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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tatgagcactctatacttcctctcactctatacttcattaagttctgcttacaaacactgaaaatagggctgaacatctggcaatgaccactatttgcagGAATGGAGCTACCTCCGCGGTGGCCTGACAACGGTGGATCGGGACTACGGGTGGATCAACAACATCCACCATGACATTGGCACCCATGTCATCCACCACC

Basic information

species Oryza sativa
transcript LOC_Os11g01340.2
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os11g01340.2 (Oryza sativa), 3'ss of exon 6
lower sequence: GLYMA11G27190.1 (Glycine max), 3'ss of exon 6
tatgagcactctatacttcctctca-ctctatacttcatt--aagttctgcttacaaacactgaaaatagggctgaa-catctggcaatgaccac-ta--tttgcagGAATGGAGCTACCTCCGCGGTGGCCTGACAACGGTGGATCGGGACTACGGGTGGATCAACAACATCCACCATGACATTGGCACCCATGTCATCCACCACC
       | | |    |||   | | |   ||||||   |  || || ||| | |   ||  ||||| |  |      ||| |  |  || | |  ||  ||  ||||||||||  || ||  | ||||| || ||||| || ||||| ||||| || |||||||||||||| ||||||||||||||||||||||||||||| ||||
-------attgttagtttcaaataaacaacatacttatgtgcaaattttgccttccttcaaagaaaagatagaaacttcatgttactctgtctatgtaatttcacagGAATGGACTTATCTAAGGGGTGGTCTTACAACCGTAGATCGTGACTATGGTTGGATCAACAACATTCACCATGACATTGGCACCCATGTCATCCATCACC

upper sequence: LOC_Os11g01340.2 (Oryza sativa), 3'ss of exon 6
lower sequence: GLYMA18G06950.1 (Glycine max), 3'ss of exon 6
-tatgagcactctatacttcctctcactctatacttcattaagttctgcttacaaacactgaaaatagggctgaaca--tctggcaatgaccactatttgcagGAATGGAGCTACCTCCGCGGTGGCCTGACAACGGTGGATCGGGACTACGGGTGGATCAACAACATCCACCATGACATTGGCACCCATGTCATCCACCACC
   |     |   |||   | | |   | |  | ||  |    | || |  |  || |  |||| |    |        |||| | ||    | | ||  ||||||||||| || ||  | ||||| || ||||| || ||||| ||||| || |||||||||||||| ||||||||||||||||||||||| ||||| ||| 
tggtagtttcaacataaaacatatttatgtgcagttt-tgccatccttcaaaagaagatagaaacttactccatgttactctgtctatatgtaat-ttcacaGGAATGGAGTTATCTAAGGGGTGGTCTTACAACAGTAGATCGCGACTATGGTTGGATCAACAACATTCACCATGACATTGGCACCCATGTTATCCATCAC-

upper sequence: LOC_Os11g01340.2 (Oryza sativa), 3'ss of exon 6
lower sequence: GLYMA02G39230.1 (Glycine max), 3'ss of exon 6
tatgagcactctatacttcctct-cactctatacttcattaagttctgcttacaaacactgaaaatagggctgaacatctggcaatgaccactatttgcagGAATGGAGCTACCTCCGCGGTGGCCTGACAACGGTGGATCGGGACTACGGGTGGATCAACAACATCCACCATGACATTGGCACCCATGTCATCCACCACC
||      ||| | |       |    |   |        | ||  ||| |       |    ||||   | |    | ||      || |  ||   ||||||||||| ||  |  | |||||||| || || |||||||| ||||| || |||||||| ||||| ||||||||||||||||||||||| |||||||| |
taccttacctcaacaaagaaagtgtggtaagtggcaacacacgtgttgcatttttggcccagcaataacac-gtgtttttgtggtgtactaaaatggacagGAATGGAGTTATTTAAGAGGTGGCCTCACCACTGTGGATCGTGACTATGGTTGGATCAATAACATTCACCATGACATTGGCACCCATGTTATCCACCATC

upper sequence: LOC_Os11g01340.2 (Oryza sativa), 3'ss of exon 6
lower sequence: GLYMA14G37350.2 (Glycine max), 3'ss of exon 6
--tatgagcactctatacttcctctcactctatacttcattaagttctgcttacaaacactgaaaatagggctgaacatctggcaatgaccactatttgcagGAATGGAGCTACCTCCGCGGTGGCCTGACAACGGTGGATCGGGACTACGGGTGGATCAACAACATCCACCATGACATTGGCACCCATGTCATCCACCACC
    | | | |   | |     | | |       |  ||  | ||  |||||       |    ||||   | |    | ||      || |  ||   ||||||||||| ||  |  | ||||| || ||||| |||||||| ||||| || |||||||| ||||| ||||||||||||||||||||||| || ||||| |
aaccttacctcaacaaagaaagtgtgataagtggcaacac-acgtgttgcttttttggcccagcaataacac-gtgtttttgtggtgtacaaaaatggacagGAATGGAGTTATTTAAGAGGTGGTCTCACAACTGTGGATCGTGACTATGGTTGGATCAATAACATTCACCATGACATTGGCACCCATGTTATTCACCATC

upper sequence: LOC_Os11g01340.2 (Oryza sativa), 3'ss of exon 6
lower sequence: Vv06s0004g06730.t01 (Vitis vinifera), 3'ss of exon 7
---------------------------------------------------------------------------tatgagcactctatacttcc----tctcactctatacttcattaagttctgcttacaa-acactgaaaatagggctgaacatctggcaatgaccactatttgcagGAATGGAGCTACCTCCGCGGTGGCCTGACAACGGTGGATCGGGACTACGGGTGGATCAACAACATCCACCATGACATTGGCACCCATGTCATCCACCACC
                                                                           |   | ||   || | |||     ||  ||  |       | ||  || |   || ||   |  ||   ||  |||  |  | |    |||           |||||||||||||| || || || || || |||||||| ||||| ||||| || ||| | |||||||||||||||||||||||||||||||| || || || |
gtactgataaacaaagatatggtcagaacactaatttgagttcttggattcttaacttgatggttagctgcagcctgcaaccaaaatagatttcaggggtccaaccttgctgagaagtacattttatgtagaatggatagagcctaatgctttagttgtcattatgttggtatggaacagGAATGGAGCTATCTACGAGGAGGGCTAACAACGGTTGATCGTGACTATGGCTGGTTTAACAACATCCACCATGACATTGGCACCCATGTTATACATCATC

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|427623|gb|D23756.1|D23756
EST:     CTTATCTGCACCACCACGGTCACAATGACCTTCCCTGGTATCGTGGAGAG                         GAATGGAGCTACCTCCGCGGTGGCCTGACAACGGTGGATCGGGACTACGGG
genomic: CTTATCTGCACCACCACGGTCACAATGACCTTCCCTGGTATCGTGGAGAGgtatatcttt ... ctatttgcagGAATGGAGCTACCTCCGCGGTGGCCTGACAACGGTGGATCGGGACTACGGG






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgcttacaaacactgaaaatagggctgaacatctggcaatgaccactatttgcagGAATGGAGCTACCTCCGCGGTGGCCTGACAACGGTGGATCGGGACTACGGGTGGATCAACAACATCCACCATGACATTGGCACCCATGTCATCCACCACC
 tgcttac  putative branch site (score: 2)
             tgaaaata  TA-rich tract