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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtctgtggcttcgcagctgcttgtgtgatacagttcatatctgtcaagaaattttcacttgccatcatcgcaagattttttaaaaaaagttcactcttttttgaacgaaaaaaaaaagttcactcttcataactgatgatgctatgcttatacagATTTCATTTTGGAGATGAACTCATCAAATCTGTAGATGCAAACAGCAGCAATGAATCGATTCTGAAAGCAGTTTGGCATCATCCGAGTGCCATACTCTGC

Basic information

species Oryza sativa
transcript LOC_Os01g10320.1
intron # 11
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|87040163|gb|CI193372.1|CI193372
EST:     GTGACTCCGGAGGCGGCGACGCTGCCCAGATGGATTTGCCAGAGCTACAG                         ATTTCATTTTGGAGATGAACTCATCAAATCTGTAGATGCAAACAGCAGCAA
genomic: GTGACTCCGGAGGCGGCGACGCTGCCCAGATGGATTTGCCAGAGCTACAGgtctgtggct ... gcttatacagATTTCATTTTGGAGATGAACTCATCAAATCTGTAGATGCAAACAGCAGCAA
EST: gi|87041427|gb|CI196049.1|CI196049
EST:     GTGAGTCCGGAGGCGGCGACGCTGCCCAGATGGATTTGCCAGAGCTACAG                         ATTTCATTTTGGAGATGAACTCATCAAATCTGTACATGCAAACAGCAGCAA
genomic: GTGACTCCGGAGGCGGCGACGCTGCCCAGATGGATTTGCCAGAGCTACAGgtctgtggct ... gcttatacagATTTCATTTTGGAGATGAACTCATCAAATCTGTAGATGCAAACAGCAGCAA
EST: gi|88233153|gb|CI233002.1|CI233002
EST:     TTTGCCAGAGCTACAG                         ATTTCATTTTGGAGATGAACTCATCAAATCTGTAGATGCAAACAGCAGCAA
genomic: TTTGCCAGAGCTACAGgtctgtggct ... gcttatacagATTTCATTTTGGAGATGAACTCATCAAATCTGTAGATGCAAACAGCAGCAA
EST: gi|87037181|gb|CI191803.1|CI191803
EST:     GTGACTCCGGAGGCGGCGACGCTGCCCAGATGGATTTGCCAGAGCTACAG                         ATTTCATTTTGGAGATGAACTCATCAAATCTGTAGATGCAAACAGCAGCAA
genomic: GTGACTCCGGAGGCGGCGACGCTGCCCAGATGGATTTGCCAGAGCTACAGgtctgtggct ... gcttatacagATTTCATTTTGGAGATGAACTCATCAAATCTGTAGATGCAAACAGCAGCAA
EST: gi|88233061|gb|CI232910.1|CI232910
EST:     GTGACTCCGGAGGCGGCGACGCTGCCCAGATGGATTTGCCAGAGCTACAG                         ATTTCATTTTGGAGATGAACTCATCAAATCTGTAGATGCAAACAGCAGCAA
genomic: GTGACTCCGGAGGCGGCGACGCTGCCCAGATGGATTTGCCAGAGCTACAGgtctgtggct ... gcttatacagATTTCATTTTGGAGATGAACTCATCAAATCTGTAGATGCAAACAGCAGCAA
EST: gi|88198498|gb|CI198348.1|CI198348
EST:     GTGACTCCGGAGCCGGCGACGCTGCCCAGATGGATTTGCCAGAGCTACAG                         ATTTCATTTTGGAGATGAACTCATCAAATCTGTAGATGCAAACAGCAGCAA
genomic: GTGACTCCGGAGGCGGCGACGCTGCCCAGATGGATTTGCCAGAGCTACAGgtctgtggct ... gcttatacagATTTCATTTTGGAGATGAACTCATCAAATCTGTAGATGCAAACAGCAGCAA
EST: gi|87039351|gb|CI193973.1|CI193973
EST:     GTGACTCCGGAGGCGGCGACGCTGCCCAGATGGATTTGCCAGAGCTACAG                         ATTTCATTTTGGAGATGAACTCATCAAATCTGTAGATGCAAACAGCAGCAA
genomic: GTGACTCCGGAGGCGGCGACGCTGCCCAGATGGATTTGCCAGAGCTACAGgtctgtggct ... gcttatacagATTTCATTTTGGAGATGAACTCATCAAATCTGTAGATGCAAACAGCAGCAA
EST: gi|88197992|gb|CI197842.1|CI197842
EST:     GTGACTCCGGAGGCGGCGACGCTGCCCAGATGGATTTGCCAGAGCTACAG                         ATTTCATTTTGGAGATGAACTCATCAAATCTGTACATGCAAACAGCAGCAA
genomic: GTGACTCCGGAGGCGGCGACGCTGCCCAGATGGATTTGCCAGAGCTACAGgtctgtggct ... gcttatacagATTTCATTTTGGAGATGAACTCATCAAATCTGTAGATGCAAACAGCAGCAA
EST: gi|87038791|gb|CI193413.1|CI193413
EST:     GTGACTCCGGAGGCGGCGACGCTGCCCAGATGGATTTGCCAGAGCTACAG                         ATTTCATTTTGGAGATGAACTCATCAAATCTGTAGATGCAAACAGCAGCAA
genomic: GTGACTCCGGAGGCGGCGACGCTGCCCAGATGGATTTGCCAGAGCTACAGgtctgtggct ... gcttatacagATTTCATTTTGGAGATGAACTCATCAAATCTGTAGATGCAAACAGCAGCAA
EST: gi|88229033|gb|CI228909.1|CI228909
EST:     GATGGATTTGCCAGAGCTACAG                         ATTTCATTTTGGAGATGAACTCATCAAATCTGTAGATGCAAACAGCAGCAA
genomic: GATGGATTTGCCAGAGCTACAGgtctgtggct ... gcttatacagATTTCATTTTGGAGATGAACTCATCAAATCTGTAGATGCAAACAGCAGCAA
EST: gi|88233255|gb|CI233104.1|CI233104
EST:     ACTCCGGAGGCGGCGACGCTGCCCAGATGGATTTGCCAGAGCTACAG                         ACTTCATTTTGGAGATGAACTCATCAAATCTGTAGATGCAAACAGCAGCAA
genomic: ACTCCGGAGGCGGCGACGCTGCCCAGATGGATTTGCCAGAGCTACAGgtctgtggct ... gcttatacagATTTCATTTTGGAGATGAACTCATCAAATCTGTAGATGCAAACAGCAGCAA
EST: gi|88197634|gb|CI197484.1|CI197484
EST:     GTGACTCCGGAGGCGGCGACGCTGCCCAGATGGATTTGCCAGAGCTACAG                         ATTTCATTTTGGAGATGAACTCATCAAATCTGTAGATGCAAACAGCAGCAA
genomic: GTGACTCCGGAGGCGGCGACGCTGCCCAGATGGATTTGCCAGAGCTACAGgtctgtggct ... gcttatacagATTTCATTTTGGAGATGAACTCATCAAATCTGTAGATGCAAACAGCAGCAA
EST: gi|88197643|gb|CI197493.1|CI197493
EST:     GTGACTCCGGAGGCGGCGACGCTGCCCAGATGGATTTGCCAGAGCTACAG                         ATTTCATTTTGGAGATGAACTCATCAAATCTGTACATGCAAACAGCAGCAA
genomic: GTGACTCCGGAGGCGGCGACGCTGCCCAGATGGATTTGCCAGAGCTACAGgtctgtggct ... gcttatacagATTTCATTTTGGAGATGAACTCATCAAATCTGTAGATGCAAACAGCAGCAA
EST: gi|87040405|gb|CI195027.1|CI195027
EST:     GTGACTCCGGAGGCGGCGACGCTGCCCAGATGGATTTGCCAGAGCTACAG                         ATTTCATTTTGGAGATGAACTCATCAAATCTGTAGATGCAAACAGCAGCAA
genomic: GTGACTCCGGAGGCGGCGACGCTGCCCAGATGGATTTGCCAGAGCTACAGgtctgtggct ... gcttatacagATTTCATTTTGGAGATGAACTCATCAAATCTGTAGATGCAAACAGCAGCAA
EST: gi|87038456|gb|CI193078.1|CI193078
EST:     GTGACTCCGGAGGCGGCGACGCTGCCCAGATGGATTTGCCAGAGCTACAG                         ATTTCATTTTGGAGATGAACTCATCAAATCTGTACATGCAAACAGCAGCAA
genomic: GTGACTCCGGAGGCGGCGACGCTGCCCAGATGGATTTGCCAGAGCTACAGgtctgtggct ... gcttatacagATTTCATTTTGGAGATGAACTCATCAAATCTGTAGATGCAAACAGCAGCAA

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: 68 (upstream exon), 14 (downstream exon)
Score: 8

CCCGCCTCGTCCCTCCCGGCGCCGGCGCCGCCGCCGCGCAGCTCTCACCGGTGACTCCGGAGGCGGCGACGCTGCCCAGATGGATTTGCCAGAGCTACAGgtctgtggct ... gcttatacagATTTCATTTTGGAGATGAACTCATCAAATCTGTAGATGCAAACAGCAGCAATGAATCGATTCTGAAAGCAGTTTGGCATCATCCGAGTGCCATACTCTGC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgaacgaaaaaaaaaagttcactcttcataactgatgatgctatgcttatacagATTTCATTTTGGAGATGAACTCATCAAATCTGTAGATGCAAACAGCAGCAATGAATCGATTCTGAAAGCAGTTTGGCATCATCCGAGTGCCATACTCTGC
       aaaaaaaaaagttca  TA-rich tract