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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtagcacattctggttgtcctggaagttaatactcttgcttatgtctacgctcaggctcacatttcagcatggaaattcatgtcatattttaaagtgagtacttatttcagGTACAGACCATTCGACAAGGCTATCTCTCAAAGCGATCTTCAAACTTGAGAGGTGACTGGAAAAGAAGGTTCTTTGTTCTTGATAGCCGAGGAATGTTAT

Basic information

species Oryza sativa
transcript LOC_Os09g33600.1
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os09g33600.1 (Oryza sativa), 3'ss of exon 11
lower sequence: GRMZM2G059225_T02 (Zea mays), 3'ss of exon 11
gtagcacattctggttgtcctggaagttaatactcttgcttatgtctacgctcaggctcacatttcagcatggaaattcatgtcatattttaaagtgagtacttattt-cagGTACAGACCATTCGACAAGGCTATCTCTCAAAGCGATCTTCAAACTTGAGAGGTGACTGGAAAAGAAGGTTCTTTGTTCTTGATAGCCGAGGAATGTTAT
        | ||||   ||    |||  |||| || ||| |   |        |   ||| |    |  ||| |  ||    | ||| |  || || || |  ||||| ||||| ||||||||||| ||||||||||| || ||| |||||||||||||||||||||| |||||||| ||||||||||| || || || ||||||||||| |
--------tgctggaactctccaaagacaatattcatgcatgcatgattaagtaatttcataaaagaagatgcatgtt----ttatactgaaacgtaaggaactattttcagGTTCAGACCATTCGCCAAGGCTATCTATCTAAGAGATCTTCAAACTTGAGAGGTGATTGGAAAAGGAGGTTCTTTGTCCTCGACAGTCGAGGAATGTTGT

upper sequence: LOC_Os09g33600.1 (Oryza sativa), 3'ss of exon 11
lower sequence: GLYMA05G38550.1 (Glycine max), 3'ss of exon 11
----------gtagcacattctggttgtcctggaagtta-atactcttgcttatgtctacgctcaggctcacatttcagcatggaaattcatgtcatattttaaagtgagtactta-tttcagGTACAGACCATTCGACAAGGCTATCTCTCAAAGCGATCTTCAAACTTGAGAGGTGACTGGAAAAGAAGGTTCTTTGTTCTTGATAGCCGAGGAATGTTAT
           |   || ||    |  | |||  | |||  || |  | | | |    ||  |     ||  | || ||    |   | |||  |   || |  |  |  | |  | ||| |||| || | |||||||||||| ||||| || || ||||| || || |||||||||||||||||||||||||  |||||| |||| || ||||||||||| |
gtattttagaatttgacgtttccttctttctgagatttatgtattacttcattttaaaacttttcaattctgagttgagtcctg---tccattgccgtttcttcatcgcttgcaaaattttagGTTCAAATCATTCGACAAGGATATCTTTCTAAACGATCCTCCAATTTGAGAGGTGACTGGAAAAGAAGGTATTTTGTTGTTGACAGTCGAGGAATGTTGT

upper sequence: LOC_Os09g33600.1 (Oryza sativa), 3'ss of exon 11
lower sequence: GLYMA08G28890.2 (Glycine max), 3'ss of exon 11
gtagcacattctggttgtcctggaagtta-atactcttgcttatgtctacgctcaggctcacatttcagcatggaaattcatgtcatattttaaagtgagtacttatttcagGTACAGACCATTCGACAAGGCTATCTCTCAAAGCGATCTTCAAACTTGAGAGGTGACTGGAAAAGAAGGTTCTTTGTTCTTGATAGCCGAGGAATGTTAT
             ||||   ||     |  | | | ||| ||     ||    ||    |    | |     |   | |  | | |  || |    | |  | | |||| |||| || || ||||||||||| |||||||||||||| || || ||||| || || ||||||||||| || || |||||||||||||| || |||||| | |
-------------gttgaattgaggcctggaaattgttgattgaagttattaacaattactttctcccagtggttgacttttataactttcttgtcttatca-tcattttagGTTCAAACTATTCGACAAGGTTATCTCTCAAAGCGTTCCTCTAACTTAAGGGGGGACTGGAAAAGGAGATTTTTTGTTCTTGATAGTCGGGGAATGCTGT

upper sequence: LOC_Os09g33600.1 (Oryza sativa), 3'ss of exon 11
lower sequence: GLYMA04G37780.1 (Glycine max), 3'ss of exon 11
gtagcacattctggttgtcctggaagttaatactcttgcttatgtctacgctcaggctcacatttcagcatggaaattcatgtcatattttaaagtgagtacttatttcagGTACAGACCATTCGACAAGGCTATCTCTCAAAGCGATCTTCAAACTTGAGAGGTGACTGGAAAAGAAGGTTCTTTGTTCTTGATAGCCGAGGAATGTTAT
   | |  ||  ||   |  ||    || | ||| |  |||   ||||       | |  |||||    |||     |  |  |  || |     |  | |||   || |||| || | |||||||||||| ||||| ||||| || || ||||| ||||| ||||||||||| |||||||  |||||||||||||| || |||||| | |
---gtat-ttaaggacataatgatgcttcacactttcacttcattctatat---agttttcattt----atgagtcctatttactgatctctccatctgcactacatttagGTTCAAATCATTCGACAAGGATATCTTTCAAAACGGTCCTCAAATTTGAGGGGTGACTGGAAGAGAAGGTATTTTGTTCTTGATAGTCGCGGAATGCTTT

upper sequence: LOC_Os09g33600.1 (Oryza sativa), 3'ss of exon 11
lower sequence: GLYMA18G51810.1 (Glycine max), 3'ss of exon 11
gtagcacattctggttgtcctggaagttaatactcttgcttatgtctacgctcaggctcacatttcagcatggaaattcatgtcatattttaaagtgagtacttatttcagGTACAGACCATTCGACAAGGCTATCTCTCAAAGCGATCTTCAAACTTGAGAGGTGACTGGAAAAGAAGGTTCTTTGTTCTTGATAGCCGAGGAATGTTAT
       |||  ||    ||||||| ||  |  |     ||||    ||  | |   ||   |   ||   |   | |  | | ||||| |    |    | | |||| |||| || || ||||||||||| |||||||||||||| || |||||||| || || ||||||||||| || || |||||||||||||| || |||||| | |
--gttgaattgagg----cctggaaattgttgattgaagttat--taacatttactttc---tcctagtg-gttgacttttataatattcttgtcttttca-tcattttagGTTCAAACTATTCGACAAGGTTATCTCTCAAAGCGTTCCTCAAACTTAAGGGGGGACTGGAAAAGGAGATTTTTTGTTCTTGATAGTCGGGGAATGCTGT

upper sequence: LOC_Os09g33600.1 (Oryza sativa), 3'ss of exon 11
lower sequence: GLYMA06G17300.1 (Glycine max), 3'ss of exon 12
gtagcacattctggttgtcctggaagttaatactcttgcttatgtctacgctcaggctcacatttca-gcatggaaattcatgtcatattttaaagtgagtacttatttcagGTACAGACCATTCGACAAGGCTATCTCTCAAAGCGATCTTCAAACTTGAGAGGTGACTGGAAAAGAAGGTTCTTTGTTCTTGATAGCCGAGGAATGTTAT
                ||  |  | |  | || |  || ||   |||      | |  | ||  ||| | |||     |  | ||  || |     |  | |||  ||  |||| || | |||||||||||| | ||| ||||| || ||  ||||  |||| ||||||||||| |||||||  |||||||||||||               
----------------gtatttaaggaca-taatgatgtttcactctttctctatgtactcacgtcatgtatgagtcctattctctgatctcgccatctgcactacttgtagGTTCAAATCATTCGACAAGGATTTCTTTCAAAACGGTCCACAAATCTGAGGGGTGACTGGAAGAGAAGGTATTTTGTTCTTGATA---------------

upper sequence: LOC_Os09g33600.1 (Oryza sativa), 3'ss of exon 11
lower sequence: AT5G13300.1 (Arabidopsis thaliana), 3'ss of exon 11
gtagcacattctggttgtcctggaagttaatactcttgcttatgtctacgctcaggctcacatttcagcatggaaattcatgtcatattttaaagtgagtacttatttcagGTACAGACCATTCGACAAGGCTATCTCTCAAAGCGATCTTCAAACTTGAGAGGTGACTGGAAAAGAAGGTTCTTTGTTCTTGATAGCCGAGGAATGTTAT
                         ||| ||   | |  |||    || | |  |   ||  || ||    |  | | |   | | ||||    |||        |||||||| || || ||  | ||||| |||||||| || |||||||||||| ||||||| ||||||||||||||||| ||||||||||| ||||| |||||| | |
-------------------------gttgatcaacgtcttta-acatatgatt-gatacatcttcca----gagagtactattaacatttcttggtgc-------tttcagGTGCAAACAATAAGGCAAGGTTATCTCTCTAAACGATCTTCAAACCTGAGAGGAGACTGGAAAAGAAGGTTTTTTGTTCTTGACAGCCGGGGAATGCTCT

upper sequence: LOC_Os09g33600.1 (Oryza sativa), 3'ss of exon 11
lower sequence: AT5G61980.1 (Arabidopsis thaliana), 3'ss of exon 11
gta-gcacattctggttgtcctggaagttaatactcttgcttatgtctacgctcaggctcacatttcagcatggaaattcatgtc-atattttaaagtgagtacttatttcagGTACAGACCATTCGACAAGGCTATCTCTCAAAGCGATCTTCAAACTTGAGAGGTGACTGGAAAAGAAGGTTCTTTGTTCTTGATAGCCGAGGAATGTTAT
||| | | ||     ||||  ||    ||| |  ||   ||  ||||      ||   | | | |      |     || || |  || | || |  | | |  |   ||||||| ||||| ||  ||||||| ||||| || || || || ||||||||||||||||||||||||||||| |||||| | ||||||||||| || ||| |||
gtaaggaaatatcttttgtattgaggcttactcgtcaaactgctgtca-----catctttatactctcttgt-----tttatatttatctgttgatataactgtt--cttcagGTTCAGACTATCAGACAAGGGTATCTGTCTAAACGTTCCTCAAACTTGAGAGGTGACTGGAAAAGAAGATTCTTTATCCTTGATAGCCGTGGGATGCTAT

upper sequence: LOC_Os09g33600.1 (Oryza sativa), 3'ss of exon 11
lower sequence: Vv17s0000g00310.t01 (Vitis vinifera), 3'ss of exon 11
-------------------gtagcacattctggttgtcctggaagttaatactcttgcttatgtctacgctcaggctcacatttcagca-tggaaattcatgt-catattttaaagtgagtacttatttcagGTACAGACCATTCGACAAGGCTATCTCTCAAAGCGATCTTCAAACTTGAGAGGTGACTGGAAAAGAAGGTTCTTTGTTCTTGATAGCCGAGGAATGTTAT
                         | |||| ||    || | | |  | | |  | | | | |     | |    ||   ||| |||| |   |||| |  |  || |    |||  || ||| | | ||||| || |||||||||||||| ||||| ||||| || || ||||| ||||| ||||||||||| ||||||||||||||||||||||||||||| ||||| |
gtaatggttgagatgaccacctttcctttctagtgactctaggaatctaaatttcttcctttctagcatccctcattcttttttaagcagtattaatttaaatatatgtagctaagacagcact-agtgcagGTTCAAACCATTCGACAAGGATATCTTTCAAAACGTTCCTCAAATTTGAGGGGTGACTGGAAGAGAAGGTTCTTTGTTCTTGATAGCCGAGGCATGTTGT

upper sequence: LOC_Os09g33600.1 (Oryza sativa), 3'ss of exon 11
lower sequence: Vv01s0150g00030.t01 (Vitis vinifera), 3'ss of exon 11
-----------------------------------gtagcacattctggttgtcctggaagttaatactcttgctt-atgtctacgctcaggctc----acatttca-gcatggaaattcatgtcatattttaaagt--gagtact--tatttcagGTACAGACCATTCGACAAGGCTATCTCTCAAAGCGATCTTCAAACTTGAGAGGTGACTGGAAAAGAAGGTTCTTTGTTCTTGATAGCCGAGGAATGTTAT
                                    |   | || ||  |        ||   ||    |||  || ||   | | ||     |     |  || |  | ||    | |  | |  | |||    ||  || ||    |||||||||| || ||||| |||||||| || |||||||| || || |||||| ||||||||||||||||||||||||| |||||||||||||||||||||||| |||
gtctgaagaagcttataagttattaaggaacttcttttatagatacttatcaaaaaaaaaaaaaaggaacttcttttatagatcctctttattttcttgatgttccttgtatttctagttgttttttgtttccgtgtctgaataacaatatttcagGTTCAAACCATCCGACAAGGTTACCTCTCAAAACGCTCCTCAAACCTGAGAGGTGACTGGAAAAGAAGGTTTTTTGTTCTTGATAGCCGAGGAATGCTAT

upper sequence: LOC_Os09g33600.1 (Oryza sativa), 3'ss of exon 11
lower sequence: EFJ08060 (Selaginella moellendorffii), 3'ss of exon 11
gtagcacattctggttgtcctggaagttaatactcttgcttatgtctacgctcaggctcacatttcagcatggaaattcatgtcatattttaaagtgagtacttatttcagGTACAGACCATTCGACAAGGCTATCTCTCAAAGCGATCTTCAAACTTGAGAGGTGACTGGAAAAGAAGGTTCTTTGTTCTTGATAGCCGAGGAATGTTAT
                                                     | |  ||  ||||| | |      |  |  | |  |   | ||| |   | ||| ||||| ||  | ||    |||||||| ||    ||||| |||||||| ||| | || |||||||||||  | ||||||||||| |||||||| |||||| | |
---------------------------------------------------gtatgggcagctttcaactt------ttgttccttcgtaacaggtgtggtgtcattgcagGTTCAACCTATAAAGCAAGGCTACCTACTTAAGCGTTCTTCAAATTTGCGTGGAGACTGGAAAAGGCGTTTCTTTGTTCTGGATAGCCGTGGAATGCTGT

upper sequence: LOC_Os09g33600.1 (Oryza sativa), 3'ss of exon 11
lower sequence: EFJ24732 (Selaginella moellendorffii), 3'ss of exon 11
gtagcacattctggttgtcctggaagttaatactcttgcttatgtctacgctcaggctcacatttcagcatggaaattcatgtcatattttaaagtgagtacttatttcagGTACAGACCATTCGACAAGGCTATCTCTCAAAGCGATCTTCAAACTTGAGAGGTGACTGGAAAAGAAGGTTCTTTGTTCTTGATAGCCGAGGAATGTTAT
                                                     | |  ||  ||||| | |     ||| | || ||     | ||| |   | ||| ||||| ||  | ||    |||||||| ||    ||||| |||||||| ||| | || |||||||||||  | ||||||||||| |||||||| |||||| | |
---------------------------------------------------gtatgggcagctttcaacttttg--ttcgt-tcgtaac---aggtgtggtgtcattgcagGTTCAACCTATAAAGCAAGGCTACCTACTTAAGCGTTCTTCAAATTTGCGTGGAGACTGGAAAAGGCGTTTCTTTGTTCTGGATAGCCGTGGAATGCTGT

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: 65 (upstream exon), 48 (downstream exon)
Score: 19

TGGCATAAACGATTCCCCTAATGGTGATGGAATACAAGCAATTGGTAGAAGTTCACACAAAATGATTGAGGCGGTGATGCAATCAGCTTCAAAGGGCAAGgtagcacatt ... cttatttcagGTACAGACCATTCGACAAGGCTATCTCTCAAAGCGATCTTCAAACTTGAGAGGTGACTGGAAAAGAAGGTTCTTTGTTCTTGATAGCCGAGGAATGTTAT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctcacatttcagcatggaaattcatgtcatattttaaagtgagtacttatttcagGTACAGACCATTCGACAAGGCTATCTCTCAAAGCGATCTTCAAACTTGAGAGGTGACTGGAAAAGAAGGTTCTTTGTTCTTGATAGCCGAGGAATGTTAT
 ggctcac  putative branch site (score: 19)
                                             cttatttc  putative PPT
                 aaattcatgtcatatt  TA-rich tract
















Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtagcacattctggttgtcctggaagttaatactcttgcttatgtctacgctcaggctcacatttcagcatggaaattcatgtcatattttaaagtgagtacttatttcagGTACAGACCATTCGACAAGGCTATCTCTCAAAGCGATCTTCAAACTTGAGAGGTGACTGGAAAAGAAGGTTCTTTGTTCTTGATAGCCGAGGAATGTTAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG