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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaggaaactgctagattaatccaacctttgaattaaattttcaaacctttctaactgcatgttcattgtttgataatcttaactcctctcaattgcagGTCTTTTGGGGATTGGATAAGAAGCTGGCTCAAAGAAAGCATTTCCCATCTGTCAATTGGCTCATCTCTTACTCAAAATACTCAAAG

Basic information

species Oryza sativa
transcript LOC_Os06g45120.2
intron # 13
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os06g45120.1 (Oryza sativa), 3'ss of exon 13
lower sequence: GLYMA08G23990.1 (Glycine max), 3'ss of exon 14
gtaaggaaactgctagattaatccaacctttgaattaaattttcaa--acctttctaactgca-tgttca--ttgtttgataatcttaactcctctcaattg-cagGTCTTTTGGGGATTGGATAAGAAGCTGGCTCAAAGAAAGCATTTCCCATCTGTCAATTGGCTCATCTCTTACTCAAAATACTCAAAG
      | | |   |   | |   | || |    |||  | |||    | || ||   ||  |   ||||  |  |||  |||  |||  |   || ||||| ||||| || ||||| ||||| || ||||| ||||| || ||||| || || ||||| || ||||| || ||||| ||||||||||||| |
------agattatcattatgaaatacccctctggttatttcttcttttatctatccttctataactttcaattcattttgtaagtttatttttgcttaattggcagGTTTTCTGGGGTTTGGACAAAAAGCTTGCTCAGAGGAAGCACTTTCCTTCTGTAAACTGGCTTATTTCTTATTCAAAATACTCAACG

upper sequence: LOC_Os06g45120.1 (Oryza sativa), 3'ss of exon 13
lower sequence: AT1G78900.2 (Arabidopsis thaliana), 3'ss of exon 14
-----------------------------------------------------------------------------------------gtaaggaaactgctagattaatccaacctttgaattaaattttcaaacctttctaactgcatgttcattgtttgataatcttaactcctctcaattgcagGTCTTTTGGGGATTGGATAAGAAGCTGGCTCAAAGAAAGCATTTCCCATCTGTCAATTGGCTCATCTCTTACTCAAAATACTCAAAG
                                                                                         ||     | ||||   |  | ||  |  ||| |      ||||    |  ||  || ||| |  || ||   |  |  |  |  ||| | ||   |||||||||| ||||| ||||| || ||||| || || ||||| ||||| || ||||| |||||| | || ||||||||||| || |||| |
gtgattatttggttcatgtctgcttccctatcttccattgtagattacatagtcgtatatgttggttgagatgaaccagatggtgtttagttttagatctgccgcag-actcgtatatttaagcattttttttctccactttgaaatgcttactc-ttccattctggttgtttctcttttcttctgcagGTCTTCTGGGGTTTGGACAAAAAGCTTGCCCAGAGAAAACATTTTCCCTCTGTTAATTGGTTGATTTCTTACTCAAAGTATTCAACG

upper sequence: LOC_Os06g45120.1 (Oryza sativa), 3'ss of exon 13
lower sequence: Vv09s0054g00890.t01 (Vitis vinifera), 3'ss of exon 14
------gtaaggaaactgc-tagattaatccaacctttgaattaaattttcaaacctttctaactgcatgttcattgtttgataatcttaactcctctcaattgcagGTCTTTTGGGGATTGGATAAGAAGCTGGCTCAAAGAAAGCATTTCCCATCTGTCAATTGGCTCATCTCTTACTCAAAATACTCAAAG
       | |  |   ||| |  || ||| ||  | ||    | | ||| |||||  |  |   ||  |   | || ||  ||| | |  |    | |    ||||||| || |||||  |||| ||||| || ||||| || || |||||||||||||| || ||||| || || |||||||||||  ||| |
tcttgtctcacaaggatgcatgaatgaatacacacgtt---ctcattttgcaaactatcttttttggcttcaccttattcaatattatgtatattttt----tgcagGTTTTCTGGGGTCTGGACAAGAAACTTGCTCAGAGGAAACATTTCCCATCTGTAAACTGGCTTATTTCATACTCAAAATATGCAACG

upper sequence: LOC_Os06g45120.1 (Oryza sativa), 3'ss of exon 13
lower sequence: Vv04s0008g02580.t01 (Vitis vinifera), 3'ss of exon 14
gtaaggaaactgctagattaatccaacctttgaattaaattttcaaacctttctaactgcatgttcattgtttgataatcttaactcctctcaat------tgcagGTCTTTTGGGGATTGGATAAGAAGCTGGCTCAAAGAAAGCATTTCCCATCTGTCAATTGGCTCATCTCTTACTCAAAATACTCAAAG
      |   | |||   ||||  ||   ||| | ||    ||  |  || | ||| | | |  |  | |  |   | | |||  |   |  ||       ||||||| || ||||| ||||| || ||||| ||||| || || |||||||||||||| || ||||| || |||||||| || |||||||  
---cccatcattctattataattgaagacttggagtatccatttga--ctctttaatttc-tccttttggcattcaagttttagttttccataaaaccttgtgcagGTGTTCTGGGGTTTGGACAAAAAGCTTGCTCAGAGGAAACATTTCCCATCTGTAAACTGGCTTATTTCTTACTCTAAGTACTCAACC

upper sequence: LOC_Os06g45120.1 (Oryza sativa), 3'ss of exon 13
lower sequence: EDP07903 (Chlamydomonas reinhardtii), 3'ss of exon 8
--------gtaaggaaactgctagattaatccaacctttgaattaaattttcaaacctttctaactgcatgttcattgtttgataatcttaactcctctcaattgcagGTCTTTTGGGGATTGGATAAGAAGCTGGCTCAAAGAAAGCATTTCCCATCTGTCAATTGGCTCATCTCTTACTCAAAATACTCAAAG-------------
        ||| || |  ||| |  || | ||| ||    | ||   | |  | | ||||    || |  |      |         | | || |  |||   | ||||| || |||||  |||| ||||||||||| ||  | ||||||||||| || ||||| ||||||||||| ||||| || ||| | |||             
ctcgaggcgtatggcacatgcaaccttgagccagcc----agtt---tctgtagagcttttgcgctacccgccgccggcacccctgacctgac-cggctctgctccagGTGTTCTGGGGCCTGGACAAGAAGCTGGCGCAGCGTAAGCATTTCCCTTCGGTCAACTGGCTCATCTCCTACTCCAAGTACACCAAGTCCCTGGAGCCCT

upper sequence: LOC_Os06g45120.1 (Oryza sativa), 3'ss of exon 13
lower sequence: PP1S8_312V6.1 (Physcomitrella patens), 3'ss of exon 14
-----------------------------------------------gtaaggaaactgctagattaatccaacctttgaattaaattttcaaaccttt----ctaactgcatgttc------attgtttgataa-----tcttaactcctctcaattgcagGTCTTTTGGGGATTGGATAAGAAGCTGGCTCAAAGAAAGCATTTCCCATCTGTCAATTGGCTCATCTCTTACTCAAAATACTCAAAG
                                                |     || | || | | |    |   ||   ||| |  |  |||| | ||    || | ||||| ||        ||  |||| ||     | |||| | |         ||||| ||||||||| | || |||||||| |||||| | || ||||| ||| |||| ||||||||||| || ||||| || ||| |  ||
gttagtcatttgtgtacttgcactgattgtgctacatcctatcgtcaatttcagaattactcgctcaccgtagattt---attgagatagcaaagcattgatcctgaatgcattttttatgtggttacttgaaaaatggatgttaaatgcatgtggagtcagGTGTTTTGGGGACTTGACAAGAAGCTTGCTCAACGTAAACATTTTCCAGCTGTGAATTGGCTCATTTCCTACTCCAAGTACACTCAG

upper sequence: LOC_Os06g45120.1 (Oryza sativa), 3'ss of exon 13
lower sequence: EFJ30330 (Selaginella moellendorffii), 3'ss of exon 14
gtaaggaaactgctagattaatccaacctttgaattaaattttcaaacctttctaactgcatgttcattgt-ttgataatcttaactcctctcaattgcagGTCTTTTGGGGATTGGATAAGAAGCTGGCTCAAAGAAAGCATTTCCCATCTGTCAATTGGCTCATCTCTTACTCAAAATACTCAAAG
                                                |||| |  | |  | ||    || ||||       | ||  | |   |||||||| ||||||||| | || |||||||| || |||||||||||||||||  ||||||| ||||| || ||||| || || ||  |  ||
----------------------------------------------gtctttgtgccagttttttttcagtgttgactgggaca-ctgttgtttgttgcagGTGTTTTGGGGACTTGACAAGAAGCTTGCGCAAAGAAAGCATTTCCCTGCTGTCAACTGGCTGATATCTTATTCGAAGTATACCCAG

upper sequence: LOC_Os06g45120.1 (Oryza sativa), 3'ss of exon 13
lower sequence: EFJ33015 (Selaginella moellendorffii), 3'ss of exon 13
gtaaggaaactgctagattaatccaacctttgaattaaattttcaaacctttctaactgcatgttcattgtttgataatcttaactcctctcaattgcagGTCTTTTGGGGATTGGATAAGAAGCTGGCTCAAAGAAAGCATTTCCCATCTGTCAATTGGCTCATCTCTTACTCAAAATACTCAAAG
                                       | ||    ||     |  ||  | |||| ||||   |       |||  | |   |||||||| ||||||||| | || |||||||| || |||||||||||||||||  ||||||| ||||| || ||||| || || ||  |  ||
--------------------------------------gtctttgtgcc-----agttgt-ttttcagtgttgactgggac--actgttgtttgttgcagGTGTTTTGGGGACTTGACAAGAAGCTTGCGCAAAGAAAGCATTTCCCTGCTGTCAACTGGCTGATATCTTATTCGAAGTATACCCAG

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|58692820|gb|CK081507.1|CK081507
EST:     GAGGTGATTTTTCAGATCCTGTTACCTCTGCAACTCTTAGTATTGTGCAG                         GTCTTTTGGGGATTGGATAAGAAGCTGGCTCAAAGAAAGCATTTCCCATCT
genomic: GAGGTGATTTTTCAGATCCTGTTACCTCTGCAACTCTTAGTATTGTGCAGgtaaggaaac ... tcaattgcagGTCTTTTGGGGATTGGATAAGAAGCTGGCTCAAAGAAAGCATTTCCCATCT
EST: gi|58611693|gb|CK039405.1|CK039405
EST:     GAGGTGATTTTTCAGATCCTGTTACCTCTGCAACTCTTAGTATTGTGCAG                         GTCTTTTGGGGATTGGATAAGAAGCTGGCTCAAAGAAAGCATTTCCCATCT
genomic: GAGGTGATTTTTCAGATCCTGTTACCTCTGCAACTCTTAGTATTGTGCAGgtaaggaaac ... tcaattgcagGTCTTTTGGGGATTGGATAAGAAGCTGGCTCAAAGAAAGCATTTCCCATCT
EST: gi|33804193|gb|CF327971.1|CF327971
EST:     GAGGTGATTTTTCAGATCCTGTTACCTCTGCAACTCTTAGTATTGTGCAG                         GTCTTTTGGGGATTGGATAAGAAGCTGGCTCAAAGAAAGCATTTCCCATCT
genomic: GAGGTGATTTTTCAGATCCTGTTACCTCTGCAACTCTTAGTATTGTGCAGgtaaggaaac ... tcaattgcagGTCTTTTGGGGATTGGATAAGAAGCTGGCTCAAAGAAAGCATTTCCCATCT
EST: gi|116875037|gb|EC365545.1|EC365545
EST:     GAGGTGATTTTTCAGATCCTGTTACCTCTGCAACTCTTAGTATTGTGCAG                         GTCTTTTGGGGATTGGATAAGAAGCTGGCTCAAAGAAAGCATTTCCCATCT
genomic: GAGGTGATTTTTCAGATCCTGTTACCTCTGCAACTCTTAGTATTGTGCAGgtaaggaaac ... tcaattgcagGTCTTTTGGGGATTGGATAAGAAGCTGGCTCAAAGAAAGCATTTCCCATCT
EST: gi|88735905|gb|CI757480.1|CI757480
EST:     TGATTTTTCAGATCCTGTTACCTCTGCAACTCTTAGTATTGTGCAG                         GTCTTTTGGGGATTGGATAAGAAGCTGGCTCAAAGAAAGCATTTCCCATCT
genomic: TGATTTTTCAGATCCTGTTACCTCTGCAACTCTTAGTATTGTGCAGgtaaggaaac ... tcaattgcagGTCTTTTGGGGATTGGATAAGAAGCTGGCTCAAAGAAAGCATTTCCCATCT
EST: gi|66919084|gb|CX105932.1|CX105932
EST:     GAGGTGATTTTTCAGATCCTGTTACCTCTGCAACTCTTAGTATTGTGCAG                         GTCTTTTGGGGATTGGATAAGAAGCTGGCTCAAAGAAAGCATTTCCCATCT
genomic: GAGGTGATTTTTCAGATCCTGTTACCTCTGCAACTCTTAGTATTGTGCAGgtaaggaaac ... tcaattgcagGTCTTTTGGGGATTGGATAAGAAGCTGGCTCAAAGAAAGCATTTCCCATCT
EST: gi|116875538|gb|EC366046.1|EC366046
EST:     GAGGTGATTTTTCAGATCCTGTTACCTCTGCAACTCTTAGTATTGTGCAG                         GTCTTTTGGGGATTGGATAAGAAGCTGGCTCAAAGAAAGCATTTCCCATCT
genomic: GAGGTGATTTTTCAGATCCTGTTACCTCTGCAACTCTTAGTATTGTGCAGgtaaggaaac ... tcaattgcagGTCTTTTGGGGATTGGATAAGAAGCTGGCTCAAAGAAAGCATTTCCCATCT
EST: gi|58657888|gb|CK046568.1|CK046568
EST:     GAGGTGATTTTTCAGATCCTGTTACCTCTGCAACTCTTAGTATTGTGCAG                         GTCTTTTGGGGATTGGATAAGAAGCTGGCTCAAAGAAAGCATTTCCCATCT
genomic: GAGGTGATTTTTCAGATCCTGTTACCTCTGCAACTCTTAGTATTGTGCAGgtaaggaaac ... tcaattgcagGTCTTTTGGGGATTGGATAAGAAGCTGGCTCAAAGAAAGCATTTCCCATCT
EST: gi|29617005|gb|CB622017.1|CB622017
EST:     GAGGGGATTTTTCAGATCCTGTTACCTCTGCAACTCTTAGTATTGTGCAG                         GTCTTTTGGGGATTGGATAACAAGCTGGCTCAAAGAAAGCATTTCCCATCT
genomic: GAGGTGATTTTTCAGATCCTGTTACCTCTGCAACTCTTAGTATTGTGCAGgtaaggaaac ... tcaattgcagGTCTTTTGGGGATTGGATAAGAAGCTGGCTCAAAGAAAGCATTTCCCATCT
EST: gi|27578142|gb|CB000837.1|CB000837
EST:     GAGGTGATTTTTCAGATCCTGTTACCTCTGCAACTCTTAGTATTGTGCAG                         GTCTTTTGGGGATTGGATAAGAAGCTGGCTCAAAGAAAGCATTTCCCATCT
genomic: GAGGTGATTTTTCAGATCCTGTTACCTCTGCAACTCTTAGTATTGTGCAGgtaaggaaac ... tcaattgcagGTCTTTTGGGGATTGGATAAGAAGCTGGCTCAAAGAAAGCATTTCCCATCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aacctttctaactgcatgttcattgtttgataatcttaactcctctcaattgcagGTCTTTTGGGGATTGGATAAGAAGCTGGCTCAAAGAAAGCATTTCCCATCTGTCAATTGGCTCATCTCTTACTCAAAATACTCAAAG
                                 tcttaactcctctc  CT-rich tract
                         tttgataatcttaa  TA-rich tract