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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacgcaagctttcctcaagatattggttccctttctctatggagtgaagaagaaattttgctgatttttgagataacatcattaagcagAATGAGCAATACCGTGCAAAAGTAGAGAAATCAAACGAGAGGTCATTGGCTCTGATCAAAGCAGGGATGGATGTAGTTGTTGCTTTCGGATTGCTTCAAT

Basic information

species Arabidopsis thaliana
transcript AT1G01820.1
intron # 6
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|164017736|gb|ES085391.1|ES085391
EST:     CATCAATTAAGAAGTTAGAAAAAGAGATAGGGAACAAGGATAAACACCAG                         AATGAGCAATAC
genomic: CATCAATTAAGAAGTTAGAAAAAGAGATAGGGAACAAGGATAAACACCAGgtacgcaagc ... cattaagcagAATGAGCAATAC
EST: gi|86078612|gb|DR374369.1|DR374369
EST:     CATCAATTAAGAAGTTAGAAAAAGAGATAGGGAACAAGGATAAACACCAG                         AATGAGCAATACCGTGCAAAAGTAGAGAAATCAAACGAGAGGTCATTGGCT
genomic: CATCAATTAAGAAGTTAGAAAAAGAGATAGGGAACAAGGATAAACACCAGgtacgcaagc ... cattaagcagAATGAGCAATACCGTGCAAAAGTAGAGAAATCAAACGAGAGGTCATTGGCT
EST: gi|86081227|gb|DR376984.1|DR376984
EST:     CATCAATTAAGAAGTTAGAWAAAGAGATAGGGAACAAGGATAAACACCAG                         AATGAGCAATACCGTGCAAAAGTAGAGAAATCAAACGAGAGGTCATTGGCT
genomic: CATCAATTAAGAAGTTAGAAAAAGAGATAGGGAACAAGGATAAACACCAGgtacgcaagc ... cattaagcagAATGAGCAATACCGTGCAAAAGTAGAGAAATCAAACGAGAGGTCATTGGCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctctatggagtgaagaagaaattttgctgatttttgagataacatcattaagcagAATGAGCAATACCGTGCAAAAGTAGAGAAATCAAACGAGAGGTCATTGGCTCTGATCAAAGCAGGGATGGATGTAGTTGTTGCTTTCGGATTGCTTCAAT
                                    agataac  putative branch site (score: 3)
               aagaaatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacgcaagctttcctcaagatattggttccctttctctatggagtgaagaagaaattttgctgatttttgagataacatcattaagcagAATGAGCAATACCGTGCAAAAGTAGAGAAATCAAACGAGAGGTCATTGGCTCTGATCAAAGCAGGGATGGATGTAGTTGTTGCTTTCGGATTGCTTCAAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GATGGA