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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGTTCTGGTCAGCAGAGTCATTGTACTATAATCCAGCTTGGCACATCATTGTCTCTTCGTGGGAAACTATCGTATATAGCCCCATTCTCGATCTGGACAGgtagccttcttgctccaagcttgcacgcgtaattatcagcttacatgtcattcttgtattaatcagttccgtcatgcaatgttttatgcag

Basic information

species Oryza sativa
transcript LOC_Os03g58240.1
intron # 16
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g58240.1 (Oryza sativa), 5'ss of exon 16
lower sequence: GRMZM2G305254_T04 (Zea mays), 5'ss of exon 15
TGTTCTGGTCAGCAGAGTCATTGTACTATAATCCAGCTTGGCACATCATTGTCTCTTCGTGGGAAACTATCGTATATAGCCCCATTCTCGATCTGGACAGgtagccttcttgctccaagcttgcacgcgtaattatcagcttacatgtcattcttgtattaatcagttccgtcatgcaatgttttatgcag
||||||||||||| || ||| |||| |||||||||||||||||||||||||| ||||| ||||| |  ||||| || ||||| ||||| ||||||||||||||| || |||  ||||   ||  ||   | | |||    |  ||||  | ||| || | | | |       ||||| ||  |||   |||
TGTTCTGGTCAGCGGAATCACTGTATTATAATCCAGCTTGGCACATCATTGTTTCTTCCTGGGAGATGATCGTGTACAGCCCTATTCTTGATCTGGACAGgtagtctccttattcca---tttaac---tgagtatattttgccatgctactct-gtctgactaa-------catgccattatttgcacag

upper sequence: LOC_Os03g58240.1 (Oryza sativa), 5'ss of exon 16
lower sequence: GRMZM2G019361_T03 (Zea mays), 5'ss of exon 15
TGTTCTGGTCAGCAGAGTCATTGTACTATAATCCAGCTTGGCACATCATTGTCTCTTCGTGGGAAACTATCGTATATAGCCCCATTCTCGATCTGGACAGgtagccttcttgctccaagctt---------gcacgcgtaattatcagcttacatgtcattcttgtattaatcagttccgtcatgcaatgttttatgcag-
||||||||||||| || ||  ||||||||||||||||||||||||||||||| ||||| |||||||| ||||| || ||||| ||||| ||||||||||||||| || |||||||| | ||          ||| ||     | || |  || |   |  | | | |  |  ||| |   | |   | || |||||  |  
TGTTCTGGTCAGCGGAATCGCTGTACTATAATCCAGCTTGGCACATCATTGTTTCTTCCTGGGAAACCATCGTGTACAGCCCAATTCTTGATCTGGACAGgtagtctccttgctcctaactgtatatattggcatgctactctgtctgactaaagccctgtttagaagcatccagattt-taagaaactggtttatatata

upper sequence: LOC_Os03g58240.1 (Oryza sativa), 5'ss of exon 16
lower sequence: GRMZM2G321413_T01 (Zea mays), 5'ss of exon 9
TGTTCTGGTCAGCAGAGTCATTGTACTATAATCCAGCTTGGCACATCATTGTCTCTTCGTGGGAAACTATCGTATATAGCCCCATTCTCGATCTGGACAGgtagccttcttgctccaagct-----tgcacgcgtaattatcagcttacat---gtcattcttgtattaatcagttccgtcatgcaatgttttatgcag-
||||||||||||| || ||  ||||||||||||||||||||||||||||||| ||||| |||||||| ||||| || ||||| ||||| ||||||||||||||| || |||||||| | ||     |    || |  |  || |  |   |   | | |  ||  |   ||| |     | |   | || |||||  |  
TGTTCTGGTCAGCGGAATCGCTGTACTATAATCCAGCTTGGCACATCATTGTTTCTTCCTGGGAAACCATCGTGTACAGCCCAATTCTTGATCTGGACAGgtagtctccttgctcctaactgtatatattggcatgctactctgtctgactaaagccctgtttagaagcatccggattttaagaaactggtttatatata

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|112785607|gb|EE591049.1|EE591049
EST:     GTCTCTTCGTGGGAAACTATCGTATATAGCCCCATTCTCGATCTGGACAG                         ATGGGCGATCCCCAGTTGCCG
genomic: GTCTCTTCGTGGGAAACTATCGTATATAGCCCCATTCTCGATCTGGACAGgtagccttct ... ttttatgcagATGGGCGATCCCCA-TTGCCG
EST: gi|88197332|gb|CI197182.1|CI197182
EST:     GTCTCTTCGTGGGAAACTATCGTATATAGCCCCATTCTCGATCTGGACAG                         ATGGGCGATCCCCATTGCCGTATTATTGTCTTTTTGGCTTCTTTACTGGCG
genomic: GTCTCTTCGTGGGAAACTATCGTATATAGCCCCATTCTCGATCTGGACAGgtagccttct ... ttttatgcagATGGGCGATCCCCATTGCCGTATTATTGTCTTTTTGGCTTCTTTACTGGCG
EST: gi|87035296|gb|CI189918.1|CI189918
EST:     GTCTCTTCGTGGGAAACTATCGTATATAGCCCCATTCTCGATCTGGACAG                         ATGGGCGATCCCCATTGCCGTATTATTGTCTTTTTGGCTTCTTTACTGGCG
genomic: GTCTCTTCGTGGGAAACTATCGTATATAGCCCCATTCTCGATCTGGACAGgtagccttct ... ttttatgcagATGGGCGATCCCCATTGCCGTATTATTGTCTTTTTGGCTTCTTTACTGGCG
EST: gi|87013871|gb|CI271262.1|CI271262
EST:     GATCTGGACAG                         ATGGGCGATCCCCATTGCCGTATTATTGTCTTTTTGGCTTCTTTACTGGCG
genomic: GATCTGGACAGgtagccttct ... ttttatgcagATGGGCGATCCCCATTGCCGTATTATTGTCTTTTTGGCTTCTTTACTGGCG
EST: gi|29672597|gb|CB668872.1|CB668872
EST:     GTCTCTTCGTGGGAAACTATCGTATATAGCCCCATTCTCGATCTGGACAG                         ATGGGCGATCCCCATTGCCGTATTATTGTCTTTTTGGCTTCTTTACTGGCG
genomic: GTCTCTTCGTGGGAAACTATCGTATATAGCCCCATTCTCGATCTGGACAGgtagccttct ... ttttatgcagATGGGCGATCCCCATTGCCGTATTATTGTCTTTTTGGCTTCTTTACTGGCG

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: 25 (upstream exon), 51 (downstream exon)
Score: 2

TGTTCTGGTCAGCAGAGTCATTGTACTATAATCCAGCTTGGCACATCATTGTCTCTTCGTGGGAAACTATCGTATATAGCCCCATTCTCGATCTGGACAGgtagccttct ... ttttatgcagATGGGCGATCCCCATTGCCGTATTATTGTCTTTTTGGCTTCTTTACTGGCGATGTTTCGGTAGAAGAAAACGGGGCAGCCGATCGTCACTCCTGCCACTC




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