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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tatgtgctcctccttctgcatatatgaacataaatacattccattgcctgcaaaatcatcccaacattaatcttatcatgctcttttattcattttgcagCTCTCCAAAGACTATCATGCATGGGCTTCGGGAGACACTTCAAGGCAACCTCTTGGGACCGGTGAGATCTGATAGTAAAGCAAAAGCTACCGTACGTACC

Basic information

species Arabidopsis thaliana
transcript AT5G04440.1
intron # 5
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|86079894|gb|DR375651.1|DR375651
EST:     AAGTTCTTGATCAAATTCTTAAACTCATGCTACCTCGATTTTTGTCACAG                         CTCTCCAAAGACTATCATGCATGGGCTTCGGGAGACACTTCAAGGCAACCT
genomic: AAGTTCTTGATCAAATTCTTAAACTCATGCTACCTCGATTTTTGTCACAGgtatgcagga ... cattttgcagCTCTCCAAAGACTATCATGCATGGGCTTCGGGAGACACTTCAAGGCAACCT
EST: gi|19741783|gb|AU227136.1|AU227136
EST:     AAGTTCTTGATCAAATTCTTAAACTCATGCTACCTCGATTTTTGTCACAG                         CTCTCCAAAGACTATCATGCATGGGCTTCGGGAGACACTTCAAGGCAACCT
genomic: AAGTTCTTGATCAAATTCTTAAACTCATGCTACCTCGATTTTTGTCACAGgtatgcagga ... cattttgcagCTCTCCAAAGACTATCATGCATGGGCTTCGGGAGACACTTCAAGGCAACCT
EST: gi|116428965|gb|EG471557.1|EG471557
EST:     AAGTTCTTGATCAAATTCTTAAACTCATGCTACCTCGATTTTTGTCACAG                         CTCTCCAAAGACTATCATGCATGGGCTTCGGGAGACACTTCAAGGCAACCT
genomic: AAGTTCTTGATCAAATTCTTAAACTCATGCTACCTCGATTTTTGTCACAGgtatgcagga ... cattttgcagCTCTCCAAAGACTATCATGCATGGGCTTCGGGAGACACTTCAAGGCAACCT
EST: gi|124954505|gb|EL029593.1|EL029593
EST:     ATCAAATTCTTAAACTCATGCTACCTCGATTTTTGTCACAG                         CTCTCCAAAGACTATCATGCATGGGCTTCGGGAGACACTTCAAGGCAACCT
genomic: ATCAAATTCTTAAACTCATGCTACCTCGATTTTTGTCACAGgtatgcagga ... cattttgcagCTCTCCAAAGACTATCATGCATGGGCTTCGGGAGACACTTCAAGGCAACCT
EST: gi|125300462|gb|EL314547.1|EL314547
EST:     ATCAAATTCTTAAACTCATGCTACCTCGATTTTTGTTCACAG                         CTCTCCAAAGACTATCATGCATGGGCTTCGGGAGACACTTCAAGGCAACC
genomic: ATCAAATTCTTAAACTCATGCTACCTCGATTTTTG-TCACAGgtatgcagga ... cattttgcagCTCTCCAAAGACTATCATGCATGGGCTTCGGGAGACACTTCAAGGCAACC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gcctgcaaaatcatcccaacattaatcttatcatgctcttttattcattttgcagCTCTCCAAAGACTATCATGCATGGGCTTCGGGAGACACTTCAAGGCAACCTCTTGGGACCGGTGAGATCTGATAGTAAAGCAAAAGCTACCGTACGTACC
                   cattaat  putative branch site (score: 3)
                                   ctcttttattcatttt  putative PPT
                                    tcttttattcatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tatgtgctcctccttctgcatatatgaacataaatacattccattgcctgcaaaatcatcccaacattaatcttatcatgctcttttattcattttgcagCTCTCCAAAGACTATCATGCATGGGCTTCGGGAGACACTTCAAGGCAACCTCTTGGGACCGGTGAGATCTGATAGTAAAGCAAAAGCTACCGTACGTACC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCAA
- -gtgctcc
- - - - - - cttctgc
- - - - - - - - - - - -atgaaca
- - - - - - - - - - - - - - - -aaataca
- - - - - - - - - - - - - - - - - - - - - - - - - caaaatc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cccaaca