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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAGGAAAGAAATGAGGAGGGGTATAGACTTGGCTACTACACTTGAACGTATTGAGAAGAATTTTGTCATCACAGATCCAAGGTTGCCTGATAATCCCATTgtaagatccatatggaatctcttttacctcttacaccgcacctgttctttttattaatatggatattaaattttcatgattgtatgttttggttcatatttcag

Basic information

species Oryza sativa
transcript LOC_Os12g01140.4
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os12g01140.1 (Oryza sativa), 5'ss of exon 6
lower sequence: GRMZM2G001457_T02 (Zea mays), 5'ss of exon 5
GAGGAAAGAAATGAGGAGGGGTATAGACTTGGCTACTACACTTGAACGTATTGAGAAGAATTTTGTCATCACAGATCCAAGGTTGCCTGATAATCCCATTgtaagatccatatgga-atctcttttacctcttacaccgcacctgttctttttattaatatggatattaaattttcatgattgtatgttttggt--tcatatttcag-----------------
|| |||||||||||| | ||| ||||| |||||||| ||||||||||||||||| ||||||||||||||||| || || ||||| || |||||||| |||||||||   |     | ||  ||| | ||| | ||| | |   |||||||| |||  | || |||||  |  |  ||| ||  |    |   ||  | ||||||                    
GAAGAAAGAAATGAGAAAGGGCATAGATTTGGCTACCACACTTGAACGTATTGAAAAGAATTTTGTCATCACCGACCCGAGGTTACCAGATAATCCAATTgtaagacaaaagctcacataccttctgcctttaacatcac---tgttctttctatcgaaatagatatcgacctaccattatattgaactacagtcattatattttttttgggtgaatgtcacag

upper sequence: LOC_Os12g01140.1 (Oryza sativa), 5'ss of exon 6
lower sequence: GLYMA12G07890.2 (Glycine max), 5'ss of exon 7
GAGGAAAGAAATGAGGAGGGGTATAGACTTGGCTACTACACTTGAACGTATTGAGAAGAATTTTGTCATCACAGATCCAAGGTTGCCTGATAATCCCATTgtaagat--ccatatggaatctcttttacctct----tacaccgcacctg------ttcttttt---attaatatggatattaaa-------ttttcatgattgtatgttttggttcatatttcag
|| ||| |||| ||| | |||| | ||  | ||||| ||||||||||||||||||||||| ||||||||||| ||||||||| |||| || || |||||||||||||   | | |   ||  | ||||   ||    | || |  |  ||      |||| | |   ||||||  |  || || |       ||   | ||||   | ||||  ||  | || |||
GAAGAAGGAAAAGAGAAAGGGTCTTGATCTTGCTACCACACTTGAACGTATTGAGAAGAACTTTGTCATCACTGATCCAAGGCTGCCGGACAACCCCATTgtaagatgatcctttttgataccatttaatactccaatgcaacaaaaatggtgaatttctctatgggattaattcgtgtactagagatgagcttaagacgattacgt-ttttatttggttttccag

upper sequence: LOC_Os12g01140.1 (Oryza sativa), 5'ss of exon 6
lower sequence: AT3G45780.1 (Arabidopsis thaliana), 5'ss of exon 6
GAGGAAAGAAATGAGGAGGGGTATAGACTTGGCTACTACACTTGAACGTATTGAGAAGAATTTTGTCATCACAGATCCAAGGTTGCCTGATAATCCCATTgtaagatccatatggaatctcttttacctcttacaccgcacctgttct-ttttattaatatggatattaaattttcatgattgtatgttttggttcatatttcag-
    || |||||||| | |||||| ||  | ||||||||||| |||||||| ||||||||||| |||||||| ||||| ||| | || ||||||||||||||||||     |   |   | |   |      | ||      |||| | ||| |||   || | | | |||   |    ||||| || ||||    || ||||   
ACAAAAGGAAATGAGAAAGGGTATTGATCTAGCTACTACACTCGAACGTATCGAGAAGAATTTCGTCATCACTGATCCTAGGCTTCCCGATAATCCCATTgtaaga-----acaaatgttttagaaaaatggaaactttttttgttatgtttcatttcgattggtctgaaaacgt----attgtttgctttgtcctatgtttctag

upper sequence: LOC_Os12g01140.1 (Oryza sativa), 5'ss of exon 6
lower sequence: Vv06s0004g03700.t01 (Vitis vinifera), 5'ss of exon 6
GAGGAAAGAAATGAGGAGGGGTATAGACTTGGCTACTACACTTGAACGTATTGAGAAGAATTTTGTCATCACAGATCCAAGGTTGCCTGATAATCCCATTgtaagatccatatggaatctcttttacctcttacaccgcacctgttctttttattaatatggatat-taaattttcatgattgtatgttttggttcatatttcag----------------------
    |  |||||||| || ||||| ||  |||| || || ||||||||||| |||||||| ||||||||||| ||||| ||  ||||||||||||||||||| |||   |||    |  |  ||     ||   | |       || |   |  | || ||   ||  | ||    |  | | |  | |||| ||  | |   ||                      
ACAAAGGGAAATGAGAAGAGGTATTGATCTGGCCACCACGCTTGAACGTATAGAGAAGAACTTTGTCATCACTGATCCCAGACTGCCTGATAATCCCATTgtgagaataatacttcaaattattggttactgcaatcatgttctttttaaattatgatttgagcatgcacataagaagaaatatgggatttg-tttgtttgatagttctaactttttgaattttcag

upper sequence: LOC_Os12g01140.1 (Oryza sativa), 5'ss of exon 6
lower sequence: PP1S174_62V6.2 (Physcomitrella patens), 5'ss of exon 3
GAGGAAAGAAATGAGGAGGGGTATAGACTTGGCTACTACACTTGAACGTATTGAGAAGAATTTTGTCATCACAGATCCAAGGTTGCCTGATAATCCCATTgtaagatcca--tatggaatctcttttac--ctcttacaccgcacctgttctttttattaatatggatattaaattttcatgattgtatgttttggttcatatttcag
 |     |  ||  |  | || || ||||||||||| ||||| || || ||||| ||||| || ||||| || |||||  || | |||||||||||||||||||| |  |    |||  |  || | |   ||| | |||   || ||      ||||   |     ||   |||| |      | ||                    
CACTCTGGGCATCCGTCGAGGAATCGACTTGGCTACAACACTGGAGCGAATTGAAAAGAACTTCGTCATAACTGATCCCCGGCTTCCTGATAATCCCATTgtaagttgtagtcttggcgttgctatcatagctcatgcacaatacatgga----ttatctgtggcagtaactaattcttggcgctctacag-----------------

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|29624477|gb|CB629488.1|CB629488
EST:     TTGAGAAGAATTTTGTCATCACAGATCCAAGGTTGCCTGATAATCCCATT                         ATATTTGCATCCGATAGCTTTCTGCAATTGACAGAATACAACCGTGAAGAA
genomic: TTGAGAAGAATTTTGTCATCACAGATCCAAGGTTGCCTGATAATCCCATTgtaagatcca ... catatttcagATATTTGCATCCGATAGCTTTCTGCAATTGACAGAATACAACCGTGAAGAA
EST: gi|29630119|gb|CB635128.1|CB635128
EST:     TTGAGAAGAATTTTGTCATCACAGATCCAAGGTTGCCTGATAATCCCATT                         ATATTTGCATCCGATAGCTTTCTGCAATTGACAGAATACAACCGTGAAGAA
genomic: TTGAGAAGAATTTTGTCATCACAGATCCAAGGTTGCCTGATAATCCCATTgtaagatcca ... catatttcagATATTTGCATCCGATAGCTTTCTGCAATTGACAGAATACAACCGTGAAGAA
EST: gi|29681859|gb|CB678134.1|CB678134
EST:     TTGAGAAGAATTTTGTCATCACAGATCCAAGGTTGCCTGATAATCCCATT                         ATATTTGCATCCGATAGCTTTCTGCAATTGACAGAATACAACCGTGAAGAA
genomic: TTGAGAAGAATTTTGTCATCACAGATCCAAGGTTGCCTGATAATCCCATTgtaagatcca ... catatttcagATATTTGCATCCGATAGCTTTCTGCAATTGACAGAATACAACCGTGAAGAA
EST: gi|29624448|gb|CB629459.1|CB629459
EST:     TTGAGAAGAATTTTGTCATCACAGATCCAAGGTTGCCTGATAATCCCATT                         ATATTTGCATCCGATAGCTTTCTGCAATTGACAGAATACAACCGTGAAGAA
genomic: TTGAGAAGAATTTTGTCATCACAGATCCAAGGTTGCCTGATAATCCCATTgtaagatcca ... catatttcagATATTTGCATCCGATAGCTTTCTGCAATTGACAGAATACAACCGTGAAGAA
EST: gi|29641853|gb|CB646860.1|CB646860
EST:     TTGAGAAGAATTTTGTCATCACAGATCCAAGGTTGCCTGATAATCCCATT                         ATATTTGCATCCGATAGCTTTCTGCAATTGACAGAATACAACCGTGAAGAA
genomic: TTGAGAAGAATTTTGTCATCACAGATCCAAGGTTGCCTGATAATCCCATTgtaagatcca ... catatttcagATATTTGCATCCGATAGCTTTCTGCAATTGACAGAATACAACCGTGAAGAA
EST: gi|2317379|gb|C22433.1|C22433
EST:     TTGAGAAGAATTTTGTCATCACAGATCCAAGGTTGCCTGATAATCCCATT                         ATATTTGCATCCGATAGCTTTCTGCAATTGACAGAATACAACCGTGAAGAA
genomic: TTGAGAAGAATTTTGTCATCACAGATCCAAGGTTGCCTGATAATCCCATTgtaagatcca ... catatttcagATATTTGCATCCGATAGCTTTCTGCAATTGACAGAATACAACCGTGAAGAA
EST: gi|29628293|gb|CB633304.1|CB633304
EST:     TTGAGAAGAATTTTGTCATCACAGATCCAAGGTTGCCTGATAATCCCATT                         ATATTTGCATCCGATAGCTTTCTGCAATTGACAGAATACAACCGTGAAGAA
genomic: TTGAGAAGAATTTTGTCATCACAGATCCAAGGTTGCCTGATAATCCCATTgtaagatcca ... catatttcagATATTTGCATCCGATAGCTTTCTGCAATTGACAGAATACAACCGTGAAGAA
EST: gi|29613611|gb|CB618624.1|CB618624
EST:     TTGAGAAGAATTTTGTCATCACAGATCCAAGGTTGCCTGATAATCCCATT                         ATATTTGCATCCGATAGCTTTCTGCAATTGACAGAATACAACCGTGAAGAA
genomic: TTGAGAAGAATTTTGTCATCACAGATCCAAGGTTGCCTGATAATCCCATTgtaagatcca ... catatttcagATATTTGCATCCGATAGCTTTCTGCAATTGACAGAATACAACCGTGAAGAA
EST: gi|29678744|gb|CB675019.1|CB675019
EST:     TTGAGAAGAATTTTGTCATCACAGATCCAAGGTTGCCTGATAATCCCATT                         ATATTTGCATCCGATAGCTTTCTGCAATTGACAGAATACAACCGTGAAGAA
genomic: TTGAGAAGAATTTTGTCATCACAGATCCAAGGTTGCCTGATAATCCCATTgtaagatcca ... catatttcagATATTTGCATCCGATAGCTTTCTGCAATTGACAGAATACAACCGTGAAGAA
EST: gi|29627346|gb|CB632357.1|CB632357
EST:     TTGAGAAGAATTTTGTCATCACAGATCCAAGGTTGCCTGATAATCCCATT                         ATATTTGCATCCGATAGCTTTCTGCAATTGACAGAATACAACCGTGAAGAA
genomic: TTGAGAAGAATTTTGTCATCACAGATCCAAGGTTGCCTGATAATCCCATTgtaagatcca ... catatttcagATATTTGCATCCGATAGCTTTCTGCAATTGACAGAATACAACCGTGAAGAA
EST: gi|29630466|gb|CB635475.1|CB635475
EST:     TTGAGAAGAATTTTGTCATCACAGATCCAAGGTTGCCTGATAATCCCATT                         ATATTTGCATCCGATAGCTTTCTGCAATTGACAGAATACAACCGTGAAGAA
genomic: TTGAGAAGAATTTTGTCATCACAGATCCAAGGTTGCCTGATAATCCCATTgtaagatcca ... catatttcagATATTTGCATCCGATAGCTTTCTGCAATTGACAGAATACAACCGTGAAGAA
EST: gi|2317377|gb|C22431.1|C22431
EST:     TTGAGAAGAATTTTGTCATCACAGATCCAAGGTTGCCTGATAATCCCATT                         ATATTTGCATCCGATAGCTTTCTGCAATTGACAGAATACAACCGTGAAGAA
genomic: TTGAGAAGAATTTTGTCATCACAGATCCAAGGTTGCCTGATAATCCCATTgtaagatcca ... catatttcagATATTTGCATCCGATAGCTTTCTGCAATTGACAGAATACAACCGTGAAGAA
EST: gi|29624450|gb|CB629461.1|CB629461
EST:     TTGAGAAGAATTTTGTCATCACAGATCCAAGGTTGCCTGATAATCCCATT                         ATATTTGCATCCGATAGCTTTCTGCAATTGACAGAATACAACCGTGAAGAA
genomic: TTGAGAAGAATTTTGTCATCACAGATCCAAGGTTGCCTGATAATCCCATTgtaagatcca ... catatttcagATATTTGCATCCGATAGCTTTCTGCAATTGACAGAATACAACCGTGAAGAA
EST: gi|58593934|gb|CF992242.1|CF992242
EST:     TTGAGAAGAATTTTGTCATCACAGATCCAAGGTTGCCTGATAATCCCATT                         ATATTTGCATCCGATAGCTTTCTGCAATTGACAGAATACAACCGTGAAGAA
genomic: TTGAGAAGAATTTTGTCATCACAGATCCAAGGTTGCCTGATAATCCCATTgtaagatcca ... catatttcagATATTTGCATCCGATAGCTTTCTGCAATTGACAGAATACAACCGTGAAGAA
EST: gi|58592396|gb|CF990704.1|CF990704
EST:     TTGAGAAGAATTTTGTCATCACAGATCCAAGGTTGCCTGATAATCCCATT                         ATATTTGCATCCGATAGCTTTCTGCAATTGACAGAATACAACCGTGAAGAA
genomic: TTGAGAAGAATTTTGTCATCACAGATCCAAGGTTGCCTGATAATCCCATTgtaagatcca ... catatttcagATATTTGCATCCGATAGCTTTCTGCAATTGACAGAATACAACCGTGAAGAA
EST: gi|29646710|gb|CB651717.1|CB651717
EST:     TTGAGAAGAATTTTGTCATCACAGATCCAAGGTTGCCTGATAATCCCATT                         ATATTTGCATCCGATAGCTTTCTGCAATTGACAGAATACAACCGTGAAGAA
genomic: TTGAGAAGAATTTTGTCATCACAGATCCAAGGTTGCCTGATAATCCCATTgtaagatcca ... catatttcagATATTTGCATCCGATAGCTTTCTGCAATTGACAGAATACAACCGTGAAGAA