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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttagtgaaaatgtaagaaattatatttgttatttgtttgaatcattaataatcttcttctccatttgtattacaagAATGAATTCAAACCCGATACACCAAACTTCCGGGAGGAAAGATCTTCAAAGTCATCACAGTGGAAGCCTTGTGCAGATAATAACAAAGCAGCTGTGGCAT

Basic information

species Arabidopsis thaliana
transcript AT1G29200.1
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|116409042|gb|EG451634.1|EG451634
EST:     ATGTATAGCCGTCTTCTAAACTTAGCTTCGGATTCTCTTGCAAAG                         AATGAATTCAAACCCGATACACCAAACTTCCGGGAGGAAAGATCTTCAAAG
genomic: ATGTATAGCCGTCTTCTAAACTTAGCTTCGGATTCTCTTGCAAAGgttagtgaaa ... gtattacaagAATGAATTCAAACCCGATACACCAAACTTCCGGGAGGAAAGATCTTCAAAG
EST: gi|116408812|gb|EG451404.1|EG451404
EST:     TTCAAATGTATAGCCGTCTTCTAAACTTAGCTTCGGATTCTCTTGCAAAG                         AATGAATTCAAACCCGATACACCAAACTTCCGGGAGGAAAGATCTTCAAAG
genomic: TTCAAATGTATAGCCGTCTTCTAAACTTAGCTTCGGATTCTCTTGCAAAGgttagtgaaa ... gtattacaagAATGAATTCAAACCCGATACACCAAACTTCCGGGAGGAAAGATCTTCAAAG
EST: gi|116408813|gb|EG451405.1|EG451405
EST:     TTCAAATGTATAGCCGTCTTCTAAACTTAGCTTCGGATTCTCTTGCAAAG                         AATGAATTCAAACCCGATACACCAAACTTCCGGGAGGAAAGATCTTCAAAG
genomic: TTCAAATGTATAGCCGTCTTCTAAACTTAGCTTCGGATTCTCTTGCAAAGgttagtgaaa ... gtattacaagAATGAATTCAAACCCGATACACCAAACTTCCGGGAGGAAAGATCTTCAAAG
EST: gi|116408811|gb|EG451403.1|EG451403
EST:     TTCAAATGTATAGCCGTCTTCTAAACTTAGCTTCGGATTCTCTTGCAAAG                         AATGAATTCAAACCCGATACACCAAACTTCCGGGAGGAAAGATCTTCAAAG
genomic: TTCAAATGTATAGCCGTCTTCTAAACTTAGCTTCGGATTCTCTTGCAAAGgttagtgaaa ... gtattacaagAATGAATTCAAACCCGATACACCAAACTTCCGGGAGGAAAGATCTTCAAAG
EST: gi|116409043|gb|EG451635.1|EG451635
EST:     ATGTATAGCCGTCTTCTAAACTTAGCTTCGGATTCTCTTGCAAAG                         AATGAATTCAAACCCGATACACCAAACTTCCGGGAGGAAAGATCTTCAAAG
genomic: ATGTATAGCCGTCTTCTAAACTTAGCTTCGGATTCTCTTGCAAAGgttagtgaaa ... gtattacaagAATGAATTCAAACCCGATACACCAAACTTCCGGGAGGAAAGATCTTCAAAG
EST: gi|116408810|gb|EG451402.1|EG451402
EST:     TTCAAATGTATAGCCGTCTTCTAAACTTAGCTTCGGATTCTCTTGCAAAG                         AATGAATTCAAACCCGATACACCAAACTTCCGGGAGGAAAGATCTTCAAAG
genomic: TTCAAATGTATAGCCGTCTTCTAAACTTAGCTTCGGATTCTCTTGCAAAGgttagtgaaa ... gtattacaagAATGAATTCAAACCCGATACACCAAACTTCCGGGAGGAAAGATCTTCAAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atatttgttatttgtttgaatcattaataatcttcttctccatttgtattacaagAATGAATTCAAACCCGATACACCAAACTTCCGGGAGGAAAGATCTTCAAAGTCATCACAGTGGAAGCCTTGTGCAGATAATAACAAAGCAGCTGTGGCAT
                     cattaat  putative branch site (score: 3)
                              tcttcttctccatttg  putative PPT
       ttatttgtttgaatca  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttagtgaaaatgtaagaaattatatttgttatttgtttgaatcattaataatcttcttctccatttgtattacaagAATGAATTCAAACCCGATACACCAAACTTCCGGGAGGAAAGATCTTCAAAGTCATCACAGTGGAAGCCTTGTGCAGATAATAACAAAGCAGCTGTGGCAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTG