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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGGTTTTTCCTATCTTGTTGTTCTGAGGGAATTCAAGAAATGCTCCAAATGGTCTGAATTCGTAGGTTTATTTGGGCTGGAATCTCTCAGAGGGTTTAAGgtaccgttcctttcgtcacttcccccaaagttttagcctgcaaagtttgttcttcttcttcttcttcttcttcttcttcttcttcttcttttttccctct...

Basic information

species Oryza sativa
transcript LOC_Os01g25820.1
intron # 1
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|88420800|gb|CI564636.1|CI564636
EST:     GGTCTGAATTCGTAGGTTTATTTGGGCTGGAATCTCTCAGAGGGTTTAAG                         AGGAAAAAGGAAAGAGGAGAAATTGTAAGGACAAGTAGAGAAGAACATGGC
genomic: GGTCTGAATTCGTAGGTTTATTTGGGCTGGAATCTCTCAGAGGGTTTAAGgtaccgttcc ... cgttgatcagAGGAAAAAGGAAAGAGGAGAAATTGTAAGGACAAGTAGAGAAGAACATGGC
EST: gi|29633927|gb|CB638936.1|CB638936
EST:     GGTCTGAATTCGTAGGTTTATTTGGGCTGGAATCTCTCAGAGGGTTTAAG                         AGGAAAAAGGAAAGAGGAGAAATTGTAAGGACAAGTAGAGAAGAACATGGC
genomic: GGTCTGAATTCGTAGGTTTATTTGGGCTGGAATCTCTCAGAGGGTTTAAGgtaccgttcc ... cgttgatcagAGGAAAAAGGAAAGAGGAGAAATTGTAAGGACAAGTAGAGAAGAACATGGC
EST: gi|29621907|gb|CB626918.1|CB626918
EST:     GTCTGAATTCGTAGGTCTT-TTTGTGTTGGAATCTCTCAGAGGGTTTAAG                         AGGAAAAAGGAAAGAGGAGAAATTGTAAGGACAAGTAGAGAAGAACATGGC
genomic: GTCTGAATTCGTAGGT-TTATTTGGGCTGGAATCTCTCAGAGGGTTTAAGgtaccgttcc ... cgttgatcagAGGAAAAAGGAAAGAGGAGAAATTGTAAGGACAAGTAGAGAAGAACATGGC
EST: gi|88730843|gb|CI754456.1|CI754456
EST:     GGTCTGAATTCGTAGGTTTATTTGGGCTGGAATCTCTCAGAGGGTTTAAG                         AGGAAAAAGGAAAGAGGAGAAATTGTAAGGACAAGTAGAGAAGAACATGGC
genomic: GGTCTGAATTCGTAGGTTTATTTGGGCTGGAATCTCTCAGAGGGTTTAAGgtaccgttcc ... cgttgatcagAGGAAAAAGGAAAGAGGAGAAATTGTAAGGACAAGTAGAGAAGAACATGGC
EST: gi|88362942|gb|CI614298.1|CI614298
EST:     GGTCTGAATTCGTAGGTTTATTTGGGCTGGAATCTCTCAGAGGGTTTAAG                         AGGAAAAAGGAAAGAGGAGAAAT-GTAAGGACAAGTAGAGAAGAACATGGC
genomic: GGTCTGAATTCGTAGGTTTATTTGGGCTGGAATCTCTCAGAGGGTTTAAGgtaccgttcc ... cgttgatcagAGGAAAAAGGAAAGAGGAGAAATTGTAAGGACAAGTAGAGAAGAACATGGC
EST: gi|88294629|gb|CI602349.1|CI602349
EST:     GGTCTGAATTCGTAGGTTTATTTGGGCTGGAATCTCTCAGAGGGTTTAAG                         AGGAAAAAGGAAAGAGGAGAAATTGTAAGGACAAGTAGAGAAGAACATGGC
genomic: GGTCTGAATTCGTAGGTTTATTTGGGCTGGAATCTCTCAGAGGGTTTAAGgtaccgttcc ... cgttgatcagAGGAAAAAGGAAAGAGGAGAAATTGTAAGGACAAGTAGAGAAGAACATGGC
EST: gi|88368139|gb|CI575021.1|CI575021
EST:     GGTCTGAATTCGTAGGTTTATTTGGGCTGGAATCTCTCAGAGGGTTTAAG                         AGGAAAAAGGAAAGAGGAGAAATTGTAAGGACAAGTAGAGAAGAACATGGC
genomic: GGTCTGAATTCGTAGGTTTATTTGGGCTGGAATCTCTCAGAGGGTTTAAGgtaccgttcc ... cgttgatcagAGGAAAAAGGAAAGAGGAGAAATTGTAAGGACAAGTAGAGAAGAACATGGC
EST: gi|426312|gb|D22176.1|D22176
EST:     GGTCTGAATTCGTAGGTTTATTTGGGCTGGAATCTCTCAGAGGGTTTAAG                         AGGAAAAAGGAAAGAGGAGAAATTGTAAGGACAAGTAGAGAAGAACATGGC
genomic: GGTCTGAATTCGTAGGTTTATTTGGGCTGGAATCTCTCAGAGGGTTTAAGgtaccgttcc ... cgttgatcagAGGAAAAAGGAAAGAGGAGAAATTGTAAGGACAAGTAGAGAAGAACATGGC
EST: gi|88453504|gb|CI563383.1|CI563383
EST:     GGTCTGAATTCGTAGGTTTATTTGGGCTGGAATCTCTCAGAGGGTTTAAG                         AGGAAAAAGGAAAGAGGAGAAATTGTAAGGACAAGTAGAGAAGAACATGGC
genomic: GGTCTGAATTCGTAGGTTTATTTGGGCTGGAATCTCTCAGAGGGTTTAAGgtaccgttcc ... cgttgatcagAGGAAAAAGGAAAGAGGAGAAATTGTAAGGACAAGTAGAGAAGAACATGGC
EST: gi|88430147|gb|CI565160.1|CI565160
EST:     GGTCTGAATTCGTAGGTTTATTTGGGCTGGAATCTCTCAGAGGGTTTAAG                         AGGAAAAAGGAAAGAGGAGAAATTGTAAGGACAAGTAGAGAAGAACATGGC
genomic: GGTCTGAATTCGTAGGTTTATTTGGGCTGGAATCTCTCAGAGGGTTTAAGgtaccgttcc ... cgttgatcagAGGAAAAAGGAAAGAGGAGAAATTGTAAGGACAAGTAGAGAAGAACATGGC
EST: gi|29631715|gb|CB636724.1|CB636724
EST:     GGTCTGAATTCGTAGGTTTATTTGGGCTGGAATCTCTCAGAGGGTTTAAG                         AGGAAAAAGGAAAGAGGAGAAATTGTAAGGACAAGTAGAGAAGAACATGGC
genomic: GGTCTGAATTCGTAGGTTTATTTGGGCTGGAATCTCTCAGAGGGTTTAAGgtaccgttcc ... cgttgatcagAGGAAAAAGGAAAGAGGAGAAATTGTAAGGACAAGTAGAGAAGAACATGGC

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: 72 (upstream exon), 75 (downstream exon)
Score: 29

GGGTTTTTCCTATCTTGTTGTTCTGAGGGAATTCAAGAAATGCTCCAAATGGTCTGAATTCGTAGGTTTATTTGGGCTGGAATCTCTCAGAGGGTTTAAGgtaccgttcc ... cgttgatcagAGGAAAAAGGAAAGAGGAGAAATTGTAAGGACAAGTAGAGAAGAACATGGCTGACCTGGAAGCAGGCATGGTTGCTGCTGCCACAGACCAGGGCAATTCA




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGGTTTTTCCTATCTTGTTGTTCTGAGGGAATTCAAGAAATGCTCCAAATGGTCTGAATTCGTAGGTTTATTTGGGCTGGAATCTCTCAGAGGGTTTAAGgtaccgttcctttcgtcacttcccccaaagttttagcctgcaaagtttgttcttcttcttcttcttcttcttcttcttcttcttcttcttttttccctct

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ttccccc