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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTCCTCCATTGGTGCCGTCTACATGGACCCGAACCGTGACCCTGAGGCTGTCGTTGACGAAAGTTGTTGGAGTGATCTTGACTTCTGCAAAAACACCAAGgtcttgcactcttgcttcgtttttttaaatattttgcatttgttaattaaacatgtttatcatgttaaaaaattgaaaaatatttaatgtctaaaaaatgtgaattttttggttctattgtgaaatagtattatctttgatgttaggtctattgaatatttgtatgtgttttgtag

Basic information

species Arabidopsis thaliana
transcript AT1G15950.2
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G15950.2 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: Vv09s0070g00240.t01 (Vitis vinifera), 5'ss of exon 3
CTCCTCCATTGGTGCCGTCTACATGGACCCGAACCGTGACCCTGAGGCTGTCGTTGACGAAAGTTGTTGGAGTGATCTTGACTTCTGCAAAAACACCAAGgtcttgcactcttgcttcgtttttttaaa------------tattttgcatt-tgttaattaaacatgttta--tcatgttaaaa----aattgaaaaa----tatttaatgtctaaaaaatgtgaattttttggttctattgtgaaatagtattatctttgatgttaggtctattgaatatttgtatgtgttttgtag
 || || ||||| || || ||||||||||| ||| |   ||| ||    || || ||||| || ||||||||||||||||| |||||||| |||||||||||||| |   ||  |||  ||| || ||             || ||| |||  | ||  || ||||| ||    || | || ||     |||    | |    | ||| |||||  |||  |   ||      ||  |||   | ||||   | |  |    |    || | | |||| ||  ||   |     || ||
ATCATCGATTGGAGCAGTGTACATGGACCCCAACAGGAGCCCAGATCAAGTTGTGGACGAGAGCTGTTGGAGTGATCTTGAATTCTGCAAGAACACCAAGgtcttcccacctatctttttttcttcaacactatttacccctaattttcatcattttttttcaacattttcgcttcttcttcaacctataatcatcagacttgtctttcatgtcccaaaggt---aacggaacggcactaaaataaaatttgactcacccaaaaacaagattt-ttgattaactgagaggaaaatgcag
















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|116464127|gb|EG506719.1|EG506719
EST:     TCGTTGACGAAAGTTGTTGGAGTGATCTTGACTTCTGCAAAAACACCAAG                         AATTGGTATTGTTACGGCAAGATGGTGGCGGAACAAGCGGCGTGGGAGACA
genomic: TCGTTGACGAAAGTTGTTGGAGTGATCTTGACTTCTGCAAAAACACCAAGgtcttgcact ... tgttttgtagAATTGGTATTGTTACGGCAAGATGGTGGCGGAACAAGCGGCGTGGGAGACA
EST: gi|125017754|gb|EL090023.1|EL090023
EST:     GACTTCTGCAAAAACAACCAAG                         AATTGGTATTGTTACGGCAAGATGGTGGCGGAACAAGCGGCGTGGGAGAC
genomic: GACTTCTGCAAAAAC-ACCAAGgtcttgcact ... tgttttgtagAATTGGTATTGTTACGGCAAGATGGTGGCGGAACAAGCGGCGTGGGAGAC
EST: gi|116438546|gb|EG481138.1|EG481138
EST:     TCGTTGACGAAAGTTGTTGGAGTGATCTTGACTTCTGCAAAAACACCAAG                         AATTGGTATTGTTACGGCAAGATGGTGGCGGAACCAGCGGCGTGGGAGACA
genomic: TCGTTGACGAAAGTTGTTGGAGTGATCTTGACTTCTGCAAAAACACCAAGgtcttgcact ... tgttttgtagAATTGGTATTGTTACGGCAAGATGGTGGCGGAACAAGCGGCGTGGGAGACA
EST: gi|116464136|gb|EG506728.1|EG506728
EST:     TCGTTGACGAAAGTTGTTGGAGTGATCTTGACTTCTGCAAAAACACCAAG                         AATTGGTATTGTTACGGCAAGATGGTGGCGGAACAAGCGGCGTGGGAGACA
genomic: TCGTTGACGAAAGTTGTTGGAGTGATCTTGACTTCTGCAAAAACACCAAGgtcttgcact ... tgttttgtagAATTGGTATTGTTACGGCAAGATGGTGGCGGAACAAGCGGCGTGGGAGACA
EST: gi|125316999|gb|EL331084.1|EL331084
EST:     TCGTTGACGAAAGTTGTTGGAGTGATCTTGACTTCTGCAAAAACACCAAG                         AATTGGTATTGTTACGGCAAGATGGTGGCGGAACAAGCGGCGTGGGAG
genomic: TCGTTGACGAAAGTTGTTGGAGTGATCTTGACTTCTGCAAAAACACCAAGgtcttgcact ... tgttttgtagAATTGGTATTGTTACGGCAAGATGGTGGCGGAACAAGCGGCGTGGGAG
EST: gi|116438547|gb|EG481139.1|EG481139
EST:     TCGTTGACGAAAGTTGTTGGAGTGATCTTGACTTCTGCAAAAACACCAAG                         AATTGGTATTGTTACGGCAAGATGGTGGCGGAACAAGCGGCGTGGGAGACA
genomic: TCGTTGACGAAAGTTGTTGGAGTGATCTTGACTTCTGCAAAAACACCAAGgtcttgcact ... tgttttgtagAATTGGTATTGTTACGGCAAGATGGTGGCGGAACAAGCGGCGTGGGAGACA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CTCCTCCATTGGTGCCGTCTACATGGACCCGAACCGTGACCCTGAGGCTGTCGTTGACGAAAGTTGTTGGAGTGATCTTGACTTCTGCAAAAACACCAAGgtcttgcactcttgcttcgtttttttaaatattttgcatttgttaattaaacatgtttatcatgttaaaaaattgaaaaatatttaatgtctaaaaaatgtgaattttttggttctattgtgaaatagtattatctttgatgttaggtctattgaatatttgtatgtgttttgtag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG