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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaacaaaaactcttaaacccaattctacctctatgtaatgtattaccttagtaagaaaccaggaatcaccttgttctgaaacttgcagGGTGAGAAAGACGACAAGATCATTGCAGTATGTGCTGATGATCCCGAGTTCCGTCACTACAGAGACATCAAAGAGCTTCCCCCTCACCGTCTAGCTGAAA

Basic information

species Arabidopsis thaliana
transcript AT2G18230.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT2G18230.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: LOC_Os02g47600.1 (Oryza sativa), 3'ss of exon 6
------------gtaacaaaaactcttaaacccaattctacctctatgtaatgtattaccttagtaagaaaccaggaatcaccttgttctgaaacttgcagGGTGAGAAAGACGACAAGATCATTGCAGTATGTGCTGATGATCCCGAGTTCCGTCACTACAGAGACATCAAAGAGCTTCCCCCTCACCGTCTAGCTGAAA
               |||| ||      ||    |||||    | |   | | |  |    | |   ||   |    | ||   |  | |||  |   |||||||||||||| ||||||||||| || || ||||||||||| || || | ||| |||| ||| |||||||| ||  | ||||||||||| ||    || |
agtcagtagcccaacacaagaaagaaataatggtattctgtaccaagtgattatgatctaatggcttgagttcttaca-catgatcatttgatgcaaacagGGTGAGAAAGATGACAAGATCATAGCTGTTTGTGCTGATGACCCTGAATACCGCCACTTCAGGGACATCAAGGAAATCCCCCCTCACCGCCTTCAAGAGA

upper sequence: AT2G18230.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GRMZM2G046587_T02 (Zea mays), 3'ss of exon 6
----gtaacaaaaactcttaaacccaattctacctctatgtaatgtattaccttagtaagaaaccaggaatc-------accttgttctgaaacttgcagGGTGAGAAAGACGACAAGATCATTGCAGTATGTGCTGATGATCCCGAGTTCCGTCACTACAGAGACATCAAAGAGCTTCCCCCTCACCGTCTAGCTGAAA
     |   | | | | | | |    ||  | | | ||    |  | |  ||  ||   |||  |  | |||       | | |  |   | |     |||| |||||||| || ||||| || ||||| ||||||||||| || || |||||||||||||  |||||||  || || || || || || ||    || |
gacctttctatagaatataatataatatagttcttgtaaactagttctgtcccaaggctgaattcttgcatcttatttaatcgttgttcaacatcactagGGCGAGAAAGATGATAAGATTATAGCAGTCTGTGCTGATGACCCTGAATTCCGTCACTACACGGACATCACGGACCTCCCACCGCATCGCCTTCAAGAGA

upper sequence: AT2G18230.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA11G07530.1 (Glycine max), 3'ss of exon 6
----------gtaacaaaaactcttaaacc---caattctacctctatgtaatgtattaccttagtaagaaaccaggaatc--accttgttctgaaacttgcagGGTGAGAAAGACGACAAGATCATTGCAGTATGTGCTGATGATCCCGAGTTCCGTCACTACAGAGACATCAAAGAGCTTCCCCCTCACCGTCTAGCTGAAA
           |  ||| |   | |||  |    |||| |  | | |  ||| |||  |  || |  | |||  |    |   | |   |||||     | ||||||||||  || ||||||||||| ||||| ||||||||||| || |||||||| || |||| ||||||||| |||||||| || || || || |||||||
tttcacttggctttcaacattgcataattcgaataattttgtcaccacttaaagtacaaatttggagaaaaattatattttctaacaaattctg----ctacagGGTGAGAGGGATGACAAGATCATAGCAGTTTGTGCTGATGACCCTGAGTTCCGCCATTACACAGACATCAAGGAGCTTCCTCCACATCGGCTTGCTGAAA

upper sequence: AT2G18230.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA01G37790.1 (Glycine max), 3'ss of exon 6
----------gtaacaaaaactcttaaacccaat--tctacctctatgtaatgtattaccttagtaagaaaccaggaatcaccttgttctgaaacttgc---agGGTGAGAAAGACGACAAGATCATTGCAGTATGTGCTGATGATCCCGAGTTCCGTCACTACAGAGACATCAAAGAGCTTCCCCCTCACCGTCTAGCTGAAA
           |  ||| |   | |||  | |||  | |  | | |  ||| ||   |  || |  | |||  |    |    || |    ||   |||   |||||||||  || ||||||||||| ||||| ||||||||||| || |||||||| || ||||  |||||||| |||||||| || || || || |||||||
tttcacttgtctttcaacattgcataattcgaataatttgtcaccacttaaagtccaaatttggagaaaaatta----tttttttctaacaaattctgctacagGGTGAGAGGGATGACAAGATCATAGCAGTTTGTGCTGATGACCCTGAGTTCCGCCATTACACTGACATCAATGAGCTTCCTCCACATCGGCTTGCTGAAA

upper sequence: AT2G18230.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: Vv04s0023g02050.t01 (Vitis vinifera), 3'ss of exon 5
-gtaacaaaaactct----taaacccaattctacct--ctatgtaatgtattaccttagtaagaaaccaggaatcaccttgttctgaaac----ttgcagGGTGAGAAAGACGACAAGATCATTGCAGTATGTGCTGATGATCCCGAGTTCCGTCACTACAGAGACATCAAAGAGCTTCCCCCTCACCGTCTAGCTGAAA
 ||  | | |  | |    || ||    || | | |    || |  |  |  ||   | | | |        | ||  |  | |  |||     ||||||||||| || || ||||| || || ||||| ||||||||||| || |||||||| ||||||| ||||||||||||| ||||||| || || || ||||| |
agtctctatatatttaaattagacgtgttttttcttgatcatatgtttcaagacaccattgaaagtgtgattaccaggtgatacacaaatccttttgcagGGTGAAAAGGATGACAAAATAATAGCAGTGTGTGCTGATGACCCTGAGTTCCGCCACTACAAAGACATCAAAGAGATTCCCCCACATCGCCTTGCTGAGA

upper sequence: AT2G18230.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: PP1S315_67V6.1 (Physcomitrella patens), 3'ss of exon 3
-------------------gtaacaaa-aactcttaaacccaattctacctctatgta-atgtattaccttagtaagaaaccaggaatcaccttgttctgaaacttgcagGGTGAGAAAGACGACAAGATCATTGCAGTATGTGCTGATGATCCCGAGTTCCGTCACTACAGAGACATCAAAGAGCTTCCCCCTCACCGTCTAGCTGAAA
                   | |        || ||     |      |    | || |  ||| ||      || || |||  |  |||    ||||| |||   ||||||||||||| |||||||||||||| || || ||||| || || ||||||| | | || | ||  |||||||| |||||||| || |||||  | || || |
gttagaagctgttgcgctcgcactgtgtggctgtttgtgtcgtggaaaaggttgtggatgtgttttctgcgggttagcaacgtgagatc----tgttcggaa---tgcagGGTGAGAAGGACGACAAGATCATCGCCGTGTGTGCCGACGACCCCGAGTACAGACATTTCAAGGACATCAACGAGCTTCCACCGCACCGATTGGCGGAGA

upper sequence: AT2G18230.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: PP1S552_1V6.1 (Physcomitrella patens), 3'ss of exon 6
-------------------gtaacaaa-aactcttaaacccaattctacctctatgta-atgtattaccttagtaagaaaccaggaatcaccttgttctgaaacttgcagGGTGAGAAAGACGACAAGATCATTGCAGTATGTGCTGATGATCCCGAGTTCCGTCACTACAGAGACATCAAAGAGCTTCCCCCTCACCGTCTAGCTGAAA
                   | |        || ||     |      |    | || |  ||| ||      || || |||  |  |||    ||||| |||   ||||||||||||| |||||||||||||| || || ||||| || || ||||||| | | || | ||  |||||||| ||                          
gttagaagctgttgcgctcgcactgtgtggctgtttgtgtcgtggaaaaggttgtggatgtgttttctgcgggttagCAACGTGAGATC----TGTTCGGAA---TGCAGGGTGAGAAGGACGACAAGATCATCGCCGTGTGTGCCGACGACCCCGAGTACAGACATTTCAAGGACATCAACGA--------------------------

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|116390031|gb|EG432623.1|EG432623
EST:     GATCATTCCTCCGTGCCCGTGCTATTGGTCTAATGCCCATGATTGATCAG                         A
genomic: GATCATTCCTCCGTGCCCGTGCTATTGGTCTAATGCCCATGATTGATCAGgtaacaaaaa ... aaacttgcag-
EST: gi|116390031|gb|EG432623.1|EG432623
EST:     GATCATTCCTCCGTGCCCGTGCTATTGGTCTAATGCCCATGATTGATCAG                         A
genomic: GATCATTCCTCCGTGCCCGTGCTATTGGTCTAATGCCCATGATTGATCAGgtaacaaaaa ... aaacttgcag-
EST: gi|116443156|gb|EG485748.1|EG485748
EST:     GATCATTCCTCCGTGCCCGTGCTATTGGTCTAATGCCCATGATTGATCAG                         GGTGAGAAAGACGACAAGATCATTGCAGTATGTGCTGATGATCCCGAGTTC
genomic: GATCATTCCTCCGTGCCCGTGCTATTGGTCTAATGCCCATGATTGATCAGgtaacaaaaa ... aaacttgcagGGTGAGAAAGACGACAAGATCATTGCAGTATGTGCTGATGATCCCGAGTTC
EST: gi|124948954|gb|EL024643.1|EL024643
EST:     GCCCGTGCTATTGGTCTAATGCCCATGATTGATCAG                         GGTGAGAAAGACGACAAGATCATTGCAGTATGTGCTGATGATCCCGAGTTC
genomic: GCCCGTGCTATTGGTCTAATGCCCATGATTGATCAGgtaacaaaaa ... aaacttgcagGGTGAGAAAGACGACAAGATCATTGCAGTATGTGCTGATGATCCCGAGTTC
EST: gi|116390040|gb|EG432632.1|EG432632
EST:     GATCATTCCTCCGTGCCCGTGCTATTGGTCTAATGCCCATGATTGATCAG                         A
genomic: GATCATTCCTCCGTGCCCGTGCTATTGGTCTAATGCCCATGATTGATCAGgtaacaaaaa ... aaacttgcag-
EST: gi|116390040|gb|EG432632.1|EG432632
EST:     GATCATTCCTCCGTGCCCGTGCTATTGGTCTAATGCCCATGATTGATCAG                         A
genomic: GATCATTCCTCCGTGCCCGTGCTATTGGTCTAATGCCCATGATTGATCAGgtaacaaaaa ... aaacttgcag-
EST: gi|116443161|gb|EG485753.1|EG485753
EST:     GATCATTCCTCCGTGCCCGTGCTATTGGTCTAATGCCCATGATTGATCAG                         GGTGAGAAAGACGACAAGATCATTGCAGTATGTGCTGATGATCCCGAGTTC
genomic: GATCATTCCTCCGTGCCCGTGCTATTGGTCTAATGCCCATGATTGATCAGgtaacaaaaa ... aaacttgcagGGTGAGAAAGACGACAAGATCATTGCAGTATGTGCTGATGATCCCGAGTTC
EST: gi|116451434|gb|EG494026.1|EG494026
EST:     GATCATTCCTCCGTGCCCGTGCTATTGGTCTAATGCCCATGATTGATCAG                         GGTGAGAAAGACGACAAGATCATTGCAGTATGTGCTGATGATCCCGAGTTC
genomic: GATCATTCCTCCGTGCCCGTGCTATTGGTCTAATGCCCATGATTGATCAGgtaacaaaaa ... aaacttgcagGGTGAGAAAGACGACAAGATCATTGCAGTATGTGCTGATGATCCCGAGTTC
EST: gi|164224212|gb|EL972207.1|EL972207
EST:     GATCATTCCTCCGTGCCCGTGCTATTGGTCTAATGCCCATGATTGATCAG                         GGTGAGAAAGACGACAAGATCATTGCAGTATGTGCTG
genomic: GATCATTCCTCCGTGCCCGTGCTATTGGTCTAATGCCCATGATTGATCAGgtaacaaaaa ... aaacttgcagGGTGAGAAAGACGACAAGATCATTGCAGTATGTGCTG
EST: gi|86075558|gb|DR371315.1|DR371315
EST:     GATCATTCCTCCGTGCCCGTGCTATTGGTCTAATGCCCATGATTGATCAG                         GGTGAGAAAGACGACAAGATCATTGCAGTATGTGCTGATGATCCCGAGTTC
genomic: GATCATTCCTCCGTGCCCGTGCTATTGGTCTAATGCCCATGATTGATCAGgtaacaaaaa ... aaacttgcagGGTGAGAAAGACGACAAGATCATTGCAGTATGTGCTGATGATCCCGAGTTC
EST: gi|116451435|gb|EG494027.1|EG494027
EST:     GATCATTCCTCCGTGCCCGTGCTATTGGTCTAATGCCCATGATTGATCAG                         GGTGAGAAAGACGACAAGATCATTGCAGTATGTGCTGATGATCCCGAGTTC
genomic: GATCATTCCTCCGTGCCCGTGCTATTGGTCTAATGCCCATGATTGATCAGgtaacaaaaa ... aaacttgcagGGTGAGAAAGACGACAAGATCATTGCAGTATGTGCTGATGATCCCGAGTTC
EST: gi|125123645|gb|EL170064.1|EL170064
EST:     GATCATTCCTCCGTGCCCGTGCTATTGGTCTAATGCCCATGATTGATCAG                         GGTGAGAAAGACGACAAGATCATTGCAGTA
genomic: GATCATTCCTCCGTGCCCGTGCTATTGGTCTAATGCCCATGATTGATCAGgtaacaaaaa ... aaacttgcagGGTGAGAAAGACGACAAGATCATTGCAGTA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgtaatgtattaccttagtaagaaaccaggaatcaccttgttctgaaacttgcagGGTGAGAAAGACGACAAGATCATTGCAGTATGTGCTGATGATCCCGAGTTCCGTCACTACAGAGACATCAAAGAGCTTCCCCCTCACCGTCTAGCTGAAA
     tgtatta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaacaaaaactcttaaacccaattctacctctatgtaatgtattaccttagtaagaaaccaggaatcaccttgttctgaaacttgcagGGTGAGAAAGACGACAAGATCATTGCAGTATGTGCTGATGATCCCGAGTTCCGTCACTACAGAGACATCAAAGAGCTTCCCCCTCACCGTCTAGCTGAAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGA