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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagtgtttttcatcaagcaaaatttggattcgatcgatctgtcgctttggatctctgtgtgtgtgagtgggggatggatagtaatgtggatcgatgtgcgttttggggtgggggttggaattctgcagGGAAGTCGACGCTCACTGACTCGCTGGTGGCGGCGGCCGGCATCATCGCGCAGGACGTGGCCGGCGACGTGCGGATGACGGACACGCGCGCGGACGAGGC

Basic information

species Oryza sativa
transcript LOC_Os01g52470.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g52470.1 (Oryza sativa), 3'ss of exon 2
lower sequence: EDO96511 (Chlamydomonas reinhardtii), 3'ss of exon 2
gtgagtgtttttcatcaagcaaaatttggattcgatcgatctgtcgctttggatctctgtgtgtgtgagtgggggatggatagtaatgtggatcgatgtgcgttt-tggggtgggggttggaattctgcagGGAAGTCGACGCTCACTGACTCGCTGGTGGCGGCGGCCGGCATCATCGCGCAGGACGTGGCCGGCGACGTGCGGATGACGGACACGCGCGCGGACGAGGC
                                                                || ||          ||  | | |  | | |   |||| |    ||| | |    |    | |||||| |||||||| ||||| |||||||||||||| |||||||| ||||| || |     |  |                                        
----------------------------------------------------------------gtaagctcctctgctatgctcaagatgcttggactgcgctaactgggcgtgtcgcgctgatgtgcagGCAAGTCGACCCTCACCGACTCGCTGGTGGCTGCGGCCGGTATCATGGC-CGTCGAGCAG----------------------------------------

upper sequence: LOC_Os01g52470.1 (Oryza sativa), 3'ss of exon 2
lower sequence: PP1S431_6V6.3 (Physcomitrella patens), 3'ss of exon 2
gtgagtgtttttcatcaagcaaaatttggattcgatcgatctgtcgctttggatctctgtgtgtgtgagtgggggatggatagtaatgtggatcgatgtgcgttttgggg-tggg-ggttggaattctgcagGGAAGTCGACGCTCACTGACTCGCTGGTGGCGGCGGCCGGCATCATCGCGCAGGACGTGGCCGGCGACGTGCGGATGACGGACACGCGCGCGGACGAGGC-----------------------------------------------------
                                                                                     || || |   ||| |  |  ||||| || | ||| |||||   |||||||||||||| || || || ||||||||||| || || || || |||||||||||   |||||| || |||||  |||||||||| ||   ||| |||||                                                     
------------------------------------------------------------------------------------catatg-acgcatgagtttaatgggggtgagtggtgggaatgtggcagggaagtcgacactgacggattcgctggtggctgctgcggggattatcgcgcagGAGACGGCCGGAGATGTGCGTCTGACGGACACCCGGCAGGATGAGGCGGATCGTGGTATTACGATCAAGTCGACCGGTATCTCGTTGTACTACGAGATGA

upper sequence: LOC_Os01g52470.1 (Oryza sativa), 3'ss of exon 2
lower sequence: PP1S3495_1V6.1 (Physcomitrella patens), 3'ss of exon 2
gtgagtgtttttcatcaagcaaaatttggattcgatcgatctgtcgctttggatctctgtgtgtgtgagtgggggatggatagtaatgtggatcgatgtgcgtttt---ggggtgggggttggaattctg-cagGGAAGTCGACGCTCACTGACTCGCTGGTGGCGGCGGCCGGCATCATCGCGCAGGACGTGGCCGGCGACGTGCGGATGACGGACACGCGCGCGGACGAGGC
                               |  |   | || |  | | |    ||     |  | | |  |   |||| |   || |    |||   | | ||    |||||| | | ||||| | || ||||||||||||| || || || ||||||||||| || || || || |||||||||||   |||||| || |||||  |||||||||| ||   ||| |||||
-------------------------------ttaactcagctctttcctcgaccatcccgacg-attactatgaactggaca--catttcttccgagccgggattaatgggggtgagtggtggaaatgtggcagGGAAGTCGACACTGACGGATTCGCTGGTGGCTGCTGCGGGGATTATCGCGCAGGAGACGGCCGGAGATGTGCGTCTGACGGACACCCGGCAGGATGAGGC

upper sequence: LOC_Os01g52470.1 (Oryza sativa), 3'ss of exon 2
lower sequence: PP1S431_2V6.1 (Physcomitrella patens), 3'ss of exon 2
gtgagtgtttttcatcaagcaaaatttggattcgatcgatctg---tcgctttggatctctgtgtgtgtgagtgggggatggatagtaatgtggatcgatgtgcgttttggggtgggggttggaattctg-cagGGAAGTCGACGCTCACTGACTCGCTGGTGGCGGCGGCCGGCATCATCGCGCAGGACGTGGCCGGCGACGTGCGGATGACGGACACGCGCGCGGACGAGGC
                             ||  || | | |||   | ||     || |  |    | ||| ||      |  |   ||  ||  | |||    |    |||||| | | ||||| | || ||||||||||||| || || || ||||||||||| || || || || |||||||||||   |||||| || |||||  |||||||||| ||   ||| |||||
-----------------------------atctgaacaaactgaattagcaaaacatttgaggaaatctga-tgataacagagtcaaaacatgcctagattaatg----ggggtgagtggtggaaatgtggcagGGAAGTCGACACTGACGGATTCGCTGGTGGCTGCTGCGGGGATTATCGCGCAGGAGACGGCCGGAGATGTGCGTCTGACGGACACCCGGCAGGATGAGGC

upper sequence: LOC_Os01g52470.1 (Oryza sativa), 3'ss of exon 2
lower sequence: PP1S431_6V6.1 (Physcomitrella patens), 3'ss of exon 2
gtgagtgtttttcatcaagcaaaatttggattcgatcgatctgtcgctttggatctctgtgtgtgtgagtgggggatggatagtaatgtggatcgatgtgcgttttgggg-tggg-ggttggaattctgcagGGAAGTCGACGCTCACTGACTCGCTGGTGGCGGCGGCCGGCATCATCGCGCAGGACGTGGCCGGCGACGTGCGGATGACGGACACGCGCGCGGACGAGGC
                            ||  ||   |        ||||     | | ||   |  |           | |   || || |   ||| |  |  ||||| || | ||| |||||   |||||||||||||| || || || ||||||||||| || || || || |||||||||||   |||||| || |||||  |||||||||| ||   ||| |||||
---------------------------agacacgtgagcgggaagacttta---ttttatg-acgacaacaaaattcaaacaaacatatg-acgcatgagtttaatgggggtgagtggtgggaatgtggcagGGAAGTCGACACTGACGGATTCGCTGGTGGCTGCTGCGGGGATTATCGCGCAGGAGACGGCCGGAGATGTGCGTCTGACGGACACCCGGCAGGATGAGGC

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|88400823|gb|CI616828.1|CI616828
EST:     TAAGAAGGACAACATCCGGAACATGTCTGTGATCGCGCACGTTGATCATG                         GGAAGTCGACGCTCACTGACTCGCTGGTGGCGGCGGCCGGCATCATCGCGC
genomic: TAAGAAGGACAACATCCGGAACATGTCTGTGATCGCGCACGTTGATCATGgtgagtgttt ... aattctgcagGGAAGTCGACGCTCACTGACTCGCTGGTGGCGGCGGCCGGCATCATCGCGC






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atggatagtaatgtggatcgatgtgcgttttggggtgggggttggaattctgcagGGAAGTCGACGCTCACTGACTCGCTGGTGGCGGCGGCCGGCATCATCGCGCAGGACGTGGCCGGCGACGTGCGGATGACGGACACGCGCGCGGACGAGGC
     tagtaat  TA-rich tract