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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TAACAGTGTGATAGAAAAGGTTTTGCTTCTCACTCGAAGAAAGGAAAAAACCCTAGTGGCTGCAGCTGTTCGATTTGTCCGCACTCTCCTCTCTGTCCATgtaagtaaagtagtcttcgatcagcattttttcttataggctcatctgtgcattctctcttgagaatgaattagacaattgattctataatggctagaaaatgttctcggatgacaataagtctttaggtaagttatgcaatttctaaaatattgttctatttcag

Basic information

species Arabidopsis thaliana
transcript AT5G49390.1
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G49390.1 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: Vv05s0077g01200.t01 (Vitis vinifera), 5'ss of exon 19
TAACAGTGTGATAGAAAAGGTTTTGCTTCTCACTCGAAGAAAGGAAAAAACCCTAGTGGCTGCAGCTGTTCGATTTGTCCGCACTCTCCTCTCTGTCCATgtaagtaaagtagtcttcgatcagcattttttcttataggctcatctgtgcattctctcttgagaatgaattagacaattgattctataatggctagaaaatgttctcggatgacaataagtctttaggtaagttatgcaatttctaaaatattgttctatttcag
 || | ||||||||| || ||| || |||| |||||||||| |||||||   ||||| | ||| |||||||||||||| |||||| | || ||   ||||||| || |  |  | || | |  | |         | |   | ||  |      || || | |     | | | |   |   ||     ||   |  | ||||   | | ||                                                      
CAATAATGTGATAGATAAAGTTCTGTTTCTAACTCGAAGAAGGGAAAAATATCTAGTAGTTGCTGCTGTTCGATTTGTTCGCACTATTCTTTCCCGCCATgtatgtgattttattttagttatgga-------gaagaaattgattgg------ctgtcataaatggaattcatatgttcattttgggtatctatgtagaatgaaatggcatc-----------------------------------------------------
















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|116464480|gb|EG507072.1|EG507072
EST:     TGCAGCTGTTCGATTTGTCCGCCCTCTCCTCTCTGTCCAT                         AATGATAATGTCCAGAGTTACATTGTTGAGAACAACACGCTGAAACCGATT
genomic: TGCAGCTGTTCGATTTGTCCGCACTCTCCTCTCTGTCCATgtaagtaaag ... tctatttcagAATGATAATGTCCAGAGTTACATTGTTGAGAACAACACGCTGAAACCGATT
EST: gi|116464443|gb|EG507035.1|EG507035
EST:     TGCAGCTGTTCGATTTGTCCGCACTCTCCTCTCTGTCCAT                         AATGATAATGTCCAGAGTTACATTGTTGAGAACAACACGCTGAAACCGATT
genomic: TGCAGCTGTTCGATTTGTCCGCACTCTCCTCTCTGTCCATgtaagtaaag ... tctatttcagAATGATAATGTCCAGAGTTACATTGTTGAGAACAACACGCTGAAACCGATT
EST: gi|116464454|gb|EG507046.1|EG507046
EST:     TGCAGCTGTTCGATTTGTCCGCACTCTCCTCTCTGTCCAT                         AATGATAATGTCCAGAGTTACATTGTTGAGAACAACACGCTGAAACCGATT
genomic: TGCAGCTGTTCGATTTGTCCGCACTCTCCTCTCTGTCCATgtaagtaaag ... tctatttcagAATGATAATGTCCAGAGTTACATTGTTGAGAACAACACGCTGAAACCGATT
EST: gi|116464465|gb|EG507057.1|EG507057
EST:     CCTCTCTGTCCAT                         AATGATAATGTCCAGAGTTACATTGTTGAGAACAACACGCTGAAACCGATT
genomic: CCTCTCTGTCCATgtaagtaaag ... tctatttcagAATGATAATGTCCAGAGTTACATTGTTGAGAACAACACGCTGAAACCGATT
EST: gi|116464476|gb|EG507068.1|EG507068
EST:     TCCTCTCTGTCCAT                         AATGATAATGTCCAGAGTTACATTGTTGAGAACAACACGCTGAAACCGATT
genomic: TCCTCTCTGTCCATgtaagtaaag ... tctatttcagAATGATAATGTCCAGAGTTACATTGTTGAGAACAACACGCTGAAACCGATT
EST: gi|116464489|gb|EG507081.1|EG507081
EST:     TGCAGCTGTTCGATTTGTCCGCACTCTCCTCTCTGTCCAT                         AATGATAATGTCCAGAGTTACATTGTTGAGAACAACACGCTGAAACCGATT
genomic: TGCAGCTGTTCGATTTGTCCGCACTCTCCTCTCTGTCCATgtaagtaaag ... tctatttcagAATGATAATGTCCAGAGTTACATTGTTGAGAACAACACGCTGAAACCGATT
EST: gi|116464469|gb|EG507061.1|EG507061
EST:     TGCAGCTGTTCGATTTGTCCGCATTCTCCTCTCTGTCCAT                         AATGATAATGTCCAGAGTTACATTGTTGAGAACAACACGCTGAAACCGATT
genomic: TGCAGCTGTTCGATTTGTCCGCACTCTCCTCTCTGTCCATgtaagtaaag ... tctatttcagAATGATAATGTCCAGAGTTACATTGTTGAGAACAACACGCTGAAACCGATT
EST: gi|116464493|gb|EG507085.1|EG507085
EST:     TGCAGCTGTTCGATTTGTCCGCACTCTCCTCTCTGTCCAT                         AATGATAATGTCCAGAGTTACATTGTTGAGAACAACACGCTGAAACCGATT
genomic: TGCAGCTGTTCGATTTGTCCGCACTCTCCTCTCTGTCCATgtaagtaaag ... tctatttcagAATGATAATGTCCAGAGTTACATTGTTGAGAACAACACGCTGAAACCGATT
EST: gi|116464420|gb|EG507012.1|EG507012
EST:     CCCTAGTGGCTGCAGCTGTTCGATTTGTCCGCACTCTCCTCTCTGTCCAT                         AATGATAATGTCCAGAGTTACATTGTTGAGAACAACACGCTGAAACCGATT
genomic: CCCTAGTGGCTGCAGCTGTTCGATTTGTCCGCACTCTCCTCTCTGTCCATgtaagtaaag ... tctatttcagAATGATAATGTCCAGAGTTACATTGTTGAGAACAACACGCTGAAACCGATT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TAACAGTGTGATAGAAAAGGTTTTGCTTCTCACTCGAAGAAAGGAAAAAACCCTAGTGGCTGCAGCTGTTCGATTTGTCCGCACTCTCCTCTCTGTCCATgtaagtaaagtagtcttcgatcagcattttttcttataggctcatctgtgcattctctcttgagaatgaattagacaattgattctataatggctagaaaatgttctcggatgacaataagtctttaggtaagttatgcaatttctaaaatattgttctatttcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTCCTC