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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gttgaaaaacaatgacaattttgtttctttcaatcctaaattttcgatttttctcactacccttatctctatttgatcgattttttgttattgtttacagGTTGGGACTGCAGTTGTTACTGGGAAAGGTGGAAGATTGGCTCTTGGACGTTTAGGAGCTATCTGTGAACAG

Basic information

species Arabidopsis thaliana
transcript AT3G55610.2
intron # 1
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|86064871|gb|DR360628.1|DR360628
EST:     TCGATCGTTCACGCGCGTTCGCCAAAGACGTTAAGCGTATCGTCGTCAAG                         GTTGGGACTGCAGTTGTTACTGGGAAAGGTGGAAGATTGGCTCTTGGACGT
genomic: TCGATCGTTCACGCGCGTTCGCCAAAGACGTTAAGCGTATCGTCGTCAAGgtttgaaatt ... ttgtttacagGTTGGGACTGCAGTTGTTACTGGGAAAGGTGGAAGATTGGCTCTTGGACGT
EST: gi|86064874|gb|DR360631.1|DR360631
EST:     TCGATCGTTCACGCGCGTTCGCCAAAGACGTTAAGCGTATCGTCGTCAAG                         GTTGGGACTGCAGTTGTTACTGGGAAAGGTGGAAGATTGGCTCTTGGACGT
genomic: TCGATCGTTCACGCGCGTTCGCCAAAGACGTTAAGCGTATCGTCGTCAAGgtttgaaatt ... ttgtttacagGTTGGGACTGCAGTTGTTACTGGGAAAGGTGGAAGATTGGCTCTTGGACGT
EST: gi|125039912|gb|EL112181.1|EL112181
EST:     CGCGTTCGCCAAAGACGTTAAGCGTATCGTCGTCAAG                         GTTGGGACTGCAGTTGTTACTGGGAAAGGTGGAAGATTGGCTCTTGGACGT
genomic: CGCGTTCGCCAAAGACGTTAAGCGTATCGTCGTCAAGgtttgaaatt ... ttgtttacagGTTGGGACTGCAGTTGTTACTGGGAAAGGTGGAAGATTGGCTCTTGGACGT
EST: gi|86064868|gb|DR360625.1|DR360625
EST:     TCGATCGTTCACGCGCGTTCGCCAAAGACGTTAAGCGTATCGTCGTCAAG                         GTTGGGACTGCAGTTGTTACTGGGAAAGGTGGAAGATTGGCTCTTGGACGT
genomic: TCGATCGTTCACGCGCGTTCGCCAAAGACGTTAAGCGTATCGTCGTCAAGgtttgaaatt ... ttgtttacagGTTGGGACTGCAGTTGTTACTGGGAAAGGTGGAAGATTGGCTCTTGGACGT
EST: gi|152033743|gb|BP562130.3|BP562130
EST:     TCGATCGTTCACGCGCGTTCGCCAAAGACGTTAAGCGTATCGTCGTCAAG                         GTTGGGACTGCAGTTGTTACTGGGAAAGGTGGAAGATTGGCTCTTGGACGT
genomic: TCGATCGTTCACGCGCGTTCGCCAAAGACGTTAAGCGTATCGTCGTCAAGgtttgaaatt ... ttgtttacagGTTGGGACTGCAGTTGTTACTGGGAAAGGTGGAAGATTGGCTCTTGGACGT
EST: gi|86064870|gb|DR360627.1|DR360627
EST:     TCGATCGTTCACGCGAGTTCGCCAAAGACGTTAAGCGTATCGTCGTCAAG                         GTTGGGACTGCAGTTGTTACTGGGAAAGGTGGAAGATTGGCTCTTGGACGT
genomic: TCGATCGTTCACGCGCGTTCGCCAAAGACGTTAAGCGTATCGTCGTCAAGgtttgaaatt ... ttgtttacagGTTGGGACTGCAGTTGTTACTGGGAAAGGTGGAAGATTGGCTCTTGGACGT
EST: gi|86064867|gb|DR360624.1|DR360624
EST:     TCGATCGTTCACGCGCGTTCGCCAAAGACGTTAAGCGTATCGTCGTCAAG                         GTTGGGACTGCAGTTGTTACTGGGAAAGGTGGAAGATTGGCTCTTGGACGT
genomic: TCGATCGTTCACGCGCGTTCGCCAAAGACGTTAAGCGTATCGTCGTCAAGgtttgaaatt ... ttgtttacagGTTGGGACTGCAGTTGTTACTGGGAAAGGTGGAAGATTGGCTCTTGGACGT
EST: gi|124918628|gb|EH992449.1|EH992449
EST:     TCGATCGTTCACGCGCGTTCGCCAAAGACGTTAAGCGTATCGTCGTCGAG                         GTTGGGACTGCAGTTGTTACTGGGAAAGGTGGAAGATTGGCT
genomic: TCGATCGTTCACGCGCGTTCGCCAAAGACGTTAAGCGTATCGTCGTCAAGgtttgaaatt ... ttgtttacagGTTGGGACTGCAGTTGTTACTGGGAAAGGTGGAAGATTGGCT
EST: gi|86064869|gb|DR360626.1|DR360626
EST:     TCGATCGTTCACGCGCGTTCGCCAAAGACGTTAAGCGTATCGTCGTCAAG                         GTTGGGACTGCAGTTGTTACTGGGAAAGGTGGAAGATTGGCTCTTGGACGT
genomic: TCGATCGTTCACGCGCGTTCGCCAAAGACGTTAAGCGTATCGTCGTCAAGgtttgaaatt ... ttgtttacagGTTGGGACTGCAGTTGTTACTGGGAAAGGTGGAAGATTGGCTCTTGGACGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gatttttctcactacccttatctctatttgatcgattttttgttattgtttacagGTTGGGACTGCAGTTGTTACTGGGAAAGGTGGAAGATTGGCTCTTGGACGTTTAGGAGCTATCTGTGAACAG
                                  attttttgttattgtt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttgaaaaacaatgacaattttgtttctttcaatcctaaattttcgatttttctcactacccttatctctatttgatcgattttttgttattgtttacagGTTGGGACTGCAGTTGTTACTGGGAAAGGTGGAAGATTGGCTCTTGGACGTTTAGGAGCTATCTGTGAACAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
- -gaaaaac
- - - - - -atgacaa
- - - - - - - - - - - - - - - - -tcctaaa