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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtattgatccatgtagcaaatatatttaatttatatgtcaataaattgtgccattgccaagatatctagaagtttcagtttgctcaagttgtcaaatttggggttatttgctcagGATTCTGCTGAGGTGCCTGATTGCACTCTTGCTTCAAAAGATTCAAATGAACCTGAAACTTTTGCCAAAGAG

Basic information

species Oryza sativa
transcript LOC_Os01g66520.1
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|88585671|gb|CI703327.1|CI703327
EST:     ATGGTGATGATGTGGCTGTTAAAATCGGTTCCTTAAAAATAGCAGAGCAG                         GATTCTGCTGAGGTGCCTGATTGCACTCTTGCTTCAAAAGATTCAAATGAA
genomic: ATGGTGATGATGTGGCTGTTAAAATCGGTTCCTTAAAAATAGCAGAGCAGgtattgatcc ... atttgctcagGATTCTGCTGAGGTGCCTGATTGCACTCTTGCTTCAAAAGATTCAAATGAA
EST: gi|88589158|gb|CI707017.1|CI707017
EST:     ATGGTGATGATGTGGCTGTTAAAATCGGTTCCTTAAAAATAGCAGAGCAG                         GATTCTGCTGAGGTGCCTGATTGCACTCTTGCTTCAAAAGATTCAAATGAA
genomic: ATGGTGATGATGTGGCTGTTAAAATCGGTTCCTTAAAAATAGCAGAGCAGgtattgatcc ... atttgctcagGATTCTGCTGAGGTGCCTGATTGCACTCTTGCTTCAAAAGATTCAAATGAA
EST: gi|88584733|gb|CI702306.1|CI702306
EST:     ATGGTGATGATGTGGCTGTTAAAATCGGTTCCTTAAAAATAGCAGAGCAG                         GATTCTGCTGAGGTGCCTGATTGCACTCTTGCTTCAAAAGATTCAAATGAA
genomic: ATGGTGATGATGTGGCTGTTAAAATCGGTTCCTTAAAAATAGCAGAGCAGgtattgatcc ... atttgctcagGATTCTGCTGAGGTGCCTGATTGCACTCTTGCTTCAAAAGATTCAAATGAA
EST: gi|86535377|gb|CI175583.1|CI175583
EST:     ATGGTGATGATGTGGCTGTTAAAATCGGTTCCTTAAAAATAGCAGAGCAG                         GATTCTGCTGAGGTGCCTGATTGCACTCTTGCTTCAAAAGATTCAAATGAA
genomic: ATGGTGATGATGTGGCTGTTAAAATCGGTTCCTTAAAAATAGCAGAGCAGgtattgatcc ... atttgctcagGATTCTGCTGAGGTGCCTGATTGCACTCTTGCTTCAAAAGATTCAAATGAA

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: 70 (upstream exon), 47 (downstream exon)
Score: 7

TGAAGAAGAGAGCTCAGATGATGATTCAACATCAGAACAAGATAATGAGGATGGTGATGATGTGGCTGTTAAAATCGGTTCCTTAAAAATAGCAGAGCAGgtattgatcc ... atttgctcagGATTCTGCTGAGGTGCCTGATTGCACTCTTGCTTCAAAAGATTCAAATGAACCTGAAACTTTTGCCAAAGAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gatatctagaagtttcagtttgctcaagttgtcaaatttggggttatttgctcagGATTCTGCTGAGGTGCCTGATTGCACTCTTGCTTCAAAAGATTCAAATGAACCTGAAACTTTTGCCAAAGAG
                                              tttgctc  CT-rich tract
                               tcaaattt  TA-rich tract