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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaacccaattccaaaaaacgtttcttttttctcgatgccttagcttctttggattctgttgtgatctaccgattttgaatttgcttgatcgatcatcggatcactgtgattagtgttattgttcctttcctttgtgtagCTTTCGCGCTTATGGAAGATTCTGGAGTGAATCCAATGGATTCACCATCTAAAGGCAGTGACTTTGGAGTCTATGGAATCATAGGAGGTGGAATCGTGGC

Basic information

species Arabidopsis thaliana
transcript AT2G04350.1
intron # 1
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|86068812|gb|DR364569.1|DR364569
EST:     AAGAAATCATCAAGAAGCTTCCTTTCACTGATTTCTCAATCTATTCGTAG                         CTTTCGCGCTTATGGAAGATTCTGGAGNGAATCCAATGGATTCACCATCTA
genomic: AAGAAATCATCAAGAAGTTTCCTTTCACTGATTTCTCAATCTATTCGTAGgtaacccaat ... ctttgtgtagCTTTCGCGCTTATGGAAGATTCTGGAGTGAATCCAATGGATTCACCATCTA
EST: gi|86068807|gb|DR364564.1|DR364564
EST:     AAGAAATCATCAAGAAGCTTCCTTTCACTGATTTCTCAATCTATTCGTAG                         CTTTCGCGCTTATGGAAGATTCTGGAGTGAATCCAATGGATTCACCATCTA
genomic: AAGAAATCATCAAGAAGTTTCCTTTCACTGATTTCTCAATCTATTCGTAGgtaacccaat ... ctttgtgtagCTTTCGCGCTTATGGAAGATTCTGGAGTGAATCCAATGGATTCACCATCTA
EST: gi|86068816|gb|DR364573.1|DR364573
EST:     AAGAAATCATCAAGAAGCTTCCTTTCACTGATTTCTCAATCTATTCGTAG                         CTTTCGCGCTTATGGAAGATTCTGGAGTGAATCCAATGGATTCACCATCTA
genomic: AAGAAATCATCAAGAAGTTTCCTTTCACTGATTTCTCAATCTATTCGTAGgtaacccaat ... ctttgtgtagCTTTCGCGCTTATGGAAGATTCTGGAGTGAATCCAATGGATTCACCATCTA
EST: gi|86068808|gb|DR364565.1|DR364565
EST:     AAGAAATCATCAAGAAGCTTCCTTTCACTGATTTCTCAATCTATTCGTAG                         CTTTCGCGCTTATGGAAGATTCTGGAGTGAATCCAATGGATTCACCATCTA
genomic: AAGAAATCATCAAGAAGTTTCCTTTCACTGATTTCTCAATCTATTCGTAGgtaacccaat ... ctttgtgtagCTTTCGCGCTTATGGAAGATTCTGGAGTGAATCCAATGGATTCACCATCTA
EST: gi|86068821|gb|DR364578.1|DR364578
EST:     AAGAAATCATCAAGAAGCTTCCTTTCACTGATTTCTCAATCTATTCGTAG                         CTTTCGCGCTTATGGAAGATTCTGGAGTGAATCCAATGGATNCACCATCTA
genomic: AAGAAATCATCAAGAAGTTTCCTTTCACTGATTTCTCAATCTATTCGTAGgtaacccaat ... ctttgtgtagCTTTCGCGCTTATGGAAGATTCTGGAGTGAATCCAATGGATTCACCATCTA
EST: gi|86068810|gb|DR364567.1|DR364567
EST:     AAGAAATCATCAAGAAGCTTCCTTTCACTGATTTCTCAATCTATTCGTAG                         CTTTCGCGCTTATGGAAGATTCTGGAGTGAATCCAATGGATTCACCATCTA
genomic: AAGAAATCATCAAGAAGTTTCCTTTCACTGATTTCTCAATCTATTCGTAGgtaacccaat ... ctttgtgtagCTTTCGCGCTTATGGAAGATTCTGGAGTGAATCCAATGGATTCACCATCTA
EST: gi|86068811|gb|DR364568.1|DR364568
EST:     AAGAAATCATCAAGAAGCTTCCTTTCACTGATTTCTCAATCTATTCGTAG                         CTTTCGCGCTTATGGAAGATTCTGGAGTGAATCCAATGGATTCACCATCTA
genomic: AAGAAATCATCAAGAAGTTTCCTTTCACTGATTTCTCAATCTATTCGTAGgtaacccaat ... ctttgtgtagCTTTCGCGCTTATGGAAGATTCTGGAGTGAATCCAATGGATTCACCATCTA
EST: gi|124955881|gb|EL030856.1|EL030856
EST:     CAATCTATTCGTAG                         CTTTCGCGCTTATGGAAGATTCTGGAGTGAATCCAATGGATTCACCATCTA
genomic: CAATCTATTCGTAGgtaacccaat ... ctttgtgtagCTTTCGCGCTTATGGAAGATTCTGGAGTGAATCCAATGGATTCACCATCTA
EST: gi|86068820|gb|DR364577.1|DR364577
EST:     AAGAAATCATCAAGAAGCTTCCTTTCACTGATTTCTCAATCTATTCGTAG                         CTTTCGCGCTTATGGAAGATTCTGGAGTGAATCCAATGGATTCACCATCTA
genomic: AAGAAATCATCAAGAAGTTTCCTTTCACTGATTTCTCAATCTATTCGTAGgtaacccaat ... ctttgtgtagCTTTCGCGCTTATGGAAGATTCTGGAGTGAATCCAATGGATTCACCATCTA
EST: gi|86068814|gb|DR364571.1|DR364571
EST:     AAGAAATCATCAAGAAGCTTCCTTTCACTGATTTCTCAATCTATTCGTAG                         CTTTCGCGCTTATGGAAGATTCTGGAGTGAATCCAATGGATTCACCATCTA
genomic: AAGAAATCATCAAGAAGTTTCCTTTCACTGATTTCTCAATCTATTCGTAGgtaacccaat ... ctttgtgtagCTTTCGCGCTTATGGAAGATTCTGGAGTGAATCCAATGGATTCACCATCTA
EST: gi|86068817|gb|DR364574.1|DR364574
EST:     AAGAAATCATCAAGAAGCTTCCTTTCACTGATTTCTCAATCTATTCGTAG                         CTTTCGCGCTTATGGAAGATTCTGGAGTGAATCCAATGGATTCACCATCTA
genomic: AAGAAATCATCAAGAAGTTTCCTTTCACTGATTTCTCAATCTATTCGTAGgtaacccaat ... ctttgtgtagCTTTCGCGCTTATGGAAGATTCTGGAGTGAATCCAATGGATTCACCATCTA
EST: gi|86068822|gb|DR364579.1|DR364579
EST:     AAGAAATCATCAAGAAGCTTCCTTTCACTGATTTCTCAATCTATTCGTAG                         CTTTCGCGCTTATGGAAGATTCTGGAGTGAATCCAATGGATTCACCATCTA
genomic: AAGAAATCATCAAGAAGTTTCCTTTCACTGATTTCTCAATCTATTCGTAGgtaacccaat ... ctttgtgtagCTTTCGCGCTTATGGAAGATTCTGGAGTGAATCCAATGGATTCACCATCTA
EST: gi|86068813|gb|DR364570.1|DR364570
EST:     TCTCAATCTATTCGTAG                         CTTTCGCGCTTATGGAAGATTCTGGAGTGAATCCAATGGATTCACCATCTA
genomic: TCTCAATCTATTCGTAGgtaacccaat ... ctttgtgtagCTTTCGCGCTTATGGAAGATTCTGGAGTGAATCCAATGGATTCACCATCTA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgatcgatcatcggatcactgtgattagtgttattgttcctttcctttgtgtagCTTTCGCGCTTATGGAAGATTCTGGAGTGAATCCAATGGATTCACCATCTAAAGGCAGTGACTTTGGAGTCTATGGAATCATAGGAGGTGGAATCGTGGC
 gcttgat  putative branch site (score: 5)
                               ttattgttcctttcct  putative PPT
                               ttattgtt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaacccaattccaaaaaacgtttcttttttctcgatgccttagcttctttggattctgttgtgatctaccgattttgaatttgcttgatcgatcatcggatcactgtgattagtgttattgttcctttcctttgtgtagCTTTCGCGCTTATGGAAGATTCTGGAGTGAATCCAATGGATTCACCATCTAAAGGCAGTGACTTTGGAGTCTATGGAATCATAGGAGGTGGAATCGTGGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA