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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gttgtatacgattctacatttttctctgctcttatagtttgactctgttccttgttcttcgttttttttctcttcttctctaacatggttaaaattgcagGGTCTTGATCTTTCTGATGTACTGGTAGAAGTAGAGAAGCGTGGATCCTCATTTGACAAATTACTGGCAGTACCTGAACTAGACGATTGGATATACAGCG

Basic information

species Arabidopsis thaliana
transcript AT5G54870.1
intron # 5
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|86058999|gb|DR354756.1|DR354756
EST:     ATGCTGCTAACATGTGGAATGAAGCCTTGAACAAGCGACTGGGAACAGAG                         GGTCTTGATCTTTCTGATGTACTGGTAGAAGTAGAGAAGCGTGGATCCTCA
genomic: ATGCTGCTAACATGTGGAATGAAGCCTTGAACAAGCGACTGGGAACAGAGgtattaacat ... aaaattgcagGGTCTTGATCTTTCTGATGTACTGGTAGAAGTAGAGAAGCGTGGATCCTCA
EST: gi|86059002|gb|DR354759.1|DR354759
EST:     ATGCTGCTAACATGTGGAATGAAGCCTTGAACAAGCGACTGGGAACAGAG                         GGTCTTGATCTTTCTGATGTACTGGTAGAAGTAGAGAAGCGTGGATCCTCA
genomic: ATGCTGCTAACATGTGGAATGAAGCCTTGAACAAGCGACTGGGAACAGAGgtattaacat ... aaaattgcagGGTCTTGATCTTTCTGATGTACTGGTAGAAGTAGAGAAGCGTGGATCCTCA
EST: gi|86059000|gb|DR354757.1|DR354757
EST:     ATGCTGCTAACATGTGGAATGAAGCCTTGAACAAGCGACTGGGAACAGAG                         GGTCTTGATCTTTCTGATGTACTGGTAGAAGTAGAGAAGCGTGGATCCTCA
genomic: ATGCTGCTAACATGTGGAATGAAGCCTTGAACAAGCGACTGGGAACAGAGgtattaacat ... aaaattgcagGGTCTTGATCTTTCTGATGTACTGGTAGAAGTAGAGAAGCGTGGATCCTCA
EST: gi|86059001|gb|DR354758.1|DR354758
EST:     TGCTAACATGTGGAATGAAGCCTTGAACAAGCGACTGGGAACAGAG                         GGTCTTGATCTTTCTGATGTACTGGTAGAAGTAGAGAAGCGTGGATCCTCA
genomic: TGCTAACATGTGGAATGAAGCCTTGAACAAGCGACTGGGAACAGAGgtattaacat ... aaaattgcagGGTCTTGATCTTTCTGATGTACTGGTAGAAGTAGAGAAGCGTGGATCCTCA
EST: gi|125304248|gb|EL318333.1|EL318333
EST:     CTGGGAACAGAG                         GGTCTTGATCTTTCTGATGTACTGGTAGAAGTAGAGAAGCGTGGATCCTCA
genomic: CTGGGAACAGAGgtattaacat ... aaaattgcagGGTCTTGATCTTTCTGATGTACTGGTAGAAGTAGAGAAGCGTGGATCCTCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgttccttgttcttcgttttttttctcttcttctctaacatggttaaaattgcagGGTCTTGATCTTTCTGATGTACTGGTAGAAGTAGAGAAGCGTGGATCCTCATTTGACAAATTACTGGCAGTACCTGAACTAGACGATTGGATATACAGCG
                                ctctaac  putative branch site (score: 2)
                ttttttttct  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttgtatacgattctacatttttctctgctcttatagtttgactctgttccttgttcttcgttttttttctcttcttctctaacatggttaaaattgcagGGTCTTGATCTTTCTGATGTACTGGTAGAAGTAGAGAAGCGTGGATCCTCATTTGACAAATTACTGGCAGTACCTGAACTAGACGATTGGATATACAGCG

- - - - - - - - - - - tctctgc
- - - - - - - - - - - - - - - - - -agtttga