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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cctccaatatatatttcttctaacagcaatttcttcatgctcaatgctaagattacatgctatctctgcagtaacatgtcattctaaattatgtcaacagATCCCTGAGAACTTTATTTCTGGAAGAGTGCCATATTACTGATAAGGGTGGTGAATGGCTTCATGAACTTGCTGTCAACAATTCTGTTCTGGTGACACTG

Basic information

species Oryza sativa
transcript LOC_Os01g63420.2
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g63420.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G035314_T01 (Zea mays), 3'ss of exon 2
---------------------------------------------------cctccaatatatatttcttctaacagcaatttc---ttcatgctcaatgctaagattacatgctatct---------ctgcagtaacatgtcattctaaattatgtcaacagATCCCTGAGAACTTTATTTCTGGAAGAGTGCCATATTACTGATAAGGGTGGTGAATGGCTTCATGAACTTGCTGTCAACAATTCTGTTCTGGTGACACTG
                                                    || ||  ||||         ||||    |||    ||| ||  |    || ||      |   ||           |  ||||||||||  |   ||||| || |  ||||||| ||||||||||| || |||||||| ||    ||| | ||| | ||  | |||||||| |||||||| || |||||||||||||||||||||||||||
gtcttttttttaatgtgttatttactgatgcacagtgaatttatcattctaactgcatgatatcacgacagaaacatgtgttttgttttcgtggacgcgacttagcacgtctttcattaagaggagaacaacagtaacatgcta---taaatcatcttgacagATCTCTGAGAACTTTGTTCCTGGAAGAATGTATAATTGCCGATGAAGGGAGCGAATGGCTCCATGAACTCGCCGTCAACAATTCTGTTCTGGTGACACTG

upper sequence: LOC_Os01g63420.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G125411_T01 (Zea mays), 3'ss of exon 1
--cctccaatatatatttcttcta-acagcaatttcttcatgctcaatgctaagattacatgctatctctgcagtaacatgtcattctaaattatgtcaacagATCCCTGAGAACTTTATTTCTGGAAGAGTGCCATATTACTGATAAGGGTGGTGAATGGCTTCATGAACTTGCTGTCAACAATTCTGTTCTGGTGACACTG
       |  || || |  |  |  ||||  | ||  |||| ||   ||||  |  | |||| |||| |  ||||||| |||||   |||||  | |  |||| || |||||||| || || |||||||| ||    |||   ||| | ||  |||||||||| |||||||| ||||||||||||||||||||||||||||||
tttacgtatcatttactgatgatgcacagtgaatttatcattctagttgctttggctgcatgatatcacaacagtaacttgtca---taaatcgtcttgacagGTCTCTGAGAACCTTGTTCCTGGAAGAATGTATAATTGAGGATGAAGGGAGTGAATGGCTCCATGAACTCGCTGTCAACAATTCTGTTCTGGTGACACTG
















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|29674615|gb|CB670890.1|CB670890
EST:     TGCATCGGCTTCTCCACTGACGCCCTCCGCCTCGTCGCCCGCTCGTGCAG                         ATCCCTGAGAACTTTATTTCTGGAAGAGTGCCATATTACTGATAAGGGTGG
genomic: TGCATCGGCTTCTCCACTGACGCCCTCCGCCTCGTCGCCCGCTCGTGCAGgtaacccagg ... atgtcaacagATCCCTGAGAACTTTATTTCTGGAAGAGTGCCATATTACTGATAAGGGTGG
EST: gi|11442919|gb|BF430818.1|BF430818
EST:     TGCATCGGCTTCTCCACTGACGCCCTCCGCCTCGTCGCCCGCTCGTGCAG                         ATCCCTGAGAACTTTATTTCTGGAAGAGTGCCATATTACTGATAAGGGTGG
genomic: TGCATCGGCTTCTCCACTGACGCCCTCCGCCTCGTCGCCCGCTCGTGCAGgtaacccagg ... atgtcaacagATCCCTGAGAACTTTATTTCTGGAAGAGTGCCATATTACTGATAAGGGTGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gctaagattacatgctatctctgcagtaacatgtcattctaaattatgtcaacagATCCCTGAGAACTTTATTTCTGGAAGAGTGCCATATTACTGATAAGGGTGGTGAATGGCTTCATGAACTTGCTGTCAACAATTCTGTTCTGGTGACACTG
                                    ttctaaa  putative branch site (score: 2)
                                 tcattctaaattat  TA-rich tract