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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CCCTTGTCCGCGCCCGCGGACACATGCTGCAGGAGCTCAAGCTCGACAAGTGCATCGGCTTCTCCACTGACGCCCTCCGCCTCGTCGCCCGCTCGTGCAGgtaacccaggagttctctctttcttgtactactcatctgtaacagtgattttttttacctccaatacttgcctaagcgaaagttagcagcagcaactgag...

Basic information

species Oryza sativa
transcript LOC_Os01g63420.3
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g63420.1 (Oryza sativa), 5'ss of exon 2
lower sequence: GRMZM2G125411_T01 (Zea mays), 5'ss of exon 1
CCCTTGTCCGCGCCCGCGGACACATGCTGCAGGAGCTCAAGCTCGACAAGTGCATCGGCTTCTCCACTGACGCCCTCCGCCTCGTCGCCCGCTCGTGCAGgtaac-ccaggagttctctctttcttgtact---actcatctgt--aacagtgattttttttacctccaatacttgcctaagcgaaagttagcagcagcaactgag
  || |||||||| ||||| |||||||| |||| |||||||||||||||||||  ||||||||| || ||||||||| |||||||||| ||||| ||||||||   || | | || | |   || |||| |     |||||||   | | |  |     | |   | |                |  ||  || |    |      
TGCTCGTCCGCGCGCGCGGCCACATGCTACAGGTGCTCAAGCTCGACAAGTGCTCCGGCTTCTCAACAGACGCCCTCTGCCTCGTCGCGCGCTCCTGCAGgtagtacccgtacttatgttcgtcgtgtagtcgtgttcatctgctgatctgcaacgccgtgtttgttcggcctgctttcccattacggtgtgcggggaaa------
















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|58655865|gb|CK044545.1|CK044545
EST:     TGCATCGGCTTCTCCACTGACGCCCTCCGCCTCGTCGCCCGCTCGTGCAG                         ATCCCTGAGAACTTTATTTCTGGAAGAGTGCCATATTACTGATAAGGGTGG
genomic: TGCATCGGCTTCTCCACTGACGCCCTCCGCCTCGTCGCCCGCTCGTGCAGgtaacccagg ... atgtcaacagATCCCTGAGAACTTTATTTCTGGAAGAGTGCCATATTACTGATAAGGGTGG
EST: gi|117242280|gb|CT848299.1|CT848299
EST:     TGCATCGGCTTCTCCACTGACGCCCTCCGCCTCGTCGCCCGCTCGTGCAG                         ATCCCTGAGAACTTTATTTCTGGAAGAGTGCCATATTACTGATAAGGGTGG
genomic: TGCATCGGCTTCTCCACTGACGCCCTCCGCCTCGTCGCCCGCTCGTGCAGgtaacccagg ... atgtcaacagATCCCTGAGAACTTTATTTCTGGAAGAGTGCCATATTACTGATAAGGGTGG
EST: gi|300215787|gb|HO088413.1|HO088413
EST:     TGCATCGGCTTCTCCACTGACGCCCTCCGCCTCGTCGCCCGCTCGTGCAG                         ATCCCTGAGAACTTTATTTCTGGAAGAGTGCCATATTACTGATAAGGGTGG
genomic: TGCATCGGCTTCTCCACTGACGCCCTCCGCCTCGTCGCCCGCTCGTGCAGgtaacccagg ... atgtcaacagATCCCTGAGAACTTTATTTCTGGAAGAGTGCCATATTACTGATAAGGGTGG
EST: gi|58664778|gb|CK053464.1|CK053464
EST:     TGCATCGGCTTCTCCACTGACGCCCTCCGCCTCGTCGCCCGCTCGTGCAG                         ATCCCTGAGAACTTTATTTCTGGAAGAGTGC-ATATTACTGATAAGGGTGG
genomic: TGCATCGGCTTCTCCACTGACGCCCTCCGCCTCGTCGCCCGCTCGTGCAGgtaacccagg ... atgtcaacagATCCCTGAGAACTTTATTTCTGGAAGAGTGCCATATTACTGATAAGGGTGG
EST: gi|11442919|gb|BF430818.1|BF430818
EST:     TGCATCGGCTTCTCCACTGACGCCCTCCGCCTCGTCGCCCGCTCGTGCAG                         ATCCCTGAGAACTTTATTTCTGGAAGAGTGCCATATTACTGATAAGGGTGG
genomic: TGCATCGGCTTCTCCACTGACGCCCTCCGCCTCGTCGCCCGCTCGTGCAGgtaacccagg ... atgtcaacagATCCCTGAGAACTTTATTTCTGGAAGAGTGCCATATTACTGATAAGGGTGG
EST: gi|29674615|gb|CB670890.1|CB670890
EST:     TGCATCGGCTTCTCCACTGACGCCCTCCGCCTCGTCGCCCGCTCGTGCAG                         ATCCCTGAGAACTTTATTTCTGGAAGAGTGCCATATTACTGATAAGGGTGG
genomic: TGCATCGGCTTCTCCACTGACGCCCTCCGCCTCGTCGCCCGCTCGTGCAGgtaacccagg ... atgtcaacagATCCCTGAGAACTTTATTTCTGGAAGAGTGCCATATTACTGATAAGGGTGG

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), 71 (downstream exon)
Score: 35

CCCTTGTCCGCGCCCGCGGACACATGCTGCAGGAGCTCAAGCTCGACAAGTGCATCGGCTTCTCCACTGACGCCCTCCGCCTCGTCGCCCGCTCGTGCAGgtaacccagg ... atgtcaacagATCCCTGAGAACTTTATTTCTGGAAGAGTGCCATATTACTGATAAGGGTGGTGAATGGCTTCATGAACTTGCTGTCAACAATTCTGTTCTGGTGACACTG




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