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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CGACATGCTGTTTGGCAAACGTGGGAAGAGTGGCCTTGTGGCCCTCAACCTAGATCTTGCTCAAGTCCGCCAATTCGTCAAAGAGCGGTTGGGAGTTGAGgtagttatacattttcccatgctttgcctctaaaaccttgttagttataactattctaagctatccggtatgcctgttatgcag

Basic information

species Oryza sativa
transcript LOC_Os12g37870.1
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os12g37870.1 (Oryza sativa), 5'ss of exon 2
lower sequence: GRMZM2G034083_T01 (Zea mays), 5'ss of exon 2
CGACATGCTGTTTGGCAAACGTGGGAAGAGTGGCCTTGTGGCCCTCAACCTAGATCTTGCTCAAGTCCGCCAATTCGTCAAAGAGCGGTTGGGAGTTGAGgta--gttat-----acattttcccatgctttgcctcta---aaaccttgttagttataactattc-taagctatccgg-----tatgcctg-ttatgcag
 |||||||| ||||| ||||||||||||||||| |||||||||||||||||||||||||| ||||| |||||||| ||||| |||||||||||||||||||||  || |      |||| |||||||| |||    |     |||| ||| |   || | |||||  | | || |  |      | |||    ||||  ||
TGACATGCTCTTTGGGAAACGTGGGAAGAGTGGGCTTGTGGCCCTCAACCTAGATCTTGCCCAAGTTCGCCAATTTGTCAAGGAGCGGTTGGGAGTTGAGgtactgtcacgactaacatattcccatgttttttaccagcacaaactttgattactaaagctatttattatctttatgaatgaatttgctcacttatctag

upper sequence: LOC_Os12g37870.1 (Oryza sativa), 5'ss of exon 2
lower sequence: GRMZM2G034083_T02 (Zea mays), 5'ss of exon 2
CGACATGCTGTTTGGCAAACGTGGGAAGAGTGGCCTTGTGGCCCTCAACCTAGATCTTGCTCAAGTCCGCCAATTCGTCAAAGAGCGGTTGGGAGTTGAGgta--gttat-----acattttcccatgctttgcctcta---aaaccttgttagttataactattc-taagctatccgg-----tatgcctg-ttatgcag------
     |||| ||||| ||||||||||||||||| |||||||||||||||||||||||||| ||||| |||||||| ||||| |||||||||||||||||||||  || |      |||| |||||||| |||    |     |||| ||| |   || | |||||  | | || |  |      | |||    ||||  ||      
-----TGCTCTTTGGGAAACGTGGGAAGAGTGGGCTTGTGGCCCTCAACCTAGATCTTGCCCAAGTTCGCCAATTTGTCAAGGAGCGGTTGGGAGTTGAGGTACTgtcacgactaacatattcccatgttttttaccagcacaaactttgattactaaagctatttattatctttatgaatgaatttgctcacttatctaggtcgag
















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|27577556|gb|CB000251.1|CB000251
EST:     CGCCAATTCGTCAAAGAGCGGNTGGGAGTTGCC                         TTTGAGATGGGTGGCTGCAAGGCTCCTATTACAACATTCATAGTTGAGCCA
genomic: CGCCAATTCGTCAAAGAGCGGTTGGGAGTTGAGgtagttatac ... tgttatgcagGTTGAGATGGGTGGCTGCAAGGCTCCTATTACAACATTCATAGTTGAGCCA
EST: gi|29669993|gb|CB666268.1|CB666268
EST:     TAGATCTTGCTCAAGTCCGCCAATTCGTCAAAGAGCGGTTGGGAGTTGAG                         GTTGAGATGGGTGGCTGCAAGGCTCCTATTACAACATTCATAGTTGAGCCA
genomic: TAGATCTTGCTCAAGTCCGCCAATTCGTCAAAGAGCGGTTGGGAGTTGAGgtagttatac ... tgttatgcagGTTGAGATGGGTGGCTGCAAGGCTCCTATTACAACATTCATAGTTGAGCCA
EST: gi|88356219|gb|CI627667.1|CI627667
EST:     TAGATCTTGCTCAAGTCCGCCAATTCGTCAAAGAGCGGTTGGGAGTTGAG                         GTTGAGATGGGTGGCTGCAAGGCTCCTATTACAACATTCATAGTTGAGCCA
genomic: TAGATCTTGCTCAAGTCCGCCAATTCGTCAAAGAGCGGTTGGGAGTTGAGgtagttatac ... tgttatgcagGTTGAGATGGGTGGCTGCAAGGCTCCTATTACAACATTCATAGTTGAGCCA
EST: gi|569539|gb|D40388.1|D40388
EST:     TAGATCTTGCTCAAGTCCGCCAATTCGTCAAAGAGCGGTTGGGAGTTGAG                         GTTGAGATGGGTGGCTGCAAGGCTCCTATTACAACATTCATAGTTGAGCCA
genomic: TAGATCTTGCTCAAGTCCGCCAATTCGTCAAAGAGCGGTTGGGAGTTGAGgtagttatac ... tgttatgcagGTTGAGATGGGTGGCTGCAAGGCTCCTATTACAACATTCATAGTTGAGCCA
EST: gi|3090568|gb|C93555.1|C93555
EST:     TAGATCTTGCTCAAGTCCGCCAATTCGTCAAAGAGCGGTTGGGAGTTGAG                         GTTGAGATGGGTGGCTGCAAGGCTCCTATTACAACATTCATAGTTGAGCCA
genomic: TAGATCTTGCTCAAGTCCGCCAATTCGTCAAAGAGCGGTTGGGAGTTGAGgtagttatac ... tgttatgcagGTTGAGATGGGTGGCTGCAAGGCTCCTATTACAACATTCATAGTTGAGCCA
EST: gi|33676456|gb|CF304695.1|CF304695
EST:     TAGATCTTGCTCAAGTCCGCCAATTCGTCAAAGAGCGGTTGGGAGTTGAG                         GTTGAGATGGGTGGCTGCAAGGCTCCTATTACAACATTCATAGTTGAGCCA
genomic: TAGATCTTGCTCAAGTCCGCCAATTCGTCAAAGAGCGGTTGGGAGTTGAGgtagttatac ... tgttatgcagGTTGAGATGGGTGGCTGCAAGGCTCCTATTACAACATTCATAGTTGAGCCA
EST: gi|2431459|gb|C73879.1|C73879
EST:     TAGATCTTGCTCAAGTCCGCCAATTCGTCAAAGAGCGGTTGGGAGTTGAG                         GTTGAGATGGGTGGCTGCAAGGCTCCTATTACAACATTCATAGTTGAGCCA
genomic: TAGATCTTGCTCAAGTCCGCCAATTCGTCAAAGAGCGGTTGGGAGTTGAGgtagttatac ... tgttatgcagGTTGAGATGGGTGGCTGCAAGGCTCCTATTACAACATTCATAGTTGAGCCA

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: 71 (upstream exon), 70 (downstream exon)
Score: 23

CGACATGCTGTTTGGCAAACGTGGGAAGAGTGGCCTTGTGGCCCTCAACCTAGATCTTGCTCAAGTCCGCCAATTCGTCAAAGAGCGGTTGGGAGTTGAGgtagttatac ... tgttatgcagGTTGAGATGGGTGGCTGCAAGGCTCCTATTACAACATTCATAGTTGAGCCATTTGTTCCACATGATCAAGAGTACTATCTTTCTATTGTATCAGAGAGGC




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