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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGGTAGCCTATACAGGATTTTGCACAAGCATGGTGCAAGGGAAAATCTAGATGAGAAGCGGCGATTGAGTATGGCTTTTGACGTGgtaaaatcatatatacttatctcaatacagaatttaggtctaacagaatgactggacatatgctttatataaagtaaaggttgaccgtagaatcaaaattgtaggtgcttctttataaaaatcattgattttgtgtaccttcgtatccag

Basic information

species Oryza sativa
transcript LOC_Os02g32610.2
intron # 11
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g32610.2 (Oryza sativa), 5'ss of exon 11
lower sequence: GRMZM2G059671_T01 (Zea mays), 5'ss of exon 9
AGGTAGCCTATACAGGATTTTGCACAAGCATGGTGCAAGGGAAAATCTAGATGAGAAGCGGCGATTGAGTATGGCTTTTGACGTGgtaaaatcatatatacttatctcaatacagaatttaggtctaacagaatgactggacata---tgctttatataaagtaaaggttgaccgtagaatcaaaattgtaggtgcttctttataaaaatcattgattttgtgtaccttcgtatccag
||||||| |||||||  |||| |||| ||||| ||||||||||||||| || |||   || || |||||||||||||| ||||||||||||        |||| | | |||| | | ||  ||||       ||   ||||  |    | |||| ||  ||    |  ||   | ||||     | ||  || |  |                                         
AGGTAGCTTATACAGACTTTTACACAGGCATGCTGCAAGGGAAAATCTGGAGGAGCGCCGCCGCTTGAGTATGGCTTTCGACGTGgtaaaaa-------acttgtttaaata-acacttgcggtccgtttagatccttggaattgaattcctttctaataatcgtaatttaggcataga---tgagtta-agctaat-----------------------------------------

upper sequence: LOC_Os02g32610.2 (Oryza sativa), 5'ss of exon 11
lower sequence: Vv08s0007g03910.t01 (Vitis vinifera), 5'ss of exon 10
AGGTAGCCTATACAGGATTTTGCACAAGCATGGTGCAAGGGAAAATCTAGATGAGAAGCGGCGATTGAGTATGGCTTTTGACGTGgtaaaatcatatatacttatctcaatacagaatttaggtctaacagaatgactggacatatgctttatataaagtaaaggttgaccgtagaatcaaaattgtaggtgcttctttataaaaatcattgattttgtgtaccttcgtatccag
||||||| |||| ||| |||||||||| | ||||||||| ||||   ||||||||| ||| |||||||||||||||| ||| ||||||        |  | ||     | || | | |||  |||   || | | | | |   |    |||| |||   |  |  ||       ||    |  |||  |   | |                                        
AGGTAGCTTATATAGGCTTTTGCACAAACCTGGTGCAAGAGAAATGTTAGATGAGAGGCGTCGATTGAGTATGGCTTATGATGTGgta--------tgcatttgaag-agtaaatattttttgtcctcca-acttattcgctctcctgtttaaatatttttgaatttttttaatgatgtcatcttgctgagtcct----------------------------------------
















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

Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGGTAGCCTATACAGGATTTTGCACAAGCATGGTGCAAGGGAAAATCTAGATGAGAAGCGGCGATTGAGTATGGCTTTTGACGTGgtaaaatcatatatacttatctcaatacagaatttaggtctaacagaatgactggacatatgctttatataaagtaaaggttgaccgtagaatcaaaattgtaggtgcttctttataaaaatcattgattttgtgtaccttcgtatccag

- - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGC