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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatcaaatctatctccgatgttgatctactctgtttctccggatttatgatttctctattcaatttccgatgattgttagatctacggggcttttgatcctgcgattactgttgctttttgtttgttaatcagAGAGAATGTTGGGAATCTTGAGGCAAAGAGCCATCGATGGAGCTTCG

Basic information

species Arabidopsis thaliana
transcript AT5G50850.1
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|164215085|gb|EL970209.1|EL970209
EST:     TTCGCCGGCGTGGTTAGATCGTACAAAGCTCAG                         AGAGAATGTTGGGAATCTTGAGGCAAAGAGCCATCGATGGAGCTTCG
genomic: TTCGCCGGCGTGGTTAGATCGTACAAAGCTCAGgtaatcaaat ... tgttaatcagAGAGAATGTTGGGAATCTTGAGGCAAAGAGCCATCGATGGAGCTTCG
EST: gi|116443796|gb|EG486388.1|EG486388
EST:     CCGCCGTCTCTCACTTTTTCGCCGGCGTGGTTAGATCGTACAAAGCTCAG                         AGAGAATGTTGGGAATCTTGAGGCAAAGAGCCATCGATGGAGCTTCG
genomic: CCGCCGTCTCTCACTTTTTCGCCGGCGTGGTTAGATCGTACAAAGCTCAGgtaatcaaat ... tgttaatcagAGAGAATGTTGGGAATCTTGAGGCAAAGAGCCATCGATGGAGCTTCG
EST: gi|116376958|gb|EG419550.1|EG419550
EST:     CTCACTTTTTCGCCGGCGTGGTTAGATCGTACAAAGCTCAG                         AGAGAATGTTGGGAATCTTGAGGCAAAGAGCCATCGATGGAGCTTCG
genomic: CTCACTTTTTCGCCGGCGTGGTTAGATCGTACAAAGCTCAGgtaatcaaat ... tgttaatcagAGAGAATGTTGGGAATCTTGAGGCAAAGAGCCATCGATGGAGCTTCG
EST: gi|125027934|gb|EL100203.1|EL100203
EST:     CCGTCTCTCACTTTTTCGCCGGCGTGGTTAGATCGTACAAAGCTCAG                         AGAGAATGTTGGGAATCTTGAGGCAAAGAGCCATCGATGGAGCTTCGACTC
genomic: CCGTCTCTCACTTTTTCGCCGGCGTGGTTAGATCGTACAAAGCTCAGgtaatcaaat ... tgttaatcagAGAGAATGTTGGGAATCTTGAGGCAAAGAGCCATCGATGGAGCTTCGACTC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agatctacggggcttttgatcctgcgattactgttgctttttgtttgttaatcagAGAGAATGTTGGGAATCTTGAGGCAAAGAGCCATCGATGGAGCTTCG
             ttttgat  putative branch site (score: 4)
                                    ctttttgttt  putative PPT
                                     tttttgtttgttaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaatcaaatctatctccgatgttgatctactctgtttctccggatttatgatttctctattcaatttccgatgattgttagatctacggggcttttgatcctgcgattactgttgctttttgtttgttaatcagAGAGAATGTTGGGAATCTTGAGGCAAAGAGCCATCGATGGAGCTTCG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT