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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgtgtgtttctcttatggattttgaatttgctgattctagttatctttatacaattatactgatagctttcaatgagtcattgttttttcctttaagGTGGCTCATGTTAGCAGCAGAGCCAAACTCACTGTTCCAAAGGAACCGAATCTTAGAACTGCAGAAAGATCTGAAAGACACAG

Basic information

species Arabidopsis thaliana
transcript AT5G62240.1
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|116430574|gb|EG473166.1|EG473166
EST:     TCTCTAAGTTACAAAACCAAGACACCAATAGGCAAAAACAGGAAGCTAAG                         GTGGCTCATGTTAGCAGCAGAGCCAAACTCACTGTTCCAAAGGAACCGAAT
genomic: TCTCTAAGTTACAAAACCAAGACACCAATAGGCAAAAACAGGAAGCTAAGgtgtgtgttt ... ttcctttaagGTGGCTCATGTTAGCAGCAGAGCCAAACTCACTGTTCCAAAGGAACCGAAT
EST: gi|116430576|gb|EG473168.1|EG473168
EST:     TCTCTAAGTTACAAAACCAAGACACCAATAGGCAAAAACAGGAAGCTAAG                         GTGGCTCATGTTAGCAGCAGAGCCAAACTCACTGTTCCAAAGGAACCGAAT
genomic: TCTCTAAGTTACAAAACCAAGACACCAATAGGCAAAAACAGGAAGCTAAGgtgtgtgttt ... ttcctttaagGTGGCTCATGTTAGCAGCAGAGCCAAACTCACTGTTCCAAAGGAACCGAAT
EST: gi|116430569|gb|EG473161.1|EG473161
EST:     TCTCTAAGTTACAAAACCAAGACACCAATAGGCAAAAACAGGAAGCTAAG                         GTGGCTCATGTTAGCAGCAGAGCCAAACTCACTGTTCCAAAGGAACCGAAT
genomic: TCTCTAAGTTACAAAACCAAGACACCAATAGGCAAAAACAGGAAGCTAAGgtgtgtgttt ... ttcctttaagGTGGCTCATGTTAGCAGCAGAGCCAAACTCACTGTTCCAAAGGAACCGAAT
EST: gi|116430567|gb|EG473159.1|EG473159
EST:     TCTCTAAGTTACAAAACCAAGACACCAATAGGCAAAAACAGGAAGCTAAG                         GTGGCTCATGTTAGCAGCAGAGCCAAACTCACTGTTCCAAAGGAACCGAAT
genomic: TCTCTAAGTTACAAAACCAAGACACCAATAGGCAAAAACAGGAAGCTAAGgtgtgtgttt ... ttcctttaagGTGGCTCATGTTAGCAGCAGAGCCAAACTCACTGTTCCAAAGGAACCGAAT
EST: gi|116430565|gb|EG473157.1|EG473157
EST:     TCTCTAAGTTACAAAACCAAGACACCAATAGGCAAAAACAGGAAGCTAAG                         GTGGCTCATGTTAGCAGCAGAGCCAAACTCACTGTTCCAAAGGAACCGAAT
genomic: TCTCTAAGTTACAAAACCAAGACACCAATAGGCAAAAACAGGAAGCTAAGgtgtgtgttt ... ttcctttaagGTGGCTCATGTTAGCAGCAGAGCCAAACTCACTGTTCCAAAGGAACCGAAT
EST: gi|116430571|gb|EG473163.1|EG473163
EST:     CCTCTAAGTTACAAAACCAAGACACCAATAGGCAAAAACAGGAAGCTAAG                         GTGGCTCATGTTAGCAGCAGAGCCAAACTCACTGTTCCAAAGGAACCGAAT
genomic: TCTCTAAGTTACAAAACCAAGACACCAATAGGCAAAAACAGGAAGCTAAGgtgtgtgttt ... ttcctttaagGTGGCTCATGTTAGCAGCAGAGCCAAACTCACTGTTCCAAAGGAACCGAAT
EST: gi|116430578|gb|EG473170.1|EG473170
EST:     TCTCTAAGTTACAAAACCAAGACACCAATAGGCAAAAACAGGAAGCTAAG                         GTGGCTCATGTTAGCAGCAGAGCCAAACTCACTGTTCCAAAGGAACCGAAT
genomic: TCTCTAAGTTACAAAACCAAGACACCAATAGGCAAAAACAGGAAGCTAAGgtgtgtgttt ... ttcctttaagGTGGCTCATGTTAGCAGCAGAGCCAAACTCACTGTTCCAAAGGAACCGAAT
EST: gi|116430582|gb|EG473174.1|EG473174
EST:     TCTCTAAGTTACAAAACCAAGACACCAATAGGCAAAAACAGGAAGCTAAG                         GTGGCTCATGTTAGCAGCAGAGCCAAACTCACTGTTCCAAAGGAACCGAAT
genomic: TCTCTAAGTTACAAAACCAAGACACCAATAGGCAAAAACAGGAAGCTAAGgtgtgtgttt ... ttcctttaagGTGGCTCATGTTAGCAGCAGAGCCAAACTCACTGTTCCAAAGGAACCGAAT
EST: gi|116430585|gb|EG473177.1|EG473177
EST:     TCTCTAAGTTACAAAACCAAGACACCAATAGGCAAAAACAGGAAGCTAAG                         GTGGCTCATGTTAGCAGCAGAGCCAAACTCACTGTTCCAAAGGAACCGAAT
genomic: TCTCTAAGTTACAAAACCAAGACACCAATAGGCAAAAACAGGAAGCTAAGgtgtgtgttt ... ttcctttaagGTGGCTCATGTTAGCAGCAGAGCCAAACTCACTGTTCCAAAGGAACCGAAT
EST: gi|116430580|gb|EG473172.1|EG473172
EST:     TCTCTAAGTTACAAAACCAAGACACCAATAGGCAAAAACAGGAAGCTAAG                         GTGGCTCATGTTAGCAGCAGAGCCAAACTCACTGTTCCAAAGGAACCGAAT
genomic: TCTCTAAGTTACAAAACCAAGACACCAATAGGCAAAAACAGGAAGCTAAGgtgtgtgttt ... ttcctttaagGTGGCTCATGTTAGCAGCAGAGCCAAACTCACTGTTCCAAAGGAACCGAAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atctttatacaattatactgatagctttcaatgagtcattgttttttcctttaagGTGGCTCATGTTAGCAGCAGAGCCAAACTCACTGTTCCAAAGGAACCGAATCTTAGAACTGCAGAAAGATCTGAAAGACACAG
               tactgat  putative branch site (score: 2)
                                   tcattgttttttcctt  putative PPT
     tatacaattatact  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgtgtgtttctcttatggattttgaatttgctgattctagttatctttatacaattatactgatagctttcaatgagtcattgttttttcctttaagGTGGCTCATGTTAGCAGCAGAGCCAAACTCACTGTTCCAAAGGAACCGAATCTTAGAACTGCAGAAAGATCTGAAAGACACAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG