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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatttctttctctactttctcaaaaatgttacctttttgttgctttggtggttatagcgtgtaaagccctcttctttgttaagttagattgatgttatattcattgggttgttaagcaaagtcactatgtcgattttggaatattgttttgccttttagGGCTAGTGATAAGTGCCAAAGAGAGAAAAGGAAGACCATCAATGGAGATGATTTGCTTTGGGCTATGGCCACTTTAGGATTCGAAGATTACATCGATCCC

Basic information

species Arabidopsis thaliana
transcript AT3G53340.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G53340.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GRMZM2G303465_T04 (Zea mays), 3'ss of exon 1
gtaatttctttctctactttctcaaaaatgttacctttttgttgctttggtggttatagcgt-gtaaagccctcttctttgttaagttagattgatgttatattcattgggttgttaagcaaagtcactatgtcgattttggaatattgttttgccttttagGGCTAGTGATAAGTGCCAAAGAGAGAAAAGGAAGACCATCAATGGAGATGATTTGCTTTGGGCTATGGCCACTTTAGGATTCGAAGATTACATCGATCCC
                        ||  ||  |  ||      || | |  |    |||||| |   |||| |  |||| |     |  | ||| | || | ||  ||    ||| | |  | ||    ||||   ||   |  |  || ||        ||||| || || || ||||| |  |||||| | ||||| ||||| || || |||||||| ||||| |||||||||||||||||||| || ||| |||| || 
----------------------gtaagttgacag-ttggcaccgcctggtagacggtagcgtagcgtagccttggtcttgg----atcgggttggtttt-tctttgttttaatgt-aggataggttctgatgtaagttcacgggtgctggttg------cagGGCCAGCGACAAATGCCAGAAGGAGAAACGAAAGACAATCAACGGGGACGATTTGCTCTGGGCGATGGCCACTTTAGGATTCGAGGAGTACGTCGAGCCT

upper sequence: AT3G53340.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GRMZM5G804893_T01 (Zea mays), 3'ss of exon 2
gtaatttctttctctactttctcaaaaatgttacctttttgttgctttggtggttatagcgtgtaaagccctcttctttgttaagttagattgatgttatattcattgggttgttaagcaaagtcactatgtcgattttggaatattgttttgccttt-tagGGCTAGTGATAAGTGCCAAAGAGAGAAAAGGAAGACCATCAATGGAGATGATTTGCTTTGGGCTATGGCCACTTTAGGATTCGAAGATTACATCGATCCC
|||| | | |   || |         | | |||| |||   |||  ||| |||  ||   | ||   |  |    ||||    || | |  ||  ||| | |   |||  ||||            | ||||| |  ||    | ||||     ||||  || || ||||| |||||||| || |||||  |||||||||||||||| || ||| |||| ||||| ||||||||  | || || ||||| ||||| || |||
gtaagtgcctcagctgcggct----gactcttacttttgc-ttggcttgttgggaatttggagtggcgttcagggcttt----agcttggctggggttttgt--gttgacttgt------------ccatgtccacgttt---ttttgtccgctctttgcagAGCGAGTGACAAGTGCCAGAGGGAGAAGCGGAAGACCATCAATGGCGACGATCTGCTGTGGGCCATGGCCACGCTGGGGTTTGAAGACTACATTGAACCC

upper sequence: AT3G53340.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GRMZM2G064426_T02 (Zea mays), 3'ss of exon 2
gtaatttctttctctactttctcaaaaatgttacctttttgttgctttggtggttatagcgtgtaaagccctcttctttgttaagttagattgatgttatattcattgggttgttaagcaaagtca-ctatgtcgattttggaatattgttttgccttt-tagGGCTAGTGATAAGTGCCAAAGAGAGAAAAGGAAGACCATCAATGGAGATGATTTGCTTTGGGCTATGGCCACTTTAGGATTCGAAGATTACATCGATCCC
|||| | | |   |  |         | | | ||  || ||||   ||||    |   |  |  | ||   |    |||   ||     | |    |||  ||   |||| | ||  |   | |   ||| ||| |  ||      |||| |    |||  ||||| ||||| |||||||| || |||||  |||||||||||||||| || ||  |||| ||||| ||||||||  | || || || || || || || |||
gtaagtccctcggccgcggct----gactctgactcttctgtttgcttggcatgttgggaattcagag---tggcgtttcgcaaaccgcact----ttagcttaggtggggttttgtgttgacttgtctacgtccacgtt----ccttgtctgctgtttgcagGGCGAGTGACAAGTGCCAGAGGGAGAAGCGGAAGACCATCAATGGCGACGACCTGCTGTGGGCCATGGCCACGCTGGGGTTTGAGGACTATATTGAACCC

upper sequence: AT3G53340.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: Vv08s0040g03260.t01 (Vitis vinifera), 3'ss of exon 1
gtaatttctttctctactttctcaaaaatgttacctttttgttgctttggtggttatagcgtgtaaagccctcttctttgttaagttagattgatgttatattcattgggttgttaagcaaagtcactatgtcgattttggaatattgttttgccttttagGGCTAGTGATAAGTGCCAAAGAGAGAAAAGGAAGACCATCAATGGAGATGATTTGCTTTGGGCTATGGCCACTTTAGGATTCGAAGATTACATCGATCCC
                                                      ||| ||   | | ||  | ||  || |||| ||     | ||    ||| || | ||||||              | | | ||||  |       || |     |||||| |||||||| || || |||||||| |||||||| || ||||| ||||||||||| ||||| ||||| |||||||| || || ||||| || ||||| 
-----------------------------------------------------gtatggc---tgatgcattttttctttttaattttaggcggtgcgtgattgatggtgttgttgg------------ttttgtttttcaa-------ttggatgcctagGGCGAGTGATAAATGTCAGAGAGAGAAGAGGAAGACTATTAATGGGGATGATTTGCTCTGGGCAATGGCGACTTTAGGGTTTGAGGATTATATTGATCCG

upper sequence: AT3G53340.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: PP1S25_89V6.1 (Physcomitrella patens), 3'ss of exon 2
gtaatttctttctctactttctcaaaaatgttacctttttgttgctttggtggttatagcgtgtaaagccctcttctttgttaagttagattgatgttatattcattgggttgttaagcaaagtcactatgtcgattttggaatattgttttgcctttta--gGGCTAGTGATAAGTGCCAAAGAGAGAAAAGGAAGACCATCAATGGAGATGATTTGCTTTGGGCTATGGCCACTTTAGGATTCGAAGATTACATCGATCCC
                                               || |||||      | | |     | | |  ||| ||  |    ||  ||||| ||  || |        |||      |    | |  | ||   | ||  ||  ||| |||  | ||||| || ||||| ||  | || || || ||||| ||||||||||||||||| |||||||| |||  ||| ||||| || ||||| ||| |||| || 
-----------------------------------------------tgatggtttc----tttgatcatgtgtacaatgtaaaact----tggcgttatttttgtttgtcctccctgca------ccgcattg--tctgccgttttccttgacctattacagAGCTAGCGACAAGTGTCAGCGGGAAAAGAGAAAGACGATCAATGGAGATGATTTACTTTGGGCCATGAGCACATTAGGGTTTGAAGACTACGTCGAGCCG

upper sequence: AT3G53340.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: EFJ24973 (Selaginella moellendorffii), 3'ss of exon 1
gtaatttctttctctactttctcaaaaatgttacctttttgttgctttggtggttatagcgtgtaaagccctcttctttgttaagttagattgatgttatattcattgggttgttaagcaaagtcactatgtcgattttggaatattgttttgccttttagGGCTAGTGATAAGTGCCAAAGAGAGAAAAGGAAGACCATCAATGGAGATGATTTGCTTTGGGCTATGGCCACTTTAGGATTCGAAGATTACATCGATCCC
                                                                                               || |   |   |||   |||      |  |  | ||  |||  |   || || || | | ||  || || ||||| ||||||||||||||||| |||||||| |||||||| ||||| ||||| ||||| |||  |||  | || ||||| || ||| | || || 
-----------------------------------------------------------------------------------------------gtaagtattgctggaa-gttctttcgatcctttgtggtgatact---atcttcttctactttgcagAGCCAGTGACAAGTGCCAAAGAGAGAAGAGGAAGACGATCAATGGCGATGACTTGCTATGGGCAATGAGCACGCTGGGCTTCGAGGAGTACTTGGAACCT

upper sequence: AT3G53340.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: EFJ15374 (Selaginella moellendorffii), 3'ss of exon 1
gtaatttctttctctactttctcaaaaatgttacctttttgttgctttggtggttatagcgtgtaaagccctcttctttgttaagttagattgatgttatattcattgggttgttaagcaaagtcactatgtcgattttgga-atattgttttgccttttagGGCTAGTGATAAGTGCCAAAGAGAGAAAAGGAAGACCATCAATGGAGATGATTTGCTTTGGGCTATGGCCACTTTAGGATTCGAAGATTACATCGATCCC
                                                                                                          |  ||  ||      |  |  | ||  ||| ||    || || || | | || ||| || ||||| ||||||||||||||||| |||||||| |||||||| ||||| ||||| ||||| |||  |||  | || ||||| || ||| | || || 
---------------------------------------------------------------------------------------------------------gtaagt-attgcttcgatcctttgtggtgatgttaactatcttcttctactttgtagAGCCAGTGACAAGTGCCAAAGAGAGAAGAGGAAGACGATCAATGGCGATGACTTGCTATGGGCAATGAGCACGCTGGGCTTCGAGGAGTACTTGGAACCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgggttgttaagcaaagtcactatgtcgattttggaatattgttttgccttttagGGCTAGTGATAAGTGCCAAAGAGAGAAAAGGAAGACCATCAATGGAGATGATTTGCTTTGGGCTATGGCCACTTTAGGATTCGAAGATTACATCGATCCC
                                       ttgttttgcctttt  CT-rich tract
                                   aatattgtttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaatttctttctctactttctcaaaaatgttacctttttgttgctttggtggttatagcgtgtaaagccctcttctttgttaagttagattgatgttatattcattgggttgttaagcaaagtcactatgtcgattttggaatattgttttgccttttagGGCTAGTGATAAGTGCCAAAGAGAGAAAAGGAAGACCATCAATGGAGATGATTTGCTTTGGGCTATGGCCACTTTAGGATTCGAAGATTACATCGATCCC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CGAAGA