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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTTTCTGCTATGAGGATGTGCTGGTAACGTAAATTTGTGGTTGCAGGTCATTCAGCTTCAAGGTGATCAGCGTAAGAATGTTGCCACGTTCCTAGTTCAGgtattgagaattatcagagcagagctatgacttctcaagagattaatgctgctaagttgacctatttatattctgaatctgattttttatctctttttgctag

Basic information

species Oryza sativa
transcript LOC_Os05g41900.3
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os05g41900.3 (Oryza sativa), 5'ss of exon 3
lower sequence: GRMZM2G073535_T01 (Zea mays), 5'ss of exon 4
TTTTCTGCTATGAGGATGTGCTGGTAACGTAAATTTGTGGTTGCAGGTCATTCAGCTTCAAGGTGATCAGCGTAAGAATGTTGCCACGTTCCTAGTTCAGgtattgagaattatcagagcagagctatgacttctcaagagattaatgctgctaagttgacctatttat--attctgaatctgattttttatctctttttgctag
                                              ||||||||||| |||||||| ||||| ||||||||||| || ||||||||||||||||| |||||  ||||| | |  |       |        |  | | | | || | ||  | || | |  || ||||   ||   || |  ||  | ||| |||
----------------------------------------------GTCATTCAGCTCCAAGGTGACCAGCGCAAGAATGTTGCTACTTTCCTAGTTCAGgtattcagaatcttcagacctggccagctgaatactgttttacca-taccgata-gatgttcaatctgttaatactgatcgtgcaattattacttgtcttggtag

upper sequence: LOC_Os05g41900.3 (Oryza sativa), 5'ss of exon 3
lower sequence: GRMZM2G073535_T05 (Zea mays), 5'ss of exon 3
----TTTTCTGCTATGAGGATGTGCTGGTAACGTAAATTTGTGGTTGCAGGTCATTCAGCTTCAAGGTGATCAGCGTAAGAATGTTGCCACGTTCCTAGTTCAGgtattgagaattatcagagcagagctatgacttctcaagagattaatgctgctaagttgacctatttat--attctgaatctgattttttatctctttttgctag
    | | | | |  | |||| | ||| |        ||    | |||||||||||||||| |||||||| ||||| ||||||||||| || ||||||||||||||||| |||||  ||||| | |  |       |        |  | | | | || | ||  | || | |  || ||||   ||   || |  ||  | ||| |||
GGTATCTGCCGGTTGGTGGATATACTGAT----CTGTTTGTCCGCTGCAGGTCATTCAGCTCCAAGGTGACCAGCGCAAGAATGTTGCTACTTTCCTAGTTCAGgtattcagaatcttcagacctggccagctgaatactgttttacca-taccgata-gatgttcaatctgttaatactgatcgtgcaattattacttgtcttggtag
















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|88528638|gb|CI456888.1|CI456888
EST:     TTCAGCTTCAAGGTGATCAGCGTAAGAATGTTGCCACGTTCCTAGTTCAG                         GCTGGGATTGGTAAGAAGGACAACATCAAGATTCACGGTTTCTAAGCTGCC
genomic: TTCAGCTTCAAGGTGATCAGCGTAAGAATGTTGCCACGTTCCTAGTTCAGgtattgagaa ... tttttgctagGCTGGGATTGCTAAGAAGGACAACATCAAGATTCACGGTTTCTAAGCTGCC
EST: gi|33682723|gb|CF310962.1|CF310962
EST:     TTCAGCTTCAAGGTGATCAGCGTAAGAATGTTGCCACGTTCCTAGTTCAG                         GCTGGGATTGCTAAGAAGGACAACATCAAGATTCACGGTTTCTAAGCTGCC
genomic: TTCAGCTTCAAGGTGATCAGCGTAAGAATGTTGCCACGTTCCTAGTTCAGgtattgagaa ... tttttgctagGCTGGGATTGCTAAGAAGGACAACATCAAGATTCACGGTTTCTAAGCTGCC
EST: gi|89171918|gb|CI040428.1|CI040428
EST:     TTCAGCTTCAAGGTGATCAGCGTAAGAATGTTGCCACGTTCCTAGTTCAG                         GCTGGGATTGCTAAGAAGGACAACATCAAGATTCACGGTTTCTAAGCTGCC
genomic: TTCAGCTTCAAGGTGATCAGCGTAAGAATGTTGCCACGTTCCTAGTTCAGgtattgagaa ... tttttgctagGCTGGGATTGCTAAGAAGGACAACATCAAGATTCACGGTTTCTAAGCTGCC
EST: gi|9884552|gb|BE607385.1|BE607385
EST:     TTCAGCTTCAAGGTGATCAGCGTAAGAATGTTGCCACGTTCCTAGTTCAG                         GCTGGGATTGCTAAGAAGGACAACATCAAGATTCACGGTTTCTAAGCTGCC
genomic: TTCAGCTTCAAGGTGATCAGCGTAAGAATGTTGCCACGTTCCTAGTTCAGgtattgagaa ... tttttgctagGCTGGGATTGCTAAGAAGGACAACATCAAGATTCACGGTTTCTAAGCTGCC
EST: gi|38481136|gb|CF965225.1|CF965225
EST:     CACGTT-CTAGTTCAG                         GCTGGGATTGCTAAGAAGGACAACATCAAGATTCACGGTTTCTAAGCTGCC
genomic: CACGTTCCTAGTTCAGgtattgagaa ... tttttgctagGCTGGGATTGCTAAGAAGGACAACATCAAGATTCACGGTTTCTAAGCTGCC
EST: gi|55431357|gb|CV728691.1|CV728691
EST:     TTCAGCTTCAAGGTGATCAGCGTAAGAATGTTGCCACGTTCCTAGTTCAG                         GCTGGGATTGCTAAGAAGGACAACATCAAGATTCACGGTTTTTAAGCTGCC
genomic: TTCAGCTTCAAGGTGATCAGCGTAAGAATGTTGCCACGTTCCTAGTTCAGgtattgagaa ... tttttgctagGCTGGGATTGCTAAGAAGGACAACATCAAGATTCACGGTTTCTAAGCTGCC
EST: gi|55412517|gb|CV724893.1|CV724893
EST:     TTCAGCTTCAAGGTGATCAGCGTAAGAATGTTGCCACGTTCCTAGTTCAG                         GCTGGGATTGCTAAGAAGGACAACATCAAGATTCCCGGTTTTTAAGCTGCC
genomic: TTCAGCTTCAAGGTGATCAGCGTAAGAATGTTGCCACGTTCCTAGTTCAGgtattgagaa ... tttttgctagGCTGGGATTGCTAAGAAGGACAACATCAAGATTCACGGTTTCTAAGCTGCC
EST: gi|568322|gb|D39166.1|D39166
EST:     TTCAGCTTCAAGGTGATCAGCGTAAGAATGTTGCCACGTTCCTAGTTCAG                         GCTGGGATTGCTAAGAAGGACAACATCAAGATTCACGGTTTCTAAGCTGCC
genomic: TTCAGCTTCAAGGTGATCAGCGTAAGAATGTTGCCACGTTCCTAGTTCAGgtattgagaa ... tttttgctagGCTGGGATTGCTAAGAAGGACAACATCAAGATTCACGGTTTCTAAGCTGCC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TTTTCTGCTATGAGGATGTGCTGGTAACGTAAATTTGTGGTTGCAGGTCATTCAGCTTCAAGGTGATCAGCGTAAGAATGTTGCCACGTTCCTAGTTCAGgtattgagaattatcagagcagagctatgacttctcaagagattaatgctgctaagttgacctatttatattctgaatctgattttttatctctttttgctag

- - - - - - - - - - - - - - - - - - - - - - - - -  TCAGCT