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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgaattatcttttcatacccattttcttagactgagaaacaataataacatgctacttttttcagatgtattacatgcgatgagaaaatggttttctgatctttttcatttattctaaacgtagGTACCAAAACCTGCCATTAAGGTGGAAACAAATTCTAATTCAAAAAAAGCTGCAGAAGGTGTAAAGCCTGTTGACAAGCCAGATGTGCAGCCGCAGCTGG

Basic information

species Arabidopsis thaliana
transcript AT2G40660.1
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|116410067|gb|EG452659.1|EG452659
EST:     CGACATTATTTGCACCAATACCTGTGAAGCTACCAGAATTTAGCTTCGAG                         GTACCAAAACCTGCCATTAAGGTGGAAACAAATTCTAATTCNNNNNNNGCT
genomic: CGACATTATTTGCACCAATACCTGTGAAGCTACCAGAATTTAGCTTCGAGgtgaattatc ... ctaaacgtagGTACCAAAACCTGCCATTAAGGTGGAAACAAATTCTAATTCAAAAAAAGCT
EST: gi|116410082|gb|EG452674.1|EG452674
EST:     CGACATTATTTGCACCAATACCTGTGAAGCTACCAGAATTTAGCTTCGAG                         GTACCAAAACCTGCCATTAAGGTGGAAACAAATTCTAATTCNNNNNNNGCT
genomic: CGACATTATTTGCACCAATACCTGTGAAGCTACCAGAATTTAGCTTCGAGgtgaattatc ... ctaaacgtagGTACCAAAACCTGCCATTAAGGTGGAAACAAATTCTAATTCAAAAAAAGCT
EST: gi|116410078|gb|EG452670.1|EG452670
EST:     CGACATTATTTGCACCAATACCCGTGAAGCTACCAGAATTTAGCTTCGAG                         GTACCAAAACCTGCCATTAAGGTGGAAACAAATTCTAATTCNNNNNNNGCT
genomic: CGACATTATTTGCACCAATACCTGTGAAGCTACCAGAATTTAGCTTCGAGgtgaattatc ... ctaaacgtagGTACCAAAACCTGCCATTAAGGTGGAAACAAATTCTAATTCAAAAAAAGCT
EST: gi|116410084|gb|EG452676.1|EG452676
EST:     CGACATTATTTGCACCAATACCTGTGAAGCTACCAGAATTTAGCTTCGAG                         GTACCAAAACCTGCCATTAAGGTGGAAACAAATTCTAATTCNNNNNNNGCT
genomic: CGACATTATTTGCACCAATACCTGTGAAGCTACCAGAATTTAGCTTCGAGgtgaattatc ... ctaaacgtagGTACCAAAACCTGCCATTAAGGTGGAAACAAATTCTAATTCAAAAAAAGCT
EST: gi|47828784|gb|CK118468.1|CK118468
EST:     CGACATTATTTGCACCAATACCTGTGAAGCTACCAGAATTTAGCTTCGAG                         GTACCAAAACCTGCCATTAAGGTGGAAACA
genomic: CGACATTATTTGCACCAATACCTGTGAAGCTACCAGAATTTAGCTTCGAGgtgaattatc ... ctaaacgtagGTACCAAAACCTGCCATTAAGGTGGAAACA
EST: gi|116410069|gb|EG452661.1|EG452661
EST:     CGACATTATTTGCACCAATACCTGTGAAGCTACCAGAATTTGGCTTCGAG                         GTACCAAAACCTGCCATTAAGGTGGAAACAAATTCTAATTCNNNNNNNGCT
genomic: CGACATTATTTGCACCAATACCTGTGAAGCTACCAGAATTTAGCTTCGAGgtgaattatc ... ctaaacgtagGTACCAAAACCTGCCATTAAGGTGGAAACAAATTCTAATTCAAAAAAAGCT
EST: gi|116410080|gb|EG452672.1|EG452672
EST:     CGACATTATTTGCACCAATACCTGTGAAGCTACCAGAATTTAGCTTCGAG                         GTACCAAAACCTGCCATTAAGGCGGAAACAAATTCTAATTCNNNNNNNGCT
genomic: CGACATTATTTGCACCAATACCTGTGAAGCTACCAGAATTTAGCTTCGAGgtgaattatc ... ctaaacgtagGTACCAAAACCTGCCATTAAGGTGGAAACAAATTCTAATTCAAAAAAAGCT
EST: gi|116411094|gb|EG453686.1|EG453686
EST:     CGACATTATTTGCACCAATACCTGTGAAGCTACCAGAATTTAGCTTCGAG                         GTACCAAAACCTGCCATTAAGGTGGAAACAAATTCTAATTCNNNNNNNGCT
genomic: CGACATTATTTGCACCAATACCTGTGAAGCTACCAGAATTTAGCTTCGAGgtgaattatc ... ctaaacgtagGTACCAAAACCTGCCATTAAGGTGGAAACAAATTCTAATTCAAAAAAAGCT
EST: gi|116411098|gb|EG453690.1|EG453690
EST:     CGACATTATTTGCACCAATACCTGCGAAGCTACCAGAATTTAGCTTCGAG                         GTACCAAAACCTGCCATTAAGGTGGAAACAAATTCTAATTCNNNNNNNGCT
genomic: CGACATTATTTGCACCAATACCTGTGAAGCTACCAGAATTTAGCTTCGAGgtgaattatc ... ctaaacgtagGTACCAAAACCTGCCATTAAGGTGGAAACAAATTCTAATTCAAAAAAAGCT
EST: gi|163977941|gb|ES050630.1|ES050630
EST:     ACATTATTTGCACCAATACCTGTGAAGCNNTACCAGAATTTAGCTTCGAG                         GTACCAAAACCT
genomic: ACATTATTTGCACCAATACCTGTGAAGC--TACCAGAATTTAGCTTCGAGgtgaattatc ... ctaaacgtagGTACCAAAACCT
EST: gi|116410076|gb|EG452668.1|EG452668
EST:     CGACATTATTTGCACCAATACCTGTGAAGCTACCAGAATTTAGCTTCGAG                         GTACCAAAACCTGCCATTAAGGTGGAAACAAATTCTAATTCNNNNNNNGCT
genomic: CGACATTATTTGCACCAATACCTGTGAAGCTACCAGAATTTAGCTTCGAGgtgaattatc ... ctaaacgtagGTACCAAAACCTGCCATTAAGGTGGAAACAAATTCTAATTCAAAAAAAGCT
EST: gi|116410074|gb|EG452666.1|EG452666
EST:     CGACATTATTTGCACCAATACCTGTGAAGCTACCAGAATTTAGCTTCGAG                         GTACCAAAACCTGCCATTAAGGTGGAAACAAATTCTAATTCNNNNNNNNGC
genomic: CGACATTATTTGCACCAATACCTGTGAAGCTACCAGAATTTAGCTTCGAGgtgaattatc ... ctaaacgtagGTACCAAAACCTGCCATTAAGGTGGAAACAAATTCTAATTCAAAAAAA-GC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attacatgcgatgagaaaatggttttctgatctttttcatttattctaaacgtagGTACCAAAACCTGCCATTAAGGTGGAAACAAATTCTAATTCAAAAAAAGCTGCAGAAGGTGTAAAGCCTGTTGACAAGCCAGATGTGCAGCCGCAGCTGG
                                           ttctaaa  putative branch site (score: 2)
                              tctttttcatttattc  CT-rich tract
                             atctttttcatttatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgaattatcttttcatacccattttcttagactgagaaacaataataacatgctacttttttcagatgtattacatgcgatgagaaaatggttttctgatctttttcatttattctaaacgtagGTACCAAAACCTGCCATTAAGGTGGAAACAAATTCTAATTCAAAAAAAGCTGCAGAAGGTGTAAAGCCTGTTGACAAGCCAGATGTGCAGCCGCAGCTGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG