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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtcaacgaactttaaatctctgttagacattcttttaactgtatgcaattagctactgtactactttggttaaaaaaagtgttgacctttagttcctaaactagtttgatcttatgatgtaggcagCTCGTGGAGGTGGAAAAATTGTTTTGAAGGGTCTTTATTCAGGATTAGCTGGAAATATCGCTGGTGTCTTACC

Basic information

species Arabidopsis thaliana
transcript AT4G39460.1
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|86037549|gb|DR333304.1|DR333304
EST:     TGAAACAGCTTTATACCCAATTGATACTATTAAGACTAGACTTCAGGCAG                         CTCGTGGAGGTGGAAAAATTGTTTTGAAGGGTCTTTATTCAGGATTAGCTG
genomic: TGAAACAGCTTTATACCCAATTGATACTATTAAGACTAGACTTCAGGCAGgtcaacgaac ... atgtaggcagCTCGTGGAGGTGGAAAAATTGTTTTGAAGGGTCTTTATTCAGGATTAGCTG
EST: gi|86037542|gb|DR333297.1|DR333297
EST:     TGAAACAGCTTTATACCCAATTGATACTATTAAGACTAGACTTCAGGCAG                         CTCGTGGAGGTGGAAAAATTGTTTTGAAGGGTCTTTATTCAGGATTAGCTG
genomic: TGAAACAGCTTTATACCCAATTGATACTATTAAGACTAGACTTCAGGCAGgtcaacgaac ... atgtaggcagCTCGTGGAGGTGGAAAAATTGTTTTGAAGGGTCTTTATTCAGGATTAGCTG
EST: gi|86037537|gb|DR333292.1|DR333292
EST:     TGAAACAGCTTTATACCCAATTGATACTATTAAGACTAGACTTCAGGCAG                         CTCGTGGAGGTGGAAAAATTGTTTTGAAGGGTCTTTATTCAGGATTAGCTG
genomic: TGAAACAGCTTTATACCCAATTGATACTATTAAGACTAGACTTCAGGCAGgtcaacgaac ... atgtaggcagCTCGTGGAGGTGGAAAAATTGTTTTGAAGGGTCTTTATTCAGGATTAGCTG
EST: gi|86037552|gb|DR333307.1|DR333307
EST:     TGAAACAGCTTTATACCCAATTGATACTATTAAGACTAGACTTCAGGCAG                         CTCGTGGAGGTGGAAAAATTGTTTTGAAGGGTCTTTATTCAGGATT
genomic: TGAAACAGCTTTATACCCAATTGATACTATTAAGACTAGACTTCAGGCAGgtcaacgaac ... atgtaggcagCTCGTGGAGGTGGAAAAATTGTTTTGAAGGGTCTTTATTCAGGATT
EST: gi|125163617|gb|EL190387.1|EL190387
EST:     AAACAGCTTTATACCCAATTGATACTATTAAGACTAGACTTCAGGCAG                         CTCGTGGAGGTGGAAAAATTGTTT-GAAGGGTCTTTATTCAGGAT
genomic: AAACAGCTTTATACCCAATTGATACTATTAAGACTAGACTTCAGGCAGgtcaacgaac ... atgtaggcagCTCGTGGAGGTGGAAAAATTGTTTTGAAGGGTCTTTATTCAGGAT
EST: gi|86037535|gb|DR333290.1|DR333290
EST:     TGAAACAGCTTTATACCCAATTGATACTATTAAGACTAGACTTCAG-C--                         -TCGTGGAGGTGGAAAAATTGTTTTGAAGGGTCTTTATTCAGGATTAGCTG
genomic: TGAAACAGCTTTATACCCAATTGATACTATTAAGACTAGACTTCAGGCAGgtcaacgaac ... atgtaggcagCTCGTGGAGGTGGAAAAATTGTTTTGAAGGGTCTTTATTCAGGATTAGCTG
EST: gi|152038462|gb|AV823633.2|AV823633
EST:     TGAAACAGCTTTATACCCAATTGATACTATTAAGACTAGACTTCAGGCAG                         CTCGTGGAGGTGGAAAAATTGTTTTGAAGGGTCTTTATTCAGGATTAGCTG
genomic: TGAAACAGCTTTATACCCAATTGATACTATTAAGACTAGACTTCAGGCAGgtcaacgaac ... atgtaggcagCTCGTGGAGGTGGAAAAATTGTTTTGAAGGGTCTTTATTCAGGATTAGCTG
EST: gi|86037532|gb|DR333287.1|DR333287
EST:     TGAAACAGCTTTATACCCAATTGATACTATTAAGACTAGACTTCAGGCAG                         CTCGTGGAGGTGGAAAAATTGTTTTGAAGGGTCTTTATTCAGGATTAGCTG
genomic: TGAAACAGCTTTATACCCAATTGATACTATTAAGACTAGACTTCAGGCAGgtcaacgaac ... atgtaggcagCTCGTGGAGGTGGAAAAATTGTTTTGAAGGGTCTTTATTCAGGATTAGCTG
EST: gi|86037548|gb|DR333303.1|DR333303
EST:     TGAAACAGCTTTATACCCAATTGATACTATTAAGACTAGACTTCAGGCAG                         CTCGTGGAGGTGGAAAAATTGTTTTGAAGGGTCTTTATTCAGGATTAGCTG
genomic: TGAAACAGCTTTATACCCAATTGATACTATTAAGACTAGACTTCAGGCAGgtcaacgaac ... atgtaggcagCTCGTGGAGGTGGAAAAATTGTTTTGAAGGGTCTTTATTCAGGATTAGCTG
EST: gi|125274718|gb|EL288803.1|EL288803
EST:     AAACAGCTTTATACCCAATTGATACTATTAAGACTAGACTTCAGGCAG                         CTCGTGGAGGTAGGAAAAATTGTTTTGAAGGGTC
genomic: AAACAGCTTTATACCCAATTGATACTATTAAGACTAGACTTCAGGCAGgtcaacgaac ... atgtaggcagCTCGTGGAGGT-GGAAAAATTGTTTTGAAGGGTC
EST: gi|86037533|gb|DR333288.1|DR333288
EST:     TGAAACAGCTATATACCCAATTGATACTATTAAGACTAGACTTCAGGSAG                         CTCGTGGAGGTGGAAAAATTGTTTTGAAGGGTCTTTATTCAGGATTAGCTG
genomic: TGAAACAGCTTTATACCCAATTGATACTATTAAGACTAGACTTCAGGCAGgtcaacgaac ... atgtaggcagCTCGTGGAGGTGGAAAAATTGTTTTGAAGGGTCTTTATTCAGGATTAGCTG
EST: gi|86037553|gb|DR333308.1|DR333308
EST:     TGAAACAGCTTTATACCCAATTGATACTATTAAGACTAGACTTCAGGCAG                         CTCGTGGAGGTGGAAAAATTGTTTTGAAGGGTCTTTATTCAGGATTAGCTG
genomic: TGAAACAGCTTTATACCCAATTGATACTATTAAGACTAGACTTCAGGCAGgtcaacgaac ... atgtaggcagCTCGTGGAGGTGGAAAAATTGTTTTGAAGGGTCTTTATTCAGGATTAGCTG
EST: gi|86037534|gb|DR333289.1|DR333289
EST:     TGAAACAGCTTTATACCCAATTGATACTATTAAGACTAGACTT----CAG                         CTCGTGGAGGTGGAAAAATTGTTTTGAAGGGTCTTTATTCAGGATTAGCTG
genomic: TGAAACAGCTTTATACCCAATTGATACTATTAAGACTAGACTTCAGGCAGgtcaacgaac ... atgtaggcagCTCGTGGAGGTGGAAAAATTGTTTTGAAGGGTCTTTATTCAGGATTAGCTG
EST: gi|86037555|gb|DR333310.1|DR333310
EST:     TGAAACAGCTTTATACCCAATTGATACTATTAAGACTAGACTTCAGGCAG                         CTCGTGGAGGTGGAAAAATTGTTTTGAAGGGTCTTTATTCAGGATTAGCTG
genomic: TGAAACAGCTTTATACCCAATTGATACTATTAAGACTAGACTTCAGGCAGgtcaacgaac ... atgtaggcagCTCGTGGAGGTGGAAAAATTGTTTTGAAGGGTCTTTATTCAGGATTAGCTG
EST: gi|86037540|gb|DR333295.1|DR333295
EST:     TGAAACAGCTTTATACCCAATTGATACTATTAAGACTAGACTTCAGGCAG                         CTCGTGGAGGTGGAAAAATTGTTTTGAAGGGTCTTTATTCAGGATTAGCTG
genomic: TGAAACAGCTTTATACCCAATTGATACTATTAAGACTAGACTTCAGGCAGgtcaacgaac ... atgtaggcagCTCGTGGAGGTGGAAAAATTGTTTTGAAGGGTCTTTATTCAGGATTAGCTG
EST: gi|86037541|gb|DR333296.1|DR333296
EST:     TGAAACAGCTTTATACCCAATTGATACTATTAAGACTAGACTTCAGGCAG                         CTCGTGGAGGTGGAAAAATTGTTTTGAAGGGTCTTTATTCAGGATTAGCTG
genomic: TGAAACAGCTTTATACCCAATTGATACTATTAAGACTAGACTTCAGGCAGgtcaacgaac ... atgtaggcagCTCGTGGAGGTGGAAAAATTGTTTTGAAGGGTCTTTATTCAGGATTAGCTG
EST: gi|86037539|gb|DR333294.1|DR333294
EST:     TGAAACAGCTTTATACCCCATTGATACTATTAAGACTAGACTTCAGGCAG                         CTCGTGGAGGTGGAAAAATTGTTTTGAAGGGTCTTTATTCAGGATTAG
genomic: TGAAACAGCTTTATACCCAATTGATACTATTAAGACTAGACTTCAGGCAGgtcaacgaac ... atgtaggcagCTCGTGGAGGTGGAAAAATTGTTTTGAAGGGTCTTTATTCAGGATTAG
EST: gi|86037546|gb|DR333301.1|DR333301
EST:     TGAAACAGCTTTATACCCAATTGATACTATTAAGACTAGACTTCAGGCAG                         CTCGTGGAGGTGGAAAAATTGTTTTGAAGGGTCTTTATTCAGGATTAGCTG
genomic: TGAAACAGCTTTATACCCAATTGATACTATTAAGACTAGACTTCAGGCAGgtcaacgaac ... atgtaggcagCTCGTGGAGGTGGAAAAATTGTTTTGAAGGGTCTTTATTCAGGATTAGCTG
EST: gi|86037536|gb|DR333291.1|DR333291
EST:     TGAAACAGCTATATACCCAATTGATACTATTAAGACTAGACTTCAGGCAG                         CTCGTGGAGGTGGAAAAATTGTTTTGAAGGGTCTTTATTCAGGATTAGCTG
genomic: TGAAACAGCTTTATACCCAATTGATACTATTAAGACTAGACTTCAGGCAGgtcaacgaac ... atgtaggcagCTCGTGGAGGTGGAAAAATTGTTTTGAAGGGTCTTTATTCAGGATTAGCTG
EST: gi|86037551|gb|DR333306.1|DR333306
EST:     TGAAACAGCTATATACCCAATTGATACTATTAAGACTAGACTTCAGGCAG                         CTCGTGGAGGTGGAAAAATTGTTTTGAAGGGTCTTTATTCAGGATTAGCTG
genomic: TGAAACAGCTTTATACCCAATTGATACTATTAAGACTAGACTTCAGGCAGgtcaacgaac ... atgtaggcagCTCGTGGAGGTGGAAAAATTGTTTTGAAGGGTCTTTATTCAGGATTAGCTG
EST: gi|152033833|gb|BP817226.2|BP817226
EST:     GAAACAGCTTTATACCCAACTTGATACTATTAAGACTAGACTTCAGGCAG                         CTCGTGGAGGTGGAAAAATTGTTTTGAAGGGTCTTTATTCAGGATTAGCTG
genomic: GAAACAGCTTTATACCCAA-TTGATACTATTAAGACTAGACTTCAGGCAGgtcaacgaac ... atgtaggcagCTCGTGGAGGTGGAAAAATTGTTTTGAAGGGTCTTTATTCAGGATTAGCTG
EST: gi|86037554|gb|DR333309.1|DR333309
EST:     TGAAACAGCTTTATACCCAATTGATACTATTAAGACTAGACTTCAGGCAG                         CTCGTGGAGGTGGAAAAATTGTTTTGAAGGGTCTTTATTCAGGATTAGCTG
genomic: TGAAACAGCTTTATACCCAATTGATACTATTAAGACTAGACTTCAGGCAGgtcaacgaac ... atgtaggcagCTCGTGGAGGTGGAAAAATTGTTTTGAAGGGTCTTTATTCAGGATTAGCTG
EST: gi|86037544|gb|DR333299.1|DR333299
EST:     TGAAACAGCTTTATACCCAATTGATACTATTAAGACTAGACTTCAGGCAG                         CTCGTGGAGGTGGAAAAATTGTTTTGAAGGGTCTTTATTCAGGATTAGCTG
genomic: TGAAACAGCTTTATACCCAATTGATACTATTAAGACTAGACTTCAGGCAGgtcaacgaac ... atgtaggcagCTCGTGGAGGTGGAAAAATTGTTTTGAAGGGTCTTTATTCAGGATTAGCTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaaaaaagtgttgacctttagttcctaaactagtttgatcttatgatgtaggcagCTCGTGGAGGTGGAAAAATTGTTTTGAAGGGTCTTTATTCAGGATTAGCTGGAAATATCGCTGGTGTCTTACC
                tttagtt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtcaacgaactttaaatctctgttagacattcttttaactgtatgcaattagctactgtactactttggttaaaaaaagtgttgacctttagttcctaaactagtttgatcttatgatgtaggcagCTCGTGGAGGTGGAAAAATTGTTTTGAAGGGTCTTTATTCAGGATTAGCTGGAAATATCGCTGGTGTCTTACC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGGA