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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CAGATCAAGAGAGCTTATAGGAAACTAGCTTTGAAGTATCATCCCGATAAGAATCAAGGAAATGAGGAAGCGACTCGCAAATTCGCTGAGATCAACAATGgtattttcgttttgcaacttgtgtgattctgctctctttgttaactcacccgtttttagttttgagaattgacgtattggtgtttgatgtaatag

Basic information

species Arabidopsis thaliana
transcript AT3G62600.1
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G62600.1 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: Vv07s0005g01220.t01 (Vitis vinifera), 5'ss of exon 2
CAGATCAAGAGAGCTTATAGGAAACTAGCTTTGAAGTATCATCCCGATAAGAATCAAGGAAATGAGGAAGCGACTCGCAAATTCGCTGAGATCAACAATGgt--attttcgttttgcaacttgtgtga-ttctgctctctttgttaactcacccgtttttagttttgaga-------attgacgtattggtgtttgatg--taatag
||||||||||| || || ||||| || || |||||||| ||||||||||||||||| ||||||||||| || | |   ||||| || ||||| |||||||||  |||||  ||||     ||||  || | ||    | |||| |   | |   |  | || ||||  ||       ||| |  || |   | | | ||  | ||||
CAGATCAAGAGGGCGTACAGGAAGCTGGCGTTGAAGTACCATCCCGATAAGAATCAGGGAAATGAGGAGGCTAATAAGAAATTTGCCGAGATTAACAATGgtgaattttaatttttttttttgttggagtccttggttgtttgatggtttatttgactgtattttttggaggtttgaattaatttaatacggctggttgattgatag
















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|86049312|gb|DR345067.1|DR345067
EST:     GAATCAAGGAAATGAGGAAGCGACTCGCAAATTCGCTGAGATCAACAATG                         CTTATGAAGTGTTATCGGATGAGGAGAAGAGGGAGATATATAACAAGTATG
genomic: GAATCAAGGAAATGAGGAAGCGACTCGCAAATTCGCTGAGATCAACAATGgtattttcgt ... gatgtaatagCTTATGAAGTGTTATCGGATGAGGAGAAGAGGGAGATATATAACAAGTATG
EST: gi|86049294|gb|DR345049.1|DR345049
EST:     GAATCAAGGAAATGAGGAAGCGACTCGCAAATTCGCTGAGATCAACAATG                         CTTATGAAGTGTTATCGGATGAGGAGAAGAGGGAGATATATAACAAGTATG
genomic: GAATCAAGGAAATGAGGAAGCGACTCGCAAATTCGCTGAGATCAACAATGgtattttcgt ... gatgtaatagCTTATGAAGTGTTATCGGATGAGGAGAAGAGGGAGATATATAACAAGTATG
EST: gi|86049291|gb|DR345046.1|DR345046
EST:     GAATCAAGGAAATGAGGAAGCGACTCGCAAATTCGCTGAGATCAACAATG                         CTTATGAAGTGTTATCGGATGAGGAGAAGAGGGAGATATATAACAAGTATG
genomic: GAATCAAGGAAATGAGGAAGCGACTCGCAAATTCGCTGAGATCAACAATGgtattttcgt ... gatgtaatagCTTATGAAGTGTTATCGGATGAGGAGAAGAGGGAGATATATAACAAGTATG
EST: gi|86049306|gb|DR345061.1|DR345061
EST:     GAATCAAGGAAATGAGGAAGCGACTCGCAAATTCGCTGAGATCAACAATG                         CTTATGAAGTGTTATCGGATGAGGAGAAGAGGGAGATATATAACAAGTATG
genomic: GAATCAAGGAAATGAGGAAGCGACTCGCAAATTCGCTGAGATCAACAATGgtattttcgt ... gatgtaatagCTTATGAAGTGTTATCGGATGAGGAGAAGAGGGAGATATATAACAAGTATG
EST: gi|86049293|gb|DR345048.1|DR345048
EST:     GAATCAAGGAAATGAGGAAGCGACTCGCAAATTCGCTGAGATCAACAATG                         CTTATGAAAGTGTTATCGGATGAGGAGAAGAGGGAGATATATAACAAGTAT
genomic: GAATCAAGGAAATGAGGAAGCGACTCGCAAATTCGCTGAGATCAACAATGgtattttcgt ... gatgtaatagCTTATGAA-GTGTTATCGGATGAGGAGAAGAGGGAGATATATAACAAGTAT
EST: gi|86049310|gb|DR345065.1|DR345065
EST:     GAATCAAGGAAATGAGGAAGCGACTCGCAAATTCGCTGAGATCAACAATG                         CTTATGAAGTGTTATCGGATGAGAAGAAGAGGGAGATATATAACAAGTATG
genomic: GAATCAAGGAAATGAGGAAGCGACTCGCAAATTCGCTGAGATCAACAATGgtattttcgt ... gatgtaatagCTTATGAAGTGTTATCGGATGAGGAGAAGAGGGAGATATATAACAAGTATG
EST: gi|125268614|gb|EL282699.1|EL282699
EST:     GAATCAAGGAAATGAGGAAGCGACTCGCAAATTCGCTGAGATCAACAATG                         CTTATGAAGTGTTATCG
genomic: GAATCAAGGAAATGAGGAAGCGACTCGCAAATTCGCTGAGATCAACAATGgtattttcgt ... gatgtaatagCTTATGAAGTGTTATCG
EST: gi|164114095|gb|ES035535.1|ES035535
EST:     GCGACTCGCAAATTCGCTGAGATCAACAATG                         CTTATGAAGTGTTATCGGATGAGGAGAAGAGGGAGATATATAACAAGTATG
genomic: GCGACTCGCAAATTCGCTGAGATCAACAATGgtattttcgt ... gatgtaatagCTTATGAAGTGTTATCGGATGAGGAGAAGAGGGAGATATATAACAAGTATG
EST: gi|86049303|gb|DR345058.1|DR345058
EST:     GAATCAAGGAAATGAGGAAGCGACTCGCAAATTCGCTGAGATCAACAATG                         CTTATGAAGTGTTATCGGATGAGGAGAAGAGG
genomic: GAATCAAGGAAATGAGGAAGCGACTCGCAAATTCGCTGAGATCAACAATGgtattttcgt ... gatgtaatagCTTATGAAGTGTTATCGGATGAGGAGAAGAGG
EST: gi|86049311|gb|DR345066.1|DR345066
EST:     GAATCAAGGAAATGAGGAAGCGACTCGCAAATTCGCTGAGATCAACAATG                         CTTATGAAGTGTTATCGGATGAGGAGAAGAGGGAGATATATAACAAGTATG
genomic: GAATCAAGGAAATGAGGAAGCGACTCGCAAATTCGCTGAGATCAACAATGgtattttcgt ... gatgtaatagCTTATGAAGTGTTATCGGATGAGGAGAAGAGGGAGATATATAACAAGTATG
EST: gi|86049292|gb|DR345047.1|DR345047
EST:     GAATCAAGGAAATGAGGAAGCGACTCGCAAATTCGCTGAGATCAACAATG                         CTTATGAAGTGTTATCGGATGAGGAGAAGAGGGAGATATATAACAAG
genomic: GAATCAAGGAAATGAGGAAGCGACTCGCAAATTCGCTGAGATCAACAATGgtattttcgt ... gatgtaatagCTTATGAAGTGTTATCGGATGAGGAGAAGAGGGAGATATATAACAAG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CAGATCAAGAGAGCTTATAGGAAACTAGCTTTGAAGTATCATCCCGATAAGAATCAAGGAAATGAGGAAGCGACTCGCAAATTCGCTGAGATCAACAATGgtattttcgttttgcaacttgtgtgattctgctctctttgttaactcacccgtttttagttttgagaattgacgtattggtgtttgatgtaatag

- - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGATCA