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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgttttgccatgaattgaagagttttggtgattcacattttgcaatcttgattttgcccatagtgttaagtatctaacactcttccactccttattacagCATTCCCGGACGCTATGAAACCTTCTGGAAGGAAGTAGACTACGCAAAGAACCTATGGAAGAACAGATCCGGTCTGAAGGTAGAAGATGCAGGAATCGCT

Basic information

species Arabidopsis thaliana
transcript AT4G29480.1
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|152034035|gb|AV821242.2|AV821242
EST:     GAGAAGTGCCAAGAGTTGTCTAAGCAGTTGCTCTACACCCGTCTTGCTAG                         CATTCCCGGACGCTATGAAACCTTCTGGAAGGAAGTAGACTACGCAAAGAA
genomic: GAGAAGTGCCAAGAGTTGTCTAAGCAGTTGCTCTACACCCGTCTTGCTAGgtcgatatct ... cttattacagCATTCCCGGACGCTATGAAACCTTCTGGAAGGAAGTAGACTACGCAAAGAA
EST: gi|86075424|gb|DR371181.1|DR371181
EST:     GAGAAGTGCCAAGAGTTGTCTAAGCAGTTGCTCTACACCCGTCTTGCTAG                         CATTCCCGGACGCTATGAAACCTTCTGGAAGGAAGTAGACTACGCAAAGAA
genomic: GAGAAGTGCCAAGAGTTGTCTAAGCAGTTGCTCTACACCCGTCTTGCTAGgtcgatatct ... cttattacagCATTCCCGGACGCTATGAAACCTTCTGGAAGGAAGTAGACTACGCAAAGAA
EST: gi|125319294|gb|EL333379.1|EL333379
EST:     AGTTGCTCTACACCCGTCTTGCTAG                         CATTCCCGGACGCTATGAAACCTTCTGGAAGGAAGTAGACTACGCAAAGAA
genomic: AGTTGCTCTACACCCGTCTTGCTAGgtcgatatct ... cttattacagCATTCCCGGACGCTATGAAACCTTCTGGAAGGAAGTAGACTACGCAAAGAA
EST: gi|164034168|gb|EL989395.1|EL989395
EST:     CACCCGTCTTGCTAG                         CATTCCCGGACGCTATGAAACCTTCTGGAAGGAAGTAGACTACGCAAAGAA
genomic: CACCCGTCTTGCTAGgtcgatatct ... cttattacagCATTCCCGGACGCTATGAAACCTTCTGGAAGGAAGTAGACTACGCAAAGAA
EST: gi|124766575|gb|EH856705.1|EH856705
EST:     CAGTTGCTCTACACCCGTCTTGCTAG                         T
genomic: CAGTTGCTCTACACCCGTCTTGCTAGgtcgatatct ... cttattacag-
EST: gi|124766575|gb|EH856705.1|EH856705
EST:     CAGTTGCTCTACACCCGTCTTGCTAG                         T
genomic: CAGTTGCTCTACACCCGTCTTGCTAGgtcgatatct ... cttattacag-
EST: gi|164143321|gb|ES089484.1|ES089484
EST:     GCCAAGAGTTGTCTAAGCAGTTGCTCTACACCCGTCTTGCTAG                         CATTCCCGGACGCTATGAAACCTTCTGGAAGGAAGTAGACTACGCAAAGAA
genomic: GCCAAGAGTTGTCTAAGCAGTTGCTCTACACCCGTCTTGCTAGgtcgatatct ... cttattacagCATTCCCGGACGCTATGAAACCTTCTGGAAGGAAGTAGACTACGCAAAGAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcttgattttgcccatagtgttaagtatctaacactcttccactccttattacagCATTCCCGGACGCTATGAAACCTTCTGGAAGGAAGTAGACTACGCAAAGAACCTATGGAAGAACAGATCCGGTCTGAAGGTAGAAGATGCAGGAATCGCT
                          atctaac  putative branch site (score: 2)
                                  ctcttccactccttat  CT-rich tract
                    ttaagtat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgttttgccatgaattgaagagttttggtgattcacattttgcaatcttgattttgcccatagtgttaagtatctaacactcttccactccttattacagCATTCCCGGACGCTATGAAACCTTCTGGAAGGAAGTAGACTACGCAAAGAACCTATGGAAGAACAGATCCGGTCTGAAGGTAGAAGATGCAGGAATCGCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGATG
tgttttg
- - - -ccatgaa
- - - - - - - - - - -gttttgg
- - - - - - - - - - - - - - - attcaca
- - - - - - - - - - - - - - - - - - - - - - - - -gattttg