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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AACTTTTCATGTGCTGGTGTGATGTACCTCTGCCAATTTATTGAGCAAAATGGTGGAAAGCTGCCAGAACGCCTGgtatgagcctgagcatttattatacaattcccagttctggcttaattatgtgtaacttatcaactattctgttcttttcatatgtatgccttgtgcttat...

Basic information

species Oryza sativa
transcript LOC_Os05g08980.4
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os05g08980.4 (Oryza sativa), 5'ss of exon 9
lower sequence: GRMZM2G558539_T01 (Zea mays), 5'ss of exon 10
AACTTTTCATGTGCTGGTGTGATGTACCTCTGCCAATTTATTGAGCAAAATGGTGGAAAGCTGCCAGAACGCCTGgtatgagcctgagcatttattatacaattcccagttctggcttaattatgtgtaacttatcaactattctgttcttttcatatgtatgccttgtgcttat------
 |||| |||||||||||||||||||||||||||||||| || |||||||||||||||||||| || || |||||||||||||| |   || ||     |   |   ||||  |  |  ||  | |     | ||  |  || | |    | ||  ||   |    |  ||||         
GACTTCTCATGTGCTGGTGTGATGTACCTCTGCCAATTCATGGAGCAAAATGGTGGAAAGCTTCCGGATCGCCTGgtatgagcatttccacttggagca---tcttcagtatttcccaaa--aagaactccctaa-atttaatttagggtgttagtaaccaaaaatcatgctccaacagtt
















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|86420361|gb|CI056350.1|CI056350
EST:     ACCTCTGCCAATTTATTGAGCAAAATGGTGGAAAGCTGCCAGAACGCCTG                         GCTCAAAAATGGCTGGGAAGCGTTTTGGAAGCCAAAATCTCATACAG
genomic: ACCTCTGCCAATTTATTGAGCAAAATGGTGGAAAGCTGCCAGAACGCCTGgtatgagcct ... gtacaggaagGCTCAAAAATGGCTGGGAAGCGTTTTGGAAGCCAAAATCTCATACAG
EST: gi|218505037|gb|FG952955.1|FG952955
EST:     ACCTCTGCCAATTTATTGAGCAAAATGGTGGAAAGCTGCCAGAACGCCTG                         GAAGGCTCAAAAATGGCTGGGAAGCGTTTTGGAAGCCAAAATCTCATACAG
genomic: ACCTCTGCCAATTTATTGAGCAAAATGGTGGAAAGCTGCCAGAACGCCTGgtatgagcct ... gtacaggaagG----CTCAAAAATGGCTGGGAAGCGTTTTGGAAGCCAAAATCTCATACAG
EST: gi|86414853|gb|CI069256.1|CI069256
EST:     ACCTCTGCCAATTTATTGAGCAAAATGGTGGAAAGCTGCCAGAACGCCTGGAAG                      
genomic: ACCTCTGCCAATTTATTGAGCAAAATGGTGGAAAGCTGCCAGAACGCCT----Ggtatgagcct ... gtacagg
EST: gi|29663313|gb|CB659588.1|CB659588
EST:     ACCTCTGCCAATTTATTGAGCAAAATGGTGGAAAGCTGCCAGAACGCCTG                         GAAGGCTCAAAAATGGCTGGGAAGCGTTTTGGAAGCCAAAATCTCATACAG
genomic: ACCTCTGCCAATTTATTGAGCAAAATGGTGGAAAGCTGCCAGAACGCCTGgtatgagcct ... gtacaggaagG----CTCAAAAATGGCTGGGAAGCGTTTTGGAAGCCAAAATCTCATACAG
EST: gi|29674385|gb|CB670660.1|CB670660
EST:     ACCTCTGCCAATTTATTGAGCAAAATGGTGGAAAGCTGCCAGAACGCCTGGAAG                      
genomic: ACCTCTGCCAATTTATTGAGCAAAATGGTGGAAAGCTGCCAGAACGCCT----Ggtatgagcct ... gtacagg
EST: gi|88962073|gb|CI097226.1|CI097226
EST:     ACCTCTGCCAATTTATTGAGCAAAATGGTGGAAAGCTGCCAGAACGCCTGGAAG                      
genomic: ACCTCTGCCAATTTATTGAGCAAAATGGTGGAAAGCTGCCAGAACGCCT----Ggtatgagcct ... gtacagg
EST: gi|33684852|gb|CF313091.1|CF313091
EST:     ACCTCTGCCAATTTATTGAGCAAAATGGTGGAAAGCTGCCAGAACGCCTGGAAG                      
genomic: ACCTCTGCCAATTTATTGAGCAAAATGGTGGAAAGCTGCCAGAACGCCT----Ggtatgagcct ... gtacagg
EST: gi|29671281|gb|CB667556.1|CB667556
EST:     ACCTCTGCCAATTTATTGAGCAAAATGGTGGAAAGCTGCCAGAACGCCTG                         GAAGGCTCAAAAATGGCTGGGAAGCGTTTTGGAAGCCAAAATCTCATACAG
genomic: ACCTCTGCCAATTTATTGAGCAAAATGGTGGAAAGCTGCCAGAACGCCTGgtatgagcct ... gtacaggaagG----CTCAAAAATGGCTGGGAAGCGTTTTGGAAGCCAAAATCTCATACAG
EST: gi|29688958|gb|CB685233.1|CB685233
EST:     ACCTCTGCCAATTTATTGAGCAAAATGGTGGAAAGCTGCCAGAACGCCTGGAAG                      
genomic: ACCTCTGCCAATTTATTGAGCAAAATGGTGGAAAGCTGCCAGAACGCCT----Ggtatgagcct ... gtacagg
EST: gi|33684851|gb|CF313090.1|CF313090
EST:     ACCTCTGCCAATTTATTGAGCAAAATGGTGGAAAGCTGCCAGAACGCCTG                         GAAGGCTCAAAAATGGCTGGGAAGCGTTTTGGAAGCCAAAATCTCATACAG
genomic: ACCTCTGCCAATTTATTGAGCAAAATGGTGGAAAGCTGCCAGAACGCCTGgtatgagcct ... gtacaggaagG----CTCAAAAATGGCTGGGAAGCGTTTTGGAAGCCAAAATCTCATACAG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AACTTTTCATGTGCTGGTGTGATGTACCTCTGCCAATTTATTGAGCAAAATGGTGGAAAGCTGCCAGAACGCCTGgtatgagcctgagcatttattatacaattcccagttctggcttaattatgtgtaacttatcaactattctgttcttttcatatgtatgccttgtgcttat

- - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - -  GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC