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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacataggctaagatacaaaaaacttgcttactatgctatacgttttggttgtccttctggttgaaggtttcttcttttgcagTTCTTGGAGCCTCTTGAGCTCTGTTACAGGTCTCTCTGTGCCTGTGGTGATAATTCTATTGCAGATGGCAGTCTTCTTGACTTTCTACGGCAAGTGTCCA

Basic information

species Oryza sativa
transcript LOC_Os01g55350.1
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g55350.1 (Oryza sativa), 3'ss of exon 9
lower sequence: GRMZM2G110714_T01 (Zea mays), 3'ss of exon 7
-------gtacataggctaagatacaaaaaacttgcttactatgcta--------tacgtttt---ggttgtccttctggttgaaggtttcttcttttgcagTTCTTGGAGCCTCTTGAGCTCTGTTACAGGTCTCTCTGTGCCTGTGGTGATAATTCTATTGCAGATGGCAGTCTTCTTGACTTTCTACGGCAAGTGTCCA
         |||||  | |||||| ||  | ||| || ||  |  |         || |||||   | || || |   |  |||   ||| |||| ||||||||||||||||||||||||||||||||||| ||||| |||||||||||||||   ||| |||| ||||| || |||||||||||  || |||||||||| |
caggttgaaacataa-ccaagata-aaggatctttctaaccgttttgggatatattatgttttatggattctcgtctcgagtgagtcttttttctcttgcagTTCTTGGAGCCTCTTGAGCTCTGTTACAGATCTCTGTGTGCCTGTGGTGATCGCTCTGTTGCGGATGGAAGCCTTCTTGACTTCTTAAGGCAAGTGTCAA

upper sequence: LOC_Os01g55350.1 (Oryza sativa), 3'ss of exon 9
lower sequence: GLYMA13G36670.1 (Glycine max), 3'ss of exon 8
gtacataggctaagatacaaaaaacttgct-tactatgctatacgttttggt----tgtccttctggttgaaggt-------------ttcttcttttgcagTTCTTGGAGCCTCTTGAGCTCTGTTACAGGTCTCTCTGTGCCTGTGGTGATAATTCTATTGCAGATGGCAGTCTTCTTGACTTTCTACGGCAAGTGTCCA
 |   |   | || |||  |   | ||    |  | |  |  |  ||||  |    |      |      || ||             || |||| ||||||||| ||||||||||||| |  || || || || ||||||||||||||||| |   |||| |||||||| || || ||||| || || |||||||| || |
-tctgtcaaccaa-atatgacttatttctcattttctcttgcaaattttaatctgatacataacacacaaaaagtctacaacctctatttattctcttgcagTTCCTGGAGCCTCTTGAACAATGCTATAGATCACTCTGTGCCTGTGGTGACAGACCTATAGCAGATGGAAGCCTCCTTGATTTCCTGCGGCAAGTTTCGA

upper sequence: LOC_Os01g55350.1 (Oryza sativa), 3'ss of exon 9
lower sequence: GLYMA20G09810.1 (Glycine max), 3'ss of exon 8
-------------gtacataggctaagatacaaaaaacttgcttactatgctatacgttttggttgtcct----tctggttgaaggtttcttcttttgcagTTCTTGGAGCCTCTTGAGCTCTGTTACAGGTCTCTCTGTGCCTGTGGTGATAATTCTATTGCAGATGGCAGTCTTCTTGACTTTCTACGGCAAGTGTCCA
              |   ||  |  |||   |   ||  |  | | | ||  | |  | ||| |  | |      ||  |  |||     || || |  |||||||||| || ||||| ||||||||||| || |||||||| ||||| |||  | | ||||| ||||| || ||||| || ||  |  | ||||| || |
agaaaagaaaaaaatgtttaaaccgagactgatgtaatata-tcattttgagagatatcttgatcttacagatacctaatcaaagtaaaattgttgtctagTTCTTGGAACCCCTTGAACTCTGTTACAGATCACTCTGTGCTTGTGGCGATCGTGCAATTGCCGATGGAAGCCTTCTAGATTTCTTGAGACAAGTCTCTA

upper sequence: LOC_Os01g55350.1 (Oryza sativa), 3'ss of exon 9
lower sequence: GLYMA06G33380.1 (Glycine max), 3'ss of exon 7
------------gtacataggctaa-gatacaaaaaacttgcttactatgctatacgttttggttgtcc---ttctggttgaaggtttcttcttttgcagTTCTTGGAGCCTCTTGAGCTCTGTTACAGGTCTCTCTGTGCCTGTGGTGATAATTCTATTGCAGATGGCAGTCTTCTTGACTTTCTACGGCAAGTGTCCA
             ||  ||  |||   ||      || |  | |  | ||  | |  | ||| |  |||     ||  |   || |    | || | ||||||||||| || ||||||||||||||||| || |||||||| ||||| |||    | ||||| ||||| || ||||| || ||  |  | ||||| || |
gagacaaaaaagatatttaaactagtaatgatgtgaaatatcattttctgagagatatcttgatcttccaaacactaatcatagttaaaatgttgtccagTTCTTGGAACCCCTTGAGCTCTGTTACAGATCACTCTGTGCTTGTGGCGATCGAGCAATTGCTGATGGAAGCCTTCTAGATTTCTTGAGACAAGTCTCTA

upper sequence: LOC_Os01g55350.1 (Oryza sativa), 3'ss of exon 9
lower sequence: AT3G14940.1 (Arabidopsis thaliana), 3'ss of exon 8
-------------------------------------------------------------------------------gtacataggctaagatacaaa---aaacttgcttact---atgctatacgt----tttggttgtccttctggttgaaggtttcttcttttgcagTTCTTGGAGCCTCTTGAGCTCTGTTACAGGTCTCTCTGTGCCTGTGGTGATAATTCTATTGCAGATGGCAGTCTTCTTGACTTTCTACGGCAAGTGTCCA
                                                                               |    |     |  || ||     | ||||| || |    ||  ||| |      ||   ||||  ||   |||      ||||  || |||||||||||||||||||||||||||||||| | || || ||| | |||||||| |   | || || ||||| || |||||||| ||  |  ||||||| || |
gtgagcaacctctatactctgaatttgttccttactaaattgtttcctgattttaacaacttgttagttcttgccattagagtttctatcattatccagccttacacttgtttccctcaataatattcacggaattcaattgtgtttactgttcttttattctatttatgcagTTCTTGGAGCCTCTTGAGCTCTGTTACCGATCACTATGTTCATGTGGTGACAGCCCGATAGCTGATGGAAGCCTTCTTGATTTCTTGAGGCAAGTCTCTA

upper sequence: LOC_Os01g55350.1 (Oryza sativa), 3'ss of exon 9
lower sequence: AT1G53310.3 (Arabidopsis thaliana), 3'ss of exon 7
gtacataggctaagatacaaaaaacttgcttactatgctatacgttttggt--tgtccttctggttgaaggtttcttcttttgcagTTCTTGGAGCCTCTTGAGCTCTGTTACAGGTCTCTCTGTGCCTGTGGTGATAATTCTATTGCAGATGGCAGTCTTCTTGACTTTCTACGGCAAGTGTCCA
           |    |   | ||  |  | |||      || | ||||||  |   |  ||   | | |    ||  || || |||||||||| |||||||||||||||||| | ||||| ||| | |||||||||  | | || |||||||| || |||||||| ||  |  ||||||| || |
------gtatcattgcaattagaatcttttaactcccggttatgatttggtactaaaccactctctcatg----ctatttgtgtagTTCTTGGAACCTCTTGAGCTCTGTTACCGATCTCTGTGTTCATGTGGTGATCGTCCAATAGCAGATGGAAGCCTTCTTGATTTCTTGAGGCAAGTCTCAA

upper sequence: LOC_Os01g55350.1 (Oryza sativa), 3'ss of exon 9
lower sequence: AT2G42600.1 (Arabidopsis thaliana), 3'ss of exon 8
---------gtacataggctaagatacaaaaaact---tgcttactatgctatacgttttg-gttgtccttctggttgaaggtttcttcttttgc----agTTCTTGGAGCCTCTTGAGCTCTGTTACAGGTCTCTCTGTGCCTGTGGTGATAATTCTATTGCAGATGGCAGTCTTCTTGACTTTCTACGGCAAGTGTCCA
         | ||  |  |||||||  ||     |   || ||  | |   ||   ||||    | | ||     ||||  ||||||  || |      |||| |||||||| |||||||| ||||||||||| |||||||  || ||||| |   ||||||| ||||| || || ||||| ||  |||| |||||||| |
atatggattgaac-cactctaagatcaaagctgttgtttgtttcttgtttgattgattttataattttctaacctttgattgtttctgtttctatccaaagTTTTTGGAGCCACTTGAGCTTTGTTACAGGTCGCTCTGTGATTGCGGTGACAGACCTATTGCTGATGGAAGCCTGCTTGATTTCTTACGCCAAGTGTCAA

upper sequence: LOC_Os01g55350.1 (Oryza sativa), 3'ss of exon 9
lower sequence: Vv19s0014g01390.t01 (Vitis vinifera), 3'ss of exon 7
-------------gtacataggctaagatacaaaaaacttgcttactatgctatacgttttggttgtcc---ttctggttgaaggtt-tcttcttttgcagTTCTTGGAGCCTCTTGAGCTCTGTTACAGGTCTCTCTGTGCCTGTGGTGATAATTCTATTGCAGATGGCAGTCTTCTTGACTTTCTACGGCAAGTGTCCA
              |  ||   | |   |         |||| || | |  | |  |||| | | |      | ||| |||    || | || ||||| |||||||||| |||||||| ||||||||||| || |||||||| ||||||||     | ||||| ||||| || ||||| || |||||  | ||||||||||
cagattgcattttattaatctaccattttttttcctttttgcatagt-tcttgtctgtttagctggattaggtactgattgggaattatatttttttgtagTTCTTGGAACCTCTTGAACTCTGTTACAGATCACTCTGTGCTTGTGGTGACCGACCAATTGCTGATGGAAGCCTTCTCGATTTTCTGAGACAAGTGTCCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttactatgctatacgttttggttgtccttctggttgaaggtttcttcttttgcagTTCTTGGAGCCTCTTGAGCTCTGTTACAGGTCTCTCTGTGCCTGTGGTGATAATTCTATTGCAGATGGCAGTCTTCTTGACTTTCTACGGCAAGTGTCCA
 tgcttac  putative branch site (score: 2)
                                        tttcttcttttgc  putative PPT
                                            ttctttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacataggctaagatacaaaaaacttgcttactatgctatacgttttggttgtccttctggttgaaggtttcttcttttgcagTTCTTGGAGCCTCTTGAGCTCTGTTACAGGTCTCTCTGTGCCTGTGGTGATAATTCTATTGCAGATGGCAGTCTTCTTGACTTTCTACGGCAAGTGTCCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGATG