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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgtttgttgcttttgggaagccttgatggtaatcttgaggataatctctcattttagattcatgattcatataatattctctgtctacacataattgcagCTTACATGCCGCATTTGAGCCTGCTTTACGCTGAGTTGACAGAGGAAGAGAAGAAGAATGCGCAGGAGAAAGCTTACACGCTCGATAGCAGCCTCGATGG

Basic information

species Arabidopsis thaliana
transcript AT4G18930.1
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|164215567|gb|ES092364.1|ES092364
EST:     GGAAGCTGGTGAACACTGTAAGAACCATTTCAATTGTTCCACTACCACAC                         CTTACATGCCGCATTTGAGCCTGCTTTACGCTGAGTTGAC
genomic: GGAAGCTGGTGAACACTGTAAGAACCATTTCAATTGTTCCACTACCACACgtaagctcct ... ataattgcagCTTACATGCCGCATTTGAGCCTGCTTTACGCTGAGTTGAC
EST: gi|125257127|gb|EL271212.1|EL271212
EST:     GGAAGCTGGTGAACACTGTAAGAACCATTTCAATTGTTCCACTACCACAC                         CTTACATGCCGCATTTGAGCCTGCTTTACGCTGAGTTGACAGAGG
genomic: GGAAGCTGGTGAACACTGTAAGAACCATTTCAATTGTTCCACTACCACACgtaagctcct ... ataattgcagCTTACATGCCGCATTTGAGCCTGCTTTACGCTGAGTTGACAGAGG
EST: gi|125045076|gb|EL117345.1|EL117345
EST:     GGAAGCTGGTGAACACTGTAAGAACCATTTCAATTGTTCCACTACCACAC                         CTTACATGCCGCATTTGAG
genomic: GGAAGCTGGTGAACACTGTAAGAACCATTTCAATTGTTCCACTACCACACgtaagctcct ... ataattgcagCTTACATGCCGCATTTGAG
EST: gi|164170373|gb|ES048420.1|ES048420
EST:     GGAAGCTGGTGAACACTGTAAGAACCATTTCAATTGTTCCACTACCACAC                         CTTACATGCCGCATTTGAGCCTGCTTTACGCTGAGTTGACAGA
genomic: GGAAGCTGGTGAACACTGTAAGAACCATTTCAATTGTTCCACTACCACACgtaagctcct ... ataattgcagCTTACATGCCGCATTTGAGCCTGCTTTACGCTGAGTTGACAGA
EST: gi|164138788|gb|ES200256.1|ES200256
EST:     GTTCCACTACCACAC                         CTTACATGCCGCATTTGAGCCTGCTTTACGCTGAGTTGACAGAGGAAAGAG
genomic: GTTCCACTACCACACgtaagctcct ... ataattgcagCTTACATGCCGCATTTGAGCCTGCTTTACGCTGAGTTGACAGAGGAA-GAG
EST: gi|163970638|gb|ES085244.1|ES085244
EST:     GCTGGTGAACACTGTAAGAACCATTTCAATTGTTCCACTACCACAC                         CTTACATGCCGCATTTGAGCCTGCTTTACGCTGAGTTGACAGAGGAAGAGA
genomic: GCTGGTGAACACTGTAAGAACCATTTCAATTGTTCCACTACCACACgtaagctcct ... ataattgcagCTTACATGCCGCATTTGAGCCTGCTTTACGCTGAGTTGACAGAGGAAGAGA
EST: gi|164233152|gb|ES162980.1|ES162980
EST:     CCACTAGCACAC                         CTTACATGCCGCATTTGAGCCTGCTTTACGCTGAGTTGACAGAGGAAGAGA
genomic: CCACTACCACACgtaagctcct ... ataattgcagCTTACATGCCGCATTTGAGCCTGCTTTACGCTGAGTTGACAGAGGAAGAGA
EST: gi|124981712|gb|EL054564.1|EL054564
EST:     GGAAGCTGGTGAACACTGTAAGAACCATTTCAATTGTTCCACTACCACAC                         CTTACATGCCGCA
genomic: GGAAGCTGGTGAACACTGTAAGAACCATTTCAATTGTTCCACTACCACACgtaagctcct ... ataattgcagCTTACATGCCGCA
EST: gi|124756717|gb|EH846847.1|EH846847
EST:     GGAAGCTGGTGAACACTGTAAGAACCATTTCAATTGTTCCACTACCACAC                         CTTACATGCCGCATTTGAGCCTGCTT
genomic: GGAAGCTGGTGAACACTGTAAGAACCATTTCAATTGTTCCACTACCACACgtaagctcct ... ataattgcagCTTACATGCCGCATTTGAGCCTGCTT
EST: gi|125145974|gb|EL181069.1|EL181069
EST:     TAAGAACCATTTCAATTGTTCCACTACCACAC                         CTTACATGCCGCATTTGAGCCTGCTTTACGCTGAGTTGACAGAGGAAGAGA
genomic: TAAGAACCATTTCAATTGTTCCACTACCACACgtaagctcct ... ataattgcagCTTACATGCCGCATTTGAGCCTGCTTTACGCTGAGTTGACAGAGGAAGAGA
EST: gi|125285121|gb|EL299206.1|EL299206
EST:     GGAAGCTGGTGAACACTGTAAGAACCATTTCAATTGTTCCACTACCACAC                         CTTACATGCCGCATTTGAGCCTGCTTTACGCTGAGTTGACAGAG
genomic: GGAAGCTGGTGAACACTGTAAGAACCATTTCAATTGTTCCACTACCACACgtaagctcct ... ataattgcagCTTACATGCCGCATTTGAGCCTGCTTTACGCTGAGTTGACAGAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctctcattttagattcatgattcatataatattctctgtctacacataattgcagCTTACATGCCGCATTTGAGCCTGCTTTACGCTGAGTTGACAGAGGAAGAGAAGAAGAATGCGCAGGAGAAAGCTTACACGCTCGATAGCAGCCTCGATGG
     attttagattcatgat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgtttgttgcttttgggaagccttgatggtaatcttgaggataatctctcattttagattcatgattcatataatattctctgtctacacataattgcagCTTACATGCCGCATTTGAGCCTGCTTTACGCTGAGTTGACAGAGGAAGAGAAGAAGAATGCGCAGGAGAAAGCTTACACGCTCGATAGCAGCCTCGATGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
tgtttgt
- - - - gcttttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ttctctg