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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGTGTTGATTTCTATGCGATAAACACGGATTCGCAAGCTCTGTTACAGTCTTCTGCTGAGAACCCACTTCAAATTGGAGAACTTTTAACTCGTGGGCTTGgttagtagagttatactattatttggtatagatgttgtgtgagttttggcacttaaagtaacaaacttgcgtctctgttacttgttttaatag

Basic information

species Arabidopsis thaliana
transcript AT5G55280.1
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G55280.1 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: Vv19s0090g01320.t01 (Vitis vinifera), 5'ss of exon 2
AGTGTTGATTTCTATGCGATAAACACGGATTCGCAAGCTCTGTTACAGTCTTCTGCTGAGAACCCACTTCAAATTGGAGAACTTTTAACTCGTGGGCTTGgttagtagagttatactattatttggtatagatgttgtgtga-gttttggcacttaaagtaacaaacttgcgt---ctctgttacttgttttaatag-----
 |||||||||||||||| ||||| || || || |||||||| ||||| ||| | |||  |||||| || ||||||||||||||||| |||||||| || |||  |   | |   ||||| || |   ||        | | | || || | |  || | |   | | ||| |    | | | | ||| |   | |||     
GGTGTTGATTTCTATGCAATAAATACAGACTCTCAAGCTCTATTACACTCTGCGGCTTCGAACCCTCTCCAAATTGGAGAACTTTTGACTCGTGGACTAGgtctg-gcactctcactatgatcttagatgttatccatttaaagtattagaatatagatttgtatatttgagggagcacagct-cttatagcactagattat
















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|86039268|gb|DR335023.1|DR335023
EST:     TTCTGCTGAGAACCCACTTCAAATTGGAGAACTTTTAACTCGTGGGCTTG                         GCACTGGTGGAAACCCGCTT
genomic: TTCTGCTGAGAACCCACTTCAAATTGGAGAACTTTTAACTCGTGGGCTTGgttagtagag ... gttttaatagGCACTGGTGGAAACCCGCTT
EST: gi|86039263|gb|DR335018.1|DR335018
EST:     TCTGCTGAGAACCCACTTCAAAATTGGAGAACTTTTAACTCGTGGGCTTG                         GCACTGGTGGAAACCC
genomic: TCTGCTGAGAACCCACTTCAAA-TTGGAGAACTTTTAACTCGTGGGCTTGgttagtagag ... gttttaatagGCACTGGTGGAAACCC
EST: gi|125140157|gb|EL178547.1|EL178547
EST:     TTCTGCTGAGAACCCACTTCAAATTGGAGAACTTTTAACTCGTGGGCTTG                         GCACTGGTGGAAACCCGCTTCTTGGAGAACAAG
genomic: TTCTGCTGAGAACCCACTTCAAATTGGAGAACTTTTAACTCGTGGGCTTGgttagtagag ... gttttaatagGCACTGGTGGAAACCCGCTTCTTGGAGAACAAG
EST: gi|86039251|gb|DR335006.1|DR335006
EST:     TTCTGCTGAGAACCCACTTCAAATTGGAGAACTTTTAACTCGTGGGCTTG                         GCACTGGTGGAAACCCGCTTCTTGGAGAACAAGCTGCAGAAGAATCAAAAG
genomic: TTCTGCTGAGAACCCACTTCAAATTGGAGAACTTTTAACTCGTGGGCTTGgttagtagag ... gttttaatagGCACTGGTGGAAACCCGCTTCTTGGAGAACAAGCTGCAGAAGAATCAAAAG
EST: gi|86039253|gb|DR335008.1|DR335008
EST:     TTCTGCTGAGAACCCACTTCAAATTGGAGAACTTTTAACTCGTGGGCTTG                         GCACTGGTGGAAACC-GCTTCTTGG
genomic: TTCTGCTGAGAACCCACTTCAAATTGGAGAACTTTTAACTCGTGGGCTTGgttagtagag ... gttttaatagGCACTGGTGGAAACCCGCTTCTTGG
EST: gi|86039254|gb|DR335009.1|DR335009
EST:     TTCTGCTGAGAACCCACTTCAAATTGGAGAACTTTTAACTCGTGGGCTTG                         GCACTGGTGGAAACCCGCTTCTTGGAGAACAAGCTGCAGA
genomic: TTCTGCTGAGAACCCACTTCAAATTGGAGAACTTTTAACTCGTGGGCTTGgttagtagag ... gttttaatagGCACTGGTGGAAACCCGCTTCTTGGAGAACAAGCTGCAGA
EST: gi|164027950|gb|ES177778.1|ES177778
EST:     GGAGAACTTTTAACTC-TGGGCTTG                         GCACTGGTGGAAACCCGCTTCTTGGAGAACAAGCTGCAGAAGAATCAAAAG
genomic: GGAGAACTTTTAACTCGTGGGCTTGgttagtagag ... gttttaatagGCACTGGTGGAAACCCGCTTCTTGGAGAACAAGCTGCAGAAGAATCAAAAG
EST: gi|86039257|gb|DR335012.1|DR335012
EST:     TCTGCTGAGAACCCACTTCAAATCTGGAGAACTTTTAACTCGTGGGCTTG                         GCACTGGTGGA
genomic: TCTGCTGAGAACCCACTTCAAAT-TGGAGAACTTTTAACTCGTGGGCTTGgttagtagag ... gttttaatagGCACTGGTGGA
EST: gi|86039272|gb|DR335027.1|DR335027
EST:     TKCTGCTGAGAACCCACTTCAAATTGGAGAACTTTTAACTCGTGGGCTTG                         GCACTGGTGGAAACC-GCTTCTTGGAGAACAAGCTGCAGAAGAAT
genomic: TTCTGCTGAGAACCCACTTCAAATTGGAGAACTTTTAACTCGTGGGCTTGgttagtagag ... gttttaatagGCACTGGTGGAAACCCGCTTCTTGGAGAACAAGCTGCAGAAGAAT
EST: gi|86039256|gb|DR335011.1|DR335011
EST:     TTCTGCTGAGAACCCACTTCAAATTGGAGAACTTTTAACTCGTGGGCTTG                         GCACTGGTGGAAACCCGCTTCTTGGAGAACAAGCTGCAGAAGAATCAAAAG
genomic: TTCTGCTGAGAACCCACTTCAAATTGGAGAACTTTTAACTCGTGGGCTTGgttagtagag ... gttttaatagGCACTGGTGGAAACCCGCTTCTTGGAGAACAAGCTGCAGAAGAATCAAAAG
EST: gi|86039271|gb|DR335026.1|DR335026
EST:     TTCTGCTGAGAACCCACTTCAAATTGGAGAACTTTTAACTCGTGGGCTTG                         GCACTGGTGGAAACCCGCTTCTTGGAGAACAAGCTGCAGAAGAATCAAAAG
genomic: TTCTGCTGAGAACCCACTTCAAATTGGAGAACTTTTAACTCGTGGGCTTGgttagtagag ... gttttaatagGCACTGGTGGAAACCCGCTTCTTGGAGAACAAGCTGCAGAAGAATCAAAAG
EST: gi|86039249|gb|DR335004.1|DR335004
EST:     TTCTGCTGAGAACCCACTTCAAATTGGAGAACTTTTAACTCGTGGGCTTG                         GCACTGGTGGAAACCCGCTTCTTGGAGAACAAGCTGCAGAAGAATCAAAA
genomic: TTCTGCTGAGAACCCACTTCAAATTGGAGAACTTTTAACTCGTGGGCTTGgttagtagag ... gttttaatagGCACTGGTGGAAACCCGCTTCTTGGAGAACAAGCTGCAGAAGAATCAAAA
EST: gi|301501112|gb|HO206652.1|HO206652
EST:     TTCTGCTGAGAACCCACTTCAAATTGGAGAACTTTTAACTCGTGGGCTTG                         GCACTGGTGGAAACCCGCTTCTTGGAGAACAAGCTGCAGAAGAATCAAAAG
genomic: TTCTGCTGAGAACCCACTTCAAATTGGAGAACTTTTAACTCGTGGGCTTGgttagtagag ... gttttaatagGCACTGGTGGAAACCCGCTTCTTGGAGAACAAGCTGCAGAAGAATCAAAAG
EST: gi|86039260|gb|DR335015.1|DR335015
EST:     TTCTGCTGAGAACCCACTTCAAATTGGAGAACTTTTAACTCGTGGGCTTG                         GCACTGGTGGAAACCCGCTTCTTGGAGAACAAGCTGCAGAAGAATCAAAAG
genomic: TTCTGCTGAGAACCCACTTCAAATTGGAGAACTTTTAACTCGTGGGCTTGgttagtagag ... gttttaatagGCACTGGTGGAAACCCGCTTCTTGGAGAACAAGCTGCAGAAGAATCAAAAG
EST: gi|86039269|gb|DR335024.1|DR335024
EST:     TTCTGCTGAGAACCCACTTCAAATTGGAGAACTTTTAACTCGTGGGCTTG                         GCACTGGTGGAAACCCGCTTCTTGGAGAACAAGCTGCAGAAGAATCAAAAG
genomic: TTCTGCTGAGAACCCACTTCAAATTGGAGAACTTTTAACTCGTGGGCTTGgttagtagag ... gttttaatagGCACTGGTGGAAACCCGCTTCTTGGAGAACAAGCTGCAGAAGAATCAAAAG
EST: gi|86039270|gb|DR335025.1|DR335025
EST:     TTCTGCTGAGAACCCACTTCAAATTGGAGAACTTTTAACTCGTGGGCKTG                         GCACTGGTGGAAACCCGCTTCTTGGAGAACAAGCTGCAGAAGAATCAAAAG
genomic: TTCTGCTGAGAACCCACTTCAAATTGGAGAACTTTTAACTCGTGGGCTTGgttagtagag ... gttttaatagGCACTGGTGGAAACCCGCTTCTTGGAGAACAAGCTGCAGAAGAATCAAAAG

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
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---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGTGTTGATTTCTATGCGATAAACACGGATTCGCAAGCTCTGTTACAGTCTTCTGCTGAGAACCCACTTCAAATTGGAGAACTTTTAACTCGTGGGCTTGgttagtagagttatactattatttggtatagatgttgtgtgagttttggcacttaaagtaacaaacttgcgtctctgttacttgttttaatag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAA