGATTTTTGTCTTCTGgtaagtttag ... tctgctgcagGCTACAGAAAATTCGACCCTCAGATAACCTCGAGTCATGGGTTGGTTAAAT
EST: gi|29627991|gb|CB633002.1|CB633002
EST:     ACTGGAAACGTTCTCGATTGGCGAAAAGTTTATGAGATTTTTGTCTTCTG                         GCTACAGAAAATTCGACCCTCAGATAACCTCGAGTCATGGGTTGGTTAAAT
genomic: ACTGGAAACGTTCTCGATTGGCGAAAAGTTTGTGAGATTTTTGTCTTCTGgtaagtttag ... tctgctgcagGCTACAGAAAATTCGACCCTCAGATAACCTCGAGTCATGGGTTGGTTAAAT
EST: gi|88412122|gb|CI566851.1|CI566851
EST:     ACTGGAAACGTTCTCGATTGGCGAAAAGTTTGTGAGATTTTTGTCTTCTG                         GCTACAGAAAATTCGACCCTCAGATAACCTCGAGTCATGGGTTGGTTAAAT
genomic: ACTGGAAACGTTCTCGATTGGCGAAAAGTTTGTGAGATTTTTGTCTTCTGgtaagtttag ... tctgctgcagGCTACAGAAAATTCGACCCTCAGATAACCTCGAGTCATGGGTTGGTTAAAT

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: 59 (upstream exon), 47 (downstream exon)
Score: 13

CTTTGGTTTTCTGAAGTACTGGAAACGTTCTCGATTGGCGAAAAGTTTGTGAGATTTTTGTCTTCTGgtaagtttag ... tctgctgcagGCTACAGAAAATTCGACCCTCAGATAACCTCGAGTCATGGGTTGGTTAAATAAAATATTTAAAGGTTCAGTAAATAGAGTTTCAAGGGGCCATTATGATG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CTTTGGTTTTCTGAAGTACTGGAAACGTTCTCGATTGGCGAAAAGTTTGTGAGATTTTTGTCTTCTGgtaagtttagggactaaaagctccccttttgccactgagcactgacttagaaatatgtataactgctgcataggaatcatgcttgacaatttggtcatta

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gctcccc