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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtactattcttctcactcatttgtagaatgtgacggcatttatttgtttttaccaaggaaaagatctaccagtttaaaatagctcatgaactttagccatgtatgctaataattcttcttgttggcagAGATCACACCAAGTAATGAAATTCACTGAAGATTTTGATTTCACAGCAATGAACGAAAAGTTCAATAAGGATGAAGTATGGGGTCATCTTGGGAAGAGTA

Basic information

species Arabidopsis thaliana
transcript AT1G26110.2
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G26110.2 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: LOC_Os01g02090.1 (Oryza sativa), 3'ss of exon 5
gtactattcttctcactcatttgtagaatgtgacggcatttatttgtttttaccaaggaaaagatctaccagtttaa-aatagctcatga-actttagccatgtatgctaataattcttcttgttggcagAGATCACACCAAGTAATGAAATTCACTGAAGATTTTGATTTCACAGCAATGAACGAAAAGTTCAATAAGGATGAAGTATGGGGTCATCTTGGGAAGAGTA
                              |||     |||   ||||||||       |     || |   || || |  | ||  |     || |   ||  || ||  | | |||  |  || ||||   || ||   |||||  || || |||||||| ||||||||||  || ||||| || ||||| || || |||||||| |||||||||||||| ||||   
-----------------------------ttgatcatgttt-catgtttttatatgattatgatgctgcttattaaagagcatctggtattgattgaagtattaatacttttgagtctgttgttttgcagTTTTCGCAGTCAGTAACAAATTTTACTGAAGAATTTGATTTCATGGCCATGAATGAGAAGTTTAACAAAGATGAAGTCTGGGGTCATCTTGGTAAGAAAT

upper sequence: AT1G26110.2 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GRMZM2G132796_T01 (Zea mays), 3'ss of exon 5
gtactattcttctcactcatttgtagaatgtgacggcatttatttgtttttaccaaggaaaagatctaccagtttaaaatagctcatgaacttta-gccatgtatgctaataattct-tcttg-ttggcagAGATCACACCAAGTAATGAAATTCACTGAAGATTTTGATTTCACAGCAATGAACGAAAAGTTCAATAAGGATGAAGTATGGGGTCATCTTGGGAAGAGTA
                             | |   | |||| | |   ||    || ||   | |      |  ||| || | | |  |  |  | | ||  | || | ||  || | ||||| || ||||   |||||    ||||    |||||||||||| ||||||||||| || ||||| || ||||| || || |||||||||||||| |||||||| ||||   
-----------------------------gagggagtatttgtataccttgggaaatgat--gctaggattgaataatattgttaaatagttaaatgtcagatttgttgatgtttgtatcttgctttgcagTTTTCACAGTCTGTAACAGCATTCACTGAAGAATTTGATTTCACGGCCATGAATGAGAAGTTTAACAAAGATGAAGTATGGGGCCATCTTGGTAAGAAAT

upper sequence: AT1G26110.2 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GRMZM2G051622_T02 (Zea mays), 3'ss of exon 5
gtactattcttctcactcatttgtagaatgtgacggcatttatttgtttttaccaaggaaaagatctaccagtttaaaatagctcatgaactttagccatgtatgctaataattcttcttgttggcagAGATCACACCAAGTAATGAAATTCACTGAAGATTTTGATTTCACAGCAATGAACGAAAAGTTCAATAAGGATGAAGTATGGGGTCATCTTGGGAAGAGTA
                  ||||||| |   ||        |  |||  ||      | | || || |     |   |||||| | | |      |    |  ||| |  ||  ||||| | |  ||||   |||||   |||||  | |||||||||||| ||||||||||| || ||||| || ||||| || || |||||||| |||||||||||||| ||||   
--------------gagtatttgtataccttgggaaatgatgcttggatt------gaataatatttgttgtt---aaatagttaa-gtgtcagatttgttaatgtttgta--tcttccttt--gcagTTTTCACAGTCAGTAACAACATTCACTGAAGAATTTGATTTCACGGCCATGAATGAGAAGTTTAACAAAGATGAAGTCTGGGGTCATCTTGGAAAGAAAT

upper sequence: AT1G26110.2 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GRMZM2G341027_T01 (Zea mays), 3'ss of exon 5
gtactattcttctcactcatttgtagaatgtgacggcatttatttgttttta--ccaaggaaaagatctaccagtttaaaatagctcatgaactttagccatgtatgctaataattcttcttgttggcagAGATCACACCAAGTAATGAAATTCACTGAAGATTTTGATTTCACAGCAATGAACGAAAAGTTCAATAAGGATGAAGTATGGGGTCATCTTGGGAAGAGTA
                            |   | | |  |  | |||||| |  ||   ||  | ||       | |  | | |||  |    ||||  |     |  | |   |  ||||   |  |||  ||| || |   |||  || ||||| || || ||||||||||  |||||||| || |||||||| || |||||||||||||| |||||||| || || |
--------------------------cttaaaatgcctctgttctgttttcagtcccttgaggacattctttgttgtcgacttgctttt---ttttaaactgtagtcttcactgtcattctctcta-cagCAATCGCATCCCATAACCAAGTTCACAGAGGACTTTGATTTCATGGCAATGAATGAGAAGTTCAACAAAGATGAAGTATGGGGCCATCTTGGTAAAAGAA

upper sequence: AT1G26110.2 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA02G11320.2 (Glycine max), 3'ss of exon 5
gtactattcttctcactcatttgtagaatgtgacggcatttatttgtttttaccaaggaaaagatctaccagtttaaaatagctcatgaactttagccatgtatgctaataattc--ttcttgttggcagAGATCACACCAAGTAATGAAATTCACTGAAGATTTTGATTTCACAGCAATGAACGAAAAGTTCAATAAGGATGAAGTATGGGGTCATCTTGGGAAGAGTA
                      | | | ||| |     || ||||  ||||            ||  |  || ||| ||| |    | |  || ||    ||     || ||||   ||  |||| |||| | |  | |  ||| |  ||||||||||||||||||||||||||||||||||| || |||||||| |||||||||||||||||||||||||| || ||||
-------------------ccagaaaattgtcaatattttgattttgttttcttct-------attgataagattataattg----taatattcagttgagttcatgaaaaatttgattaatgtttgcagGGTTTCCGCTCAGTCACAAAATTCACTGAAGATTTTGATTTCACAGCAATGAATGAGAAGTTCAAAAAGGATGAAGTATGGGGTCATCTTGGTAAAAGTA

upper sequence: AT1G26110.2 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA02G11300.2 (Glycine max), 3'ss of exon 6
gtactattcttctcactcatttgtagaatgtgacggcatttatttgtttttaccaaggaaaagatctaccagtttaaaatagctcatgaactttagccatgtatgctaataattcttcttgttggcagAGATCACACCAAGTAATGAAATTCACTGAAGATTTTGATTTCACAGCAATGAACGAAAAGTTCAATAAGGATGAAGTATGGGGTCATCTTGGGAAGAGTA
                  || |||| ||| |      || | |||  || ||   | |  |  ||      | ||  || |     |  | || |   |   || | | |||| ||| |     |||| | |  |||| ||| |  ||||||||||| ||||||||||||||||||||||| || |||||||| |||||||||||||||||||||||||| || ||||
---------------tatatatgta-aatatacttttatgtttttccttctattgatgggattat------gattgtaacattcagttgagttca-tgaaaaattcaattaatgctttt-----gcagGGTTTGCACCCAGTCACAAAATTCACTGAGGATTTTGATTTCACAGCAATGAATGAGAAGTTCAAAAAGGATGAAGTATGGGGTCATCTTGGTAAAAGTA

upper sequence: AT1G26110.2 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA01G22680.3 (Glycine max), 3'ss of exon 4
gtactattcttctcactcatttgtagaatgtgacggcatttatttgtttttaccaaggaaaagatctaccagtttaaaatagctcatgaactttagccatgtatgctaataattcttcttgttggcagAGATCACACCAAGTAATGAAATTCACTGAAGATTTTGATTTCACAGCAATGAACGAAAAGTTCAATAAGGATGAAGTATGGGGTCATCTTGGGAAGAGTA
                  || || | ||| ||     |||| |||   ||  | |  ||   ||| ||  | | ||| ||   |||      ||    |   || ||| |||| |||       |||| | | ||||| ||| |  ||||||||||| |||||||||||||  |||||||| || |||||||| ||||||||||||||||| |||||||| || ||||
---------------tatatctgca-aatatgcttttatttttttccctt--ctattgatgggat-tatgattgtaacat---tcagttgagttcatgaaaaattctattaatgcttt------gcagGGTTTACACCCAGTCACAAAATTCACTGAGGATTTTGATTTCATGGCAATGAATGAGAAGTTCAAAAAGGATGAAGTATGGGGCCATCTTGGTAAAAGTA

upper sequence: AT1G26110.2 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA04G17050.1 (Glycine max), 3'ss of exon 6
gtactattcttctcactcatttgtagaatgtgacggcatttatttgtttttaccaaggaaaagatctaccagtttaaaatagctcatgaactttagccatgtatgctaataattcttcttgttggcagAGATCACACCAAGTAATGAAATTCACTGAAGATTTTGATTTCACAGCAATGAACGAAAAGTTCAATAAGGATGAAGTATGGGGTCATCTTGGGAAGAGTA
                  || |||| ||| ||     ||||  || ||  | |||  ||   ||| ||  | | ||| ||   |||      ||    |   || | | |||| |||       |||| | |  | || ||| |  |||||||| || ||||||||||| |  |||||||| || |||||||| |||||||||||||||||||||||||| || ||||
---------------tatatctgta-aatatgcttttattt--ttcttccttccattgatgggat-tatgattgtaacat---tcagttgagttcatgaaaaattcaattaatgcttt------gcagGGTTTGCGCCCAGTCACAAAATTCACAGAGGATTTTGATTTTATGGCAATGAATGAGAAGTTCAAAAAGGATGAAGTATGGGGTCATCTTGGTAAAAGTA

upper sequence: AT1G26110.2 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: Vv01s0011g02820.t01 (Vitis vinifera), 3'ss of exon 5
gtactattcttctcactcatttgtagaatgtgacggcatttatttgtttttaccaaggaaaagatctacca---gttt----aaaatagctcatgaactttagccatgtatgctaataattcttcttgttggcagAGATCACACCAAGTAATGAAATTCACTGAAGATTTTGATTTCACAGCAATGAACGAAAAGTTCAATAAGGATGAAGTATGGGGTCATCTTGGGAAGAGTA
                                     ||   |||| |||||    ||| || || | | |   ||||    |||||   |   ||| |||  |    |    || | |   ||    ||| ||| | ||||  | ||| |  ||||||||||| |||||||||||||  |||||||| || || ||||| |||||||||||||||||||||||||| ||  |||
--------------------------------ctattataggtttgattttat-ggggagaatatttgcaatgagtttctccaaaattaattg-gaaatttgacggcatggaatatttaacatttgccttg-cagGGCTCACGTCCAGTGACAAAATTCACTGAGGATTTTGATTTCATGGCAATGAATGAGAAATTCAAGAAGGATGAAGTATGGGGTCATCTTGGTAAAGGTA

upper sequence: AT1G26110.2 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: PP1S198_51V6.2 (Physcomitrella patens), 3'ss of exon 7
---------------------------------------------------------------gtactattcttctcactcatttgtagaatgtgacggcatttatttgtt--tttaccaaggaaaagatctaccagttta--aaatagctcatgaactttagccatg--tatgctaataattcttcttgttggcagAGATCACACCAAGTAATGAAATTCACTGAAGATTTTGATTTCACAGCAATGAACGAAAAGTTCAATAAGGATGAAGTATGGGGTCATCTTGGGAAGAGTA
                                                                ||||     |       || |    | |||  |    |  | | |||   |  | || |     ||| | ||  ||    | | | || ||    | |  | ||   |||   | | || |   |  |  |||    |  | |       | |||||||||||||||| || |||||||| ||||| || |||||||| ||||| ||||| |||||    || ||    |   
gtaattttttatactttcctaaggttttaaggccccgtttgttcttgtttcaacttacaggttatactggcactaattgatatctaataattgtctcattgtgcactcgttaactctcaaaagttggcatccaacatcttcttgagttgttc-tgtgtctcattcctgatcatgacgaaacttgtaacttgtttcagCTGGCGAATCCCACGCAGCAATTCACTGAAGATTTCGACTTCACAGCCATGAATGAGAAGTTCAACAAGGACGAAGTTTGGGGAACGCTCGGAGGAAAGG

upper sequence: AT1G26110.2 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: PP1S35_195V6.1 (Physcomitrella patens), 3'ss of exon 7
gtactattcttctcactcatttgtagaatgtgacggcatttatttgtttt-taccaaggaaaagatctaccagtttaaaatagctcatgaactttagccatgtatgctaataattcttcttgttggcagAGATCACACCAAGTAATGAAATTCACTGAAGATTTTGATTTCACAGCAATGAACGAAAAGTTCAATAAGGATGAAGTATGGGGTCATCTTGGGAAGAGTA
          | |   |   ||   || | |      | ||    ||||  |||    | |   |   || |||    |||   | |||   ||  | ||  | || |||  |        | ||||  |   |||||        | ||||||| ||||||||||| |||||||| ||||| || ||||| || ||||| ||||| |||||    ||||||   |   
----------tgttgtttggtttccgattatagtactactttcaagtttcatactttcgtagcaa--gacgagtggtcaatgattgatgtggtt--gtcaattgtgataagca--------gCTGGCGAATCCCACACA-------GCAATTCACAGAAGATTTTGACTTCACAGCCATGAATGAGAAGTTTAACAAGGACGAAGTTTGGGGAACCCTTGGGGGAAAGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttaaaatagctcatgaactttagccatgtatgctaataattcttcttgttggcagAGATCACACCAAGTAATGAAATTCACTGAAGATTTTGATTTCACAGCAATGAACGAAAAGTTCAATAAGGATGAAGTATGGGGTCATCTTGGGAAGAGTA
                              tgctaat  putative branch site (score: 2)
                                       ttcttcttgtt  putative PPT
                                 taataattcttctt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtactattcttctcactcatttgtagaatgtgacggcatttatttgtttttaccaaggaaaagatctaccagtttaaaatagctcatgaactttagccatgtatgctaataattcttcttgttggcagAGATCACACCAAGTAATGAAATTCACTGAAGATTTTGATTTCACAGCAATGAACGAAAAGTTCAATAAGGATGAAGTATGGGGTCATCTTGGGAAGAGTA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA