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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgtaccttaatatccatttcttttgatttcatatgaatgtaaaggatatgagaaaatatgggtgcggaaaggttcaaacacacacaaaatgactaaccttacattggtggataaagctagtcaatactcatgctaagctacacttgtgcttttttctaactccattctttttgcattcagGTCTTGTTTGGAGAAGTTGAGAATGCATCGCCTCAGAAAGTTCCAACCCCAATAGTAAATGGTGATGAGACTGGTGGATTGCCCATTGAAGCCTTTTCTA

Basic information

species Arabidopsis thaliana
transcript AT1G31810.1
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|116473995|gb|EG516587.1|EG516587
EST:     ATATTCTTTGGGAGGCCAAGGATCATTACCCAAAAGGGTTTCGAGCAGAG                         GTCTTGTTTGGAGAAGTTGAGAATGCATCGCCTCAGAAAGTTCCAACCCCA
genomic: ATATTCTTTGGGAGGCCAAGGATCATTACCCAAAAGGGTTTCGAGCAGAGgtatgtacct ... ttgcattcagGTCTTGTTTGGAGAAGTTGAGAATGCATCGCCTCAGAAAGTTCCAACCCCA
EST: gi|116447074|gb|EG489666.1|EG489666
EST:     ATATTCTTTGGGAGGCCAAGGATCATTACCCAAAAGGGTTTCGAGCAGAG                         GTCTTGTTTGGAGAAGTTGAGAATGCATCGCCTCAGAAAGTTCCAACCCCA
genomic: ATATTCTTTGGGAGGCCAAGGATCATTACCCAAAAGGGTTTCGAGCAGAGgtatgtacct ... ttgcattcagGTCTTGTTTGGAGAAGTTGAGAATGCATCGCCTCAGAAAGTTCCAACCCCA
EST: gi|164164719|gb|ES188056.1|ES188056
EST:     TATTCTTTGGGAGGCCAAGGATCATTACCCAAAAGGGTTTACGAGCAGAG                         GTCTTGTTTGGAGAAGTTGAGA
genomic: TATTCTTTGGGAGGCCAAGGATCATTACCCAAAAGGGTTT-CGAGCAGAGgtatgtacct ... ttgcattcagGTCTTGTTTGGAGAAGTTGAGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

actcatgctaagctacacttgtgcttttttctaactccattctttttgcattcagGTCTTGTTTGGAGAAGTTGAGAATGCATCGCCTCAGAAAGTTCCAACCCCAATAGTAAATGGTGATGAGACTGGTGGATTGCCCATTGAAGCCTTTTCTA
                            ttctaac  putative branch site (score: 1)
                       cttttttctaactcca  CT-rich tract
                        ttttttctaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgtaccttaatatccatttcttttgatttcatatgaatgtaaaggatatgagaaaatatgggtgcggaaaggttcaaacacacacaaaatgactaaccttacattggtggataaagctagtcaatactcatgctaagctacacttgtgcttttttctaactccattctttttgcattcagGTCTTGTTTGGAGAAGTTGAGAATGCATCGCCTCAGAAAGTTCCAACCCCAATAGTAAATGGTGATGAGACTGGTGGATTGCCCATTGAAGCCTTTTCTA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGC