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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CGTATGAGGTATCGAGTCATCAGACTTCCAAAGTATCTGATCCTTCACATGCGACGGTTTACCAAAAATAACTTCTTTGTAGAGAAGAATCCTACTCTAGgtaaaatccttgttttgatttaattagcctctgcagtccacttggtacatttctaagatgtttacatatttatcttacag

Basic information

species Oryza sativa
transcript LOC_Os09g24250.1
intron # 7
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os09g24250.1 (Oryza sativa), 5'ss of exon 7
lower sequence: GRMZM2G091151_T01 (Zea mays), 5'ss of exon 7
CGTATGAGGTATCGAGTCATCAGACTTCCAAAGTATCTGATCCTTCACATGCGACGGTTTACCAAAAATAACTTCTTTGTAGAGAAGAATCCTACTCTAGgtaaaatc-----cttgttt---tgatttaattagcctctgcagtccact-tggtacat--ttctaagatgtttacatatttatctta-cag
|| |||||||| |||||||  ||||| || ||||||||||||||||| |||||| ||||||||||||||||||| ||||| ||||| || |||||||||||| | ||      |||| ||   | | ||   |  |  |||   | | |  |||||  |  || ||| ||||||  ||||| | |||  |||
CGAATGAGGTACCGAGTCACTAGACTGCCGAAGTATCTGATCCTTCATATGCGAAGGTTTACCAAAAATAACTTTTTTGTCGAGAAAAACCCTACTCTAGgtgagattttacacttgcttgattaactttgctgtcgcctgtcatgctccatggtagctgattttaatatgttttaatattcaacttggcag
















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|33811333|gb|CF331556.1|CF331556
EST:     GCGACGGTTTACCAAAAATAACTTCTTTGTAGAGAAGAATCCTACTCTAG                         TGAATTTCCCCGTGAAGAACTTGGAATTGAAAGATTACATCCCATTACCTA
genomic: GCGACGGTTTACCAAAAATAACTTCTTTGTAGAGAAGAATCCTACTCTAGgtaaaatcct ... tatcttacagTGAATTTCCCCGTGAAGAACTTGGAATTGAAAGATTACATCCCATTACCTA
EST: gi|33687261|gb|CF315500.1|CF315500
EST:     AATCCTACTCTAG                         TGAATTTCCCCGTGAAGAACTTGGAATTGAAAGATTACATCCCATTACCTA
genomic: AATCCTACTCTAGgtaaaatcct ... tatcttacagTGAATTTCCCCGTGAAGAACTTGGAATTGAAAGATTACATCCCATTACCTA
EST: gi|86902109|gb|CI300348.1|CI300348
EST:     GCGACGGTTTACCAAAAATAACTTCTTTGTAGAGAAGAATCCTACTCTAG                         TGAATTTCCCCGTGAAGAACTTGGAATTGAAAGATTACATCCCATTACCTA
genomic: GCGACGGTTTACCAAAAATAACTTCTTTGTAGAGAAGAATCCTACTCTAGgtaaaatcct ... tatcttacagTGAATTTCCCCGTGAAGAACTTGGAATTGAAAGATTACATCCCATTACCTA
EST: gi|33683169|gb|CF311408.1|CF311408
EST:     GCGACGGTTTACCAAAAATAACTTCTTTGTAGAGAAGAATCCTACTCTAG                         TGAATTTCCCCGTGAAGAACTTGGAATTGAAAGATTACATCCCATTACCTA
genomic: GCGACGGTTTACCAAAAATAACTTCTTTGTAGAGAAGAATCCTACTCTAGgtaaaatcct ... tatcttacagTGAATTTCCCCGTGAAGAACTTGGAATTGAAAGATTACATCCCATTACCTA
EST: gi|29661389|gb|CB657664.1|CB657664
EST:     GCGACGGTTTACCAAAAATAACTTCTTTGTAGAGAAGAATCCTACTCTAG                         TGAATTTCCCCGTGAAGAACTTGGAATTGAAAGATTACATCCCATTACCTA
genomic: GCGACGGTTTACCAAAAATAACTTCTTTGTAGAGAAGAATCCTACTCTAGgtaaaatcct ... tatcttacagTGAATTTCCCCGTGAAGAACTTGGAATTGAAAGATTACATCCCATTACCTA
EST: gi|88224775|gb|CI224624.1|CI224624
EST:     GCGACGGTTTACCAAAAATAACTTCTTTGTAGAGAAGAATCCTACTCTAG                         TGAATTTCCCCGTGAAGAACTTGGAATTGAAAGATTACATCCCATTACCTA
genomic: GCGACGGTTTACCAAAAATAACTTCTTTGTAGAGAAGAATCCTACTCTAGgtaaaatcct ... tatcttacagTGAATTTCCCCGTGAAGAACTTGGAATTGAAAGATTACATCCCATTACCTA
EST: gi|29629631|gb|CB634640.1|CB634640
EST:     GCGACGGTTTACCAAAAATAACTTCTTTGTAGAGAAGAATCCTACTCTAG                         TGAATTTCCCCGTGAAGAACTTGGAATTGAAAGATTACATCCCATTACCTA
genomic: GCGACGGTTTACCAAAAATAACTTCTTTGTAGAGAAGAATCCTACTCTAGgtaaaatcct ... tatcttacagTGAATTTCCCCGTGAAGAACTTGGAATTGAAAGATTACATCCCATTACCTA
EST: gi|58596598|gb|CK007126.1|CK007126
EST:     GCGACGGTTTACCAAAAATAACTTCTTTGTAGAGAAGAATCCTACTCTAG                         TGAATTTCCCCGTGAAGAACTTGGAATTGAAAGATTACATCCCATTACCTA
genomic: GCGACGGTTTACCAAAAATAACTTCTTTGTAGAGAAGAATCCTACTCTAGgtaaaatcct ... tatcttacagTGAATTTCCCCGTGAAGAACTTGGAATTGAAAGATTACATCCCATTACCTA

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), 74 (downstream exon)
Score: 51

CGTATGAGGTATCGAGTCATCAGACTTCCAAAGTATCTGATCCTTCACATGCGACGGTTTACCAAAAATAACTTCTTTGTAGAGAAGAATCCTACTCTAGgtaaaatcct ... tatcttacagTGAATTTCCCCGTGAAGAACTTGGAATTGAAAGATTACATCCCATTACCTAAGCCAAAAGATTCCGAGAAGCTACGCTCAAAGTATGATCTCATAGCCAA




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