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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGAATTCTCAATAACTAGCATGACTGGTGGTTATAGACGTGTTTTCCAGAAACCAATAGACTTTGAATGgtacgctatatgtatagttagagattcctccagttttgagatcaaacattatatggaagtagagactaatgttgtctgtaaattgctgcag

Basic information

species Arabidopsis thaliana
transcript AT3G04820.1
intron # 18
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G04820.1 (Arabidopsis thaliana), 5'ss of exon 18
lower sequence: Vv14s0030g01850.t01 (Vitis vinifera), 5'ss of exon 13
GGAATTCTCAATAACTAGCATGACTGGTGGTTATAGACGTGTTTTCCAGAAACCAATAGACTTTGAATGgtacgctatatgtata-gttagagattcctccagttttgagatcaaacattatatggaagtagagactaatgttgtctgtaaattgctgcag
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GGAATTCTCAATAACCAACATGACTGGAGGTTTTAGGAGGGTTTTCCAAAAGCCAATCGACTTTGAATGgtattgtattcctttatgttggcaacttttatgtctgagatattcaa-ataatattg--ttgactaattattttgttt-tctattattgcag
















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|124755919|gb|EH846049.1|EH846049
EST:     ACGTGTTTTCCAGAAACCAATAGACTTTGAATG                         GGAATTACTGACTTACACTGACAGCAATAAACCATTGGCAGAGACGGATCT
genomic: ACGTGTTTTCCAGAAACCAATAGACTTTGAATGgtacgctata ... attgctgcagGGAATTACTGACTTACACTGACAGCAATAAACCATTGGCAGAGACGGATCT
EST: gi|116457909|gb|EG500501.1|EG500501
EST:     ATGACTGGTGGTTATAGACGTGTTTTCCAGAAACCAATAGACTTTGAATG                         GGAATTACTGACTTACACTGACAGCAATAAACCATTGGCAGAGACGGATCT
genomic: ATGACTGGTGGTTATAGACGTGTTTTCCAGAAACCAATAGACTTTGAATGgtacgctata ... attgctgcagGGAATTACTGACTTACACTGACAGCAATAAACCATTGGCAGAGACGGATCT
EST: gi|116457913|gb|EG500505.1|EG500505
EST:     ATGACTGGTGGTTATAGACGTGTTTTCCAGAAACCAATAGACTTTGAATG                         GGAATTACTGACTTACACTGACAGCAATAAACCATTGGCAGAGACGGATCT
genomic: ATGACTGGTGGTTATAGACGTGTTTTCCAGAAACCAATAGACTTTGAATGgtacgctata ... attgctgcagGGAATTACTGACTTACACTGACAGCAATAAACCATTGGCAGAGACGGATCT
EST: gi|116462939|gb|EG505531.1|EG505531
EST:     ATGACTGGTGGTTATAGACGTGTTTTCCAGAAACCAATAGACTTTGAATG                         GGAATTACTGACTTACACTGACAGCAATAAACCATTGGCAGAGACGGATCT
genomic: ATGACTGGTGGTTATAGACGTGTTTTCCAGAAACCAATAGACTTTGAATGgtacgctata ... attgctgcagGGAATTACTGACTTACACTGACAGCAATAAACCATTGGCAGAGACGGATCT
EST: gi|116457908|gb|EG500500.1|EG500500
EST:     ATGACTGGTGGTTATAGACGTGTTTTCCAGAAACCAATAGACTTTGAATG                         GGAATTACTGACTTACACTGACAGCAATAAACCATTGGCAGAGACGGATCT
genomic: ATGACTGGTGGTTATAGACGTGTTTTCCAGAAACCAATAGACTTTGAATGgtacgctata ... attgctgcagGGAATTACTGACTTACACTGACAGCAATAAACCATTGGCAGAGACGGATCT
EST: gi|116457917|gb|EG500509.1|EG500509
EST:     ATGACTGGTGGTTATAGACGTGTTTTCCAGAAACCAATAGACTTTGAATG                         GGAATTACTGACTTACACTGACAGCAATAAACCATTGGCAGGGACGGATCT
genomic: ATGACTGGTGGTTATAGACGTGTTTTCCAGAAACCAATAGACTTTGAATGgtacgctata ... attgctgcagGGAATTACTGACTTACACTGACAGCAATAAACCATTGGCAGAGACGGATCT
EST: gi|116457902|gb|EG500494.1|EG500494
EST:     ATGACTGGTGGTTATAGACGTGTTTTCCAGAAACCAATAGACTTTGAATG                         GGAATTACTGACTTACACTGACAGCAATAAACCATTGGCAGAGACGGATTT
genomic: ATGACTGGTGGTTATAGACGTGTTTTCCAGAAACCAATAGACTTTGAATGgtacgctata ... attgctgcagGGAATTACTGACTTACACTGACAGCAATAAACCATTGGCAGAGACGGATCT
EST: gi|116457914|gb|EG500506.1|EG500506
EST:     ATGACTGGTGGTTATAGACGTGTTTTCCAGAAACCAATAGACTTTGAATG                         GGAATTACTGACTTACACTGACAGCAATAAACCATTGGCAGAGACGGATCT
genomic: ATGACTGGTGGTTATAGACGTGTTTTCCAGAAACCAATAGACTTTGAATGgtacgctata ... attgctgcagGGAATTACTGACTTACACTGACAGCAATAAACCATTGGCAGAGACGGATCT
EST: gi|116457920|gb|EG500512.1|EG500512
EST:     ATGACTGGTGGTTATAGACGTGTTTTCCAGAAACCAATAGACTTTGAATG                         GGAATTACTGACTTACACTGACAGCAATAAACCATTGGCAGAGACGGATCT
genomic: ATGACTGGTGGTTATAGACGTGTTTTCCAGAAACCAATAGACTTTGAATGgtacgctata ... attgctgcagGGAATTACTGACTTACACTGACAGCAATAAACCATTGGCAGAGACGGATCT
EST: gi|116457916|gb|EG500508.1|EG500508
EST:     ATGACTGGTGGTTATAGACGTGTTTTCCAGAAACCAATAGACTTTGAATG                         GGAATTACTGACTTACACTGACAGCAATAAACCATTGGCAGGGACGGATCT
genomic: ATGACTGGTGGTTATAGACGTGTTTTCCAGAAACCAATAGACTTTGAATGgtacgctata ... attgctgcagGGAATTACTGACTTACACTGACAGCAATAAACCATTGGCAGAGACGGATCT
EST: gi|116457919|gb|EG500511.1|EG500511
EST:     ATGACTGGTGGTTATAGACGTGTTTTCCAGAAACCAATAGACTTTGAATG                         GGAATTACTGACTTACACTGACAGCAATAAACCATTGGCAGAGACGGATCT
genomic: ATGACTGGTGGTTATAGACGTGTTTTCCAGAAACCAATAGACTTTGAATGgtacgctata ... attgctgcagGGAATTACTGACTTACACTGACAGCAATAAACCATTGGCAGAGACGGATCT
EST: gi|125140581|gb|EL178773.1|EL178773
EST:     TTATAGACGTGTTTTCCAGAAACCAATAGACTTTGAATG                         GGAATTACTGACTTACACTGACAGCAATAAACCATTGGCAGAGACGGA
genomic: TTATAGACGTGTTTTCCAGAAACCAATAGACTTTGAATGgtacgctata ... attgctgcagGGAATTACTGACTTACACTGACAGCAATAAACCATTGGCAGAGACGGA
EST: gi|116457911|gb|EG500503.1|EG500503
EST:     ATGACTGGTGGTTATAGACGTGTTTTCCAGAAACCAATAGACTTTGAATG                         GGAATTACTGACTTACACTGACAGCAATAAACCATTGGCAGAGACGGATCT
genomic: ATGACTGGTGGTTATAGACGTGTTTTCCAGAAACCAATAGACTTTGAATGgtacgctata ... attgctgcagGGAATTACTGACTTACACTGACAGCAATAAACCATTGGCAGAGACGGATCT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGAATTCTCAATAACTAGCATGACTGGTGGTTATAGACGTGTTTTCCAGAAACCAATAGACTTTGAATGgtacgctatatgtatagttagagattcctccagttttgagatcaaacattatatggaagtagagactaatgttgtctgtaaattgctgcag

- - - - - - - - - - - - TGGTGG