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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AAATGTGGCAAAAGCAGAAGGCAGGCCTGAGCCTGCATTGTATGGTAGTGAGGACATTCGTCCTCTGACCTTAGATGATTTCAAATCTGCCCATGAGCAGgtgagaccagcacattttatatttattttgagctctttacttgaaagttcataatctgatcaatttatttaccacag

Basic information

species Oryza sativa
transcript LOC_Os11g43970.1
intron # 27
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os11g43970.1 (Oryza sativa), 5'ss of exon 27
lower sequence: GRMZM2G126453_T01 (Zea mays), 5'ss of exon 22
AAATGTGGCAAAAGCAGAAGGCAGGCCTGAGCCTGCATTGTATGGTAGTGAGGACATTCGTCCTCTGACCTTAGATGATTTCAAATCTGCCCATGAGCAGgtgagaccagcacattttatatttattttgagctctttacttgaaagttcat----aatctga---tcaatttatttaccacag----------------------------------------------------
 ||| |||| ||| ||||||| ||||| ||||||||||| ||||| || |||||||| || ||||| | | ||||||| ||||||||||||||||||||||||||| || || | || ||     ||   | ||| |  |    |   |  |    |||||         ||| | | | ||                                                      
GAATTTGGCTAAAACAGAAGGTAGGCCGGAGCCTGCATTATATGGAAGCGAGGACATCCGCCCTCTTAGCATAGATGACTTCAAATCTGCCCATGAGCAGgtgagaacaccaaagttgatcccatttcgcatctcctccccccgacccttctctgcaatctacgttcttgtttgtatgcaaccatgtattcttgtttcttagagcggcatcctaatctctccttggtcgggcgcag

upper sequence: LOC_Os11g43970.1 (Oryza sativa), 5'ss of exon 27
lower sequence: GRMZM2G052403_T01 (Zea mays), 5'ss of exon 18
AAATGTGGCAAAAGCAGAAGGCAGGCCTGAGCCTGCATTGTATGGTAGTGAGGACATTCGTCCTCTGACCTTAGATGATTTCAAATCTGCCCATGAGCAGgtgagaccagcacattttatatttattttgagctctttacttgaaagttcataatctgatcaatttatttaccacag------------------------
 | | |||| ||| ||||||| ||||| ||||| ||||||||||| || ||| |||| |||||||| | | |||| || |||||||| |||||||||||||||||| || |||    | |    | | |     | | |      |  || || |||  ||      ||  | ||                          
GAGTTTGGCTAAAACAGAAGGTAGGCCAGAGCCCGCATTGTATGGAAGCGAGCACATCCGTCCTCTTAGCATAGACGACTTCAAATCCGCCCATGAGCAGgtgagaacaccaccaagtttgccgagtctacaaacatcaacctgcatatcgta-tctactcccgaccttctctacgatctacattcttgtttctagagcat
















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|58653111|gb|CK041791.1|CK041791
EST:     AGGACATTCGTCCTCTGACCTTAGATGATTTCAAATCTGCCCATGAGCAG                         GTTTGTGCAAGCGTTTCATCTGATTCAGCAAACATGAATGAACTTCTTCAA
genomic: AGGACATTCGTCCTCTGACCTTAGATGATTTCAAATCTGCCCATGAGCAGgtgagaccag ... tttaccacagGTTTGTGCAAGCGTTTCATCTGATTCAGCAAACATGAATGAACTTCTTCAA
EST: gi|86422679|gb|CI060252.1|CI060252
EST:     CTCTGACCTTAGATGATTTCAAATCTGCCCATGAGCAG                         GTTTGTGCAAGCGTTTCATCTGATTCAGCAAACATGAATGAACTTCTTCAA
genomic: CTCTGACCTTAGATGATTTCAAATCTGCCCATGAGCAGgtgagaccag ... tttaccacagGTTTGTGCAAGCGTTTCATCTGATTCAGCAAACATGAATGAACTTCTTCAA
EST: gi|7274059|gb|AU031974.2|AU031974
EST:     AGNACATTCGTCCTCTGACCTTAGATGATTTCAAATCTGCCCATGAGCAG                         GTTTGTGCAAGCGTTTCATCTGATTCAGCAAACATGAATGAACTTCTTCAA
genomic: AGGACATTCGTCCTCTGACCTTAGATGATTTCAAATCTGCCCATGAGCAGgtgagaccag ... tttaccacagGTTTGTGCAAGCGTTTCATCTGATTCAGCAAACATGAATGAACTTCTTCAA
EST: gi|33659831|gb|CF282444.1|CF282444
EST:     AGGACATTCGTCCTCTGACCTTAGATGATTTCAAATCTGCCCATGAGCAG                         GTTTGTGCAAGCGTTTCATCTGATTCAGCAAACATGAATGAACTTCTTCAA
genomic: AGGACATTCGTCCTCTGACCTTAGATGATTTCAAATCTGCCCATGAGCAGgtgagaccag ... tttaccacagGTTTGTGCAAGCGTTTCATCTGATTCAGCAAACATGAATGAACTTCTTCAA
EST: gi|29614541|gb|CB619554.1|CB619554
EST:     AGGACATTCGTCCTCTGACCTTAGATGATTTCAAATCTGCCCATGAGCAG                         GTTTGTGCAAGCGTTTCATCTGATTCAGCAAACATGAATGAACTTCTTCAA
genomic: AGGACATTCGTCCTCTGACCTTAGATGATTTCAAATCTGCCCATGAGCAGgtgagaccag ... tttaccacagGTTTGTGCAAGCGTTTCATCTGATTCAGCAAACATGAATGAACTTCTTCAA
EST: gi|88830949|gb|CI080373.1|CI080373
EST:     TCCTCTGACCTTAGATGATTTCAAATCTGCCCATGAGCAG                         GTTTGTGCAAGCGTTTCATCTGATTCAGCAAACATGAATG-ACTTCTTCAA
genomic: TCCTCTGACCTTAGATGATTTCAAATCTGCCCATGAGCAGgtgagaccag ... tttaccacagGTTTGTGCAAGCGTTTCATCTGATTCAGCAAACATGAATGAACTTCTTCAA
EST: gi|86480548|gb|CI123181.1|CI123181
EST:     AGGACATTCGTCCTCTGACCTTAGATGATTTCAAATCTGCCCATGAGCAG                         GTTTGTGCAAGCGTTTCATCTGATTCAGCAAACATGAATGAACTTCTTCAA
genomic: AGGACATTCGTCCTCTGACCTTAGATGATTTCAAATCTGCCCATGAGCAGgtgagaccag ... tttaccacagGTTTGTGCAAGCGTTTCATCTGATTCAGCAAACATGAATGAACTTCTTCAA
EST: gi|8860068|gb|AU097386.1|AU097386
EST:     AGGACATTCGTCCTCTGACCTTAGATGATTTCAAATCTGCCCATGAGCAG                         GTTTGTGCAAGCGTTTCATCTGATTCAGCAAACATGAATGAACTTCTTCAA
genomic: AGGACATTCGTCCTCTGACCTTAGATGATTTCAAATCTGCCCATGAGCAGgtgagaccag ... tttaccacagGTTTGTGCAAGCGTTTCATCTGATTCAGCAAACATGAATGAACTTCTTCAA
EST: gi|11171080|gb|AU163614.1|AU163614
EST:     AGGACATTCGTCCTCTGACCTTAGATGATTTCAAATCTGCCCATGAGCAG                         GTTTGTGCAAGCGTTTCATCTGATTCAGCAAACATGAATGAACTTCTTCAA
genomic: AGGACATTCGTCCTCTGACCTTAGATGATTTCAAATCTGCCCATGAGCAGgtgagaccag ... tttaccacagGTTTGTGCAAGCGTTTCATCTGATTCAGCAAACATGAATGAACTTCTTCAA
EST: gi|88842637|gb|CI081893.1|CI081893
EST:     GATGATTTCAAATCTGCCCATGAGCAG                         GTTTGTGCAAGCGTTTCATCTGATTCAGCAAACATGAATGAACTTCTTCAA
genomic: GATGATTTCAAATCTGCCCATGAGCAGgtgagaccag ... tttaccacagGTTTGTGCAAGCGTTTCATCTGATTCAGCAAACATGAATGAACTTCTTCAA
EST: gi|29682150|gb|CB678425.1|CB678425
EST:     AGGACATTCGTCCTCTGACCTTAGATGATTTCAAATCTGCCCATGAGCAG                         GTTTGTGCAAGCGTTTCATCTGATTCAGCAAACATGAATGAACTTCTTCAA
genomic: AGGACATTCGTCCTCTGACCTTAGATGATTTCAAATCTGCCCATGAGCAGgtgagaccag ... tttaccacagGTTTGTGCAAGCGTTTCATCTGATTCAGCAAACATGAATGAACTTCTTCAA
EST: gi|15857794|gb|BI810606.1|BI810606
EST:     AGGACATTCGTCCTCTGACCTTAGATGATTTCAAATCTGCCCATGAGCAG                         GTTTGTGCAAGCGTTTCATCTGATTCAGCAAACATGAATGAACTTCTTCAA
genomic: AGGACATTCGTCCTCTGACCTTAGATGATTTCAAATCTGCCCATGAGCAGgtgagaccag ... tttaccacagGTTTGTGCAAGCGTTTCATCTGATTCAGCAAACATGAATGAACTTCTTCAA
EST: gi|8860101|gb|AU097419.1|AU097419
EST:     AGGACATTCGTCCTCTGACCTTAGATGATTTCAAATCTGCCCATGAGCAG                         GTTTGTGCAAGCGTTTCATCTGATTCAGCAAACATGAATGAACTTCTTCAA
genomic: AGGACATTCGTCCTCTGACCTTAGATGATTTCAAATCTGCCCATGAGCAGgtgagaccag ... tttaccacagGTTTGTGCAAGCGTTTCATCTGATTCAGCAAACATGAATGAACTTCTTCAA
EST: gi|86479265|gb|CI121898.1|CI121898
EST:     AGGACATTCGTCCTCTGACCTTAGATGATTTCAAATCTGCCCATGAGCAG                         GTTTGTGCAAGCGTTTCATCTGATTCAGCAAACATGAATGAACTTCTTCAA
genomic: AGGACATTCGTCCTCTGACCTTAGATGATTTCAAATCTGCCCATGAGCAGgtgagaccag ... tttaccacagGTTTGTGCAAGCGTTTCATCTGATTCAGCAAACATGAATGAACTTCTTCAA
EST: gi|86849466|gb|CI299672.1|CI299672
EST:     AGGACATTCGTCCTCTGACCTTAGATGATTTCAAATCTGCCCATGAGCAG                         GTTTGTGCAAGCGTTTCATCTGATTCAGCAAACATGAATGAACTTCTTCAA
genomic: AGGACATTCGTCCTCTGACCTTAGATGATTTCAAATCTGCCCATGAGCAGgtgagaccag ... tttaccacagGTTTGTGCAAGCGTTTCATCTGATTCAGCAAACATGAATGAACTTCTTCAA
EST: gi|5038858|gb|AU070968.1|AU070968
EST:     AGGACATTCGTCCTCTGACCTTAGATGATTTCAAATCTGCCCATGAGCAG                         GTTTGTGCAAGCGTTTCATCTGATTCAGCAAACATGAATGAACTTCTTCAA
genomic: AGGACATTCGTCCTCTGACCTTAGATGATTTCAAATCTGCCCATGAGCAGgtgagaccag ... tttaccacagGTTTGTGCAAGCGTTTCATCTGATTCAGCAAACATGAATGAACTTCTTCAA
EST: gi|27554453|gb|CA998353.1|CA998353
EST:     AGGACATTCGTCCTCTGACCTTAGATGATTTCAAATCTGCCCATGAGCAC                         GTTTGTGCAAGCGTTTCATCTGAT
genomic: AGGACATTCGTCCTCTGACCTTAGATGATTTCAAATCTGCCCATGAGCAGgtgagaccag ... tttaccacagGTTTGTGCAAGCGTTTCATCTGAT
EST: gi|58686681|gb|CK075368.1|CK075368
EST:     AGGACATTCGTCCTCTGACCTTAGATGATTTCAAATCTGCCCATGAGCAG                         GTTTGTGCAAGCGTTTCATCTGATTCAGCAAACATGAATGAACTTCTTCAA
genomic: AGGACATTCGTCCTCTGACCTTAGATGATTTCAAATCTGCCCATGAGCAGgtgagaccag ... tttaccacagGTTTGTGCAAGCGTTTCATCTGATTCAGCAAACATGAATGAACTTCTTCAA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AAATGTGGCAAAAGCAGAAGGCAGGCCTGAGCCTGCATTGTATGGTAGTGAGGACATTCGTCCTCTGACCTTAGATGATTTCAAATCTGCCCATGAGCAGgtgagaccagcacattttatatttattttgagctctttacttgaaagttcataatctgatcaatttatttaccacag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG