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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaagtagttgcttattccgaatgttttctctaagcctcacattacactcaaagtcatggttttggtgagcagACGAATTTGATGGAGTCACGAGGATGCAGATGGGTAGAGTAAGAAAAGGGCTTCGACTTGTTGAAGCAAAGACCAAAGACGACCCAAACGAAGTATCAGA

Basic information

species Arabidopsis thaliana
transcript AT2G39690.2
intron # 3
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|116384056|gb|EG426648.1|EG426648
EST:     CTCTTACGCTCCTGATTTCTTGGATGCCACTTCTTCAGGTGGCTTCACAG                         ACGAATTTGATGGAGTCACGAGGATGCAGATGGGTAGAGTAAGAAAAGGGC
genomic: CTCTTACGCTCCTGATTTCTTGGATGCCACTTCTTCAGGTGGCTTCACAGgtaaagtagt ... tggtgagcagACGAATTTGATGGAGTCACGAGGATGCAGATGGGTAGAGTAAGAAAAGGGC
EST: gi|116384064|gb|EG426656.1|EG426656
EST:     CTCTTACGCTCCTGATTTCTTGGATGCCACTTCTTCAGGTGGCTTCACAG                         ACGAATTTGATGGAGTCACGAGGATGCAGATGGGTAGAGTAAGAAAAGGGC
genomic: CTCTTACGCTCCTGATTTCTTGGATGCCACTTCTTCAGGTGGCTTCACAGgtaaagtagt ... tggtgagcagACGAATTTGATGGAGTCACGAGGATGCAGATGGGTAGAGTAAGAAAAGGGC
EST: gi|116384062|gb|EG426654.1|EG426654
EST:     CTCTTACGCTCCTGATTTCTTGGATGCCACTTCTTCAGGTGGCTTCACAG                         ACGAATTTGATGGAGTCACGAGGATGCAGATGGGTAGAGTAAGAAAAGGGC
genomic: CTCTTACGCTCCTGATTTCTTGGATGCCACTTCTTCAGGTGGCTTCACAGgtaaagtagt ... tggtgagcagACGAATTTGATGGAGTCACGAGGATGCAGATGGGTAGAGTAAGAAAAGGGC
EST: gi|116384069|gb|EG426661.1|EG426661
EST:     CTCTTACGCTCCTGATTTCTTGGATGCCACTTCTTCAGGTGGCTTCACAG                         ACGAATTTGATGGAGTCACGAGGATGCAGATGGGTAGAGTAAGAAAAGGGC
genomic: CTCTTACGCTCCTGATTTCTTGGATGCCACTTCTTCAGGTGGCTTCACAGgtaaagtagt ... tggtgagcagACGAATTTGATGGAGTCACGAGGATGCAGATGGGTAGAGTAAGAAAAGGGC
EST: gi|116384054|gb|EG426646.1|EG426646
EST:     CTCTTACGCTCCTGATTTCTTGGATGCCACTTCTTCAGGTGGCTTCACAG                         ACGAATTTGATGGAGTCACGAGGATGCAGATGGGTAGAGTAAGAAAAGGGC
genomic: CTCTTACGCTCCTGATTTCTTGGATGCCACTTCTTCAGGTGGCTTCACAGgtaaagtagt ... tggtgagcagACGAATTTGATGGAGTCACGAGGATGCAGATGGGTAGAGTAAGAAAAGGGC
EST: gi|116384057|gb|EG426649.1|EG426649
EST:     CTCTTACGCTCCTGATTTCTTGGATGCCACTTCTTCAGGTGGCTTCACAG                         ACGAATTTGATGGAGTCACGAGGATGCAGATGGGTAGAGTAAGAAAAGGGC
genomic: CTCTTACGCTCCTGATTTCTTGGATGCCACTTCTTCAGGTGGCTTCACAGgtaaagtagt ... tggtgagcagACGAATTTGATGGAGTCACGAGGATGCAGATGGGTAGAGTAAGAAAAGGGC
EST: gi|116384067|gb|EG426659.1|EG426659
EST:     CTCTTACGCTCCTGATTTCTTGGATGCCACTTCTTCAGGTGGCTTCACAG                         ACGAATTTGATGGAGTCACGAGGATGCAGATGGGTAGAGTAAGAAAAGGGC
genomic: CTCTTACGCTCCTGATTTCTTGGATGCCACTTCTTCAGGTGGCTTCACAGgtaaagtagt ... tggtgagcagACGAATTTGATGGAGTCACGAGGATGCAGATGGGTAGAGTAAGAAAAGGGC
EST: gi|116384070|gb|EG426662.1|EG426662
EST:     CTCTTACGCTCCTGATTTCTTGGATGCCACTTCTTCAGGTGGCTTCACAG                         ACGAATTTGATGGAGTCACGAGGATGCAGATGGGTAGAGTAAGAAAAGGGC
genomic: CTCTTACGCTCCTGATTTCTTGGATGCCACTTCTTCAGGTGGCTTCACAGgtaaagtagt ... tggtgagcagACGAATTTGATGGAGTCACGAGGATGCAGATGGGTAGAGTAAGAAAAGGGC
EST: gi|116384055|gb|EG426647.1|EG426647
EST:     CTCTTACGCTCCTGATTTCTTGGATGCCACTTCTTCAGGTGGCTTCACAG                         ACGAATTTGATGGAGTCACGAGGATGCAGATGGGTAGAGTAAGAAAAGGGC
genomic: CTCTTACGCTCCTGATTTCTTGGATGCCACTTCTTCAGGTGGCTTCACAGgtaaagtagt ... tggtgagcagACGAATTTGATGGAGTCACGAGGATGCAGATGGGTAGAGTAAGAAAAGGGC
EST: gi|116384068|gb|EG426660.1|EG426660
EST:     CTCTTACGCTCCTGATTTCTTGGATGCCACTTCTTCAGGTGGCTTCACAG                         ACGAATTTGATGGAGTCACGAGGATGCAGATGGGTAGAGTAAGAAAAGGGC
genomic: CTCTTACGCTCCTGATTTCTTGGATGCCACTTCTTCAGGTGGCTTCACAGgtaaagtagt ... tggtgagcagACGAATTTGATGGAGTCACGAGGATGCAGATGGGTAGAGTAAGAAAAGGGC
EST: gi|116384066|gb|EG426658.1|EG426658
EST:     CTCTTACGCTCCTGATTTCTTGGATGCCACTTCTTCAGGTGGCTTCACAG                         ACGAATTTGATGGAGTCACGAGGATGCAGATGGGTAGAGTAAGAAAAGGGC
genomic: CTCTTACGCTCCTGATTTCTTGGATGCCACTTCTTCAGGTGGCTTCACAGgtaaagtagt ... tggtgagcagACGAATTTGATGGAGTCACGAGGATGCAGATGGGTAGAGTAAGAAAAGGGC
EST: gi|116384072|gb|EG426664.1|EG426664
EST:     CTCTTACGCTCCTGATTTCTTGGATGCCACTTCTTCAGGTGGCTTCACAG                         ACGAATTTGATGGAGTCACGAGGATGCAGATGGGTAGAGTAAGAAAAGGGC
genomic: CTCTTACGCTCCTGATTTCTTGGATGCCACTTCTTCAGGTGGCTTCACAGgtaaagtagt ... tggtgagcagACGAATTTGATGGAGTCACGAGGATGCAGATGGGTAGAGTAAGAAAAGGGC
EST: gi|116384061|gb|EG426653.1|EG426653
EST:     CTCTTACGCTCCTGATTTCTTGGATGCCACTTCTTCAGGTGGCTTCACAG                         ACGAATTTGATGGAGTCACGAGGATGCAGATGGGTAGAGTAAGAAAAGGGC
genomic: CTCTTACGCTCCTGATTTCTTGGATGCCACTTCTTCAGGTGGCTTCACAGgtaaagtagt ... tggtgagcagACGAATTTGATGGAGTCACGAGGATGCAGATGGGTAGAGTAAGAAAAGGGC
EST: gi|116384059|gb|EG426651.1|EG426651
EST:     CTCTTACGCTCCTGATTTCTTGGATGCCACTTCTTCAGGTGGCTTCACAG                         ACGAATTTGATGGAGTCACGAGGATGCAGATGGGTAGAGTAAGAAAAGGGC
genomic: CTCTTACGCTCCTGATTTCTTGGATGCCACTTCTTCAGGTGGCTTCACAGgtaaagtagt ... tggtgagcagACGAATTTGATGGAGTCACGAGGATGCAGATGGGTAGAGTAAGAAAAGGGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cgaatgttttctctaagcctcacattacactcaaagtcatggttttggtgagcagACGAATTTGATGGAGTCACGAGGATGCAGATGGGTAGAGTAAGAAAAGGGCTTCGACTTGTTGAAGCAAAGACCAAAGACGACCCAAACGAAGTATCAGA
                gcctcac  putative branch site (score: 3)
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaagtagttgcttattccgaatgttttctctaagcctcacattacactcaaagtcatggttttggtgagcagACGAATTTGATGGAGTCACGAGGATGCAGATGGGTAGAGTAAGAAAAGGGCTTCGACTTGTTGAAGCAAAGACCAAAGACGACCCAAACGAAGTATCAGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAAG