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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CAAATGGCAGGCATTTAAGTTGGCAACACTCTCTGGTTTAGCTGAGCCTCTAGGTGTAATTATCGTGGgtaagttgcattggttttctttgctcaagttgcttcttatatacgagtccctgttctcttaagagttctaaaaagagtattataaattctgctttgatccatcttccttacgatgcag

Basic information

species Arabidopsis thaliana
transcript AT3G20870.1
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G20870.1 (Arabidopsis thaliana), 5'ss of exon 9
lower sequence: LOC_Os02g10230.1 (Oryza sativa), 5'ss of exon 9
CAAATGGCAGGCATTTAAGTTGGCAACACTCTCTGGTTTAGCTGAGCCTCTAGGTGTAATTATCGTGGgtaagttgcattg-gttttctttgctcaagttgcttcttatatacgagtccctgttctcttaagagttctaaaaagagtattataaattctgctttgatccatcttccttacgatgcag
||||||||| ||||||||  | ||||| ||||||||||| |||||||| ||||| || || || || |||| | |   |    |   |||  ||  | |   ||  |      |  |  |  ||   |   ||   || |    | | | ||   ||| |                           
CAAATGGCAAGCATTTAAAGTTGCAACCCTCTCTGGTTTCGCTGAGCCACTAGGAGTGATCATTGTTGgtatgctatgtcatatgcacttctctgtaatatttttcttctggtgtatatccattgagtgctgaaggctgatgcaaatgtgattgcttcag---------------------------
















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|125185722|gb|EL200676.1|EL200676
EST:     GTTGGCAACACTCTCTGGTTTAGCTGAGCCTCTAGGTGTAATTATCGTGG                         CCTATCTATTCCCGAGAAGCTTAAGTCCAGAAATCCTTGAAGGTTTGTTGG
genomic: GTTGGCAACACTCTCTGGTTTAGCTGAGCCTCTAGGTGTAATTATCGTGGgtaagttgca ... tacgatgcagCCTATCTATTCCCGAGAAGCTTAAGTCCAGAAATCCTTGAAGGTTTGTTGG
EST: gi|86083065|gb|DR378824.1|DR378824
EST:     GTTGGCAACACTCTCTGGTTTAGCTGAGCCTCTAGGTGTAATTATCGTGG                         CCTATCTATTCCCGAGAAGCTTAAGTCCAGAAATCCTTGAAGGTTTGTTGG
genomic: GTTGGCAACACTCTCTGGTTTAGCTGAGCCTCTAGGTGTAATTATCGTGGgtaagttgca ... tacgatgcagCCTATCTATTCCCGAGAAGCTTAAGTCCAGAAATCCTTGAAGGTTTGTTGG
EST: gi|116396456|gb|EG439048.1|EG439048
EST:     GTTGGCAACACTTTCTGGTTTAGCTGAGCCTCTAGGTGTAATTATCGTGG                         CCTATTTATTCCCGAGAAGCTTAAGTCCAGAAATCCTTGAAGGTTTGTTGG
genomic: GTTGGCAACACTCTCTGGTTTAGCTGAGCCTCTAGGTGTAATTATCGTGGgtaagttgca ... tacgatgcagCCTATCTATTCCCGAGAAGCTTAAGTCCAGAAATCCTTGAAGGTTTGTTGG
EST: gi|116396457|gb|EG439049.1|EG439049
EST:     GTTGGCAACACTCTCTGGTTTAGCTGAGCCTCTAGGTGTAATTATCGTGG                         CCTATCTATTCCCGAGAAGCTTAAGTCCAGAAATCCTTGAAGGTTTGTTGG
genomic: GTTGGCAACACTCTCTGGTTTAGCTGAGCCTCTAGGTGTAATTATCGTGGgtaagttgca ... tacgatgcagCCTATCTATTCCCGAGAAGCTTAAGTCCAGAAATCCTTGAAGGTTTGTTGG
EST: gi|116403229|gb|EG445821.1|EG445821
EST:     GTTGGCAACACTCTCTGGTTTAGCTGAGCCTCTAGGTGTAATTATCGTGG                         CCTATCTATTCCCGAGAAGCTTAAGTCCAGAAATCCTTGAAGGTTTGTTGG
genomic: GTTGGCAACACTCTCTGGTTTAGCTGAGCCTCTAGGTGTAATTATCGTGGgtaagttgca ... tacgatgcagCCTATCTATTCCCGAGAAGCTTAAGTCCAGAAATCCTTGAAGGTTTGTTGG
EST: gi|86082548|gb|DR378307.1|DR378307
EST:     GTTGGCAACACTCTCTGGTTTAGCTGAGCCTCTAGGTGTAATTATCGTGG                         CCTATCTATTCCCGAGAAGCTTAAGTCCAGAAATCCTTGAAGGTTTGTTGG
genomic: GTTGGCAACACTCTCTGGTTTAGCTGAGCCTCTAGGTGTAATTATCGTGGgtaagttgca ... tacgatgcagCCTATCTATTCCCGAGAAGCTTAAGTCCAGAAATCCTTGAAGGTTTGTTGG
EST: gi|164182555|gb|ES129932.1|ES129932
EST:     GTTGGCAACACTCTCTGGTTTAGCTGAGCCTCTAGGTGTAATTATCGTGG                         CCTATCTATTCCCGAGAAG
genomic: GTTGGCAACACTCTCTGGTTTAGCTGAGCCTCTAGGTGTAATTATCGTGGgtaagttgca ... tacgatgcagCCTATCTATTCCCGAGAAG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CAAATGGCAGGCATTTAAGTTGGCAACACTCTCTGGTTTAGCTGAGCCTCTAGGTGTAATTATCGTGGgtaagttgcattggttttctttgctcaagttgcttcttatatacgagtccctgttctcttaagagttctaaaaagagtattataaattctgctttgatccatcttccttacgatgcag

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