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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cttcttttgaatattgacttacattcacattaatctttagttgagaaattaaaaatcaatggagttgttgagctaatgatatgtttttggtgtataacagGCGACTTGGTGATATGTCCGGAAGGCACGACGTGTAGAGAAGAGTATCTACTGAGATTTAGCGCTCTATTCGCAGAGCTAAGCGACCGGATTGTGCCAGT

Basic information

species Arabidopsis thaliana
transcript AT4G00400.1
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|163985229|gb|ES030596.1|ES030596
EST:     CCGTGACCGTGCCACCGATGCTGCCAACATGAGAAAACTTCTCGAGAAAG                         GCGACTTGGTGATATGTCC
genomic: CCGTGACCGTGCCACCGATGCTGCCAACATGAGAAAACTTCTCGAGAAAGgtactttaca ... tgtataacagGCGACTTGGTGATATGTCC
EST: gi|125127193|gb|EL172166.1|EL172166
EST:     CCGTGACCGTGCCACCGATGCTGCCAACATGAGAAAACTTCTCGAGAAAG                         GCGACTTGGTGATATGTCCGGAAGGCACGACG
genomic: CCGTGACCGTGCCACCGATGCTGCCAACATGAGAAAACTTCTCGAGAAAGgtactttaca ... tgtataacagGCGACTTGGTGATATGTCCGGAAGGCACGACG
EST: gi|164194617|gb|EL987122.1|EL987122
EST:     CCGTGACCGTGCCACCGATGCTGCCAACATGAGAAAACTTCTCGAGAAAG                         GCGACTTGGTGATATGTCCGGAAGGCACGACGTGTAGAGAAGAGTA
genomic: CCGTGACCGTGCCACCGATGCTGCCAACATGAGAAAACTTCTCGAGAAAGgtactttaca ... tgtataacagGCGACTTGGTGATATGTCCGGAAGGCACGACGTGTAGAGAAGAGTA
EST: gi|125314116|gb|EL328201.1|EL328201
EST:     CCGTGACCGTGCCACCGATGCTGCCAACATGAGAAAACTTCTCGAGAAAG                         GCGACTTGGTGA
genomic: CCGTGACCGTGCCACCGATGCTGCCAACATGAGAAAACTTCTCGAGAAAGgtactttaca ... tgtataacagGCGACTTGGTGA
EST: gi|164052983|gb|EL990695.1|EL990695
EST:     CCGTGACCGTGCCACCGATGCTGCCAACATGNGAAAACTTCTCGAGAAAG                         GCGACTTGGTGATATGTCCGGAAGGCACGACGTGTAGAGAAGAGTA
genomic: CCGTGACCGTGCCACCGATGCTGCCAACATGAGAAAACTTCTCGAGAAAGgtactttaca ... tgtataacagGCGACTTGGTGATATGTCCGGAAGGCACGACGTGTAGAGAAGAGTA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaattaaaaatcaatggagttgttgagctaatgatatgtttttggtgtataacagGCGACTTGGTGATATGTCCGGAAGGCACGACGTGTAGAGAAGAGTATCTACTGAGATTTAGCGCTCTATTCGCAGAGCTAAGCGACCGGATTGTGCCAGT
                         agctaat  putative branch site (score: 3)
                            taatgatatgttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cttcttttgaatattgacttacattcacattaatctttagttgagaaattaaaaatcaatggagttgttgagctaatgatatgtttttggtgtataacagGCGACTTGGTGATATGTCCGGAAGGCACGACGTGTAGAGAAGAGTATCTACTGAGATTTAGCGCTCTATTCGCAGAGCTAAGCGACCGGATTGTGCCAGT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCT
- - - - - - - - - - - attcaca
- - - - - - - - - - - - - - - - - - - - - - - - - - aaatcaa