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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tcctttttatattttaaacttatatttatttgggaattgtatgttagtatacagtacatactacagttgaattcaacagttaattttgtatgatgttcagGCATTTGCTCAGTTGTTGAAAGCTCCACGTGAGGAAACTGATTCGATAATCAAGGAGCGCTTTCCTGTTCCTCGTTTGGTCGTGTGTGATCAATATGGTT

Basic information

species Oryza sativa
transcript LOC_Os08g36994.1
intron # 12
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|87016525|gb|CI273735.1|CI273735
EST:     CCATTGCGCAGTGGCGAAAGGCTGGCTACCAAGATCAGCAAGGGCATGAG                         GCATTTGCTCAGTTGTTGAAAGCTCCACGTGAGGAAACTGATTCGATAATC
genomic: CCATTGCGCAGTGGCGAAAGGCTGGCTACCAAGATCAGCAAGGGCATGAGgtaatgtttt ... tgatgttcagGCATTTGCTCAGTTGTTGAAAGCTCCACGTGAGGAAACTGATTCGATAATC
EST: gi|88839144|gb|CI378068.1|CI378068
EST:     CCATTGCCCAGTGGCGAAAGGCTGGCTACCAAGATCAGCAAGGGCATGAG                         GCATTTGCTCAGTTGTTGAAAGCTCCACGTGAGGAAACTGATTCGATAATC
genomic: CCATTGCGCAGTGGCGAAAGGCTGGCTACCAAGATCAGCAAGGGCATGAGgtaatgtttt ... tgatgttcagGCATTTGCTCAGTTGTTGAAAGCTCCACGTGAGGAAACTGATTCGATAATC
EST: gi|9865041|gb|AU100791.1|AU100791
EST:     CCATTGCGCAGTGGCGAAAGGCTGGCTACCAAGATCAGCAAGGGCNTGAG                         GCATTTGCTCAGTTGTTGAAAGCTCCACGTGAGGAAACTGATTCGATAATC
genomic: CCATTGCGCAGTGGCGAAAGGCTGGCTACCAAGATCAGCAAGGGCATGAGgtaatgtttt ... tgatgttcagGCATTTGCTCAGTTGTTGAAAGCTCCACGTGAGGAAACTGATTCGATAATC
EST: gi|29622603|gb|CB627614.1|CB627614
EST:     CCATTGCGCAGTGGCGAAAGGCTGGCTACCAAGATCAGCAAGGGCATGAG                         GCATTTGCTCAGTTGTTGAAAGCTCCACATGAGGAAACTGATTCGATAATC
genomic: CCATTGCGCAGTGGCGAAAGGCTGGCTACCAAGATCAGCAAGGGCATGAGgtaatgtttt ... tgatgttcagGCATTTGCTCAGTTGTTGAAAGCTCCACGTGAGGAAACTGATTCGATAATC
EST: gi|89175029|gb|CI041107.1|CI041107
EST:     CCATTGCGCAGTGGCGAAAGGCTGGCTACCAAGATCAGCAAGGGCATGAG                         GCATTTGCTCAGTTGTTGAAAGCTCCACGTGAGGAAACTGATTCGATAATC
genomic: CCATTGCGCAGTGGCGAAAGGCTGGCTACCAAGATCAGCAAGGGCATGAGgtaatgtttt ... tgatgttcagGCATTTGCTCAGTTGTTGAAAGCTCCACGTGAGGAAACTGATTCGATAATC
EST: gi|88838779|gb|CI376317.1|CI376317
EST:     TGGCTACCAAGATCAGCAAGGGCATGAG                         GCATTTGCTCAGTTGTT-AAAGCTCCACGTGAGGAAACTGATTCGATAATC
genomic: TGGCTACCAAGATCAGCAAGGGCATGAGgtaatgtttt ... tgatgttcagGCATTTGCTCAGTTGTTGAAAGCTCCACGTGAGGAAACTGATTCGATAATC
EST: gi|86494160|gb|CI136793.1|CI136793
EST:     CCATTGCGCAGTGGCGAAAGGCTGGCTACCAAGATCAGCAAGGGCATGAG                         GCATTTGCTCAGTTGTTGAAAGCTCCACGTGAGGAAACTGATTCGATAATC
genomic: CCATTGCGCAGTGGCGAAAGGCTGGCTACCAAGATCAGCAAGGGCATGAGgtaatgtttt ... tgatgttcagGCATTTGCTCAGTTGTTGAAAGCTCCACGTGAGGAAACTGATTCGATAATC
EST: gi|58693961|gb|CK082648.1|CK082648
EST:     CCATTGCGCAGTGGCGAAAGGCTGGCTACCAAGATCAGCAAGGGCATGAG                         GCATTTGCTCAGTTGTTGAAAGCTCCACATGAGGAAACTGATTCGATAATC
genomic: CCATTGCGCAGTGGCGAAAGGCTGGCTACCAAGATCAGCAAGGGCATGAGgtaatgtttt ... tgatgttcagGCATTTGCTCAGTTGTTGAAAGCTCCACGTGAGGAAACTGATTCGATAATC
EST: gi|86885390|gb|CI318541.1|CI318541
EST:     CAAGGGCATGAG                         GCATTTGCTCAGTTGTTGAAAGCTCCACGTGA-GAAACTGATTCGATAATC
genomic: CAAGGGCATGAGgtaatgtttt ... tgatgttcagGCATTTGCTCAGTTGTTGAAAGCTCCACGTGAGGAAACTGATTCGATAATC
EST: gi|86477675|gb|CI120308.1|CI120308
EST:     CCATTGCGCAGTGGCGAAAGGCTGGCTACCAAGATCAGCAAGGGCATGAG                         GCATTTGCTCAGTTGTTGAAAGCTCCACGTGAGGAAACTGATTCGATAATC
genomic: CCATTGCGCAGTGGCGAAAGGCTGGCTACCAAGATCAGCAAGGGCATGAGgtaatgtttt ... tgatgttcagGCATTTGCTCAGTTGTTGAAAGCTCCACGTGAGGAAACTGATTCGATAATC
EST: gi|86437940|gb|CI119860.1|CI119860
EST:     GCTACCAAGATCAGCAAGGGCATGGG                         GCATTTGCTCAGTTGTTGAAAGCTCCACGTGAGGAAACTGATTCGATAATC
genomic: GCTACCAAGATCAGCAAGGGCATGAGgtaatgtttt ... tgatgttcagGCATTTGCTCAGTTGTTGAAAGCTCCACGTGAGGAAACTGATTCGATAATC
EST: gi|86888989|gb|CI314605.1|CI314605
EST:     GCGAAAGGCTGGCTACCAAGATCAGCAAGGGCATGAG                         GCATTTGCTCAGTTGTTGAAAGCTCCACGTGAGGAAACTGATTCTATAATC
genomic: GCGAAAGGCTGGCTACCAAGATCAGCAAGGGCATGAGgtaatgtttt ... tgatgttcagGCATTTGCTCAGTTGTTGAAAGCTCCACGTGAGGAAACTGATTCGATAATC
EST: gi|89186541|gb|CI048213.1|CI048213
EST:     CCATTGCGCAGTGGCGAAAGGCTGGCTACCAAGATCAGCAAGGGCATGAG                         GCATTTGCTCAGTTGTTGAAAGCTCCACGTGAGGAAACTGATTCGATAATC
genomic: CCATTGCGCAGTGGCGAAAGGCTGGCTACCAAGATCAGCAAGGGCATGAGgtaatgtttt ... tgatgttcagGCATTTGCTCAGTTGTTGAAAGCTCCACGTGAGGAAACTGATTCGATAATC
EST: gi|58653330|gb|CK042010.1|CK042010
EST:     CCATTGCGCAGTGGCGAAAGGCTGGCTACCAAGATCAGCAAGGGCATGAG                         GCATTTGCTCAGTTGTTGAAAGCTCCACATGAGGAAACTGATTCGATAATC
genomic: CCATTGCGCAGTGGCGAAAGGCTGGCTACCAAGATCAGCAAGGGCATGAGgtaatgtttt ... tgatgttcagGCATTTGCTCAGTTGTTGAAAGCTCCACGTGAGGAAACTGATTCGATAATC
EST: gi|86481033|gb|CI123666.1|CI123666
EST:     CCATTGCGCAGTGGCGAAAGGCTGGCTACCAAGATCAGCAAGGGCATGAG                         GCATTTGCTCAGTTGTTGAAAGCTCCACGTGAGGAAACTGATTCGATAATC
genomic: CCATTGCGCAGTGGCGAAAGGCTGGCTACCAAGATCAGCAAGGGCATGAGgtaatgtttt ... tgatgttcagGCATTTGCTCAGTTGTTGAAAGCTCCACGTGAGGAAACTGATTCGATAATC
EST: gi|29622674|gb|CB627685.1|CB627685
EST:     CCATTGCGCAGTGGCGAAAGGCTGGCTACCAAGATCAGCAAGGGCATGAG                         GCATTTGCTCAGTTGTTGAAAGCTCCACATGAGGAAACTGATTCGATAATC
genomic: CCATTGCGCAGTGGCGAAAGGCTGGCTACCAAGATCAGCAAGGGCATGAGgtaatgtttt ... tgatgttcagGCATTTGCTCAGTTGTTGAAAGCTCCACGTGAGGAAACTGATTCGATAATC
EST: gi|88273091|gb|CI388547.1|CI388547
EST:     CGAAAGGCTGGGTACCAAGATCAGCAAGGGCATGAG                         GCATTTGCTCAGTTGTTGAAAGCTCCACGTGAGGAAACTGATTCGATAATC
genomic: CGAAAGGCTGGCTACCAAGATCAGCAAGGGCATGAGgtaatgtttt ... tgatgttcagGCATTTGCTCAGTTGTTGAAAGCTCCACGTGAGGAAACTGATTCGATAATC
EST: gi|86504504|gb|CI147137.1|CI147137
EST:     CATTGCGCAGTGGCGAAAGGCTGGCTACCCAAGATCAGCAAGGGCATGAG                         GCATTTGCTCAGTTGTTGAAAGCTCCACGTGAGGAAACTGATTCGATAATC
genomic: CATTGCGCAGTGGCGAAAGGCTGGCTA-CCAAGATCAGCAAGGGCATGAGgtaatgtttt ... tgatgttcagGCATTTGCTCAGTTGTTGAAAGCTCCACGTGAGGAAACTGATTCGATAATC
EST: gi|86519048|gb|CI159254.1|CI159254
EST:     GGCTGGCTACCAAGATCAGCAAGGGCATGAG                         GCATTTGCTCAGTTGTTGAAAGCTCCACGTGAGGAAACTGATTCGATAATC
genomic: GGCTGGCTACCAAGATCAGCAAGGGCATGAGgtaatgtttt ... tgatgttcagGCATTTGCTCAGTTGTTGAAAGCTCCACGTGAGGAAACTGATTCGATAATC
EST: gi|29678731|gb|CB675006.1|CB675006
EST:     CCATTGCGCAGTGGCGAAAGGCTGGCTACCAAGATCAGCAAGGGCATGAG                         GCATTTGCTCAGTTGTTGAAAGCTCCACGTGAGGAAACTGATTGGATAATC
genomic: CCATTGCGCAGTGGCGAAAGGCTGGCTACCAAGATCAGCAAGGGCATGAGgtaatgtttt ... tgatgttcagGCATTTGCTCAGTTGTTGAAAGCTCCACGTGAGGAAACTGATTCGATAATC

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: 64 (upstream exon), 69 (downstream exon)
Score: 18

GATCCTTTTGTTGGATTCTTATTTTACTATCGTCATATTCCATGGGATAACCATTGCGCAGTGGCGAAAGGCTGGCTACCAAGATCAGCAAGGGCATGAGgtaatgtttt ... tgatgttcagGCATTTGCTCAGTTGTTGAAAGCTCCACGTGAGGAAACTGATTCGATAATCAAGGAGCGCTTTCCTGTTCCTCGTTTGGTCGTGTGTGATCAATATGGTT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agtatacagtacatactacagttgaattcaacagttaattttgtatgatgttcagGCATTTGCTCAGTTGTTGAAAGCTCCACGTGAGGAAACTGATTCGATAATCAAGGAGCGCTTTCCTGTTCCTCGTTTGGTCGTGTGTGATCAATATGGTT
                                agttaat  putative branch site (score: 18)
                                  ttaattttgtatgat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tcctttttatattttaaacttatatttatttgggaattgtatgttagtatacagtacatactacagttgaattcaacagttaattttgtatgatgttcagGCATTTGCTCAGTTGTTGAAAGCTCCACGTGAGGAAACTGATTCGATAATCAAGGAGCGCTTTCCTGTTCCTCGTTTGGTCGTGTGTGATCAATATGGTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAG
- - - - - - - - - - - - - - - - - - ttgtatg