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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttttttgccattttccacttttcttcactctcgaaactatggattctttagattaacttagggattgtgtttgcagGAAGACGAATAAGTTAGTTAGCGATAGAAAGAATTGGAAGAATTCAACTCCGAAAGCTGTATATTCCGGCAATCTCTGGACACCGGAGATTCCGTCTCCT

Basic information

species Arabidopsis thaliana
transcript AT1G02560.1
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|164156938|gb|EL994131.1|EL994131
EST:     CGATTCTCCCAAGCTTTCTCTTCCTTTCGAGCCTCTCCGTTCAAG                         GAAGACGAATAAGTTAGTTAGCGATAGAAAGAATTGGAAGAA
genomic: CGATTCTCCCAAGCTTTCTCTTCCTTTCGAGCCTCTCCGTTCAAGgtttttttgc ... gtgtttgcagGAAGACGAATAAGTTAGTTAGCGATAGAAAGAATTGGAAGAA
EST: gi|125301425|gb|EL315510.1|EL315510
EST:     TTCTCCCAAGCTTTCTCTTCCTTTCGAGCCTCTCCGTTCAAG                         GAAGACGAATAAGTTAGTTAGCGATAGAAAGAATTGGAAGAATTCAACTCC
genomic: TTCTCCCAAGCTTTCTCTTCCTTTCGAGCCTCTCCGTTCAAGgtttttttgc ... gtgtttgcagGAAGACGAATAAGTTAGTTAGCGATAGAAAGAATTGGAAGAATTCAACTCC
EST: gi|124717675|gb|EH809077.1|EH809077
EST:     TCTTTCGATTCTCCCAAGCTTTCTCTTCCTTTCGAGCCTCTCCGTTCAAG                         GAAGACGAATAAG
genomic: TCTTTCGATTCTCCCAAGCTTTCTCTTCCTTTCGAGCCTCTCCGTTCAAGgtttttttgc ... gtgtttgcagGAAGACGAATAAG
EST: gi|125290511|gb|EL304596.1|EL304596
EST:     TCTTTCGATTCTCCCGAGCTTTCTCTTCCTTTCGAGCCTCTCCGTTCAAG                         GAAGACGAATAAGTTAGTTAGCGATAGAAAGAATTGGAAGAATTCAACTCC
genomic: TCTTTCGATTCTCCCAAGCTTTCTCTTCCTTTCGAGCCTCTCCGTTCAAGgtttttttgc ... gtgtttgcagGAAGACGAATAAGTTAGTTAGCGATAGAAAGAATTGGAAGAATTCAACTCC
EST: gi|124707491|gb|EH798893.1|EH798893
EST:     CGATTCTCCCAAGCTTTCTCTTCCTTTCGAGCCTCTCCGTTCAAG                         GAAGACGAATAAGTTAGTTAGCGATAGAAAGAATT
genomic: CGATTCTCCCAAGCTTTCTCTTCCTTTCGAGCCTCTCCGTTCAAGgtttttttgc ... gtgtttgcagGAAGACGAATAAGTTAGTTAGCGATAGAAAGAATT
EST: gi|125233713|gb|EL247798.1|EL247798
EST:     TCTTTCGATTCTCCCAAGCTTTCTCTTCCTTTCGAGCCTCTCCGTTCAAG                         GAAGACGAATAAG
genomic: TCTTTCGATTCTCCCAAGCTTTCTCTTCCTTTCGAGCCTCTCCGTTCAAGgtttttttgc ... gtgtttgcagGAAGACGAATAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcttcactctcgaaactatggattctttagattaacttagggattgtgtttgcagGAAGACGAATAAGTTAGTTAGCGATAGAAAGAATTGGAAGAATTCAACTCCGAAAGCTGTATATTCCGGCAATCTCTGGACACCGGAGATTCCGTCTCCT
                             gattaac  putative branch site (score: 2)
                     attctttagattaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtttttttgccattttccacttttcttcactctcgaaactatggattctttagattaacttagggattgtgtttgcagGAAGACGAATAAGTTAGTTAGCGATAGAAAGAATTGGAAGAATTCAACTCCGAAAGCTGTATATTCCGGCAATCTCTGGACACCGGAGATTCCGTCTCCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT