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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaaaattttgagctgacttttttggtagctttgagttaatgtgtgtttctgttaacttatgtcctgagacatttactctcttccctattggcagGCTCGGATTTATCACCGCTTGACTTAATCAACGTACAGACCTTTGCTCAGAAAGTTATGGACCTTGCTGACTACAGGAAGAAGCTCTATGATTATCTTGT

Basic information

species Arabidopsis thaliana
transcript AT1G56110.1
intron # 4
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|164188323|gb|EL983759.1|EL983759
EST:     GGATGAAGATAAGGCAAAGGAGGTCATCGAAGCTGGAAAAGCATCCATGG                         GCTCGGATTTATCACCGCTTGACTTA
genomic: GGATGAAGATAAGGCAAAGGAGGTCATCGAAGCTGGAAAAGCATCCATGGgtaaaaattt ... ctattggcagGCTCGGATTTATCACCGCTTGACTTA
EST: gi|164202444|gb|ES050464.1|ES050464
EST:     GGCAAAGGAGGTCATCGAAGCTGGTTAAAAGCATCCATGG                         GCTCGGATTTATCACCGCTTGACTTAATCAACGTACAGACCTTTGCTCAGA
genomic: GGCAAAGGAGGTCATCGAAGCTGG--AAAAGCATCCATGGgtaaaaattt ... ctattggcagGCTCGGATTTATCACCGCTTGACTTAATCAACGTACAGACCTTTGCTCAGA
EST: gi|125298276|gb|EL312361.1|EL312361
EST:     GGATGAAGATAAGGCAAAGGAGGTCATCGAAGCTGGAAAAGCATCCATGG                         GCTCGGATTTATCACCGCTTGACTTAATCAACGTACAGA
genomic: GGATGAAGATAAGGCAAAGGAGGTCATCGAAGCTGGAAAAGCATCCATGGgtaaaaattt ... ctattggcagGCTCGGATTTATCACCGCTTGACTTAATCAACGTACAGA
EST: gi|124811928|gb|EH896794.1|EH896794
EST:     GGATGAAGATAAGGCAAAGGAGGTCATCGAAGCTGGAAAAGCATCCATGG                         GCTCGGATTTATCACCGCTTGACTTAAT
genomic: GGATGAAGATAAGGCAAAGGAGGTCATCGAAGCTGGAAAAGCATCCATGGgtaaaaattt ... ctattggcagGCTCGGATTTATCACCGCTTGACTTAAT
EST: gi|116482901|gb|EG525493.1|EG525493
EST:     GGATGAAGATAAGGCAAAGGAGGTCATCGAAGCTGGAAAAGCATCCATGG                         GCTCGGATTTATCACCGCTTGACTTAATCAACGTACAGACCTTTGCTCAGA
genomic: GGATGAAGATAAGGCAAAGGAGGTCATCGAAGCTGGAAAAGCATCCATGGgtaaaaattt ... ctattggcagGCTCGGATTTATCACCGCTTGACTTAATCAACGTACAGACCTTTGCTCAGA
EST: gi|164186264|gb|ES052552.1|ES052552
EST:     GGATGAAGATAAGGCAAAGGAGGTCATCGAAGCTGGAAAAGCATCCATGG                         GCTCGGATTTATCACCGCTTGACTTAATCAACGTACAGACCTTTGCTC
genomic: GGATGAAGATAAGGCAAAGGAGGTCATCGAAGCTGGAAAAGCATCCATGGgtaaaaattt ... ctattggcagGCTCGGATTTATCACCGCTTGACTTAATCAACGTACAGACCTTTGCTC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgtgtgtttctgttaacttatgtcctgagacatttactctcttccctattggcagGCTCGGATTTATCACCGCTTGACTTAATCAACGTACAGACCTTTGCTCAGAAAGTTATGGACCTTGCTGACTACAGGAAGAAGCTCTATGATTATCTTGT
          tgttaac  putative branch site (score: 2)
                                tttactctcttcccta  putative PPT
            ttaacttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaaaattttgagctgacttttttggtagctttgagttaatgtgtgtttctgttaacttatgtcctgagacatttactctcttccctattggcagGCTCGGATTTATCACCGCTTGACTTAATCAACGTACAGACCTTTGCTCAGAAAGTTATGGACCTTGCTGACTACAGGAAGAAGCTCTATGATTATCTTGT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC