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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtagaaatcctgtttcattctaatattcttttgtattatattttgttctattctccatttgttgggtgatgcatcgttaaaacctcatatggtctcatactttgttatgtcatgtattttaatcttttgtgtttcatttctgttacttatcttttcagAAAAACGAAGTGTTTGATGCTTTGAGAAGATATAGCAAACCTACTCATCTGTGGGATCTATATGCATTTTCTTGTGATCCCTCCACTGTTTATCAGAAAT

Basic information

species Oryza sativa
transcript LOC_Os08g44260.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os08g44260.2 (Oryza sativa), 3'ss of exon 6
lower sequence: AC194264.3_FGT006 (Zea mays), 3'ss of exon 6
gtagaaatcctgtttcattctaatattcttttgtattatattttgttctattctccatttgttgggtgatgcatcgttaaaacctcatatggtctcatactttgttatgtcatgtatttt-aatcttttgtgtttcatttctgttacttatcttttcagAAAAACGAAGTGTTTGATGCTTTGAGAAGATATAGCAAACCTACTCATCTGTGGGATCTATATGCATTTTCTTGTGATCCCTCCACTGTTTATCAGAAAT
                                                     | | ||  ||   | ||| || |    |      | |  |  |||| ||  ||   ||||| ||  | ||||||||   ||| | || || | ||| |||||||||||||| |||||||||||||||||||| ||||| |  |||||| || || ||||||||||||||||||||||||||||||| |||||  || | ||  | |
----------------------------------------------------gtaccttatttcaattatgtatgg----agttgtttcttttagcatatttattt---tcatgcatgctgaatcttttagattttacttgtgattcttgtcttttcagAAAAATGAAGTGTTTGATGCTTTGAGGAGATACACTAAACCTGCTAATTTGTGGGATCTATATGCATTTTCTTGTGATCCATCCACCATTAAGCATGATT
















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|701989|gb|D48280.1|D48280
EST:     GTAAAGACATGAGGGTCATTGTGTTCGATTTTCTTCCTAAAACCAAGCAG                         AAAAACGAAGTTCTTTGATGCTTTGAGAAGATATAGCAAACCTACTCATCT
genomic: GTAAAGACATGAGGGTCATTGTGTTCGATTTTCTTCCTAAAACCAAGCAGgtagaaatcc ... atcttttcagAAAAACGAAGTG-TTTGATGCTTTGAGAAGATATAGCAAACCTACTCATCT






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gttatgtcatgtattttaatcttttgtgtttcatttctgttacttatcttttcagAAAAACGAAGTGTTTGATGCTTTGAGAAGATATAGCAAACCTACTCATCTGTGGGATCTATATGCATTTTCTTGTGATCCCTCCACTGTTTATCAGAAAT
             ttttaat  putative branch site (score: 3)
                                       ttacttatcttttc  putative PPT
        atgtattttaatcttt  TA-rich tract