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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtattggggaaatgttgacttgtcagtttttcctccctttctacagcatctttcttatgtttttgctaattgaattatctttcatgcttttagGTAAATTGGAAAAGGGGGCAGTGCTTAAGGCTATGTGTTCGGGTTTTCAAGAGTCAACGGAACCAGCTATCTGTCTTACTGAAG

Basic information

species Arabidopsis thaliana
transcript AT3G52850.1
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|164009148|gb|ES078018.1|ES078018
EST:     AGACGTGACTATACTCCCAACTCTTGTCGTGAACAACAGACAATACAGAG                         GTAAATTGGAAAAGGGGGACAGTGCTTAAGGCTATGTGTTCGGGTTT
genomic: AGACGTGACTATACTCCCAACTCTTGTCGTGAACAACAGACAATACAGAGgtattgggga ... atgcttttagGTAAATTGGAAAAGGGGG-CAGTGCTTAAGGCTATGTGTTCGGGTTT
EST: gi|125083796|gb|EL144232.1|EL144232
EST:     AGACGTGACTATACTCCCAACTCTTGTCGTGAACAACAGACAATACAGAG                         GTAAATTGGAAAAGGGGGCAGTGCTTAAGGTCTATGTGT
genomic: AGACGTGACTATACTCCCAACTCTTGTCGTGAACAACAGACAATACAGAGgtattgggga ... atgcttttagGTAAATTGGAAAAGGGGGCAGTGCTTAAGG-CTATGTGT
EST: gi|86037689|gb|DR333444.1|DR333444
EST:     AGACGTGACTATACTCCCAACTCTTGTCGTGAACAACAGACAATACAGAG                         GTAAATTGGAAAAGGGGGCAGTGCTTAAGGCTATGTGTTCGGGTTTTCAAG
genomic: AGACGTGACTATACTCCCAACTCTTGTCGTGAACAACAGACAATACAGAGgtattgggga ... atgcttttagGTAAATTGGAAAAGGGGGCAGTGCTTAAGGCTATGTGTTCGGGTTTTCAAG
EST: gi|164006595|gb|ES152809.1|ES152809
EST:     AGACGTGACTATACTCCCAACTCTTGTCGTGAACAACAGACAATACAGAG                         GTAAATTGGAAAAGGGG-CAGTGCTTAAG
genomic: AGACGTGACTATACTCCCAACTCTTGTCGTGAACAACAGACAATACAGAGgtattgggga ... atgcttttagGTAAATTGGAAAAGGGGGCAGTGCTTAAG
EST: gi|86037688|gb|DR333443.1|DR333443
EST:     AGACGTGACTATACTCCCAACTCTTGTCGTGAACAACAGACAATACAGAG                         GTAAATTGGAAAAGGGGGCAGTGCTTAAGGCTATGTGTTCGGGTTTTCAAG
genomic: AGACGTGACTATACTCCCAACTCTTGTCGTGAACAACAGACAATACAGAGgtattgggga ... atgcttttagGTAAATTGGAAAAGGGGGCAGTGCTTAAGGCTATGTGTTCGGGTTTTCAAG
EST: gi|163996267|gb|ES015849.1|ES015849
EST:     AGACGTGACTATACTCCCAACTCTTGTCGTGAACAACAGACAATACAGAG                         GTAAATTGGAAAAGGGGGCAGTGCTTAAGGCTATGTGTTCGGGTTT
genomic: AGACGTGACTATACTCCCAACTCTTGTCGTGAACAACAGACAATACAGAGgtattgggga ... atgcttttagGTAAATTGGAAAAGGGGGCAGTGCTTAAGGCTATGTGTTCGGGTTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttctacagcatctttcttatgtttttgctaattgaattatctttcatgcttttagGTAAATTGGAAAAGGGGGCAGTGCTTAAGGCTATGTGTTCGGGTTTTCAAGAGTCAACGGAACCAGCTATCTGTCTTACTGAAG
                         tgctaat  putative branch site (score: 2)
                                       tctttcatgctttt  putative PPT
                            taattgaattatcttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtattggggaaatgttgacttgtcagtttttcctccctttctacagcatctttcttatgtttttgctaattgaattatctttcatgcttttagGTAAATTGGAAAAGGGGGCAGTGCTTAAGGCTATGTGTTCGGGTTTTCAAGAGTCAACGGAACCAGCTATCTGTCTTACTGAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGAAG