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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTTGCTGATTTTGGCCTTGCAAGACTAGCTATGGATGCAGTCACGCATGTAACTACACGGGTGATGGGAACTTTTGGgtaagtaaattactgcctgccttactgagggcacaagagaacatcgtacattttcatatgatctaatgattatttgttatgcag

Basic information

species Oryza sativa
transcript LOC_Os01g02040.1
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g02040.1 (Oryza sativa), 5'ss of exon 5
lower sequence: GRMZM5G872442_T02 (Zea mays), 5'ss of exon 6
GTTGCTGATTTTGGCCTTGCAAGACTAGCTATGGATGCAGTCACGCATGTAACTACACGGGTGATGGGAACTTTTGGgtaagtaaattactgcctgccttactgagggcacaagagaacatcgtacattttcatatgatctaatgattatttgttatgcag
|||||||||||||| ||||||||  |||||||||||||   ||| |||||||| ||||| |||||||||||||| |||| ||||||  |            | |   |  ||||||||||    | |  | | | | |||| |       || ||||  ||
GTTGCTGATTTTGGTCTTGCAAGGTTAGCTATGGATGCTTGCACTCATGTAACCACACGAGTGATGGGAACTTTCGGgttagtaaaaca-----------gcggcaagttcaagagaacagttaaaacctgcttgtaatctgacacacgcttcttatttag

upper sequence: LOC_Os01g02040.1 (Oryza sativa), 5'ss of exon 5
lower sequence: GRMZM2G355636_T01 (Zea mays), 5'ss of exon 6
GTTGCTGATTTTGGCCTTGCAAGACTAGCTATGGATGCAGTCACGCATGTAACTACACGGGTGATGGGAACTTTTGGgtaagtaaattactgcctgccttactgagggcacaagagaacatcgtacattttcatatgatctaatgattatttgttatgcag
|||||||||||||| ||||||||  |||||||||||||   ||| |||||||||||||| ||||||||||||||||||| ||||||  |  | |             |  ||||||| ||    | |  | | | | |||| | |  | ||| |||   ||
GTTGCTGATTTTGGTCTTGCAAGGATAGCTATGGATGCTTGCACTCATGTAACTACACGAGTGATGGGAACTTTTGGgttagtaaagcagcgac-----------aagtccaagagagcagttaaaacatgcttgtaatctgacgcatgtttcttaattag
















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|27554568|gb|CA998468.1|CA998468
EST:     GCTATGGATGCAGTCACGCATGTAACTACACGGGTGATGGGAACTTTTGG                         TTATCTGGCTCCGGAGTATGCTTCGAGTGG
genomic: GCTATGGATGCAGTCACGCATGTAACTACACGGGTGATGGGAACTTTTGGgtaagtaaat ... tgttatgcagTTATCTGGCTCCGGAGTATGCTTCGAGTGG
EST: gi|66929099|gb|CX115947.1|CX115947
EST:     GCTATGGATGCAGTCACGCATGTAACTACACGGGTGATGGGAACTTTTGG                         TTATCTGGCTCCGGAGTATGCTTCGAGTGGCAAGTTGACTGAGAGATCTGA
genomic: GCTATGGATGCAGTCACGCATGTAACTACACGGGTGATGGGAACTTTTGGgtaagtaaat ... tgttatgcagTTATCTGGCTCCGGAGTATGCTTCGAGTGGCAAGTTGACTGAGAGATCTGA
EST: gi|86481600|gb|CI124233.1|CI124233
EST:     GCTATGGATGCAGTCACGCATGTAACTACACGGGTGATGGGAACTTTTGG                         TTATCTGGCTCCGGAGTATGCTTCTAGTGGCAAGTTGACTGAGAGATCTGA
genomic: GCTATGGATGCAGTCACGCATGTAACTACACGGGTGATGGGAACTTTTGGgtaagtaaat ... tgttatgcagTTATCTGGCTCCGGAGTATGCTTCGAGTGGCAAGTTGACTGAGAGATCTGA
EST: gi|27576561|gb|CA999255.1|CA999255
EST:     GCTATGGATGCAGTCACGCATGTAACTACACGGGTGATGGGAACTTTTGG                         TTATCTGGCTCCGGAGTATGCTTCGAGTGGCAAGTTGACTGAGAGATCTGA
genomic: GCTATGGATGCAGTCACGCATGTAACTACACGGGTGATGGGAACTTTTGGgtaagtaaat ... tgttatgcagTTATCTGGCTCCGGAGTATGCTTCGAGTGGCAAGTTGACTGAGAGATCTGA
EST: gi|86436777|gb|CI118499.1|CI118499
EST:     ACGGGTGATGGGAACTTTTGG                         TTATCTGGCTCCGGAGTATGCTTCGAGTGGCAAGTTGACTGAGAGATCTGA
genomic: ACGGGTGATGGGAACTTTTGGgtaagtaaat ... tgttatgcagTTATCTGGCTCCGGAGTATGCTTCGAGTGGCAAGTTGACTGAGAGATCTGA

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: 63 (upstream exon), 69 (downstream exon)
Score: 11

GTTGCTGATTTTGGCCTTGCAAGACTAGCTATGGATGCAGTCACGCATGTAACTACACGGGTGATGGGAACTTTTGGgtaagtaaat ... tgttatgcagTTATCTGGCTCCGGAGTATGCTTCGAGTGGCAAGTTGACTGAGAGATCTGATGTATTCTCTTTTGGCGTTGTTCTCTTAGAGCTTATTACCGGTAGAAAG




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