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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttagaactcgcagcagctacaacatctaagctttgattagcagttttcaatattttttatttgttttcgtatttcagGTGGTTTACGGGTCTGGCGGAAGGAAATTCGCATTCCAGAACTTGGCACCGTTAGGTTGCTTACCGGCCGTGAAACAAGCAAGCGGAAATGTTCAAGAAT

Basic information

species Arabidopsis thaliana
transcript AT1G54030.1
intron # 3
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|116463066|gb|EG505658.1|EG505658
EST:     AACAAGCTTTTGTTGATCAAGTCATCACTACCATAAAAGCAGAAATAAAG                         GTGGTTTACGGGTCTGGCGGAAGGAAATTCGCATTCCAGAACTTGGCACCG
genomic: AACAAGCTTTTGTTGATCAAGTCATCACTACCATAAAAGCAGAAATAAAGgttagaactc ... cgtatttcagGTGGTTTACGGGTCTGGCGGAAGGAAATTCGCATTCCAGAACTTGGCACCG
EST: gi|124771056|gb|EH861186.1|EH861186
EST:     ACAAGCTTTTGTTTGATCAAGTCATCACTACCATAAAAGCAGAAATAAAG                         GTGGTTTACGGGTCTGGCGGAAGGAAATTCGCATTCCAG
genomic: ACAAGCTTTTG-TTGATCAAGTCATCACTACCATAAAAGCAGAAATAAAGgttagaactc ... cgtatttcagGTGGTTTACGGGTCTGGCGGAAGGAAATTCGCATTCCAG
EST: gi|125135561|gb|EL175816.1|EL175816
EST:     CACTACCATAAAAGCAGAAATAAAG                         GTGGTTTACGGGTCTGGCGGAAGGAAATTCGCATTCCAGAACTTGGCACCG
genomic: CACTACCATAAAAGCAGAAATAAAGgttagaactc ... cgtatttcagGTGGTTTACGGGTCTGGCGGAAGGAAATTCGCATTCCAGAACTTGGCACCG
EST: gi|164086410|gb|ES039173.1|ES039173
EST:     CACTACCATAAAAGCAGAAATAAAG                         GTGGTTTACGGGTCTGGCGGAAGGAAATTCGCATTCCAGAACTTGGCACCG
genomic: CACTACCATAAAAGCAGAAATAAAGgttagaactc ... cgtatttcagGTGGTTTACGGGTCTGGCGGAAGGAAATTCGCATTCCAGAACTTGGCACCG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

catctaagctttgattagcagttttcaatattttttatttgttttcgtatttcagGTGGTTTACGGGTCTGGCGGAAGGAAATTCGCATTCCAGAACTTGGCACCGTTAGGTTGCTTACCGGCCGTGAAACAAGCAAGCGGAAATGTTCAAGAAT
        ctttgat  putative branch site (score: 5)
                              ttttttatttgttttc  putative PPT
                     ttttcaatatttttta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttagaactcgcagcagctacaacatctaagctttgattagcagttttcaatattttttatttgttttcgtatttcagGTGGTTTACGGGTCTGGCGGAAGGAAATTCGCATTCCAGAACTTGGCACCGTTAGGTTGCTTACCGGCCGTGAAACAAGCAAGCGGAAATGTTCAAGAAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCAAG