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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaattctctctgtctgtcttcattattgactgtgaatttttttcgcgtattggttatgaaaagagatgtatttgataaatgctattgttttcgcagATGTTTCGAAGAGGGTAATGCAGAGTTCACAGCTCAAAATAAACAAAGGCTTTTTTGCATCTGTTAATACACAAGAAGATAAACCCTTTGATTTCTTCCG

Basic information

species Arabidopsis thaliana
transcript AT4G39460.2
intron # 2
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|86037549|gb|DR333304.1|DR333304
EST:     TCCTCTTACTCTCTCCGTTGATGTGAAGAGCTCTTCAGCGACCTCTCATG                         ATGTTTCGAAGAGGGTAATGCAGAGTCCACAGCTCAAAATAAACAAAGGCC
genomic: TCCTCTTACTCTCTCCGTTGATGTGAAGAGCTCTTCAGCGACCTCTCATGgtaaattctc ... gttttcgcagATGTTTCGAAGAGGGTAATGCAGAGTTCACAGCTCAAAATAAACAAAGGCT
EST: gi|86037541|gb|DR333296.1|DR333296
EST:     TCCTCTTACTCTCTCCGTTGATGTGAAGAGCTCTTCAGCGACCTCTCATG                         ATGTTTCGAAGAGGGTAATGCAGAGTCCACAGCTCAAAATAAACAAAGGCT
genomic: TCCTCTTACTCTCTCCGTTGATGTGAAGAGCTCTTCAGCGACCTCTCATGgtaaattctc ... gttttcgcagATGTTTCGAAGAGGGTAATGCAGAGTTCACAGCTCAAAATAAACAAAGGCT
EST: gi|86037552|gb|DR333307.1|DR333307
EST:     TCCTCTTACTCTCTCCGTTGATGTGAAGAGCTCTTCAGCGACCTCTCATG                         ATGTTTCGAAGAGGGTAATGCAGAGTCCACAGCTCAAAATAAACAAAGGCT
genomic: TCCTCTTACTCTCTCCGTTGATGTGAAGAGCTCTTCAGCGACCTCTCATGgtaaattctc ... gttttcgcagATGTTTCGAAGAGGGTAATGCAGAGTTCACAGCTCAAAATAAACAAAGGCT
EST: gi|86037540|gb|DR333295.1|DR333295
EST:     TCCTCTTACTCTCTCCGTTGATGTGAAGAGCTCTTCAGCGACCTCTCATG                         ATGTTTCGAAGAGGGTAATGCAGAGTCCACAGCTCAAAATAAACAAAGGCT
genomic: TCCTCTTACTCTCTCCGTTGATGTGAAGAGCTCTTCAGCGACCTCTCATGgtaaattctc ... gttttcgcagATGTTTCGAAGAGGGTAATGCAGAGTTCACAGCTCAAAATAAACAAAGGCT
EST: gi|86037532|gb|DR333287.1|DR333287
EST:     TCCTCTTACTCTCTCCGTTGATGTGAAGAGCTCTTCAGCGACCTCTCATG                         ATGTTTCGAAGAGGGTAATGCAGAGTCCACAGCTCAAAATAAACAAAGGCT
genomic: TCCTCTTACTCTCTCCGTTGATGTGAAGAGCTCTTCAGCGACCTCTCATGgtaaattctc ... gttttcgcagATGTTTCGAAGAGGGTAATGCAGAGTTCACAGCTCAAAATAAACAAAGGCT
EST: gi|86037555|gb|DR333310.1|DR333310
EST:     TCCTCTTACTCTCTCCGTTGATGTGAAGAGCTCTTCAGCGACCTCTCATG                         ATGTTTCGAAGAGGGTAATGCAGAGTCCACAGCTCAAAATAAACAAAGGCT
genomic: TCCTCTTACTCTCTCCGTTGATGTGAAGAGCTCTTCAGCGACCTCTCATGgtaaattctc ... gttttcgcagATGTTTCGAAGAGGGTAATGCAGAGTTCACAGCTCAAAATAAACAAAGGCT
EST: gi|125235502|gb|EL249587.1|EL249587
EST:     CTTACTCTCTCCGTTGATGTGAAGAGCTCTTCAGCGACCTCTCATG                         ATGTTTCGAAGAGGGTAATGCAGAGTTCACAGCTC
genomic: CTTACTCTCTCCGTTGATGTGAAGAGCTCTTCAGCGACCTCTCATGgtaaattctc ... gttttcgcagATGTTTCGAAGAGGGTAATGCAGAGTTCACAGCTC
EST: gi|86037534|gb|DR333289.1|DR333289
EST:     TCCTCTTACTCTCTCCGTTGATGTGAAGAGCTCTTCAGCGACCTCTCATG                         ATGTTTCGAAGAGGGTAATGCAGAGTCCACAGCTCAAAATAAACAAAGGCT
genomic: TCCTCTTACTCTCTCCGTTGATGTGAAGAGCTCTTCAGCGACCTCTCATGgtaaattctc ... gttttcgcagATGTTTCGAAGAGGGTAATGCAGAGTTCACAGCTCAAAATAAACAAAGGCT
EST: gi|86037548|gb|DR333303.1|DR333303
EST:     TCCTCTTACTCTCTCCGTTGATGTGAAGAGCTCTTCAGCGACCTCTCATG                         ATGTTTCGAAGAGGGTAATGCAGAGTCCACAGCTCAAAATAAACAAAGGCT
genomic: TCCTCTTACTCTCTCCGTTGATGTGAAGAGCTCTTCAGCGACCTCTCATGgtaaattctc ... gttttcgcagATGTTTCGAAGAGGGTAATGCAGAGTTCACAGCTCAAAATAAACAAAGGCT
EST: gi|152033833|gb|BP817226.2|BP817226
EST:     TCCTCTTACTCTCTCCGTTGATGTGAAGAGCTCTTCAGCGACCTCTCATG                         ATGTTTCGAAGAGGGTAATGCAGAGTTCACAGCTCAAAATAAACAAAGGCT
genomic: TCCTCTTACTCTCTCCGTTGATGTGAAGAGCTCTTCAGCGACCTCTCATGgtaaattctc ... gttttcgcagATGTTTCGAAGAGGGTAATGCAGAGTTCACAGCTCAAAATAAACAAAGGCT
EST: gi|86037553|gb|DR333308.1|DR333308
EST:     TCCTCTTACTCTCTCCGTTGATGTGAAGAGCTCTTCAGCGACCTCTCATG                         ATGTTTCGAAGAGGGTAATGCAGAGTCCACAGCTCAAAATAAACAAAGGCT
genomic: TCCTCTTACTCTCTCCGTTGATGTGAAGAGCTCTTCAGCGACCTCTCATGgtaaattctc ... gttttcgcagATGTTTCGAAGAGGGTAATGCAGAGTTCACAGCTCAAAATAAACAAAGGCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttcgcgtattggttatgaaaagagatgtatttgataaatgctattgttttcgcagATGTTTCGAAGAGGGTAATGCAGAGTTCACAGCTCAAAATAAACAAAGGCTTTTTTGCATCTGTTAATACACAAGAAGATAAACCCTTTGATTTCTTCCG
                            atttgat  putative branch site (score: 5)
                                           ttgttttc  putative PPT
                        atgtatttgataaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaattctctctgtctgtcttcattattgactgtgaatttttttcgcgtattggttatgaaaagagatgtatttgataaatgctattgttttcgcagATGTTTCGAAGAGGGTAATGCAGAGTTCACAGCTCAAAATAAACAAAGGCTTTTTTGCATCTGTTAATACACAAGAAGATAAACCCTTTGATTTCTTCCG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG