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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtctgttattctttctatcaatatgttcatcaagtatactaaatctaatttggcaatgagtctggtgttggagagaaattctcccttaaaaaagtttccctgcttaatactgacaagaaacaacggttttctgtttcatctgtgctagGTTCGTGAAGTTAAACCTGATGTGCTTCTTGGTTTATCAGCAGTTGGAGGGTTATTCTCAAAAGAG

Basic information

species Arabidopsis thaliana
transcript AT2G13560.1
intron # 11
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|124888476|gb|EH967378.1|EH967378
EST:     AGAAATGGAGCCGTCAGGGATTAAAAGAAGGAGCAACTCTTGTGGAAGTG                         GTTCGTGAAGTTAAACCTGAGTGTGCTT
genomic: AGAAATGGAG-CGTCAGGGATTAAAAGAAGGAGCAACTCTTGTGGAAGTGgtctgttatt ... tctgtgctagGTTCGTGAAGTTAAACCTGA-TGTGCTT
EST: gi|125095515|gb|EL152623.1|EL152623
EST:     AAGAAATGGAGCGTCAGGGATTAAAAGAAGGAGCAACTCTTGTGGAAGTG                         GTTCGTGAAGTTAAACCTGATGTGCTTCTTGGTTTATCAGCAGTTGG
genomic: AAGAAATGGAGCGTCAGGGATTAAAAGAAGGAGCAACTCTTGTGGAAGTGgtctgttatt ... tctgtgctagGTTCGTGAAGTTAAACCTGATGTGCTTCTTGGTTTATCAGCAGTTGG
EST: gi|125327132|gb|EL341212.1|EL341212
EST:     AAGAAATGGAGCGTCAGGGATTAAAAGAAGGAGCAACTCTTGTGGAAGTG                         GTTCGTGAAGTTAAACCTGA
genomic: AAGAAATGGAGCGTCAGGGATTAAAAGAAGGAGCAACTCTTGTGGAAGTGgtctgttatt ... tctgtgctagGTTCGTGAAGTTAAACCTGA
EST: gi|116453720|gb|EG496312.1|EG496312
EST:     AAGAAATGGAGCGTCAGGGATTAAAAGAAGGAGCAACTCTTGTGGAAGTG                         GTTCGTGAAGTTAAACCTGATGTGCTTCTTGGTTTATCAGCAGTTGGAGGG
genomic: AAGAAATGGAGCGTCAGGGATTAAAAGAAGGAGCAACTCTTGTGGAAGTGgtctgttatt ... tctgtgctagGTTCGTGAAGTTAAACCTGATGTGCTTCTTGGTTTATCAGCAGTTGGAGGG
EST: gi|124864652|gb|EH949089.1|EH949089
EST:     TGGAGCGTCAGGGATTAAAAGAAGGAGCAACTCTTGTGGAAGTG                         GTTCGTGAAGTTAAACCTGATGTGCTTCTTGGTTTATCAGCAGTTGGAGGG
genomic: TGGAGCGTCAGGGATTAAAAGAAGGAGCAACTCTTGTGGAAGTGgtctgttatt ... tctgtgctagGTTCGTGAAGTTAAACCTGATGTGCTTCTTGGTTTATCAGCAGTTGGAGGG
EST: gi|47828604|gb|CK118288.1|CK118288
EST:     AAGAAATGGAGCGTCAGGGATTAAAAGAAGGAGCAACTCTTGTGGAAGTG                         GTTCGTGAAGTTAAACCTGATGTGCTTCTTGGTTTATCAGCAGTTGGAGGG
genomic: AAGAAATGGAGCGTCAGGGATTAAAAGAAGGAGCAACTCTTGTGGAAGTGgtctgttatt ... tctgtgctagGTTCGTGAAGTTAAACCTGATGTGCTTCTTGGTTTATCAGCAGTTGGAGGG
EST: gi|124864904|gb|EH949341.1|EH949341
EST:     AAGAAATGGAGCGTCAGGGATTAAAAGAAGGAGCAACTCTTGTGGAAGTG                         GTTCGTGAAGTTAAACCTGATGTGCTTCTTGGTTTATCAGCAGTTGGAGGG
genomic: AAGAAATGGAGCGTCAGGGATTAAAAGAAGGAGCAACTCTTGTGGAAGTGgtctgttatt ... tctgtgctagGTTCGTGAAGTTAAACCTGATGTGCTTCTTGGTTTATCAGCAGTTGGAGGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtttccctgcttaatactgacaagaaacaacggttttctgtttcatctgtgctagGTTCGTGAAGTTAAACCTGATGTGCTTCTTGGTTTATCAGCAGTTGGAGGGTTATTCTCAAAAGAG
              tactgac  putative branch site (score: 1)
                                 ttttctgtttcatct  putative PPT
          ttaatact  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtctgttattctttctatcaatatgttcatcaagtatactaaatctaatttggcaatgagtctggtgttggagagaaattctcccttaaaaaagtttccctgcttaatactgacaagaaacaacggttttctgtttcatctgtgctagGTTCGTGAAGTTAAACCTGATGTGCTTCTTGGTTTATCAGCAGTTGGAGGGTTATTCTCAAAAGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG