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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtacactcacattttttttctctcatctccatcttgttggttaaactgaacgcaatgccaaaaatattttcagGTCCTAGAGAGGTGTTCATGTGCGGAATCGCGCAGTACGTCAACCTGTGGGGCACCATGGTCGGCTACACAATCACCGCAACCATAAGCATGGT

Basic information

species Oryza sativa
transcript LOC_Os01g65660.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g65660.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G096407_T01 (Zea mays), 3'ss of exon 2
--------gtaagtacact-cacattttttttctctcatctccatcttgttggttaaactgaacgcaatgccaaaaatat----------tttcagGTCCTAGAGAGGTGTTCATGTGCGGAATCGCGCAGTACGTCAACCTGTGGGGCACCATGGTCGGCTACACAATCACCGCAACCATAAGCATGGT
             ||| |  | ||    |   |   | ||    || | || | ||| |||| |||  ||||   || ||          |  ||||||| || |||||||||||||||||  ||||||||||||| ||||||||||||||||||||||| ||||| ||||| || ||||||||||||| 
gtacgcctacgcctacgcgacgcacggctccacgtccgtccgtctcgtcttagctaa-ctgaccgcggtgccctgaacatgcgtacgtcgtcgcagGTCCCAGGGAGGTGTTCATGTGCGGGGTCGCGCAGTACGTGAACCTGTGGGGCACCATGGTCGGGTACACCATCACGGCGACCATAAGCATGGC

upper sequence: LOC_Os01g65660.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM5G830545_T02 (Zea mays), 3'ss of exon 2
----------gtaagtacactca-cattttttttctctcatctccat-----cttgttggttaaactgaacgcaatgccaaaa-atatttt-cagGTCCTAGAGAGGTGTTCATGTGCGGAATCGCGCAGTACGTCAACCTGTGGGGCACCATGGTCGGCTACACAATCACCGCAACCATAAGCATGGT------
            | | || | |  ||| | |  ||||    |  ||      |  ||  ||     | |||  |||||| ||| |    |  ||||||| || ||||||||||||||||| |||||||||||||| |||||||||||||||||||| || ||||| ||||| || |||||||||||||       
gtacgcgccgccacgcacccccgtcatctctcctctcgacacggcacagctccacgtccgtctcgtttaactgaatgcctaaacacgcatcgcagGTCCCAGGGAGGTGTTCATGTGCGGGATCGCGCAGTACGTGAACCTGTGGGGCACCATGGTTGGGTACACCATCACGGCGACCATAAGCATGGCGTAAGT

upper sequence: LOC_Os01g65660.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM5G830545_T03 (Zea mays), 3'ss of exon 2
----------gtaagtacactca-cattttttttctctcatctccat-----cttgttggttaaactgaacgcaatgccaaaa-atatttt-cagGTCCTAGAGAGGTGTTCATGTGCGGAATCGCGCAGTACGTCAACCTGTGGGGCACCATGGTCGGCTACACAATCACCGCAACCATAAGCATGGT
            | | || | |  ||| | |  ||||    |  ||      |  ||  ||     | |||  |||||| ||| |    |  ||||||| || ||||||||||||||||| |||||||||||||| |||||||||||||||||||| || ||||| ||||| || ||||||||||||| 
gtacgcgccgccacgcacccccgtcatctctcctctcgacacggcacagctccacgtccgtctcgtttaactgaatgcctaaacacgcatcgcagGTCCCAGGGAGGTGTTCATGTGCGGGATCGCGCAGTACGTGAACCTGTGGGGCACCATGGTTGGGTACACCATCACGGCGACCATAAGCATGGC

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|29641020|gb|CB646027.1|CB646027
EST:     CACCGGCACCAGGAACCGCACATACATGGACGCCGTCAGATCATACCTCA                         GTCCTAGAGAGGTGTTCATGTGCGGAATCGCGCAGTACGTCAACCTGTGGG
genomic: CACCGGCACCAGGAACCGCACATACATGGACGCCGTCAGATCATACCTCAgtaagtacac ... atattttcagGTCCTAGAGAGGTGTTCATGTGCGGAATCGCGCAGTACGTCAACCTGTGGG
EST: gi|88423122|gb|CI613423.1|CI613423
EST:     CACCGGCACCAGGAACCGCACATACATGGACGCCGTCAGATCATACCTCA                         GTC-TAGAGAGGTGTTCATGTGCGGAATCGCGCAGTACG
genomic: CACCGGCACCAGGAACCGCACATACATGGACGCCGTCAGATCATACCTCAgtaagtacac ... atattttcagGTCCTAGAGAGGTGTTCATGTGCGGAATCGCGCAGTACG
EST: gi|29641091|gb|CB646098.1|CB646098
EST:     CACCGGCACCAGGAACCGCACATACATGGACGCCGTCAGATCATACCTCA                         GTCCTAGAGAGGTGTTCATGTGCGGAATCGCGCAGTACGTCAACCTGTGGG
genomic: CACCGGCACCAGGAACCGCACATACATGGACGCCGTCAGATCATACCTCAgtaagtacac ... atattttcagGTCCTAGAGAGGTGTTCATGTGCGGAATCGCGCAGTACGTCAACCTGTGGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tctctcatctccatcttgttggttaaactgaacgcaatgccaaaaatattttcagGTCCTAGAGAGGTGTTCATGTGCGGAATCGCGCAGTACGTCAACCTGTGGGGCACCATGGTCGGCTACACAATCACCGCAACCATAAGCATGGT
                                              tattttc  CT-rich tract
                                         aaaaatattttca  TA-rich tract