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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaggcaggaaattttctttttctgagccatatcttgctgttgcttcttgtttgaactatagatgcagaaaataacctgtaatacatgacagaactaacaaaagcatttttcagctctaacttttaattgttccttcttgctagGAATCTGCAAACTCTAAAATCGACGACAGCGACGACGACGCTAGT

Basic information

species Oryza sativa
transcript LOC_Os03g61670.1
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|86498981|gb|CI141614.1|CI141614
EST:     AAGCTGAGAAGAAGAGGCTTGAGGAG                         GAATCTGCAAACTCTAAAATCGACGACAGCGACGACGACGCTAGT
genomic: AAGCTGAGAAGAAGAGGCTTGAGGAGgtaggcagga ... ttcttgctagGAATCTGCAAACTCTAAAATCGACGACAGCGACGACGACGCTAGT
EST: gi|86433374|gb|CI093717.1|CI093717
EST:     ATGAAGCTGAGAAGAAGAGGCTTGAGGAG                         GAATCTGCAAACTCTAAAATCGACGACAGCGACGACGACGCTAGT
genomic: ATGAAGCTGAGAAGAAGAGGCTTGAGGAGgtaggcagga ... ttcttgctagGAATCTGCAAACTCTAAAATCGACGACAGCGACGACGACGCTAGT
EST: gi|58666692|gb|CK055378.1|CK055378
EST:     GCTGAGAAAGCCGCCTTTGATGAAGCTGAGAAGAAGAGGCTTGAGGAG                         GAATCTGCAAACTCTAAAATCGACGACAGCGACGACGACGCTAGT
genomic: GCTGAGAAAGCCGCCTTTGATGAAGCTGAGAAGAAGAGGCTTGAGGAGgtaggcagga ... ttcttgctagGAATCTGCAAACTCTAAAATCGACGACAGCGACGACGACGCTAGT
EST: gi|86484126|gb|CI126759.1|CI126759
EST:     GCTGAGAAAGCCGCCTTTGATGAAGCTGAGAAGAAGAGGCTTGAGGAG                         GAATCTGCAAACTCTAAAATCGACGACAGCGACGACGACGCTAGT
genomic: GCTGAGAAAGCCGCCTTTGATGAAGCTGAGAAGAAGAGGCTTGAGGAGgtaggcagga ... ttcttgctagGAATCTGCAAACTCTAAAATCGACGACAGCGACGACGACGCTAGT
EST: gi|88996487|gb|CI259991.1|CI259991
EST:     GCTGAGAAAGCCGCCTTTGATGAAGCTGAGAAGAAGAGGCTTGAGGAG                         GAATCTGCAAACTCTAAAATCGACGACAGCGACGACGACGCTAGT
genomic: GCTGAGAAAGCCGCCTTTGATGAAGCTGAGAAGAAGAGGCTTGAGGAGgtaggcagga ... ttcttgctagGAATCTGCAAACTCTAAAATCGACGACAGCGACGACGACGCTAGT
EST: gi|88968007|gb|CI098249.1|CI098249
EST:     GCTGAGAAAGCCGCCTCTGATGAAGCTGAGAAGAAGAGGCTTGAGGAG                         GAATCTGCAAACTCTAAAATCGACGACAGCGACGACGACGCTAGT
genomic: GCTGAGAAAGCCGCCTTTGATGAAGCTGAGAAGAAGAGGCTTGAGGAGgtaggcagga ... ttcttgctagGAATCTGCAAACTCTAAAATCGACGACAGCGACGACGACGCTAGT
EST: gi|86484726|gb|CI127359.1|CI127359
EST:     GCTGAGAAAGCCGCCTTTGATGAAGCTGAGAAGAAGAGGCTTGAGGAG                         GAATCTGCAAACTCTAAAATCGACGACAGCGACGACGACGCTAGT
genomic: GCTGAGAAAGCCGCCTTTGATGAAGCTGAGAAGAAGAGGCTTGAGGAGgtaggcagga ... ttcttgctagGAATCTGCAAACTCTAAAATCGACGACAGCGACGACGACGCTAGT
EST: gi|58664711|gb|CK053397.1|CK053397
EST:     GCTGAGAAAGCCGCCTTTGATGAAGCTGAGAAGAAGAGGCTTGAGGAG                         GAATCTGCAAACTCTAAAATCGACGACAGCGACGACGACGCTAGT
genomic: GCTGAGAAAGCCGCCTTTGATGAAGCTGAGAAGAAGAGGCTTGAGGAGgtaggcagga ... ttcttgctagGAATCTGCAAACTCTAAAATCGACGACAGCGACGACGACGCTAGT

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: 74 (upstream exon), 69 (downstream exon)
Score: 12

GCTGAGAAAGCCGCCTTTGATGAAGCTGAGAAGAAGAGGCTTGAGGAGgtaggcagga ... ttcttgctagGAATCTGCAAACTCTAAAATCGACGACAGCGACGACGACGCTAGT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cagaactaacaaaagcatttttcagctctaacttttaattgttccttcttgctagGAATCTGCAAACTCTAAAATCGACGACAGCGACGACGACGCTAGT
                                      ttgttccttcttgct  CT-rich tract
                            taacttttaattgtt  TA-rich tract