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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagttctcttcgccacttttttccttttgatttctaatttctctgtatccatttagttgaagtttttggtttcatagagctcctacttcttcgtgtttctgattttgttcttcgtttgtttcatgtaatgcagGTACATGGACAAGAAACTCCAAA

Basic information

species Arabidopsis thaliana
transcript AT3G11500.1
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|125241957|gb|EL256042.1|EL256042
EST:     TCCGATTCTGCAAGTATGAGTCGATCAGGTCAGCCTCCAGATCTCAAGAA                         GTACATGGACAAGAAACTCCAAA
genomic: TCCGATTCTGCAAGTATGAGTCGATCAGGTCAGCCTCCAGATCTCAAGAAgtaagttctc ... tgtaatgcagGTACATGGACAAGAAACTCCAAA
EST: gi|152038476|gb|AV823925.2|AV823925
EST:     TCCGATTCTGCAAGTATGAGTCGATCAGGTCAGCCTCCAGATCTCAAGAA                         GTACATGGACAAGAAACTCCAAA
genomic: TCCGATTCTGCAAGTATGAGTCGATCAGGTCAGCCTCCAGATCTCAAGAAgtaagttctc ... tgtaatgcagGTACATGGACAAGAAACTCCAAA
EST: gi|163994963|gb|ES158211.1|ES158211
EST:     TCCGATTCTGCAAGTATGAGTCGATCAGGTCAGCCTCCTGATCTCAAGAA                         GTACATGGACAAGAAACTCCAAATTAAGCT
genomic: TCCGATTCTGCAAGTATGAGTCGATCAGGTCAGCCTCCAGATCTCAAGAAgtaagttctc ... tgtaatgcagGTACATGGACAAGAAACTCCAAATTAAGCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gctcctacttcttcgtgtttctgattttgttcttcgtttgtttcatgtaatgcagGTACATGGACAAGAAACTCCAAA
                  ttctgat  putative branch site (score: 3)
                       attttgtt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagttctcttcgccacttttttccttttgatttctaatttctctgtatccatttagttgaagtttttggtttcatagagctcctacttcttcgtgtttctgattttgttcttcgtttgtttcatgtaatgcagGTACATGGACAAGAAACTCCAAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA