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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgaccctttgattcccttcccttttcatagttttcgattggcggttagattgtcttgctgactgtctttttgagctctgcagGTGCACCATTTAAGAAATTCGCATCACTGCGTGAAGAATGGGCATTGAAGAACCGATACATCAGCCCAG

Basic information

species Arabidopsis thaliana
transcript AT1G12000.1
intron # 14
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|86088437|gb|DR384196.1|DR384196
EST:     GTAAGTTCAAGCCTGTGATCAAGAAAGCAATGGTGGAACTTGAAG                         GTGCACCATTTAAGAAATTCGCATCACTGCGTGAAGAATGGGCATTGAAGA
genomic: GTAAGTTCAAGCCTGTGATCAAGAAAGCAATGGTGGAACTTGAAGgtgacccttt ... agctctgcagGTGCACCATTTAAGAAATTCGCATCACTGCGTGAAGAATGGGCATTGAAGA
EST: gi|86060419|gb|DR356176.1|DR356176
EST:     GTAAGTTCAAGCCTGTGATCAAGAAAGCAATGGTGGAACTTGAAG                         GTGCACCATTTAAGAAATTCGCATCACTGCGTGAAGAATGGGCATTGAAGA
genomic: GTAAGTTCAAGCCTGTGATCAAGAAAGCAATGGTGGAACTTGAAGgtgacccttt ... agctctgcagGTGCACCATTTAAGAAATTCGCATCACTGCGTGAAGAATGGGCATTGAAGA
EST: gi|124796242|gb|EH885921.1|EH885921
EST:     GTAAGTTCAAGCCTGTGATCAAGAAAGCAATGGTGGAACTTGAAG                         GTGCACCATTTAAGAAATT
genomic: GTAAGTTCAAGCCTGTGATCAAGAAAGCAATGGTGGAACTTGAAGgtgacccttt ... agctctgcagGTGCACCATTTAAGAAATT
EST: gi|86060418|gb|DR356175.1|DR356175
EST:     GTAAGTTCAAGCCTGTGATCAAGAAAGCAATGGTGGAACTTGAAG                         GTGCACCATTTAAGAAATTCGCATCACTGCGTGAAGAATGGGCATTGAAGA
genomic: GTAAGTTCAAGCCTGTGATCAAGAAAGCAATGGTGGAACTTGAAGgtgacccttt ... agctctgcagGTGCACCATTTAAGAAATTCGCATCACTGCGTGAAGAATGGGCATTGAAGA
EST: gi|125269642|gb|EL283727.1|EL283727
EST:     TTCAAGCCTGTGATCAAGAAAGCAATGGTGGAACTTGAAG                         GTGCACCATTTAAGAAATTCGCATCACTGCGTGAAGAATGGGCATTGAAGA
genomic: TTCAAGCCTGTGATCAAGAAAGCAATGGTGGAACTTGAAGgtgacccttt ... agctctgcagGTGCACCATTTAAGAAATTCGCATCACTGCGTGAAGAATGGGCATTGAAGA
EST: gi|124743697|gb|EH834859.1|EH834859
EST:     GTAAGTTCAAGCCTGTGATCAAGAAAGCAATGGTGGAACTTGAAG                         GTGCACCATTTAAGAAATTCGCATCACTGCG
genomic: GTAAGTTCAAGCCTGTGATCAAGAAAGCAATGGTGGAACTTGAAGgtgacccttt ... agctctgcagGTGCACCATTTAAGAAATTCGCATCACTGCG
EST: gi|125297233|gb|EL311318.1|EL311318
EST:     GTAAGTTCAAGCCTGTGATCAAGTAAGCAATGGTGGAACTTGAAG                         GTGCACCATTTAAGAAA
genomic: GTAAGTTCAAGCCTGTGATCAAGAAAGCAATGGTGGAACTTGAAGgtgacccttt ... agctctgcagGTGCACCATTTAAGAAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tagttttcgattggcggttagattgtcttgctgactgtctttttgagctctgcagGTGCACCATTTAAGAAATTCGCATCACTGCGTGAAGAATGGGCATTGAAGAACCGATACATCAGCCCAG
                            tgctgac  putative branch site (score: 2)
                 ttagatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgaccctttgattcccttcccttttcatagttttcgattggcggttagattgtcttgctgactgtctttttgagctctgcagGTGCACCATTTAAGAAATTCGCATCACTGCGTGAAGAATGGGCATTGAAGAACCGATACATCAGCCCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC