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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagaatctaacattgatacttcatgctttgattagtcaatttattcatgtgttctcttagattataatattggatttcacagATTTGGACAGCCTATGAAAGTTAATTGGGCGTATGCAACTGGTCAAAGGGAAGATACATCAA

Basic information

species Arabidopsis thaliana
transcript AT1G54080.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G54080.2 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA16G01230.1 (Glycine max), 3'ss of exon 4
gtaagaatctaacattgatacttcatgctttgattagtcaatttattcatgtgttctcttagattataatattggatttcacagATTTGGACAGCCTATGAAAGTTAATTGGGCGTATGCAACTGGTCAAAGGGAAGATACATCAA
          |   ||| |  ||     | || | | |  ||||  |  ||| ||||     ||| ||||       ||  ||||||||| |||||||| |||||||||||||| ||||| | |||||| || || ||||| ||| 
-------gtaagtgttgctctttagatttatgttaaattgatttcattttgtattct----aattttaattcaatgctttgcagATTTGGGCAGCCTATCAAAGTTAATTGGGCATATGCGAGTGGTCAGAGAGAGGATACGTCAG

upper sequence: AT1G54080.2 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA07G04640.1 (Glycine max), 3'ss of exon 4
gtaagaatctaacattgatacttcatgctttgattagtcaatttattcatgtgttctcttagattataatattggatttcacagATTTGGACAGCCTATGAAAGTTAATTGGGCGTATGCAACTGGTCAAAGGGAAGATACATCAA
          |   ||| |  |      | || | | |  ||||  |  |||||||    | ||| ||||       ||  ||||||||| |||||||| |||||||||||||| ||||| | |||||| || || ||||| ||| 
-------gtaagtgttgctgttaagatttatgttaaattgatttcattttgtgttc----aaattctaattcaatgctttgcagATTTGGGCAGCCTATCAAAGTTAATTGGGCATATGCTAGTGGTCAGAGAGAGGATACGTCAG

upper sequence: AT1G54080.2 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: Vv09s0002g00880.t01 (Vitis vinifera), 3'ss of exon 4
gtaagaatctaacattgatacttcatgctttgattagtcaatttattcatgtgttctcttagattataatattggatttcacagATTTGGACAGCCTATGAAAGTTAATTGGGCGTATGCAACTGGTCAAAGGGAAGATACATCAA
         ||| |   |  ||| ||  |||  |||    |  | ||    | || | |  | |  | || ||| | ||  ||| ||||| |||||||| |||||||||||||| ||||| | |||||||||||| || |||||| 
--------gtaagaagaacccttgat-ttttatttatgttacatgttgggat-ttgtttctgttgctcattttgtaatttgcagGTTTGGGCAGCCTATCAAAGTTAATTGGGCATATGCTAGTGGTCAAAGGGAGGACACATCAG

upper sequence: AT1G54080.2 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: PP1S84_50V6.2 (Physcomitrella patens), 3'ss of exon 5
--------------gtaagaatctaacattgatacttcatgctttgattagtcaatttattcatgtgttctcttagat-tataatattgg-atttcacagATTTGGACAGCCTATGAAAGTTAATTGGGCGTATGCAACTGGTCAAAGGGAAGATACATCAA
              ||      ||||  ||  |     ||||   ||  |   |  |  |   |   || ||| |  |   |  |  ||    |    ||||||||||||||||| |||||||||||||| |||||||  || || || || |||||  || 
cgtcttcactttttgtgctttcctaattttccttacgaatgcaaggaccaaatagatagtaatttctttttctgatctgcgtggtgatgatgctgtgtagATTTGGACAGCCTATCAAAGTTAATTGGGCATATGCAAGCGGGCAGAGAGAGGATACTACAG

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|124985768|gb|EL058337.1|EL058337
EST:     GATCGAAGATGTGCTAGTATGGCTATAATGACTCTTAACGGAAGGCATAT                         ATTTGGACAGCCTATGAAAGTTAATTGGGCGTATGCA
genomic: GATCGAAGATGTGCTAGTATGGCTATAATGACTCTTAACGGAAGGCATATgtaagaatct ... gatttcacagATTTGGACAGCCTATGAAAGTTAATTGGGCGTATGCA
EST: gi|86052517|gb|DR348274.1|DR348274
EST:     GATCGAAGATGTGCTAGTATGGCTATAATGACTCTTAACGGAAGGCATAT                         ATTTGGACAGCCTATGAAAGTTAATTGGGCGTATGCAACTGGTCAAAGGGA
genomic: GATCGAAGATGTGCTAGTATGGCTATAATGACTCTTAACGGAAGGCATATgtaagaatct ... gatttcacagATTTGGACAGCCTATGAAAGTTAATTGGGCGTATGCAACTGGTCAAAGGGA
EST: gi|164156707|gb|EL979502.1|EL979502
EST:     GTATGGCTATAATGACTCTTAACGGAAGGCATAT                         ATTTGGACAGCCTATGAAAGTTAATTGGGCGTATGCAACTGGTCAAAGGGA
genomic: GTATGGCTATAATGACTCTTAACGGAAGGCATATgtaagaatct ... gatttcacagATTTGGACAGCCTATGAAAGTTAATTGGGCGTATGCAACTGGTCAAAGGGA
EST: gi|124767745|gb|EH857875.1|EH857875
EST:     TGGCTATAATGACTCTTAACGGAAGGCATAT                         ATTTGGACAGCCTATGAAAGTTAATTGGGCGTATGCAACTGGTCAAAGGGA
genomic: TGGCTATAATGACTCTTAACGGAAGGCATATgtaagaatct ... gatttcacagATTTGGACAGCCTATGAAAGTTAATTGGGCGTATGCAACTGGTCAAAGGGA
EST: gi|164227306|gb|ES160704.1|ES160704
EST:     AGATGTGCTAGTATGGCTATAATGACTCTTAACGGAAGGCATAT                         ATTTGGACAGCCTATGAAAGTTAATTGGGCGTACGCAACTGGTCAAAGGGA
genomic: AGATGTGCTAGTATGGCTATAATGACTCTTAACGGAAGGCATATgtaagaatct ... gatttcacagATTTGGACAGCCTATGAAAGTTAATTGGGCGTATGCAACTGGTCAAAGGGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgattagtcaatttattcatgtgttctcttagattataatattggatttcacagATTTGGACAGCCTATGAAAGTTAATTGGGCGTATGCAACTGGTCAAAGGGAAGATACATCAA
 ctttgat  putative branch site (score: 5)
                             ttagattataatattg  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagaatctaacattgatacttcatgctttgattagtcaatttattcatgtgttctcttagattataatattggatttcacagATTTGGACAGCCTATGAAAGTTAATTGGGCGTATGCAACTGGTCAAAGGGAAGATACATCAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA