Skip to another splice site:
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 5'  3'   		2  
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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cttagtgataaatataaaaacattttatgtatattatactattagtgaaattaaatataaataatcaaaccggtctgacttgattcacattacttggcagGAAATCAAGTACTCGGTATCTTTGCGCCGAAAGACCTTAGAGGAGGAGGATCCAATAATAAAAATGTGTGTCGACTTCAAAGTACCTGCCCCAGCTCCTG

Basic information

species Arabidopsis thaliana
transcript AT5G23820.1
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|125147832|gb|EL181846.1|EL181846
EST:     ACTCTTTCCGACGTTCTTTATGTTGGTTATGATTGAG                         GAAATCAAGTACTCGGTATCTTTGCGCCGAAAGACCTTAGAGGAGGAGGA
genomic: ACTCTTTCCGACGTTCTTTATGTTGGTTATGA-TGAGgtaactacat ... tacttggcagGAAATCAAGTACTCGGTATCTTTGCGCCGAAAGACCTTAGAGGAGGAGGA
EST: gi|125313306|gb|EL327391.1|EL327391
EST:     CCAACTTTGAGTTAACTCTT-CCGACGTTCTTTATGTTGGTTATGATGAG                         GAAATCAAGTAC
genomic: CCAACTTTGAGTTAACTCTTTCCGACGTTCTTTATGTTGGTTATGATGAGgtaactacat ... tacttggcagGAAATCAAGTAC
EST: gi|124856671|gb|EH941108.1|EH941108
EST:     CTCTTTCCGACGTTCTTTATGTTGGTTATGATGAG                         GAAATCAAGTACTCGGTATCTTTGCGCCGAAAG
genomic: CTCTTTCCGACGTTCTTTATGTTGGTTATGATGAGgtaactacat ... tacttggcagGAAATCAAGTACTCGGTATCTTTGCGCCGAAAG
EST: gi|124919953|gb|EH993691.1|EH993691
EST:     TCCGACGTTCTTTATGTTGGTTATGATGAG                         GTAAATCAAGTACTCGGTATCTTTGCGCCGAAAGACCTTAGAGGAGGAGGA
genomic: TCCGACGTTCTTTATGTTGGTTATGATGAGgtaactacat ... tacttggcagG-AAATCAAGTACTCGGTATCTTTGCGCCGAAAGACCTTAGAGGAGGAGGA
EST: gi|86027528|gb|DR323281.1|DR323281
EST:     CCAACTTTGAGTTAACTCTTTCCGACGTTCTTTATGTTGGTTATGATGAG                         GAAATCAAGTACTCGGTATCTTTGCGCCAAAAGACCTTAGAGGAGGAGGAT
genomic: CCAACTTTGAGTTAACTCTTTCCGACGTTCTTTATGTTGGTTATGATGAGgtaactacat ... tacttggcagGAAATCAAGTACTCGGTATCTTTGCGCCGAAAGACCTTAGAGGAGGAGGAT
EST: gi|86027524|gb|DR323277.1|DR323277
EST:     CCAACTTTGAGTTAACTCTTTCCGACGTTCTTTATGTTGGTTATGATGAG                         GAAATCAAGTACTCGGTATCTTTGCGCC
genomic: CCAACTTTGAGTTAACTCTTTCCGACGTTCTTTATGTTGGTTATGATGAGgtaactacat ... tacttggcagGAAATCAAGTACTCGGTATCTTTGCGCC
EST: gi|125155070|gb|EL185380.1|EL185380
EST:     CTTTCCGACGTTCTTTATGTTGGTTATGATGAG                         GAAATCAAGTACTCGGTATCTTTGCGCCGAAAGACCTTAGAGGAGGAGGAT
genomic: CTTTCCGACGTTCTTTATGTTGGTTATGATGAGgtaactacat ... tacttggcagGAAATCAAGTACTCGGTATCTTTGCGCCGAAAGACCTTAGAGGAGGAGGAT
EST: gi|124750305|gb|EH840435.1|EH840435
EST:     CCAACTTTGAGTTAACTCTTTCCGACGTTCTTTATGTTGGTTATGATGAG                         GAAATCAAGTACTCGGTATCTTTGCGCCGAAAGACCTTAGAGG
genomic: CCAACTTTGAGTTAACTCTTTCCGACGTTCTTTATGTTGGTTATGATGAGgtaactacat ... tacttggcagGAAATCAAGTACTCGGTATCTTTGCGCCGAAAGACCTTAGAGG
EST: gi|86027555|gb|DR323308.1|DR323308
EST:     CCAACTTTGAGTTAACTCTTTCCGACGTTCTTTATGTTGGTTATGATGAG                         GAAATCAAGTACTCGGTATCTTTGCGCCAAAAGACCTTAGAGGAGGAGGAT
genomic: CCAACTTTGAGTTAACTCTTTCCGACGTTCTTTATGTTGGTTATGATGAGgtaactacat ... tacttggcagGAAATCAAGTACTCGGTATCTTTGCGCCGAAAGACCTTAGAGGAGGAGGAT
EST: gi|125288684|gb|EL302769.1|EL302769
EST:     TCCGACGTTCTTTATGTTGGTTATGATGAG                         GAAATCAAGTACTCGGTATCTTTGCGCCGAAAGACCTTAGAGGAGGAGGAT
genomic: TCCGACGTTCTTTATGTTGGTTATGATGAGgtaactacat ... tacttggcagGAAATCAAGTACTCGGTATCTTTGCGCCGAAAGACCTTAGAGGAGGAGGAT
EST: gi|86081443|gb|DR377200.1|DR377200
EST:     CCAACTTTGAGTTAACTCTTTCCGACGTTCTTTATGTTGGTTATGATGAG                         GAAATCAAGTACTCGGTATCTTTGCGCCAAAAGACCTTAGAGGAGGAGGAT
genomic: CCAACTTTGAGTTAACTCTTTCCGACGTTCTTTATGTTGGTTATGATGAGgtaactacat ... tacttggcagGAAATCAAGTACTCGGTATCTTTGCGCCGAAAGACCTTAGAGGAGGAGGAT
EST: gi|86027535|gb|DR323288.1|DR323288
EST:     CCAACTTTGAGTTAACTCTTTCCGACGTTCTTTATGTTGGTTATGATGAG                         GAAATCAAGTACTCGGTATCTT
genomic: CCAACTTTGAGTTAACTCTTTCCGACGTTCTTTATGTTGGTTATGATGAGgtaactacat ... tacttggcagGAAATCAAGTACTCGGTATCTT
EST: gi|124704702|gb|EH796104.1|EH796104
EST:     TGGTTATGATGAG                         GAAATCAAGTACTCGGTATCTTTGCGCCGAAAGACCTTAGAGGAGGAGGAT
genomic: TGGTTATGATGAGgtaactacat ... tacttggcagGAAATCAAGTACTCGGTATCTTTGCGCCGAAAGACCTTAGAGGAGGAGGAT
EST: gi|86027546|gb|DR323299.1|DR323299
EST:     CCAACTTTGAGTTAACTCTTTCCGACGTTCTTTATGTTGGTTATGATGAG                         GAAATCAAGTACTCGGTATCTTTGCGCCAAAAGACCTTAGAGGAGGAGGAT
genomic: CCAACTTTGAGTTAACTCTTTCCGACGTTCTTTATGTTGGTTATGATGAGgtaactacat ... tacttggcagGAAATCAAGTACTCGGTATCTTTGCGCCGAAAGACCTTAGAGGAGGAGGAT
EST: gi|124912029|gb|EH986109.1|EH986109
EST:     CAACTTTGAGTTAACTCTTTTCCGACGTTCTTTATGTTGGTTATGATGAG                         GAAATCAAGTACTCGGTATCTTTGCGCCGAAAGACCTTAGAGGAGGAGGAT
genomic: CAACTTTGAGTTAACTC-TTTCCGACGTTCTTTATGTTGGTTATGATGAGgtaactacat ... tacttggcagGAAATCAAGTACTCGGTATCTTTGCGCCGAAAGACCTTAGAGGAGGAGGAT
EST: gi|125220797|gb|EL234882.1|EL234882
EST:     CTTTATGTTGGTTATGATGAG                         GAAATCAAGTACTCGGTATCTTTGCGCCGAAAGACCTTAGAGGAGGGGGAT
genomic: CTTTATGTTGGTTATGATGAGgtaactacat ... tacttggcagGAAATCAAGTACTCGGTATCTTTGCGCCGAAAGACCTTAGAGGAGGAGGAT
EST: gi|125103014|gb|EL157566.1|EL157566
EST:     TTGAGTTAACTCTTTCCGACGTTCTTTATGTTGGTTATGATGAG                         GAAATCAAGTACTCGGTATCTTTGCGCCGAAAGACCTTAGAGGAGGAGGAT
genomic: TTGAGTTAACTCTTTCCGACGTTCTTTATGTTGGTTATGATGAGgtaactacat ... tacttggcagGAAATCAAGTACTCGGTATCTTTGCGCCGAAAGACCTTAGAGGAGGAGGAT
EST: gi|125235299|gb|EL249384.1|EL249384
EST:     CCAACTTTGAGTTAACTCTTTCCGACGTTCTTTATGTTGGTTATGATGAG                         GAAATCAAGTACTCGGTATCTTTGCGCCGAAAGA
genomic: CCAACTTTGAGTTAACTCTTTCCGACGTTCTTTATGTTGGTTATGATGAGgtaactacat ... tacttggcagGAAATCAAGTACTCGGTATCTTTGCGCCGAAAGA
EST: gi|125082797|gb|EL143582.1|EL143582
EST:     CCAACTTTGAGTTAACTCTTTCCGACGTTCTTTATGTTGGTTATGATGAG                         GAAATCAAGTACTCGGTATCTTTGCG
genomic: CCAACTTTGAGTTAACTCTTTCCGACGTTCTTTATGTTGGTTATGATGAGgtaactacat ... tacttggcagGAAATCAAGTACTCGGTATCTTTGCG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgaaattaaatataaataatcaaaccggtctgacttgattcacattacttggcagGAAATCAAGTACTCGGTATCTTTGCGCCGAAAGACCTTAGAGGAGGAGGATCCAATAATAAAAATGTGTGTCGACTTCAAAGTACCTGCCCCAGCTCCTG
     ttaaatataaataatc  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cttagtgataaatataaaaacattttatgtatattatactattagtgaaattaaatataaataatcaaaccggtctgacttgattcacattacttggcagGAAATCAAGTACTCGGTATCTTTGCGCCGAAAGACCTTAGAGGAGGAGGATCCAATAATAAAAATGTGTGTCGACTTCAAAGTACCTGCCCCAGCTCCTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTC
- - - - - - - taaaaac
- - - - - - - - - - - - - - - - - - - - - - - - aattaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aatcaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - attcaca