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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTCACACACTTGTACTGCTGGAGCATTTGGTCAATTTGCTACAGGGATTGGAAACACTGATGCAGGTTTTGTGTTAGGCACTGGAAAAATCCTCCTTAAGgtttgtagaatagctgattcctttgattctctatgatatagttttattcagtgtgttaaatggaaatcagtgatgcctgtttcaacttgaaaaaggcttgttagaatagtttccccctctccaaattatactgtagtgtctgaagctcatatcctgacttcgcag

Basic information

species Arabidopsis thaliana
transcript AT4G13430.1
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT4G13430.1 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: LOC_Os02g03260.1 (Oryza sativa), 5'ss of exon 5
CTCACACACTTGTACTGCTGGAGCATTTGGTCAATTTGCTACAGGGATTGGAAACACTGATGCAGGTTTTGTGTTAGGCACTGGAAAAATCCTCCTTAAGgtttgtagaatagctgattcctttgattctctatgatatagttttattcagtgtgttaaatggaaatcagtgatgcctgtttcaacttgaaaaaggcttgttagaatagtttccccctctccaaattatactgtagtgtctgaagctcatatcctgacttcgcag
 || || || || | ||||||||| ||||| |||||||| || || ||||||||||||||||| ||||||||| | |||||||| ||    || |||||||| |||||||       |||   | | ||  |||   ||    | |   |      |  || | ||  |||| | |   | |    | |  |   | |  |  ||||  | |                                                     
TTCTCATACATGCAATGCTGGAGCCTTTGGCCAATTTGCAACTGGAATTGGAAACACTGATGCTGGTTTTGTGATGGGCACTGGGAAGGCTCTTCTTAAGgtatgtagaa-----agttctgattactccgtatcgaat----tcaaatatcagccttgatagtaaaaagtggttcagatattggttagtga---gttcatctgaatgatgt-----------------------------------------------------

upper sequence: AT4G13430.1 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: GRMZM2G370852_T02 (Zea mays), 5'ss of exon 5
-----CTCACACACTTGTACTGCTGGAGCATTTGGTCAATTTGCTACAGGGATTGGAAACACTGATGCAGGTTTTGTGTTAGGCACTGGAAAAATCCTCCTTAAGgtttg--tagaatagctgattcctttgattctct-atgatatagtttta--ttcagtgtgttaaatggaaatcagtgatgcctgtttcaacttgaaaaaggcttgttagaatagtttccccctctccaaattatactgtagtgtctgaagctcatatcctgacttcgcag
      || || || || | ||||||||| |||||||||||||| || || ||||||||||||||||||||||||||| | |||||||||||    || || |||||  |   |   | | || ||  | | | ||||  | |  | | |||||    |||| |  ||      |  || || |    | | | || |||                                                                           
ACTGATTCTCATACGTGCAATGCTGGAGCCTTTGGTCAATTTGCAACCGGAATTGGAAACACTGATGCAGGTTTTGTGATGGGCACTGGAAAGGCTCTTCtcaaggtacgcccatggttgttggttgttgttactctcggaaggcaaaattttaaaaccagtcttatagggcatacccaatggtagaggctcccacatga---------------------------------------------------------------------------

upper sequence: AT4G13430.1 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: GRMZM2G370852_T01 (Zea mays), 5'ss of exon 5
CTCACACACTTGTACTGCTGGAGCATTTGGTCAATTTGCTACAGGGATTGGAAACACTGATGCAGGTTTTGTGTTAGGCACTGGAAAAATCCTCCTTAAGgtttgt--agaatagctgattcctttgattctct-atgatatagttttat--tcagtgtgttaaatggaaatcagtgatgcctgtttcaacttgaaaaaggcttgttagaatagtttccccctctccaaattatactgtagtgtctgaagctcatatcctgacttcgcag
 || || || || | ||||||||| |||||||||||||| || || ||||||||||||||||||||||||||| | |||||||||||    || || |||||  |   |   | | || ||  | | | ||||  | |  | | |||||    |||| |  ||      |  || || |    | | | || ||||  ||                                                                      
TTCTCATACGTGCAATGCTGGAGCCTTTGGTCAATTTGCAACCGGAATTGGAAACACTGATGCAGGTTTTGTGATGGGCACTGGAAAGGCTCTTCTCAAGgtacgcccatggttgttggttgttgttactctcggaaggcaaaattttaaaaccagtcttatagggcatacccaatggtagaggctcccacatgaatgag----------------------------------------------------------------------

upper sequence: AT4G13430.1 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: GRMZM2G010044_T02 (Zea mays), 5'ss of exon 5
CTCACACACTTGTACTGCTGGAGCATTTGGTCAATTTGCTACAGGGATTGGAAACACTGATGCAGGTTTTGTGTTAGGCACTGGAAAAATCCTCCTTAAGgtttgtagaatagctgattcctttgattctctatgatatagttttattcagtgtgttaaatggaaatcagtgatgcctgtttcaacttgaaaaaggcttgttagaatagtttccccctctccaaattatactgtagtgtctgaagctcatatcctgacttcgcag
 || || || || | ||||||||| |||||||| ||||| || || || |||||||||||||||||||||||||| |||||||||||    || || ||||| ||   |     || ||| | |  ||||  |  | |||  |||               || ||| ||||        || ||     ||||| |   |  | ||  ||       | | |||| |                                      
TTCTCATACATGCAATGCTGGAGCTTTTGGTCAGTTTGCAACTGGAATCGGAAACACTGATGCAGGTTTTGTGTTGGGCACTGGAAAGGCTCTTCTCAAGgtatgccca-----tggttcttgttgttcta-agaagataaattt---------------tgaaaaccagtc-------ttacagaaccaaaaaaggaagagaaaagggtcagggtatatgcaaactg-------------------------------------

upper sequence: AT4G13430.1 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: GLYMA14G40570.1 (Glycine max), 5'ss of exon 6
CTCACACACTTGTACTGCTGGAGCATTTGGTCAATTTGCTACAGGGATTGGAAACACTGATGCAGGTTTTGTGTTAGGCACTGGAAAAATCCTCCTTAAGgtttgtagaatagctgattcctttgattctctatgatatagttttattcagtgtgttaaatggaaatcagtgatgcctgtttcaacttgaaaaaggcttgttagaatagtttccccctctccaaattatactgtagtgtctgaagctcatatcctgacttcgcag
 || ||||||||||||||||||||||||||||||||||||||||||||||| || |||||||| || |||||| | || ||||| ||| | || || |||||         || |  | |    ||| |  | | |  |  |     ||||    |     |  ||  || ||  ||| | |  | |||     |  | | |    |   |                                                      
TTCTCACACTTGTACTGCTGGAGCATTTGGTCAATTTGCTACAGGGATTGGTAATACTGATGCCGGCTTTGTGCTGGGAACTGGGAAACTTCTGCTCAAGgt---------agtttctgctcaagatccattctaacttgatacc-ctcagaagatagggagagaaggagagagacctctctttaattgttgggg--tcgctgatcttactg-----------------------------------------------------

upper sequence: AT4G13430.1 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: GLYMA17G37540.1 (Glycine max), 5'ss of exon 6
-CTCACACACTTGTACTGCTGGAGCATTTGGTCAATTTGCTACAGGGATTGGAAACACTGATGCAGGTTTTGTGTTAGGCACTGGAAAAATCCTCCTTAAGgtttgtagaatagctgattcctttgattctctatgatatagttttattcagtgtgttaaatggaaatcagtgatgcctgtttcaacttgaaaaaggcttgttagaatagtttccccctctccaaattatactgtagtgtctgaagctcatatcctgacttcgcag
  || |||||||||||||||||||||||||| |||||||||||||||||||| || |||||||| || |||||| | || ||||| ||| | || ||||||||             | |||   | |    | ||  | ||  || |       |   | |    |  ||  ||| ||      |  | |  | ||       |||  |   || |                                                  
ATTCTCACACTTGTACTGCTGGAGCATTTGGCCAATTTGCTACAGGGATTGGTAATACTGATGCTGGCTTTGTGCTGGGAACTGGGAAACTTCTGCTTAAggta------------gtttctgctaaaggcccat--tctaacttgagggttccttccagaaaccagccatagataccctcagtagatagggagaga---aggagagaaacctctct-------------------------------------------------

upper sequence: AT4G13430.1 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: GLYMA20G34160.1 (Glycine max), 5'ss of exon 6
CTCACACACTTGTACTGCTGGAGCATTTGGTCAATTTGCTACAGGGATTGGAAACACTGATGCAGGTTTTGTGTTAGGCACTGGAAAAATCCTCCTTAAGgtttgtagaatagctgattcctttgattctctatgatatagttttattcagtgtgttaaatggaaatcagtgatgcctgtttcaacttgaaaaaggcttgttagaatagtttccccctctccaaattatactgtagtgtctgaagctcatatcctgacttcgcag
    |||||     | |||||||||||||| || ||||| |||||  |||| ||||||||||||| |||||| ||||| || || || ||| | || ||||   ||| |  |      ||  || |||   | ||| | |    ||   | | |  |  ||| |    |    |     | |   | |  |       ||  ||  || | ||   ||  |||                                          
----CACACCACATCAGCTGGAGCATTTGGCCAGTTTGCCACAGGAGTTGGTAACACTGATGCAGCTTTTGTATTAGGGACAGGGAAGATCTTACTCAAGGCAAgtaaacaaatatcatcactttattaaatgtgaaaaacaccta---aattttattgatgaaggctaagacttttcatcttgccctacattcaagatgaaagttta-tatctttcttcccag-----------------------------------------

upper sequence: AT4G13430.1 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: Vv05s0049g01980.t01 (Vitis vinifera), 5'ss of exon 6
CTCACACACTTGTACTGCTGGAGCATTTGGTCAATTTGCTACAGGGATTGGAAACACTGATGCAGGTTTTGTGTTAGGCACTGGAAAAATCCTCCTTAAGgtttgtagaatagctgattcctttgattctctatgatatagttttattcagtgtgttaaatgg-aaatcagtg-atgcctgtttcaacttgaaaaaggcttgttagaatagtttccccctctccaaattatactgtagtgtctgaagctcatatcctgacttcgcag
||| ||||| ||||||||||| |||||||| || || ||||| || || || ||||||||||| | ||| || |||||||||||||| ||||| || |||||||| |    |  || ||  | |   || |||   | | | |   |||      | ||||    | |  |||  ||  |  |  ||||   | |   ||||||                                                               
CTCCCACACATGTACTGCTGGGGCATTTGGCCAGTTCGCTACTGGAATAGGTAACACTGATGCTGCTTTCGTATTAGGCACTGGAAAGATCCTGCTGAAGgtttgca----aattgttttttatatctccctactcttttgatcacttccccccctcaaattttgagtttgtgtgtggatcctgtaactgatagacatcttgtt---------------------------------------------------------------

upper sequence: AT4G13430.1 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: Vv08s0056g01640.t01 (Vitis vinifera), 5'ss of exon 6
CTCACACACTTGTACTGCTGGAGCATTTGGTCAATTTGCTACAGGGATTGGAAACACTGATGCAGGTTTTGTGTTAGGCACTGGAAAAATCCTCCTTAAGgtttgtagaatagctgattcctttgattctcta-tgatatagttttattcagtgtgttaaatggaaatcagtgatgcctgtttcaacttgaaaaaggcttgttagaatagtttccccctctccaaattatactgtagtgtctgaagctcatatcctgacttcgcag
||| ||||| ||||||||||| |||||||| || |||||||| || || || ||||| ||||| |||||||| || ||||||||||| ||||| || ||||||  |  |         || ||||  ||  || || | ||||| | ||       | || | ||  |      ||  ||||  ||||   | |   |||| |                                                               
CTCCCACACATGTACTGCTGGGGCATTTGGCCAGTTTGCTACTGGAATAGGTAACACCGATGCTGGTTTTGTATTGGGCACTGGAAAGATCCTGCTCAAGgttactgaatc------ctcttttgtctccttaatgttttagttatgtttttcccctcaatttgagtttctgtgtggatgttgtaactcatagatatcttggtttt------------------------------------------------------------

upper sequence: AT4G13430.1 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: PP1S227_66V6.1 (Physcomitrella patens), 5'ss of exon 6
CTCACACACTTGTACTGCTGGAGCATTTGGTCAATTTGCTACAGGGATTGGAAACACTGATGCAGGTTTTGTGTTAGGCACTGGAAAAATCCTCCTTAAGgtttgtagaatagctgattcctttgattctctatgatatagttttattcagtgtgttaaatggaaatcagtgatgcctgtttcaacttgaaaaaggcttgttagaatagtttccccctctccaaattatactgtagtgtctgaagctcatatcctgacttcgcag
 || |||||||| | ||||||||| |||||||| ||||| |||||||| || |||||||||||||| ||| |  | ||||| || ||  ||||  |||||||       |||| | |    | ||  ||     ||| |   | | |   ||  |  || |  | |  | |||     |||  |      |   | |  |  | |                                                            
TTCCCACACTTGCAATGCTGGAGCGTTTGGTCAGTTTGCAACAGGGATCGGTAACACTGATGCAGGCTTTATTATGGGCACCGGCAAGCTCCTGATTAAGgtacagttgatagttcaaatttgtggctc-----gatgtgaatatttaaggtagggcaatttcatacgactgacata-gttgtagtggacatttgccacgccacat-----------------------------------------------------------

upper sequence: AT4G13430.1 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: EFJ32611 (Selaginella moellendorffii), 5'ss of exon 5
CTCACACACTTGTACTGCTGGAGCATTTGGTCAATTTGCTACAGGGATTGGAAACACTGATGCAGGTTTTGTGTTAGGCACTGGAAAAATCCTCCTTAAGgtttgtagaatagctgattcctttgattctctatgatatagttttattcagtgtgttaaatggaaatcagtgatgcctgtttcaacttgaaaaaggcttgttagaatagtttccccctctccaaattatactgtagtgtctgaagctcatatcctgacttcgcag
||| || ||||| ||||||||||| ||||| ||||| ||||| || || |||||||| ||||| |||||  |  | || |||||||||||  | || ||||   ||||    |||  || | |   |  |   |  || |   ||    | ||| |                                                                                                             
CTCGCATACTTGCACTGCTGGAGCGTTTGGACAATTCGCTACTGGAATAGGAAACACCGATGCTGGTTTCATCATGGGAACTGGAAAAATTTTACTAAAGgcaagtagg--cgctttttgcatctttgtttcttcttacaagcttcgctactgtctag-----------------------------------------------------------------------------------------------------------

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|125242694|gb|EL256779.1|EL256779
EST:     AAACACTGATTGCAGGTTTTGTGTTAGGCACTGGAAAAATCCTCCTTAAG                         GTTCCACCAACGATGAGGTTTATCTTGGATGGTGAGATG
genomic: AAACACTGA-TGCAGGTTTTGTGTTAGGCACTGGAAAAATCCTCCTTAAGgtttgtagaa ... gacttcgcagGTTCCACCAACGATGAGGTTTATCTTGGATGGTGAGATG
EST: gi|164172976|gb|ES145403.1|ES145403
EST:     GAAACACTGATGCAGGTTTTGTGTTAGGCACTGGAAAAATCCTCCCTAAG                         GTTCCACCAACG
genomic: GAAACACTGATGCAGGTTTTGTGTTAGGCACTGGAAAAATCCTCCTTAAGgtttgtagaa ... gacttcgcagGTTCCACCAACG
EST: gi|125303542|gb|EL317627.1|EL317627
EST:     GGTTTTGTGTTAGGCACTGGAAAAATCCTCCTTAAG                         GTTCCACCAACGATGAGGTTTATCTTGGATGGTGAGATGCCTAGTTATTTG
genomic: GGTTTTGTGTTAGGCACTGGAAAAATCCTCCTTAAGgtttgtagaa ... gacttcgcagGTTCCACCAACGATGAGGTTTATCTTGGATGGTGAGATGCCTAGTTATTTG
EST: gi|124802169|gb|EH891202.1|EH891202
EST:     GAAACACTGATGCAGGTTTTGTGTTAGGCACTGGAAAAATCCTCCTTAAG                         GTTCCACCAACGATGAGGTTTATCTTGGATGGTGAGATGCCTAGTTA
genomic: GAAACACTGATGCAGGTTTTGTGTTAGGCACTGGAAAAATCCTCCTTAAGgtttgtagaa ... gacttcgcagGTTCCACCAACGATGAGGTTTATCTTGGATGGTGAGATGCCTAGTTA