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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...caatatggatccccactatttttttaagtatgtcaacattatttgctttctcatataagttgaggaggtcgtactgaagtgtgctgaattctctccacagGTGAATGGAGTGGCTGAGTTACACAGCAACATTTTGAAGGAAGAGCTTTTTGCAGACTATCTCTCTATATGGCCCAACAAATTTCAGAACAAAACAAATG

Basic information

species Oryza sativa
transcript LOC_Os01g63270.1
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g63270.1 (Oryza sativa), 3'ss of exon 9
lower sequence: GRMZM2G085577_T01 (Zea mays), 3'ss of exon 9
----caatatggatccccactattt-ttttaagtatgtcaacattatttgctttctcatataagttgaggaggtcgtactgaagtgtgctgaattctctcc-acagGTGAATGGAGTGGCTGAGTTACACAGCAACATTTTGAAGGAAGAGCTTTTTGCAGACTATCTCTCTATATGGCCCAACAAATTTCAGAACAAAACAAATG
       |  | ||  |  | || |  |  |||||  ||   ||| |    |||||  |   |  | |       || |||||| ||  | ||   | ||  |||||||||||||||||||||||| || ||||||||||||||| |||| || |||||||| ||| ||||||||||||| | |||||| || |||||||| ||||
gaaattgttggcataacttcaatgtactccaagtagttctggattctccattttctactgctatatta------tgtcctgaagcgtattcaaaattttctgacagGTGAATGGAGTGGCTGAGTTGCATAGCAACATTTTGAAGCAAGAACTATTTGCAGATTATGTCTCTATATGGCCTACCAAATTCCAAAACAAAACTAATG

upper sequence: LOC_Os01g63270.1 (Oryza sativa), 3'ss of exon 9
lower sequence: AT3G46970.1 (Arabidopsis thaliana), 3'ss of exon 10
caatatggatccccactatttttttaagtatgtcaacattatttgctttctcatataagttgaggaggtcgtactgaagtgtgctgaattctctccacagGTGAATGGAGTGGCTGAGTTACACAGCAACATTTTGAAGGAAGAGCTTTTTGCAGACTATCTCTCTATATGGCCCAACAAATTTCAGAACAAAACAAATG
   || |    |||||| |      |  ||||| |  ||| |||   ||| ||| ||   |  |      ||||| |    |        || |   ||||||||||| || ||| ||||||||||  | || |||||||  ||| | || ||||||||| ||||||||||||| ||||| ||||| ||||| || ||||
--gtaagtggtcccactgtcaa---agttatgtta-tattgttt--cttcccatgtagtcttggtttcaagtactcat---tatgagggcctttttgcagGTGAATGGCGTTGCTCAGTTACACAGTGATATCTTGAAGGCTGAGTTATTCGCAGACTATGTCTCTATATGGCCAAACAAGTTTCAAAACAAGACTAATG

upper sequence: LOC_Os01g63270.1 (Oryza sativa), 3'ss of exon 9
lower sequence: Vv06s0004g06020.t01 (Vitis vinifera), 3'ss of exon 9
--------caatatggatccccactatttttttaagtatgtcaacattatttgctttctcatataagttgaggaggtcgtactgaagtgtgctgaattctctc-cacagGTGAATGGAGTGGCTGAGTTACACAGCAACATTTTGAAGGAAGAGCTTTTTGCAGACTATCTCTCTATATGGCCCAACAAATTTCAGAACAAAACAAATG
            ||   || |  |   | || |   | ||||  |||| |||  || | | || || ||    | |        || | |   ||   | ||    ||||| ||||| || ||| ||||||||||  | ||||| || |  ||| | |||||||||||| ||||||||||||||| ||| || ||||| ||||| ||||
tttcttcctttaatttctctcttcctctcttctctctctgtctccatttttt--ttgcacgtacaaatttgaaaagc-------aactttctcgaccacccttgtgcagGTAAATGGTGTTGCTCAGTTACACAGTGATATTTTAAAAGCCGAGTTATTTGCAGACTATGTCTCTATATGGCCCACCAAGTTCCAGAATAAAACCAATG

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|29623807|gb|CB628818.1|CB628818
EST:     AGAAGCCAGTAGTGCGCATGGCAAATTTGTGCGTAGTGTCTGCCCATACG                         GTGAATGGAGTGGCTGAGTTACACAGCAACATTTTGAAGGAAGAGCTTTTT
genomic: AGAAGCCAGTAGTGCGCATGGCAAATTTGTGCGTAGTGTCTGCCCATACGgtaagtgcag ... ctctccacagGTGAATGGAGTGGCTGAGTTACACAGCAACATTTTGAAGGAAGAGCTTTTT
EST: gi|29635801|gb|CB640810.1|CB640810
EST:     AGAAGCCAGTAGTGCGCATGGCAAATTTGTGCGTAGTGTCTGCCCATACG                         GTGAATGGAGTGGCTGAGTT-CACAGCAACATTTTGAAGGAAGAGCTTTTT
genomic: AGAAGCCAGTAGTGCGCATGGCAAATTTGTGCGTAGTGTCTGCCCATACGgtaagtgcag ... ctctccacagGTGAATGGAGTGGCTGAGTTACACAGCAACATTTTGAAGGAAGAGCTTTTT
EST: gi|58610009|gb|CK038042.1|CK038042
EST:     AGAAGCCAGTAGTGCGCATGGCAAATTTGTGCGTAGTGTCTGCCCATACG                         GTGAATGGAGTGGCTGAGTTACACAGCAACATTTTGAAGGAAGAGCTTTTT
genomic: AGAAGCCAGTAGTGCGCATGGCAAATTTGTGCGTAGTGTCTGCCCATACGgtaagtgcag ... ctctccacagGTGAATGGAGTGGCTGAGTTACACAGCAACATTTTGAAGGAAGAGCTTTTT
EST: gi|58688682|gb|CK077369.1|CK077369
EST:     AGAAGCCAGTAGTGCGCATGGCAAATTTGTGCGTAGTGTCTGCCCATACG                         GTGAATGGAGTGGCTGAGTTACACAGCAACATTTTGAAGGAAGAGCTTTTT
genomic: AGAAGCCAGTAGTGCGCATGGCAAATTTGTGCGTAGTGTCTGCCCATACGgtaagtgcag ... ctctccacagGTGAATGGAGTGGCTGAGTTACACAGCAACATTTTGAAGGAAGAGCTTTTT
EST: gi|29623647|gb|CB628658.1|CB628658
EST:     AGAAGCCAGTAGTGCGCATGGCAAATTTGTGCGTAGTGTCTGCCCATACG                         GTGAATGGAGTGGCTGAGTTACACAGCAACATTTTGAAGGAAGAGCTTTTT
genomic: AGAAGCCAGTAGTGCGCATGGCAAATTTGTGCGTAGTGTCTGCCCATACGgtaagtgcag ... ctctccacagGTGAATGGAGTGGCTGAGTTACACAGCAACATTTTGAAGGAAGAGCTTTTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctttctcatataagttgaggaggtcgtactgaagtgtgctgaattctctccacagGTGAATGGAGTGGCTGAGTTACACAGCAACATTTTGAAGGAAGAGCTTTTTGCAGACTATCTCTCTATATGGCCCAACAAATTTCAGAACAAAACAAATG
                                           ttctctccac  CT-rich tract
       atataagtt  TA-rich tract