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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCTTACATTGAGAAAGAAGATGGTAAGAAATTGAAGCAAAAGCAACGGGAGAGAATGCAACCAAAAATGGGAAAGATGGACATTGACTACCAGgtttctattttttttaatctttgttttgtgatgagtatttgctgatatctgttctataactgacaagtgaagctattctttcctttctcag

Basic information

species Arabidopsis thaliana
transcript AT4G21660.2
intron # 7
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT4G21660.1 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: LOC_Os02g58090.1 (Oryza sativa), 5'ss of exon 7
GCTTACATTGAGAAAGAAGATGGTAAGAAATTGAAGCAAAAGCAACGGGAGAGAATGCAACCAAAAATGGGAAAGATGGACATTGACTACCAGgtttctattttttttaatctttgttttgtgatgagtatttgctgatatctgt-tctataactgacaagtgaagc--tattctttccttt--ctcag--------
|| || |||||||| || ||| |||| || ||||| |||||||| |||||| | ||||||||||||||||| |||||||| || || || |||||    ||||  |   ||  |     | |   ||  ||||| || ||||    | |||     |||          || |||||||||   ||||         
GCATATATTGAGAAGGAGGATAGTAAAAAGTTGAAACAAAAGCAGCGGGAGCGTATGCAACCAAAAATGGGCAAGATGGATATAGATTATCAGgtaaaaatttactcctattgtc----tatagagatcatttgatggtatcaacatttattgtaaacacacattttcatactctttccttaagctcaagttctaat

upper sequence: AT4G21660.1 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: GLYMA13G31550.2 (Glycine max), 5'ss of exon 7
GCTTACATTGAGAAAGAAGATGGTAAGAAATTGAAGCAAAAGCAACGGGAGAGAATGCAACCAAAAATGGGAAAGATGGACATTGACTACCAGgtttctattttttttaatctttgttttgtgatg-----agtatttgct-gatatctgtt--ctataactg-acaagtgaagctattctttcctttctcag-----------
||||| ||||||||||| ||| |||||||  |||| ||||||||| ||||| | ||||||||||||||||| || ||||| || || || ||||||||  || | |||    || ||||||          | |  ||||| | | | ||||  || ||  |  | || |      || |||   | | |              
GCTTATATTGAGAAAGAGGATAGTAAGAAGCTGAAACAAAAGCAAAGGGAGCGCATGCAACCAAAAATGGGGAAAATGGATATAGATTATCAGgtttcatttgtgtttgcctttggttttgcaccatttgcattgcttgcttggtttttgtttactctagtttcagaactattctcatccttagttctttttattggttgccag

upper sequence: AT4G21660.1 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: GLYMA15G07760.1 (Glycine max), 5'ss of exon 7
GCTTACATTGAGAAAGAAGATGGTAAGAAATTGAAGCAAAAGCAACGGGAGAGAATGCAACCAAAAATGGGAAAGATGGACATTGACTACCAGgtttc---tattttttttaatctttgttttgt---gatgagtatttgctgatatctgttctataactga---caagtgaagctattctttcctttctcag-------
||||| ||||||||||| ||| |||||||  |||| ||||||||| ||||| | ||||||||||||||||| || ||||| || || || ||||||||   | | ||||  |   ||||  |||      ||  | |||| | |     ||   | ||||     ||         ||  ||   |||||  |       
GCTTATATTGAGAAAGAGGATAGTAAGAAGCTGAAACAAAAGCAAAGGGAGCGCATGCAACCAAAAATGGGGAAAATGGATATAGATTATCAGgtttcatttgtgttttgcaccatttgcattgcttgcttggttttttgtttactcaagtgtcagaactattttcatcctttctaatagttctttttcttggttgctag

upper sequence: AT4G21660.1 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: GLYMA13G25110.1 (Glycine max), 5'ss of exon 7
GCTTACATTGAGAAAGAAGATGGTAAGAAATTGAAGCAAAAGCAACGGGAGAGAATGCAACCAAAAATGGGAAAGATGGACATTGACTACCAGgtttc----tattttttttaatctttgttttgtgatgagtat-ttgctgatatctgttctataactgacaagtgaagctattctt-tcctttctcag----------------------
||||| ||||||||||||||  |||| ||  |||||||||||||| | ||  | ||||||||||||||||| || ||||| ||||| || |||||||     ||| |||    ||  | ||||||   |   | | |||||    | | | ||  |      |     | | |||  |  |||||||||                       
GCTTATATTGAGAAAGAAGACAGTAAAAAGCTGAAGCAAAAGCAAAGAGAACGCATGCAACCAAAAATGGGGAAAATGGATATTGATTATCAGgttttattatatctttacctattctagttttgccctctttgtcttgcttgcttttatgctgcattcagaagtcagaacaatttctaccctttctcaagtgactgtttcttggctgctag

upper sequence: AT4G21660.1 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: PP1S98_7V6.1 (Physcomitrella patens), 5'ss of exon 7
GCTTACATTGAGAAAGAAGATGGTAAGAAATTGAAGCAAAAGCAACGGGAGAGAATGCAACCAAAAATGGGAAAGATGGACATTGACTACCAGgtt-tctattttttttaatctttgttttgtgatgagtatttgctgatatctgttctataactgacaagtgaagctattctttcctttctcag----------------------------------------------------------------
|||||||||||||| |||||  | |||||  | |||||||||||  |||||| |||||| || || ||||||||||||||||| || || |||||| | ||     |   ||   | |  | ||  ||||  ||  ||| |   ||   |||| ||     ||   |  |   ||| |  |  |                                                                 
GCTTACATTGAGAAGGAAGACAGCAAGAAGCTCAAGCAAAAGCAGAGGGAGAAAATGCAGCCTAAGATGGGAAAGATGGACATCGATTATCAGgttatttaacgcgtcacatgcctctcat-tgtcgagttatta-tgaaaatggtc--ataattgttgtttggttcattagattcttcgcagaagattatagagtatacggagagccaagatgggtttgtattgatacatgtttcttgtgatccgcag

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|124706325|gb|EH797727.1|EH797727
EST:     AACGGGAGAGAATGCAACCAAAAATGGGAAAGATGGACATTGACTACCAG                         GTACTTCATGATGCATTTTTCAAATACCAAACAAAGCCTAAG
genomic: AACGGGAGAGAATGCAACCAAAAATGGGAAAGATGGACATTGACTACCAGgtttctattt ... cctttctcagGTACTTCATGATGCATTTTTCAAATACCAAACAAAGCCTAAG
EST: gi|125316557|gb|EL330642.1|EL330642
EST:     CAAAAATAGGGAAAGATGGACATTGACTACCAG                         GTACTTCATGATGCATTTTTCAAATACCAAACAAAGCCTAAGCTGTCAGCT
genomic: CAAAAAT-GGGAAAGATGGACATTGACTACCAGgtttctattt ... cctttctcagGTACTTCATGATGCATTTTTCAAATACCAAACAAAGCCTAAGCTGTCAGCT
EST: gi|164173697|gb|ES126652.1|ES126652
EST:     TGCAACCAAAAATGGGAAAGATGGACATTGACTACCAG                         GTACTTCATGATGCATTTTTCAAATACCAAACAAAGCCTAAGCTGTCAGCT
genomic: TGCAACCAAAAATGGGAAAGATGGACATTGACTACCAGgtttctattt ... cctttctcagGTACTTCATGATGCATTTTTCAAATACCAAACAAAGCCTAAGCTGTCAGCT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCTTACATTGAGAAAGAAGATGGTAAGAAATTGAAGCAAAAGCAACGGGAGAGAATGCAACCAAAAATGGGAAAGATGGACATTGACTACCAGgtttctattttttttaatctttgttttgtgatgagtatttgctgatatctgttctataactgacaagtgaagctattctttcctttctcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA