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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaatctcgatcttgttcgatctctatttttggtggaattgagattgttaattaggtcaaaaattcgtgattgtattagGATGAAGCAATGGGACTGGTGTTGAGTGCAGCTTCGGTTAAAGGATGGACAACCGGTTCCGGTATGGAAGGACCGTCTCTACCGGCTAAAACCGATACAG

Basic information

species Arabidopsis thaliana
transcript AT5G27280.1
intron # 2
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|125274239|gb|EL288324.1|EL288324
EST:     CTTCCGGAATCGAACTCTCTCCAAT                         GATGAAGCAATGGGACTGGTGTTGAGCGCAGCTTCGGTTAAAGGATGGAAC
genomic: CTTCCGGAATCGAACTCTCTCCAATgtaaatctcg ... attgtattagGATGAAGCAATGGGACTGGTGTTGAGTGCAGCTTCGGTTAAAGGATGGA-C
EST: gi|86014973|gb|DR310719.1|DR310719
EST:     ATTCCGAATCGAACTCACCAAGCCTCTTCCGGAATCGAATTCTCTCCAAT                         GATGAAGCAATGGGACTGGTGTTGAGTGCAGCTTCGGTTAAAGGATGGACA
genomic: ATTCCGAATCGAACTCATCAAGCCTCTTCCGGAATCGAACTCTCTCCAATgtaaatctcg ... attgtattagGATGAAGCAATGGGACTGGTGTTGAGTGCAGCTTCGGTTAAAGGATGGACA
EST: gi|86077887|gb|DR373644.1|DR373644
EST:     ATTCCGAATCGAACTCACCAAGCCTCTTCCGGAATCGAATTCTCTCCAAT                         GATGAAGCAATGGGACTGGTGTTGAGTGCAGCTTCGGTTAAAGGATGGACA
genomic: ATTCCGAATCGAACTCATCAAGCCTCTTCCGGAATCGAACTCTCTCCAATgtaaatctcg ... attgtattagGATGAAGCAATGGGACTGGTGTTGAGTGCAGCTTCGGTTAAAGGATGGACA
EST: gi|163979472|gb|ES116113.1|ES116113
EST:     ATTCCGAATCGAACTCATCAAGCCTCTTCCGGAATCGAACTCTCTCCAAT                         GATGAAGCAATGGGATTGGTGTTGAGT
genomic: ATTCCGAATCGAACTCATCAAGCCTCTTCCGGAATCGAACTCTCTCCAATgtaaatctcg ... attgtattagGATGAAGCAATGGGACTGGTGTTGAGT
EST: gi|124959432|gb|EL034136.1|EL034136
EST:     ATTCCGAATCGAACTCATCAAGCCTCTTCCGGAGTCGAACTCTCTCCAAT                         GATGAAGCAATGGGACTGGT
genomic: ATTCCGAATCGAACTCATCAAGCCTCTTCCGGAATCGAACTCTCTCCAATgtaaatctcg ... attgtattagGATGAAGCAATGGGACTGGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatttttggtggaattgagattgttaattaggtcaaaaattcgtgattgtattagGATGAAGCAATGGGACTGGTGTTGAGTGCAGCTTCGGTTAAAGGATGGACAACCGGTTCCGGTATGGAAGGACCGTCTCTACCGGCTAAAACCGATACAG
                     tgttaat  putative branch site (score: 3)
                   attgttaatta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaatctcgatcttgttcgatctctatttttggtggaattgagattgttaattaggtcaaaaattcgtgattgtattagGATGAAGCAATGGGACTGGTGTTGAGTGCAGCTTCGGTTAAAGGATGGACAACCGGTTCCGGTATGGAAGGACCGTCTCTACCGGCTAAAACCGATACAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG