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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaactaattttgtatgtttaccaaaaggaaggaacttgtcttatatttattgcttagttaacttttgaaagGTGGGGAATGTCGAAGAAGCTAGAAAGGCTGTTGCTGTAGGAGTAGACGCCATTATTGTCCAAGGGCGTGAAGCAGGTGGGCATGTTATTGGCAAGGATG

Basic information

species Arabidopsis thaliana
transcript AT5G64250.2
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|164064463|gb|EL985259.1|EL985259
EST:     GGATGATGCTCACTTTGCCGGTGTCAAAGGTTATTCCTCAG                         GTGGGGAATGTCGAAGAAGCTAGAA
genomic: GGATGATGCTCACTTTGCCGGTGTCAAA-GTTATTCCTCAGgtaactaatt ... cttttgaaagGTGGGGAATGTCGAAGAAGCTAGAA
EST: gi|116453508|gb|EG496100.1|EG496100
EST:     AGGAGCTTGTGGATGATGCTCACTTTGCCGGTGTCAAAGTTATTCCTCAG                         GTGGGGAATGTCGAAGAAGCTAGAAAGGCTGTTGCTGTAGGAGTAGACGCC
genomic: AGGAGCTTGTGGATGATGCTCACTTTGCCGGTGTCAAAGTTATTCCTCAGgtaactaatt ... cttttgaaagGTGGGGAATGTCGAAGAAGCTAGAAAGGCTGTTGCTGTAGGAGTAGACGCC
EST: gi|116453507|gb|EG496099.1|EG496099
EST:     AGGAGCTTGTGGATGATGCTCACTTTGCCGGTGTCAAAGTTATTCCTCAG                         GTGGGGAATGTCGAAGAAGCTAGAAAGGCTGTTGCTGTAGGAGTAGACGCC
genomic: AGGAGCTTGTGGATGATGCTCACTTTGCCGGTGTCAAAGTTATTCCTCAGgtaactaatt ... cttttgaaagGTGGGGAATGTCGAAGAAGCTAGAAAGGCTGTTGCTGTAGGAGTAGACGCC
EST: gi|116453498|gb|EG496090.1|EG496090
EST:     AGGAGCTTGTGGATGATGCTCACTTTGCCGGTGTCAAAGTTATTCCTCAG                         GTGGGGAATGTCGAAGAAGCTAGAAAGGCTGTTGCTGTAGGAGTAGACGCC
genomic: AGGAGCTTGTGGATGATGCTCACTTTGCCGGTGTCAAAGTTATTCCTCAGgtaactaatt ... cttttgaaagGTGGGGAATGTCGAAGAAGCTAGAAAGGCTGTTGCTGTAGGAGTAGACGCC
EST: gi|116453517|gb|EG496109.1|EG496109
EST:     AGGAGCTTGTGGATGATGCTCACTTTGCCGGTGTCAAAGTTATTCCTCAG                         GTGGGGAATGTCGAAGAAGCTAGAAAGGCTGTTGCTGTAGGAGTAGACGCC
genomic: AGGAGCTTGTGGATGATGCTCACTTTGCCGGTGTCAAAGTTATTCCTCAGgtaactaatt ... cttttgaaagGTGGGGAATGTCGAAGAAGCTAGAAAGGCTGTTGCTGTAGGAGTAGACGCC
EST: gi|116453516|gb|EG496108.1|EG496108
EST:     AGGAGCTTGTGGATGATGCTCACTTTGCCGGTGTCAAAGTTATTCCTCAG                         GTGGGGAATGTCGAAGAAGCTAGAAAGGCTGTTGCTGTAGGAGTAGACGCC
genomic: AGGAGCTTGTGGATGATGCTCACTTTGCCGGTGTCAAAGTTATTCCTCAGgtaactaatt ... cttttgaaagGTGGGGAATGTCGAAGAAGCTAGAAAGGCTGTTGCTGTAGGAGTAGACGCC
EST: gi|164137454|gb|EL968568.1|EL968568
EST:     GGATGATGCTCACTTTGCCGGTGTCAAAGTTATTCCTCAG                         GTGGGGAATGTCGAAGAAGCTAGAAA
genomic: GGATGATGCTCACTTTGCCGGTGTCAAAGTTATTCCTCAGgtaactaatt ... cttttgaaagGTGGGGAATGTCGAAGAAGCTAGAAA
EST: gi|86039417|gb|DR335172.1|DR335172
EST:     AGGAGCTTGTGGATGATGCTCACTTTGCCGGTGTCAAAGTTATTCCTCAG                         GTGGGGAATGTCGAAGAAGCTAGAAAGGCTGTTGCTGTAGGAGTAGACGCC
genomic: AGGAGCTTGTGGATGATGCTCACTTTGCCGGTGTCAAAGTTATTCCTCAGgtaactaatt ... cttttgaaagGTGGGGAATGTCGAAGAAGCTAGAAAGGCTGTTGCTGTAGGAGTAGACGCC
EST: gi|164206941|gb|EL967982.1|EL967982
EST:     GGATGATGCTCACTTTGCCGGTGTCAAAGGTTATTCCTCAG                         GTGGGGAATGTCGAAGAAGCTAGAAA
genomic: GGATGATGCTCACTTTGCCGGTGTCAAA-GTTATTCCTCAGgtaactaatt ... cttttgaaagGTGGGGAATGTCGAAGAAGCTAGAAA
EST: gi|116453501|gb|EG496093.1|EG496093
EST:     AGGAGCTTGTGGATGATGCTCACTTTGCCGGTGTCAAAGTTATTCCTCAG                         GTGGGGAATGTCGAAGAAGCTAGAAAGGCTGTTGCTGTAGGAGTAGACGCC
genomic: AGGAGCTTGTGGATGATGCTCACTTTGCCGGTGTCAAAGTTATTCCTCAGgtaactaatt ... cttttgaaagGTGGGGAATGTCGAAGAAGCTAGAAAGGCTGTTGCTGTAGGAGTAGACGCC
EST: gi|116453499|gb|EG496091.1|EG496091
EST:     AGGAGCTTGTGGATGATGCTCACTTTGCCGGTGTCAAAGTTATTCCTCAG                         GTGGGGAATGTCGAAGAAGCTAGAAAGGCTGTTGCTGTAGGAGTAGACGCC
genomic: AGGAGCTTGTGGATGATGCTCACTTTGCCGGTGTCAAAGTTATTCCTCAGgtaactaatt ... cttttgaaagGTGGGGAATGTCGAAGAAGCTAGAAAGGCTGTTGCTGTAGGAGTAGACGCC
EST: gi|86039418|gb|DR335173.1|DR335173
EST:     AGGAGCTTGTGGATGATGCTCACTTTGCCGGTGTCAAAGTTATTCCTCAG                         GTGGGGAATGTCGAAGAAGCTAGAAAGGCTGTTGCTGTAGGAGTAGACGCC
genomic: AGGAGCTTGTGGATGATGCTCACTTTGCCGGTGTCAAAGTTATTCCTCAGgtaactaatt ... cttttgaaagGTGGGGAATGTCGAAGAAGCTAGAAAGGCTGTTGCTGTAGGAGTAGACGCC
EST: gi|86039416|gb|DR335171.1|DR335171
EST:     AGGAGCTTGTGGATGATGCTCACTTTGCCGGTGTCAAAGTTATTCCTCAG                         GTGGGGAATGTCGAAGAAGCTAGAAAGGCTGTTGCTGTAGGAGTAGACGCC
genomic: AGGAGCTTGTGGATGATGCTCACTTTGCCGGTGTCAAAGTTATTCCTCAGgtaactaatt ... cttttgaaagGTGGGGAATGTCGAAGAAGCTAGAAAGGCTGTTGCTGTAGGAGTAGACGCC
EST: gi|86039415|gb|DR335170.1|DR335170
EST:     AGGAGCTTGTGGATGATGCTCACTTTGCCGGTGTCAAAGTTATTCCTCAG                         GTGGGGAATGTCGAAGAAGCTAGAAAGGCTGTTGCTGTAGGAGTAGACGCC
genomic: AGGAGCTTGTGGATGATGCTCACTTTGCCGGTGTCAAAGTTATTCCTCAGgtaactaatt ... cttttgaaagGTGGGGAATGTCGAAGAAGCTAGAAAGGCTGTTGCTGTAGGAGTAGACGCC
EST: gi|86039419|gb|DR335174.1|DR335174
EST:     AGGAGCTTGTGGATGATGCTCACTTTGCCGGTGTCAAAVTTATTCCTCAG                         GTGGGGAATGTCGAAGAAGCTARMAAAGGCTGTTGCTGTAGGAGTAGACGC
genomic: AGGAGCTTGTGGATGATGCTCACTTTGCCGGTGTCAAAGTTATTCCTCAGgtaactaatt ... cttttgaaagGTGGGGAATGTCGAAGAAGCTAG-AAAGGCTGTTGCTGTAGGAGTAGACGC
EST: gi|116453500|gb|EG496092.1|EG496092
EST:     AGGAGCTTGTGGATGATGCTCACTTTGCCGGTGTCAAAGTTATTCCTCAG                         GTGGGGAATGTCGAAGAAGCTAGAAAGGCTGTTGCTGTAGGAGTAGACGCC
genomic: AGGAGCTTGTGGATGATGCTCACTTTGCCGGTGTCAAAGTTATTCCTCAGgtaactaatt ... cttttgaaagGTGGGGAATGTCGAAGAAGCTAGAAAGGCTGTTGCTGTAGGAGTAGACGCC
EST: gi|116453502|gb|EG496094.1|EG496094
EST:     AGGAGCTTGTGGATGATGCTCACTTTGCCGGTGCCAAAGTTATTCCCCAG                         GTGGGGAATGTCGAAGAAGCTAGAAAGGCTGTTGCTGTAGGAGTAGACGCC
genomic: AGGAGCTTGTGGATGATGCTCACTTTGCCGGTGTCAAAGTTATTCCTCAGgtaactaatt ... cttttgaaagGTGGGGAATGTCGAAGAAGCTAGAAAGGCTGTTGCTGTAGGAGTAGACGCC
EST: gi|86039413|gb|DR335168.1|DR335168
EST:     AGGAGCTTGTGGATGATGCTCACTTTGCCGGTGTCAAAGTTATTCCTCAG                         GTGGGGAATGTCGAAGAAGCTAGAAAGGCTGTTGCTGTAGGAGTAGACGCC
genomic: AGGAGCTTGTGGATGATGCTCACTTTGCCGGTGTCAAAGTTATTCCTCAGgtaactaatt ... cttttgaaagGTGGGGAATGTCGAAGAAGCTAGAAAGGCTGTTGCTGTAGGAGTAGACGCC
EST: gi|86039414|gb|DR335169.1|DR335169
EST:     AGGAGCTTGTGGATGATGCTCACTTTGCCGGTGTCAAAGTTATTCCTCAG                         GTGGGGAATGTCGAAGAAGCTAGAAAGGCTGTTGCTGTAGGAGTAGACGCC
genomic: AGGAGCTTGTGGATGATGCTCACTTTGCCGGTGTCAAAGTTATTCCTCAGgtaactaatt ... cttttgaaagGTGGGGAATGTCGAAGAAGCTAGAAAGGCTGTTGCTGTAGGAGTAGACGCC
EST: gi|116453497|gb|EG496089.1|EG496089
EST:     AGGAGCTTGTGGATGATGCTCACTTTGCCGGTGTCAAAGTTATTCCTCAG                         GTGGGGAATGTCGAAGAAGCTAGAAAGGCTGTTGCTGTAGGAGTAGACGCC
genomic: AGGAGCTTGTGGATGATGCTCACTTTGCCGGTGTCAAAGTTATTCCTCAGgtaactaatt ... cttttgaaagGTGGGGAATGTCGAAGAAGCTAGAAAGGCTGTTGCTGTAGGAGTAGACGCC
EST: gi|116453503|gb|EG496095.1|EG496095
EST:     AGGAGCTTGTGGATGATGCTCACTTTGCCGGTGCCAAAGTTATTCCCCAG                         GTGGGGAATGTCGAAGAAGCTAGAAAGGCTGTTGCTGTAGGAGTAGACGCC
genomic: AGGAGCTTGTGGATGATGCTCACTTTGCCGGTGTCAAAGTTATTCCTCAGgtaactaatt ... cttttgaaagGTGGGGAATGTCGAAGAAGCTAGAAAGGCTGTTGCTGTAGGAGTAGACGCC
EST: gi|86039420|gb|DR335175.1|DR335175
EST:     AGGAGCTTGTGGATGATGCTCACTTTGCCGGTGTCAAAGTTATTCCTCAG                         GTGGGGAATGTCGAAGAAGCTAGAAAGGCTGTTGCTGTAGGAGTAGACGCC
genomic: AGGAGCTTGTGGATGATGCTCACTTTGCCGGTGTCAAAGTTATTCCTCAGgtaactaatt ... cttttgaaagGTGGGGAATGTCGAAGAAGCTAGAAAGGCTGTTGCTGTAGGAGTAGACGCC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttaccaaaaggaaggaacttgtcttatatttattgcttagttaacttttgaaagGTGGGGAATGTCGAAGAAGCTAGAAAGGCTGTTGCTGTAGGAGTAGACGCCATTATTGTCCAAGGGCGTGAAGCAGGTGGGCATGTTATTGGCAAGGATG
                                       agttaac  putative branch site (score: 3)
                                             ctttt  CT-rich tract
                        ttatatttattgctta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaactaattttgtatgtttaccaaaaggaaggaacttgtcttatatttattgcttagttaacttttgaaagGTGGGGAATGTCGAAGAAGCTAGAAAGGCTGTTGCTGTAGGAGTAGACGCCATTATTGTCCAAGGGCGTGAAGCAGGTGGGCATGTTATTGGCAAGGATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG