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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...caaatgaattgaattgtctttattatgattagtgaacataatgcacgcaaaattttcaactataccttttcctatgcttatcatctgctgttacttgcagGGGAATTGTCAATGATACTTACAAGATGGATCTTATTCTCATACACCCACCATATATGATAGCATTAGCCTGCATCTACATTGCAAGCGTTCTTAAAGAC

Basic information

species Oryza sativa
transcript LOC_Os09g32680.4
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os09g32680.4 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G408242_T03 (Zea mays), 3'ss of exon 7
caaatgaattgaattgtctttat-tatgattagtgaacataatgcacgcaaaattttcaactataccttttcctatgctta----tcatctgctgttacttgcagGGGAATTGTCAATGATACTTACAAGATGGATCTTATTCTCATACACCCACCATATATGATAGCATTAGCCTGCATCTACATTGCAAGCGTTCTTAAAGAC
    |  | | |   ||  | || |||| | |||   ||   |   |        |     || | |||||  ||     |    | | ||  ||| |||||||||||  |||| |||||||| ||||||||||| ||||| |||||| |||| || || ||||| ||| | |||||||| ||||| || || ||| | ||||| 
----tctaattatgggtgataatgtatgctcagtcttca-gctattcctgttgcctgttgttacatctttttttaaagaaaaaactgaccttatgtgacttgcagGGGCCTTGTTAATGATACATACAAGATGGACCTTATCCTCATATACCCTCCCTACATGATTGCACTGGCCTGCATATACATAGCGAGTGTTTTGAAAGAT

upper sequence: LOC_Os09g32680.4 (Oryza sativa), 3'ss of exon 6
lower sequence: AT5G48640.1 (Arabidopsis thaliana), 3'ss of exon 7
----------------caaatgaattgaattgt-ctttattatgattagtgaacataatgcacgcaaaattttcaactataccttttcctatgcttatcatctgctgttact--tgcagGGGAATTGTCAATGATACTTACAAGATGGATCTTATTCTCATACACCCACCATATATGATAGCATTAGCCTGCATCTACATTGCAAGCGTTCTTAAAGAC
                 | ||  |||| || |  ||  |||   |      | | |||        | || |   ||             ||  | |  | ||  | |   |  | |||||||||||| ||||||||||| |||||||| || |||||  ||||||| || ||    |||||  |||| ||||| ||||| ||||| || |  | ||| 
gtaagtccttctatatgagatatattgcatagaactcaattcctagctccaaccttaaaatctaagagatctctgacctgtataaaaagcattttgaaaacctattttccgtgtttcagGGGAATTGTTAATGATACTTATAAGATGGACCTCATTCTTGTACACCCTCCCTACCGCATAGCGCTAGCATGCATATACATAGCAAGTGTCCACAGAGAG

upper sequence: LOC_Os09g32680.4 (Oryza sativa), 3'ss of exon 6
lower sequence: Vv00s0360g00050.t01 (Vitis vinifera), 3'ss of exon 7
caaatgaattgaattgtctttattatgattagtgaacataat--gcacgcaaaattttcaactataccttttcctatgcttatcatctgctgttacttgcagGGGAATTGTCAATGATACTTACAAGATGGATCTTATTCTCATACACCCACCATATATGATAGCATTAGCCTGCATCTACATTGCAAGCGTTCTTAAAGAC
    ||  |    || ||    |  ||       | | |  |  | | |  |  || |  | | |||       | |  |  |    |  ||   | |  ||||||||||||||||| || ||||| |||||||||||||||||  | || ||| || |||| || ||||| ||||| ||||||||||| || |  ||||| 
-ttgtgtgtgtgcttttcagcttcctgcccgccaagctttctttgtatgtgaggttgtgca-tgtactacaagatctaatgttggaattttggatcataaagGGGAATTGTCAATGACACCTACAAAATGGATCTTATTCTCATTTATCCTCCACATCTGATTGCCTTAGCTTGCATATACATTGCAAGTGTACACAAAGAT

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|24468776|gb|CA305725.1|CA305725
EST:     GTTATTGCAGGATGCTGGCATAACAGATCTGACACAATTTGCCTG                         GGGAATTGTCAATGATACTTACAAGATGGATCTTATTCTCATACACCCACC
genomic: GTTATTGCAGGATGCTGGCATAACAGATCTGACACAATTTGCCTGgtactcttct ... ttacttgcagGGGAATTGTCAATGATACTTACAAGATGGATCTTATTCTCATACACCCACC
EST: gi|86493556|gb|CI136189.1|CI136189
EST:     GTTATTGCAGGATGCTGGCATAACAGATCTGACACAATTTGCCTG                         GGGAATTGTCAATGATACTTACAAGATGGATCTTATTCTCATACACCCACC
genomic: GTTATTGCAGGATGCTGGCATAACAGATCTGACACAATTTGCCTGgtactcttct ... ttacttgcagGGGAATTGTCAATGATACTTACAAGATGGATCTTATTCTCATACACCCACC
EST: gi|29660228|gb|CB656503.1|CB656503
EST:     GTTATTGCAGGATGCTGGCATAACAGATCTGACACAATTTGCCTG                         GGGAATTGTCAATGATACTTACAAGATGGATCTTATTCTCATACACCCACC
genomic: GTTATTGCAGGATGCTGGCATAACAGATCTGACACAATTTGCCTGgtactcttct ... ttacttgcagGGGAATTGTCAATGATACTTACAAGATGGATCTTATTCTCATACACCCACC
EST: gi|88833089|gb|CI369979.1|CI369979
EST:     ATCTGACACAATTTGCCTG                         GGGAATTGTCAATGATACTTACAAGATGGATCTTATTCTCATACACCCACC
genomic: ATCTGACACAATTTGCCTGgtactcttct ... ttacttgcagGGGAATTGTCAATGATACTTACAAGATGGATCTTATTCTCATACACCCACC
EST: gi|88258947|gb|CI363240.1|CI363240
EST:     CATAACAGATCTGACACAATTTGCCTG                         GGGAATTGTCAATGATACTTACAAGATGGATCTTATTCTCATACACCCACC
genomic: CATAACAGATCTGACACAATTTGCCTGgtactcttct ... ttacttgcagGGGAATTGTCAATGATACTTACAAGATGGATCTTATTCTCATACACCCACC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cgcaaaattttcaactataccttttcctatgcttatcatctgctgttacttgcagGGGAATTGTCAATGATACTTACAAGATGGATCTTATTCTCATACACCCACCATATATGATAGCATTAGCCTGCATCTACATTGCAAGCGTTCTTAAAGAC
     aattttcaactata  TA-rich tract