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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacattccacacctcagcttaagaagatgactaactcttattattgccacattgtgttaccttacctctgtttttgggtgacaccgccggatattttaacttgttggctctgtaatttgatatttgatgttcttgaacactatctataaggatctttcttgattacagGTGCAAAGATGTGGCAAGAGAACAGGGAAAAATGGGTGGGAGATCAATCTCGACAAAGAAAAAACACTGCAAAGGATCAGATTATAAG

Basic information

species Arabidopsis thaliana
transcript AT3G54880.1
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|125039536|gb|EL111805.1|EL111805
EST:     AAGCTCGGTGAAAACGAACAGCGAAAACACCCTTACACTTGTGAATCATG                         GTGCAAAGATGTGGCAAGAGAACAGGGAAAAATGGGTGGGAGATCA
genomic: AAGCTCGGTGAAAACGAACAGCGAAAACACCCTTACACTTGTGAATCATGgtacattcca ... ttgattacagGTGCAAAGATGTGGCAAGAGAACAGGGAAAAATGGGTGGGAGATCA
EST: gi|125234625|gb|EL248710.1|EL248710
EST:     AAGCTCGGTGAAAACGAACAGCGAAAACACCCTTACACTTGTGAATCATG                         GTGCAAAGATGTGG
genomic: AAGCTCGGTGAAAACGAACAGCGAAAACACCCTTACACTTGTGAATCATGgtacattcca ... ttgattacagGTGCAAAGATGTGG
EST: gi|124881694|gb|EH960596.1|EH960596
EST:     CGGTGAAAACGAACAGCGAAAACACCCTTACACTTGTGAATCATG                         GTGCAAAGATGTGGCAAGAGAACAGGGAAAAATGGGTGGGGGATCAATCTC
genomic: CGGTGAAAACGAACAGCGAAAACACCCTTACACTTGTGAATCATGgtacattcca ... ttgattacagGTGCAAAGATGTGGCAAGAGAACAGGGAAAAATGGGTGGGAGATCAATCTC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aatttgatatttgatgttcttgaacactatctataaggatctttcttgattacagGTGCAAAGATGTGGCAAGAGAACAGGGAAAAATGGGTGGGAGATCAATCTCGACAAAGAAAAAACACTGCAAAGGATCAGATTATAAG
                                           tcttgat  putative branch site (score: 4)
                                       tctttctt  CT-rich tract
      atatttgat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacattccacacctcagcttaagaagatgactaactcttattattgccacattgtgttaccttacctctgtttttgggtgacaccgccggatattttaacttgttggctctgtaatttgatatttgatgttcttgaacactatctataaggatctttcttgattacagGTGCAAAGATGTGGCAAGAGAACAGGGAAAAATGGGTGGGAGATCAATCTCGACAAAGAAAAAACACTGCAAAGGATCAGATTATAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGATCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAAG