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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AAATGAATTACACCTCTGAGGATGAACCATATCCTCGTGGAGAAATCTGTGTTAGGGGACCTACGATATTCTGTGGTTACTATAAAGACGAAATCCAAACgtaatttgctatatatttctatcttctactatttaaattcataaatatttgatgagtttcagcaattaaatttgaaaacctgcag

Basic information

species Oryza sativa
transcript LOC_Os12g04990.3
intron # 16
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os12g04990.3 (Oryza sativa), 5'ss of exon 16
lower sequence: GRMZM2G176546_T01 (Zea mays), 5'ss of exon 8
AAATGAATTACACCTCTGAGGATGAACCATATCCTCGTGGAGAAATCTGTGTTAGGGGACCTACGATATTCTGTGGTTACTATAAAGACGAAATCCAAACgtaatttgctatatatttctatcttctactatttaaattcataaatatttgat---gagtt-tcagcaattaaatttgaaaacctgcag
|||||||||| || ||||| ||| |||| ||||||||||||||||| |||||||| |||||||  ||||||   ||||||||||| || ||| | ||||||||| || ||||   |  ||      ||   |||  | | |   || ||  |     | || |||  || || |||| |||| || |||
AAATGAATTATACATCTGATGATCAACCTTATCCTCGTGGAGAAATTTGTGTTAGAGGACCTATAATATTCCAGGGTTACTATAAGGATGAAGTTCAAACgtaaatttctatccgtcacttaaacatagc-tttgtactgaatgatcttcaactgcaacttatcaataaatacattttaaaaactacag

upper sequence: LOC_Os12g04990.3 (Oryza sativa), 5'ss of exon 16
lower sequence: AT5G27600.1 (Arabidopsis thaliana), 5'ss of exon 17
AAATGAATTACACCTCTGAGGATGAACCATATCCTCGTGGAGAAATCTGTGTTAGGGGACCTACGATATTCTGTGGTTACTATAAAGACGAAATCCAAACgtaatttgctatatatttctatc--ttctactatttaaattcataaatatttg---atgagtttcagcaattaaatttgaaaacctgcag
||||||||||||| || || ||| ||||||| || ||||| ||||||||||| || ||||| |  || |||   || ||||| ||||| |||   |||||||||     | |  | |   ||   |    ||| ||| ||  ||| |||  ||   |||||| |   ||  |  | ||||  |       
AAATGAATTACACATCAGACGATCAACCATACCCACGTGGTGAAATCTGTGTAAGAGGACCAATCATCTTCAAAGGCTACTACAAAGATGAAGAACAAACgtaacacattttccagtatcattagtggctctagttatatgtatagataagtggacatgagtcttgacacatttacttgagcag------

upper sequence: LOC_Os12g04990.3 (Oryza sativa), 5'ss of exon 16
lower sequence: Vv05s0020g03080.t01 (Vitis vinifera), 5'ss of exon 17
AAATGAATTACACCTCTGAGGATGAACCATATCCTCGTGGAGAAATCTGTGTTAGGGGACCTACGATATTCTGTGGTTACTATAAAGACGAAATCCAAACgtaatttgctatatatttctatcttctactatttaaattcataaatatttgatgagtttca-gcaattaaatttgaaaacctgcag-----
||||||| ||||| ||||||||| | || ||||||||||| |||||||||||| |||| || |   | ||    |||||| ||||||| ||| | || |||||     |  |   | |    ||  | || || ||  |  |  || ||     | ||  |  ||  | | | ||  | |     |     
AAATGAACTACACATCTGAGGATCAGCCCTATCCTCGTGGTGAAATCTGTGTTCGGGGTCCCATTCTTTTTCTAGGTTACCATAAAGATGAAGTGCAGACgta-cccaccttgcctgttctgctggttcttttgaatgttgtgcattttgtcaaaattggatacatctgattatgtgatcaaattgaacag

upper sequence: LOC_Os12g04990.3 (Oryza sativa), 5'ss of exon 16
lower sequence: Vv14s0128g00720.t01 (Vitis vinifera), 5'ss of exon 17
AAATGAATTACACCTCTGAGGATGAACCATATCCTCGTGGAGAAATCTGTGTTAGGGGACCTACGATATTCTGTGGTTACTATAAAGACGAAATCCAAACgtaatttgctat---atatttctat--cttctactattta---aattcataaatatttgatgagtttcagcaat---taaatttgaaaacctgcag-------------------
||||||||||||||||||||||| | || |||||||| || ||||| ||||| ||||| ||     | |||   || ||||| ||||| ||| |||| ||||| |   || |   ||||||||||  ||| || |  |||   ||| || | || | |    | | |||   ||   |||||     | |   | |                   
AAATGAATTACACCTCTGAGGATCAGCCCTATCCTCGCGGTGAAATATGTGTCAGGGGTCCCGTTCTCTTCCAAGGCTACTACAAAGATGAAGTCCAGACgtactcaactttcttatatttctatttcttgtattgcttatcaaatacacatatttcttgcaattgtcactcatgtgtaaataatggatctacctgactccagttactttgacag

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:     TAGGGGACCTACGATATTCTGTGGTTACTATAAAGACGAAATCCAAAC                         TAGAGAGGCTGTTGACGAGGATGGTTGGTTACACACTGGAGACATAGGTTT
genomic: TAGGGGACCTACGATATTCTGTGGTTACTATAAAGACGAAATCCAAACgtaatttgct ... aaacctgcagTAGAGAGGCTGTTGACGAGGATGGTTGGTTACACACTGGAGACATAGGTTT
EST: gi|568356|gb|D39204.1|D39204
EST:     GTTAGGGG-CCTACGATATTCTGTGGTTACTATAAAGACGGAATCCAAAC                         TAGAGAGGCTGTTGACGAGGNTGGGTTGGT-ACACACTGGAG
genomic: GTTAGGGGACCTACGATATTCTGTGGTTACTATAAAGACGAAATCCAAACgtaatttgct ... aaacctgcagTAGAGAGGCTGTTGACGAGGATGG-TTGGTTACACACTGGAG
EST: gi|58659745|gb|CK048425.1|CK048425
EST:     GTTAGGGGACCTACGATATTCTGTGGTTACTATAAAGACGAAATCCAAAC                         TAGAGAGGCTGTTGACGAGGATGGTTGGTTACACACTGGAGACATAGGTTT
genomic: GTTAGGGGACCTACGATATTCTGTGGTTACTATAAAGACGAAATCCAAACgtaatttgct ... aaacctgcagTAGAGAGGCTGTTGACGAGGATGGTTGGTTACACACTGGAGACATAGGTTT
EST: gi|29622085|gb|CB627096.1|CB627096
EST:     GGTTACTATAAAGACGAAATCCAAAC                         TAGAGAGGCTGTTGACGAGGATGGTTGGTTACACACTGGAGACATAGGTTT
genomic: GGTTACTATAAAGACGAAATCCAAACgtaatttgct ... aaacctgcagTAGAGAGGCTGTTGACGAGGATGGTTGGTTACACACTGGAGACATAGGTTT
EST: gi|313081138|gb|HO213724.1|HO213724
EST:     GTTAGGGGACCTACGATATTCTGTGGTTACTATAAAGACGAAATCCAAAC                         TAGAGAGGCTGTTGACGAGGATGGTTGGTTACACACTGGAGACATAGGTTT
genomic: GTTAGGGGACCTACGATATTCTGTGGTTACTATAAAGACGAAATCCAAACgtaatttgct ... aaacctgcagTAGAGAGGCTGTTGACGAGGATGGTTGGTTACACACTGGAGACATAGGTTT