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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgattgacttcaaattctgattctttagggtttaatataacctaattttcgtttcttgtaccttcagTGTAAACCTTAGACTGTACAGAACCCTTGTGGAAGAACTTGCCAGAGAATTAAAAGAAGAGTTTTCCGCAAACGCTGAATCTAGAGCTTCTGGGATGGTG

Basic information

species Arabidopsis thaliana
transcript AT5G39930.1
intron # 4
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|116437659|gb|EG480251.1|EG480251
EST:     TTTCCTCTTGATAAGGCTCTTATTCACTACTTTGGTCTCACAAATCCAAG                         TGTAAACCTTAGACTGTACAGAACCCTTGTGGAAGAACTTGCCAGAGAATT
genomic: TTTCCTCTTGATAAGGCTCTTATTCACTACTTTGGTCTCACAAATCCAAGgtgattgact ... gtaccttcagTGTAAACCTTAGACTGTACAGAACCCTTGTGGAAGAACTTGCCAGAGAATT
EST: gi|116437653|gb|EG480245.1|EG480245
EST:     TTTCCTCTTGATAAGGCTCTTATTCACTACTTTGGTCTCACAAATCCAAG                         TGTAAACCTTAGACTGTACAGAACCCTTGTGGAAGAACTTGCCAGAGAATT
genomic: TTTCCTCTTGATAAGGCTCTTATTCACTACTTTGGTCTCACAAATCCAAGgtgattgact ... gtaccttcagTGTAAACCTTAGACTGTACAGAACCCTTGTGGAAGAACTTGCCAGAGAATT
EST: gi|116437665|gb|EG480257.1|EG480257
EST:     TTTCCTCTTGATAAGGCTCTTATTCACTACTTTGGTCTCACAAATCCAAG                         TGTAAACCTTAGACTGTACAGAACCCTTGTGGAAGAACTTGCCAGAGAATT
genomic: TTTCCTCTTGATAAGGCTCTTATTCACTACTTTGGTCTCACAAATCCAAGgtgattgact ... gtaccttcagTGTAAACCTTAGACTGTACAGAACCCTTGTGGAAGAACTTGCCAGAGAATT
EST: gi|116437661|gb|EG480253.1|EG480253
EST:     TTTCCTCTTGATAAGGCTCTTATTCACTACTTTGGTCTCACAAATCCAAG                         TGTAAACCTTAGACTGTACAGAACCCTTGTGGAAGAACTTGCC
genomic: TTTCCTCTTGATAAGGCTCTTATTCACTACTTTGGTCTCACAAATCCAAGgtgattgact ... gtaccttcagTGTAAACCTTAGACTGTACAGAACCCTTGTGGAAGAACTTGCC
EST: gi|116463908|gb|EG506500.1|EG506500
EST:     TTTCCTCTTGATAAGGCTCTTATTCACTACTTTGGTCTCACAAATCCAAG                         TGTAAACCTTAGACTGTACAGAACCCTTGTGGAAGAACTTGCCAGAGAATT
genomic: TTTCCTCTTGATAAGGCTCTTATTCACTACTTTGGTCTCACAAATCCAAGgtgattgact ... gtaccttcagTGTAAACCTTAGACTGTACAGAACCCTTGTGGAAGAACTTGCCAGAGAATT
EST: gi|116437666|gb|EG480258.1|EG480258
EST:     TTTCCTCTTGATAAGGCTCTTATTCACTACTTTGGTCTCACAAATCCAAG                         TGTAAACCTTAGACTGTACAGAACCCTTGTGGAAGAACTTGCCAGAGAATT
genomic: TTTCCTCTTGATAAGGCTCTTATTCACTACTTTGGTCTCACAAATCCAAGgtgattgact ... gtaccttcagTGTAAACCTTAGACTGTACAGAACCCTTGTGGAAGAACTTGCCAGAGAATT
EST: gi|116463918|gb|EG506510.1|EG506510
EST:     TTTCCTCTTGATAAGGCTCTTATTCACTACTTTGGTCTCACAAATCCAAG                         TGTAAACCTTAGACTGTACAGAACCCTTGTGGAAGAACTTGCCAGAGAATT
genomic: TTTCCTCTTGATAAGGCTCTTATTCACTACTTTGGTCTCACAAATCCAAGgtgattgact ... gtaccttcagTGTAAACCTTAGACTGTACAGAACCCTTGTGGAAGAACTTGCCAGAGAATT
EST: gi|116437669|gb|EG480261.1|EG480261
EST:     TTTCCTCTTGATAAGGCTCTTATTCACTACTTTGGTCTCACAAATCCAAG                         TGTAAACCTTAGACTGTACAGAACCCTTGTGGAAGAACTTGCCAGAGAATT
genomic: TTTCCTCTTGATAAGGCTCTTATTCACTACTTTGGTCTCACAAATCCAAGgtgattgact ... gtaccttcagTGTAAACCTTAGACTGTACAGAACCCTTGTGGAAGAACTTGCCAGAGAATT
EST: gi|116437664|gb|EG480256.1|EG480256
EST:     TTTCCTCTTGATAAGGCTCTTATTCACTACTTTGGTCTCACAAATCCAAG                         TGTAAACCTTAGACTGTACAGAACCCTTGTGGAAGAACTTGCCAGAGAATT
genomic: TTTCCTCTTGATAAGGCTCTTATTCACTACTTTGGTCTCACAAATCCAAGgtgattgact ... gtaccttcagTGTAAACCTTAGACTGTACAGAACCCTTGTGGAAGAACTTGCCAGAGAATT
EST: gi|116463874|gb|EG506466.1|EG506466
EST:     TTTCCTCTTGATAAGGCTCTTATTCACCACTTTGGTCTCACAAATCCAAG                         TGTAAACCTTAGACCGTACAGAACCCTTGTGGAAGAACTTGCCAGAGAATT
genomic: TTTCCTCTTGATAAGGCTCTTATTCACTACTTTGGTCTCACAAATCCAAGgtgattgact ... gtaccttcagTGTAAACCTTAGACTGTACAGAACCCTTGTGGAAGAACTTGCCAGAGAATT
EST: gi|116437658|gb|EG480250.1|EG480250
EST:     TTTCCTCTTGATAAGGCTCTTATTCACTACTTTGGTCTCACAAATCCAAG                         TGTAAACCTTAGACTGTACAGAACCCTTGTGGAAGAACTTGCCAGAGAATT
genomic: TTTCCTCTTGATAAGGCTCTTATTCACTACTTTGGTCTCACAAATCCAAGgtgattgact ... gtaccttcagTGTAAACCTTAGACTGTACAGAACCCTTGTGGAAGAACTTGCCAGAGAATT
EST: gi|116463877|gb|EG506469.1|EG506469
EST:     GCTCTTATTCACTACTTTGGTCTCACAAATCCGAG                         TGTAAACCTTAGACTGTACAGAACCCTTGTGGAAGAACTTGCCAGAGAATT
genomic: GCTCTTATTCACTACTTTGGTCTCACAAATCCAAGgtgattgact ... gtaccttcagTGTAAACCTTAGACTGTACAGAACCCTTGTGGAAGAACTTGCCAGAGAATT
EST: gi|116463913|gb|EG506505.1|EG506505
EST:     TGGTCTCACAAATCCAAG                         TGTAAACCTTAGACTGTACAGAACCCTTGTGGAAGAACTTGCCAGAGAATT
genomic: TGGTCTCACAAATCCAAGgtgattgact ... gtaccttcagTGTAAACCTTAGACTGTACAGAACCCTTGTGGAAGAACTTGCCAGAGAATT
EST: gi|116463891|gb|EG506483.1|EG506483
EST:     TTTCCTCTTGATAAGGCTCTTATTCACTACTTTGGTCTCACAAATCCAAG                         TGTAAACCTTAGACTGTACAGAACCCTTGTGGAAGAACTTGCCAGAGAATT
genomic: TTTCCTCTTGATAAGGCTCTTATTCACTACTTTGGTCTCACAAATCCAAGgtgattgact ... gtaccttcagTGTAAACCTTAGACTGTACAGAACCCTTGTGGAAGAACTTGCCAGAGAATT
EST: gi|116463879|gb|EG506471.1|EG506471
EST:     TTTCCTCTTGATAAGGCTCTTATTCACTACTTTGGTCTCACAAATCCAAG                         TGTAAACCTTAGACTGTACAGAACCCTTGTGGAAGAACTTGCCAGAGAATT
genomic: TTTCCTCTTGATAAGGCTCTTATTCACTACTTTGGTCTCACAAATCCAAGgtgattgact ... gtaccttcagTGTAAACCTTAGACTGTACAGAACCCTTGTGGAAGAACTTGCCAGAGAATT
EST: gi|116463884|gb|EG506476.1|EG506476
EST:     TTTCCTCTTGATAAGGCTCTTATTCACTACTTTGGTCTCACAAATCCAAG                         TGTAAACCTTAGACTGTACAGAACCCTTGTGGAAGAACTTGCCAGAGAATT
genomic: TTTCCTCTTGATAAGGCTCTTATTCACTACTTTGGTCTCACAAATCCAAGgtgattgact ... gtaccttcagTGTAAACCTTAGACTGTACAGAACCCTTGTGGAAGAACTTGCCAGAGAATT
EST: gi|116463901|gb|EG506493.1|EG506493
EST:     TTTCCTCTTGATAAGGCTCTTATTCACTACTTTGGTCTCACAAATCCAAG                         TGTAAACCTTAGACTGTACAGAACCCTTGTGGAAGAACTTGCCAGAGAATT
genomic: TTTCCTCTTGATAAGGCTCTTATTCACTACTTTGGTCTCACAAATCCAAGgtgattgact ... gtaccttcagTGTAAACCTTAGACTGTACAGAACCCTTGTGGAAGAACTTGCCAGAGAATT
EST: gi|116437642|gb|EG480234.1|EG480234
EST:     TTTCCTCTTGATAAGGCTCTTATTCACTACTTTGGTCTCACAAATCCAAG                         TGTAAACCTTAGACTGTACAGAACCCTTGTGGAAGAACTTGCCAGAGAATT
genomic: TTTCCTCTTGATAAGGCTCTTATTCACTACTTTGGTCTCACAAATCCAAGgtgattgact ... gtaccttcagTGTAAACCTTAGACTGTACAGAACCCTTGTGGAAGAACTTGCCAGAGAATT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aattctgattctttagggtttaatataacctaattttcgtttcttgtaccttcagTGTAAACCTTAGACTGTACAGAACCCTTGTGGAAGAACTTGCCAGAGAATTAAAAGAAGAGTTTTCCGCAAACGCTGAATCTAGAGCTTCTGGGATGGTG
                           acctaat  putative branch site (score: 3)
                                 ttttcgtttcttgt  CT-rich tract
                  tttaatataacctaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgattgacttcaaattctgattctttagggtttaatataacctaattttcgtttcttgtaccttcagTGTAAACCTTAGACTGTACAGAACCCTTGTGGAAGAACTTGCCAGAGAATTAAAAGAAGAGTTTTCCGCAAACGCTGAATCTAGAGCTTCTGGGATGGTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCTT