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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatttcaattttatgtgccttgaagagatcttctgtcacctcaatttttttattctccatctgtaattcttgcaaattcatttgtgctgacaatgcattatttttctgtagGCAATTTTCTTGTTAGCAAGGAACCTCCACACAAGCCGATTCTCCTTGATTTTGGGCTTACTAAACGCATATCTCAATCAATGAGGCAGGCACTAGCAAA

Basic information

species Oryza sativa
transcript LOC_Os06g48770.2
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os06g48770.2 (Oryza sativa), 3'ss of exon 8
lower sequence: GRMZM2G140917_T01 (Zea mays), 3'ss of exon 9
gtatttcaattttatgtgccttgaagagatcttctgtcacctcaatttttttattctccatctgtaattcttgcaaattcatttgtgctgacaatgcattatttttct--gtagGCAATTTTCTTGTTAGCAAGGAACCTCCACACAAGCCGATTCTCCTTGATTTTGGGCTTACTAAACGCATATCTCAATCAATGAGGCAGGCACTAGCAAA
||||||  | | |||     ||||  ||  ||||  ||||||        || ||||| |  ||      | ||| ||| |||  | ||     |||||| || |  |  ||||||||||||||||| ||||||||||||||||| || ||||||||||||||||||||||| ||||| ||||||||| |||| ||||||||||||||||||||
gtatttagaatatattcattttgagaagg-cttcgttcacct--------ttcttctctaattga-----tcgcacattaattcatacttgtg-tgcatttttctcttatgtagGCAATTTTCTTGTGAGCAAGGAACCTCCACATAAACCGATTCTCCTTGATTTTGGGCTCACTAAGCGCATATCTGAATCTATGAGGCAGGCACTAGCAAA

upper sequence: LOC_Os06g48770.2 (Oryza sativa), 3'ss of exon 8
lower sequence: Vv04s0008g02740.t01 (Vitis vinifera), 3'ss of exon 7
gtatttcaattttatgtgccttgaagagatcttctgtcacctcaatttttttattctccatctgtaattcttgcaaattcatttgtgctgacaatgcattat----ttttctgtagGCAATTTTCTTGTTAGCAAGGAACCTCCACACAAGCCGATTCTCCTTGATTTTGGGCTTACTAAACGCATATCTCAATCAATGAGGCAGGCACTAGCAAA
     | |||||  |    | ||| | | | |||   ||         || ||   |  |  | | | |  |  ||| | | |||     |   |     |     || |||| ||| ||||||||||| |||||||||||||||||    ||  || | ||||| ||||||||||| ||     ||||    || ||||  || |||||||| ||
----gtaaatttgcta---cctgatgggctattcatcca---------ttctaccttttagttatgactgctaaaaaattaattgaataaatgctttcccacatgattctctgcagGAAATTTTCTTGTCAGCAAGGAACCTCCACATCGTCCAGTTTTGCTTGACTTTGGGCTTACAAAGTCACTATCAAGCTCTATGAAACAAGCACTAGCGAA
















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|86498768|gb|CI141401.1|CI141401
EST:     TGCTCATCAAATATACGTTGATGGCTTCTTTAACGGCGATCCTCACCCTG                         GCAATTTTCTTGTTAGCAAGGAACCTCCACACAAGCCGATTCTCCTTGATT
genomic: TGCTCATCAAATATACGTTGATGGCTTCTTTAACGGCGATCCTCACCCTGgtatttcaat ... ttttctgtagGCAATTTTCTTGTTAGCAAGGAACCTCCACACAAGCCGATTCTCCTTGATT
EST: gi|569556|gb|D40405.1|D40405
EST:     TGCTCATCAAATATACGTTGATGGCTTCTTTAACGGCGATCCTCACCCTG                         GCAATTTTCTTGTTAGCAAGGAACCTCCACACAAGCCGATTCTCCTTGATT
genomic: TGCTCATCAAATATACGTTGATGGCTTCTTTAACGGCGATCCTCACCCTGgtatttcaat ... ttttctgtagGCAATTTTCTTGTTAGCAAGGAACCTCCACACAAGCCGATTCTCCTTGATT
EST: gi|29621872|gb|CB626883.1|CB626883
EST:     TGCTCATCAAATATACGTTGATGGCTTCTTTAACGGCGATCCTCACCCTG                         GCAATTTTCTTGTTAGCAAGGAACCTCCACACAAGCCGATTCTCCTTGATT
genomic: TGCTCATCAAATATACGTTGATGGCTTCTTTAACGGCGATCCTCACCCTGgtatttcaat ... ttttctgtagGCAATTTTCTTGTTAGCAAGGAACCTCCACACAAGCCGATTCTCCTTGATT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ccatctgtaattcttgcaaattcatttgtgctgacaatgcattatttttctgtagGCAATTTTCTTGTTAGCAAGGAACCTCCACACAAGCCGATTCTCCTTGATTTTGGGCTTACTAAACGCATATCTCAATCAATGAGGCAGGCACTAGCAAA
                            tgctgac  putative branch site (score: 2)
                                         ttatttttct  putative PPT
                                   aatgcattattttt  TA-rich tract