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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTTTTCGAAGGATATGTTGGAGTATTACTTCTTAAGACGGCTTTGCACGGGCTTGCATCGGAATGGCAGgcaagaattatcaactatgtaatgtttgcagttgatagttaatcagatcttcatgagacttaggctgagtttgtttcttagagttcccaattccccttat...

Basic information

species Oryza sativa
transcript LOC_Os02g01720.1
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g01720.1 (Oryza sativa), 5'ss of exon 9
lower sequence: GRMZM2G159142_T01 (Zea mays), 5'ss of exon 9
GTTTTCGAAGGATATGTTGGAGTATTACTTCTTAAGACGGCTTTGCACGGGCTTGCATCGGAATGGCAGgcaagaattat-caactatg--taatgtttgcagttgatagttaatcagatcttcatgagacttaggctgagtttgtttcttagagttcccaattccccttat
| |||||||| |||||||||||| || |||||| ||||||||||||| |||||||| || ||||||||||||||||| || ||||  |    | | ||  |||| ||  || |   ||   |  |  | | |    ||   |    ||    || ||          |  | 
GGTTTCGAAGCATATGTTGGAGTTTTGCTTCTTCAGACGGCTTTGCATGGGCTTGCTTCCGAATGGCAGgcaagaatgattcaacagttatcactattgacagtcgaatgtcagataggattaaaaaaaattct--ctagctgcccttgaatgaatttattgcctttccca-
















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|88282214|gb|CI403610.1|CI403610
EST:     GAGTATTACTTCTTAAGACGGCTTTGCACGGGCTTGCATCGGAATGGCAG                         GTTGTAGTTTGTGGGATCTTGCTGGTGGTAATGGCAGTCGGCAACTTTGTC
genomic: GAGTATTACTTCTTAAGACGGCTTTGCACGGGCTTGCATCGGAATGGCAGgcaagaatta ... cacttgccagGTTGTAGTTTGTGGGATCTTGCTGGTGGTAATGGCAGTCGGCAACTTTGTC
EST: gi|86541107|gb|CI181313.1|CI181313
EST:     GAGTATTACTTCTTAAGACGGCTTTGCACGGGCTTGCATCGGAATGTCAG                         GTTGTAGTTTGTGGGATCTTGCTGGTGGTAATGGCAGTCGGCAACTTTGTC
genomic: GAGTATTACTTCTTAAGACGGCTTTGCACGGGCTTGCATCGGAATGGCAGgcaagaatta ... cacttgccagGTTGTAGTTTGTGGGATCTTGCTGGTGGTAATGGCAGTCGGCAACTTTGTC
EST: gi|88534385|gb|CI463105.1|CI463105
EST:     TTTGCACGGGCTTGCATCGGAATGGCAG                         GTTGTAGTTTGTGAGATCTTGCTGGTGGTAATGGCAGTCGGCAACTTTGTC
genomic: TTTGCACGGGCTTGCATCGGAATGGCAGgcaagaatta ... cacttgccagGTTGTAGTTTGTGGGATCTTGCTGGTGGTAATGGCAGTCGGCAACTTTGTC
EST: gi|88519758|gb|CI447412.1|CI447412
EST:     GAGTATTACTTCTTAAGACGGCTTTGCACGGGCTTGCATCGGAATGGCAG                         GTTGTAGTTTGTGGGATCTTGCTGGTGGTAATGGCAGTCGGCAACTTTGTC
genomic: GAGTATTACTTCTTAAGACGGCTTTGCACGGGCTTGCATCGGAATGGCAGgcaagaatta ... cacttgccagGTTGTAGTTTGTGGGATCTTGCTGGTGGTAATGGCAGTCGGCAACTTTGTC
EST: gi|88502836|gb|CI430342.1|CI430342
EST:     CTTAAGACGGCTTTGCACGGGCTTGCATCGGAATGGCAG                         GTTGTAGTTTGTGGGATCTTGCTGGTGGTAATGGCAGTCGGCAACTTTGTC
genomic: CTTAAGACGGCTTTGCACGGGCTTGCATCGGAATGGCAGgcaagaatta ... cacttgccagGTTGTAGTTTGTGGGATCTTGCTGGTGGTAATGGCAGTCGGCAACTTTGTC
EST: gi|29661903|gb|CB658178.1|CB658178
EST:     GAGTATTACTTCTTAAGACGGCTTTGCACGGGCTTGCATCGGAATGGCAG                         GTTGTAGTTTGTGGGATCTTGCTGGTGGTAATGGCAGTCGGCAACTTTGTC
genomic: GAGTATTACTTCTTAAGACGGCTTTGCACGGGCTTGCATCGGAATGGCAGgcaagaatta ... cacttgccagGTTGTAGTTTGTGGGATCTTGCTGGTGGTAATGGCAGTCGGCAACTTTGTC
EST: gi|88994869|gb|CI036450.1|CI036450
EST:     GAGTATTACTTCTTAAGACGGCTTTGCACGGGCTTGCATCGGAATGGCAG                         GTTGTAGTTTGTGGGATCTTGCTGGTGGTAATGGCAGTCGGCAACTTTGTC
genomic: GAGTATTACTTCTTAAGACGGCTTTGCACGGGCTTGCATCGGAATGGCAGgcaagaatta ... cacttgccagGTTGTAGTTTGTGGGATCTTGCTGGTGGTAATGGCAGTCGGCAACTTTGTC
EST: gi|29664288|gb|CB660563.1|CB660563
EST:     GAGTATTACTTCTTAAGACGGCTTTGCACGGGCTTGCATCGGAATGGCAG                         GTTGTAGTTTGTGGGATCTTGCTGGTGGTAATGGCAGTCGGCAACTTTGTC
genomic: GAGTATTACTTCTTAAGACGGCTTTGCACGGGCTTGCATCGGAATGGCAGgcaagaatta ... cacttgccagGTTGTAGTTTGTGGGATCTTGCTGGTGGTAATGGCAGTCGGCAACTTTGTC
EST: gi|88280040|gb|CI401238.1|CI401238
EST:     TTTGCACGGGCTTGCATCGGAATGGCAG                         GTTTTAGTTTGTGGAATCTTGCTGGTGGTAATGGCAGTCGGCAACTTTGTC
genomic: TTTGCACGGGCTTGCATCGGAATGGCAGgcaagaatta ... cacttgccagGTTGTAGTTTGTGGGATCTTGCTGGTGGTAATGGCAGTCGGCAACTTTGTC
EST: gi|25802938|gb|CA758899.1|CA758899
EST:     GAGTATTACTTCTTAAGACGGCTTTGCACGGGCTTGCATCGGAATGGCAG                         GTTGTAGTTTGTGGGATCTTGCTGGTGGTAATGGCAGTCGGCAACTTTGTC
genomic: GAGTATTACTTCTTAAGACGGCTTTGCACGGGCTTGCATCGGAATGGCAGgcaagaatta ... cacttgccagGTTGTAGTTTGTGGGATCTTGCTGGTGGTAATGGCAGTCGGCAACTTTGTC
EST: gi|86539481|gb|CI179687.1|CI179687
EST:     GAGTATTACTTCTTAAGACGGCTTTGCACGGGCTTGCATCGGAATGGCAG                         GTTGTAGTTTGTGGGATCTTGCTGGTGGTAATGGCAGTCGGCAACTTTGTC
genomic: GAGTATTACTTCTTAAGACGGCTTTGCACGGGCTTGCATCGGAATGGCAGgcaagaatta ... cacttgccagGTTGTAGTTTGTGGGATCTTGCTGGTGGTAATGGCAGTCGGCAACTTTGTC
EST: gi|88980837|gb|CI022527.1|CI022527
EST:     GAGTATTACTTCTTAAGACGGCTTTGCACGGGCTTGCATCGGAAGGGCAG                         GTTGTAGTTTGTGGGATCTTGCTGGTGGTAATGGCAGTCGGCAACTTTGTC
genomic: GAGTATTACTTCTTAAGACGGCTTTGCACGGGCTTGCATCGGAATGGCAGgcaagaatta ... cacttgccagGTTGTAGTTTGTGGGATCTTGCTGGTGGTAATGGCAGTCGGCAACTTTGTC
EST: gi|88200565|gb|CI200415.1|CI200415
EST:     GAGTATTACTTCTTAAGACGGCTTTGCACGGGCTTGCATCGGAATGGCAG                         GTTGTAGTTTGTGGGATCTTGCTGGTGGTAATGGCAGTCGGCAACTTTGTC
genomic: GAGTATTACTTCTTAAGACGGCTTTGCACGGGCTTGCATCGGAATGGCAGgcaagaatta ... cacttgccagGTTGTAGTTTGTGGGATCTTGCTGGTGGTAATGGCAGTCGGCAACTTTGTC
EST: gi|58687887|gb|CK076574.1|CK076574
EST:     GAGTATTACTTCTTAAGACGGCTTTGCACGGGCTTGCATCGGAATGGCAG                         GTTGTAGTTTGTGGGATCTTGCTGGTGGTAATGGCAGTCGGCAACTTTGTC
genomic: GAGTATTACTTCTTAAGACGGCTTTGCACGGGCTTGCATCGGAATGGCAGgcaagaatta ... cacttgccagGTTGTAGTTTGTGGGATCTTGCTGGTGGTAATGGCAGTCGGCAACTTTGTC
EST: gi|88507512|gb|CI435018.1|CI435018
EST:     CGGCTTTGCACGGGCTTGCATCGGAATGGCAG                         GTTGTAGTTTGTGGGATCTTGCTGGTGGTAATGGCAGTCGGCAACTTTGTC
genomic: CGGCTTTGCACGGGCTTGCATCGGAATGGCAGgcaagaatta ... cacttgccagGTTGTAGTTTGTGGGATCTTGCTGGTGGTAATGGCAGTCGGCAACTTTGTC
EST: gi|86541101|gb|CI181307.1|CI181307
EST:     GAGTATTACTTCTTAAGACGGCTTTGCACGGGCTTGCATCGGAATGGCAG                         GTTGTAGTTTGTGGGATCTTGCTGGTGGTAATGGCAGTCGGCAACTTTGTC
genomic: GAGTATTACTTCTTAAGACGGCTTTGCACGGGCTTGCATCGGAATGGCAGgcaagaatta ... cacttgccagGTTGTAGTTTGTGGGATCTTGCTGGTGGTAATGGCAGTCGGCAACTTTGTC
EST: gi|88542899|gb|CI472257.1|CI472257
EST:     GAGTATTACTTCTTAAGACGGCTTTGCACGGGCTTGCATCGGAATGGCAG                         GTTGTAGTTTGTGAGATCTTGCTGGTGGTAATGGCAGTCGGCAACTTTGTC
genomic: GAGTATTACTTCTTAAGACGGCTTTGCACGGGCTTGCATCGGAATGGCAGgcaagaatta ... cacttgccagGTTGTAGTTTGTGGGATCTTGCTGGTGGTAATGGCAGTCGGCAACTTTGTC
EST: gi|88470024|gb|CI407295.1|CI407295
EST:     ACGGCTTTGCACGGGCTTGCATCGGAATGGCAG                         GTTGTAGTTTGTGGGATCTTGCTGGTGGTAATGGCAGTCGGCAACTTTGTC
genomic: ACGGCTTTGCACGGGCTTGCATCGGAATGGCAGgcaagaatta ... cacttgccagGTTGTAGTTTGTGGGATCTTGCTGGTGGTAATGGCAGTCGGCAACTTTGTC

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: 69 (upstream exon), 66 (downstream exon)
Score: 21

GTTTTCGAAGGATATGTTGGAGTATTACTTCTTAAGACGGCTTTGCACGGGCTTGCATCGGAATGGCAGgcaagaatta ... cacttgccagGTTGTAGTTTGTGGGATCTTGCTGGTGGTAATGGCAGTCGGCAACTTTGTCAACACGATGGAGACTTTGATGTTAAAATTGAGGTTCAAAGCAAAAATGA




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