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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGAGTTTCAGTTCATGGTTGATGAGGCTCCTGTGGATGATAAGATCCACATCGAAGTAGTAAGCAAACGCCGTGGGCTCCGGCTTCCCTTCCGCAATAAGgtcagtcagtcactgttgttacctgctgattgcaaaaccatctcttctgataatgatattcacaaccagttgttaaaaaaaaacagagagaatataatcacatccagttcatagtgccttctaaaatcaacctctcatttctccgaaaatttcag

Basic information

species Oryza sativa
transcript LOC_Os06g47130.3
intron # 11
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os06g47130.2 (Oryza sativa), 5'ss of exon 10
lower sequence: GRMZM2G140443_T02 (Zea mays), 5'ss of exon 11
------AGAGTTTCAGTTCATGGTTGATGAGGCTCCTGTGGATGATAAGATCCACATCGAAGTAGTAAGCAAACGCCGTGGGCTCCGGCTTCCCTTCCGCAATAAGgtcagtcagtcactgttgttacctgctgattgcaa-aaccatctctt--ctgataatgatattcacaaccagttgttaaaaaaaaacagagagaatataatcacatccagttcatagtgccttctaaaatcaacctctcatttctccgaaaatttcag
       ||||| ||||||||||| || ||| |||| ||||| ||||||||||||||| ||||   |||||||||||| |||||      |||||||||||| ||||  |||||  ||    |  |   |||||  ||| | ||| | ||| |  ||||   |     |  ||                                                                                           
GAGCGAGGAGTTCCAGTTCATGGTAGACGAGCCTCCGGTGGAAGATAAGATCCACATCCAAGTCAAAAGCAAACGCCGCGGGCT------TCCCTTCCGCAACAAGgcaagtcacgcagctctaatctttgctgtctgccataactaactcatagctgacggtccgtcttccag------------------------------------------------------------------------------------------
















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|88505624|gb|CI433130.1|CI433130
EST:     GTGGGCTCCGGCTTCCCTTCCGCAATAAG                         GAATCATTGGGGCATGTGGATATAAACCTAGTGGACGTCGTGAACAACGGA
genomic: GTGGGCTCCGGCTTCCCTTCCGCAATAAGgtcagtcagt ... aaaatttcagGAATCATTGGGGCATGTGGATATAAACCTAGTGGACGTCGTGAACAACGGA
EST: gi|88281509|gb|CI402905.1|CI402905
EST:     TCGAAGTAGTAAGCAAACGCCGTGGGCTCCGGCTTCCCTTCCGCAATAAG                         GAATCATTGGGGCATGTGGATATAAACCTAGTGGACGTCGTGAACAACGGA
genomic: TCGAAGTAGTAAGCAAACGCCGTGGGCTCCGGCTTCCCTTCCGCAATAAGgtcagtcagt ... aaaatttcagGAATCATTGGGGCATGTGGATATAAACCTAGTGGACGTCGTGAACAACGGA
EST: gi|88470704|gb|CI407975.1|CI407975
EST:     TCGAAGTAGTAAGCAAACGCCGTGGGCTCCGGCTTCCCTTCCGCAATAAG                         GAATCATTGGGGCATGTGGATATAAACCTAGTGGACGTCGTGAACAACGGA
genomic: TCGAAGTAGTAAGCAAACGCCGTGGGCTCCGGCTTCCCTTCCGCAATAAGgtcagtcagt ... aaaatttcagGAATCATTGGGGCATGTGGATATAAACCTAGTGGACGTCGTGAACAACGGA
EST: gi|88516986|gb|CI444640.1|CI444640
EST:     TCGAAGTAGTAAGCAAACGCCGTGGGCTCCGGCTTCCCTTCCGCAATAAG                         GAATCATTGGGGCATGTGGATATAAACCTAGTGGACGTCGTGAACAACGGA
genomic: TCGAAGTAGTAAGCAAACGCCGTGGGCTCCGGCTTCCCTTCCGCAATAAGgtcagtcagt ... aaaatttcagGAATCATTGGGGCATGTGGATATAAACCTAGTGGACGTCGTGAACAACGGA
EST: gi|88486628|gb|CI423899.1|CI423899
EST:     TCGAAGTAGTAAGCAAACGCCGTGGGCTCCGGCTTCCCTTCCGCAATAAG                         GAATCATTGGGGCATGTGGATATAAACCTAGTGGACGTCGTGAACAACGGA
genomic: TCGAAGTAGTAAGCAAACGCCGTGGGCTCCGGCTTCCCTTCCGCAATAAGgtcagtcagt ... aaaatttcagGAATCATTGGGGCATGTGGATATAAACCTAGTGGACGTCGTGAACAACGGA
EST: gi|4715980|gb|AU057096.1|AU057096
EST:     TCGAAGTAGTAAGCAAACGCCGTGGGCTCCGGCTTCCCTTCCGCAATAAG                         GAATCATTGGGGCATGTGGATATAAACCTAGTGGACGTCGTGAACAACGGA
genomic: TCGAAGTAGTAAGCAAACGCCGTGGGCTCCGGCTTCCCTTCCGCAATAAGgtcagtcagt ... aaaatttcagGAATCATTGGGGCATGTGGATATAAACCTAGTGGACGTCGTGAACAACGGA
EST: gi|4715981|gb|AU057097.1|AU057097
EST:     TCGAAGTAGTAAGCAAACGCCGTGGGCTCCGGCTTCCCTTCCGCAATAAG                         GAATCATTGGGGCATGTGGATATAAACCTAGTGGACGTCGTGAACAACGGA
genomic: TCGAAGTAGTAAGCAAACGCCGTGGGCTCCGGCTTCCCTTCCGCAATAAGgtcagtcagt ... aaaatttcagGAATCATTGGGGCATGTGGATATAAACCTAGTGGACGTCGTGAACAACGGA
EST: gi|88478208|gb|CI415479.1|CI415479
EST:     CGCCGTGGGCTCCGGCTTCCCTTCCGCAATAAG                         GAATCATTGGGGCATGTGGATATAAACCTAGTGGACGTCGTGAACAACGGA
genomic: CGCCGTGGGCTCCGGCTTCCCTTCCGCAATAAGgtcagtcagt ... aaaatttcagGAATCATTGGGGCATGTGGATATAAACCTAGTGGACGTCGTGAACAACGGA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGAGTTTCAGTTCATGGTTGATGAGGCTCCTGTGGATGATAAGATCCACATCGAAGTAGTAAGCAAACGCCGTGGGCTCCGGCTTCCCTTCCGCAATAAGgtcagtcagtcactgttgttacctgctgattgcaaaaccatctcttctgataatgatattcacaaccagttgttaaaaaaaaacagagagaatataatcacatccagttcatagtgccttctaaaatcaacctctcatttctccgaaaatttcag

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