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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaatttggtagcaaaattagtagcaaggagtacttgattttggacccaagattcctccaaatatgctgctggctatagtcaggttccaagtattcattccgaatgctcttgttgtcccacagGATACATGCAATAGGAAAAGTAACCAGCAGAATTTGGGCACAATTAAATCTTCAAACTTATGCACTGAGATAATTGAGTACACAAGCCCTACTGAAACTG

Basic information

species Oryza sativa
transcript LOC_Os06g07210.1
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os06g07210.1 (Oryza sativa), 3'ss of exon 8
lower sequence: GRMZM2G304362_T01 (Zea mays), 3'ss of exon 8
gtaaatttggtagcaaaattagtagcaaggagtacttgattttggacccaagattcctccaaatatgctgctggctatagtcaggttccaagtattcattccgaatgctcttgttgtcccacagGATACATGCAATAGGAAAAGTAACCAGCAGAATTTGGGCACAATTAAATCTTCAAACTTATGCACTGAGATAATTGAGTACACAAGCCCTACTGAAACTG
||| ||||||||||        || |||  |||| |   || | ||        |  | | || ||  |     | |  || |||         ||  ||   |  ||| ||         |||||||| ||||||||||||||||||||||||||| |||||||||||||||| |||||| | |||||||| ||||||||||  |||||||||||||| || |
gtacatttggtagc--------tatcaaatagtagtaccttctagatttgtctgttttgccaaaatttt-----ccacggtaagg--------gtttcttgtaatggctattaactgtatgcagGATACTTGCAATAGGAAAAGTAACCAGCAGAATCTGGGCACAATTAAATCGTCAAACCTGTGCACTGAAATAATTGAGTTTACAAGCCCTACTGAGACCG

upper sequence: LOC_Os06g07210.1 (Oryza sativa), 3'ss of exon 8
lower sequence: GRMZM2G340527_T01 (Zea mays), 3'ss of exon 8
gtaaatttggtagcaaaattagtagcaaggagtacttgattttggacccaagattcctccaaatatgctgctggctatagtcaggttccaagtattcattccgaatgctcttgttgtcccacagGATACATGCAATAGGAAAAGTAACCAGCAGAATTTGGGCACAATTAAATCTTCAAACTTATGCACTGAGATAATTGAGTACACAAGCCCTACTGAAACTG
||| |||| || ||     ||  |   |||||||| |  | ||          ||  ||        ||  || | | |||        ||| |||  ||   |  ||| ||         |||||||| ||||||||||||||||||||||||||| |||||||||||||||| |||||||| |||||||||||||||||||  |||||||||||||||||||
gtacatttagtggc-----tatcaaataggagtacctcctatt----------tttgtct-------cttttgccaaaagtttccagttaaggatttcttgtaatggctattaactgtatgcagGATACTTGCAATAGGAAAAGTAACCAGCAGAATCTGGGCACAATTAAATCGTCAAACTTGTGCACTGAGATAATTGAGTTTACAAGCCCTACTGAAACTG

upper sequence: LOC_Os06g07210.1 (Oryza sativa), 3'ss of exon 8
lower sequence: GLYMA08G15360.1 (Glycine max), 3'ss of exon 9
gtaaatttggtagcaaaattagtagcaaggagtacttgattttggacccaagattcctccaaatatgctgctggctatagtcaggttccaagtattcattccgaatgctcttgttgtcccacagGATACATGCAATAGGAAAAGTAACCAGCAGAATTTGGGCACAATTAAATCTTCAAACTTATGCACTGAGATAATTGAGTACACAAGCCCTACTGAAACTG
         ||    ||| | ||     |   || |||| | |     ||||  |||  || | | |  ||||  |  |    ||   ||| |  ||   |  |||        |||   | || |                                                                                                  
---------gtcatgaaacttgtgcactgagataattgagtata----caag-

upper sequence: LOC_Os06g07210.1 (Oryza sativa), 3'ss of exon 8
lower sequence: GLYMA06G15350.1 (Glycine max), 3'ss of exon 8
gtaaatttggtagcaaaattagtagcaaggagtacttgattttggacccaagattcctccaaatatgctgctggctatagtcaggttccaagtattcattccgaatgctcttgttgtcccac-agGATACATGCAATAGGAAAAGTAACCAGCAGAATTTGGGCACAATTAAATCTTCAAACTTATGCACTGAGATAATTGAGTACACAAGCCCTACTGAAACTG
                            || || |||     ||      |  ||||||   | ||  || |   ||| ||      ||    | | |||||      | |  ||   | || ||||||| |||||||||||||| || || ||||||||||| ||||||||||| |||||||| || |||||||||||||| ||  |||| || ||||||||||
--------------------------gtggtgttcttaga--tgtctttgactttcctcatgagattttg-tatttattgttttcacccgttgagtaattccagcatttttgtttacactactagGATACTTGCAATAGGAAAAGCAATCAACAGAATTTGGGTACAATTAAATCGTCAAACTTGTGTACTGAGATAATTGAATATTCAAGTCCAACTGAAACTG

upper sequence: LOC_Os06g07210.1 (Oryza sativa), 3'ss of exon 8
lower sequence: GLYMA08G15360.1 (Glycine max), 3'ss of exon 8
gtaaatttggtagcaaaattagtagcaaggagtacttgattttggacccaagattcctccaaatatgctgctggctatagtcaggttccaagtattcattccgaatgctcttgttgtcccacagGATACATGCAATAGGAAAAGTAACCAGCAGAATTTGGGCACAATTAAATCTTCAAACTTATGCACTGAGATAATTGAGTACACAAGCCCTACTGAAACTG
                  ||   |  || |  |  |||| ||| |  | ||| |||   ||       |||    | || | |  |||     ||| |  ||   |  | ||  | |  |  |||| || |||||||||||||| ||||| ||||||||||||||||| ||                                                     
--------------gtggtttaca--aatgcttgtttgacttttg--ctaagtttctgtcag------tgcattttgtatttattttc-----attgaaacctcttcatttttctatatcctagGACACTTGCAATAGGAAAAGCAACCAACAGAATTTGGGCACAATCAA-----------------------------------------------------

upper sequence: LOC_Os06g07210.1 (Oryza sativa), 3'ss of exon 8
lower sequence: GLYMA04G39500.1 (Glycine max), 3'ss of exon 8
gtaaatttggtagcaaaattagtagcaaggagtacttgattttggacccaagattcctccaaatatgctgctggctatagtcaggttccaagtattcattccgaatgctcttgttgtcccac-agGATACATGCAATAGGAAAAGTAACCAGCAGAATTTGGGCACAATTAAATCTTCAAACTTATGCACTGAGATAATTGAGTACACAAGCCCTACTGAAACTG
                            |||  ||||   | |            ||   | || |  |  |   | |  |||  |    | ||   | ||| |    | |  ||   | || ||||||| |||||||||||||| ||||| ||||||||||| ||||||||||| |||||||| || |||||||||||||||||  |||| || ||||||||||
--------------------------gtggaacacttagatgtcttttactttccccatgagattttgtatttattgttttcacctgttgaata---aatccaacatttttatttacactactagGATACTTGCAATAGGAAAAGCAACCAACAGAATTTGGGTACAATTAAATCATCAAACTTGTGTACTGAGATAATTGAGTATTCAAGTCCAACTGAAACTG

upper sequence: LOC_Os06g07210.1 (Oryza sativa), 3'ss of exon 8
lower sequence: GLYMA05G32070.1 (Glycine max), 3'ss of exon 8
gtaaatttggtagcaaaattagtagcaaggagtacttgattttggacccaagattcctccaaatatgctgctggctatagtcaggttccaagtattcattccgaatgctcttgttgtcccacagGATACATGCAATAGGAAAAGTAACCAGCAGAATTTGGGCACAATTAAATCTTCAAACTTATGCACTGAGATAATTGAGTACACAAGCCCTACTGAAACTG
                  ||   |  || |  |  || | ||| |   | || || ||   | |    |||    | || | |  || ||    || |  ||   | || ||  | |  |  |||| || |||||||  ||||| ||||| ||||||||||||||||| || || |||||||| |||||||||||||||||||| ||||| || || ||||| |
--------------gtggtttaca--aatgcatgtttaacttttg---ctaggtttct---atttcagtgcattttgtatttatttttca----ttgaaacctcttcctttttctatatcctagGACACTTGCAATAAAAAAAGCAACCAACAGAATTTGGGCACAATCAAGTCATCAAACTTGTGCACTGAGATAATTGAGTATACAAGTCCAACAGAAACGG

upper sequence: LOC_Os06g07210.1 (Oryza sativa), 3'ss of exon 8
lower sequence: AT2G21790.1 (Arabidopsis thaliana), 3'ss of exon 8
gtaaatttggtagcaaaattagtagcaaggagtacttgattttggacccaagattcctccaaatatgctgctggctatagtcaggttccaagtattcattccgaatgctcttgttgtcccacagGATACATGCAATAGGAAAAGTAACCAGCAGAATTTGGGCACAATTAAATCTTCAAACTTATGCACTGAGATAATTGAGTACACAAGCCCTACTGAAACTG
                        | ||| |  | |     ||    |      | | |   ||   ||  |    || |    ||||  | |    | |  ||||||||||      | | ||||| |||||||  | |||||||| ||||| ||| |||| || || || || || |||||||||||||| || ||||||||||| || || || |||||||
------------------------gtaagtaacagtcatcatt----ctgtagctacacgttatggccttataatcattg----gttcttact-ccaaatttgaatgctcttaaa---ctatagGATTCATGCAACCGAAAAAGTAATCAGCAAAATCTGGGTACCATAAAGTCGTCCAACTTATGCACTGAAATCATTGAGTACACTAGTCCAACAGAAACTG

upper sequence: LOC_Os06g07210.1 (Oryza sativa), 3'ss of exon 8
lower sequence: Vv07s0031g01990.t01 (Vitis vinifera), 3'ss of exon 8
gtaaatttggtagcaaaattagtagcaaggagtacttgattttggacccaagattcctccaaatatgctgctggctatagtcaggttccaagtattcattccgaatgctcttgttgtcccacagGATACATGCAATAGGAAAAGTAACCAGCAGAATTTGGGCACAATTAAATCTTCAAACTTATGCACTGAGATAATTGAGTACACAAGCCCTACTGAAACTG
       ||||    |||||    ||||       |   || ||  |||| ||||| |   | |    || ||| |      | |||  || | |    ||    |    |     ||  | ||||| | |||||||  |||||||| || |||||| |||| || |||||||||||||||||||| |||||||| ||||||||||| ||  ||  ||||||||
------gtggtttataaattctatgcaaaa-----tcatttctgctcccatgattctttttatt----tggtggtt-----tatgttttaattttgttctctttttctcttacccttcttatagGATTCTTGCAATAAAAAAAGTAATCAACAGAATCTGGGTACCATTAAATCTTCAAACTTATGTACTGAGATCATTGAGTACACCAGTGCTGATGAAACTG

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: 75 (upstream exon), 74 (downstream exon)
Score: 13

GGCAAGGCAAAGAAAATTGTCCCAGCTCAGACCCTCTGGTTTGACATTTTAAAGGCACAGATAGAAACTGGTACACCATATATGCTTTACAAGgtaaatttgg ... tgtcccacagGATACATGCAATAGGAAAAGTAACCAGCAGAATTTGGGCACAATTAAATCTTCAAACTTATGCACTGAGATAATTGAGTACACAAGCCCTACTGAAACTG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gctggctatagtcaggttccaagtattcattccgaatgctcttgttgtcccacagGATACATGCAATAGGAAAAGTAACCAGCAGAATTTGGGCACAATTAAATCTTCAAACTTATGCACTGAGATAATTGAGTACACAAGCCCTACTGAAACTG
                                      ctcttgtt  CT-rich tract
                       tattcatt  TA-rich tract