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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagaaatgctgttttttctagggcttctcgcaatgtaatattcgcaatgaggaagctaataatgtgaattttcgtttttagGGATACAGCTGGACAAGAAAGATTCAGGAGTTTAATACCAAGTTACATAAGAGATTCTTCTGTTGCAGTTGTTGTTTATGATGTAGCCAATAGACTCTCA

Basic information

species Arabidopsis thaliana
transcript AT2G22290.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT2G22290.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: LOC_Os03g09140.1 (Oryza sativa), 3'ss of exon 2
----------------gtaagaaatgctgttttttctagggcttctcgcaatgtaa--tattcgcaatgaggaagctaataatgtgaattttcgtttttagGGATACAGCTGGACAAGAAAGATTCAGGAGTTTAATACCAAGTTACATAAGAGATTCTTCTGTTGCAGTTGTTGTTTATGATGTAGCCAATAGACTCTCA
                | |  | |   |     |  |      |       | | |  || |   ||   |||   |  ||  |||| |  |  | |  |||||||||||||| || || || ||| |||| || || ||||||||||| || ||||||||||| |||||  ||||||| |||||  |             
tgaactgaaatcacgcgcacaagacaattcagctagtgaaaactgggaggttttcagctagtaaaaaccgggagagttttatggtga-tgataatgtgcagGGATACAGCTGGGCAGGAGAGGTTCCGGAGCTTGATCCCAAGTTACATCAGGGATTCTTCTGTGGCAGTGATTGTTTACGATGTGACTG-----------

upper sequence: AT2G22290.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GRMZM2G128771_T01 (Zea mays), 3'ss of exon 2
gtaagaaatgctgttttttc----------tagggcttc--tcgcaatgtaa---tattcgcaatgagga-agctaataatgtga-attttcgtttttagGGATACAGCTGGACAAGAAAGATTCAGGAGTTTAATACCAAGTTACATAAGAGATTCTTCTGTTGCAGTTGTTGTTTATGATGTAGCCAATAGACTCTCA
                   |          | | | ||   | ||  ||| |    |||  |   ||| | || ||  | |      || | | | | |||||||| || ||||| || || || |||||| | || ||||| ||||| || || ||||||||||| || ||||||||||||||| |||           
nnnnnnnnnnnnnnnnnnncacattactatttgagttttggtagctttgttagttcattttcttggagaacagttagcatttcattgttcttgctgtcagGGATACTGCAGGACAGGAGAGGTTTAGGAGTCTTATTCCAAGCTACATCAGGGACTCTTCTGTTGCGGTGGTTGTTTATGATGTATCCA-----------

upper sequence: AT2G22290.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA18G02040.1 (Glycine max), 3'ss of exon 2
-----------------------------------------------------------------gtaagaaatgctgtt-ttttctagg-gcttctcgcaatgtaatattcgcaatgaggaagctaataatgtgaattttcgtttttagGGATACAGCTGGACAAGAAAGATTCAGGAGTTTAATACCAAGTTACATAAGAGATTCTTCTGTTGCAGTTGTTGTTTATGATGTAGCCAATAGACTCTCA
                                                                  | |||  |    || || | ||||  ||| |   ||   | | || | | ||   ||  |  |  |   | |||   ||   |||||||| || || ||||||||||| || ||| | || ||||| |||||||||||||||||||||||||||||||| || ||||||||||           
gtaggccatattcctctttaactcatgccacaagacctatttatatttttttttctaaaagttatattagatttcacattgttgtgtaggcactttttttaacccattctttgta-tgttaaaattgtt--tcatattttaacttcacagGGATACTGCAGGGCAAGAAAGATTTAGAAGTCTGATTCCAAGCTACATAAGAGATTCTTCTGTTGCAGTTGTTGTATACGATGTAGCCA-----------

upper sequence: AT2G22290.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA11G38110.1 (Glycine max), 3'ss of exon 2
---------------------------------------------------------------gtaagaaatgctgttttttctagggcttctc--gcaatgtaatat-tcgcaatgaggaagctaataatgt---gaattttcgtttt-tagGGATACAGCTGGACAAGAAAGATTCAGGAGTTTAATACCAAGTTACATAAGAGATTCTTCTGTTGCAGTTGTTGTTTATGATGTAGCCAATAGACTCTCA
                                                                 |||  ||  |   |||   |  | |      ||||| |  | |  ||   |  | | | ||| | |||   | |||||   ||   |||||||| || || |||||||| || || ||| | || ||||| ||||||||||||||||||||||||||| |||| |||||||||||||           
gtaggccatattcctcttcaactcataccacaagatctatttatatttgtttttttgtattttaaaagttatattagatttcacattgttatgtaggcaattttttttaccgttctttgtatgttaaaagtgtgtcgtattttaacttcacagGGATACTGCAGGGCAAGAAAGGTTTAGAAGTCTCATTCCAAGCTACATAAGAGATTCTTCTGTTGCAGTTATTGTATATGATGTAGCCA-----------

upper sequence: AT2G22290.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA08G14390.1 (Glycine max), 3'ss of exon 2
-----------------------------------------------------------------------------gtaagaaatgctgttttttctagggcttctcg-caatgta-atattcgcaatgaggaagctaataatgtgaattttcgtttttagGGATACAGCTGGACAAGAAAGATTCAGGAGTTTAATACCAAGTTACATAAGAGATTCTTCTGTTGCAGTTGTTGTTTATGATGTAGCCAATAGACTCTCA
                                                                              | |||       ||  |  || | ||  | | || |||  || ||  ||||     |||| |  || ||   ||   ||   |||||||| || || ||||||||||| || ||| | || ||||| ||||||||||||||||||||||||||| | || |||||||| || |           
gtaggatgaattcctcttcaaatcatatatacaagctcagtctttttatatttgtttgtttatttttcaacaattatattagagtgcacattgctggtatgcctagtaggcattgtttatttttacaatttctgagcttagtatatg---ttaacttcacagGGATACTGCAGGGCAAGAAAGATTTAGAAGTCTCATTCCAAGCTACATAAGAGATTCTTCTGTTGCAGTTATAGTATATGATGTTGCTA-----------

upper sequence: AT2G22290.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA05G31200.1 (Glycine max), 3'ss of exon 2
-------------------------------------------------------------------------gtaagaaatgctgttttttctagggcttctcgcaatgtaatattc--gcaatgaggaagctaataatgtgaattttcgtttttagGGATACAGCTGGACAAGAAAGATTCAGGAGTTTAATACCAAGTTACATAAGAGATTCTTCTGTTGCAGTTGTTGTTTATGATGTAGCCAATAGACTCTCA
                                                                          | |||       ||  |  || | ||| | |  |     |||||   ||||     |||| |  || ||   ||   ||   |||||||| || || ||||||||||| || ||| | || ||||| ||||||||||||||||||||||| ||| | || |||||||| || |           
gtaggatgactcctcttcaaatcataaatacaagctcagtctatttatatttgttttatttttcaacaattatattagagtacacattgctggtacgccttataggcactctttattcttacaatttctgagcttagtatatg---ttaacttcacagGGATACTGCAGGGCAAGAAAGATTTAGAAGTCTCATTCCAAGCTACATAAGAGATTCTTCTGTTGCGGTTATAGTATATGATGTTGCTA-----------

upper sequence: AT2G22290.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: Vv00s0665g00040.t01 (Vitis vinifera), 3'ss of exon 2
----------gtaagaaatgctgtttt---ttctagggcttctcgcaatgtaatattcgcaa---tgaggaagctaataatgtgaattttcg--tttttagGGATACAGCTGGACAAGAAAGATTCAGGAGTTTAATACCAAGTTACATAAGAGATTCTTCTGTTGCAGTTGTTGTTTATGATGTAGCCAATAGACTCTCA
            ||    |   | |||   | ||   | | || | | | |  | ||   |    |   |   |||| | | ||  ||||    ||   |||||||| ||||| ||||||||||| |||||| | |||||||| ||||||||||||||||| ||||| ||  ||||||||||||| |  |           
gattggtttctcaaattgtttaggtttacatgctgtagatacttgtattatt-tgtttatatacttctagtttctaaaattttggcttttgaaattcacagGGATACTGCTGGCCAAGAAAGATTTAGGAGTCTTATACCAAGCTACATAAGAGATTCTTCAGTTGCTGTGATTGTTTATGATGTTGGAA-----------

upper sequence: AT2G22290.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: PP1S346_29V6.1 (Physcomitrella patens), 3'ss of exon 3
-----gtaa-gaaatgctgttttttctagggcttctcgcaatgtaatattcgcaatgag-----gaagcta--ataatgtgaa----ttttcgtttttagGGATACAGCTGGACAAGAAAGATTCAGGAGTTTAATACCAAGTTACATAAGAGATTCTTCTGTTGCAGTTGTTGTTTATGATGTAGCCAATAGACTCTCA
      ||| || |||  | || |  |   | |||| |   | |  |  | | || ||      ||| | |  ||||| ||      || |    |  |||||||| |||||||| || || |||||||||||||| || ||||||||  | ||||| || || ||||| ||||| || |||||  | |           
attagataacgagatggaggttgtcttcttgtttcttgacgtcttgttgtagaaacgaaatactgaatccatcataatttggggctgttatgaaatgcagGGATACCGCTGGACAGGAGAGGTTCAGGAGTTTAATTCCTAGTTACATTCGGGATTCGTCCGTGGCAGTGGTTGTGTACGATGTTTCAA-----------

upper sequence: AT2G22290.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: PP1S456_9V6.1 (Physcomitrella patens), 3'ss of exon 3
----------gtaagaaatgctgttttttctagggct--tctcgcaatgta-atattcgcaatgagga--agctaataatgtga--attttcgtttttagGGATACAGCTGGACAAGAAAGATTCAGGAGTTTAATACCAAGTTACATAAGAGATTCTTCTGTTGCAGTTGTTGTTTATGATGTAGCCAATAGACTCTCA
          || | ||  | | | |||| |     |    | ||  |||  | |||| || |||     | |  | |||| ||   || |    | |||||| |||||||||||||| || |||||||||||||| || || |||||  |||| || ||||| ||||| |||||||| |||||  | |           
agtactccttgtgataatggttatcttttttgcacatgacattgccttgtggaaattcccattgaatttcatcagaaaatgggactgttatgaaatgtagGGACACAGCTGGACAAGAGAGGTTCAGGAGTTTAATTCCCAGCTACATTCGAGACTCGTCTGTGGCAGTAGTTGTTTACGATGTTTCGA-----------


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctcgcaatgtaatattcgcaatgaggaagctaataatgtgaattttcgtttttagGGATACAGCTGGACAAGAAAGATTCAGGAGTTTAATACCAAGTTACATAAGAGATTCTTCTGTTGCAGTTGTTGTTTATGATGTAGCCAATAGACTCTCA
                           agctaat  putative branch site (score: 3)
                                          ttttcgttttt  putative PPT
                              taataatgtgaatttt  TA-rich tract