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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtaaaaaattgagaatgacttttgctgctttcatttatccgtctggatattttctaattgtaattgttattcttgtttcagGTCAGGGATTTCGTTGGAGAGCAGATGTCTTTAAGAGGTATTGAGTTTCACACTGAAGAATCCCCTGAAGCCATCATCAAAGCTGGAGATGGCTCGTTCT

Basic information

species Arabidopsis thaliana
transcript AT3G54660.1
intron # 3
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|86059409|gb|DR355166.1|DR355166
EST:     TTCATGTATTTATAAGGCAAAAGAAGGTGCTGAGGGGATTTGATGAAGAT                         GTCAGGGATTTCGTTGGAGAGCAGATGTCTTTAAGAGGTATTGAGTTTCAC
genomic: TTCATGTATTTATAAGGCAAAAGAAGGTGCTGAGGGGATTTGATGAAGATgtaagtaaaa ... cttgtttcagGTCAGGGATTTCGTTGGAGAGCAGATGTCTTTAAGAGGTATTGAGTTTCAC
EST: gi|116469965|gb|EG512557.1|EG512557
EST:     TTCATGTATTTATAAGGCAAAAGAAGGTGCTGAGGGGATTTGATGAAGAT                         GTCAGGGATTTCGTTGGAGAGC
genomic: TTCATGTATTTATAAGGCAAAAGAAGGTGCTGAGGGGATTTGATGAAGATgtaagtaaaa ... cttgtttcagGTCAGGGATTTCGTTGGAGAGC
EST: gi|86059408|gb|DR355165.1|DR355165
EST:     TTCATGTATTTATAAGGCAAAAGAAGGTGCTGAGGGGATTTGATGAAGAT                         GTCAGGGATTTCGTTGGAGAGCAGATGTCTTTAAGAGGTATTGAGTTTCAC
genomic: TTCATGTATTTATAAGGCAAAAGAAGGTGCTGAGGGGATTTGATGAAGATgtaagtaaaa ... cttgtttcagGTCAGGGATTTCGTTGGAGAGCAGATGTCTTTAAGAGGTATTGAGTTTCAC
EST: gi|124942153|gb|EL018443.1|EL018443
EST:     TTCATGTATTTGTAAGGCAAAAGAAGGTGCTGAGGGGATTTGGTGAAGAT                         GTCAGGGATTTCGTTGGAGAGCAG
genomic: TTCATGTATTTATAAGGCAAAAGAAGGTGCTGAGGGGATTTGATGAAGATgtaagtaaaa ... cttgtttcagGTCAGGGATTTCGTTGGAGAGCAG
EST: gi|116445247|gb|EG487839.1|EG487839
EST:     TTCATGTATTTATAAGGCAAAAGAAGGTGCTGAGGGGATTTGATGAAGAT                         GTCAGGGATTTCGTTGGAGAGCAGATGTCTTTAAGAGGTATTGAGTTTCAC
genomic: TTCATGTATTTATAAGGCAAAAGAAGGTGCTGAGGGGATTTGATGAAGATgtaagtaaaa ... cttgtttcagGTCAGGGATTTCGTTGGAGAGCAGATGTCTTTAAGAGGTATTGAGTTTCAC
EST: gi|125293569|gb|EL307654.1|EL307654
EST:     TTCATGTATTTATAAGGCAAAAGAAGGTGCTGAGGGGATTTGATGAAGAT                         GTCAGGGATTTCGTTGGAGAGCAGATGTC
genomic: TTCATGTATTTATAAGGCAAAAGAAGGTGCTGAGGGGATTTGATGAAGATgtaagtaaaa ... cttgtttcagGTCAGGGATTTCGTTGGAGAGCAGATGTC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gctttcatttatccgtctggatattttctaattgtaattgttattcttgtttcagGTCAGGGATTTCGTTGGAGAGCAGATGTCTTTAAGAGGTATTGAGTTTCACACTGAAGAATCCCCTGAAGCCATCATCAAAGCTGGAGATGGCTCGTTCT
                         ttctaat  putative branch site (score: 2)
                                           ttcttgtttc  putative PPT
                    atattttctaattgta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtaaaaaattgagaatgacttttgctgctttcatttatccgtctggatattttctaattgtaattgttattcttgtttcagGTCAGGGATTTCGTTGGAGAGCAGATGTCTTTAAGAGGTATTGAGTTTCACACTGAAGAATCCCCTGAAGCCATCATCAAAGCTGGAGATGGCTCGTTCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG