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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tatgcttactaggcaaaagtccatatttagttgaatcacactatacaatatctgtaatttcccttcaatgtgctattctaaaatgattgttgcattgcagGTACAGTGTATCATTGGTTTGTCTTGTTTGCGGTTTGGCTTTGTGGCAGCCAGCATGTTCTTTCGCAGAAAACACCACTTGAACCAAAAGATAAATTCCT

Basic information

species Oryza sativa
transcript LOC_Os10g38980.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os10g38980.2 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G162251_T01 (Zea mays), 3'ss of exon 1
tatgcttactaggcaaaagtccatatttagttgaatcacacta---tacaatatctgtaatttcccttcaatgtgctattctaaaatgattgttgcattgcagGTACAGTGTATCATTGGTTTGTCTTGTTTGCGGTTTGGCTTTGTGGCAGCCAGCATGTTCTTTCGCAGAAAACACCACTTGAACCAAAAGATAAATTCCT
  | | |  |  |     ||   || | |     ||   | |    | || | | |||    |  |||  || |||| | || ||   |   |  |||||||||||||||| |||| ||| ||||  || ||| ||||||||||||||| |||||||||||| | || |||||| |  |||||||||||||||||||||||||
--tacatgttttgtttt-gtttctactgaaagtgatgtgattgaagtgcattctttgtttgctgtctttgatatgctttgctgaatataacatcacattgcagGTACAGTGCATCACTGGCTTGTGCTGATTGTGGTTTGGCTTTGTGGAAGCCAGCATGTTGTGTCTCAGAAATCGACACTTGAACCAAAAGATAAATTCCT
















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|58667257|gb|CK055943.1|CK055943
EST:     TATTGGGGCTAAAAGAATGGAGAGTTCCAGCTCTGGTTCTTGTCCTCAGG                         GTACAGTGTATCATTGGTTTGTCTTGTTTGCGGTTTGGCTTTGTGGCAGCC
genomic: TATTGGGGCTAAAAGAATGGAGAGTTCCAGCTCTGGTTCTTGTCCTCAGGgtgagtatgt ... tgcattgcagGTACAGTGTATCATTGGTTTGTCTTGTTTGCGGTTTGGCTTTGTGGCAGCC






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

caatatctgtaatttcccttcaatgtgctattctaaaatgattgttgcattgcagGTACAGTGTATCATTGGTTTGTCTTGTTTGCGGTTTGGCTTTGTGGCAGCCAGCATGTTCTTTCGCAGAAAACACCACTTGAACCAAAAGATAAATTCCT
                              ttctaaa  putative branch site (score: 2)
                            tattctaaaatgatt  TA-rich tract