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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgattttttcgtctcatgctgacttagcctaaaagtagagttagtaaaaagatcctgactctatcattacccgtttgtatcgaactctcaaatgcagAGATATCACCGAGCAGAACAAGAAAGATTTGCAAGGCAACGACCTCCGGTGCCTAATTTTCCTCCTCCACCACCTTCGCCGCCTCCACCAGTTTTAATCA

Basic information

species Arabidopsis thaliana
transcript AT1G28240.1
intron # 8
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|116429469|gb|EG472061.1|EG472061
EST:     GGACAGTAAGCATGTTCCTTGATTGTGAAAGACGCAATTTTGTAGTTCAG                         AGATATCACCGAGCAGAACAAGAAAGATTTGCAAGGCAACGACCTCCGGTG
genomic: GGACAGTAAGCATGTTCCTTGATTGTGAAAGACGCAATTTTGTAGTTCAGgtgatttttt ... tcaaatgcagAGATATCACCGAGCAGAACAAGAAAGATTTGCAAGGCAACGACCTCCGGTG
EST: gi|124823862|gb|EH908728.1|EH908728
EST:     CCTTGATTGTGAAAGACGCAATTTTGTAGTTCAG                         AGATATCACCGAGCAGAACAAGAAAGATTTGCAAGGCAACGACCTCCGGTG
genomic: CCTTGATTGTGAAAGACGCAATTTTGTAGTTCAGgtgatttttt ... tcaaatgcagAGATATCACCGAGCAGAACAAGAAAGATTTGCAAGGCAACGACCTCCGGTG
EST: gi|125009453|gb|EL081722.1|EL081722
EST:     TTCCTTGATTGTGAAAGACGCAATTTTGTAGTTCAG                         AGATATCACCGAGCAGAACAAGAAAGATTTGCAAGGCAACGACCTCCGGTG
genomic: TTCCTTGATTGTGAAAGACGCAATTTTGTAGTTCAGgtgatttttt ... tcaaatgcagAGATATCACCGAGCAGAACAAGAAAGATTTGCAAGGCAACGACCTCCGGTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agtaaaaagatcctgactctatcattacccgtttgtatcgaactctcaaatgcagAGATATCACCGAGCAGAACAAGAAAGATTTGCAAGGCAACGACCTCCGGTGCCTAATTTTCCTCCTCCACCACCTTCGCCGCCTCCACCAGTTTTAATCA
          tcctgac  putative branch site (score: 2)
                                          ctctc  putative PPT
                   tatcatta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgattttttcgtctcatgctgacttagcctaaaagtagagttagtaaaaagatcctgactctatcattacccgtttgtatcgaactctcaaatgcagAGATATCACCGAGCAGAACAAGAAAGATTTGCAAGGCAACGACCTCCGGTGCCTAATTTTCCTCCTCCACCACCTTCGCCGCCTCCACCAGTTTTAATCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTCCTC