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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...taatagatgataaaaatgaaactctgtttcatatgaagtcccaagagtgtggtccagaataattatgtcttgcctcacatatagctattctaactctcagAGCTTGAAGCACAACCCTAATGGGAGGTTTGTCGTAGTCTGCGGTGATGGAGAGTACATAATCTACACTGCTTTGGCGTGGAGAAATAGATCTTTTGGGT

Basic information

species Arabidopsis thaliana
transcript AT3G15980.2
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G15980.2 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: LOC_Os02g11840.2 (Oryza sativa), 3'ss of exon 2
taatagatgataaaaatgaaactctgtttcatatgaagtccca-agagtgtggtc-cagaata-attatgtcttgcctcacatatagctattctaactctcagAGCTTGAAGCACAACCCTAATGGGAGGTTTGTCGTAGTCTGCGGTGATGGAGAGTACATAATCTACACTGCTTTGGCGTGGAGAAATAGATCTTTTGGGT
 | |   |  |   | | ||| |   ||  || | || ||    | |||||  |   ||  ||  |||    ||     |  |||||    |  |  | ||||||||| | |||||| || |||||||| ||||| || || || || |||||||| ||||||||||||||||| || || |||||||||||||| || ||||
gattctgttgttgtagtaaaattaaatta-atctcaaatctagtatagtgtaattatagtgtatgttagtaattatagtaattatagtgtattca--tttcagAGCTTAAGGCACAATCCGAATGGGAGATTTGTTGTTGTATGTGGAGATGGAGAATACATAATCTACACTGCATTAGCATGGAGAAATAGATCATTCGGGT

upper sequence: AT3G15980.2 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: LOC_Os02g11830.2 (Oryza sativa), 3'ss of exon 11
taatagatgataaaaatgaaactct-gtttcatatgaagtcccaagagtgtggtccagaataatt-atgtct-tgcctcacatatagctat-tctaactctcagAGCTTGAAGCACAACCCTAATGGGAGGTTTGTCGTAGTCTGCGGTGATGGAGAGTACATAATCTACACTGCTTTGGCGTGGAGAAATAGATCTTTTGGGT
     | |  | ||| || |  | | |  | | || ||        | | |  | |    |  || |||| |     | |   |||    | | |   | |||||| || | |||||| || ||||| || ||||| || || || || |||||||| |||||||||||||| || ||||| |||||||||||||| || ||||
----cggttttgaaattgtacttgtcgggttaaataaatgtgatgaacttttctacgttctggtttatgtttgcatgttattaataatagtgtattcatttcagAGTTTAAGGCACAATCCAAATGGAAGATTTGTTGTTGTATGTGGAGATGGAGAATACATAATCTACACCGCATTGGCATGGAGAAATAGATCATTCGGGT

upper sequence: AT3G15980.2 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: LOC_Os06g05180.1 (Oryza sativa), 3'ss of exon 11
taatagatgataaaaatgaaactctgtttcatatgaagtcccaagagtgtg----gtccagaataattatgtcttgcctcacatatagctattctaactc-tcagAGCTTGAAGCACAACCCTAATGGGAGGTTTGTCGTAGTCTGCGGTGATGGAGAGTACATAATCTACACTGCTTTGGCGTGGAGAAATAGATCTTTTGGGT
     |   | || | |     ||| | |  || | | |   |   || ||     ||  ||||| |  |   |      |  | |     || |   |  ||||||||| ||||| ||||| ||||| || ||||||||||| || || ||||| || | |||||| || ||||| ||||| ||||| ||||| || ||||| |
-----ggctacaacatttcttttctttctactaggtaatgttagttgtttgtcatatcttgaatagtattcaatcttactatgtgtcatctttttgtttggtcagAGCTTAAAGCATAACCCCAATGGAAGATTTGTCGTAGTTTGTGGAGATGGTGAATTCATAATTTATACTGCATTGGCTTGGAGGAATAGGTCATTTGGAT

upper sequence: AT3G15980.2 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: GRMZM2G000645_T01 (Zea mays), 3'ss of exon 11
----taatagatgataaaaatgaaactctgtttcatatgaagtcccaagagtgtggtccagaataattatgtcttgcctcacatatagctattctaactc-tcagAGCTTGAAGCACAACCCTAATGGGAGGTTTGTCGTAGTCTGCGGTGATGGAGAGTACATAATCTACACTGCTTTGGCGTGGAGAAATAGATCTTTTGGGT
       ||||    |   |||        | |   |    |||    |    |  | ||| | |  |||    ||  |      ||   ||| |   |  ||||||||||||||| |||||||||||  |||| || || || || || ||||| ||||||||||| || |||||  |||| ||||| |||||||| |||||||
ccttccctagaccccacccatgcggaagcctctggcaccgggtct---gcccttttttcagta-atgtataatctgatt-gtgagtaatcattttggttggtcagAGCTTGAAGCATAACCCTAATGGACGGTTCGTTGTTGTATGTGGAGATGGCGAGTACATAATTTATACTGCCCTGGCCTGGAGGAATAGATCATTTGGGT

upper sequence: AT3G15980.2 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: GRMZM2G443953_T03 (Zea mays), 3'ss of exon 12
-taatagatgataaaaatgaaac-tctgtttcatatgaagtcccaagagtgtggtccagaataattatgtcttgcctcacatatagctattctaactctcagAGCTTGAAGCACAACCCTAATGGGAGGTTTGTCGTAGTCTGCGGTGATGGAGAGTACATAATCTACACTGCTTTGGCGTGGAGAAATAGATCTTTTGGGT
 |  |  |||  |  ||  |  |  | ||||  ||  |  |      |   |   | || ||| |||       |   |  ||   || |     ||  ||||| ||   |||||| || |||||||||||||| |  || || || |||||||||||||| |||||||| ||  | || |||||||||||||| |||||||
tttttttatggaaggaaaaaggcaccggttttttaaaagttagttctaacttatgctaggatatttaaaaa--acagtaactaatcctttctgttcttccagAGTTTACGGCACAATCCAAATGGGAGGTTTGTTGCTGTATGTGGAGATGGAGAGTACATTATCTACACAGCGCTAGCATGGAGAAATAGATCCTTTGGGT

upper sequence: AT3G15980.2 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: GRMZM2G124886_T01 (Zea mays), 3'ss of exon 11
taatagatgataaaaatgaaactctgtttcatatgaagtcccaagagtgtggtccagaataattatgtcttgcctcacatatagctattctaact--ctcagAGCTTGAAGCACAACCCTAATGGGAGGTTTGTCGTAGTCTGCGGTGATGGAGAGTACATAATCTACACTGCTTTGGCGTGGAGAAATAGATCTTTTGGGT
   |  || || |  ||          ||  | ||  |||       | |  |      |  || |   ||   | | |||  | | |  ||  |   ||||||||| |  ||||| || |||||||| ||||| || || || || |||||||| |||||||| ||||| || || || |||||||||||||| |||||||
gtttgaattatcatgattttttaaaacttgttttgtggtcatgtatatcttttttgtgctggtt-tacattat-taatatactggtgtgatatttgtttcagAGCTTAAGACACAATCCGAATGGGAGATTTGTTGTTGTATGTGGAGATGGAGAATACATAATATACACAGCATTAGCATGGAGAAATAGATCATTTGGGT

upper sequence: AT3G15980.2 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: GRMZM2G095348_T02 (Zea mays), 3'ss of exon 10
-----------------------------------------------------------taatagatgataaaaatgaaactctgtttcatatgaagtcccaagagtg-tggtccagaataat-tatgtcttgcctcacatatagctattctaactc--tcagAGCTTGAAGCACAACCCTAATGGGAGGTTTGTCGTAGTCTGCGGTGATGGAGAGTACATAATCTACACTGCTTTGGCGTGGAGAAATAGATCTTTTGGGT
                                                           || |      |  || || |  ||| |||| | | |          ||| |  |   |  |    |||    ||  |   || ||  |||| |   |   ||||||||||||||| || ||||||||  |||| || || || || || ||||| ||||||||||| || |||||  |||| ||||| ||||| || ||||| |
gtacttttggatgctgatgtgttctttgtattttaaaacttgttactattgtaggtttatagtgtggtttttaagtggacatct-tttcgttttattatttggtggtgctcattttgtgtggcgtataatctgattgtgat-taattatttttggttggtcagAGCTTGAAGCATAATCCTAATGGACGGTTCGTTGTTGTATGTGGAGATGGTGAGTACATAATTTATACTGCCCTGGCCTGGAGGAATAGGTCATTTGGAT

upper sequence: AT3G15980.2 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: GLYMA13G43680.2 (Glycine max), 3'ss of exon 11
--taatagatgataaaaatgaaactctgtttcata--tgaagtcccaagagtgtggtccagaataattatgtcttgcctcacatatagctattctaactctcagAGCTTGAAGCACAACCCTAATGGGAGGTTTGTCGTAGTCTGCGGTGATGGAGAGTACATAATCTACACTGCTTTGGCGTGGAGAAATAGATCTTTTGGGT
   | |   |  |||||    |   ||  ||  |   | || |  ||| | | |       |    |  || |||       || ||  |    |      ||||  || |||||||| || |||||||||||||| || || || || ||||| |||||||| || |||||||| ||||| ||||||||||| || ||||| |
agaagtgagttttaaaacaatagtccttattgctggttcaattatcaacaatatttgtttcatgggtggtgacttattgttgatttaatt----tgttgtgcagAATTTAAAGCACAATCCAAATGGGAGGTTTGTTGTTGTGTGTGGAGATGGTGAGTACATTATATACACTGCATTGGCATGGAGAAATAGGTCATTTGGTT

upper sequence: AT3G15980.2 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: GLYMA15G01680.1 (Glycine max), 3'ss of exon 11
-taatagatgataaaaatgaaactctgtttcatatgaagtcccaagagtgtggtccagaataattatgtcttgcctcacatatagctattctaactct-cagAGCTTGAAGCACAACCCTAATGGGAGGTTTGTCGTAGTCTGCGGTGATGGAGAGTACATAATCTACACTGCTTTGGCGTGGAGAAATAGATCTTTTGGGT
  ||  ||   | ||||| | | ||  | |     |       |  ||     |      ||  |  ||  || || |    |   |    | | | | ||||  || |||||||| || |||||||||||||| || || || || ||||| |||||||| || |||||||| ||||| ||||||||||| || ||||| |
agaagtgagttttaaaataatagtccttattgcgggttcaattatcagcaatatttgtttta--tgggtggtggctgattgttgatttcatttattgtgcagAATTTAAAGCACAATCCAAATGGGAGGTTTGTTGTTGTATGTGGAGATGGTGAGTACATTATATACACTGCATTGGCATGGAGAAATAGGTCATTTGGTT

upper sequence: AT3G15980.2 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: GLYMA07G03890.1 (Glycine max), 3'ss of exon 11
taatagatgataaaaatgaaactct--gtttca--tatgaagtcccaagagtgtggtccagaataattatgtcttgcctcacatat-agctattctaactctca-gAGCTTGAAGCACAACCCTAATGGGAGGTTTGTCGTAGTCTGCGGTGATGGAGAGTACATAATCTACACTGCTTTGGCGTGGAGAAATAGATCTTTTGGGT
      |  |||| |||  | | ||  |||| |  ||| |   |  |    | |  ||  | ||  | |  |  || || || | | |  || | | |  |||| ||| || | |||||| || |||||||||||||| || || || || ||||| ||||| || || ||||||| |||||| |||||||||||||| ||||| |
-----taaaataataatccaccccttagttttaattatcaccacttatttattttttcatgcatgttgac-tggtgtctgacttgtgatttacttttatactcaagAGTTTAAGGCACAATCCGAATGGGAGGTTTGTTGTTGTTTGTGGAGATGGGGAGTATATTATATACACTGGTTTGGCATGGAGAAATAGATCATTTGGTT

upper sequence: AT3G15980.2 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: GLYMA08G22140.1 (Glycine max), 3'ss of exon 11
taatagatgataaaaatgaaactctgtttcatatgaagtcccaagagtgtggtccagaataattatgtcttgcctcacatatagct-attctaactctcagAGCTTGAAGCACAACCCTAATGGGAGGTTTGTCGTAGTCTGCGGTGATGGAGAGTACATAATCTACACTGCTTTGGCGTGGAGAAATAGATCTTTTGGGT
   |  |  |||| |||    | ||   |  ||   | | |||    | |  |  || ||  | |  |  || || || | |   | | | | | ||||||||  | | |||||| || ||||||||||| || || || || || ||||| || || || || |||||||||||||| |||||||||||||| ||||| |
agctttaaaataataatctgccccttagttttaattatttccacttttttttttaagcatgttgac-tggtgtctgacttgtgatttacttttattctcagAGTCTAAGGCACAATCCAAATGGGAGGTTCGTTGTTGTTTGTGGAGATGGGGAATATATTATATACACTGCTTTGGCATGGAGAAATAGATCATTTGGTT

upper sequence: AT3G15980.2 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: Vv09s0002g04810.t01 (Vitis vinifera), 3'ss of exon 11
taatagatgataaaaatgaaactctgtttcatatgaagtcccaag--agtgtggtccaga---ataattatgtcttgcctcacatatagctattctaactctcagAGCTTGAAGCACAACCCTAATGGGAGGTTTGTCGTAGTCTGCGGTGATGGAGAGTACATAATCTACACTGCTTTGGCGTGGAGAAATAGATCTTTTGGGT
    |       |  |||||    ||||||  |  |  |   ||   | |||  |  |     | | |||| |||| | |    | |   | || |   | ||||||| | || || ||||| |||||||||||||| || || || || ||||| |||||||| || || || |||||||| ||||| ||||| |||||||| |
--gcattaagctaggatgaatgattgtttc-caccatattttaatttattgttatttatgtttacatttatttcttccttttttttt--tttttttgtgtttcagAGCCTAAAACATAACCCAAATGGGAGGTTTGTTGTTGTTTGTGGAGATGGTGAGTACATTATATATACAGCTTTGGCATGGAGGAATAGGTCTTTTGGTT

upper sequence: AT3G15980.2 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: Vv11s0016g04180.t01 (Vitis vinifera), 3'ss of exon 11
taatagatgataaaaatgaaactc-tgtttcatatgaagtcccaagagtgtggtccagaataattatgtct--tgcctcacatatagctattctaactctcagAGCTTGAAGCACAACCCTAATGGGAGGTTTGTCGTAGTCTGCGGTGATGGAGAGTACATAATCTACACTGCTTTGGCGTGGAGAAATAGATCTTTTGGGT
 | |   |    || | | |   | |     || ||  | | ||    | | ||   |    ||||||  |  || ||    | |   |  | | | | |||||| |||||||||||  ||||||| |||| ||| || || || || ||||| || |||||||| |||||  ||||||| |||||||||||||| ||||| |
-actttttctctaagaggcagtgcatagaatatgtgcgggctcagtttttttgtt--gtcacattatggttaatgacttttgtttttttggttttaatttcagAGTTTGAAGCACAATTCTAATGGAAGGTCTGTTGTTGTTTGTGGGGATGGGGAATACATAATATACACATCTTTGGCATGGAGAAATAGATCATTTGGCT

upper sequence: AT3G15980.2 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: PP1S61_1V6.1 (Physcomitrella patens), 3'ss of exon 11
taatagatgataaaaatgaaactctgtttcatatgaagtcc---caagagtgtggtccagaataattatgtcttgcctcacatatagctattctaactctcagAGCTTGAAGCACAACCCTAATGGGAGGTTTGTCGTAGTCTGCGGTGATGGAGAGTACATAATCTACACTGCTTTGGCGTGGAGAAATAGATCTTTTGGGT
    || || |  |  || |||   ||   |  |   |||    |  ||     ||| |  |||| |||   | |       | |   | |  |      ||||||||| |||| || |||||||| || ||||| || || |||||||||||||||||||| || || |||||  |||| ||||| || ||||||||||| |
---gaggtgcttgaggtgtaacctggtcataattattgtctgtgcttgaaacatgtcaattataaatattcatggatgtgtgtgtttgtgtcttgttgtgcagAGCTTGGAGCATAATCCTAATGGCAGATTTGTGGTCGTATGCGGTGATGGAGAGTACATTATTTATACTGCCCTGGCATGGAGGAACAGATCTTTTGGCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agtgtggtccagaataattatgtcttgcctcacatatagctattctaactctcagAGCTTGAAGCACAACCCTAATGGGAGGTTTGTCGTAGTCTGCGGTGATGGAGAGTACATAATCTACACTGCTTTGGCGTGGAGAAATAGATCTTTTGGGT
                                          ttctaac  putative branch site (score: 1)
                                       ctattct  CT-rich tract
            aataattatgtctt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
taatagatgataaaaatgaaactctgtttcatatgaagtcccaagagtgtggtccagaataattatgtcttgcctcacatatagctattctaactctcagAGCTTGAAGCACAACCCTAATGGGAGGTTTGTCGTAGTCTGCGGTGATGGAGAGTACATAATCTACACTGCTTTGGCGTGGAGAAATAGATCTTTTGGGT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAA
- - - - -ataaaaa
- - - - - - - - - aaactct
- - - - - - - - - - - - - - - - - - - -cccaaga
- - - - - - - - - - - - - - - - - - - - - - - - - - - -agaataa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - acatata