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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGCTGGTCTGGCCAAGCTTAGTTCATTTGGCTTGGATAGGATTCCGGATGCAAATGTTCTAATGAGGGCTGAACAGTCTGCAAAGCAGCAGAAACTCAAGgtaaccacttctattcttgaactacacaaggagaaaacatgctgacatccttttctttttcaag

Basic information

species Oryza sativa
transcript LOC_Os02g32350.1
intron # 12
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g32350.1 (Oryza sativa), 5'ss of exon 12
lower sequence: AC207890.3_FGT002 (Zea mays), 5'ss of exon 12
GGCTGGTCTGGCCAAGCTTAGTTCATTTGGCTTGGATAGGATTCCGGATGCAAATGTTCTAATGAGGGCTGAACAGTCTGCAAAGCAGCAGAAACTCAAGgtaaccacttc--tattcttgaactacacaaggagaaaacatgctgac-atccttttctttttcaag
 ||||| || |||||||| ||||||||||||||||||||||   | |||||  || | ||||  || |||||||||||||| ||||| |||||  | ||||||||   | |  | | | ||| ||  | ||     ||| |   | ||   |  ||   ||||||||
AGCTGGACTTGCCAAGCTGAGTTCATTTGGCTTGGATAGGACCTCAGATGCTTATATCCTAACAAGAGCTGAACAGTCTGCGAAGCAACAGAAGATTAAGgtaacttttccattctccctgagctgtaaaaaagctaaaaacatttactgacgcttaacttttcaag

upper sequence: LOC_Os02g32350.1 (Oryza sativa), 5'ss of exon 12
lower sequence: GRMZM2G136296_T01 (Zea mays), 5'ss of exon 13
GGCTGGTCTGGCCAAGCTTAGTTCATTTGGCTTGGATAGGATTCCGGATGCAAATGTTCTAATGAGGGCTGAACAGTCTGCAAAGCAGCAGAAACTCAAGgtaacc----acttctattcttgaactacacaag-gagaaaacatgctgacatccttttctttttcaag
 ||||| ||||| ||||| ||||| |||||||||||||||||  | |||||  |||| ||||  || |||||||||| ||| ||||| || ||  | |||||||||    | || | | | ||| ||  | ||  | ||||||    |     |  ||   ||||||||
AGCTGGGCTGGCGAAGCTGAGTTCTTTTGGCTTGGATAGGATGTCAGATGCTCATGTCCTAACAAGAGCTGAACAGTTTGCGAAGCAACAAAAGATTAAGgtaacctttaatttttctccctgagctgtaaaaaagggaaaacccattactgacacttaacttttcaag
















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|2799427|gb|AA752416.1|AA752416
EST:     AGCAGAAACTCAAG                         ATCTGGGAGAATTATGTAGAGGGTGAAGAAGTTTCCAATGGATCTGCATCT
genomic: AGCAGAAACTCAAGgtaaccactt ... ctttttcaagATCTGGGAGAATTATGTAGAGGGTGAAGAAGTTTCCAATGGATCTGCATCT
EST: gi|2311450|gb|C27605.1|C27605
EST:     AAATGTTCTAATGAGGGCTGAACAGTCTGCAAAGCA-CNAGAAACTCAAG                         ATCTGGGAGAATTATGTAGAGGGTGAAGAAGTTTCCAATGGATCTGCATCT
genomic: AAATGTTCTAATGAGGGCTGAACAGTCTGCAAAGCAGC-AGAAACTCAAGgtaaccactt ... ctttttcaagATCTGGGAGAATTATGTAGAGGGTGAAGAAGTTTCCAATGGATCTGCATCT
EST: gi|29622581|gb|CB627592.1|CB627592
EST:     CAAATGTTCTAATGAGGGCTGAACAGTCTGCAAAGCAGCAGAAACTCAAG                         ATCTGGGAGAATTATGTAGAGGGTGAAGAAGTTTCCAATGGATCTGCATCT
genomic: CAAATGTTCTAATGAGGGCTGAACAGTCTGCAAAGCAGCAGAAACTCAAGgtaaccactt ... ctttttcaagATCTGGGAGAATTATGTAGAGGGTGAAGAAGTTTCCAATGGATCTGCATCT
EST: gi|29674464|gb|CB670739.1|CB670739
EST:     CAAATGTTCTAATGAGGGCTGAACAGTCTGCAAAGCAGCAGAAACTCAAG                         ATCTGGGAGAATTATGTAGAGGGTGAAGAAGTTTCCAATGGATCTGCATCT
genomic: CAAATGTTCTAATGAGGGCTGAACAGTCTGCAAAGCAGCAGAAACTCAAGgtaaccactt ... ctttttcaagATCTGGGAGAATTATGTAGAGGGTGAAGAAGTTTCCAATGGATCTGCATCT
EST: gi|218498571|gb|FG951792.1|FG951792
EST:     AGCAGCAGAGACTCAAG                         ATCTGGGAGAATTATGTAGA-GGTCGAAGAAGTTTCCAATGGATCTGCATC
genomic: AGCAGCAGAAACTCAAGgtaaccactt ... ctttttcaagATCTGGGAGAATTATGTAGAGGGT-GAAGAAGTTTCCAATGGATCTGCATC
EST: gi|29623578|gb|CB628589.1|CB628589
EST:     CAAATGTTCTAATGAGGGCTGAACAGTCTGCAAAGCAGCAGAAACTCAAG                         ATCTGGGAGAATTATGTAGAGGGTGAAGAAGTTTCCAATGGATCTGCATCT
genomic: CAAATGTTCTAATGAGGGCTGAACAGTCTGCAAAGCAGCAGAAACTCAAGgtaaccactt ... ctttttcaagATCTGGGAGAATTATGTAGAGGGTGAAGAAGTTTCCAATGGATCTGCATCT
EST: gi|66916134|gb|CX102982.1|CX102982
EST:     CAAATGTTCTAATGAGGGCTGAACAGTCTGCAAAGCAGCAGAAACTCAAG                         ATCTGGGAGAATTATGTAGAGGGTGAAGAAGTTTCCAATGGATCTGCATCT
genomic: CAAATGTTCTAATGAGGGCTGAACAGTCTGCAAAGCAGCAGAAACTCAAGgtaaccactt ... ctttttcaagATCTGGGAGAATTATGTAGAGGGTGAAGAAGTTTCCAATGGATCTGCATCT
EST: gi|88329612|gb|CI650071.1|CI650071
EST:     CAAATGTTCTAATGAGGGCTGAACAGTCTGCAAAGCAGCAGAAACTCAAG                         ATCTGGGAGAATTATGTAGAGGGTGAAGAAGTTTCCAATGGATCTGCATCT
genomic: CAAATGTTCTAATGAGGGCTGAACAGTCTGCAAAGCAGCAGAAACTCAAGgtaaccactt ... ctttttcaagATCTGGGAGAATTATGTAGAGGGTGAAGAAGTTTCCAATGGATCTGCATCT
EST: gi|13420819|gb|AU174909.1|AU174909
EST:     CAAATGTTCTAATGAGGGCTGAACAGTCTGCAAAGCAGCAGAAACTCAAG                         ATCTGGGAGAATTATGTAGAGGGTGAAGAAGTTTCCAATGGATCTGCATCT
genomic: CAAATGTTCTAATGAGGGCTGAACAGTCTGCAAAGCAGCAGAAACTCAAGgtaaccactt ... ctttttcaagATCTGGGAGAATTATGTAGAGGGTGAAGAAGTTTCCAATGGATCTGCATCT
EST: gi|29627293|gb|CB632304.1|CB632304
EST:     CAAATGTTCTAATGAGGGCTGAACAGTCTGCAAAGCAGCAGAAACTCAAG                         ATCTGGGAGAATTATGTAGAGGGTGAAGAAGTTTCCAATGGATCTGCATCT
genomic: CAAATGTTCTAATGAGGGCTGAACAGTCTGCAAAGCAGCAGAAACTCAAGgtaaccactt ... ctttttcaagATCTGGGAGAATTATGTAGAGGGTGAAGAAGTTTCCAATGGATCTGCATCT
EST: gi|29631512|gb|CB636521.1|CB636521
EST:     CAAATGTTCTAATGAGGGCTGAACAGTCTGCAAAGCAGCAGAAACTCAAG                         ATCTGGGAGAATTATGTAGAGGGTGAAGAAGTTTCCAATGGATCTGCATCT
genomic: CAAATGTTCTAATGAGGGCTGAACAGTCTGCAAAGCAGCAGAAACTCAAGgtaaccactt ... ctttttcaagATCTGGGAGAATTATGTAGAGGGTGAAGAAGTTTCCAATGGATCTGCATCT
EST: gi|38565897|gb|CK085350.1|CK085350
EST:     CAAATGTTCTAATGAGGGCTGAACAGTCTGCAAAGCAGCAGAAACTCAAG                         ATCTGGGAGAATTATGTAGAGGGTGAAGAAGTTTCCAATGGATCTGCATCT
genomic: CAAATGTTCTAATGAGGGCTGAACAGTCTGCAAAGCAGCAGAAACTCAAGgtaaccactt ... ctttttcaagATCTGGGAGAATTATGTAGAGGGTGAAGAAGTTTCCAATGGATCTGCATCT
EST: gi|218500523|gb|FG958817.1|FG958817
EST:     CAAATGTTCTAATGAGGGCTGAACAGTCTGCAAAGCAGCAGAAACTCAAG                         ATCTGGGAGAATTATGTAGAGGGTGAAGAAGTTTCCAATGGATCTGCATCT
genomic: CAAATGTTCTAATGAGGGCTGAACAGTCTGCAAAGCAGCAGAAACTCAAGgtaaccactt ... ctttttcaagATCTGGGAGAATTATGTAGAGGGTGAAGAAGTTTCCAATGGATCTGCATCT
EST: gi|29644259|gb|CB649266.1|CB649266
EST:     CAAATGTTCTAATGAGGGCTGAACAGTCTGCAAAGCAGCAGAAACTCAAG                         ATCTGGGAGAATTATGTAGAGGGTGAAGAAGTTTCCAATGGATCTGCATCT
genomic: CAAATGTTCTAATGAGGGCTGAACAGTCTGCAAAGCAGCAGAAACTCAAGgtaaccactt ... ctttttcaagATCTGGGAGAATTATGTAGAGGGTGAAGAAGTTTCCAATGGATCTGCATCT
EST: gi|58692787|gb|CK081474.1|CK081474
EST:     CAAATGTTCTAATGAGGGCTGAACAGTCTGCAAAGCAGCAGAAACTCAAG                         ATCTGGGAGAATTATGTAGAGGGTGAAGAAGTTTCCAATGGATCTGCATCT
genomic: CAAATGTTCTAATGAGGGCTGAACAGTCTGCAAAGCAGCAGAAACTCAAGgtaaccactt ... ctttttcaagATCTGGGAGAATTATGTAGAGGGTGAAGAAGTTTCCAATGGATCTGCATCT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGCTGGTCTGGCCAAGCTTAGTTCATTTGGCTTGGATAGGATTCCGGATGCAAATGTTCTAATGAGGGCTGAACAGTCTGCAAAGCAGCAGAAACTCAAGgtaaccacttctattcttgaactacacaaggagaaaacatgctgacatccttttctttttcaag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAAG