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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatggcaaccacaaaaagaagactcttagtctcttagaccagttccaccatctgttcttcaagggttcaaagtcagtcttttattgatactacccttttacttgttctttttcatcagTTGTGCTCGTGGTAGCCCCAAACGGCAGGTATTGCTTGAGAAAGCTGGTCACTTTCAG

Basic information

species Arabidopsis thaliana
transcript AT5G03880.1
intron # 10
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|125050172|gb|EL122441.1|EL122441
EST:     TAGAACTGGAGTTACCACACATTCAGCGCAG                         TTGTGCTCGTGGTAGCCCCAAACGGCAGGTATTGCTTGAAGAAAAGCTGGT
genomic: TAGAACTGGAGTTACCACACATTCAGCGCAGgtatggcaac ... ttttcatcagTTGTGCTCGTGGTAGCCCCAAACGGCAGGTATTGCTTGA-GAAA-GCTGGT
EST: gi|116475228|gb|EG517820.1|EG517820
EST:     CTTGTACGCGAAGTTCTTGTAGAACTGGAGTTACCACACATTCAGCGCAG                         TTGTGCTCGTGGT
genomic: CTTGTACGCGAAGTTCTTGTAGAACTGGAGTTACCACACATTCAGCGCAGgtatggcaac ... ttttcatcagTTGTGCTCGTGGT
EST: gi|124794445|gb|EH884124.1|EH884124
EST:     TACGCGAAGTTCTTGTAGAACTGGAGTTACCACACATTCAGCGCAG                         TTGTGCTCGTGGTAGCCCCAAACGGCAGGTNTTGCTTGAGAAAGCTGGTCA
genomic: TACGCGAAGTTCTTGTAGAACTGGAGTTACCACACATTCAGCGCAGgtatggcaac ... ttttcatcagTTGTGCTCGTGGTAGCCCCAAACGGCAGGTATTGCTTGAGAAAGCTGGTCA
EST: gi|116475229|gb|EG517821.1|EG517821
EST:     CTTGTACGCGAAGTTCTTGTAGAACTGGAGTTACCACACATTCAGCGCAG                         TTGTGCTCGTGGT
genomic: CTTGTACGCGAAGTTCTTGTAGAACTGGAGTTACCACACATTCAGCGCAGgtatggcaac ... ttttcatcagTTGTGCTCGTGGT
EST: gi|164195183|gb|ES143411.1|ES143411
EST:     GAACTGGAGTTACCACACATTCAGCGCAG                         TTGTGCTCGTGGTAGCCCCAAACGGCAGGTATTGCTTGAGAAAGCTGGTCA
genomic: GAACTGGAGTTACCACACATTCAGCGCAGgtatggcaac ... ttttcatcagTTGTGCTCGTGGTAGCCCCAAACGGCAGGTATTGCTTGAGAAAGCTGGTCA
EST: gi|86080278|gb|DR376035.1|DR376035
EST:     CTTGTACGCGAAGTTCTTGTAGAACTGGAGTTACCACACATTCAGCGCAG                         TTGTGCTCGTGGTAGCCCCAAACGGCAGGTATTGCTTGAGAAAGCTGGTCA
genomic: CTTGTACGCGAAGTTCTTGTAGAACTGGAGTTACCACACATTCAGCGCAGgtatggcaac ... ttttcatcagTTGTGCTCGTGGTAGCCCCAAACGGCAGGTATTGCTTGAGAAAGCTGGTCA
EST: gi|125303306|gb|EL317391.1|EL317391
EST:     CTTGTACGCGAAGTTCTTGTAGAACTGGAGTTACCACACATTCAGCGCAG                         TTGTGCTCGTGGTAG
genomic: CTTGTACGCGAAGTTCTTGTAGAACTGGAGTTACCACACATTCAGCGCAGgtatggcaac ... ttttcatcagTTGTGCTCGTGGTAG
EST: gi|124728425|gb|EH819827.1|EH819827
EST:     CACATTCAGCGCAG                         TTGTGCTCGTGGTAGCCCCAAACGGCAGGTATTGCTTGAGAAAGCTGGTCA
genomic: CACATTCAGCGCAGgtatggcaac ... ttttcatcagTTGTGCTCGTGGTAGCCCCAAACGGCAGGTATTGCTTGAGAAAGCTGGTCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggttcaaagtcagtcttttattgatactacccttttacttgttctttttcatcagTTGTGCTCGTGGTAGCCCCAAACGGCAGGTATTGCTTGAGAAAGCTGGTCACTTTCAG
                  tattgat  putative branch site (score: 3)
                          ctacccttttacttgt  CT-rich tract
               ttttattgatacta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatggcaaccacaaaaagaagactcttagtctcttagaccagttccaccatctgttcttcaagggttcaaagtcagtcttttattgatactacccttttacttgttctttttcatcagTTGTGCTCGTGGTAGCCCCAAACGGCAGGTATTGCTTGAGAAAGCTGGTCACTTTCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG