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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaataggcagtgcgtggtgtcttagggttttgcacagatgagtgctacaaatactcatacaactcattgaattaaatggatggaaatttgattggattcttggatttgttcttgcagGATTTACTGCAAAAATCAAATGCAACTGATGCATCAGGAAATGTAATACTTAGTGACTTTGGTGTCCACATGCAACAGAAG

Basic information

species Oryza sativa
transcript LOC_Os09g24910.1
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os09g24910.2 (Oryza sativa), 3'ss of exon 11
lower sequence: GRMZM2G127717_T01 (Zea mays), 3'ss of exon 11
gtaataggcagtgcgtggtgtcttagggttttgcacagatgagtgctacaaatactcatacaactcattgaattaaatggatggaaatttgat-tggattcttggatttgttcttgcagGATTTACTGCAAAAATCAAATGCAACTGATGCATCAGGAAATGTAATACTTAGTGACTTTGGTGTCCACATGCAACAGAAG
||||  | ||||||  |  |    |  ||||  |     ||| |||| | |||  ||||  |  | | |  | | ||| | || ||||| ||  || ||| ||| | |  ||    |||||||||||||||||||||||||||||||| || ||||||||||| ||||||||||||||||||||||||||||| ||||||
gtaa--gacagtgca-gtagctaaacagtttatccttcttgactgcttctaat-ttcat--aggtgaat--actgaatag-tgaaaattagaaatgtatttttgtactc-ttggcacagGATTTACTGCAAAAATCAAATGCAACTGACGCTTCAGGAAATGTGATACTTAGTGACTTTGGTGTCCACATGCAGCAGAAG
















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|86493701|gb|CI136334.1|CI136334
EST:     TGGNNNNNNNGGGATTTTGCGTGGTTTGTGTTGCTGAAGGTGCAGGGCAG                         GATTTACTGCAAAAATCAAATGCAACTGATGCATCAGGAAATGTAATACTT
genomic: TGGAAAAAAAGGGATTTTGCGTGGTTTGTGTTGCTGAAGGTGCAGGGCAGgtaataggca ... gttcttgcagGATTTACTGCAAAAATCAAATGCAACTGATGCATCAGGAAATGTAATACTT
EST: gi|86504245|gb|CI146878.1|CI146878
EST:     GGGATTTTGCGTGGTTTGTGTTGCTGAAGGTGCAGGGCAG                         GATTTACTGCAAAAATCAAATGCAACTGATGCATCAGGAAATGTAATACTT
genomic: GGGATTTTGCGTGGTTTGTGTTGCTGAAGGTGCAGGGCAGgtaataggca ... gttcttgcagGATTTACTGCAAAAATCAAATGCAACTGATGCATCAGGAAATGTAATACTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctcattgaattaaatggatggaaatttgattggattcttggatttgttcttgcagGATTTACTGCAAAAATCAAATGCAACTGATGCATCAGGAAATGTAATACTTAGTGACTTTGGTGTCCACATGCAACAGAAG
                       atttgat  putative branch site (score: 5)
                                          tttgttctt  putative PPT
     tgaattaaat  TA-rich tract