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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atagctaataattgaaagcatatgcttggattgtggatataatatattcgacaagtgttaaaattttaaatattgataattttgtgtggtgtatttgtagGGTTTGTGACATCGAAGGTGGCATGTTGTGGACAAGGACCGTACAATGGCATAGGACTATGCACACCAGTCTCGAATTTGTGTCCGAATAGAGACTTATA

Basic information

species Arabidopsis thaliana
transcript AT3G04290.1
intron # 4
splice site 3'
intron type U2

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|124972474|gb|EL046166.1|EL046166
EST:     CAATGCCTATCAAATGAACATGGATTATCTATCTAATCCTGAACAATTTG                         GGTTTGTGACATCGAAGGTGG
genomic: CAATGCCTATCAAATGAACATGGATTATCTATCTAATCCTGAACAATTTGgtaattacaa ... gtatttgtagGGTTTGTGACATCGAAGGTGG
EST: gi|125118454|gb|EL167172.1|EL167172
EST:     TGGATTATCTATCTAATCCTGAACAATTTG                         GGTTTGTGACATCGAAGGTGGCATGTTGTGGACAAAGGACCGTACAATGGC
genomic: TGGATTATCTATCTAATCCTGAACAATTTGgtaattacaa ... gtatttgtagGGTTTGTGACATCGAAGGTGGCATGTTGTGGACAA-GGACCGTACAATGGC
EST: gi|164098019|gb|ES174021.1|ES174021
EST:     AATGAACATGGATTATCTATCTAATCCCTGAACAATTTG                         GGTTTGTGACATCGAAGGTGGCATGTTGTGGACAAGGACCGTACAATGGCA
genomic: AATGAACATGGATTATCTATCTAAT-CCTGAACAATTTGgtaattacaa ... gtatttgtagGGTTTGTGACATCGAAGGTGGCATGTTGTGGACAAGGACCGTACAATGGCA
EST: gi|125112298|gb|EL163431.1|EL163431
EST:     AATGCCTATCAAATGAACATGGATTATCTATCTAATCCTAGAACAATTTG                         GGTTTGTGACATCGAAGGTGG
genomic: AATGCCTATCAAATGAACATGGATTATCTATCTAATCCT-GAACAATTTGgtaattacaa ... gtatttgtagGGTTTGTGACATCGAAGGTGG
EST: gi|86085296|gb|DR381055.1|DR381055
EST:     CAATGCCTATCAAATGAACATGGATTATCTATCTAATCCTGAACAATTTG                         GGTTTGTGACATCGAAGGTGGCATGTTGTGGACAAGGACCGTACAATGGCA
genomic: CAATGCCTATCAAATGAACATGGATTATCTATCTAATCCTGAACAATTTGgtaattacaa ... gtatttgtagGGTTTGTGACATCGAAGGTGGCATGTTGTGGACAAGGACCGTACAATGGCA
EST: gi|47831098|gb|CK120782.1|CK120782
EST:     CAATGCCTATCAAATGAACATGGATTATCTATCTAATCCTGAACAATTTG                         GGTTTGTGACATCGAAGGTGGCATGTTGTGGACAAGGACCGTACAATGGCA
genomic: CAATGCCTATCAAATGAACATGGATTATCTATCTAATCCTGAACAATTTGgtaattacaa ... gtatttgtagGGTTTGTGACATCGAAGGTGGCATGTTGTGGACAAGGACCGTACAATGGCA
EST: gi|164178703|gb|EL999885.1|EL999885
EST:     CAATGCCTATCAAATGAACATGGATTATCTATCTAATCCTGAACAATTTG                         GGTTTGTGACATCGAAGGTGGCATGTTGTGG
genomic: CAATGCCTATCAAATGAACATGGATTATCTATCTAATCCTGAACAATTTGgtaattacaa ... gtatttgtagGGTTTGTGACATCGAAGGTGGCATGTTGTGG
EST: gi|125233101|gb|EL247186.1|EL247186
EST:     GATTATCTATCTAATCCTGAACAATTTG                         GGTTTGTGACATCGAAGGTGGCATGTTGTGGACAAGGACCGTACAATGGCA
genomic: GATTATCTATCTAATCCTGAACAATTTGgtaattacaa ... gtatttgtagGGTTTGTGACATCGAAGGTGGCATGTTGTGGACAAGGACCGTACAATGGCA
EST: gi|125280521|gb|EL294606.1|EL294606
EST:     TGCCTATCAAATGAACATGGATTATCTATCTAATCCTGAACTAATTTG                         GGTTTGTGACATCGAAGGTGGCATGTTGTGGACAAGGACCGTACAATGGC
genomic: TGCCTATCAAATGAACATGGATTATCTATCTAATCCTGAAC-AATTTGgtaattacaa ... gtatttgtagGGTTTGTGACATCGAAGGTGGCATGTTGTGGACAAGGACCGTACAATGGC
EST: gi|86020684|gb|DR316430.1|DR316430
EST:     CAATGCCTATCAAATGAACATGGATTATCTATCTAATCCTGAACAATTTG                         GGTTTGTGACATCGAAGGTGGCATGTTGTGGACAAGGACCGTACAATGGCA
genomic: CAATGCCTATCAAATGAACATGGATTATCTATCTAATCCTGAACAATTTGgtaattacaa ... gtatttgtagGGTTTGTGACATCGAAGGTGGCATGTTGTGGACAAGGACCGTACAATGGCA
EST: gi|164012852|gb|ES120499.1|ES120499
EST:     TGAACATGGATTATCTATCTAATCCTGAACAATTTG                         GGTTTGTGACATCGAAGGTGGCATGTTGTGGACAAGGACCGTACAATGGCA
genomic: TGAACATGGATTATCTATCTAATCCTGAACAATTTGgtaattacaa ... gtatttgtagGGTTTGTGACATCGAAGGTGGCATGTTGTGGACAAGGACCGTACAATGGCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attcgacaagtgttaaaattttaaatattgataattttgtgtggtgtatttgtagGGTTTGTGACATCGAAGGTGGCATGTTGTGGACAAGGACCGTACAATGGCATAGGACTATGCACACCAGTCTCGAATTTGTGTCCGAATAGAGACTTATA
                         tattgat  putative branch site (score: 3)
     acaagtgttaaaattt  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atagctaataattgaaagcatatgcttggattgtggatataatatattcgacaagtgttaaaattttaaatattgataattttgtgtggtgtatttgtagGGTTTGTGACATCGAAGGTGGCATGTTGTGGACAAGGACCGTACAATGGCATAGGACTATGCACACCAGTCTCGAATTTGTGTCCGAATAGAGACTTATA

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