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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTTGATCCTCTTACTCATCAAGTCAAAATCTGTGACTTTGGCAGTGCGAAACAGCTCgtaagactttgtgacatataaactcattcgacttgtagcggttgttgttttctgtgatcttgtcatttactgttgaaatttacttttgcttcag

Basic information

species Arabidopsis thaliana
transcript AT4G18710.1
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT4G18710.1 (Arabidopsis thaliana), 5'ss of exon 5
lower sequence: LOC_Os01g10840.1 (Oryza sativa), 5'ss of exon 6
GTTGATCCTCTTACTCATCAAGTCAAAATCTGTGACTTTGGCAGTGCGAAACAGCTCgtaagact-ttgtgacatataaactcattcgacttgtagcggttgttgttttctgtgatcttgtcatttactgttgaaatttacttttg-cttcag------
||||||||||| ||||||||||||||  | ||||||||||| ||||| ||    || ||| |    ||   ||   |||    | |      || |   ||| ||| | |||  ||  |   | |    |   |    || | ||| |  ||       
GTTGATCCTCTCACTCATCAAGTCAAGCTATGTGACTTTGGAAGTGCAAAGGTTCTGgtatgttgatttccacccttaagagtaatttctcagtggt--ttgatgtatgctgaaattattctagtggtaggctagtcataatgttgacagcataagtgg

upper sequence: AT4G18710.1 (Arabidopsis thaliana), 5'ss of exon 5
lower sequence: LOC_Os05g11730.1 (Oryza sativa), 5'ss of exon 6
GTTGATCCTCTTACTCATCAAGTCAAAATCTGTGACTTTGGCAGTGCGAAACAGCTCgtaa-gactttgtgacatataaactcattcgacttgtagcggttgttgttttctgtgatcttgtcatttactgttgaaatttacttttgcttcag------
|| |||||||| ||||||||||||||  ||||||||||||| || || |||   || |||  | | || |      |||| |  |   |   | |    ||  | |   || |  | || | | ||    || | |   | | |||||  ||      
GTGGATCCTCTAACTCATCAAGTCAAGCTCTGTGACTTTGGGAGCGCAAAAACACTGgtattggccttttccaccctaaagttttgtaatacgcacacattactttagactttcttttttttaattggactttagacg-attcttgctgtagactagt
















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|125309971|gb|EL324056.1|EL324056
EST:     TTACTCATCAAGTCAAAATCTGTGACTTTGGCAGTGCGAAACAGCTC                         GTTAAAGGTGAAGCCAACATTTCTTACATCTGCTCACGATTCTACCGTGCA
genomic: TTACTCATCAAGTCAAAATCTGTGACTTTGGCAGTGCGAAACAGCTCgtaagacttt ... tttgcttcagGTTAAAGGTGAAGCCAACATTTCTTACATCTGCTCACGATTCTACCGTGCA
EST: gi|86056751|gb|DR352508.1|DR352508
EST:     CTCTTACTCATCAAGTCAAAATCTGTGACTTTGGCAGTGCGAAACAGCTC                         GTTAAAGGTGA
genomic: CTCTTACTCATCAAGTCAAAATCTGTGACTTTGGCAGTGCGAAACAGCTCgtaagacttt ... tttgcttcagGTTAAAGGTGA
EST: gi|125051890|gb|EL123936.1|EL123936
EST:     TCAAAATCTGTGACTTTGGCAGTGCGAAACAGCTC                         GTTAAAGGTGAAGCCAACATTTCTTACATCTGCTCACGATTCTACCGTGCA
genomic: TCAAAATCTGTGACTTTGGCAGTGCGAAACAGCTCgtaagacttt ... tttgcttcagGTTAAAGGTGAAGCCAACATTTCTTACATCTGCTCACGATTCTACCGTGCA
EST: gi|116451981|gb|EG494573.1|EG494573
EST:     CTCTTACTCATCAAGTCAAAATCTGTGACTTTGGCAGTGCGAAACAGCTC                         GTTAAAGGTGAAGCCAACATTTCTTACATCTGCTCACGATTCTACCGTGCA
genomic: CTCTTACTCATCAAGTCAAAATCTGTGACTTTGGCAGTGCGAAACAGCTCgtaagacttt ... tttgcttcagGTTAAAGGTGAAGCCAACATTTCTTACATCTGCTCACGATTCTACCGTGCA
EST: gi|125092868|gb|EL150668.1|EL150668
EST:     CTCTTACTCATCAAGTCAAAATCTGTGACTTTGGCAGTGCGAAACAGCTC                         GTTAAAGGTGAAGCCAACATTTCTTACA
genomic: CTCTTACTCATCAAGTCAAAATCTGTGACTTTGGCAGTGCGAAACAGCTCgtaagacttt ... tttgcttcagGTTAAAGGTGAAGCCAACATTTCTTACA
EST: gi|116452048|gb|EG494640.1|EG494640
EST:     CTCTTACTCATCAAGTCAAAATCTGTGACTTTGGCAGTGCGAAACAGCTC                         GTTAAAGGTGAAGCCAACATTTCTTACATCTGCTCACGATTCTACCGTGCA
genomic: CTCTTACTCATCAAGTCAAAATCTGTGACTTTGGCAGTGCGAAACAGCTCgtaagacttt ... tttgcttcagGTTAAAGGTGAAGCCAACATTTCTTACATCTGCTCACGATTCTACCGTGCA
EST: gi|125060675|gb|EL129352.1|EL129352
EST:     GTGACTTTGGCAGTGCGAAACAGCTC                         GTTAAAGGTGAAGCCAACATTTCTTACATCTGCTCACGATTCTACCGTGCA
genomic: GTGACTTTGGCAGTGCGAAACAGCTCgtaagacttt ... tttgcttcagGTTAAAGGTGAAGCCAACATTTCTTACATCTGCTCACGATTCTACCGTGCA
EST: gi|125047580|gb|EL119849.1|EL119849
EST:     CTCTTACTCATCAAGTCAAAATCTGTGACTTTGGCAGTGCGAAACAGCTC                         GTTAAAGGTGAAG
genomic: CTCTTACTCATCAAGTCAAAATCTGTGACTTTGGCAGTGCGAAACAGCTCgtaagacttt ... tttgcttcagGTTAAAGGTGAAG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTTGATCCTCTTACTCATCAAGTCAAAATCTGTGACTTTGGCAGTGCGAAACAGCTCgtaagactttgtgacatataaactcattcgacttgtagcggttgttgttttctgtgatcttgtcatttactgttgaaatttacttttgcttcag

- - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTC