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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagtacttgaattcatcttcctgttgcggaaaatttagaaacttgagtaaatgttgaaattttagGTCAGAAAGAGGGAGGTCAGGAATTAGTTGGTGGCCTTGATTGCACCGTACATAGGAACTTCTTCGGTAGCCAG

Basic information

species Arabidopsis thaliana
transcript AT5G60540.1
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|86052475|gb|DR348232.1|DR348232
EST:     TGTTTGGGGGACATGCGCAGGTCTTATATTCTTGGCAGACAGAGCAGTTG                         GTCAGAAAGAGGGAGGTCAGGAATTAGTTGGTGGCCTTGATTGCACCGTAC
genomic: TGTTTGGGGGACATGCGCAGGTCTTATATTCTTGGCAGACAGAGCAGTTGgtgagtactt ... gaaattttagGTCAGAAAGAGGGAGGTCAGGAATTAGTTGGTGGCCTTGATTGCACCGTAC
EST: gi|124756951|gb|EH847081.1|EH847081
EST:     TGTTTGGGGGACATGCGCAGGTCTTATATTCTTGGCAGACAGAGCAGTTG                         GTCAGAAAGAGGGAGGTCAGGAATTAGTTGGTGG
genomic: TGTTTGGGGGACATGCGCAGGTCTTATATTCTTGGCAGACAGAGCAGTTGgtgagtactt ... gaaattttagGTCAGAAAGAGGGAGGTCAGGAATTAGTTGGTGG
EST: gi|47828146|gb|CK117830.1|CK117830
EST:     TGTTTGGGGGACATGCGCAGGTCTTATATTCTTGGCAGACAGAGCAGTTG                         GTCAGAAAGAGGGAGGTCAGGAATTAGTTGGTGGCCTTGATTGCACCGTAC
genomic: TGTTTGGGGGACATGCGCAGGTCTTATATTCTTGGCAGACAGAGCAGTTGgtgagtactt ... gaaattttagGTCAGAAAGAGGGAGGTCAGGAATTAGTTGGTGGCCTTGATTGCACCGTAC
EST: gi|86052480|gb|DR348237.1|DR348237
EST:     TGTTTGGGGGACATGCGCAGGTCTTATATTCTTGGCAGACAGAGCAGTTG                         GTCAGAAAGAGGGAGGTCAGGAATTAGTTGGTGGCCTTGATTGCACCGTAC
genomic: TGTTTGGGGGACATGCGCAGGTCTTATATTCTTGGCAGACAGAGCAGTTGgtgagtactt ... gaaattttagGTCAGAAAGAGGGAGGTCAGGAATTAGTTGGTGGCCTTGATTGCACCGTAC
EST: gi|86052481|gb|DR348238.1|DR348238
EST:     TGTTTGGGGGACATGCGCAGGTCTTATATTCTTGGCAGACAGAGCAGTTG                         GTCAGAAAGAGGGAGGTCAGGAATTAGTTGGTGGCCTTGATTGCACCGTAC
genomic: TGTTTGGGGGACATGCGCAGGTCTTATATTCTTGGCAGACAGAGCAGTTGgtgagtactt ... gaaattttagGTCAGAAAGAGGGAGGTCAGGAATTAGTTGGTGGCCTTGATTGCACCGTAC
EST: gi|19877313|gb|AU238144.1|AU238144
EST:     TGTTTGGGGGACATGCGCAGGTCTTATATTCTTGGCAGACAGAGCAGTTG                         GTCAGAAAGAGGGAGGTCAGGAATTAGTTGGTGGCCTTGATTGCACCGTAC
genomic: TGTTTGGGGGACATGCGCAGGTCTTATATTCTTGGCAGACAGAGCAGTTGgtgagtactt ... gaaattttagGTCAGAAAGAGGGAGGTCAGGAATTAGTTGGTGGCCTTGATTGCACCGTAC
EST: gi|86052483|gb|DR348240.1|DR348240
EST:     TGTTTNGGGGACATGCGCAGGTCTTATATTCTTGGCAGACAGAGCAGTTG                         GTCAGAAAGAGGGAGGTCAGGAATTAGTTGGTGGCSTTGATTGCAC-GTAC
genomic: TGTTTGGGGGACATGCGCAGGTCTTATATTCTTGGCAGACAGAGCAGTTGgtgagtactt ... gaaattttagGTCAGAAAGAGGGAGGTCAGGAATTAGTTGGTGGCCTTGATTGCACCGTAC
EST: gi|86052478|gb|DR348235.1|DR348235
EST:     TGTTTGGGGGACATGCGCAGGTCTTATATTCTTGGCAGACAGAGCAGTTG                         GTCAGAAAGAGGGAGGTCAGGAATTAGTTGGTGGCCTTGATTGCACCGTAC
genomic: TGTTTGGGGGACATGCGCAGGTCTTATATTCTTGGCAGACAGAGCAGTTGgtgagtactt ... gaaattttagGTCAGAAAGAGGGAGGTCAGGAATTAGTTGGTGGCCTTGATTGCACCGTAC
EST: gi|86052482|gb|DR348239.1|DR348239
EST:     TGTTTGGGGGACATGCGCAGGTCTTATATTCTTGGCAGACAGAGCAGTTG                         GTCAGAAAGAGGGAGGTCAGGAATTAGTTGGTGGCCTTGATTGCACCGTAC
genomic: TGTTTGGGGGACATGCGCAGGTCTTATATTCTTGGCAGACAGAGCAGTTGgtgagtactt ... gaaattttagGTCAGAAAGAGGGAGGTCAGGAATTAGTTGGTGGCCTTGATTGCACCGTAC
EST: gi|86052484|gb|DR348241.1|DR348241
EST:     TGTTTGGGGGACATGCGCAGGTCTTATATTCTTGGCAGACAGAGCAGTTG                         GTCAGAAAGAGGGAGGTCAGGAATTAGTTGGTGGCCTTGATTGCACCGTAC
genomic: TGTTTGGGGGACATGCGCAGGTCTTATATTCTTGGCAGACAGAGCAGTTGgtgagtactt ... gaaattttagGTCAGAAAGAGGGAGGTCAGGAATTAGTTGGTGGCCTTGATTGCACCGTAC
EST: gi|124801222|gb|EH890657.1|EH890657
EST:     TGTTTGGGGGACANGCGCAGGTCTTATATTCTTGGCAGACAGAGCAGTTG                         GTCAGAAAGAGGGAGGTCAGGAATTAGTTGGTG
genomic: TGTTTGGGGGACATGCGCAGGTCTTATATTCTTGGCAGACAGAGCAGTTGgtgagtactt ... gaaattttagGTCAGAAAGAGGGAGGTCAGGAATTAGTTGGTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attcatcttcctgttgcggaaaatttagaaacttgagtaaatgttgaaattttagGTCAGAAAGAGGGAGGTCAGGAATTAGTTGGTGGCCTTGATTGCACCGTACATAGGAACTTCTTCGGTAGCCAG
                                     taaatgttgaaatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagtacttgaattcatcttcctgttgcggaaaatttagaaacttgagtaaatgttgaaattttagGTCAGAAAGAGGGAGGTCAGGAATTAGTTGGTGGCCTTGATTGCACCGTACATAGGAACTTCTTCGGTAGCCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGTGG