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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagaaagcttcatatactcttacaaatacctgatgctacttctctattaacgggttctggttggcacgcagGTCGACTTCAATCTTCCTCAGAGATTTGACATTACCTATGTAGACACAAACTCAGATAAGAAACGTCCTATAATGATCCACAGAGCGGTTTTAGGATCAT

Basic information

species Arabidopsis thaliana
transcript AT2G04842.1
intron # 6
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|116385886|gb|EG428478.1|EG428478
EST:     TTAAGATTGAAGATGCATTGGGTAGAAAATGGCAGTGCTCAACTATTCAG                         GTCGACTTCAATCTTCCTCAGAGATTTGACATTACCTATGTAGACACAAAC
genomic: TTAAGATTGAAGATGCATTGGGTAGAAAATGGCAGTGCTCAACTATTCAGgtaagaaagc ... tggcacgcagGTCGACTTCAATCTTCCTCAGAGATTTGACATTACCTATGTAGACACAAAC
EST: gi|116385828|gb|EG428420.1|EG428420
EST:     TTAAGATTGAAGATGCATTGGGTAGAAAATGGCAGTGCTCAACTATTCAG                         GTCGACTTCAATCTTCCTCAGAGATTTGACATTACCTATGTAGACACAAAC
genomic: TTAAGATTGAAGATGCATTGGGTAGAAAATGGCAGTGCTCAACTATTCAGgtaagaaagc ... tggcacgcagGTCGACTTCAATCTTCCTCAGAGATTTGACATTACCTATGTAGACACAAAC
EST: gi|124780578|gb|EH870521.1|EH870521
EST:     ATTGGGTAGAAAATGGCAGTGCTCAACTATTCAG                         GTCGACTTCAATCTTCCTCAGAGATTTGACATTACCTATGTAGACACAAAC
genomic: ATTGGGTAGAAAATGGCAGTGCTCAACTATTCAGgtaagaaagc ... tggcacgcagGTCGACTTCAATCTTCCTCAGAGATTTGACATTACCTATGTAGACACAAAC
EST: gi|116385892|gb|EG428484.1|EG428484
EST:     TTAAGATTGAAGATGCATTGGGTAGAAAATGGCAGTGCTCAACTATTCAG                         GTCGAC-TCAATCTTCTTCAGAGATTTGACATTACCTATGTAGACACAAAC
genomic: TTAAGATTGAAGATGCATTGGGTAGAAAATGGCAGTGCTCAACTATTCAGgtaagaaagc ... tggcacgcagGTCGACTTCAATCTTCCTCAGAGATTTGACATTACCTATGTAGACACAAAC
EST: gi|116385904|gb|EG428496.1|EG428496
EST:     TTAAGATTGAAGATGCATTGGGTAGAAAATGGCAGTGCTCAGCTATTCAG                         GTCGACTTCAATCTTCCTCAGAGATTTGACATTACCTATGTAGACACAAAC
genomic: TTAAGATTGAAGATGCATTGGGTAGAAAATGGCAGTGCTCAACTATTCAGgtaagaaagc ... tggcacgcagGTCGACTTCAATCTTCCTCAGAGATTTGACATTACCTATGTAGACACAAAC
EST: gi|116385897|gb|EG428489.1|EG428489
EST:     TTAAGATTGAAGATGCATTGGGTAGAAAATGGCAGTGCTCAACTATTCAG                         GTCGACTTCAATCTTCCTCAGAGATTTGACATTACCTATGTAGACACAA-C
genomic: TTAAGATTGAAGATGCATTGGGTAGAAAATGGCAGTGCTCAACTATTCAGgtaagaaagc ... tggcacgcagGTCGACTTCAATCTTCCTCAGAGATTTGACATTACCTATGTAGACACAAAC
EST: gi|116385885|gb|EG428477.1|EG428477
EST:     TTAAGATTGAAGATGCATTGGGTAGAAAATGGCAGTGCTCAACTATTCAG                         GTCGACTTCAATCTTCCTCAGAGATTTGACATTACCTATGTAGACACAAAC
genomic: TTAAGATTGAAGATGCATTGGGTAGAAAATGGCAGTGCTCAACTATTCAGgtaagaaagc ... tggcacgcagGTCGACTTCAATCTTCCTCAGAGATTTGACATTACCTATGTAGACACAAAC
EST: gi|116385903|gb|EG428495.1|EG428495
EST:     TTAAGATTGAAGATGCATTGGGTAGAAAATGGCAGTGCTCAGCTATTCAG                         GTCGACTTCAATCTTCCTCAGAGATTTGACATTACCTATGTAGACACAAAC
genomic: TTAAGATTGAAGATGCATTGGGTAGAAAATGGCAGTGCTCAACTATTCAGgtaagaaagc ... tggcacgcagGTCGACTTCAATCTTCCTCAGAGATTTGACATTACCTATGTAGACACAAAC
EST: gi|116385899|gb|EG428491.1|EG428491
EST:     CTAAGATTGAAGATGCATTGGGTAGAAAATGGCAGTGCTCAACTATTCAG                         GTCGACTTCAATCTTCCTCAGAGATTTGACATTACCTATGTAGACACAAAC
genomic: TTAAGATTGAAGATGCATTGGGTAGAAAATGGCAGTGCTCAACTATTCAGgtaagaaagc ... tggcacgcagGTCGACTTCAATCTTCCTCAGAGATTTGACATTACCTATGTAGACACAAAC
EST: gi|116386174|gb|EG428766.1|EG428766
EST:     CTCAACTATTCAG                         GTCGACTTCAATCTTCCTCAGAGATTTGACATTACCTATGTAGACACAAAC
genomic: CTCAACTATTCAGgtaagaaagc ... tggcacgcagGTCGACTTCAATCTTCCTCAGAGATTTGACATTACCTATGTAGACACAAAC
EST: gi|116386169|gb|EG428761.1|EG428761
EST:     AGAAAATGGCAGTGCTCAACTATTCAG                         GTCGACTTCAATCTTCCTCAGAGATTTGACATTACCTATGTAGACACAAAC
genomic: AGAAAATGGCAGTGCTCAACTATTCAGgtaagaaagc ... tggcacgcagGTCGACTTCAATCTTCCTCAGAGATTTGACATTACCTATGTAGACACAAAC
EST: gi|116386172|gb|EG428764.1|EG428764
EST:     TTAAGATTGAAGATGCATTGGGTAGAAAATGGCAGTGCTCAACTATTCAG                         GTCGACTTCAATCTTCCTCAGAGATTTGACATTACCTATGTAGACACAAAC
genomic: TTAAGATTGAAGATGCATTGGGTAGAAAATGGCAGTGCTCAACTATTCAGgtaagaaagc ... tggcacgcagGTCGACTTCAATCTTCCTCAGAGATTTGACATTACCTATGTAGACACAAAC
EST: gi|116385887|gb|EG428479.1|EG428479
EST:     TTAAGATTGAAGATGCATTGGGTAGAAAATGGCAGTGCTCAACTATTCAG                         GTCGACTTCAATCTTCCTCAGAGATTTGACATTACCTATGTAGACACAAAC
genomic: TTAAGATTGAAGATGCATTGGGTAGAAAATGGCAGTGCTCAACTATTCAGgtaagaaagc ... tggcacgcagGTCGACTTCAATCTTCCTCAGAGATTTGACATTACCTATGTAGACACAAAC
EST: gi|116386176|gb|EG428768.1|EG428768
EST:     CTCAACTATTCAG                         GTCGACTTCAATCTTCCTCAGAGATTTGACATTACCTATGTAGACACAAAC
genomic: CTCAACTATTCAGgtaagaaagc ... tggcacgcagGTCGACTTCAATCTTCCTCAGAGATTTGACATTACCTATGTAGACACAAAC
EST: gi|116385830|gb|EG428422.1|EG428422
EST:     TTAAGATTGAAGATGCATTGGGTAGAAAATGGCAGTGCTCAACTATTCAG                         GTCGACTTCAATCTTCCTCAGAGATTTGACATTACCTATGTAGACACAAAC
genomic: TTAAGATTGAAGATGCATTGGGTAGAAAATGGCAGTGCTCAACTATTCAGgtaagaaagc ... tggcacgcagGTCGACTTCAATCTTCCTCAGAGATTTGACATTACCTATGTAGACACAAAC
EST: gi|116386168|gb|EG428760.1|EG428760
EST:     TTAAGATTGAAGAGGCATTGGGTAGAAAATGGCAGTGCTCAACTATTCAG                         GTCGACTTCAATCTTCCTCAGAGATTTGACATTACCTATGTAGACACAAAC
genomic: TTAAGATTGAAGATGCATTGGGTAGAAAATGGCAGTGCTCAACTATTCAGgtaagaaagc ... tggcacgcagGTCGACTTCAATCTTCCTCAGAGATTTGACATTACCTATGTAGACACAAAC
EST: gi|116385834|gb|EG428426.1|EG428426
EST:     TTAAGATTGAAGATGCATTGGGTAGAAAATGGCAGTGCTCAACTATTCAG                         GTCGACTTCAATCTTCCTCAGAGATTTGACATTACCTATGTAGACACAAAC
genomic: TTAAGATTGAAGATGCATTGGGTAGAAAATGGCAGTGCTCAACTATTCAGgtaagaaagc ... tggcacgcagGTCGACTTCAATCTTCCTCAGAGATTTGACATTACCTATGTAGACACAAAC
EST: gi|116385888|gb|EG428480.1|EG428480
EST:     TTAAGATTGAAGATGCATTGGGTAGAAAATGGCAGTGCTCAACTATTCAG                         GTCGACTTCAATCTTCCTCAGAGATTTGACATTACCTATGTAGACACAAAC
genomic: TTAAGATTGAAGATGCATTGGGTAGAAAATGGCAGTGCTCAACTATTCAGgtaagaaagc ... tggcacgcagGTCGACTTCAATCTTCCTCAGAGATTTGACATTACCTATGTAGACACAAAC
EST: gi|116385835|gb|EG428427.1|EG428427
EST:     TTAAGATTGAAGATGCATTGGGTAGAAAATGGCAGTGCTCAACTATTCAG                         GTCGACTTCAATCTTCCTCAGAGATTTGACATTACCTATGTAGACACAAAC
genomic: TTAAGATTGAAGATGCATTGGGTAGAAAATGGCAGTGCTCAACTATTCAGgtaagaaagc ... tggcacgcagGTCGACTTCAATCTTCCTCAGAGATTTGACATTACCTATGTAGACACAAAC
EST: gi|116385831|gb|EG428423.1|EG428423
EST:     TTAAGATTGAAGATGCATTGGGTAGAAAATGGCAGTGCTCAACTATTCAG                         GTCGACTTCAATCTTCCTCAGAGATTTGACATTACCTATGTAGACACAAAC
genomic: TTAAGATTGAAGATGCATTGGGTAGAAAATGGCAGTGCTCAACTATTCAGgtaagaaagc ... tggcacgcagGTCGACTTCAATCTTCCTCAGAGATTTGACATTACCTATGTAGACACAAAC
EST: gi|116385891|gb|EG428483.1|EG428483
EST:     TTAAGATTGAAGATGCATTGGGTAGAAAATGGCAGTGCTCAACTATTCAG                         GTCGACTTCAATCTTCCTCAGAGATTTGACATTACCTATGTAGACACAAAC
genomic: TTAAGATTGAAGATGCATTGGGTAGAAAATGGCAGTGCTCAACTATTCAGgtaagaaagc ... tggcacgcagGTCGACTTCAATCTTCCTCAGAGATTTGACATTACCTATGTAGACACAAAC
EST: gi|116385895|gb|EG428487.1|EG428487
EST:     TTAAGATTGAAGATGCATTGGGTAGAAAATGGCAGTGCTCAACTATTCAG                         GTCGACTTCGATCTTCCTCAGAGATTTGACATTACCTATGTAGACACAAAC
genomic: TTAAGATTGAAGATGCATTGGGTAGAAAATGGCAGTGCTCAACTATTCAGgtaagaaagc ... tggcacgcagGTCGACTTCAATCTTCCTCAGAGATTTGACATTACCTATGTAGACACAAAC
EST: gi|116386170|gb|EG428762.1|EG428762
EST:     TTAAGATTGAAGATGCATTGGGTAGAAAATGGCAGTGCTCAACTATTCAG                         GTCGACTTCAATCTTCCTCAGAGATTTGACATTACCTATGTAGACACAAAC
genomic: TTAAGATTGAAGATGCATTGGGTAGAAAATGGCAGTGCTCAACTATTCAGgtaagaaagc ... tggcacgcagGTCGACTTCAATCTTCCTCAGAGATTTGACATTACCTATGTAGACACAAAC
EST: gi|116385898|gb|EG428490.1|EG428490
EST:     TTAAGATTGAAGATGCATTGGGTAGAAAATGGCAGTGCTCAACTATTCAG                         GTCGACTTCAATCTTCCTCAGAGATTTGACATTACCTATGTAGACACAAAC
genomic: TTAAGATTGAAGATGCATTGGGTAGAAAATGGCAGTGCTCAACTATTCAGgtaagaaagc ... tggcacgcagGTCGACTTCAATCTTCCTCAGAGATTTGACATTACCTATGTAGACACAAAC
EST: gi|116385832|gb|EG428424.1|EG428424
EST:     TTAAGATTGAAGATGCATTGGGTAGAAAATGGCAGTGCTCAACTATTCAG                         GTCGACTTCAATCTTCCTCAGAGATTTGACATTACCTATGTAGACACAAAC
genomic: TTAAGATTGAAGATGCATTGGGTAGAAAATGGCAGTGCTCAACTATTCAGgtaagaaagc ... tggcacgcagGTCGACTTCAATCTTCCTCAGAGATTTGACATTACCTATGTAGACACAAAC
EST: gi|116385896|gb|EG428488.1|EG428488
EST:     TTAAGATTGAAGATGCATTGGGTAGAAAATGGCAGTGCTCAACTATTCAG                         GTCGACTTC-ATCTTCCTCAGAGATTTGACATTACCTATGTAGACACAAAC
genomic: TTAAGATTGAAGATGCATTGGGTAGAAAATGGCAGTGCTCAACTATTCAGgtaagaaagc ... tggcacgcagGTCGACTTCAATCTTCCTCAGAGATTTGACATTACCTATGTAGACACAAAC
EST: gi|116385902|gb|EG428494.1|EG428494
EST:     CTAAGATTGAAGATGCATTGGGTAGAAAATGGCAGTGCTCAACTATTCAG                         GTCGACTTCAATCTTCCTCAGAGATTTGACATTACCTATGTAGACACAAAC
genomic: TTAAGATTGAAGATGCATTGGGTAGAAAATGGCAGTGCTCAACTATTCAGgtaagaaagc ... tggcacgcagGTCGACTTCAATCTTCCTCAGAGATTTGACATTACCTATGTAGACACAAAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctcttacaaatacctgatgctacttctctattaacgggttctggttggcacgcagGTCGACTTCAATCTTCCTCAGAGATTTGACATTACCTATGTAGACACAAACTCAGATAAGAAACGTCCTATAATGATCCACAGAGCGGTTTTAGGATCAT
                            tattaac  putative branch site (score: 1)
                          tctattaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagaaagcttcatatactcttacaaatacctgatgctacttctctattaacgggttctggttggcacgcagGTCGACTTCAATCTTCCTCAGAGATTTGACATTACCTATGTAGACACAAACTCAGATAAGAAACGTCCTATAATGATCCACAGAGCGGTTTTAGGATCAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA