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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGTCTTTGCAGCATTCCAGTTTATCCTAGTTCAATTGTTAATCTAATGAGTTACACGGAGGAAAAAAATTTCATCACGGAAGTTCCAGAGCAAGTTTAATgtgagttgatggttttcccttgttttattggtccctctgataaaaatccagagatgattttggtgctgaagtttccatttcttgatgcag

Basic information

species Oryza sativa
transcript LOC_Os02g54510.2
intron # 9
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|88274260|gb|CI394666.1|CI394666
EST:     TTACACGGAGGNNNNNNNTTTCATCACGGAAGTTCCAGAGCAAGTTTAAT                         GGATTTTCGATCCTGGAATCATCAGCTGTCGTTTGCCTTCCTCGGGGAACA
genomic: TTACACGGAGGAAAAAAATTTCATCACGGAAGTTCCAGAGCAAGTTTAATgtgagttgat ... cttgatgcagGGATTTTCGATCCTGGAATCATCAGCTGTCGTTTGCCTTCCTCGGGGAACA
EST: gi|86872733|gb|CI341943.1|CI341943
EST:     TTACACGGAGGNNNNNNNTTTCATCACGGAAGTTCCAGAGCAAGTTTAAT                         GGATTTTCGATCCTGGAATCATCAGCTGTCGTTTGCCTTCCTCGGGGAACA
genomic: TTACACGGAGGAAAAAAATTTCATCACGGAAGTTCCAGAGCAAGTTTAATgtgagttgat ... cttgatgcagGGATTTTCGATCCTGGAATCATCAGCTGTCGTTTGCCTTCCTCGGGGAACA
EST: gi|29621712|gb|CB626723.1|CB626723
EST:     TTACACGGAGGNNNNNNNTTTCATCACGGAAGTTCCAGAGCAAGTTTGAT                         GGATTTTCGATCCTGGAATCATCAGCTGTCGTTTGCCTTCCTCGGGGAACA
genomic: TTACACGGAGGAAAAAAATTTCATCACGGAAGTTCCAGAGCAAGTTTAATgtgagttgat ... cttgatgcagGGATTTTCGATCCTGGAATCATCAGCTGTCGTTTGCCTTCCTCGGGGAACA
EST: gi|88512805|gb|CI440311.1|CI440311
EST:     TTACACGGAGGNNNNNNNTTTCATCACGGAAGTTCCAGAGCAAGTTTAAT                         GGATTTTCGATCCTGGAATCATCAGCTGTCGTTTGCCTTCCTCGGGGAACA
genomic: TTACACGGAGGAAAAAAATTTCATCACGGAAGTTCCAGAGCAAGTTTAATgtgagttgat ... cttgatgcagGGATTTTCGATCCTGGAATCATCAGCTGTCGTTTGCCTTCCTCGGGGAACA
EST: gi|88374409|gb|CI515893.1|CI515893
EST:     TTACACGGAGGNNNNNNNTTTCATCACGGAAGTTCCAGAGCAAGTTTAAT                         GGATTTTCGATCCTGGAATCATCAGCTGTCGTTTGCCTTCCTCGGGGAACA
genomic: TTACACGGAGGAAAAAAATTTCATCACGGAAGTTCCAGAGCAAGTTTAATgtgagttgat ... cttgatgcagGGATTTTCGATCCTGGAATCATCAGCTGTCGTTTGCCTTCCTCGGGGAACA
EST: gi|86896552|gb|CI328904.1|CI328904
EST:     TTACACGGAGGNNNNNNNTTTCATCACGGAAGTTCCAGAGCAAGTTTAAT                         GGATTTTCGATCCTGGAATCATCAGCTGTCGTTTGCCTTCCTCGGGGAACA
genomic: TTACACGGAGGAAAAAAATTTCATCACGGAAGTTCCAGAGCAAGTTTAATgtgagttgat ... cttgatgcagGGATTTTCGATCCTGGAATCATCAGCTGTCGTTTGCCTTCCTCGGGGAACA
EST: gi|88492076|gb|CI429348.1|CI429348
EST:     TTACACGGAGGNNNNNNNTTTCATCACGGAAGTTCCAGAGCAAGTTTAAT                         GGATTTTCGATCCTGGAATCATCAGCTGTCGTTTGCCTTCCTCGGGGAACA
genomic: TTACACGGAGGAAAAAAATTTCATCACGGAAGTTCCAGAGCAAGTTTAATgtgagttgat ... cttgatgcagGGATTTTCGATCCTGGAATCATCAGCTGTCGTTTGCCTTCCTCGGGGAACA
EST: gi|29677569|gb|CB673844.1|CB673844
EST:     TTACACGGAGGNNNNNNNTTTCATCACGGAAGTTCCAGAGCAAGTTTAAT                         GGATTTTCGATCCTGGAATCATCAGCTGTCGTTTGCCTTCCTCGGGGAACA
genomic: TTACACGGAGGAAAAAAATTTCATCACGGAAGTTCCAGAGCAAGTTTAATgtgagttgat ... cttgatgcagGGATTTTCGATCCTGGAATCATCAGCTGTCGTTTGCCTTCCTCGGGGAACA
EST: gi|88520199|gb|CI447853.1|CI447853
EST:     TTACACGGAGGNNNNNNNTTTCATCACGGAAGTTCCAGAGCAAGTTTAAT                         GGATTTTCGATCCTGGAATCATCAGCTGTCGTTTGCCTTCCTCGGGGAACA
genomic: TTACACGGAGGAAAAAAATTTCATCACGGAAGTTCCAGAGCAAGTTTAATgtgagttgat ... cttgatgcagGGATTTTCGATCCTGGAATCATCAGCTGTCGTTTGCCTTCCTCGGGGAACA
EST: gi|29623880|gb|CB628891.1|CB628891
EST:     TTACACGGAGGNNNNNNNTTTCATCACGGAAGTTCCAGAGCAAGTTTGAT                         GGATTTTCGATCCTGGAATCATCAGCTGTCGTTTGCCTTCCTCGGGGAACA
genomic: TTACACGGAGGAAAAAAATTTCATCACGGAAGTTCCAGAGCAAGTTTAATgtgagttgat ... cttgatgcagGGATTTTCGATCCTGGAATCATCAGCTGTCGTTTGCCTTCCTCGGGGAACA
EST: gi|86436755|gb|CI118477.1|CI118477
EST:     TTACACGGAGGNNNNNNNTTTCATCACGGAAGTTCCAGAGCAAGTTTAAT                         GGATTTTCGATCCTGGAATCATCAGCTGTCGTTTGCCTTCCTCGGGGAACA
genomic: TTACACGGAGGAAAAAAATTTCATCACGGAAGTTCCAGAGCAAGTTTAATgtgagttgat ... cttgatgcagGGATTTTCGATCCTGGAATCATCAGCTGTCGTTTGCCTTCCTCGGGGAACA
EST: gi|86852008|gb|CI317768.1|CI317768
EST:     TTTCATCACGGAAGTTCCAGACCAAGTTTAAT                         GGATTTTCGATCCTGGAATCATCAGCTGTCGTTTGCCTTCCTCGGGGAACA
genomic: TTTCATCACGGAAGTTCCAGAGCAAGTTTAATgtgagttgat ... cttgatgcagGGATTTTCGATCCTGGAATCATCAGCTGTCGTTTGCCTTCCTCGGGGAACA
EST: gi|88435866|gb|CI514005.1|CI514005
EST:     TTACACGGAGGNNNNNNNTTTCATCACGGAAGTTCCAGAGCAAGTTTAAT                         GGATTTTCGATCCTGGAATCATCAGCTGTCGTTTGCCTTCCTCGGGGAACA
genomic: TTACACGGAGGAAAAAAATTTCATCACGGAAGTTCCAGAGCAAGTTTAATgtgagttgat ... cttgatgcagGGATTTTCGATCCTGGAATCATCAGCTGTCGTTTGCCTTCCTCGGGGAACA
EST: gi|88252274|gb|CI350702.1|CI350702
EST:     TTACACGGAGGNNNNNNNTTTCATCACGGAAGTTCCAGAGCAAGTTTAAT                         GGATTTTCGATCCTGGAATCATCAGCTGTCGTTTGCCTTCCTCGGGGAACA
genomic: TTACACGGAGGAAAAAAATTTCATCACGGAAGTTCCAGAGCAAGTTTAATgtgagttgat ... cttgatgcagGGATTTTCGATCCTGGAATCATCAGCTGTCGTTTGCCTTCCTCGGGGAACA
EST: gi|88505935|gb|CI433441.1|CI433441
EST:     TTACACGGAGGNNNNNNNTTTCATCACGGAAGTTCCAGAGCAAGTTTAAT                         GGATTTTCGATCCTGGAATCATCAGCTGTCGTTTGCCTTCCTCGGGGAACA
genomic: TTACACGGAGGAAAAAAATTTCATCACGGAAGTTCCAGAGCAAGTTTAATgtgagttgat ... cttgatgcagGGATTTTCGATCCTGGAATCATCAGCTGTCGTTTGCCTTCCTCGGGGAACA
EST: gi|86841644|gb|CI337351.1|CI337351
EST:     TTACACGGAGGNNNNNNNTTTCATCACGGAAGTTCCAGAGCAAGTTTAAT                         GGATTTTCGATCCTGGAATCATCAGCTGTCGTTTGCCTTCCTCGGGGAACA
genomic: TTACACGGAGGAAAAAAATTTCATCACGGAAGTTCCAGAGCAAGTTTAATgtgagttgat ... cttgatgcagGGATTTTCGATCCTGGAATCATCAGCTGTCGTTTGCCTTCCTCGGGGAACA
EST: gi|86878737|gb|CI340606.1|CI340606
EST:     TTACACGGAGGNNNNNNNTTTCATCACGGAAGTTCCAGAGCAAGTTTAAT                         GGATTTTCGATCCTGGAATCATCAGCTGTCGTTTGCCTTCCTCGGGGAACA
genomic: TTACACGGAGGAAAAAAATTTCATCACGGAAGTTCCAGAGCAAGTTTAATgtgagttgat ... cttgatgcagGGATTTTCGATCCTGGAATCATCAGCTGTCGTTTGCCTTCCTCGGGGAACA
EST: gi|86865351|gb|CI330872.1|CI330872
EST:     TTACACGGAGGNNNNNNNTTTCATCACGGAAGTTCCAGAGCAAGTTTAAT                         GGATTTTCGATCCTGGAATCATCAGCTGTCGTTTGCCTTCCTCGGGGAACA
genomic: TTACACGGAGGAAAAAAATTTCATCACGGAAGTTCCAGAGCAAGTTTAATgtgagttgat ... cttgatgcagGGATTTTCGATCCTGGAATCATCAGCTGTCGTTTGCCTTCCTCGGGGAACA
EST: gi|88488042|gb|CI425313.1|CI425313
EST:     TTACACGGAGGNNNNNNNTTTCATCACGGAAGTTCCAGAGCAAGTTTAAT                         GGATTTTCGATCCTGGAATCATCAGCTGTCGTTTGCCTTCCTCGGGGAACA
genomic: TTACACGGAGGAAAAAAATTTCATCACGGAAGTTCCAGAGCAAGTTTAATgtgagttgat ... cttgatgcagGGATTTTCGATCCTGGAATCATCAGCTGTCGTTTGCCTTCCTCGGGGAACA
EST: gi|396941216|gb|HO188425.1|HO188425
EST:     TTACACGGAGGNNNNNNNTTTCATCACGGAAGTTCCAGAGCAAGTTTGAT                         GGATTTTCGATCCTGGAATCATCAGCTGTCGTTTGCCTTCCTCGGGGAACA
genomic: TTACACGGAGGAAAAAAATTTCATCACGGAAGTTCCAGAGCAAGTTTAATgtgagttgat ... cttgatgcagGGATTTTCGATCCTGGAATCATCAGCTGTCGTTTGCCTTCCTCGGGGAACA
EST: gi|29624045|gb|CB629056.1|CB629056
EST:     TTACACGGAGGNNNNNNNTTTCATCACGGAAGTTCCAGAGCAAGTTTGAT                         GGATTTTCGATCCTGGAATCATCAGCTGTCGTTTGCCTTCCTCGGGGAACA
genomic: TTACACGGAGGAAAAAAATTTCATCACGGAAGTTCCAGAGCAAGTTTAATgtgagttgat ... cttgatgcagGGATTTTCGATCCTGGAATCATCAGCTGTCGTTTGCCTTCCTCGGGGAACA
EST: gi|88455418|gb|CI519439.1|CI519439
EST:     TTACACGGAGGNNNNNNNTTTCATCACGGAAGTTCCAGAGCAAGTTTAAT                         GGATTTTCGATCCTGGAATCATCAGCTGTCGTTTGCCTTCCTCGGGGAACA
genomic: TTACACGGAGGAAAAAAATTTCATCACGGAAGTTCCAGAGCAAGTTTAATgtgagttgat ... cttgatgcagGGATTTTCGATCCTGGAATCATCAGCTGTCGTTTGCCTTCCTCGGGGAACA
EST: gi|88505583|gb|CI433089.1|CI433089
EST:     TTACACGGAGGNNNNNNNTTTCATCACGGAAGTTCCAGAGCAAGTTTAAT                         GGATTTTCGATCCTGGAATCATCAGCTGTCGTTTGCCTTCCTCGGGGAACA
genomic: TTACACGGAGGAAAAAAATTTCATCACGGAAGTTCCAGAGCAAGTTTAATgtgagttgat ... cttgatgcagGGATTTTCGATCCTGGAATCATCAGCTGTCGTTTGCCTTCCTCGGGGAACA
EST: gi|88509459|gb|CI436965.1|CI436965
EST:     TTACACGGAGGNNNNNNNTTTCATCACGGAAGTTCCAGAGCAAGTTTAAT                         GGATTTTCGATCCTGGAATCATCAGCTGTCGTTTGCCTTCCTCGGGGAACA
genomic: TTACACGGAGGAAAAAAATTTCATCACGGAAGTTCCAGAGCAAGTTTAATgtgagttgat ... cttgatgcagGGATTTTCGATCCTGGAATCATCAGCTGTCGTTTGCCTTCCTCGGGGAACA
EST: gi|88513637|gb|CI441143.1|CI441143
EST:     TTACACGGAGGNNNNNNNTTTCATCACGGAAGTTCCAGAGCAAGTTTAAT                         GGATTTTCGATCCTGGAATCATCAGCTGTCGTTTGCCTTCCTCGGGGAACA
genomic: TTACACGGAGGAAAAAAATTTCATCACGGAAGTTCCAGAGCAAGTTTAATgtgagttgat ... cttgatgcagGGATTTTCGATCCTGGAATCATCAGCTGTCGTTTGCCTTCCTCGGGGAACA
EST: gi|88250609|gb|CI348839.1|CI348839
EST:     TTACACGGAGGNNNNNNNTTTCATCACGGAAGTTCCAGAGCAAGTTTAAT                         GGATTTTCGATCCTGGAATCATCAGCTGTCGTTTGCCTTCCTCGGGGAACA
genomic: TTACACGGAGGAAAAAAATTTCATCACGGAAGTTCCAGAGCAAGTTTAATgtgagttgat ... cttgatgcagGGATTTTCGATCCTGGAATCATCAGCTGTCGTTTGCCTTCCTCGGGGAACA

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: 65 (upstream exon), 69 (downstream exon)
Score: 24

TGTCTTTGCAGCATTCCAGTTTATCCTAGTTCAATTGTTAATCTAATGAGTTACACGGAGGAAAAAAATTTCATCACGGAAGTTCCAGAGCAAGTTTAATgtgagttgat ... cttgatgcagGGATTTTCGATCCTGGAATCATCAGCTGTCGTTTGCCTTCCTCGGGGAACAGTATGCTATATACCTTATCCTCTGGACGGGAACTATAGAAATAGAAATG




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Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGTCTTTGCAGCATTCCAGTTTATCCTAGTTCAATTGTTAATCTAATGAGTTACACGGAGGAAAAAAATTTCATCACGGAAGTTCCAGAGCAAGTTTAATgtgagttgatggttttcccttgttttattggtccctctgataaaaatccagagatgattttggtgctgaagtttccatttcttgatgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG