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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtattgtaatcttcttcttctctatttgttttttaagagaatcgatttttgttcgattttgatttggtttgtgttatggagcagAAGGAGAACGATGTTGTTGTTGAGGATGTGAAAGATGGAGACGAAGACGATGATGATGTTGATGACGACGACGATGAGATTGCTGATG

Basic information

species Arabidopsis thaliana
transcript AT4G10480.1
intron # 1
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|164057520|gb|ES158904.1|ES158904
EST:     CATTAAAGAGCAGATGAAGCTCCAG                         AAGGAGAACGATGTTGTTGTTGAGGATGTGAAAGATGGAGACGAAGACGAT
genomic: CATTAAAGAGCAGATGAAGCTCCAGgtattgtaat ... tatggagcagAAGGAGAACGATGTTGTTGTTGAGGATGTGAAAGATGGAGACGAAGACGAT
EST: gi|124927948|gb|EL005636.1|EL005636
EST:     TGAATGAGGAGGCTCTTATGGATGCCATTAAAGGGCAGATGAAGCTCCAG                         AAGGAGAACGATGTTGTTGTTG
genomic: TGAATGAGGAGGCTCTTATGGATGCCATTAAAGAGCAGATGAAGCTCCAGgtattgtaat ... tatggagcagAAGGAGAACGATGTTGTTGTTG
EST: gi|164147130|gb|ES029380.1|ES029380
EST:     AGCAGATGAAGCTCCAG                         AAGGAGAACGATGTTGTTGTTGAGGATGTGAAAGATGGAGACGAAGACGAT
genomic: AGCAGATGAAGCTCCAGgtattgtaat ... tatggagcagAAGGAGAACGATGTTGTTGTTGAGGATGTGAAAGATGGAGACGAAGACGAT
EST: gi|164203486|gb|ES044215.1|ES044215
EST:     GAGCAGATGAAGCTCCAG                         AAGGAGAACGATGTTGTTGTTGAGGATGTGAAAGATGGAGACGAAGACGAT
genomic: GAGCAGATGAAGCTCCAGgtattgtaat ... tatggagcagAAGGAGAACGATGTTGTTGTTGAGGATGTGAAAGATGGAGACGAAGACGAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttttaagagaatcgatttttgttcgattttgatttggtttgtgttatggagcagAAGGAGAACGATGTTGTTGTTGAGGATGTGAAAGATGGAGACGAAGACGATGATGATGTTGATGACGACGACGATGAGATTGCTGATG
                           ttttgat  putative branch site (score: 4)
                          attttgattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtattgtaatcttcttcttctctatttgttttttaagagaatcgatttttgttcgattttgatttggtttgtgttatggagcagAAGGAGAACGATGTTGTTGTTGAGGATGTGAAAGATGGAGACGAAGACGATGATGATGTTGATGACGACGACGATGAGATTGCTGATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGAT