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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAGTTGCATTCAACAAGAGGAGTTCTTGCAGGAGAAAGAGCAAGAGCGTTCCAGTTGCAGgtgtcatcataatcatcaatagactctattcaaatttgcattttcaaaatgtagtattgttctaaaaacttgagatgaacgcag

Basic information

species Arabidopsis thaliana
transcript AT5G18590.1
intron # 16
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G18590.1 (Arabidopsis thaliana), 5'ss of exon 16
lower sequence: GLYMA17G02680.1 (Glycine max), 5'ss of exon 14
GAGTTGCATTCAACAAGAGGAGTTCTTGCAGGAGAAAGAGCAAGAGCGTTCCAGTTGCAGgtgtcatcataatc---atcaatagactctattcaaatttgcattttca-aaatgtagtattgttctaaaaacttgagatgaacgcag----------------------------------------------------------
|||||||| ||||||||||||||| |||||||||||||||||||||| |||||  | |||||       |          |||  |  || |||| || |  | |  || | |||  | ||  |||||   |  || |       | |                                                          
GAGTTGCACTCAACAAGAGGAGTTATTGCAGGAGAAAGAGCAAGAGCATTCCAACTACAGgtacatgtttggcttcagctaatctaaccttttcatatgtcaaatcccatatatgatgaatgtttctacttatctgggtccggtccggtgattacgttataatgttttgaccaaacttccttggacttgtcatatgtgttgtacag

upper sequence: AT5G18590.1 (Arabidopsis thaliana), 5'ss of exon 16
lower sequence: GLYMA07G38020.1 (Glycine max), 5'ss of exon 15
GAGTTGCATTCAACAAGAGGAGTTCTTGCAGGAGAAAGAGCAAGAGCGTTCCAGTTGCAGgtgtcatcataatcatcaatagactctattcaaatt--tgcattttcaaaatgtagtat-tgttctaaaaacttgagatgaacgcag------------------------------------------------------------
|||||||| || |||||||||||| ||||||||||||||||||| || |||||  | |||||       |     | ||  ||    |    | ||  |  || |   |||     ||| || | |  | | ||  |||  |  ||                                                             
GAGTTGCACTCGACAAGAGGAGTTATTGCAGGAGAAAGAGCAAGGGCATTCCAACTTCAGgtacatatttggcttttaactgatctaacattatttgttttatatgtcaaaccccatatatgatgtttacatttatgatctattcattcgatcattgttcctacttatcttatctgtgtccggttcattataatattttgaccgtag

upper sequence: AT5G18590.1 (Arabidopsis thaliana), 5'ss of exon 16
lower sequence: Vv05s0020g01740.t01 (Vitis vinifera), 5'ss of exon 16
GAGTTGCATTCAACAAGAGGAGTTCTTGCAGGAGAAAGAGCAAGAGCGTTCCAGTTGCAGgtgtcatcataatcatcaatagactctattcaaatttgcattttcaaaatgtagtattgttctaaaaacttgagatgaacgcag----------------
||| | |||||||| |||||||| ||||||||||| || |||||||| |||||  ||||||| |  |  | | |   || |||    |   |||     |     |||  |  | |  |    ||| |  ||| |  ||   |                 
GAGCTTCATTCAACTAGAGGAGTGCTTGCAGGAGAGAGGGCAAGAGCATTCCAACTGCAGgtatggttttgaaccaaaaaagagaaaaaaaaaaagaaaaagaaaaaagcgagggagagaagaaaagatgtgaaagaaaatgaaactacacatctggctg

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|124947000|gb|EL022872.1|EL022872
EST:     AGAGGAGTTCTTGCAGGAGAAAGAGCAAGAGCGTTCCAGTTGCAG                         GTTGAAGTGTTTCATCTGAAGCAAAGATTACAATCTCTAGAGAA
genomic: AGAGGAGTTCTTGCAGGAGAAAGAGCAAGAGCGTTCCAGTTGCAGgtgtcatcat ... atgaacgcagGTTGAAGTGTTTCATCTGAAGCAAAGATTACAATCTCTAGAGAA
EST: gi|86055075|gb|DR350832.1|DR350832
EST:     CAACAAGAGGAGTTCTTGCAGGAGAAAGAGCAAGAGCGTTCCAGTTGCAG                         GTTGAAGTGTTTCATCTGAAGCAAAGATTACAATCTCTAGAGAACAGAGCT
genomic: CAACAAGAGGAGTTCTTGCAGGAGAAAGAGCAAGAGCGTTCCAGTTGCAGgtgtcatcat ... atgaacgcagGTTGAAGTGTTTCATCTGAAGCAAAGATTACAATCTCTAGAGAACAGAGCT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GAGTTGCATTCAACAAGAGGAGTTCTTGCAGGAGAAAGAGCAAGAGCGTTCCAGTTGCAGgtgtcatcataatcatcaatagactctattcaaatttgcattttcaaaatgtagtattgttctaaaaacttgagatgaacgcag

- - - - - - - AAGAGG
- - - - - - -  AGAGGA
- - - - - - - - GAGGAG
- - - - - - - - - - - - - -  AGGAGA
- - - - - - - - - - - - - - - GGAGAA
- - - - - - - - - - - - - - - - - - AGAGCA
- - - - - - - - - - - - - - - - - - - AGCAAG
- - - - - - - - - - - - - - - - - - -  GCAAGA