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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CAGAACTCACTTTGGAGGTGGTAAATCTTCTGGATATGGTTTGATCTATGATACTGTCGAGAACGCTAAGAAGTTTGAGCCTAAGTACAGACTTATCAGGgtaatttctctttacttgtttgatagttaagtaaaacttttggttctagtttttagtctagcttactcttggtgctttgattttcactgctttgcgatgaaacaatggtgttgcaatctcatactgaaatgattgttgatgtgattgacag

Basic information

species Arabidopsis thaliana
transcript AT5G28060.1
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G28060.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: GLYMA19G43190.1 (Glycine max), 5'ss of exon 3
CAGAACTCACTTTGGAGGTGGTAAATCTTCTGGATATGGTTTGATCTATGATACTGTCGAGAACGCTAAGAAGTTTGAGCCTAAGTACAGACTTATCAGGgtaatttctctttacttgtttgatagttaagtaaaacttttggttctagtttttagtctagcttactct-tggtgctttgattttcactgctttgcgatgaaacaatggtgttgcaatctcatactgaaatgattgttgatgtgattgacag
| |||| || ||||||||||| |||||  |||||| ||||||||| |||||||| || ||||| || ||||||| |||||| || ||||| ||||||||||| | |   |   | |      |    |   |     ||||  ||  | | |  | ||    ||  | | ||||  || |||||| || |   |||  |    |  ||                                            
CCGAACACATTTTGGAGGTGGCAAATCCACTGGATTTGGTTTGATTTATGATACAGTGGAGAATGCCAAGAAGTATGAGCCCAAATACAGGCTTATCAGGgtcagtcaaca--attaacacaacctctgcttg---tttttttttacaatctgaaatcacatttgttttatggtatttagatttttacagtcctgcact----ccttgc-------------------------------------------

upper sequence: AT5G28060.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: GLYMA10G30200.1 (Glycine max), 5'ss of exon 3
CAGAACTCACTTTGGAGGTGGTAAATCTTCTGGATATGGTTTGATCTATGATACTGTCGAGAACGCTAAGAAGTTTGAGCCTAAGTACAGACTTATCAGGgtaatttctctttacttgtttgatagttaagtaaaacttttggttctagtttttagtctagcttactcttggtgctttgattttcactgctttgcgatgaaacaatggtgttgcaatctcatactgaaatgattgttgatgtgattgacag
| ||||||| ||||| ||||| || ||  |||| | |||||||||||||||| | || ||||| |||||||||| ||||||||| ||||| ||||||||||| | |||  |  |  | | ||   || ||       || |  || || |||||    | ||||  | |   ||||||  |||| | |  |    | |      ||    ||                                       
CCGAACTCATTTTGGTGGTGGCAAGTCCACTGGGTTTGGTTTGATCTATGATTCAGTTGAGAATGCTAAGAAGTATGAGCCTAAATACAGGCTTATCAGGgtgagttcattaaatctttctgt--gtcaa-------ttgtcattataattttt---ttggctttgtttgaatgctttttttttta-tattagatggtctgtttataaattta--------------------------------------

upper sequence: AT5G28060.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: GLYMA20G37190.1 (Glycine max), 5'ss of exon 3
CAGAACTCACTTTGGAGGTGGTAAATCTTCTGGATATGGTTTGATCTATGATACTGTCGAGAACGCTAAGAAGTTTGAGCCTAAGTACAGACTTATCAGGgtaatttctctttacttgtttgatagttaagtaaaacttttggttctagtttttagtctagcttactcttggtgctttgattttcactgctttgcgatgaaacaatggtgttgcaatctcatactgaaatgattgttgatgtgattgacag
  ||||||| ||||| ||||| || ||  |||| | |||||||||||||||| | || ||||| || |||||||  |||||||||||||| ||||||||||| | || | |  |  | | ||   || || ||  | | |   || |    |||    ||   | |  ||  |  ||| | ||  || |  |    || ||| |||                                             
TCGAACTCATTTTGGTGGTGGCAAGTCCACTGGGTTTGGTTTGATCTATGATTCAGTTGAGAATGCCAAGAAGTACGAGCCTAAGTACAGGCTTATCAGGgtgagttatttaaatctttctgt--gtcaattatgattataatttttcccctttg--ttaaaatgccttt--tttttttaattagacgggctgtttat-aaataata--------------------------------------------

upper sequence: AT5G28060.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: GLYMA03G40530.1 (Glycine max), 5'ss of exon 3
CAGAACTCACTTTGGAGGTGGTAAATCTTCTGGATATGGTTTGATCTATGATACTGTCGAGAACGCTAAGAAGTTTGAGCCTAAGTACAGACTTATCAGGgtaatttctctttacttgtttgatagttaagtaaaacttttggttctagtttttagtctagcttactct-tggtgctttgattttcactgctttgcgatgaaacaatggtgttgcaatctcatactgaaatgattgttgatgtgattgacag
| |||| || ||||||||||| |||||  |||||| ||||||||| ||||| ||  | || || ||||| |||| |||||| || ||||| ||||||||||| | |   |  |  ||      |  |    | ||| ||||| || || | |  | ||     |  | | |||| |||||||||| || |   |||  |                                                     
CCGAACACATTTTGGAGGTGGCAAATCCACTGGATTTGGTTTGATTTATGACACAATGGAAAATGCTAAAAAGTATGAGCCCAAATACAGGCTTATCAGGgtgagtcaacaattattacaacctc-tgcttttaaatttttgtttataatctgaaatcacttctgttttatggtactttgatttttacagtgctgcattcc---------------------------------------------------

upper sequence: AT5G28060.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: Vv14s0030g01620.t01 (Vitis vinifera), 5'ss of exon 3
CAGAACTCACTTTGGAGGTGGTAAATCTTCTGGATATGGTTTGATCTATGATACTGTCGAGAACGCTAAGAAGTTTGAGCCTAAGTACAGACTTATCAGGgtaatttct------ctttacttgtttgatagttaagtaaaacttttggttctagtttttagtctagct-tac-tcttggtgctttgattttcactgctttgcgatgaaacaatggtgttgcaatctcatactgaaatgattgttgatgtgattgacag
| | ||||||||||||||||| || ||| |||||| ||||||||| |||||| | || ||||| || |||||||  |||||||||||||| || |||||||||| || |      || |  || |    |  ||   | || | |   | | |  | | ||     | | | | | || ||  || |||  ||  |  ||                                                           
CCGGACTCACTTTGGAGGTGGGAAGTCTACTGGATTTGGTTTGATTTATGATTCAGTTGAGAATGCGAAGAAGTACGAGCCTAAGTACAGGCTCATCAGGgtaaattatataaatctctttttctcatttgatttcatcaagcatcaagctattctgtatatgagggttgtgcgtttttgtatttagatgatctttattt-----------------------------------------------------------

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|124939744|gb|EL016259.1|EL016259
EST:     ATACTGTCGAGAACGCTAAGAAGTTTGAGCCTAAGTACAGACTTATCAGG                         AATGGACTTGACACCAAGATTGAGAAATCAAGGAAA
genomic: ATACTGTCGAGAACGCTAAGAAGTTTGAGCCTAAGTACAGACTTATCAGGgtaatttctc ... tgattgacagAATGGACTTGACACCAAGATTGAGAAATCAAGGAAA
EST: gi|125280798|gb|EL294883.1|EL294883
EST:     ATACTGTCGAGAACGCTAAGAAGTTTGAGCCTAAGTACAGACTTATCAGG                         AATGGACTTGACACCAAGATTG
genomic: ATACTGTCGAGAACGCTAAGAAGTTTGAGCCTAAGTACAGACTTATCAGGgtaatttctc ... tgattgacagAATGGACTTGACACCAAGATTG
EST: gi|124877461|gb|EH956898.1|EH956898
EST:     TCGAGAACGCTAAGAAGTTTGAGCCTAAGTACAGGCTTATCAGG                         AATGGACTTGACACCAAGATTGAGAAAT
genomic: TCGAGAACGCTAAGAAGTTTGAGCCTAAGTACAGACTTATCAGGgtaatttctc ... tgattgacagAATGGACTTGACACCAAGATTGAGAAAT
EST: gi|124905973|gb|EH980053.1|EH980053
EST:     ATACTGTCGAGAACGCTAAGAAGTTTGAGCCTAAGTACAGACTTATCAGG                         AATGGACTTGACACCAAGATTGAGAAA
genomic: ATACTGTCGAGAACGCTAAGAAGTTTGAGCCTAAGTACAGACTTATCAGGgtaatttctc ... tgattgacagAATGGACTTGACACCAAGATTGAGAAA
EST: gi|125304289|gb|EL318374.1|EL318374
EST:     CCTAAGTACAGACTTATCAGG                         AGTGGACTTGACACCAAGATTGAGAAATCAAGGAAACAGATCAAGGAGAGG
genomic: CCTAAGTACAGACTTATCAGGgtaatttctc ... tgattgacagAATGGACTTGACACCAAGATTGAGAAATCAAGGAAACAGATCAAGGAGAGG
EST: gi|86084565|gb|DR380324.1|DR380324
EST:     ATACTGTCGAGAACGCTAAGAAGTTTGAGCCTAAGTACAGACTTATCAGG                         AATGGACTTGACACCAAGATTGAGAAATCAAGGAAACAGATCAAGGAGAGG
genomic: ATACTGTCGAGAACGCTAAGAAGTTTGAGCCTAAGTACAGACTTATCAGGgtaatttctc ... tgattgacagAATGGACTTGACACCAAGATTGAGAAATCAAGGAAACAGATCAAGGAGAGG
EST: gi|86078425|gb|DR374182.1|DR374182
EST:     ATACTGTCGAGAACGCTAAGAAGTTTGAGCCTAAGTACAGACTTATCAGG                         AATGGACTTGACACCAAGATTGAGAAATCAAGGAAACAGATCAAGGAGAGG
genomic: ATACTGTCGAGAACGCTAAGAAGTTTGAGCCTAAGTACAGACTTATCAGGgtaatttctc ... tgattgacagAATGGACTTGACACCAAGATTGAGAAATCAAGGAAACAGATCAAGGAGAGG
EST: gi|125166852|gb|EL192450.1|EL192450
EST:     AACGCTAAGAAGTTTGAGCCTAAGTACAGACTTATCAGG                         AATGGACTTGACACCAAGATTGAGAAATCAAAGGAAACAGATCAAGGAGAG
genomic: AACGCTAAGAAGTTTGAGCCTAAGTACAGACTTATCAGGgtaatttctc ... tgattgacagAATGGACTTGACACCAAGATTGAGAAATCAA-GGAAACAGATCAAGGAGAG
EST: gi|86081226|gb|DR376983.1|DR376983
EST:     ATACTGTCGAGAACGCTAAGAAGTTTGAGCCTAAGTACAGACTTATCAGG                         AATGGACTTGACACCAAGATTGAGAAATCAAGGAAACAGATCAAGGAGAGG
genomic: ATACTGTCGAGAACGCTAAGAAGTTTGAGCCTAAGTACAGACTTATCAGGgtaatttctc ... tgattgacagAATGGACTTGACACCAAGATTGAGAAATCAAGGAAACAGATCAAGGAGAGG
EST: gi|125193763|gb|EL208717.1|EL208717
EST:     AACGCTAAGAAGTTTGAGCCTAAGTACAGACTTATCAGG                         AATGGACTTGACACCAAGATTGAGAAATCAAGGAAACAGATCAAGGAG
genomic: AACGCTAAGAAGTTTGAGCCTAAGTACAGACTTATCAGGgtaatttctc ... tgattgacagAATGGACTTGACACCAAGATTGAGAAATCAAGGAAACAGATCAAGGAG
EST: gi|125197851|gb|EL212805.1|EL212805
EST:     TACAGACTTATCAGG                         AATGGACTTGACACCAAGATTGAGAAATCAAGGAAACAGATCAAGGAGAGG
genomic: TACAGACTTATCAGGgtaatttctc ... tgattgacagAATGGACTTGACACCAAGATTGAGAAATCAAGGAAACAGATCAAGGAGAGG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CAGAACTCACTTTGGAGGTGGTAAATCTTCTGGATATGGTTTGATCTATGATACTGTCGAGAACGCTAAGAAGTTTGAGCCTAAGTACAGACTTATCAGGgtaatttctctttacttgtttgatagttaagtaaaacttttggttctagtttttagtctagcttactcttggtgctttgattttcactgctttgcgatgaaacaatggtgttgcaatctcatactgaaatgattgttgatgtgattgacag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT