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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttatcctaagaatcaaatgtttgttaatcattgtcaaaacatattatttggaaaggaagtaactgtgcatgtcttgtaattttcagCAATGTTGTGGCTGCAACTGATTTAACACTGATGGCATTGGCAGGAATAGGCCTGCGTCACGATAAG

Basic information

species Oryza sativa
transcript LOC_Os05g39230.2
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os05g39230.2 (Oryza sativa), 3'ss of exon 5
lower sequence: AC197705.4_FGT011 (Zea mays), 3'ss of exon 6
gttatcctaagaatcaaatgtttgttaatcat-tgtcaa--aacatattatttggaaaggaagtaactgtgcatgtc--ttgtaattttcagCAATGTTGTGGCTGCAACTGATTTAACACTGATGGCATTGGCAGGAATAGGCCTGCGTCACGATAAG
|||  |    |||| |  | ||| ||  |    ||||||  || | |  |||| || |||| ||||||||| || |   |||| |||||||||||||| || |||||||||||||| ||  ||||||||||||||||||||||||| ||   | | |||
gttgcctgctgaatgatttttttcttcttggggtgtcaatcaataaaacattttgacaggatgtaactgtggattttgtttgtcattttcagCAATGTGGTTGCTGCAACTGATTTGACCATGATGGCATTGGCAGGAATAGGCCTTCGATGCAACAAG
















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|29689746|gb|CB686021.1|CB686021
EST:     CAATGGCTTTACCAAAATGGCAGAAAAGGCGCAACTGTACGTCAAGTCAG                         CAATGTTGTGGCTGCAACTGATTTAACACTGATGGCATTGGCAGGAATAGG
genomic: CAATGGCTTTACCAAAATGGCAGAAAAGGCGCAACTGTACGTCAAGTCAGgttatcctaa ... taattttcagCAATGTTGTGGCTGCAACTGATTTAACACTGATGGCATTGGCAGGAATAGG
EST: gi|58602199|gb|CK012727.1|CK012727
EST:     CAATGGCTTTACCAAAATGGCAGAAAAGGCGCAACTGTACGTCAAGTCAG                         CAATGTTGTGGCTGCAACTGATTTAACACTGATGGCATTGGCAGGAATAGG
genomic: CAATGGCTTTACCAAAATGGCAGAAAAGGCGCAACTGTACGTCAAGTCAGgttatcctaa ... taattttcagCAATGTTGTGGCTGCAACTGATTTAACACTGATGGCATTGGCAGGAATAGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgtcaaaacatattatttggaaaggaagtaactgtgcatgtcttgtaattttcagCAATGTTGTGGCTGCAACTGATTTAACACTGATGGCATTGGCAGGAATAGGCCTGCGTCACGATAAG
                         aagtaac  putative branch site (score: 2)
                                                ttttc  putative PPT
     aaacatattattt  TA-rich tract