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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaaatcatatatacttatctcaatacagaatttaggtctaacagaatgactggacatatgctttatataaagtaaaggttgaccgtagaatcaaaattgtaggtgcttctttataaaaatcattgattttgtgtaccttcgtatccagGCTAAGGGGATGAATTACCTTCACAAGCGCAATCCTCCTATAGTCCACCGGGATCTAAAGTCACCAAATCTGTTGGTTGATAAAAAGTACACTGTGAAG

Basic information

species Oryza sativa
transcript LOC_Os02g32610.2
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g32610.2 (Oryza sativa), 3'ss of exon 11
lower sequence: GRMZM2G059671_T01 (Zea mays), 3'ss of exon 9
gtaaaatcatatatacttatctcaatacagaatttaggtctaacagaatgac-tggacatatgctttatataaagtaaaggttgaccgtagaatcaaaattgtaggtgcttctttataaaaatcattgattttgtgtaccttc-gtatccagGCTAAGGGGATGAATTACCTTCACAAGCGCAATCCTCCTATAGTCCACCGGGATCTAAAGTCACCAAATCTGTTGGTTGATAAAAAGTACACTGTGAAG
                                                || |   |  |||| ||| | ||||||   |  ||| || |  | |  |||||| ||         | ||| | ||    ||| | || | ||||  | | ||||| || |||||||| || ||||| ||||| |||||||| ||||||||||||||||| ||||||||||| ||||||||||| ||||||||||||||||| 
------------------------------------------------tggcaccgctatatacttca-ataaagctgacattggcctttcagttgaaattgaagcaatcgtcgtttaatactct---attgtttgcatcttctatgtacagGCAAAAGGGATGAACTATCTTCATAAGCGTAATCCTCCAATAGTCCACCGGGATCTTAAGTCACCAAACCTGTTGGTTGACAAAAAGTACACTGTGAAA

upper sequence: LOC_Os02g32610.2 (Oryza sativa), 3'ss of exon 11
lower sequence: GRMZM2G059671_T03 (Zea mays), 3'ss of exon 9
gtaaaatcatatatacttatctcaatacagaatttaggtctaacagaatgac-tggacatatgctttatataaagtaaaggttgaccgtagaatcaaaattgtaggtgcttctttataaaaatcattgattttgtgtaccttc-gtatccagGCTAAGGGGATGAATTACCTTCACAAGCGCAATCCTCCTATAGTCCACCGGGATCTAAAGTCACCAAATCTGTTGGTTGATAAAAAGTACACTGTGAAG-
                                                || |   |  |||| ||| | ||||||   |  ||| || |  | |  |||||| ||         | ||| | ||    ||| | || | ||||  | | ||||| || |||||||| || ||||| ||||| |||||||| ||||||||||||||||| ||||||||||| ||||||||||| |||||||||||||||||  
------------------------------------------------tggcaccgctatatacttca-ataaagctgacattggcctttcagttgaaattgaagcaatcgtcgtttaatactct---attgtttgcatcttctatgtacagGCAAAAGGGATGAACTATCTTCATAAGCGTAATCCTCCAATAGTCCACCGGGATCTTAAGTCACCAAACCTGTTGGTTGACAAAAAGTACACTGTGAAAG

upper sequence: LOC_Os02g32610.2 (Oryza sativa), 3'ss of exon 11
lower sequence: GLYMA19G37570.2 (Glycine max), 3'ss of exon 11
gtaaaatcatatatacttatctcaatacagaatttaggtctaacagaatgactggacatatgctttatataaagtaa-aggttgaccgtagaatcaaaattgtaggtgcttctttataaaaatcattgattttgtgtaccttcgtatccagGCTAAGGGGATGAATTACCTTCACAAGCGCAATCCTCCTATAGTCCACCGGGATCTAAAGTCACCAAATCTGTTGGTTGATAAAAAGTACACTGTGAAG
                   |     | |||||  ||  | | |  |  |   |||   |||   || | | || ||| | | | |   |    ||| ||   | | | |   ||  | ||        | |||||  |  ||| | | ||||||||||| |||||||| ||||| || ||||||||||| || || ||  | ||||| || || ||||| ||  | ||||| || || || || ||||||
------------------gtaaactttcagaaaataaatattattgttt--ttggttctatttattttttgaattaatatgatcattatgatgtcataacctttg-tacccattggttaagt------aatttgt-cattttcatgtgcagGCTAAGGGAATGAATTATCTTCATAAACGCAATCCTCCCATTGTTCATAGAGATCTGAAATCTCCAAACCTTCTTGTTGACAAGAAATATACAGTGAAG

upper sequence: LOC_Os02g32610.2 (Oryza sativa), 3'ss of exon 11
lower sequence: GLYMA03G34890.1 (Glycine max), 3'ss of exon 11
gtaaaatcatatatacttatctcaatacagaatttaggtctaacagaatgactggacatatgctttatataaagtaaaggttgaccgtagaatcaaaattgtaggtgcttctttataaaaatca-ttgattttgtgt-accttcgtatccagGCTAAGGGGATGAATTACCTTCACAAGCGCAATCCTCCTATAGTCCACCGGGATCTAAAGTCACCAAATCTGTTGGTTGATAAAAAGTACACTGTGAAG
                                 | |  | ||| | ||| |      | ||   || | |  |||     ||     | |||| || ||  |        |||| ||   ||   || | | | ||| |  ||| | | |||||||||||||||||||| ||||| || ||||||||||| || || ||  | ||||| || || ||||| ||  | ||||| || || || || ||||||
--------------------------------gtaaactttaagaaaataa------acatcaattgttttcagttctatttattttttgaattaatatgatgtcataacctttgtacccattggttaagtatttgtcattttcatgtgcagGCTAAGGGGATGAATTATCTTCATAAACGCAATCCTCCCATTGTTCATAGAGATCTGAAATCTCCAAACCTTCTTGTTGACAAGAAATATACAGTGAAG

upper sequence: LOC_Os02g32610.2 (Oryza sativa), 3'ss of exon 11
lower sequence: AT5G03730.1 (Arabidopsis thaliana), 3'ss of exon 10
gtaaaatcatatatacttatctcaatacagaatttaggtctaacagaatgactggacatatgctttatataaagtaaaggttgaccgtagaatcaaaattgtaggtgcttctttataaaaatcattgattttgtgtaccttcgtatccagGCTAAGGGGATGAATTACCTTCACAAGCGCAATCCTCCTATAGTCCACCGGGATCTAAAGTCACCAAATCTGTTGGTTGATAAAAAGTACACTGTGAAG
                                             | |||  |       |   ||| ||  |     | ||       ||        | | |||| ||||| | |   | | ||   |||      ||  ||   ||||||||||| |||||||| |||||||| ||||||||||| || || ||  | |||||||| || |||||  | |||||||| ||||| || || || |||
---------------------------------------------gtatgtttaattccttatgttacatgtatgggtgattacttcctga--------tcttggtgtttcttcacatggaacttt--ctttccaattctctgt-cacagGCTAAGGGAATGAATTATCTTCACAATCGCAATCCTCCAATTGTGCATAGAGATCTAAAATCTCCAAACTTATTGGTTGACAAAAAATATACAGTCAAG

upper sequence: LOC_Os02g32610.2 (Oryza sativa), 3'ss of exon 11
lower sequence: Vv08s0007g03910.t01 (Vitis vinifera), 3'ss of exon 10
gtaaaatcatatatacttatctcaatacagaatttaggtctaacagaatgactggacatatgctttatataaagtaaaggttgaccgtagaatcaaaattgtaggtgcttctttataaaaatcattgattttgtgtaccttcgtatc---cagGCTAAGGGGATGAATTACCTTCACAAGCGCAATCCTCCTATAGTCCACCGGGATCTAAAGTCACCAAATCTGTTGGTTGATAAAAAGTACACTGTGAAG
                                                    |     | |  |   | | |  |  | |       ||  | | ||| |  |  || ||  |||| |    | |   |||| | |   ||   | |   ||||| ||||| |||||||| ||||| || ||||||||||| || || || || ||| | ||||| ||||| || |||||||| ||||| ||||| ||||||
----------------------------------------------------tatttttttagtgattgttatttggatgcaccttttaccagctaaaata-acttgttttattatcatttccgtgctttttttttttttttaaaacaaacagGCCAAGGGCATGAATTATCTTCATAAACGCAATCCTCCCATTGTTCATCGAGATTTGAAGTCTCCAAACCTTTTGGTTGACAAAAAATACACCGTGAAG

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|29660723|gb|CB656998.1|CB656998
EST:     ATTGAGTATGGCTTTTGACGTG                         GCTAAGGGGATGAATTACCTTCACAAGCGCAATCCTCCTATAGTCCACCGG
genomic: ATTGAGTATGGCTTTTGACGTGgtaaaatcat ... tcgtatccagGCTAAGGGGATGAATTACCTTCACAAGCGCAATCCTCCTATAGTCCACCGG
EST: gi|29639477|gb|CB644486.1|CB644486
EST:     ATGAGAAGCGGCGA-TGNAGTATGGCTTTTGACGTG                         GCTAAGGGGATGAATTACCTTCACAAGCGCAATCCTCCTATAGTCCACCGG
genomic: ATGAGAAGCGGCGATTG-AGTATGGCTTTTGACGTGgtaaaatcat ... tcgtatccagGCTAAGGGGATGAATTACCTTCACAAGCGCAATCCTCCTATAGTCCACCGG
EST: gi|29678550|gb|CB674825.1|CB674825
EST:     ATGAGAAGCGGCGATTGAGTATGGCTTTTGACGTG                         GCTAGGGGGATGAATTACCTTCACAAGCGCAATCCTCCTATAGTCCACCGG
genomic: ATGAGAAGCGGCGATTGAGTATGGCTTTTGACGTGgtaaaatcat ... tcgtatccagGCTAAGGGGATGAATTACCTTCACAAGCGCAATCCTCCTATAGTCCACCGG
EST: gi|88585426|gb|CI703056.1|CI703056
EST:     CAAGGGAAAATCTAGATGAGAAGCGGCGATTGAGTATGGCTTTTGACGTG                         GCTAAGGGGATGAATTACCTTCACAAGCGCAATCCTCCTATAGTCCACCGG
genomic: CAAGGGAAAATCTAGATGAGAAGCGGCGATTGAGTATGGCTTTTGACGTGgtaaaatcat ... tcgtatccagGCTAAGGGGATGAATTACCTTCACAAGCGCAATCCTCCTATAGTCCACCGG
EST: gi|29662085|gb|CB658360.1|CB658360
EST:     CAAGGGACAATCTAGATGAGAAGCGGCGATTGAGTATGGCTTTTGACGTG                         GCTAAGGGGATGAATTACCTTCACAAGCGCAATCCTCCTATAGTCCACCGG
genomic: CAAGGGAAAATCTAGATGAGAAGCGGCGATTGAGTATGGCTTTTGACGTGgtaaaatcat ... tcgtatccagGCTAAGGGGATGAATTACCTTCACAAGCGCAATCCTCCTATAGTCCACCGG
EST: gi|29680716|gb|CB676991.1|CB676991
EST:     CAAGGGAAAATCTAGATGAGAAGCGGCGATTGAGTATGGCTTTTGACGTG                         GCTAAGGGGATGAATTACCTTCACAAGCGCAATCCTCCTATAGTCCACCGG
genomic: CAAGGGAAAATCTAGATGAGAAGCGGCGATTGAGTATGGCTTTTGACGTGgtaaaatcat ... tcgtatccagGCTAAGGGGATGAATTACCTTCACAAGCGCAATCCTCCTATAGTCCACCGG
EST: gi|29664340|gb|CB660615.1|CB660615
EST:     AGTATGGCTTTTGACGTG                         GCTAAGGGGATGAATTACCTTCACAAGCGCAATCCTCCTATAGTCCACCGG
genomic: AGTATGGCTTTTGACGTGgtaaaatcat ... tcgtatccagGCTAAGGGGATGAATTACCTTCACAAGCGCAATCCTCCTATAGTCCACCGG
EST: gi|33675051|gb|CF303290.1|CF303290
EST:     CAAGGGAAAATCTAGATGAGAAGCGGCGATTGAGTATGGCTTTTGACGTG                         GCTAAGGGGATGAATTACCTTCACAAGCGCAATCCTCCTATAGTCCACCGG
genomic: CAAGGGAAAATCTAGATGAGAAGCGGCGATTGAGTATGGCTTTTGACGTGgtaaaatcat ... tcgtatccagGCTAAGGGGATGAATTACCTTCACAAGCGCAATCCTCCTATAGTCCACCGG
EST: gi|29665412|gb|CB661687.1|CB661687
EST:     CAAGGGAAAATCTAGATGAGAAGCGGCGATTGAGTATGGCTTTTGACGTG                         GCTAAGGGGATGAATTACCTTCACAAGCGCAATCCTCCTATAGTCCA
genomic: CAAGGGAAAATCTAGATGAGAAGCGGCGATTGAGTATGGCTTTTGACGTGgtaaaatcat ... tcgtatccagGCTAAGGGGATGAATTACCTTCACAAGCGCAATCCTCCTATAGTCCA
EST: gi|29664339|gb|CB660614.1|CB660614
EST:     CAAGGGAAAATCTAGATGAGAAGCGGCGATTGAGTATGGCTTTTGACGTG                         GCTAAGGGGATGAATTACCTTCACAAGCGCAATCCTCCTATAGTCCACCGG
genomic: CAAGGGAAAATCTAGATGAGAAGCGGCGATTGAGTATGGCTTTTGACGTGgtaaaatcat ... tcgtatccagGCTAAGGGGATGAATTACCTTCACAAGCGCAATCCTCCTATAGTCCACCGG
EST: gi|29628356|gb|CB633367.1|CB633367
EST:     GATTGAGTATGGCTTTTGACGTG                         GCTAAGGGGATGAATTACCTTCACAAGCGCAATCCTCCTATAGTCCACCGG
genomic: GATTGAGTATGGCTTTTGACGTGgtaaaatcat ... tcgtatccagGCTAAGGGGATGAATTACCTTCACAAGCGCAATCCTCCTATAGTCCACCGG
EST: gi|58595275|gb|CF993583.1|CF993583
EST:     CAAGGGAAAATCTAGATGAGAAGCGGCGATTGAGTATGGCTTTTGACGTG                         GCTAAGGGGATGAATTACCTTCACAAGCGCAATCCTCCTATAGTCCACCGG
genomic: CAAGGGAAAATCTAGATGAGAAGCGGCGATTGAGTATGGCTTTTGACGTGgtaaaatcat ... tcgtatccagGCTAAGGGGATGAATTACCTTCACAAGCGCAATCCTCCTATAGTCCACCGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaattgtaggtgcttctttataaaaatcattgattttgtgtaccttcgtatccagGCTAAGGGGATGAATTACCTTCACAAGCGCAATCCTCCTATAGTCCACCGGGATCTAAAGTCACCAAATCTGTTGGTTGATAAAAAGTACACTGTGAAG
                           cattgat  putative branch site (score: 4)
                                        taccttc  putative PPT
             ttctttataaaaatca  TA-rich tract