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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CATTGCACAATCAACCATTCTGTGGTTGGACTCCGGTCCTGTATATCTGAAGGCGCAGTGATAGAGGACTCTCTGCTAATGGGTGCAGACTATTATGAGgtaaaataaaacaaaactatactatattatggtgtattggtgttgtgggaacttaattgtgctttttgttcag

Basic information

species Oryza sativa
transcript LOC_Os09g12660.2
intron # 7
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os09g12660.2 (Oryza sativa), 5'ss of exon 7
lower sequence: GRMZM2G106213_T02 (Zea mays), 5'ss of exon 7
CATTGCACAATCAACCATTCTGTGGTTGGACTCCGGTCCTGTATATCTGAAGGCGCAGTGATAGAGGACTCTCTGCTAATGGGTGCAGACTATTATGAGgtaaaataaaacaaaactatactatattatggtgtattgg---tgttgtgggaacttaattgtgctttttgttcag-----
|||||||||||||| ||||| || ||||||||||| ||||| || |||||||| ||||| |||||||||||| |||||||||||||||||||||| |||||||| || |   ||||   ||| || ||| ||| | |||   | |  || ||||||| |  | |||| ||||  |     
CATTGCACAATCAATCATTCCGTAGTTGGACTCCGTTCCTGCATTTCTGAAGGTGCAGTTATAGAGGACTCTTTGCTAATGGGTGCAGACTATTACGAGgtaaagtagagtcaaacagaactctaatatcgtgcaatggaaatatcatgagaactta-tcattctttctgttttgttcag
















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|86858990|gb|CI275175.1|CI275175
EST:     AAGGCGCAGTGATAGAGGACTCTCTGCTAATGGGTGCAGACTATTATGAG                         ACGGAGACGGACAAGAAAGCCCTTTCTGAGACTGGTGGCATTCCCATTGGT
genomic: AAGGCGCAGTGATAGAGGACTCTCTGCTAATGGGTGCAGACTATTATGAGgtaaaataaa ... ttttgttcagACGGAGACGGACAAGAAAGCCCTTTCTGAGACTGGTGGCATTCCCATTGGT
EST: gi|86496727|gb|CI139360.1|CI139360
EST:     AAGGCGCAGTGATAGAGGACTCTCTGCTAATGGGTGCAGACTATTATGAG                         ACGGAGACGGACAAGAAAGCCCTTTCTGAGACTGGTGGCATTCCCATTGGT
genomic: AAGGCGCAGTGATAGAGGACTCTCTGCTAATGGGTGCAGACTATTATGAGgtaaaataaa ... ttttgttcagACGGAGACGGACAAGAAAGCCCTTTCTGAGACTGGTGGCATTCCCATTGGT
EST: gi|24468914|gb|CA305863.1|CA305863
EST:     ACGGCGCAGTGATAGAGGACTCTCTGCTAATGGGTGCAGACTATTATGAG                         ACGGAGACGGACAAGAAAGCCCTTTCTGAGACTGGTGGCATTCCCATTGGT
genomic: AAGGCGCAGTGATAGAGGACTCTCTGCTAATGGGTGCAGACTATTATGAGgtaaaataaa ... ttttgttcagACGGAGACGGACAAGAAAGCCCTTTCTGAGACTGGTGGCATTCCCATTGGT
EST: gi|87009864|gb|CI277365.1|CI277365
EST:     AAGGCGCAGTGATAGAGGACTCTCTGCTAATGGGTGCAGACTATTATGAG                         ACGGAGACGGACAAGAAAGCCCTTTCTGAGACTGGTGGCATTCCCATTGGT
genomic: AAGGCGCAGTGATAGAGGACTCTCTGCTAATGGGTGCAGACTATTATGAGgtaaaataaa ... ttttgttcagACGGAGACGGACAAGAAAGCCCTTTCTGAGACTGGTGGCATTCCCATTGGT
EST: gi|88222446|gb|CI222402.1|CI222402
EST:     AAGGCGCAGTGATAGAGGACTCTCTGCTAATGGGTGCAGACTATTATGAG                         ACGGAGACGGACAAGAAAGCCCTTTCTGAGACTGGTGGCATTCCCATTGGT
genomic: AAGGCGCAGTGATAGAGGACTCTCTGCTAATGGGTGCAGACTATTATGAGgtaaaataaa ... ttttgttcagACGGAGACGGACAAGAAAGCCCTTTCTGAGACTGGTGGCATTCCCATTGGT
EST: gi|88222920|gb|CI220666.1|CI220666
EST:     AAGGCGCAGTGATAGAGGGCTCTCTGCTAATGGGTGCAGACTATTATGAG                         ACGGAGACGGACAAGAAAGCCCTTTCTGAGACTGGTGGCATTCCCATTGGT
genomic: AAGGCGCAGTGATAGAGGACTCTCTGCTAATGGGTGCAGACTATTATGAGgtaaaataaa ... ttttgttcagACGGAGACGGACAAGAAAGCCCTTTCTGAGACTGGTGGCATTCCCATTGGT
EST: gi|87018057|gb|CI275871.1|CI275871
EST:     AAGGCGCAGTGATAGAGGACTCTCTGCTAATGGGTGCAGACTATTATGAG                         ACGGAGACGGACAAGAAAGCCCTTTCTGAGACTGGTGGCATTCCCATTGGT
genomic: AAGGCGCAGTGATAGAGGACTCTCTGCTAATGGGTGCAGACTATTATGAGgtaaaataaa ... ttttgttcagACGGAGACGGACAAGAAAGCCCTTTCTGAGACTGGTGGCATTCCCATTGGT
EST: gi|89164207|gb|CI101295.1|CI101295
EST:     AAGGCGCAGTGATAGAGGACTCTCTGCTAATGGGTGCAGACTATTATGAG                         ACGGAGACGGACAAGAAAGCCCTTTCTGAGACTGGTGGCATTCCCATTGGT
genomic: AAGGCGCAGTGATAGAGGACTCTCTGCTAATGGGTGCAGACTATTATGAGgtaaaataaa ... ttttgttcagACGGAGACGGACAAGAAAGCCCTTTCTGAGACTGGTGGCATTCCCATTGGT
EST: gi|88967313|gb|CI002497.1|CI002497
EST:     AAGGCGCAGTGATAGAGGACTCTCTGCTAATGGGTGCAGACTATTATGAG                         ACGGAGACGGACAAGAAAGCCCTTTCTGAGACTGGTGGCATTCCCATTGGT
genomic: AAGGCGCAGTGATAGAGGACTCTCTGCTAATGGGTGCAGACTATTATGAGgtaaaataaa ... ttttgttcagACGGAGACGGACAAGAAAGCCCTTTCTGAGACTGGTGGCATTCCCATTGGT
EST: gi|86517463|gb|CI157669.1|CI157669
EST:     AAGGCGCAGTGATAGAGGACTCTCTGCTAATGGGTGCAGACTATTATGAG                         ACGGAGACGGACAAGAAAGCCCTTTCTGAGACTGGTGGCATTCCCATTGGT
genomic: AAGGCGCAGTGATAGAGGACTCTCTGCTAATGGGTGCAGACTATTATGAGgtaaaataaa ... ttttgttcagACGGAGACGGACAAGAAAGCCCTTTCTGAGACTGGTGGCATTCCCATTGGT
EST: gi|58683758|gb|CK072445.1|CK072445
EST:     AAGGCGCAGTGATAGAGGACTCTCTGCTAATGGGTGCAGACTATTATGAG                         ACGGAGACGGACAAGAAAGCCCTTTCTGAGACTGGTGGCATTCCCATTGGT
genomic: AAGGCGCAGTGATAGAGGACTCTCTGCTAATGGGTGCAGACTATTATGAGgtaaaataaa ... ttttgttcagACGGAGACGGACAAGAAAGCCCTTTCTGAGACTGGTGGCATTCCCATTGGT
EST: gi|88957454|gb|CI095395.1|CI095395
EST:     AAGGCGCAGTGATAGAGGACTCTCTGCTAATGGGTGCAGACTATTATGAG                         ACGGAGACGGACAAGAAAGCCCTTTCTGAGACTGGTGGCATTCCCATTGGT
genomic: AAGGCGCAGTGATAGAGGACTCTCTGCTAATGGGTGCAGACTATTATGAGgtaaaataaa ... ttttgttcagACGGAGACGGACAAGAAAGCCCTTTCTGAGACTGGTGGCATTCCCATTGGT
EST: gi|29675781|gb|CB672056.1|CB672056
EST:     AAGGCGCAGTGATAGAGGACTCTCTGCTAATGGGTGCAGACTATTATGAG                         ACGGAGACGGACAAGAAAGCCCTTTCTGAGACTGGTGGCATTCCCATTGGT
genomic: AAGGCGCAGTGATAGAGGACTCTCTGCTAATGGGTGCAGACTATTATGAGgtaaaataaa ... ttttgttcagACGGAGACGGACAAGAAAGCCCTTTCTGAGACTGGTGGCATTCCCATTGGT
EST: gi|86494922|gb|CI137555.1|CI137555
EST:     AAGGCGCAGTGATAGAGGACTCTCTGCTAATGGGTGCAGACTATTATGAG                         ACGGAGACGGACAAGAAAGCCCTTTCTGAGACTGGTGGCATTCCCATTGGT
genomic: AAGGCGCAGTGATAGAGGACTCTCTGCTAATGGGTGCAGACTATTATGAGgtaaaataaa ... ttttgttcagACGGAGACGGACAAGAAAGCCCTTTCTGAGACTGGTGGCATTCCCATTGGT
EST: gi|218485015|gb|FG946141.1|FG946141
EST:     ACGGCGCAGTGATAGAGGACTCTCTGCTAATGGGTGCAGACTATTATGAG                         ACGGAGACGGACAAGAAAGCCCTTTCTGAGACTGGTGGCATTCCCATTGGT
genomic: AAGGCGCAGTGATAGAGGACTCTCTGCTAATGGGTGCAGACTATTATGAGgtaaaataaa ... ttttgttcagACGGAGACGGACAAGAAAGCCCTTTCTGAGACTGGTGGCATTCCCATTGGT
EST: gi|86504993|gb|CI147626.1|CI147626
EST:     AAGGCGCAGTGATAGAGGACTCTCTGCTAATGGGTGCAGACTATTATGAG                         ACGGAGACGGACAAGAAAGCCCTTTCTGAGACTGGTGGCATTCCCATTGGT
genomic: AAGGCGCAGTGATAGAGGACTCTCTGCTAATGGGTGCAGACTATTATGAGgtaaaataaa ... ttttgttcagACGGAGACGGACAAGAAAGCCCTTTCTGAGACTGGTGGCATTCCCATTGGT
EST: gi|88232188|gb|CI230646.1|CI230646
EST:     AAGGCGCAGTGATAGAGGACTCTCTGCTAATGGGTGCAGACTATTATGAG                         ACGGAGGCGGACAAGAAAGCCCTTTCTGAGACTGGTGGCATTCCCATTGGT
genomic: AAGGCGCAGTGATAGAGGACTCTCTGCTAATGGGTGCAGACTATTATGAGgtaaaataaa ... ttttgttcagACGGAGACGGACAAGAAAGCCCTTTCTGAGACTGGTGGCATTCCCATTGGT
EST: gi|86520775|gb|CI160981.1|CI160981
EST:     AAGGCGCAGTGATAGAGGACTCTCTGCTAATGGGTGCAGACTATTATGAG                         ACGGAGACGGACAAGAAAGCCCTTTCTGAGACTGGTGGCATTCCCATTGGT
genomic: AAGGCGCAGTGATAGAGGACTCTCTGCTAATGGGTGCAGACTATTATGAGgtaaaataaa ... ttttgttcagACGGAGACGGACAAGAAAGCCCTTTCTGAGACTGGTGGCATTCCCATTGGT
EST: gi|87010148|gb|CI279245.1|CI279245
EST:     AAGGCGCAGTGATAGAGGACTCTCTGCTAATGGGTGCAGACTATTATGAG                         ACGGAGACGGACAAGAAAGCCCTTTCTGAGACTGGTGGCATTCCCATTGGT
genomic: AAGGCGCAGTGATAGAGGACTCTCTGCTAATGGGTGCAGACTATTATGAGgtaaaataaa ... ttttgttcagACGGAGACGGACAAGAAAGCCCTTTCTGAGACTGGTGGCATTCCCATTGGT
EST: gi|86500004|gb|CI142637.1|CI142637
EST:     AAGGCGCAGTGATAGAGGACTCTCTGCTAATGGGTGCAGACTATTATGAG                         ACGGAGACGGACAAGAAAGCCCTTTCTGAGACTGGTGGCATTCCCATTGGT
genomic: AAGGCGCAGTGATAGAGGACTCTCTGCTAATGGGTGCAGACTATTATGAGgtaaaataaa ... ttttgttcagACGGAGACGGACAAGAAAGCCCTTTCTGAGACTGGTGGCATTCCCATTGGT
EST: gi|86504994|gb|CI147627.1|CI147627
EST:     AAGGCGCAGTGATAGAGGACTCTCTGCTAATGGGTGCAGACTATTATGAG                         ACGGAGACGGACAAGAAAGCCCTTTCTGAGACTGGTGGCATTCCCATTGGT
genomic: AAGGCGCAGTGATAGAGGACTCTCTGCTAATGGGTGCAGACTATTATGAGgtaaaataaa ... ttttgttcagACGGAGACGGACAAGAAAGCCCTTTCTGAGACTGGTGGCATTCCCATTGGT
EST: gi|86500640|gb|CI143273.1|CI143273
EST:     AAGGCGCAGTGATAGAGGACTCTCTGCTAATGGGTGCAGACTATTATGAG                         ACGGAGACGGACAAGAAAGCCCTTTCTGAGACTGGTGGCATTCCCATTGGT
genomic: AAGGCGCAGTGATAGAGGACTCTCTGCTAATGGGTGCAGACTATTATGAGgtaaaataaa ... ttttgttcagACGGAGACGGACAAGAAAGCCCTTTCTGAGACTGGTGGCATTCCCATTGGT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CATTGCACAATCAACCATTCTGTGGTTGGACTCCGGTCCTGTATATCTGAAGGCGCAGTGATAGAGGACTCTCTGCTAATGGGTGCAGACTATTATGAGgtaaaataaaacaaaactatactatattatggtgtattggtgttgtgggaacttaattgtgctttttgttcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA