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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGATTATCAAAGTCTTATAACAAGATCTGTGTATGATAAGCAGCTAGACAGTGGAAGAGGTACTCTGCTTCACTTGTGTGATGAAGTCATCCAACAAGAGgtgctaattatcccctgttattttttatgtcgtattctctttctttttttgcttacaaactgataaaatgtag

Basic information

species Arabidopsis thaliana
transcript AT5G13940.1
intron # 19
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G13940.1 (Arabidopsis thaliana), 5'ss of exon 19
lower sequence: Vv14s0068g00980.t01 (Vitis vinifera), 5'ss of exon 12
AGATTATCAAAGTCTTATAACAAGATCTGTGTATGATAAGCAGCTAGACAGTGGAAGAGGTACTCTGCTTCACTTGTGTGATGAAGTCATCCAACAAGAGgtgctaattatcccctgt---tattttttatgtcgtattctctttctttttttgcttacaaactg-----ataaaatgtag-------------------
 || || || |   | || ||| | ||  |||| || || || || || |||||||| || ||||||||||||||||||||||| || || |||||||| ||    |||   |         ||||||||    ||    ||||| |    |||  ||    |       || | ||||||                   
TGAGTACCAGAACTTAATCACACGGTCCATGTACGACAAACAACTGGATAGTGGAAGGGGAACTCTGCTTCACTTGTGTGATGATGTGATTCAACAAGAAgtaagtattgatctagaagaacattttttaatatgttaagtctttttaaaattgactatgctccatttgtatcacatgtagtattagtgaaagataaaaa
















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|116480284|gb|EG522876.1|EG522876
EST:     GTGGAAGAGGTACTCTGCTTCACTTGTGTGATGAAGTCATCCAACAAGAG                         GTTAAAGAGGTCATCATTTCGTTTTTCATGCTGATCAAGAAAGGGTGTCCC
genomic: GTGGAAGAGGTACTCTGCTTCACTTGTGTGATGAAGTCATCCAACAAGAGgtgctaatta ... taaaatgtagGTTAAAGAGGTCATCATTTCGTTTTTCATGCTGATCAAGAAAGGGTGTCCC
EST: gi|116481915|gb|EG524507.1|EG524507
EST:     GTGGAAGAGGTACTCTGCTTCACTTGTGTGATGAAGTCATCCAACAAGAG                         GTTAAAGAGGTCATCATTTCGTTTTTCATGCTGATCAAGAAAGGGTGTCCC
genomic: GTGGAAGAGGTACTCTGCTTCACTTGTGTGATGAAGTCATCCAACAAGAGgtgctaatta ... taaaatgtagGTTAAAGAGGTCATCATTTCGTTTTTCATGCTGATCAAGAAAGGGTGTCCC
EST: gi|116481924|gb|EG524516.1|EG524516
EST:     GTGGAAGAGGTACTCTGCTTCACTTGTGTGATGAAGTCATCCAACAAGAG                         GTTAAAGAGGTCATCATTTCGTTTTTCATGCTGATCAA
genomic: GTGGAAGAGGTACTCTGCTTCACTTGTGTGATGAAGTCATCCAACAAGAGgtgctaatta ... taaaatgtagGTTAAAGAGGTCATCATTTCGTTTTTCATGCTGATCAA
EST: gi|116480243|gb|EG522835.1|EG522835
EST:     GTGGAAGAGGTACTCTGCTTCACTTGTGTGATGAAGTCATCCAACAAGAG                         GTTAAAGAGGTCATCATTTCGTTTTTCATGCTGATCAAGAAAGGGTGTCCC
genomic: GTGGAAGAGGTACTCTGCTTCACTTGTGTGATGAAGTCATCCAACAAGAGgtgctaatta ... taaaatgtagGTTAAAGAGGTCATCATTTCGTTTTTCATGCTGATCAAGAAAGGGTGTCCC
EST: gi|116481923|gb|EG524515.1|EG524515
EST:     GTGGAAGAGGTACTCTGCTTCACTTGTGTGATGAAGTCATCCAACAAGAG                         GTTAAAGAGGTCATCATTTCGTTTTTCATGCTGATCAAGAAAGGGTGTCCC
genomic: GTGGAAGAGGTACTCTGCTTCACTTGTGTGATGAAGTCATCCAACAAGAGgtgctaatta ... taaaatgtagGTTAAAGAGGTCATCATTTCGTTTTTCATGCTGATCAAGAAAGGGTGTCCC
EST: gi|116480191|gb|EG522783.1|EG522783
EST:     GTGGAAGAGGTACTCTGCTTCACTTGTGTGATGAAGTCATCCAACAAGAG                         GTTAAAGAGGTCATCATTTCGTTTTTCATGCTGATCAAGAAAGGGTGTCCC
genomic: GTGGAAGAGGTACTCTGCTTCACTTGTGTGATGAAGTCATCCAACAAGAGgtgctaatta ... taaaatgtagGTTAAAGAGGTCATCATTTCGTTTTTCATGCTGATCAAGAAAGGGTGTCCC
EST: gi|116481912|gb|EG524504.1|EG524504
EST:     GTGGAAGAGGTACTCTGCTTCACTTGTGTGATGAAGTCATCCAACAAGAG                         GTTAAAGAGGTCATCATTTCGTTTTTCATGCTGATCAAGAAAGGGTGTCCC
genomic: GTGGAAGAGGTACTCTGCTTCACTTGTGTGATGAAGTCATCCAACAAGAGgtgctaatta ... taaaatgtagGTTAAAGAGGTCATCATTTCGTTTTTCATGCTGATCAAGAAAGGGTGTCCC
EST: gi|116481910|gb|EG524502.1|EG524502
EST:     GTGGAAGAGGTACTCTGCTTCACTTGTGTGATGAAGTCATCCAACAAGAG                         GTTAAAGAGGTCATCATTTCGTTTTTCATGCTGATCAAGAAAGGGTGTCCC
genomic: GTGGAAGAGGTACTCTGCTTCACTTGTGTGATGAAGTCATCCAACAAGAGgtgctaatta ... taaaatgtagGTTAAAGAGGTCATCATTTCGTTTTTCATGCTGATCAAGAAAGGGTGTCCC
EST: gi|116481918|gb|EG524510.1|EG524510
EST:     GTGGAAGAGGTACTCTGCTTCACTTGTGTGATGAAGTCATCCAACAAGAG                         GTTAAAGAGGTCATCATTTCGTTTTTCATGCTGATCAAGAAAGGGTGTCCC
genomic: GTGGAAGAGGTACTCTGCTTCACTTGTGTGATGAAGTCATCCAACAAGAGgtgctaatta ... taaaatgtagGTTAAAGAGGTCATCATTTCGTTTTTCATGCTGATCAAGAAAGGGTGTCCC
EST: gi|116481916|gb|EG524508.1|EG524508
EST:     GTGGAAGAGGTACTCTGCTTCACTTGTGTGATGAAGTCATCCAACAAGAG                         GTTAAAGAGGTCATCATTTCGTTTTTCATGCTGATCAAGAAAGGGTGTCCC
genomic: GTGGAAGAGGTACTCTGCTTCACTTGTGTGATGAAGTCATCCAACAAGAGgtgctaatta ... taaaatgtagGTTAAAGAGGTCATCATTTCGTTTTTCATGCTGATCAAGAAAGGGTGTCCC
EST: gi|116481922|gb|EG524514.1|EG524514
EST:     GTGGAAGAGGTACTCTGCTTCACTTGTGTGATGAAGTCATCCAACAAGAG                         GTTAAAGAGGTCATCATTTCGTTTTTCATGCTGATCAAGAAAGGGTGTCCC
genomic: GTGGAAGAGGTACTCTGCTTCACTTGTGTGATGAAGTCATCCAACAAGAGgtgctaatta ... taaaatgtagGTTAAAGAGGTCATCATTTCGTTTTTCATGCTGATCAAGAAAGGGTGTCCC
EST: gi|116480168|gb|EG522760.1|EG522760
EST:     GTGGAAGAGGTACTTTGCTTCACTTGTGTGATGAAGTCATCCAACAAGAG                         GTTAAAGAGGTCATCATTTCGTTTTTCATGCTGATCAAGAAAGGGTGTCCC
genomic: GTGGAAGAGGTACTCTGCTTCACTTGTGTGATGAAGTCATCCAACAAGAGgtgctaatta ... taaaatgtagGTTAAAGAGGTCATCATTTCGTTTTTCATGCTGATCAAGAAAGGGTGTCCC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGATTATCAAAGTCTTATAACAAGATCTGTGTATGATAAGCAGCTAGACAGTGGAAGAGGTACTCTGCTTCACTTGTGTGATGAAGTCATCCAACAAGAGgtgctaattatcccctgttattttttatgtcgtattctctttctttttttgcttacaaactgataaaatgtag

- - - - - - - - - - - - - - - - - - - - - - - - -  TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG