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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tctccactgggtgtcatattctcggtacttaagcaactgagacggtgccattgcaaagcgtacctataaataagtccacactcttgcattgtctttgcagCTCCAAGTCTTGAGGGTTCTTGCATTGGGAGAGGGGGAGATGAGCGGCCCAATGCAACGCTCGTCGCAGCCACAGTTTATCTCTAGCGTCGAGCGGAACA

Basic information

species Oryza sativa
transcript LOC_Os06g46310.1
intron # 1
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|88326220|gb|CI660033.1|CI660033
EST:     GTTCGCTTTGCAGAACTCCCTAACAAGAACCAGATCCAACCCGACCACCG                         CTCCAAGTCTTGAGGGTTCTTGCATTGGGAGAGGGGGAGATGAGCGGCCCA
genomic: GTTCGCTTTGCAGAACTCCCTAACAAGAACCAGATCCAACCCGACCACCGgtaacttctc ... gtctttgcagCTCCAAGTCTTGAGGGTTCTTGCATTGGGAGAGGGGGAGATGAGCGGCCCA
EST: gi|44677020|gb|CR290454.1|CR290454
EST:     GTTCGCTTTGCAGAACTCCCTAACAAGAACCAGATCCAANCCGANCACCG                         CTCCAAGTCTTGAGGGTTCTTGCATTGGGAGAGGGGGAGATGAGCGGCCCA
genomic: GTTCGCTTTGCAGAACTCCCTAACAAGAACCAGATCCAACCCGACCACCGgtaacttctc ... gtctttgcagCTCCAAGTCTTGAGGGTTCTTGCATTGGGAGAGGGGGAGATGAGCGGCCCA

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), 75 (downstream exon)
Score: 36

GACTCCCCACCCATCCCAGGTACGGCGCCTCGCCGCGTTCTCTTCTCCAGGTTCGCTTTGCAGAACTCCCTAACAAGAACCAGATCCAACCCGACCACCGgtaacttctc ... gtctttgcagCTCCAAGTCTTGAGGGTTCTTGCATTGGGAGAGGGGGAGATGAGCGGCCCAATGCAACGCTCGTCGCAGCCACAGTTTATCTCTAGCGTCGAGCGGAACA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgccattgcaaagcgtacctataaataagtccacactcttgcattgtctttgcagCTCCAAGTCTTGAGGGTTCTTGCATTGGGAGAGGGGGAGATGAGCGGCCCAATGCAACGCTCGTCGCAGCCACAGTTTATCTCTAGCGTCGAGCGGAACA
                                           ttgtcttt  CT-rich tract
                   tataaataagt  TA-rich tract