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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaaacacttaatgtccatgtctcgtagactaatgaactctagttgaagacttatctgtattgtatgtttaacgatggcaaacaaaattttgttctgcagTATCCTCCTTGTTACAAGGACATCAGTTTCTGGATAAGTGATTTGTTCACAGAGAATAATTTTTGTGAAGTTGTTAGAGGAATTGCTGGGGATCTTGTTG

Basic information

species Arabidopsis thaliana
transcript AT3G58140.1
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G58140.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: LOC_Os12g34860.1 (Oryza sativa), 3'ss of exon 7
--gtaaaacacttaatgtccatgtctcgtagactaatgaactctagttgaagacttatctgtattgtatgtttaacgatggcaaacaaaattttgttctgcagTATCCTCCTTGTTACAAGGACATCAGTTTCTGGATAAGTGATTTGTTCACAGAGAATAATTTTTGTGAAGTTGTTAGAGGAATTGCTGGGGATCTTGTTG
  | |  |  | ||    |||    |  |  ||   |  | | | ||  |  | ||  |    |   |  |||  |  |           |  |||||| |||| ||| ||||| |||||||| || ||||| ||||| | |||   ||| |||||||| ||||| ||||| ||||| |||||||||||||| |||||||| |
ttgcatcaagcatatccaccaataattttttacatgtttatttttgtatataaattgccc---tctgacttttttcccttttcctttttctgctgttctacagTTTCCACCTTGCTACAAGGATATGAGTTTTTGGATCAATGAAGAGTTTACAGAGAACAATTTATGTGAGGTTGTCAGAGGAATTGCTGGAGATCTTGTAG

upper sequence: AT3G58140.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: AC211349.4_FGT001 (Zea mays), 3'ss of exon 7
gtaaaacacttaatgtccatgtctcgtagactaatgaac------tctagttgaaga-------cttatct--gtattg--tatgtttaacgatggcaaacaaaattttgttctgcagTATCCTCCTTGTTACAAGGACATCAGTTTCTGGATAAGTGATTTGTTCACAGAGAATAATTTTTGTGAAGTTGTTAGAGGAATTGCTGGGGATCTTGTTG
||| ||  ||  ||||   |||||| ||   ||||| ||      | |  ||||  |        | ||||  || | |  |||| | |  ||  |   |  |   ||  || |  ||| |||||||||||||||||| || ||||||||||| | ||||   || |||||||| || || ||||| ||||| |||||||||||||| ||||||||||
gtataat-ctctatgtttctgtctcttat-ttaatgtacacttcatttttttgagaaaatagtcttcatcttggtgtcgattatgctcactgacagtttatcactattgtttgtttagTTTCCTCCTTGTTACAAGGATATGAGTTTCTGGATCAATGATGCATTTACAGAGAACAACTTATGTGAGGTTGTCAGAGGAATTGCTGGTGATCTTGTTG

upper sequence: AT3G58140.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA02G10060.1 (Glycine max), 3'ss of exon 7
gtaaaacacttaatgtccatgtctcgtagactaatgaactctagttgaa--gacttatctgtattgtat-gtttaacgatggcaaac--aaaattttgttctgcagTATCCTCCTTGTTACAAGGACATCAGTTTCTGGATAAGTGATTTGTTCACAGAGAATAATTTTTGTGAAGTTGTTAGAGGAATTGCTGGGGATCTTGTTG
     |   | | | |  |  ||| |  || |    |  | || || |   |||  ||   ||   | | ||   |  ||   ||        |||   | |||||||||||||||||||||||||||| ||||||||||| ||||| |  || || || || ||| | |||||||||||||||||||| || ||||||||||| |
-----attttgagtcttga-atcttgaggaatttatatttttatttcagtggacacattcctaaaatcttgtgagaacattctaattttggtgtttgcctttgcagTATCCTCCTTGTTACAAGGACATGAGTTTCTGGATCAGTGAATCATTTACTGAAAACAATCTGTGTGAAGTTGTTAGAGGAATAGCCGGGGATCTTGTAG

upper sequence: AT3G58140.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA18G52890.1 (Glycine max), 3'ss of exon 9
gtaaaacacttaatgtccatgtctcgtagactaatgaactctagttgaagacttatctgtattgtatgtttaacgatggcaaacaaaattttgt-------tctgcagTATCCTCCTTGTTACAAGGACATCAGTTTCTGGATAAGTGATTTGTTCACAGAGAATAATTTTTGTGAAGTTGTTAGAGGAATTGCTGGGGATCTTGTTG
      |  || || |  | |||| | |   | | ||| ||||  |    | ||   || |    | || |   ||  |||  | || ||||||       | |||||||||||||||||||||||||||| ||||||||||| | ||| |  ||||| || || ||| | |||||||||||||||||||| || ||||||||||| |
----tgctattcattttga-gtcttgaatcttgaggaa-tctatatttttatttcagtggac-aca-gtcttgtgagagcattctaatttttgtgtttgcctttgcagTATCCTCCTTGTTACAAGGACATGAGTTTCTGGATCAATGAATCATTCACCGAAAACAATCTGTGTGAAGTTGTTAGAGGAATAGCCGGGGATCTTGTCG

upper sequence: AT3G58140.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: Vv19s0027g01200.t01 (Vitis vinifera), 3'ss of exon 7
gtaaaacacttaatgtccatgtctcgtagactaatgaactctagttga-agacttatctgta---ttgtatgtttaacgatggcaaacaa--aattttgttctgcagTATCCTCCTTGTTACAAGGACATCAGTTTCTGGATAAGTGATTTGTTCACAGAGAATAATTTTTGTGAAGTTGTTAGAGGAATTGCTGGGGATCTTGTTG
       | | | |   ||   |      |||||  |  | ||  ||  |||      ||||   || | | ||    | | | ||   |  | | |  || |||||||||||||||||||||||| ||| ||||| ||||| | ||| | ||||||||| || ||||| ||||| ||||| |||||| ||||||| ||| ||||  
-------attaattacacacaacataataactaaatatttatacctgttagagccccttgtaaccttctctattggctgctagaaactgactattgtctttttgcagTATCCTCCTTGTTACAAGGGCATGAGTTTTTGGATTAATGAGTCGTTCACAGAAAACAATTTATGTGAGGTTGTAAGAGGAGTTGCTGGAGATTTTGTCC

upper sequence: AT3G58140.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: Vv11s0103g00120.t01 (Vitis vinifera), 3'ss of exon 7
gtaaaacacttaatgtccatgtctcgtagactaatgaactctagttgaagacttatctgtattgtatgtttaacgatggcaaacaaaattttgt---tctgcagTATCCTCCTTGTTACAAGGACATCAGTTTCTGGATAAGTGATTTGTTCACAGAGAATAATTTTTGTGAAGTTGTTAGAGGAATTGCTGGGGATCTTGTTG
    |  |||||    | || |       |   ||  |  |  |||  || |  || |    |      ||  |      ||||  | | ||||   | ||||||||||||||||||| |||||||| ||||| ||||| | ||| |  |||||||| || ||||| ||||| |||||||||||| ||||||| |||||||| |
----attacttacacacaatataataactaagtatttatacctgttagagccccatgtaaccttctctattggctgctagaaactgactattgtctttttgcagTATCCTCCTTGTTATAAGGACATGAGTTTTTGGATTAATGAGTCATTCACAGAAAACAATTTATGTGAGGTTGTTAGAGGAGTTGCTGGAGATCTTGTCG

upper sequence: AT3G58140.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: Vv19s0027g01480.t01 (Vitis vinifera), 3'ss of exon 2
-------gtaaaacacttaatgtccatgtctcgtagactaatgaactctagttgaagacttatctgtattgtatgtttaacgatggcaaacaaaattttgttctgcagTATCCTCCTTGTTACAAGGACATCAGTTTCTGGATAAGTGATTTGTTCACAGAGAATAATTTTTGTGAAGTTGTTAGAGGAATTGCTGGGGATCTTGTTG
         | |  || ||||  | |  | |      ||  |  |  | | |  ||      ||| |||||  || |  |   || | | |      |  || |||||||||||||||||||||||||||  ||||| ||||| | ||| ||||||||||| || ||||| ||||| ||||| |||||| ||||||| |||||||| |
attaattacacacaacataataactaaatatttatacctgttagagcccaatgtaa---ccttctctattggctgctagaaactgactatcg-----tctttttgcagTATCCTCCTTGTTACAAGGACAAGAGTTTTTGGATTAATGAGTTGTTCACAGAAAACAATTTATGTGATGTTGTAAGAGGAGTTGCTGGAGATCTTGTCG

upper sequence: AT3G58140.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: Vv19s0027g01150.t01 (Vitis vinifera), 3'ss of exon 8
-------gtaaaacacttaatgtccatgtctcgtagactaatgaactctagttgaagacttatctgtattgtatgtttaacgatggcaaacaaaattttgttctgcagTATCCTCCTTGTTACAAGGACATCAGTTTCTGGATAAGTGATTTGTTCACAGAGAATAATTTTTGTGAAGTTGTTAGAGGAATTGCTGGGGATCTTGTTG
         | |  || ||||  | |  | |  || ||   | |   |   ||| |  |||  || |||||  || |  |   || | | |      |  || |||||||||||||| ||||||||||||| ||||| ||||| | ||| | ||||||||| || ||||| ||||| ||| | |||||| ||||||| ||        
attaattacacacaacataataactaaatatt-tatacctgttagagccccttgtaacctt--ctctattggctgctagaaactgactatcg-----tctttttgcagTATCCTCCTCGTTACAAGGACATGAGTTTTTGGATTAATGAGTCGTTCACAGAAAACAATTTATGTGAGGTTATAAGAGGAGTTGCTGGAGA--------

upper sequence: AT3G58140.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: EFJ33041 (Selaginella moellendorffii), 3'ss of exon 7
gtaaaacacttaatgtccatgtctcgtagactaatgaactctagttgaagacttatctgtattgtatgtttaacgatggcaaacaaaattttgttctg-cagTATCCTCCTTGTTACAAGGACATCAGTTTCTGGATAAGTGATTTGTTCACAGAGAATAATTTTTGTGAAGTTGTTAGAGGAATTGCTGGGGATCTTGTTG
                                                       |  |   |    | |      |   ||      || || | || ||||||||||| |||||||||||||| || |||||||| |  |||   ||||| ||||| ||  | || ||  | || ||||   | ||||| ||  |||  |
------------------------------------------------------gtacgccatacgcgctcgcttcttctaactttcgttctggtttggcagTATCCTCCCTGTTACAAGGACATAAGCTTCTGGATTACCGATGCTTTCACGGAGAACAACCTGTGCGAGCTCGTCAGAGATGTCGCTGGTGACATTGCCG

Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|124750940|gb|EH841070.1|EH841070
EST:     GGAGTGAAATTCAAGCCATATTCAAAG                         TATCCTCCTTGTTACAAGGACATCAGTTTCTGGATAAGTGATTTGTT
genomic: GGAGTGAAATTCAAGCCATATTCAAAGgtaaaacact ... tgttctgcagTATCCTCCTTGTTACAAGGACATCAGTTTCTGGATAAGTGATTTGTT
EST: gi|124732314|gb|EH823716.1|EH823716
EST:     CCCAGTTTGGAAAAGGAGAACTTGGAGTGAAATTCAAGCCATATTCAAAG                         TATCCTCCTTGTTACAAGGACATCAGTTTCTGGATAAGTGATTTGTTCACA
genomic: CCCAGTTTGGAAAAGGAGAACTTGGAGTGAAATTCAAGCCATATTCAAAGgtaaaacact ... tgttctgcagTATCCTCCTTGTTACAAGGACATCAGTTTCTGGATAAGTGATTTGTTCACA
EST: gi|116411244|gb|EG453836.1|EG453836
EST:     TTTGGAAAAGGAGAACTTGGAGTGAAATTCAAGCCATATTCAAAG                         TATCCTCCTTGTTACAAGGACATCAGTTTCTGGATAAGTGATTTGTTCACA
genomic: TTTGGAAAAGGAGAACTTGGAGTGAAATTCAAGCCATATTCAAAGgtaaaacact ... tgttctgcagTATCCTCCTTGTTACAAGGACATCAGTTTCTGGATAAGTGATTTGTTCACA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gaagacttatctgtattgtatgtttaacgatggcaaacaaaattttgttctgcagTATCCTCCTTGTTACAAGGACATCAGTTTCTGGATAAGTGATTTGTTCACAGAGAATAATTTTTGTGAAGTTGTTAGAGGAATTGCTGGGGATCTTGTTG
                     gtttaac  putative branch site (score: 3)
                                          ttttgttct  putative PPT
                                  aaacaaaattttgtt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaaacacttaatgtccatgtctcgtagactaatgaactctagttgaagacttatctgtattgtatgtttaacgatggcaaacaaaattttgttctgcagTATCCTCCTTGTTACAAGGACATCAGTTTCTGGATAAGTGATTTGTTCACAGAGAATAATTTTTGTGAAGTTGTTAGAGGAATTGCTGGGGATCTTGTTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA