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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgtaatccatttaccgatgagaatacaacttgctaccttcctgtatgaatacttctatcctaactgtaagcttcttttcttgcttttagCTCCCAGATGCGATCAGTGAGAGGATTTTCATCCAGTTCAG

Basic information

species Arabidopsis thaliana
transcript AT3G13930.1
intron # 5
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|164006323|gb|ES136045.1|ES136045
EST:     AAACTAAGCAGCCCAATGGCAGGACCAAAACTATTTAAAGAATTTATAAG                         CTCCCAGATGCGATCAGTGAGAGGATTTTCATCCAGTTCAG
genomic: AAACTAAGCAGCCCAATGGCAGGACCAAAACTATTTAAAGAATTTATAAGgtatgtaatc ... ttgcttttagCTCCCAGATGCGATCAGTGAGAGGATTTTCATCCAGTTCAG
EST: gi|164225022|gb|EL974653.1|EL974653
EST:     GAATTTATAAG                         CTCCCAGATGCGATCAGTGAGAGGATTTTCATCCAGTTCAG
genomic: GAATTTATAAGgtatgtaatc ... ttgcttttagCTCCCAGATGCGATCAGTGAGAGGATTTTCATCCAGTTCAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

accttcctgtatgaatacttctatcctaactgtaagcttcttttcttgcttttagCTCCCAGATGCGATCAGTGAGAGGATTTTCATCCAGTTCAG
                       tcctaac  putative branch site (score: 1)
                                    cttcttttcttgcttt  putative PPT
         tatgaata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgtaatccatttaccgatgagaatacaacttgctaccttcctgtatgaatacttctatcctaactgtaagcttcttttcttgcttttagCTCCCAGATGCGATCAGTGAGAGGATTTTCATCCAGTTCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT