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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CGGACTGAGCGGGAGGCGAGGCGATCGACGGCGAACTGAATTCCTAGTTTGTTGCAGGCTCAAGgtctgtgaatgcttcttgatttcttagatgctaggacaatttgagttgctctttttcagttcagacttcatagttttccagctttcttgtgctaacctgctttgcttccttttcag

Basic information

species Oryza sativa
transcript LOC_Os12g40490.1
intron # 2
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:     GGCGAGGCGATCGACGGCGAACTGAATTCCTAGTTTGTTGCAGGCTCAAG                         CTTTGGTTTTCTGAAGTACTGGAAACGTTCTCGATTGGCGAAAAGTTTGTG
genomic: GGCGAGGCGATCGACGGCGAACTGAATTCCTAGTTTGTTGCAGGCTCAAGgtctgtgaat ... tccttttcagCTTTGGTTTTCTGAAGTACTGGAAACGTTCTCGATTGGCGAAAAGTTTGTG
EST: gi|88322002|gb|CI673152.1|CI673152
EST:     GGCGAGGCGATCGACGGCGAACTGAATTCCTAGTTTGTTGCAGGCTCAAG                         CTTTGGTTTTCTGAAGTACTGGAAACGTTCTCGATTGGCGAAAAGTTTGTG
genomic: GGCGAGGCGATCGACGGCGAACTGAATTCCTAGTTTGTTGCAGGCTCAAGgtctgtgaat ... tccttttcagCTTTGGTTTTCTGAAGTACTGGAAACGTTCTCGATTGGCGAAAAGTTTGTG
EST: gi|88391277|gb|CI595531.1|CI595531
EST:     GGCGAGGCGATCGACGGCGAACTGAATTCCTAGTTTGTTGCAGGCTCAAG                         CTTTGGTTTTCTGAAGTACTGGAAACGTTCTCGATTGGCGAAAAGTTTGTG
genomic: GGCGAGGCGATCGACGGCGAACTGAATTCCTAGTTTGTTGCAGGCTCAAGgtctgtgaat ... tccttttcagCTTTGGTTTTCTGAAGTACTGGAAACGTTCTCGATTGGCGAAAAGTTTGTG
EST: gi|29632389|gb|CB637398.1|CB637398
EST:     GGCGAGGCGATCGACTGCGAACTGAATTCCTAGTTTGTTGCAGGCTCAAG                         CTTTGGTTTTCTGAAGTACTGGAAACGTTCTCGATTGGCGAAAAGTTTGTG
genomic: GGCGAGGCGATCGACGGCGAACTGAATTCCTAGTTTGTTGCAGGCTCAAGgtctgtgaat ... tccttttcagCTTTGGTTTTCTGAAGTACTGGAAACGTTCTCGATTGGCGAAAAGTTTGTG
EST: gi|88733513|gb|CI756690.1|CI756690
EST:     GGCGAGGCGATCGACGGCGAACTGAATTCCTAGTTTGTTGCAGGCTCAAG                         CTTTGGTTTTCTGAAGTACTGGAAACGTTCTCGATTGGCGAAAAGTTTGTG
genomic: GGCGAGGCGATCGACGGCGAACTGAATTCCTAGTTTGTTGCAGGCTCAAGgtctgtgaat ... tccttttcagCTTTGGTTTTCTGAAGTACTGGAAACGTTCTCGATTGGCGAAAAGTTTGTG
EST: gi|88593039|gb|CI711188.1|CI711188
EST:     GGCGAGGCGATCGACGGCGAACTGAATTCCTAGTTTGTTGCAGGCTCAAG                         CTTTGGTTTTCTGAAGTACTGGAAACGTTCTCGATTGGCGAAAAGTTTGTG
genomic: GGCGAGGCGATCGACGGCGAACTGAATTCCTAGTTTGTTGCAGGCTCAAGgtctgtgaat ... tccttttcagCTTTGGTTTTCTGAAGTACTGGAAACGTTCTCGATTGGCGAAAAGTTTGTG
EST: gi|88737536|gb|CI759417.1|CI759417
EST:     GGCGAGGCGATCGACGGCGAACTGAATTCCTAGTTTGTTGCAGGCTCAAG                         CTTTGGTTTTCTGAAGTACTGGAAACGTTCTCGATTGGCGAAAAGTTTGTG
genomic: GGCGAGGCGATCGACGGCGAACTGAATTCCTAGTTTGTTGCAGGCTCAAGgtctgtgaat ... tccttttcagCTTTGGTTTTCTGAAGTACTGGAAACGTTCTCGATTGGCGAAAAGTTTGTG
EST: gi|88367909|gb|CI572630.1|CI572630
EST:     GGCGAGGCGATCGACGGCGAACTGAATTCCTAGTTTGTTGCAGGCTCAAG                         CTTTGGTTTTCTGAAGTACTGGAAACGTTCTCGATTGGCGAAAAGTTTGTG
genomic: GGCGAGGCGATCGACGGCGAACTGAATTCCTAGTTTGTTGCAGGCTCAAGgtctgtgaat ... tccttttcagCTTTGGTTTTCTGAAGTACTGGAAACGTTCTCGATTGGCGAAAAGTTTGTG
EST: gi|88581980|gb|CI699200.1|CI699200
EST:     GGCGAGGCGATCGACGGCGAACTGAATTCCTAGTTTGTTGCAGGCTCAAG                         CTTTGGTTTTCTGAAGTACTGGAAACGTTCTCGATTGGCGAAAAGTTTGTG
genomic: GGCGAGGCGATCGACGGCGAACTGAATTCCTAGTTTGTTGCAGGCTCAAGgtctgtgaat ... tccttttcagCTTTGGTTTTCTGAAGTACTGGAAACGTTCTCGATTGGCGAAAAGTTTGTG
EST: gi|33678894|gb|CF307133.1|CF307133
EST:     GGCGAGGCGATCGACGGCGAACTGAATTCCTAGTTTGTTGCAGGCTCAAG                         CTTTGGTTTTCTGAAGTACTGGAAACGTTCTCGATTGGCGAAAAGTTTGTG
genomic: GGCGAGGCGATCGACGGCGAACTGAATTCCTAGTTTGTTGCAGGCTCAAGgtctgtgaat ... tccttttcagCTTTGGTTTTCTGAAGTACTGGAAACGTTCTCGATTGGCGAAAAGTTTGTG
EST: gi|88826328|gb|CI776893.1|CI776893
EST:     GGCGAGGCGATCGACGGCGAACTGAATTCCTAGTTTGTTGCAGGCTCAAG                         CTTTGGTTTTCTGAAGTACTGGAAACGTTCTCGATTGGCGAAAAGTTTGTG
genomic: GGCGAGGCGATCGACGGCGAACTGAATTCCTAGTTTGTTGCAGGCTCAAGgtctgtgaat ... tccttttcagCTTTGGTTTTCTGAAGTACTGGAAACGTTCTCGATTGGCGAAAAGTTTGTG
EST: gi|88317739|gb|CI672328.1|CI672328
EST:     GGCGAGGCGATCGACGGCGAACTGAATTCCTAGTTTGTTGCAGGCTCAAG                         CTTTGGTTTTCTGAAGTACTGGAAACGTTCTCGATTGGCGAAAAGTTTGTG
genomic: GGCGAGGCGATCGACGGCGAACTGAATTCCTAGTTTGTTGCAGGCTCAAGgtctgtgaat ... tccttttcagCTTTGGTTTTCTGAAGTACTGGAAACGTTCTCGATTGGCGAAAAGTTTGTG
EST: gi|29635157|gb|CB640166.1|CB640166
EST:     GGCGAGGCGATCGACGGCGAACTGAATTCCTAGTTTGTTGCAGGCTCAAG                         CTTTGGTTTTCTGAAGTACTGGAAACGTTCTCGATTGGCGAAAAGTTTGTG
genomic: GGCGAGGCGATCGACGGCGAACTGAATTCCTAGTTTGTTGCAGGCTCAAGgtctgtgaat ... tccttttcagCTTTGGTTTTCTGAAGTACTGGAAACGTTCTCGATTGGCGAAAAGTTTGTG
EST: gi|29630464|gb|CB635473.1|CB635473
EST:     GGCGAGGCGATCGACGGCGAACTGAATTCCTAGTTTGTTGCAGGCTCAAG                         CTTTGGTTTTCTGAAGTACTGGAAACGTTCTCGATTGGCGAAAAGTTTATG
genomic: GGCGAGGCGATCGACGGCGAACTGAATTCCTAGTTTGTTGCAGGCTCAAGgtctgtgaat ... tccttttcagCTTTGGTTTTCTGAAGTACTGGAAACGTTCTCGATTGGCGAAAAGTTTGTG
EST: gi|29627991|gb|CB633002.1|CB633002
EST:     GGCGAGGCGATCGACGGCGAACTGAATTCCTAGTTTGTTGCAGGCTCAAG                         CTTTGGTTTTCTGAAGTACTGGAAACGTTCTCGATTGGCGAAAAGTTTATG
genomic: GGCGAGGCGATCGACGGCGAACTGAATTCCTAGTTTGTTGCAGGCTCAAGgtctgtgaat ... tccttttcagCTTTGGTTTTCTGAAGTACTGGAAACGTTCTCGATTGGCGAAAAGTTTGTG
EST: gi|88412122|gb|CI566851.1|CI566851
EST:     GGCGAGGCGATCGACGGCGAACTGAATTCCTAGTTTGTTGCAGGCTCAAG                         CTTTGGTTTTCTGAAGTACTGGAAACGTTCTCGATTGGCGAAAAGTTTGTG
genomic: GGCGAGGCGATCGACGGCGAACTGAATTCCTAGTTTGTTGCAGGCTCAAGgtctgtgaat ... tccttttcagCTTTGGTTTTCTGAAGTACTGGAAACGTTCTCGATTGGCGAAAAGTTTGTG

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: 55 (upstream exon), 41 (downstream exon)
Score: 12

CGGACTGAGCGGGAGGCGAGGCGATCGACGGCGAACTGAATTCCTAGTTTGTTGCAGGCTCAAGgtctgtgaat ... tccttttcagCTTTGGTTTTCTGAAGTACTGGAAACGTTCTCGATTGGCGAAAAGTTTGTGAGATTTTTGTCTTCTG




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