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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttggcaagcaactccaatgatcgaattcttttgctagtgaccatatttgaagttgagtctaactcgtgcattgtcaattatgtttttcagTATCTGAAGAATGTACAGATAAGAGATATTCCAATACTGGAGAGGTTCTCCCTGTTCATCTGCATCGCGTTGGTTTGGGCCTATGCTCAAATCCTCACTG

Basic information

species Oryza sativa
transcript LOC_Os01g55500.2
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g55500.4 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G437859_T03 (Zea mays), 3'ss of exon 6
----gtttggcaagcaa------ctcca-atgatcgaattcttttgctagtgaccatatttgaagttgagtctaactcgtgcattgtcaatta------------tgtttttcagTATCTGAAGAATGTACAGATAAGAGATATTCCAATACTGGAGAGGTTCTCCCTGTTCATCTGCATCGCGTTGGTTTGGGCCTATGCTCAAATCCTCACTG
    |  ||||||  ||      ||||| || ||  | |||| |  |||   |||| |||     |   | | |  |   || |     ||              |||||  ||||||||||||||  ||||||||| ||| || || |||||||| ||||||||||| ||||||||  |||||||||| ||||| || ||||| ||||||||| 
gtctgactggcaaaaaaaaaaaactccagattattcagttctct--ctacgcaccaaattcatgatcttggcgagtttaagcgtacctgatctctgcatttcggttgtttcgcagTATCTGAAGAACATACAGATAAAAGAAATCCCCATACTGGAAAGGTTCTCCCTTTTCATCTGTGTCGCGTTGGTATGGGCGTACGCTCAGATCCTCACTT
















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|58599082|gb|CK009610.1|CK009610
EST:     GCGTTGAGGTTGGACTTCCAATGTTAATTCTGTTCGTCGTGCTTTCTCAG                         TATCTGAAGAATGTACAGATAAGAGATATTCCAATACTGGAGAGGTTCTCC
genomic: GCGTTGAGGTTGGACTTCCAATGTTAATTCTGTTTGTCGTGCTTTCTCAGgtttggcaag ... tgtttttcagTATCTGAAGAATGTACAGATAAGAGATATTCCAATACTGGAGAGGTTCTCC
EST: gi|88358900|gb|CI619404.1|CI619404
EST:     GCGTTGAGGTTGGACTTCCAATGTTAATTCTGTTTGTCGTGCTTTCTCAG                         TATCTGAAGAATGTACAGATAAGAGATATTCCAATACTGGAGAGGTTCTCC
genomic: GCGTTGAGGTTGGACTTCCAATGTTAATTCTGTTTGTCGTGCTTTCTCAGgtttggcaag ... tgtttttcagTATCTGAAGAATGTACAGATAAGAGATATTCCAATACTGGAGAGGTTCTCC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agtgaccatatttgaagttgagtctaactcgtgcattgtcaattatgtttttcagTATCTGAAGAATGTACAGATAAGAGATATTCCAATACTGGAGAGGTTCTCCCTGTTCATCTGCATCGCGTTGGTTTGGGCCTATGCTCAAATCCTCACTG
                     gtctaac  putative branch site (score: 2)
                                             tgtttttc  putative PPT
                                      tcaattatgttttt  TA-rich tract