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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagctgatttaacgatctttcaatataatccaagatcatattagttcattcattcatattatcttctagttactaaagatttgcctatgttaatttacagGCTTGGAGCTTGTATGAAAAGGAGCAAGCACTCGGGATTGTTGACCCAAGACTTGAGGAATTCAGCAGGGATGAAGTGTATAGAGTCATCCATGTCGCAC

Basic information

species Oryza sativa
transcript LOC_Os08g10310.2
intron # 23
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|29626561|gb|CB631572.1|CB631572
EST:     CGAACACCGACAATTCTCTTGAGGAAAGTAAGATCTATCTCTTTGAGTGG                         GCTTGGAGCTTGTATGAAAAGGAGCAAGCACTCGGGATTGTTGACCCAAGA
genomic: CGAACACCGACAATTCTCTTGAGGAAAGTAAGATCTATCTCTTTGAGTGGgtaagctgat ... taatttacagGCTTGGAGCTTGTATGAAAAGGAGCAAGCACTCGGGATTGTTGACCCAAGA
EST: gi|29677636|gb|CB673911.1|CB673911
EST:     CGAACACCGACAATTCTCTTGAGGAAAGTAAGATCTATCTCTTTGAGTGG                         GCTTGGAGCTTGTATGAAAAGGAGCAAGCACTCGGGATTGTTGACCCAAGA
genomic: CGAACACCGACAATTCTCTTGAGGAAAGTAAGATCTATCTCTTTGAGTGGgtaagctgat ... taatttacagGCTTGGAGCTTGTATGAAAAGGAGCAAGCACTCGGGATTGTTGACCCAAGA
EST: gi|27548698|gb|CA766608.2|CA766608
EST:     CGAACACCGACAATTCTCTTGAGGAAAGTAAGATCTATTTCTTTGAGTGG                         GCTTGGAGCTTGTATGAAAAGGAGCAAGCACTCGGGATTGTTGACCCAAGA
genomic: CGAACACCGACAATTCTCTTGAGGAAAGTAAGATCTATCTCTTTGAGTGGgtaagctgat ... taatttacagGCTTGGAGCTTGTATGAAAAGGAGCAAGCACTCGGGATTGTTGACCCAAGA
EST: gi|29644824|gb|CB649831.1|CB649831
EST:     CGAACACCGACAATTCTCTTGAGGAAAGTAAGATCTATCTCTTTGAGTGG                         GCTTGGAGCTTGTATGAAAAGGAGCAAGCACTCGGGATTGTTGACCCAAGA
genomic: CGAACACCGACAATTCTCTTGAGGAAAGTAAGATCTATCTCTTTGAGTGGgtaagctgat ... taatttacagGCTTGGAGCTTGTATGAAAAGGAGCAAGCACTCGGGATTGTTGACCCAAGA
EST: gi|29664653|gb|CB660928.1|CB660928
EST:     CGAACACCGACAATTCTCTTGAGGAAAGTAAGATCTATCTCTTTGAGTGG                         GCTTGGAGCTTGTATGAAAAGGAGCAAGCACTCGGGATTGTTGACCCAAGA
genomic: CGAACACCGACAATTCTCTTGAGGAAAGTAAGATCTATCTCTTTGAGTGGgtaagctgat ... taatttacagGCTTGGAGCTTGTATGAAAAGGAGCAAGCACTCGGGATTGTTGACCCAAGA
EST: gi|29664654|gb|CB660929.1|CB660929
EST:     CGAACACCGACAATTCTCTTGAGGAAAGTAAGATCTATCTCTTTGAGTGG                         GCTTGGAGCTTGTATGAAAAGGAGCAAGCACTCGGGATTGTTGACCCAAGA
genomic: CGAACACCGACAATTCTCTTGAGGAAAGTAAGATCTATCTCTTTGAGTGGgtaagctgat ... taatttacagGCTTGGAGCTTGTATGAAAAGGAGCAAGCACTCGGGATTGTTGACCCAAGA
EST: gi|29677594|gb|CB673869.1|CB673869
EST:     CGAACACCGACAATTCTCTTGAGGAAAGTAAGATCTATCTCTTTGAGTGG                         GCTTGGAGCTTGTATGAAAAGGAGCAAGCACTCGGGATTGTTGACCCAAGA
genomic: CGAACACCGACAATTCTCTTGAGGAAAGTAAGATCTATCTCTTTGAGTGGgtaagctgat ... taatttacagGCTTGGAGCTTGTATGAAAAGGAGCAAGCACTCGGGATTGTTGACCCAAGA

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: 50 (upstream exon), 40 (downstream exon)
Score: 5

TGATGTTTTCGCATTCGGGGTGGTAGCACTAGAGATTGTTGCTGGTCGGTCGAACACCGACAATTCTCTTGAGGAAAGTAAGATCTATCTCTTTGAGTGGgtaagctgat ... taatttacagGCTTGGAGCTTGTATGAAAAGGAGCAAGCACTCGGGATTGTTGACCCAAGACTTGAGGAATTCAGCAGGGATGAAGTGTATAGAGTCATCCATGTCGCAC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcattcattcatattatcttctagttactaaagatttgcctatgttaatttacagGCTTGGAGCTTGTATGAAAAGGAGCAAGCACTCGGGATTGTTGACCCAAGACTTGAGGAATTCAGCAGGGATGAAGTGTATAGAGTCATCCATGTCGCAC
      attcatattatctt  TA-rich tract