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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgatatagataaaatctgatctcgtttctgtaaacaagcacgattcttgtatttatatgcttatgtttacaatgtttctctctgtgcgatagTGAGGATCCTGAGATCCATTTCAAGTACATTGAAGCAGCTGCCAAGACTGGTCAAATAAAGGAGGTTGAGCGTGTAACTAGAGAGTCTAACTTCTATGAT

Basic information

species Arabidopsis thaliana
transcript AT3G08530.1
intron # 20
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G08530.1 (Arabidopsis thaliana), 3'ss of exon 20
lower sequence: LOC_Os11g01380.1 (Oryza sativa), 3'ss of exon 20
gtgatatagataaaatctgatctcgtttctgtaaacaagcacgattcttgtatttatatgcttatgtttacaatgtttctctctgtgcgatagTGAGGATCCTGAGATCCATTTCAAGTACATTGAAGCAGCTGCCAAGACTGGTCAAATAAAGGAGGTTGAGCGTGTAACTAGAGAGTCTAACTTCTATGAT
      ||| |||   ||  |   |||  | |   | |   | ||| |    || |  ||       |||  ||  |||| |   | | | ||||||||||| || || |||||||| ||||| ||||||||||| | |||||| || || || || ||||| |||||||| || || || ||||| ||||||
-----gtagttaactactcctgatgttgatatgtgcgaa-gcaattttgtccttaacgtggcgcaccttaatatcgttctttacattcaacagTGAGGATCCAGATATTCATTTCAAATACATAGAAGCAGCTGCTAGGACTGGACAGATCAAAGAAGTTGAACGTGTAACCAGGGAATCCAACTTTTATGAT

upper sequence: AT3G08530.1 (Arabidopsis thaliana), 3'ss of exon 20
lower sequence: LOC_Os12g01390.1 (Oryza sativa), 3'ss of exon 20
gtgatatagataaaatctgatctcgtttctgtaaacaagcacgattcttgtatttatatgcttatgtttacaatgtttctctctgtgcgatagTGAGGATCCTGAGATCCATTTCAAGTACATTGAAGCAGCTGCCAAGACTGGTCAAATAAAGGAGGTTGAGCGTGTAACTAGAGAGTCTAACTTCTATGAT
  |   |  |  | | |||||   |||  | |   | |   | ||| |    || |  ||       |||  ||  |||| |   | | | ||||||||||| || || |||||||| ||||| ||||||||||| | |||||| || || || || ||||| |||||||| || || || ||||| ||||||
--gtagttaactacacctgat---gttgatatgtgcgaa-gcaattttgtccttaacgtggcgcaccttaatatcgttctttacattcaacagTGAGGATCCAGATATTCATTTCAAATACATAGAAGCAGCTGCTAGGACTGGACAGATCAAAGAAGTTGAACGTGTAACCAGGGAATCCAACTTTTATGAT

upper sequence: AT3G08530.1 (Arabidopsis thaliana), 3'ss of exon 20
lower sequence: GRMZM2G057576_T02 (Zea mays), 3'ss of exon 18
----------------gtgatatagataaaatctgatctcgtttctgtaaacaagcacgattcttgtatttatatgcttatgtttacaatgtttctctctgtgcgatagTGAGGATCCTGAGATCCATTTCAAGTACATTGAAGCAGCTGCCAAGACTGGTCAAATAAAGGAGGTTGAGCGTGTAACTAGAGAGTCTAACTTCTATGAT
                 |||| | | ||     | |  | |  |   | || |   |   ||||     |   |||| |   | |  ||| ||||| | | | | ||||||||||||| || ||||||||||| ||||| ||||||||||| |  ||||| || || || || |||||||||||||| ||||||||||| |||||||||
gtagttactcttactcctgatgttggtatttcttaaggtggcataccttaatat-taaatttctcaacatggcatgcattgatattaaat-tttctttatattc-atagTGAGGATCCAGATATCCATTTCAAATACATAGAAGCAGCTGCAAGAACTGGACAGATCAAAGAAGTTGAGCGTGTAACCAGAGAGTCTAATTTCTATGAT

upper sequence: AT3G08530.1 (Arabidopsis thaliana), 3'ss of exon 20
lower sequence: GRMZM2G430947_T01 (Zea mays), 3'ss of exon 6
----gtgatatagataaaatctgatctcgtttctgtaaacaagcacgattcttgtatttatatgcttatgtttacaatgtttctctctgtgcgatagTGAGGATCCTGAGATCCATTTCAAGTACATTGAAGCAGCTGCCAAGACTGGTCAAATAAAGGAGGTTGAGCGTGTAACTAGAGAGTCTAACTTCTATGAT
     |  | | | | | | | ||   | |||||  ||    |   |  | |   |   | ||||  |        | |||||| |   ||| | || ||||| || || ||||||||||||||||| |||||||| || | |||||| ||||| || || ||||| |||||||| |||||||| ||||||||||||
gtaatttctcttgttgacagcggaatgcctttctcaaattttgtgtgtctttctca---aaatgca-acacacctgaggtttctttacatgcaacagCGAGGACCCAGATATCCATTTCAAGTACATAGAAGCAGCAGCAAGGACTGGACAAATCAAAGAAGTTGAACGTGTAACCAGAGAGTCAAACTTCTATGAT

upper sequence: AT3G08530.1 (Arabidopsis thaliana), 3'ss of exon 20
lower sequence: GRMZM2G453474_T01 (Zea mays), 3'ss of exon 4
-------gtgatatagataaaatctgatctcgtttctgtaaacaagcacgattcttgtatttatatgcttatgtttacaatgtttctctctgtgcgatagTGAGGATCCTGAGATCCATTTCAAGTACATTGAAGCAGCTGCCAAGACTGGTCAAATAAAGGAGGTTGAGCGTGTAACTAGAGAGTCTAACTTCTATGAT----
        |  | | | | | | | ||   | |||||  ||    |   |  | |   |   | ||||  |        | |||||| |   ||| | || ||||| || || ||||||||||||||||| |||||||| || |  ||||| ||||| || || ||||| | |||||| |||||||| ||||| ||||||    
caggtaatttctcttgctgacagcggaatgcctttctcaaattttgtgtgtctttctca---aaatgca-acacacctgaggtttctttacatgcaacagcgagGACCCAGATATCCATTTCAAGTACATAGAAGCAGCAGCAAGAACTGGACAAATCAAAGAAGTTGAACATGTAACCAGAGAGTCAAACTTATATGATGCTG

upper sequence: AT3G08530.1 (Arabidopsis thaliana), 3'ss of exon 20
lower sequence: GRMZM2G102756_T01 (Zea mays), 3'ss of exon 4
----gtgatatagataaaatctgatctcgtttctgtaaacaagcacgattcttgtatttatatgcttatgtttacaatgtttctctctgtgcgatagTGAGGATCCTGAGATCCATTTCAAGTACATTGAAGCAGCTGCCAAGACTGGTCAAATAAAGGAGGTTGAGCGTGTAACTAGAGAGTCTAACTTCTATGAT
     |  | | | | | | | ||   | |||||  ||  | ||  |  | |   |   | ||||  |        | |||||| |   ||| | || ||||| || || ||||||||||||||||| |||||||| || || | ||| ||||| || || ||||| | |||||| |||||||| ||||| ||||||
gtaatttctcttgctgacagcggaatgcctttctcaaattatgcgtgtctttctca---aaatgca-acacacctgaggtttctttacatgcaacagCGAGGACCCAGATATCCATTTCAAGTACATAGAAGCAGCAGCAAAAATTGGACAAATCAAAGAAGTTGAACATGTAACCAGAGAGTCAAACTTATATGAT

upper sequence: AT3G08530.1 (Arabidopsis thaliana), 3'ss of exon 20
lower sequence: GLYMA14G06340.1 (Glycine max), 3'ss of exon 20
--------gtgatatagataaaa--tctgatctcgtttctgtaaacaagcacgattctt----gtattt----atatgcttatgtttaca-atgtttctctc-----tgtgcgatagTGAGGATCCTGAGATCCATTTCAAGTACATTGAAGCAGCTGCCAAGACTGGTCAAATAAAGGAGGTTGAGCGTGTAACTAGAGAGTCTAACTTCTATGAT
         | || | || ||||    || | |  | |  ||||   | | |  ||  |     ||||     || |  || || | |   ||||| ||||      | ||  | |||||||||||||| || || || ||||||||||| ||||| || |||||||||||||| ||||||||||||||||| || ||||| || || |||||||||
gtaattctttcatttggaaaaaaaacttgtttttctgttggtaattgacctcattttattgagatattgtccgatgtatttctgctgatgtatgttcctctaaataatatggaacagTGAGGATCCTGACATTCACTTTAAGTACATTGAGGCAGCAGCAAAGACTGGTCAAATCAAGGAGGTTGAGCGTGTGACAAGAGAATCAAATTTCTATGAT

upper sequence: AT3G08530.1 (Arabidopsis thaliana), 3'ss of exon 20
lower sequence: GLYMA02G42560.1 (Glycine max), 3'ss of exon 20
-----------gtgatatagataaaatctgatctcgtttctgtaaacaagcacgattctt----gtattt----atatgcttatgtttaca-atgtttctctc-----tgtgcgatagTGAGGATCCTGAGATCCATTTCAAGTACATTGAAGCAGCTGCCAAGACTGGTCAAATAAAGGAGGTTGAGCGTGTAACTAGAGAGTCTAACTTCTATGAT
            |     | | ||||  || | |  | |  ||||   | | |  ||  |     ||||     || |  || || | |   ||||| ||||      | ||  | |||||||||||||| || || || ||||||||||| ||||| || |||||||||||||| ||||||||||||||||| || ||||| || || |||||||||
gtaattctttcatttggaaaaaaaaacttgtttttctgttggtaatagacctcatttaattgagatattatccaatgtatttctgctgatgtatgttcctctaaataatatggaacagTGAGGATCCTGATATTCACTTTAAGTACATTGAGGCAGCGGCAAAGACTGGTCAAATCAAGGAGGTTGAGCGTGTGACAAGAGAATCAAATTTCTATGAT

upper sequence: AT3G08530.1 (Arabidopsis thaliana), 3'ss of exon 20
lower sequence: GLYMA11G35460.1 (Glycine max), 3'ss of exon 19
---------------------------gtgatatagataaaatctgatctcgtttctgtaaacaagcacgattcttgtatttatatgcttatgtttacaatgtttctctctgtgcgatagTGAGGATCCTGAGATCCATTTCAAGTACATTGAAGCAGCTGCCAAGACTGGTCAAATAAAGGAGGTTGAGCGTGTAACTAGAGAGTCTAACTTCTATGAT
                            |    | |     |  ||||  | |||  |||||   | | | |   ||   | ||  ||| || |||    |    ||     || || |||||||||||||| || || || |||||||||||||||||||| |||||||| ||||| || |||||||||||||| |||||||| || |  |||||||||
gtaattccttcatttttatagaactgttttggctggtgggcaagtgatgccattt--gtaaagggg-atgttgtctgatatcatcagctaatatttttt-tccccctaaacttgggacagTGAGGATCCTGACATTCACTTTAAGTACATTGAAGCAGCTGCAAAGACTGGACAAATCAAAGAGGTTGAGCGTGTGACTAGAGAATCAAGTTTCTATGAT

upper sequence: AT3G08530.1 (Arabidopsis thaliana), 3'ss of exon 20
lower sequence: GLYMA18G02960.1 (Glycine max), 3'ss of exon 19
--------gtgatatagataaaatctgatctcgtttctgta-aacaagcacgattcttgtat------ttatatgcttatgtttacaatgtttctctctg----tgcgatagTGAGGATCCTGAGATCCATTTCAAGTACATTGAAGCAGCTGCCAAGACTGGTCAAATAAAGGAGGTTGAGCGTGTAACTAGAGAGTCTAACTTCTATGAT
         | || |   || || ||| | | | |  || | ||      | |||  |  |       || | ||||      ||  || ||| || |||    || || |||||||||||||| || || |||||||||||||| ||||| || |||||||| ||||| || |||||||||||||| |||||||| || |  || ||||||
gtaactctttcatgtttttagaa-ctgttttggctggtggacaagtgatgcaatttgtaaaggggatattgtctgctatcagctaatatttttttccctgaacttgggacagTGAGGATCCTGACATTCACTTCAAGTACATTGAGGCAGCAGCAAAGACTGGACAAATCAAAGAGGTTGAGCGTGTGACTAGAGAATCAAGTTTTTATGAT

upper sequence: AT3G08530.1 (Arabidopsis thaliana), 3'ss of exon 20
lower sequence: Vv13s0067g01290.t01 (Vitis vinifera), 3'ss of exon 20
gtgatatagataaaatctgatctcgtttctgtaaacaagcacgattcttgta-tttatatgcttatgtttacaatgtttctctctg-----tgcgatagTGAGGATCCTGAGATCCATTTCAAGTACATTGAAGCAGCTGCCAAGACTGGTCAAATAAAGGAGGTTGAGCGTGTAACTAGAGAGTCTAACTTCTATGAT
|| || |   ||  |    |   | || || |    | |  || | | |  |  |||| |  | || || | |  ||||   | ||     ||  | |||||||||||||| || || |||||||| |||||||| ||||| || ||||| ||||| ||||||||||||||||| ||| |||| || ||||||||||||
gtaatttgtttagtaaggaagaactttgctttctttaggtgcggtacatccaacttattttgtgattttcatatcgttttcttttggttcatggaacagTGAGGATCCTGACATTCACTTCAAGTATATTGAAGCTGCTGCTAAAACTGGACAAATTAAGGAGGTTGAGCGTGTGACTCGAGAATCAAACTTCTATGAT

upper sequence: AT3G08530.1 (Arabidopsis thaliana), 3'ss of exon 20
lower sequence: PP1S452_30V6.1 (Physcomitrella patens), 3'ss of exon 20
---------------------------------------------------------------gtgatata-gataa--aatctgatctcgtttctgtaaacaagcacgattcttgtatttatatgcttatgtttacaatgtttctctctgtgcgatagTGAGGATCCTGAGATCCATTTCAAGTACATTGAAGCAGCTGCCAAGACTGGTCAAATAAAGGAGGTTGAGCGTGTAACTAGAGAGTCTAACTTCTATGAT
                                                                || |||| | |||  |   |||| | | |    |    | ||| ||   || |   |  |   |     |   ||  | | ||| | || |  || ||||| ||||||||||| | |||||||||||| || || || |||||||| ||||| ||||| || || ||||| || |||||||| |||||||||  |
gtgggaatttatgtcttttctttctttctgtttttttttttaattttaattttggcttggaatctggtatacggtaagcagattgatatgggtgagtttgggatgcatgaag-ttatgcatgcacaatccgcctagtaaactatatctttttgtgtcagCGAGGACCCTGAGATCCACTACAAGTACATTGAGGCTGCAGCAAAGACTGGCCAAATCAAGGAAGTGGAACGTGTCACAAGAGAGTCCAACTTCTATCCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gcacgattcttgtatttatatgcttatgtttacaatgtttctctctgtgcgatagTGAGGATCCTGAGATCCATTTCAAGTACATTGAAGCAGCTGCCAAGACTGGTCAAATAAAGGAGGTTGAGCGTGTAACTAGAGAGTCTAACTTCTATGAT
                                   tgtttctctct  CT-rich tract
     attcttgtatttatat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgatatagataaaatctgatctcgtttctgtaaacaagcacgattcttgtatttatatgcttatgtttacaatgtttctctctgtgcgatagTGAGGATCCTGAGATCCATTTCAAGTACATTGAAGCAGCTGCCAAGACTGGTCAAATAAAGGAGGTTGAGCGTGTAACTAGAGAGTCTAACTTCTATGAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAG