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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_Os06g45120.1
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|116875538|gb|EC366046.1|EC366046
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|58657888|gb|CK046568.1|CK046568
EST:     GAGGTGATTTTTCAGATCCTGTTACCTCTGCAACTCTTAGTATTGTGCAG                         GTCTTTTGGGGATTGGATAAGAAGCTGGCTCAAAGAAAGCATTTCCCATCT
genomic: GAGGTGATTTTTCAGATCCTGTTACCTCTGCAACTCTTAGTATTGTGCAGgtaaggaaac ... tcaattgcagGTCTTTTGGGGATTGGATAAGAAGCTGGCTCAAAGAAAGCATTTCCCATCT
EST: gi|29667460|gb|CB663735.1|CB663735
EST:     GAGGTGATTTTTCAGATCCTGTTACCTCTGCAACTCTTAGTATTGTGCAG                         GTCTTTTGGGGATTGGATAAGAAGCTGGCTCAAAGAAAGCATTTCCCATCT
genomic: GAGGTGATTTTTCAGATCCTGTTACCTCTGCAACTCTTAGTATTGTGCAGgtaaggaaac ... tcaattgcagGTCTTTTGGGGATTGGATAAGAAGCTGGCTCAAAGAAAGCATTTCCCATCT
EST: gi|29617005|gb|CB622017.1|CB622017
EST:     GAGGGGATTTTTCAGATCCTGTTACCTCTGCAACTCTTAGTATTGTGCAG                         GTCTTTTGGGGATTGGATAACAAGCTGGCTCAAAGAAAGCATTTCCCATCT
genomic: GAGGTGATTTTTCAGATCCTGTTACCTCTGCAACTCTTAGTATTGTGCAGgtaaggaaac ... tcaattgcagGTCTTTTGGGGATTGGATAAGAAGCTGGCTCAAAGAAAGCATTTCCCATCT
EST: gi|116875037|gb|EC365545.1|EC365545
EST:     GAGGTGATTTTTCAGATCCTGTTACCTCTGCAACTCTTAGTATTGTGCAG                         GTCTTTTGGGGATTGGATAAGAAGCTGGCTCAAAGAAAGCATTTCCCATCT
genomic: GAGGTGATTTTTCAGATCCTGTTACCTCTGCAACTCTTAGTATTGTGCAGgtaaggaaac ... tcaattgcagGTCTTTTGGGGATTGGATAAGAAGCTGGCTCAAAGAAAGCATTTCCCATCT
EST: gi|27578142|gb|CB000837.1|CB000837
EST:     GAGGTGATTTTTCAGATCCTGTTACCTCTGCAACTCTTAGTATTGTGCAG                         GTCTTTTGGGGATTGGATAAGAAGCTGGCTCAAAGAAAGCATTTCCCATCT
genomic: GAGGTGATTTTTCAGATCCTGTTACCTCTGCAACTCTTAGTATTGTGCAGgtaaggaaac ... tcaattgcagGTCTTTTGGGGATTGGATAAGAAGCTGGCTCAAAGAAAGCATTTCCCATCT

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 1 RNA-Seqlibrary.


Block sizes: 67 (upstream exon), 38 (downstream exon)
Score: 87

TCCAGATCGGACAGGCAGTGTCACAATTGTTGGTGCTGTCTCTCCACCTGGAGGTGATTTTTCAGATCCTGTTACCTCTGCAACTCTTAGTATTGTGCAGgtaaggaaac ... tcaattgcagGTCTTTTGGGGATTGGATAAGAAGCTGGCTCAAAGAAAGCATTTCCCATCTGTCAATTGGCTCATCTCTTACTCAAAATACTCAAAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aacctttctaactgcatgttcattgtttgataatcttaactcctctcaattgcagGTCTTTTGGGGATTGGATAAGAAGCTGGCTCAAAGAAAGCATTTCCCATCTGTCAATTGGCTCATCTCTTACTCAAAATACTCAAAG
                                 tcttaactcctctc  CT-rich tract
                         tttgataatcttaa  TA-rich tract