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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtctctgttgctttttttaactgaaacatatacatgtaaaatgtttagtaacaagtcatgtgttgttccttagGGTTTGCTTGAGCCTACACTTGAGGTTCTACGACTTGACGGGAACCCATTAAGAAG

Basic information

species Arabidopsis thaliana
transcript AT3G15410.2
intron # 20
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|164067489|gb|ES092624.1|ES092624
EST:     TTCCTCCAGAACTG                         GGTTTGCTTGAGCCTACACTTGAGGTTCTACGACTTGACGGGAACCCATTA
genomic: TTCCTCCAGAACTGgtaagtctct ... tgttccttagGGTTTGCTTGAGCCTACACTTGAGGTTCTACGACTTGACGGGAACCCATTA
EST: gi|124921698|gb|EL000060.1|EL000060
EST:     TTCCTCCAGAACTG                         GGTTTGCTTGAGCCTACACTTGAGGTTCTACGACTTGACGGGAACCCATTA
genomic: TTCCTCCAGAACTGgtaagtctct ... tgttccttagGGTTTGCTTGAGCCTACACTTGAGGTTCTACGACTTGACGGGAACCCATTA
EST: gi|124730675|gb|EH822077.1|EH822077
EST:     AACATCTAGACATATCCAACAACAACATTTCAAGTCTTCCTCCAGAACTG                         GGTTTGCTTTGAGCCTACACTTGAGGTTCTACGACTTGACGGGAACCCATT
genomic: AACATCTAGACATATCCAACAACAACATTTCAAGTCTTCCTCCAGAACTGgtaagtctct ... tgttccttagGGTTTGCTT-GAGCCTACACTTGAGGTTCTACGACTTGACGGGAACCCATT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aactgaaacatatacatgtaaaatgtttagtaacaagtcatgtgttgttccttagGGTTTGCTTGAGCCTACACTTGAGGTTCTACGACTTGACGGGAACCCATTAAGAAG
                           tagtaac  putative branch site (score: 1)
                                            ttgttcctt  putative PPT
         atatacatgtaaaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtctctgttgctttttttaactgaaacatatacatgtaaaatgtttagtaacaagtcatgtgttgttccttagGGTTTGCTTGAGCCTACACTTGAGGTTCTACGACTTGACGGGAACCCATTAAGAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG