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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...agtttccgtgtattagattgatttaagccaacatgttttgtgtcttagcatgacgtggtcttatcgtttgaaagaataacaatatctatgccttttgcagGCTGCTTGTAATGAACAGCTGGAAAAGTCTGAAAGGGCATTTCTTCTCCACCTGTTACAATGGAATAGTTACAACAACGTGAAAGAG

Basic information

species Arabidopsis thaliana
transcript AT5G18420.1
intron # 2
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|164042206|gb|ES071091.1|ES071091
EST:     AAATGATAAGT                         GCTGCTTGTAATGAACAGCTGG-AAAGTCTGAAAGGGCATTTCTTCTCCAC
genomic: AAATGATAAGTgtaagcaccc ... ccttttgcagGCTGCTTGTAATGAACAGCTGGAAAAGTCTGAAAGGGCATTTCTTCTCCAC
EST: gi|125123088|gb|EL169537.1|EL169537
EST:     TTCTTCACAGAAGCCATCTTTCAACCCGTTTTTATCTGAAATGATAAGT                         GCTGCTTGTAATGAACAGCTAGGAAAAAGTCTGAAAGGGCATTTCTTCTCC
genomic: TTCTTCACAGAAGCCATCTTTCAACCCGTTTTTATCTGAAATGATAAGTgtaagcaccc ... ccttttgcagGCTGCTTGTAATGAACAGCT-GGAAAA-GTCTGAAAGGGCATTTCTTCTCC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tagcatgacgtggtcttatcgtttgaaagaataacaatatctatgccttttgcagGCTGCTTGTAATGAACAGCTGGAAAAGTCTGAAAGGGCATTTCTTCTCCACCTGTTACAATGGAATAGTTACAACAACGTGAAAGAG
                            gaataac  putative branch site (score: 2)
                                           tgcctttt  putative PPT
                         aaagaataacaatat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
agtttccgtgtattagattgatttaagccaacatgttttgtgtcttagcatgacgtggtcttatcgtttgaaagaataacaatatctatgccttttgcagGCTGCTTGTAATGAACAGCTGGAAAAGTCTGAAAGGGCATTTCTTCTCCACCTGTTACAATGGAATAGTTACAACAACGTGAAAGAG

- - - - - - - - - - - - aagccaa
- - - - - - - - - - - - - - - - -tgttttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gaaagaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aacaata