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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtagtgaaaagtttgatgattattgtttacaagttgatagttcaaagatatacatttatagtaatctgacaatcatactgctgcttcagATACTGTGAGGAGAGAAGCAACTACAATAATGGCTGTATTTCCTTCTCCAAATGAGGTCATGTCAATTCTTGTGCAG

Basic information

species Oryza sativa
transcript LOC_Os12g13590.2
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os12g13590.1 (Oryza sativa), 3'ss of exon 9
lower sequence: GRMZM2G316815_T01 (Zea mays), 3'ss of exon 1
-------gtagtgaaaagtttgatgattattgtttacaagttgatagttcaaagatatacatttatagtaatctgaca-atcatactgctgcttcagATACTGTGAGGAGAGAAGCAACTACAATAATGGCTGTATTTCCTTCTCCAAATGAGGTCATGTCAATTCTTGTGCAG
         ||    |   ||    ||| ||||||  ||  | ||| ||  | ||| | || || | | | ||||| | ||||||||  | |||||||||||||||||| ||| ||| ||||||||| |||||| ||||||||||| |||||||||||| |||||||||| |||
gtatttatgagctgcactctttgcaatttttgtttctaaact-atactttgatgattttcaattttggcactctgatatatcatacttgt-cttcagATACTGTGAGGAAAGAGGCAGCTACAATAACGGCTGTCTTTCCTTCTCCGAATGAGGTCATGGCAATTCTTGTCCAG

upper sequence: LOC_Os12g13590.1 (Oryza sativa), 3'ss of exon 9
lower sequence: Vv15s0046g02200.t01 (Vitis vinifera), 3'ss of exon 9
gtagtgaaaagtttgatgattattgtttacaagttgatagttcaaagatatacatttatagtaatctgacaatcatactgct-gcttcagATACTGTGAGGAGAGAAGCAACTACAATAATGGCTGTATTTCCTTCTCCAAATGAGGTCATGTCAATTCTTGTGCAG
          |||||| || ||  || |  |  ||  ||  |        | | |  || |   ||  | | |  |  || | | ||||||||||||| | | ||||||| | ||||||||||||||||| || ||||| ||||| |||||| ||||| | || |||
----------gtttgaagaatag-gtattgatcttagtaactggg-----ttcttggatggatttcatatatttgttttgtttgtttcagATACTGTGCGAAAAGAAGCAGCCACAATAATGGCTGTATTCCCCTCTCCTAATGATGTCATGGCAATTTTGGTTCAG
















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|29632378|gb|CB637387.1|CB637387
EST:     CCACATTTGTATTGCAGAGGGCCTCTCTGTATTGTACAAGGAAATTGCAG                         ATACTGTGAGGAGAGAAGCAACTACAATAATGGCTGTATTTCCTTCTCCAA
genomic: CCACATTTGTATTGCAGAGGGCCTCTCTGTATTGTACAAGGAAATTGCAGgtagtgaaaa ... gctgcttcagATACTGTGAGGAGAGAAGCAACTACAATAATGGCTGTATTTCCTTCTCCAA
EST: gi|29669744|gb|CB666019.1|CB666019
EST:     CCACATTTGTATTGCAGAGGGCCTCTCTGTATTGTACAAGGAAATTGCAG                         ATACTGTGAGGAGAGAAGCAACTACAATAATGGCTGTATTTCCTTCTCCAG
genomic: CCACATTTGTATTGCAGAGGGCCTCTCTGTATTGTACAAGGAAATTGCAGgtagtgaaaa ... gctgcttcagATACTGTGAGGAGAGAAGCAACTACAATAATGGCTGTATTTCCTTCTCCAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgatagttcaaagatatacatttatagtaatctgacaatcatactgctgcttcagATACTGTGAGGAGAGAAGCAACTACAATAATGGCTGTATTTCCTTCTCCAAATGAGGTCATGTCAATTCTTGTGCAG
                             atctgac  putative branch site (score: 3)
                                              ctgcttc  putative PPT
         aaagatatacatttat  TA-rich tract