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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaatctattctgacgaattttctgtgcccctctaatgttacggtcacttttagcttggcacttaatcctaaaatgactttatgcctactgcttttaagGGTTGAAAATGCGGAAGTGTTGTGCCTGGGAATTGTTTCAGTGGCAGTGTTCATGCTTGTTTTGCCACTCTTTAAGGCTACTGGTAATATCCTTCTGCAA

Basic information

species Oryza sativa
transcript LOC_Os02g58580.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g58580.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G017365_T08 (Zea mays), 3'ss of exon 7
-------------gtaaatctattctgacgaattttctgtgcccctctaatgttacggtcacttttagcttggcacttaatcctaaaatgactttatgcctactgcttttaagGGTTGAAAATGCGGAAGTGTTGTGCCTGGGAATTGTTTCAGTGGCAGTGTTCATGCTTGTTTTGCCACTCTTTAAGGCTACTGGTAATATCCTTCTGCAA
              |    ||||| | |||  ||| ||||||  | |   | | | ||| |||| | ||       ||| ||||        ||| ||| |||| |   || || |||| ||||| || ||  ||||||||||||| || |||||||||||||| ||||||||||||||  | ||||| ||||||||||||||||| ||||||
gtaaaatctattttttttactattttcacg--tttcctgtgcttcccatttatcatggtgacttgtggccatctgtttattcct--------tttgtgc-tactacccgta-gGATTGAGAATGCTGAGGTTCTGTGCCTGGGAATCGTCTCAGTGGCAGTGTTTATGCTTGTTTTGCCGTTATTTAAAGCTACTGGTAATATCCTACTGCAA
















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|8858691|gb|AU096009.1|AU096009
EST:     TGCAGGCTTGATACTAGCTTCCTGGTTTCTTTCATTGGG                         GGTTGAAAATGCGGAAGTGTTGTGCCTGGGAATTGTTTCAGTGGCAGTGTT
genomic: TGCAGGCTTGATACTAGCTTCCTGGTTTCTTTCATTGGGgtaaatctat ... tgcttttaagGGTTGAAAATGCGGAAGTGTTGTGCCTGGGAATTGTTTCAGTGGCAGTGTT
EST: gi|29661174|gb|CB657449.1|CB657449
EST:     TGCAGGCTTGATACTAGCTTCCTGGTTTCTTTCATTGGG                         GGTTGAAAATGCGGAAGTGTTGTGCCTGGGAATTGTTTCAGTGGCAGTGTT
genomic: TGCAGGCTTGATACTAGCTTCCTGGTTTCTTTCATTGGGgtaaatctat ... tgcttttaagGGTTGAAAATGCGGAAGTGTTGTGCCTGGGAATTGTTTCAGTGGCAGTGTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcacttttagcttggcacttaatcctaaaatgactttatgcctactgcttttaagGGTTGAAAATGCGGAAGTGTTGTGCCTGGGAATTGTTTCAGTGGCAGTGTTCATGCTTGTTTTGCCACTCTTTAAGGCTACTGGTAATATCCTTCTGCAA
                      tcctaaa  putative branch site (score: 2)
                                            ctgctttt  putative PPT
                         taaaatgactttat  TA-rich tract