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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATACGGGAAGTACAAGCCTATCGTTGAGCCGGCAAAATGgtaccttctcttgccctttttcgtaattatcgcactcactcgattgatggaactatggaggagtgggcagtgatggatgctgatagttctcgtttggtttttgcag

Basic information

species Oryza sativa
transcript LOC_Os01g55730.1
intron # 3
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|88302743|gb|CI668589.1|CI668589
EST:     ATACGGGAAGTACAAGCCTATCGTTGAGCCGGCAAAATG                         TCAGAAGTGTGGGAAACGGAACGTCCGACAGGCGTATCACAACGTCTGCAC
genomic: ATACGGGAAGTACAAGCCTATCGTTGAGCCGGCAAAATGgtaccttctc ... gtttttgcagTCAGAAGTGTGGGAAACGGAACGTCCGACAGGCGTATCACAACGTCTGCAC
EST: gi|88739397|gb|CI762905.1|CI762905
EST:     ATACGGGAAGTACAAGCCTATCGTTGAGCCGGCAAAATG                         TCAGAAGTGTGGGAAACGGAACGTCCGACAGGCGTATCACAACGTCTGCAC
genomic: ATACGGGAAGTACAAGCCTATCGTTGAGCCGGCAAAATGgtaccttctc ... gtttttgcagTCAGAAGTGTGGGAAACGGAACGTCCGACAGGCGTATCACAACGTCTGCAC
EST: gi|33381195|gb|CF196538.1|CF196538
EST:     ATACGGGAAGTACAAGCCTATCGTTGAGCCGGCAAAATG                         TCAGAAGTGTGGGAAACGGAACGTCCGACAGGCGTATCACAACGTCTGCAC
genomic: ATACGGGAAGTACAAGCCTATCGTTGAGCCGGCAAAATGgtaccttctc ... gtttttgcagTCAGAAGTGTGGGAAACGGAACGTCCGACAGGCGTATCACAACGTCTGCAC
EST: gi|38470771|gb|CF954902.1|CF954902
EST:     ATACGGGAAGTACAAGCCTATCGTTGAGCCGGCAAAATG                         TCAGAAGTGTGGGAAACGGAACGTCCGACAGGCGTATCACAACGTCTGCAC
genomic: ATACGGGAAGTACAAGCCTATCGTTGAGCCGGCAAAATGgtaccttctc ... gtttttgcagTCAGAAGTGTGGGAAACGGAACGTCCGACAGGCGTATCACAACGTCTGCAC
EST: gi|3767261|gb|AU031371.1|AU031371
EST:     GGGAAGTACAAGCCTATCGTTGAGCCGGCAAAATG                         TCAGAAGTGTGGGAAACGGAACGTCCGACAGGCGTATCACAACGTCTGCAC
genomic: GGGAAGTACAAGCCTATCGTTGAGCCGGCAAAATGgtaccttctc ... gtttttgcagTCAGAAGTGTGGGAAACGGAACGTCCGACAGGCGTATCACAACGTCTGCAC
EST: gi|428826|gb|D24982.1|D24982
EST:     ATACGGGAAGTACAAGCCTATCGTTGAGCCGGCAAAATG                         TCAGAAGTNTGGGAAACGGAACGTCCGACAGGCGTATCACAACGTCTGCAC
genomic: ATACGGGAAGTACAAGCCTATCGTTGAGCCGGCAAAATGgtaccttctc ... gtttttgcagTCAGAAGTGTGGGAAACGGAACGTCCGACAGGCGTATCACAACGTCTGCAC
EST: gi|88718954|gb|CI742464.1|CI742464
EST:     ATACGGGAAGTACAAGCCTATCGTTGAGCCGGCAAAATG                         TCAGAAGTGTGGGAAACGGAACGTCCGACAGGCGTATCACAACGTCTGCAC
genomic: ATACGGGAAGTACAAGCCTATCGTTGAGCCGGCAAAATGgtaccttctc ... gtttttgcagTCAGAAGTGTGGGAAACGGAACGTCCGACAGGCGTATCACAACGTCTGCAC
EST: gi|88727187|gb|CI750842.1|CI750842
EST:     ATACGGGAAGTACAAGCCTATCGTTGAGCCGGCAAAATG                         TCAGAAGTGTGGGAAACGGAACGTCCGACAGGCGTATCACAACGTCTGCAC
genomic: ATACGGGAAGTACAAGCCTATCGTTGAGCCGGCAAAATGgtaccttctc ... gtttttgcagTCAGAAGTGTGGGAAACGGAACGTCCGACAGGCGTATCACAACGTCTGCAC
EST: gi|88420754|gb|CI564590.1|CI564590
EST:     ATACGGGAAGTACAAGCCTATCGTTGAGCCGGCAAAATG                         TCAGAAGTGTGGGAAACGGAACGTCCGACAGGCGTATCACAACGTCTGCAC
genomic: ATACGGGAAGTACAAGCCTATCGTTGAGCCGGCAAAATGgtaccttctc ... gtttttgcagTCAGAAGTGTGGGAAACGGAACGTCCGACAGGCGTATCACAACGTCTGCAC
EST: gi|88296284|gb|CI667674.1|CI667674
EST:     ATACGGGAAGTACAAGCCTATCGTTGAGCCGGNAAAATG                         TCAGAAGTGTGGGAAACGGAACGTCCGACAGGCGTATCACAACGTCTGCAC
genomic: ATACGGGAAGTACAAGCCTATCGTTGAGCCGGCAAAATGgtaccttctc ... gtttttgcagTCAGAAGTGTGGGAAACGGAACGTCCGACAGGCGTATCACAACGTCTGCAC
EST: gi|66932185|gb|CX119033.1|CX119033
EST:     ATACGGGAAGTACAAGCCTATCGTTGAGCCGGCAAAATG                         TCAGAAGTGTGGGAAACGGAACGTCCGACAGGCGTATCACAACGTCTGCAC
genomic: ATACGGGAAGTACAAGCCTATCGTTGAGCCGGCAAAATGgtaccttctc ... gtttttgcagTCAGAAGTGTGGGAAACGGAACGTCCGACAGGCGTATCACAACGTCTGCAC

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: 43 (upstream exon), 64 (downstream exon)
Score: 20

ATACGGGAAGTACAAGCCTATCGTTGAGCCGGCAAAATGgtaccttctc ... gtttttgcagTCAGAAGTGTGGGAAACGGAACGTCCGACAGGCGTATCACAACGTCTGCACGG




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