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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cacattttcttaggtaatttaagcccctggaactgtatttgatctgattagttttcttattaaataaattattaattgattgtgttttaatggtctcaagGAAAAAGAACATTTTCAAGTTAGCTCAAGGAGAATACATAGCTCCCGAGAAGATTGAGAATGTCTATGCTAAGTGCAAGTTTATTGCGCAGTCCTTTATA

Basic information

species Oryza sativa
transcript LOC_Os12g04990.3
intron # 17
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os12g04990.3 (Oryza sativa), 3'ss of exon 17
lower sequence: GRMZM2G176546_T01 (Zea mays), 3'ss of exon 9
--------------------------------------------------------cacattttcttaggta--------atttaagcc--cctggaactgtatttgatctgattagttttcttattaaataaattattaattgattgtgttttaatggtctcaagGAAAAAGAACATTTTCAAGTTAGCTCAAGGAGAATACATAGCTCCCGAGAAGATTGAGAATGTCTATGCTAAGTGCAAGTTTATTGCGCAGTCCTTTATA
                                                        ||| ||| ||| | ||        |||||      ||     |  | |||||||| |    |||||||  || || | | ||   || | |   || |  |||  |  ||||||||||||||||||||||||||||||||||||||||||||||| ||||||||||| ||||||||||| || |||||||| ||||| || |  ||||||
gtaaaaacgtgcactgttttatattttatccattcagaacttgtgttcttgcagaacacttttccttggctatattgttgatttacattttccctaggcgctgtttgatctcaccgtttttcttcctatattattaatgccttaaat---ttctcctggattttagGAAAAAGAACATTTTCAAGTTAGCTCAAGGAGAATACATAGCTCCAGAGAAGATTGAAAATGTCTATGCCAAATGCAAGTTCATTGCCCAATGTTTTATA

upper sequence: LOC_Os12g04990.3 (Oryza sativa), 3'ss of exon 17
lower sequence: AT5G27600.1 (Arabidopsis thaliana), 3'ss of exon 18
cacattttcttaggtaatttaagcccctggaactgtatttgatctgattagttttcttattaaataaatt--attaattgattgtgttttaatggtctcaa--gGAAAAAGAACATTTTCAAGTTAGCTCAAGGAGAATACATAGCTCCCGAGAAGATTGAGAATGTCTATGCTAAGTGCAAGTTTATTGCGCAGTCCTTTATA
             ||  | |||  |     ||   |  ||| | |   |   |||       || || ||  | |  ||| |     || ||||  |   |  |||| |||||||| || ||||| || ||||||||||| ||||| || |||||||| || ||||| ||| | || || |  ||  || ||||||  || || 
-------------gttttataaatc----aaaacattcttgttatttctttctttgcggaagaaaaagttgaaatgtttgttaaaacttcaatgtgcatgacagGAAGAAGAACATATTTAAGTTGGCGCAAGGAGAATATATAGCACCAGAGAAGATCGAAAATGTTTATACCAAATGTAGATTCGTTTCGCAGTGTTTCATT

upper sequence: LOC_Os12g04990.3 (Oryza sativa), 3'ss of exon 17
lower sequence: Vv14s0128g00720.t01 (Vitis vinifera), 3'ss of exon 18
cacattttcttaggtaatttaagcccctggaactgtatttgatctgattagttttcttattaaataaattattaattgattgtgttttaatggtc---tca----agGAAAAAGAACATTTTCAAGTTAGCTCAAGGAGAATACATAGCTCCCGAGAAGATTGAGAATGTCTATGCTAAGTGCAAGTTTATTGCGCAGTCCTTTATA
   | || ||||   ||   || |     |||  | |   || |     |  |||    |   | |  ||| |   | |  |    || |||| |   | |    |||||||||||||| |||||| | || || || ||||| ||||| || ||||| ||||||||||| ||||| |||||||| ||| || | || |  ||||| 
---aattgcttacaaaag--aaactttgtgaagagcag--gaacatgccaactttaagttatgaaattttagtctcttagcgaaaattgatggccaacttatgacagGAAAAAGAACATCTTCAAGCTGGCACAGGGTGAATATATAGCACCAGAGAAAATTGAGAATGTATATGCCAAGTGCAAATTTGTTTCCCAATGTTTTATC

upper sequence: LOC_Os12g04990.3 (Oryza sativa), 3'ss of exon 17
lower sequence: Vv05s0020g03080.t01 (Vitis vinifera), 3'ss of exon 18
-----------------------------------------------------------------------------cacattttcttaggtaatttaagcccctggaactgtatttgatctgattagtttt-----cttattaaataaatt----attaattgattgtgttttaatggtc-tca------agGAAAAAGAACATTTTCAAGTTAGCTCAAGGAGAATACATAGCTCCCGAGAAGATTGAGAATGTCTATGCTAAGTGCAAGTTTATTGCGCAGTCCTTTATA
                                                                                 | |   |   ||  ||   ||  ||    |||  ||||| | ||    | |     | || |  || |  |    |||  ||   | ||| ||||  ||  | |      ||||| ||||||||||| ||||| || |||||||| ||||||||||| ||||| ||||||||||| |||||||| ||||| ||| |||| |||| |||| ||
gtaaagaccatatcatttttgttgacagttcttagacgaattaataatgactcctctctagttttggatgactcaattgactgtatgttcatatcttggtcctgtgattttgttattgatataatcgactataattacatacttcattacctgtgcatttcttagctttgtattaaaagttgttatatgacagGAAGAAGAACATTTTTAAGTTGGCACAAGGAGAGTACATAGCTCCAGAGAAAATTGAGAATGTATATGCTAAATGCAAATTTGTTGCCCAGTGCTTTGTA

upper sequence: LOC_Os12g04990.3 (Oryza sativa), 3'ss of exon 17
lower sequence: PP1S408_23V6.1 (Physcomitrella patens), 3'ss of exon 20
---------cacattttcttaggtaatttaagcccctggaactgtatttgatctgattagttttcttattaaataaattattaattgattgtgttttaatggtctcaagGAAAAAGAACATTTTCAAGTTAGCTCAAGGAGAATACATAGCTCCCGAGAAGATTGAGAATGTCTATGCTAAGTGCAAGTTTATTGCGCAGTCCTTTATA
            ||    |||| |  ||||        | | ||| |   |  |  |  ||| | || ||        | ||  |||| |   |  | |     |  ||||| ||||| || || ||||| ||||||||||| ||||| || || |||||||| |||||||||||   |    |    || ||  | ||||  |  |||
tgtcgtgagtggatcaatttagct--tttactttttcaggaatgt-tcacaagtagtatgttctgttcttcg------tgtttgttgagtcattcatcacacattgcagGAAGAAGAATATCTTTAAGTTGGCTCAAGGAGAGTACATTGCCCCGGAGAAGATCGAGAATGTCTACCTTCGCAGTCGTTTCATAACACAGTGTTACATA

upper sequence: LOC_Os12g04990.3 (Oryza sativa), 3'ss of exon 17
lower sequence: PP1S33_126V6.1 (Physcomitrella patens), 3'ss of exon 21
-----------------------------------------------------------------------------cacattttcttaggtaatttaagcccctggaactgtatttgatctgattagttttct-tattaaataaatt---attaattgattgtgttttaat-ggtc--tcaagGAAAAAGAACATTTTCAAGTTAGCTCAAGGAGAATACATAGCTCCCGAGAAGATTGAGAATGTCTATGCTAAGTGCAAGTTTATTGCGCAGTCCTTTATA
                                                                                |     ||  |||  ||   | | |  ||   |    ||||     |  |||   ||||  |  |  |   || | |||   ||  |||  | |||   |  || || ||||| || |||||||| ||||| ||||| ||||| || ||||||||||||||||| |||||        |   ||| ||||| |||| |||||| 
gtactctggactagcgtcacccttagatgtatgctattgatatttttcatcattcaacgtctggtagtctagatcagtgtacccagttgagtatgttctactcttctaatgttcgaagatcaatccaactttgaatatttcaggagctttcatgagttgtacgttctttccttggttattgcagAAAGAAGAATATCTTCAAGTTGGCTCAGGGAGAGTACATTGCGCCCGAGAAGATTGAGAACGTCTACCTGCGAAGTCGGTTCATTGCACAGTGCTTTATT

upper sequence: LOC_Os12g04990.3 (Oryza sativa), 3'ss of exon 17
lower sequence: PP1S12_178V6.2 (Physcomitrella patens), 3'ss of exon 20
----cacattttcttaggtaatttaagcccctggaactgtatttgatctgattagttttcttattaaataaattattaattgattgtgttttaatggtctcaagGAAAAAGAACATTTTCAAGTTAGCTCAAGGAGAATACATAGCTCCCGAGAAGATTGAGAATGTCTATGCTAAGTGCAAGTTTATTGCGCAGTCCTTTATA
       ||| |  |  | || |  | |      || | ||| ||        |||| |  |  |    |  ||  |  |  ||  | |  | |  ||||  ||||| ||||||||||||||||||||||||||||||||||| || || || |||||||||||  | |||  |    |   ||||||| ||||||  ||  ||
aagttttattcttctctgaaactgtaactagaaaaaat-tatctggaagtggcagttcttatgct---catgtttgttttgtatcctttaatcactgtctgcagGAAGAAGAACATTTTCAAGTTAGCTCAAGGAGAATACATTGCACCGGAAAAGATTGAGAACATTTATCTTCGCAGTCGGTTTATTTCGCAGTGTTTCGTA

upper sequence: LOC_Os12g04990.3 (Oryza sativa), 3'ss of exon 17
lower sequence: EFJ37488 (Selaginella moellendorffii), 3'ss of exon 19
cacattttcttaggtaatttaagcccctggaactgtatttgatctgattagttttcttattaaataaattattaattgattgtgttttaatggtctcaagGAAAAAGAACATTTTCAAGTTAGCTCAAGGAGAATACATAGCTCCCGAGAAGATTGAGAATGTCTATGCTAAGTGCAAGTTTATTGCGCAGTCCTTTATA
                                               | |  |   || |   ||    | ||  ||||     ||||     |  | ||||||||||||||||| ||| | || || || ||||||||||| || |||||||||||||||||||||   ||  |||||||  |||| ||||  ||  | 
----------------------------------------------gtaacgtgctttgtgtcattcgattttgcttgacgtcatttt-----ttgccagGAAAAAGAACATTTTTAAGCTTGCACAGGGTGAATACATAGCGCCAGAGAAGATTGAGAATGTCTATCAAAAAAGCAAGTTCGTTGCTCAGTGTTTCGTC

upper sequence: LOC_Os12g04990.3 (Oryza sativa), 3'ss of exon 17
lower sequence: EFJ33980 (Selaginella moellendorffii), 3'ss of exon 19
cacattttcttaggtaatttaagcccctggaactgtatttgatctgattagttttcttattaaataaattattaattgattgtgttttaatggtctcaagGAAAAAGAACATTTTCAAGTTAGCTCAAGGAGAATACATAGCTCCCGAGAAGATTGAGAATGTCTATGCTAAGTGCAAGTTTATTGCGCAGTCCTTTATA
                                               | |  |   || |   ||    | ||  ||||     ||||     |  | ||||||||||||||||| ||| | || || || ||||||||||| || |||||||||||||||||||||  |||  |||||||  |||| ||||  ||  | 
----------------------------------------------gtaacgtgctttgtgtcattcgattttgcttgacgtcatttt-----ttgccagGAAAAAGAACATTTTTAAGCTTGCACAGGGTGAATACATAGCGCCAGAGAAGATTGAGAATGTCTATCATAAAAGCAAGTTCGTTGCTCAGTGTTTCGTC

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|29630787|gb|CB635796.1|CB635796
EST:     GGAGACATAGGTTTGTGGATGCCTGGAGGGCGTCTAAAAATTATAGATAG                         GAAAAAGAACATTTTCAAGTTAGCTCAAGGAGAATACATAGCTCCCGAGAA
genomic: GGAGACATAGGTTTGTGGATGCCTGGAGGGCGTCTAAAAATTATAGATAGgtaaaactga ... tggtctcaagGAAAAAGAACATTTTCAAGTTAGCTCAAGGAGAATACATAGCTCCCGAGAA
EST: gi|29625658|gb|CB630669.1|CB630669
EST:     GGAGACATAGGTTTGTGGATGCCTGGAGGGCGTCTAAAAATTATAGATAG                         GAAAAAGAACATTTTCAAGTTAGCTCAAGGAGAATACATAGCTCCCGAGAA
genomic: GGAGACATAGGTTTGTGGATGCCTGGAGGGCGTCTAAAAATTATAGATAGgtaaaactga ... tggtctcaagGAAAAAGAACATTTTCAAGTTAGCTCAAGGAGAATACATAGCTCCCGAGAA
EST: gi|58659745|gb|CK048425.1|CK048425
EST:     GGAGACATAGGTTTGTGGATGCCTGGAGGGCGTCTAAAAATTATAGATAG                         GAAAAAGAACAT
genomic: GGAGACATAGGTTTGTGGATGCCTGGAGGGCGTCTAAAAATTATAGATAGgtaaaactga ... tggtctcaagGAAAAAGAACAT
EST: gi|29622085|gb|CB627096.1|CB627096
EST:     GGAGACATAGGTTTGTGGATGCCTGGAGGGCGTCTAAAAATTATAGATAG                         GAAAAAGAACATTTTCAAGTTAGCTCAAGGAGAATACATAGCTCCCGAGAA
genomic: GGAGACATAGGTTTGTGGATGCCTGGAGGGCGTCTAAAAATTATAGATAGgtaaaactga ... tggtctcaagGAAAAAGAACATTTTCAAGTTAGCTCAAGGAGAATACATAGCTCCCGAGAA
EST: gi|29626658|gb|CB631669.1|CB631669
EST:     AGACATAGGTTTGTGGATGCCTGGAGGGCGTCTAAAAATTATAGATAG                         GAAAAAGAACATTTTCAAGTTAGCTCAAGGAGAATACATAGCTCCCGAGAA
genomic: AGACATAGGTTTGTGGATGCCTGGAGGGCGTCTAAAAATTATAGATAGgtaaaactga ... tggtctcaagGAAAAAGAACATTTTCAAGTTAGCTCAAGGAGAATACATAGCTCCCGAGAA
EST: gi|313081138|gb|HO213724.1|HO213724
EST:     GGAGACATAGGTTTGTGGATGCCTGGAGGGCGTCTAAAAATTATAGATAG                         GAAAAAGAACATTTTCAAGTTAGCTCAAGGAGAATACATAGCTCCCGAGAA
genomic: GGAGACATAGGTTTGTGGATGCCTGGAGGGCGTCTAAAAATTATAGATAGgtaaaactga ... tggtctcaagGAAAAAGAACATTTTCAAGTTAGCTCAAGGAGAATACATAGCTCCCGAGAA
EST: gi|29674288|gb|CB670563.1|CB670563
EST:     GGAGACATAGGTTTGTGGATGCCTGGAGGGCGTCTAAAAATTATAGATAG                         GAAAAAGAACATTTTCAAGTTAGCTCAAGGAGAATACATAGCTCCCGAGAA
genomic: GGAGACATAGGTTTGTGGATGCCTGGAGGGCGTCTAAAAATTATAGATAGgtaaaactga ... tggtctcaagGAAAAAGAACATTTTCAAGTTAGCTCAAGGAGAATACATAGCTCCCGAGAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gattagttttcttattaaataaattattaattgattgtgttttaatggtctcaagGAAAAAGAACATTTTCAAGTTAGCTCAAGGAGAATACATAGCTCCCGAGAAGATTGAGAATGTCTATGCTAAGTGCAAGTTTATTGCGCAGTCCTTTATA
      ttttcttattaaataa  TA-rich tract