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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tctgaaaattttgcatacagatgtttagttttaataattaattgtttgatttaaccatttgacaatatactaaagattgctgttggaatccctttttcagGATAGGATTGCAGGGGACAAAGGAACTGTCTGACAATAAGATAGATAAGAGAACATTGCAGAAAGGCCTGCTTCTTGAATTTCAGAAAGATTCTGAGAGA

Basic information

species Oryza sativa
transcript LOC_Os01g62440.2
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g62440.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G082260_T01 (Zea mays), 3'ss of exon 1
tctgaaaattttgcatacagatgtttagttt--taataattaatt-gtttgatttaaccatttgacaatatactaaagattgctgttggaatccctt------tttcagGATAGGATTGCAGGGGACAAAGGAACTGTCTGACAATAAGATAGATAAGAGAACATTGCAGAAAGGCCTGCTTCTTGAATTTCAGAAAGATTCTGAGAGA
      |||  | ||||  | | || |  ||  | || | || ||  |||  | |||| ||   | ||   ||| ||  || ||||||||||  |||       |||||||||||||||||||| || |||||| || |||||||||||||||  ||||||||||| ||||||||  |||| |||||||||||||||||| ||||||||
------aatggttcatatggctattaaaattggttatcactatttcatttcttctaacaat---aaaactcactgaaatttactgttggaatttcttattctacttcagGATAGGATTGCAGGGCACGAAGGAATTGCCTGACAATAAGATAGTCAAGAGAACATTACAGAAAGGATTGCTGCTTGAATTTCAGAAAGATCCTGAGAGA
















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|29670923|gb|CB667198.1|CB667198
EST:     TCCGTCCTGGAGGAGCTCCGATCACAGAGGCGTGGTCGGGTTTCGGCAAA                         GATAGGATTGCAGGGGACAAAGGAACTGTCTGACAATAAGATAGATAAGAG
genomic: TCCGTCCTGGAGGAGCTCCGATCACAGAGGCGTGGTCGGGTTTCGGCAAAgtaacgcgcc ... cctttttcagGATAGGATTGCAGGGGACAAAGGAACTGTCTGACAATAAGATAGATAAGAG
EST: gi|88300755|gb|CI589747.1|CI589747
EST:     TCCGTCCTGGAGGAGCTCCGATCACAGAGGCGTGGTCGGGTTTCGGCAAA                         GATAGGATTGCAGGGGACAAAGGAACTGTCTGACAATAAGATAGATAAGAG
genomic: TCCGTCCTGGAGGAGCTCCGATCACAGAGGCGTGGTCGGGTTTCGGCAAAgtaacgcgcc ... cctttttcagGATAGGATTGCAGGGGACAAAGGAACTGTCTGACAATAAGATAGATAAGAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgatttaaccatttgacaatatactaaagattgctgttggaatccctttttcagGATAGGATTGCAGGGGACAAAGGAACTGTCTGACAATAAGATAGATAAGAGAACATTGCAGAAAGGCCTGCTTCTTGAATTTCAGAAAGATTCTGAGAGA
                      tactaaa  putative branch site (score: 1)
                                           tccctttttc  putative PPT
                  aatatactaaagatt  TA-rich tract