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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttcttgtgacattatacttttatctatgattattgttctgtcattttccttttggttgtttggattatgtctgctgacaatttaaacttatgttactcagGATTCAATGTTGAGAAAGTTCAGTACAAGAATGTGATGTTCACAGTTTGGGATGTTGGTGGCCAAGAGAAACTGAGACCTCTTTGGAGGCATTACTTCAA

Basic information

species Arabidopsis thaliana
transcript AT5G17060.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G17060.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: LOC_Os02g47110.1 (Oryza sativa), 3'ss of exon 2
ttcttgtgacattatacttttatctatgattatt-----gttctgtcattttccttttggttgtttggattatgtctgctgacaatttaaacttatgttactcagGATTCAATGTTGAGAAAGTTCAGTACAAGAATGTGATGTTCACAGTTTGGGATGTTGGTGGCCAAGAGAAACTGAGACCTCTTTGGAGGCATTACTTCAA
   |  |  ||| ||   ||| | |  | |||||       |||| ||| |  ||||  | ||      | ||   ||||      ||     | |   || |||| ||||||||||||||||| ||||||||||| |||||||| ||||| |||||||| ||||||||||||||  |||| ||||| |||||||||||||||||
-gatattatcatcatggcttt-tatggggttatttgaaaaatctgacatctcacttt--gctgggacactgattgatgcttctgcctttgtgctgtaccac-cagGGTTCAATGTTGAGAAAGTACAGTACAAGAACGTGATGTTTACAGTATGGGATGTCGGTGGCCAAGAGAAGTTGAGGCCTCTGTGGAGGCATTACTTCAA

upper sequence: AT5G17060.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: LOC_Os10g42940.1 (Oryza sativa), 3'ss of exon 2
----ttcttgtgacattatacttttatctatgattattgt-tctgtcattttccttttggtt--gtttggattatgtctgctgacaatttaaacttatgttactcagGATTCAATGTTGAGAAAGTTCAGTACAAGAATGTGATGTTCACAGTTTGGGATGTTGGTGGCCAAGAGAAACTGAGACCTCTTTGGAGGCATTACTTCAA
     |    |  |||    |  |         | || |  ||| | |||||  |||  |     |    |      ||     ||   | | | |   | |  |||| ||||| || ||||||||||| |||||||||||| ||||||| || ||||||||||||||||| || ||| |||| ||  | |||||||| ||||||||
gtaggttcactctcatccctccctccctccgcctcatcgaatcttttattttgttttgagccaaatccaaacccaacctaacatcatcatcatcat-catcatgcagGCTTCAACGTGGAGAAAGTTCAATACAAGAATGTGGTGTTCACTGTGTGGGATGTTGGTGGCCAGGAAAAATTGAGGCCCTTATGGAGGCACTACTTCAA

upper sequence: AT5G17060.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GRMZM2G106795_T03 (Zea mays), 3'ss of exon 2
ttcttgtgacattatacttttatctatgattattgttctgtcattttccttttggttgtttggattatgtctgctgacaatttaaacttatgttact--cagGATTCAATGTTGAGAAAGTTCAGTACAAGAATGTGATGTTCACAGTTTGGGATGTTGGTGGCCAAGAGAAACTGAGACCTCTTTGGAGGCATTACTTCAA
    | ||   ||| |  |||    | ||||| |        || || |  || |         | |||| || ||| |  |    || ||| ||||   ||| |||||||| ||||||||||| ||||||||||||||||| || ||||||||||||||||||||||| ||  |||| ||  | |||||||| ||||||||
ccaatatgttcttaaaggttttatgaggattactaaaaataaatgtttcactttgcctgcaaattcatgtgtgatgatatctct--ctgatgctactactagGTTTCAATGTCGAGAAAGTTCAATACAAGAATGTGATGTTTACTGTTTGGGATGTTGGTGGCCAAGAAAAGTTGAGGCCCTTGTGGAGGCACTACTTCAA

upper sequence: AT5G17060.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GRMZM2G011518_T03 (Zea mays), 3'ss of exon 2
------------------------------------ttcttgtgacatta--tacttttatctatgattattgttctgt-cattttccttttggttgtttggat------tatgtctgctgacaatttaaactt-atgttact-cagGATTCAATGTTGAGAAAGTTCAGTACAAGAATGTGATGTTCACAGTTTGGGATGTTGGTGGCCAAGAGAAACTGAGACCTCTTTGGAGGCATTACTTCAA
                                      ||| ||   | |   | |  ||  ||   || |    || | ||  | || |    ||| || |        ||||| |  |||||   |  |||| ||   | |  ||| |||||||||||||| ||||| |||||||||||  ||||||| || ||||||||||||||||| ||||| || || || || |||||||| ||||||||
gtccgattgtaccacctatctgcttgtgcatttcataacttttggtttcaaccattgctaattacagttgtccaactctgcacctgccatgcaattgattcgtccgttcatatgtttagtgacagcatgcactttatcacattgtagGTTTCAATGTTGAGAAGGTTCAATACAAGAATGTAGTGTTCACCGTGTGGGATGTTGGTGGCCAGGAGAAGCTCAGGCCCCTGTGGAGGCACTACTTCAA

upper sequence: AT5G17060.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GRMZM2G113995_T03 (Zea mays), 3'ss of exon 2
ttcttgtgacattatacttttatctatgattattgttctgtcattttccttttggttgtttgg--attatgtctgctgacaatttaaactta-tgttac--tcagGATTCAATGTTGAGAAAGTTCAGTACAAGAATGTGATGTTCACAGTTTGGGATGTTGGTGGCCAAGAGAAACTGAGACCTCTTTGGAGGCATTACTTCAA
||| |||   |    | |   |   | |  |  ||   |  |||||         ||     |  | |  ||||| |||| || |     |  || ||     ||| ||||| || ||||||||||| ||||||||||||||||| || || |||||||||||||||||||| ||  |||| ||  | |||||||| ||||||||
ttcctgtctta----attgaaaggcagggctcctgccattacatttaaaacaaactttccctgcaaattcgtctg-tgacgatatgtctctggtgctatcactagGTTTCAACGTCGAGAAAGTTCAATACAAGAATGTGATGTTTACTGTGTGGGATGTTGGTGGCCAAGAAAAGTTGAGGCCCTTGTGGAGGCACTACTTCAA

upper sequence: AT5G17060.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA01G43910.2 (Glycine max), 3'ss of exon 3
ttcttgtgacattatacttttatctatgattattgttctgtcattttccttttggttgtttggattatgtctgctgacaatttaaacttatgttact---cagGATTCAATGTTGAGAAAGTTCAGTACAAGAATGTGATGTTCACAGTTTGGGATGTTGGTGGCCAAGAGAAACTGAGACCTCTTTGGAGGCATTACTTCAA
 |    || |  |||  | ||  |   | || ||  | |         |   ||  | |    | | | ||| ||     |||||| |||| || |    |||| |||||||| |||||||||||||| |||||||| || |||||||| ||||||||||| || ||||||||||| || || ||||||||||| |||||  |
gttgaatgtctatatggtattggcgccgcttgttagttt--tggccagcaaatgagtctacataatgtttct-ctaggtttttaaatttatattgccttgcagGTTTCAATGTGGAGAAAGTTCAGTATAAGAATGTTATTTTCACAGTCTGGGATGTTGGAGGACAAGAGAAACTAAGGCCACTTTGGAGGCACTACTTTGA

upper sequence: AT5G17060.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA11G01380.2 (Glycine max), 3'ss of exon 3
ttcttgtgacattatacttttatctatgattattgttctgtcattttccttttggttgtttggattatgtctgctgacaatttaaacttatgttact---cagGATTCAATGTTGAGAAAGTTCAGTACAAGAATGTGATGTTCACAGTTTGGGATGTTGGTGGCCAAGAGAAACTGAGACCTCTTTGGAGGCATTACTTCAA
 |   ||| |  |||  | ||  |   | || ||  | |       | |   ||  | |    ||| | ||| ||     | |||| |||| || |    |||| |||||||| |||||||||||||| || ||||| || |||||||||||||||||||| || ||||||||||| || || ||||||||||| || || ||
attaagtgtctatatggtattgacctggcttgttagttt--tggcctgcaaatgagtctacatattgtttct-ctatgtttataaatttatattgccttgcagGTTTCAATGTGGAGAAAGTTCAGTATAAAAATGTTATTTTCACAGTTTGGGATGTTGGAGGACAAGAGAAACTAAGGCCACTTTGGAGGCACTATTTTAA

upper sequence: AT5G17060.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA12G02110.1 (Glycine max), 3'ss of exon 2
-----ttcttgtgacattatacttttatcta-tgattattgttctgtcattttccttttggttgtttggattatgtctgctgacaatttaaacttatgttactcagGATTCAATGTTGAGAAAGTTCAGTACAAGAATGTGATGTTCACAGTTTGGGATGTTGGTGGCCAAGAGAAACTGAGACCTCTTTGGAGGCATTACTTCAA
      | |      || | ||||   | ||         |  ||   | |  ||| |  |||||||   | | |  | | ||   |||  |    || |   |||| || ||||| ||||| |||||||| ||||||||  | ||||| |||||||||||||| || ||||||||| | ||  | ||||||||||| || || ||
caaacatgtaccagtatcacacttaagtttaacaggggaagaactagaaataacctatatgttgtttatttaaggcttacgga---tttgta---gtgctttgcagGTTTTAATGTGGAGAAGGTTCAGTATAAGAATGTTGTTTTCACGGTTTGGGATGTTGGAGGGCAAGAGAAATTAAGGGCACTTTGGAGGCACTATTTTAA

upper sequence: AT5G17060.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA11G09790.3 (Glycine max), 3'ss of exon 1
----ttcttgtgacattatacttttatctatgattatt--gttctgtcattttccttttggttgtttggattatgtctgctgacaatttaaacttatgttactcagGATTCAATGTTGAGAAAGTTCAGTACAAGAATGTGATGTTCACAGTTTGGGATGTTGGTGGCCAAGAGAAACTGAGACCTCTTTGGAGGCATTACTTCAA
        | | ||| |  | |||     | ||  | |  |   |   | |  ||| |   |||||||  | | |  |   ||   |||  |    || |   |||| || ||||| ||||| |||||||| ||||||||  | ||||| |||||||||||||| || ||||||||| | ||  | ||||||||||| || || ||
tgtaccagtatcacacttaagtttagctgaggaagaattagaagtagaaataacctatatattgtttgattaaggcttataga---tttgta---gtgctttgcagGTTTTAATGTGGAGAAGGTTCAGTATAAGAATGTTGTTTTCACGGTTTGGGATGTTGGAGGGCAAGAGAAATTAAGGGCACTTTGGAGGCACTATTTTAA

upper sequence: AT5G17060.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: Vv16s0039g02240.t01 (Vitis vinifera), 3'ss of exon 2
----ttcttgtgacattatacttttatctatgattattgttctgtcattttccttttggttgtttggatt-atgtctgctgacaatttaaacttatgttactcagGATTCAATGTTGAGAAAGTTCAGTACAAGAATGTGATGTTCACAGTTTGGGATGTTGGTGGCCAAGAGAAACTGAGACCTCTTTGGAGGCATTACTTCAA
       |  | | ||| ||| | ||| ||| | ||| | | | | || |  |   |||   ||  |||| || |    |||  ||||   ||  |  ||   ||| |||||||| |||||||||||||| ||||| |||||||||||||| |||||||| ||||| ||||||||||| || || || |||||||||||||| ||
taacagttgatcatattgtacatgtat-tat-actatggatgt-tgatgtgtcgaatggagcttcagattgattttaattgatcatttt--ctggtaatatatagGTTTCAATGTGGAGAAAGTTCAGTATAAGAACGTGATGTTCACAGTGTGGGATGTAGGTGGACAAGAGAAACTCAGGCCACTCTGGAGGCATTACTTTAA

upper sequence: AT5G17060.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: PP1S37_304V6.1 (Physcomitrella patens), 3'ss of exon 2
------------------------------------------------------------------ttcttgtgacattatacttttatctatgattat-------tgttctgtcattttccttttggttgttt---ggattatgtctgctgacaatttaaacttatgttac-----tcagGATTCAATGTTGAGAAAGTTCAGTACAAGAATGTGATGTTCACAGTTTGGGATGTTGGTGGCCAAGAGAAACTGAGACCTCTTTGGAGGCATTACTTCAA
                                                                  |     || || | |  ||||||  |   ||         | | ||| ||  | | | |  ||  |||   || | |  |||| ||  || ||| | ||    | |     ||||| |||||||| ||||||||||| |||||||||||   ||| ||||| ||||| ||||| |||||||||||| || ||||||| ||| |||||||||||||
gtaatttgacttatcacttgtagtcaatccttcatttttttggtagtgcgcctcttcgtttctgagtatagatggcactgttgttttatacaatgttgcaaccgtatttcctgccaagtgcatgtgagtgtttttgagggtaacatctgttgctaaattacattttccattcaattttcagGGTTCAATGTAGAGAAAGTTCAATACAAGAATGTTGAGTTTACAGTGTGGGACGTTGGAGGCCAAGAGAAATTGCGACCTCTGTGGCGGCATTACTTCAA

upper sequence: AT5G17060.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: PP1S91_59V6.1 (Physcomitrella patens), 3'ss of exon 2
----------------------------------------------------------------------------------ttcttgtgacattatacttttatctatgattattgttctgt-cattttccttttggttgtttggatta-tgtctgctgacaatttaaacttatg--ttactcagGATTCAATGTTGAGAAAGTTCAGTACAAGAATGTGATGTTCACAGTTTGGGATGTTGGTGGCCAAGAGAAACTGAGACCTCTTTGGAGGCATTACTTCAA
                                                                                   |  | |     |  ||||||     | | |||||| |||  | ||      | || || ||  |||    | || | ||    |    |   |  |  ||||||||| ||||| || |||||||| |||||||||||   ||||||||| ||||||||||| || || |||||| || | || |||||| |||||||||||||
gtaaagtgacacatgacacttgccgcaggtcttgatgattctcaaatggagtgtctcgtcgttcctagttgaaggtagttgtgttatctattgatgaacttttgcaccttaatattgtgctgagcgttgatgagtcggctggttatattggcatttgttcacttcctgtgttcccgcatctctcagGATTTAATGTGGAAAAAGTTCAATACAAGAATGTCGAGTTCACAGTATGGGATGTTGGAGGTCAGGAGAAATTGCGGCCCCTTTGGCGGCATTACTTCAA

upper sequence: AT5G17060.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: PP1S47_298V6.1 (Physcomitrella patens), 3'ss of exon 2
--------------------------------------------------------------------------------ttcttgtgacattatactttt--atctatgattat-tgttctgtcattttccttttggttgtttggattatgtctgctgacaatttaaacttatgt--tactcagGATTCAATGTTGAGAAAGTTCAGTACAAGAATGTGATGTTCACAGTTTGGGATGTTGGTGGCCAAGAGAAACTGAGACCTCTTTGGAGGCATTACTTCAA
                                                                                 |  | ||||  | |  | ||  || ||| ||| | |||   ||  |  |   |||| ||    ||||    | || | |    ||    |||||   || ||||| |||||||| |||||||||||||||||||| ||   ||| ||||| ||||||||||| || ||||||||| || | ||||| ||| ||||||| |||||
gtagcttgacttaacacttccagttgatccttttgtatttgaaagagcccctcttcgtttctgcttatttgatgtatttgcttatttgacggtgttttgtttgatgtattattctgtgtcgagtgctggtgaatttgctttcgaggatgtcatttgttaagttgttgtggttatgcaatattcagGGTTCAATGTGGAGAAAGTTCAGTACAAGAACGTCGAGTTTACAGTGTGGGATGTTGGAGGTCAAGAGAAATTGCGGCCTCTGTGGCGGCATTATTTCAA

upper sequence: AT5G17060.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: EFJ08154 (Selaginella moellendorffii), 3'ss of exon 2
ttcttgtgacattatacttttatctatgattattgttctgtcattttccttttggttgtttggattatgtctgctgacaatttaaacttatgttactcagGATTCAATGTTGAGAAAGTTCAGTACAAGAATGTGATGTTCACAGTTTGGGATGTTGGTGGCCAAGAGAAACTGAGACCTCTTTGGAGGCATTACTTCAA
                          | ||  || || | |  |||      |      ||||  |   |   |     || | ||    || ||    ||||| || || ||||| || ||||||||||||||| ||||||| || |||||||| |||||||| ||||| || ||||| || |||| ||| ||||| | 
-------------------------gtaatcctttttttctggtttcttggctttcatcttggccttcttgctcgactgatgtgaatccttgcta----gGATTTAACGTGGAGAAGGTCCAGTACAAGAATGTGGTGTTCACGGTGTGGGATGTGGGTGGCCAGGAGAAGCTAAGACCGCTCTGGAAGCACTACTTTAG

upper sequence: AT5G17060.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: EFJ24533 (Selaginella moellendorffii), 3'ss of exon 2
ttcttgtgacattatacttttatctatgattattgttctgtcattttccttttggttgtttggattatgtctgctgacaatttaaacttatgttactcagGATTCAATGTTGAGAAAGTTCAGTACAAGAATGTGATGTTCACAGTTTGGGATGTTGGTGGCCAAGAGAAACTGAGACCTCTTTGGAGGCATTACTTCAA
                   | |||  |  || | |||   |   |||| | |||    | | | |    |   |     || | ||    || ||    ||||| || || ||||| || ||||||||||||||| ||||||| || ||||||||||||||||| ||||| || ||||| || |||| ||| ||||| | 
------------------gtaatccttttttctggtttcttggctttcatcttgaccttcttgctcgatttctcgactgatgtgaatccttgcta----gGATTTAACGTGGAGAAGGTCCAGTACAAGAATGTGGTGTTCACGGTGTGGGATGTTGGTGGCCAGGAGAAGCTAAGACCGCTCTGGAAGCACTACTTTAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttccttttggttgtttggattatgtctgctgacaatttaaacttatgttactcagGATTCAATGTTGAGAAAGTTCAGTACAAGAATGTGATGTTCACAGTTTGGGATGTTGGTGGCCAAGAGAAACTGAGACCTCTTTGGAGGCATTACTTCAA
                          tgctgac  putative branch site (score: 2)
                                 aatttaaacttatgtt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttcttgtgacattatacttttatctatgattattgttctgtcattttccttttggttgtttggattatgtctgctgacaatttaaacttatgttactcagGATTCAATGTTGAGAAAGTTCAGTACAAGAATGTGATGTTCACAGTTTGGGATGTTGGTGGCCAAGAGAAACTGAGACCTCTTTGGAGGCATTACTTCAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - tgtttgg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ctgctga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aaactta