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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagttcttgctttcctttgatattagtcattgatgtatctgaatctttgtttttcttttgcctaatgtttttttttcctacagTGTACAAGAAACATTACCCACCTGCTTTGGATGATGAGGTCTGGAGGTTGGAAAAGATTGGAAAGGACGGGGCTTTCCATAAGAAACTCAATAAAGCAGG

Basic information

species Arabidopsis thaliana
transcript AT2G18750.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT2G18750.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: LOC_Os02g08120.1 (Oryza sativa), 3'ss of exon 5
gtaagttcttgctttcctttgatattagtcattgatgt-atctgaatctttgtttttcttttgcctaatgttt----ttttttcctacagTGTACAAGAAACATTACCCACCTGCTTTGGATGATGAGGTCTGGAGGTTGGAAAAGATTGGAAAGGACGGGGCTTTCCATAAGAAACTCAATAAAGCAGG
||||||         ||| ||| |  |  ||| ||| | ||  || ||||  |  |  || |    | |||||    ||  ||     |||||| ||||| || ||||||||||| ||| | ||||||||||||||||| |||||||| || ||||| ||  |||||||||||| ||| || ||||| ||
gtaagt---------cctctga-agcaaccat-gatatgatacgattcttcatgatatttctattaactgtttgaatttcatttgattagTGTATAAGAAGCACTACCCACCTGCGTTGAAAGATGAGGTCTGGAGGTTAGAAAAGATAGGGAAGGATGGATCTTTCCATAAGAGACTGAACAAAGCTGG

upper sequence: AT2G18750.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: LOC_Os04g36660.1 (Oryza sativa), 3'ss of exon 5
--gtaagttcttgctttcctttgatatta-gtcattgatgtatctgaatctttgtttttcttttgcctaatgtttttttttcctacagTGTACAAGAAACATTACCCACCTGCTTTGGATGATGAGGTCTGGAGGTTGGAAAAGATTGGAAAGGACGGGGCTTTCCATAAGAAACTCAATAAAGCAGG
   | | | | |    |    |||| ||  || | || |  ||     ||||    | |   |     |||  |  |   || |  ||||||||||||||| ||||| |||||  |  | ||||| || ||||| ||||| |||||||||||||| || || || || ||||| || ||   |   ||
gtatgattccatatactttactgatcttgtgtaactgttacat----gtcttaacatatagatc-ttaaattataatccctcttgtagTGTACAAGAAACACTACCCTCCTGCCCTAAAGGATGATGTTTGGAGATTGGAGAAGATTGGAAAGGATGGTGCATTTCACAAGAAGCTAAACTCAAATGG

upper sequence: AT2G18750.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GRMZM2G018837_T04 (Zea mays), 3'ss of exon 5
gtaagttcttgctttcctttgatattagtcattgatgtatctgaatctttgtttttcttttgcctaatgtt-tttttttcctacagTGTACAAGAAACATTACCCACCTGCTTTGGATGATGAGGTCTGGAGGTTGGAAAAGATTGGAAAGGACGGGGCTTTCCATAAGAAACTCAATAAAGCAGG
         |   | ||    || |   |   |  |||||    | |||    | | | |   ||| |    |||  ||  |  |||||||||||| || || |||||| |  || | ||||||||||||||||||||||| || || ||||| ||| | ||||||||||  || || ||| | ||
--------gtaagtcccaaaaatgtatctgtgtactgtattccca-cttgacatatatctaaactatttcaatttcatttatctagTGTACAAGAAGCACTATCCACCTACACTGAAAGATGAGGTCTGGAGGTTGGAAAAAATAGGGAAGGATGGGTCATTCCATAAGAGGCTGAACAAATCTGG

upper sequence: AT2G18750.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GRMZM2G010471_T01 (Zea mays), 3'ss of exon 1
gtaagttcttgctttcctttgatattagtcattgatgtatctgaatctttgtttttcttttgcctaatgtt-tttttttcctacagTGTACAAGAAACATTACCCACCTGCTTTGGATGATGAGGTCTGGAGGTTGGAAAAGATTGGAAAGGACGGGGCTTTCCATAAGAAACTCAATAAAGCAGG
|||||| |      |       |||| ||   || |||||    | |||    | | | |   ||| |    |||  ||  |  |||||||||||| || || |||||| |  || | ||||||||||||||||||||||| || || ||||| ||| | ||||||||||  || || ||| | ||
gtaagtcccaaaaat------gtatttgtg--tgctgtattctca-cttgacatatatctaaactatttcaatttcatttatctagTGTACAAGAAGCACTATCCACCTACACTGAAAGATGAGGTCTGGAGGTTGGAAAAAATAGGGAAGGATGGGTCATTCCATAAGAGGCTGAACAAATCTGG

upper sequence: AT2G18750.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GRMZM2G451882_T01 (Zea mays), 3'ss of exon 5
gtaagttcttgct--ttcctttgatattagtcattgatgtatctgaatctttgtttttcttttgcctaatgtttttttttcctacagTGTACAAGAAACATTACCCACCTGCTTTGGATGATGAGGTCTGGAGGTTGGAAAAGATTGGAAAGGACGGGGCTTTCCATAAGAAACTCAATAAAGCAGG
|||||| |       ||  |||  ||||  | |||||   ||    ||||    | |||           | ||  ||| ||||  ||||||||||| || || |||||| |  |  | ||||||||||||||||||||||| || |||||||| ||  | ||||||||||  || || ||| | ||
gtaagtcccaaaaaattgtttttgtatttct-attgacacat----atctaaactattcca---------gattcatttaccta--gTGTACAAGAAGCACTATCCACCTACGCTAAAAGATGAGGTCTGGAGGTTGGAAAAAATAGGAAAGGATGGCTCATTCCATAAGAGGCTGAACAAATCTGG

upper sequence: AT2G18750.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GRMZM2G113453_T01 (Zea mays), 3'ss of exon 5
---------gtaagttcttgctttcctt-tgatattagtcattgatgtatctgaatcttt-gtttttcttttgcctaatgt-----ttttttttcctacagTGTACAAGAAACATTACCCACCTGCTTTGGATGATGAGGTCTGGAGGTTGGAAAAGATTGGAAAGGACGGGGCTTTCCATAAGAAACTCAATAAAGCAGG
           |   | ||| ||| ||  | | || |  ||  ||| || ||| || ||| |  |||   | ||| |   |     |||| | |     |||||||||||| || |||||||||||  || | ||||| || ||||| || ||||||||||| ||||| || || ||||| |||||  | |||      ||
gtatgtgtgacacactgttgatttactcattagatgaaacaaagat-tacctgtatttttagaatttgcatcgccaagcatgctgattttgtatttattagTGTACAAGAAGCACTACCCACCTGCGCTGAAGGATGATGTTTGGAGATTAGAAAAGATTGGCAAGGATGGCGCATTCCACAAGAAGTTAAATGCCAGTGG

upper sequence: AT2G18750.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: PP1S336_7V6.1 (Physcomitrella patens), 3'ss of exon 4
-------------------------------------------------------------gtaagttcttgctttcctttgatattagtcattgatgta-tctgaatctttgtttttcttt---tgcctaatgtttttt---------tttcctacagTGTACAAGAAACATTACCCACCTGCTTTGGATGATGAGGTCTGGAGGTTGGAAAAGATTGGAAAGGACGGGGCTTTCCATAAGAAACTCAAT-AAAGCAGG
                                                              |      ||  |||| ||| |      | ||  | | | | ||||| ||| | |   |     |    ||| |||| |         |||| | ||||||||||||| || || |||||||| ||| |||| ||||| ||| | ||||| |||||||| |||||||| || || || |||   |||||| ||| |   
gtacgttgactgttttgaaccttgggtcatcttacgctataagagtttgtctgcgttcctaatttacagttagtttcgttttaggcagttaataaaagcagtttgaatatttatctagatggaagtattgaatcttttctacttgggaatttcgtgcagTGTACAAGAAGCACTATCCACCTGCCTTGAATGACGAGGTATGGCGCTTGGACAAGATTGGGAAGGACGGAGCCTTTCACAAGCGCCTCAATCAAAACCA-

upper sequence: AT2G18750.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: PP1S84_168V6.1 (Physcomitrella patens), 3'ss of exon 4
gtaagttcttgctttcctttga-----tattagtcattgatgtatct-----gaatctttgtttttcttttgcctaatgtttttttt-------tcctacagTGTACAAGAAACATTACCCACCTGCTTTGGATGATGAGGTCTGGAGGTTGGAAAAGATTGGAAAGGACGGGGCTTTCCATAAGAAACTCAATAAAGCAGG
     || || |  ||| | ||     ||  |   ||   || |  |     ||||   |   ||||| || |  |   |  || |        | || |||| |||||||| || ||||| ||| | ||| |||||||||||||| | ||||| || ||||| |||||||| ||||| || |||   |||||| |  |  |
--gcctttttacggtccctggaagaagtacgaaggatcagtggaaatattaggaatggatacgtttctgtttctaagaatcgttgtcggtcacattctgcagTTTACAAGAAGCACTACCCGCCTTCCTTGAATGATGAGGTCTGGCGATTGGACAAAATTGGCAAGGACGGTGCTTTTCACAAGCGTCTCAATCAGTCTCG

upper sequence: AT2G18750.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: PP1S98_167V6.1 (Physcomitrella patens), 3'ss of exon 4
--------gtaagttcttgctttcctt--tgatattagtcattgatgtatctgaatctttgtttttcttttgcctaatgtttttt-----tttcctacagTGTACAAGAAACATTACCCACCTGCTTTGGATGATGAGGTCTGGAGGTTGGAAAAGATTGGAAAGGACGGGGCTTTCCATAAGAAACTCAATAAAGCAGG
        | |  | | | | |||  |  |||     || ||| |   |    ||    | | | | | |    ||||  || ||       |  |||||| |||||||| || || || ||||||||  |||| ||||| ||| | ||||| ||||||||||| ||||| |||||||| ||    || ||| ||||| |
tgccctgtgcacatccattcgttctgtgctgaatgccgtgattaacagaagaaaaatcatatctctatatctaataattgttgttggtcaccttgtacagTCTACAAGAAGCACTATCCGCCTGCTTTAAATGACGAGGTTTGGCGATTGGACAAGATTGGAAAAGACGGTGCTTTCCACAAACGTCTAAATCAAGCAAG

upper sequence: AT2G18750.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: PP1S51_322V6.1 (Physcomitrella patens), 3'ss of exon 4
---gtaagttcttgctttcctttgata-----ttagtcattgatgtatctgaatctttgt------ttttcttttgcctaatgttttt-ttttcctacagTGTACAAGAAACATTACCCACCTGCTTTGGATGATGAGGTCTGGAGGTTGGAAAAGATTGGAAAGGACGGGGCTTTCCATAAGAAACTCAATAAAGCAGG
    |  || |     ||  |   | |     | || ||     |||  ||| |   ||       ||    ||| | |  || |     |||| | |||||||||| || || ||||||||||| ||| |||| ||||| ||| | ||||| |||||||| || || || |||||||| |||   || ||| ||||   
ttgttcggtgccaaagtttttgaaaaaaagaatcaggcagcatggtacttgattggatgcaaccacttacagttttctttgtgctgaaactttcgtgcagTGTACAAAAAGCACTACCCACCTGCCTTGAATGACGAGGTGTGGCGCTTGGACAAGATTGGGAAAGATGGTGCTTTCCACAAGCGTCTTAATCAAGCCAA

upper sequence: AT2G18750.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: PP1S21_379V6.1 (Physcomitrella patens), 3'ss of exon 6
gtaagttcttgctttcctttga-----tattagtcattgatg----tatctgaat-----ctttgtttttcttttgcctaatgttt--ttttttcctacagTGTACAAGAAACATTACCCACCTGCTTTGGATGATGAGGTCTGGAGGTTGGAAAAGATTGGAAAGGACGGGGCTTTCCATAAGAAACTCAATAAAGCAGG
 |   || ||| | ||  ||||     | | |   |||  ||    |||   |||        | || ||  |  ||||  |  ||  | |  | || |||||||||||||||||||||| || ||  ||  ||||||||| ||| ||||||| || ||||| |||||||| ||||| || |||   |||||| || |  |
-tgcatttttgttatcacttgaagaagtgtgaacaatttgtggaaatataaaaatgagtataatattgtttctgagcctcgttgttggtctcattctgcagTGTACAAGAAACATTACCCGCCAGCCCTGACTGATGAGGTTTGGCGGTTGGATAAAATTGGCAAGGACGGTGCTTTTCACAAGCGTCTCAATCAATCTCG

upper sequence: AT2G18750.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: EFJ05811 (Selaginella moellendorffii), 3'ss of exon 4
gtaagttcttgctttcctttgatattagtcattgatgtatctgaatctttgtttttcttttgcctaa-tgttttttt-ttcctacagTGTACAAGAAACATTACCCACCTGCTTTGGATGATGAGGTCTGGAGGTTGGAAAAGATTGGAAAGGACGGGGCTTTCCATAAGAAACTCAATAAAGCAGG
                           || |  || ||  |     ||      || | |||| ||  ||||| | | ||    |||| ||||| ||||| || || || |||||||  ||||| || |||||| | || |||||||||||||||||||| ||||| ||||  ||||| ||||| ||
---------------------------gtaa--gaagtccccactcctcgcagattttcttgcttacctgtttatatatttgcgcagTTTACAAAAAACACTATCCTCCCGCTTTGGGCGATGATGTGTGGAGGCTTGACAAGATTGGAAAGGACGGGGCATTCCACAAGAGGCTCAACAAAGCTGG

upper sequence: AT2G18750.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: EFJ34469 (Selaginella moellendorffii), 3'ss of exon 4
gtaagttcttgctttcctttgatattagtcattgatgtatctgaatctttgtttttcttttgcctaatgtttttttttcctacagTGTACAAGAAACATTACCCACCTGCTTTGGATGATGAGGTCTGGAGGTTGGAAAAGATTGGAAAGGACGGGGCTTTCCATAAGAAACTCAATAAAGCAGG
                        | ||||     |        ||   ||| || ||  | |||    || | | ||    |||| ||||| ||||| || || || |||||||  ||||| || |||||| | || |||||||||||||||||||| ||||| ||||  ||||| ||||| ||
-----------------------gtaagtccccactcctcgcagat---tgtcttgct--tacctgt--ttatatatttgcgcagTTTACAAAAAACACTATCCTCCCGCTTTGGGCGATGATGTGTGGAGGCTTGACAAGATTGGAAAGGACGGGGCATTCCACAAGAGGCTCAACAAAGCTGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attgatgtatctgaatctttgtttttcttttgcctaatgtttttttttcctacagTGTACAAGAAACATTACCCACCTGCTTTGGATGATGAGGTCTGGAGGTTGGAAAAGATTGGAAAGGACGGGGCTTTCCATAAGAAACTCAATAAAGCAGG
                               gcctaat  putative branch site (score: 3)
               tctttgtttttctttt  CT-rich tract
                                  taatgttttttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagttcttgctttcctttgatattagtcattgatgtatctgaatctttgtttttcttttgcctaatgtttttttttcctacagTGTACAAGAAACATTACCCACCTGCTTTGGATGATGAGGTCTGGAGGTTGGAAAAGATTGGAAAGGACGGGGCTTTCCATAAGAAACTCAATAAAGCAGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA