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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaatcaagaatcatcccctaaaaccacaaatggcaaatgctaatgttacataacctaattgttttttttgttttgtttgttgtagATTAAGTTCGAGCAAGGTGTTATAGGGACTCCTCAGCTAACGGATTCGATTGAAATACCGGAATCCGTGGAGGTTCTTGGTCAGAAAATCGATCTCAATC

Basic information

species Arabidopsis thaliana
transcript AT4G04020.1
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|124781909|gb|EH871852.1|EH871852
EST:     CGTTTAGCACCAACGCTAAGTTTGAAATCCGAAGTCCTAAACGTGTCCAG                         ATTAAGTTCGAGCAAGGTGTTATAGGGACTCCT
genomic: CGTTTAGCACCAACGCTAAGTTTGAAATCCGAAGTCCTAAACGTGTCCAGgtaaatcaag ... tttgttgtagATTAAGTTCGAGCAAGGTGTTATAGGGACTCCT
EST: gi|86074440|gb|DR370197.1|DR370197
EST:     CGTTTAGCACCAACGCTAAGTTTGAAATCCGAAGTCCTAAACGTGTCCAG                         ATTAAGTTCGAGCAAGGTGTTATAGGGACTCCTCAGCTAACGGATTCGATT
genomic: CGTTTAGCACCAACGCTAAGTTTGAAATCCGAAGTCCTAAACGTGTCCAGgtaaatcaag ... tttgttgtagATTAAGTTCGAGCAAGGTGTTATAGGGACTCCTCAGCTAACGGATTCGATT
EST: gi|124743599|gb|EH834761.1|EH834761
EST:     CGTTTAGCACCAACGCTAAGTTTGAAATCCGAAGTCCTAAACGTGTCCAG                         ATTAAGTTCGAGCAAGGTGTTATAGGGACTCCTCAGCTAACGGATTCGATT
genomic: CGTTTAGCACCAACGCTAAGTTTGAAATCCGAAGTCCTAAACGTGTCCAGgtaaatcaag ... tttgttgtagATTAAGTTCGAGCAAGGTGTTATAGGGACTCCTCAGCTAACGGATTCGATT
EST: gi|124963541|gb|EL037870.1|EL037870
EST:     AGCACCAACGCTAAGTTTGAAATCCGAAGTCCTAAACGTGTCCAG                         ATTAAGTTCGAGCAAGGTGTTATAGGGACTCCTCAGCTAACGGATTCGATT
genomic: AGCACCAACGCTAAGTTTGAAATCCGAAGTCCTAAACGTGTCCAGgtaaatcaag ... tttgttgtagATTAAGTTCGAGCAAGGTGTTATAGGGACTCCTCAGCTAACGGATTCGATT
EST: gi|125031122|gb|EL103391.1|EL103391
EST:     GAAGTCCTAAACGTGTCCAG                         ATTAAGTTCGAGCAAGGTGTTATAGGGACTCCTCAGCTAACGGATTCGATT
genomic: GAAGTCCTAAACGTGTCCAGgtaaatcaag ... tttgttgtagATTAAGTTCGAGCAAGGTGTTATAGGGACTCCTCAGCTAACGGATTCGATT
EST: gi|124955342|gb|EL030363.1|EL030363
EST:     GTTTAGCACCAACGCTAAGTTTGTAAATCCGAAGTCCTAAACGTGTCCAG                         ATTAAGTTCGAGCAAGGTGTTATAGGGACTCCTCAGCTAACGGATTCGATT
genomic: GTTTAGCACCAACGCTAAGTTTG-AAATCCGAAGTCCTAAACGTGTCCAGgtaaatcaag ... tttgttgtagATTAAGTTCGAGCAAGGTGTTATAGGGACTCCTCAGCTAACGGATTCGATT
EST: gi|124705617|gb|EH797019.1|EH797019
EST:     CGTTTAGCACCAACGCTAAGTTTGAAATCCGAAGTCCTAAACGTGTCCAG                         ATTAAGTTCGAGTAAGGTGTTATAGGGACTCCTCAGCTAACGGATTCGATT
genomic: CGTTTAGCACCAACGCTAAGTTTGAAATCCGAAGTCCTAAACGTGTCCAGgtaaatcaag ... tttgttgtagATTAAGTTCGAGCAAGGTGTTATAGGGACTCCTCAGCTAACGGATTCGATT
EST: gi|86080656|gb|DR376413.1|DR376413
EST:     CGAAGTCCTAAACGTGTCCAG                         ATTAAGTTCGAGCAAGGTGTTAT-RGGACTCCTCAGCTAACGGATTCGATT
genomic: CGAAGTCCTAAACGTGTCCAGgtaaatcaag ... tttgttgtagATTAAGTTCGAGCAAGGTGTTATAGGGACTCCTCAGCTAACGGATTCGATT
EST: gi|125254396|gb|EL268481.1|EL268481
EST:     CACCAACGCTAAGTTTGAAATCCGAAGTCCTAAACGTGTCCAG                         ATTAAGTTCGAGCAAGGTGTTATAGGGACTCCTCAGCTAACGGATTCGATT
genomic: CACCAACGCTAAGTTTGAAATCCGAAGTCCTAAACGTGTCCAGgtaaatcaag ... tttgttgtagATTAAGTTCGAGCAAGGTGTTATAGGGACTCCTCAGCTAACGGATTCGATT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tggcaaatgctaatgttacataacctaattgttttttttgttttgtttgttgtagATTAAGTTCGAGCAAGGTGTTATAGGGACTCCTCAGCTAACGGATTCGATTGAAATACCGGAATCCGTGGAGGTTCTTGGTCAGAAAATCGATCTCAATC
                               ttttttttgttttgtt  CT-rich tract
                         taattgttttttttgt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaatcaagaatcatcccctaaaaccacaaatggcaaatgctaatgttacataacctaattgttttttttgttttgtttgttgtagATTAAGTTCGAGCAAGGTGTTATAGGGACTCCTCAGCTAACGGATTCGATTGAAATACCGGAATCCGTGGAGGTTCTTGGTCAGAAAATCGATCTCAATC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG