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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtataatatgcttcccttttgatattctctttaacacttagatgatggtggttggggatctgatgatgtctactcttatctttttacttgtttagACTGGTGGATACAGTGAAGACATGATTCCTACG

Basic information

species Arabidopsis thaliana
transcript AT3G49870.1
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|124891155|gb|EH970057.1|EH970057
EST:     TGATAGGACTTCAAAATGCAGGAAAGACATCACTTGTAAATGTTGTTGCA                         ACTGGTGGATACAGTGAAGACATGATTCCTACGGT
genomic: TGATAGGACTTCAAAATGCAGGAAAGACATCACTTGTAAATGTTGTTGCAgtaagtataa ... acttgtttagACTGGTGGATACAGTGAAGACATGATTCCTACGGT
EST: gi|164133832|gb|ES007414.1|ES007414
EST:     GGACTTCAAAATGCAGGAAAGACATCACTTGTAAATGTTGTTGCA                         ACTGGTGGATACAGTGAAGACATGATTCCTACG
genomic: GGACTTCAAAATGCAGGAAAGACATCACTTGTAAATGTTGTTGCAgtaagtataa ... acttgtttagACTGGTGGATACAGTGAAGACATGATTCCTACG
EST: gi|125039344|gb|EL111613.1|EL111613
EST:     ACTTCAAAATGCAGGAAAGACATCACTTGTAAATAGTTGTTGCA                         ACTGGTGGATACAGTG
genomic: ACTTCAAAATGCAGGAAAGACATCACTTGTAAAT-GTTGTTGCAgtaagtataa ... acttgtttagACTGGTGGATACAGTG
EST: gi|86072842|gb|DR368599.1|DR368599
EST:     TGATAGGACTTCAAAATGCAGGAAAGACATCACTTGTAAATGTTGTTGCA                         ACTGGTGGATACAGTGAAGACATGATTCCTACG
genomic: TGATAGGACTTCAAAATGCAGGAAAGACATCACTTGTAAATGTTGTTGCAgtaagtataa ... acttgtttagACTGGTGGATACAGTGAAGACATGATTCCTACG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gatgatggtggttggggatctgatgatgtctactcttatctttttacttgtttagACTGGTGGATACAGTGAAGACATGATTCCTACG
                 atctgat  putative branch site (score: 4)
                            tctactcttatctttt  putative PPT
                                   ttatctttttactt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtataatatgcttcccttttgatattctctttaacacttagatgatggtggttggggatctgatgatgtctactcttatctttttacttgtttagACTGGTGGATACAGTGAAGACATGATTCCTACG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA