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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aaatctagtccttttaataccacggtttatgctgatttcttaagtattatatcattcaagtcacctctacttaccttttctctgtctttcctcacatcagGTTTCTGCAGCTCGAGAGGAAGTACCTGGACGGCGTGGTTATCCTGGTTATATGTATACTGATTTGGCAACTATCTATGAGCGTGCTGGTCGCATAGAAG

Basic information

species Oryza sativa
transcript LOC_Os01g51380.1
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g51380.2 (Oryza sativa), 3'ss of exon 9
lower sequence: PP1S85_75V6.1 (Physcomitrella patens), 3'ss of exon 8
-----------------------------------------------------------------------aaat-ctagtccttttaataccacggtt-tatgctgatttcttaagtattatatcatt--caagtcacctctacttaccttttctctgtctttcctcac-atcagGTTTCTGCAGCTCGAGAGGAAGTACCTGGACGGCGTGGTTATCCTGGTTATATGTATACTGATTTGGCAACTATCTATGAGCGTGCTGGTCGCATAGAAG
                                                                       ||||  ||||  | | || |   |   | |||  || |   |  |    |  | | ||   | | ||     || ||   ||    |   |  |    | | ||||||||||||||||| || ||||||||||| || ||||| ||||||||||| ||||| || ||| | || ||||| || || |||||||| || || || |
gtaccagtctttaccttaaagatctgcttgcccttgtggtatggtacttctgactctgtttttggtttttgaaatgttagtgttctaaaaaatgcccctctattttgttggttctaagtctgcacctttagtatgccagaatgacatattcttatgatccttaactatgcgaacagGTTTCTGCAGCTCGTGAAGAAGTACCTGGGCGTCGTGGATATCCTGGTTACATGTACACGGATCTTGCCACTATTTACGAACGTGCTGGGCGAATTGAGG

upper sequence: LOC_Os01g51380.2 (Oryza sativa), 3'ss of exon 9
lower sequence: PP1S425_12V6.1 (Physcomitrella patens), 3'ss of exon 8
---------------------------------------------------------------------------------------------aaatctagtccttt--taataccacggtttatgctgatttcttaagtattatatcattcaagtcacctctacttaccttttctctgtctttcctcacatcagGTTTCTGCAGCTCGAGAGGAAGTACCTGGACGGCGTGGTTATCCTGGTTATATGTATACTGATTTGGCAACTATCTATGAGCGTGCTGGTCGCATAGAAG
                                                                                               |  ||||  ||    ||        | |||     ||  ||    ||||   | ||||     |  | | ||   ||| | || ||  | ||   |  |||||||||| ||||| || ||||| ||||| || ||||| ||||||||||| |||||||||||| |||| || || ||||| |||||||| || || ||||
gtacaagtgtttctcttaaagacttttcgcttggactcctttttcagaagttagctcctgtgaaattctacatgctactccgcagttggtatctgaaatagtttttaagcaaatttgtaatctat-tcagttggtttttaattaagaccttcagtgtgctacaaatt--ttttccactctcaattcttcaaatagGTTTCTGCTGCTCGTGAAGAAGTGCCTGGGCGTCGTGGATATCCTGGTTACATGTATACTGATCTGGCCACCATTTATGAACGTGCTGGACGAATCGAAG

upper sequence: LOC_Os01g51380.2 (Oryza sativa), 3'ss of exon 9
lower sequence: EFJ11911 (Selaginella moellendorffii), 3'ss of exon 8
aaatctagtccttttaataccacggtttatgctgatttcttaagtattatatcattcaagtcacctctacttaccttttctctgtctttcctcacatcagGTTTCTGCAGCTCGAGAGGAAGTACCTGGACGGCGTGGTTATCCTGGTTATATGTATACTGATTTGGCAACTATCTATGAGCGTGCTGGTCGCATAGAAG
                                           ||||  |||  |||||||    ||     | || |  |        | |    | |||| ||||| ||||| ||||| || ||||| || ||||| |||||||||||||||||||| ||||||||||| || || ||||||||||| || || ||||
-------------------------------------------gtatggtatgtttcaagtt-tgtcatgagagctatgataaccagggctttgtgt-agGTGTCTGCCGCTCGTGAGGAGGTGCCTGGTCGTCGTGGATATCCTGGTTATATGTATACAGATTTGGCAACAATTTACGAGCGTGCTGGACGAATTGAAG

upper sequence: LOC_Os01g51380.2 (Oryza sativa), 3'ss of exon 9
lower sequence: EFJ13375 (Selaginella moellendorffii), 3'ss of exon 8
aaatctagtccttttaataccacggtttatgctgatttcttaagtattatatcattcaagtcacctctacttaccttttctctgtctttcctcacatcagGTTTCTGCAGCTCGAGAGGAAGTACCTGGACGGCGTGGTTATCCTGGTTATATGTATACTGATTTGGCAACTATCTATGAGCGTGCTGGTCGCATAGAAG
                                |    || || || | |  |  |||| |  |  | |  | ||| |  || ||| |           |||| ||||| ||||| ||||| || ||||| || ||||| |||||||||||||||||||| ||||||||||| || || ||||||||||| || || ||||
-------------------------------gtatgatcgtatgtttcaagtttttcatgagagttatgataaccatggctttgtgt-----------agGTGTCTGCCGCTCGTGAGGAGGTGCCTGGTCGTCGTGGATATCCTGGTTATATGTATACAGATTTGGCAACAATTTACGAGCGTGCTGGACGAATTGAAG

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|33811101|gb|CF331441.1|CF331441
EST:     TTCTTGTCATCCTGACTGACATGAGCTCATATGCCGATGCACTTCTTGAA                         GTTTCTGCAGCTCGAGAGGAAGTACCTGGACGGCGTGGTTATCCTGGTTAT
genomic: TTCTTGTCATCCTGACTGACATGAGCTCATATGCCGATGCACTTCGTGAAgtaagggcct ... ctcacatcagGTTTCTGCAGCTCGAGAGGAAGTACCTGGACGGCGTGGTTATCCTGGTTAT






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attatatcattcaagtcacctctacttaccttttctctgtctttcctcacatcagGTTTCTGCAGCTCGAGAGGAAGTACCTGGACGGCGTGGTTATCCTGGTTATATGTATACTGATTTGGCAACTATCTATGAGCGTGCTGGTCGCATAGAAG
               tcacctctacttacct  CT-rich tract