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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagcagatagatacatatgaatggcaagtccccagaagtgattagcttttttcacttatactggaacccaccatttacatttttggtacagCTTGATGACGTTATTGATCTTGTGATCCCAAGAGGCAGCAACAAGCTTGTTTCTCAAATAAAAAACTCGACGAAAATCCCAGTGCTAGGCCATGCTG

Basic information

species Arabidopsis thaliana
transcript AT3G55610.2
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G55610.2 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: LOC_Os05g38150.1 (Oryza sativa), 3'ss of exon 11
gtaagcagatagatacatatg-aatggcaagtccccagaagtgattagcttttttcacttatactggaacccaccatttacatttttggtacagCTTGATGACGTTATTGATCTTGTGATCCCAAGAGGCAGCAACAAGCTTGTTTCTCAAATAAAAAACTCGACGAAAATCCCAGTGCTAGGCCATGCTG
             |   |||| |||   |  |   || ||| | | |  |  |  || ||   ||  |||||   ||  ||| |    || ||||||||||| || ||||||||||| || |||||||| || || |||||||| |||||||| ||    || || || || || || || || |||||||
------------gtgtgtatgcaattctatattttca-aagcgttga--tactaccaatttggcta-aacccgtaat--acact----gtgcagCTTGATGATGTCATTGATCTTGTCATTCCAAGAGGAAGTAATAAGCTTGTCTCTCAAATCAAGGCGTCAACTAAGATTCCTGTTCTTGGGCATGCTG

upper sequence: AT3G55610.2 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: LOC_Os01g62900.1 (Oryza sativa), 3'ss of exon 12
gtaagcagatagatacatatgaatggcaagtccccagaagtgattagcttttttcacttatactggaacccaccatttacatttttggtacagCTTGATGACGTTATTGATCTTGTGATCCCAAGAGGCAGCAACAAGCTTGTTTCTCAAATAAAAAACTCGACGAAAATCCCAGTGCTAGGCCATGCTG
             |   |||| |  |  | ||    |  ||||| |  |||    | |||  ||  |     |||     | | |  || ||||||||||| || ||||||||||| || |||||||| ||||| ||||| ||||| || || |||    | || || || || || || || |||||||
------------gtgagtatgtaaagtgattctttgg--gtgataaa-tttaagaatttaatctaaa-----ccagaagtactct--gtgcagCTTGATGATGTGATTGATCTTGTAATACCAAGAGGTAGCAATAAGCTCGTTTCCCAGATCAAAGCAGCAACCAAGATTCCTGTTCTTGGTCATGCTG

upper sequence: AT3G55610.2 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: GRMZM2G375504_T03 (Zea mays), 3'ss of exon 11
gtaagcagatagatacatatgaatggcaagtccccagaagtgattagcttttttcacttatactggaacccaccatttaca-tttttggtacagCTTGATGACGTTATTGATCTTGTGATCCCAAGAGGCAGCAACAAGCTTGTTTCTCAAATAAAAAACTCGACGAAAATCCCAGTGCTAGGCCATGCTG
                   | | ||  |  |  |  |||   | |   | |    |  |  |    || ||   | | | | | | |  ||||||||||||| || ||||||||||| || |||||||||||||| ||||| ||||| ||||| |||   || || || || || || || || ||||| |
------------------gtaagtgtaatatatcatgaaaataatgattctaccaatatgcatgataagcctaaactcataatatgttctacagCTTGATGATGTCATTGATCTTGTCATTCCAAGAGGCAGCAATAAGCTGGTTTCGCAAATCAAAGCATCAACTAAGATACCTGTCCTCGGTCATGCGG

upper sequence: AT3G55610.2 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: AC203754.4_FGT008 (Zea mays), 3'ss of exon 11
------gtaagcagatagatacatatgaatggcaagt-ccccagaagtgattagc-ttttttcacttatactggaacccaccatttacatttttggtacagCTTGATGACGTTATTGATCTTGTGATCCCAAGAGGCAGCAACAAGCTTGTTTCTCAAATAAAAAACTCGACGAAAATCCCAGTGCTAGGCCATGCTG
       |       |   || |  |||  |  |  |       || |||| |   |    | |    || |    |  | |   || ||      |||||||| |||| || ||||||||||| || |||||||||||||| ||||| ||||| ||||| || |  || || || ||||| || || || |||||||
acgaaaattgctgatttactaaaggtgagcgtaatatattatgaaaatgatgattgtaccattatgcctaataagcctaaactcata-atacactctacagCTTCATGATGTAATTGATCTTGTCATTCCAAGAGGCAGCAATAAGCTGGTTTCACAAATCAAGACATCAACTAAGATCCCTGTTCTTGGTCATGCTG

upper sequence: AT3G55610.2 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: GRMZM2G094309_T01 (Zea mays), 3'ss of exon 4
gtaagca-gatagatacatatgaatggcaagtccccagaagtgattagcttttttcacttatactggaacccaccatttacatttttggtacagCTTGATGACGTTATTGATCTTGTGATCCCAAGAGGCAGCAACAAGCTTGTTTCTCAAATAAAAAACTCGACGAAAATCCCAGTGCTAGGCCATGCTG
|| |||   ||| ||  ||   ||||   | |   |     ||  ||            ||  |   ||| ||  ||  ||| | |    ||||||| |||| || ||||||||||| || |||||||| ||||| ||||| ||||| ||||| ||    || || || ||||| || || || |||||||
gtgagcgtaatatat-tatgaaaatgatgattgtaccattatgcctaa-----------taagcctaaactcataat--acactct----acagCTTCATGATGTAATTGATCTTGTCATTCCAAGAGGTAGCAATAAGCTGGTTTCACAAATCAAGGCATCAACTAAGATCCCTGTTCTTGGTCATGCTG

upper sequence: AT3G55610.2 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: GLYMA14G07120.1 (Glycine max), 3'ss of exon 9
gtaagcagatagatacatatgaatggcaagtccccagaagtgattagcttttttcacttatactggaacccaccatttacatttttggtacagCTTGATGACGTTATTGATCTTGTGATCCCAAGAGGCAGCAACAAGCTTGTTTCTCAAATAAAAAACTCGACGAAAATCCCAGTGCTAGGCCATGCTG
|| | |  ||   |  |  | |||  ||| | |         || ||| | ||    |||  |     ||  |  |  | | ||    | ||||| |||||||| |||||||| ||||| ||||||||||||||||| |||||||||||||| || |  || || ||||| || ||  |||| || ||||
gtgaactaatcagtggagcttaatttcaatttc---------ataagcctgttcactttaagcattggccacctttaaatacttaaatttcagCTGGATGACGTAATTGATCTGGTGATTCCAAGAGGCAGCAACAAACTTGTTTCTCAAATCAAGAGTTCCACTAAAATTCCTGTTTTAGGTCACGCTG

upper sequence: AT3G55610.2 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: GLYMA02G41850.1 (Glycine max), 3'ss of exon 9
gtaagcagatagatacatatgaatggcaagtccccagaagtgattagcttttttcacttatactggaacccaccatttacatttttggtacagCTTGATGACGTTATTGATCTTGTGATCCCAAGAGGCAGCAACAAGCTTGTTTCTCAAATAAAAAACTCGACGAAAATCCCAGTGCTAGGCCATGCTG
|| | |  ||   |  |  | |||  ||  | |  |    || | | | ||   || |   ||     |   | ||||| ||||      ||||| ||||| || || ||||| ||||| ||||||||||||||||| ||||||||||| || || |  || || ||||| || ||  |||| |||||||
gtgaactaatcagtggagcttaatttcagtttcataaccctgttca-ccttaagcattggcac-----ctttctatttaaattt------cagCTGGATGATGTAATCGATCTGGTGATTCCAAGAGGCAGCAACAAACTTGTTTCTCAGATCAAGAGTTCCACTAAAATTCCTGTTTTAGGTCATGCTG

upper sequence: AT3G55610.2 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: GLYMA18G03830.1 (Glycine max), 3'ss of exon 12
-------gtaagcagatagatacatatgaatggcaagtccccagaagtg----attagcttttttcacttatactggaacccaccatttacatttttggtacagCTTGATGACGTTATTGATCTTGTGATCCCAAGAGGCAGCAACAAGCTTGTTTCTCAAATAAAAAACTCGACGAAAATCCCAGTGCTAGGCCATGCTG
         ||| |||||   |  ||||| |   |   |  |  |  |     ||| |    ||| ||  |  || ||     |  | ||| ||| |  | ||| | ||||| || |||||||| ||||| ||||||||||||||||| |||||  |||| || || |  || || ||||| || || || || ||||| |
gtgaatacaaagtagatattcatttatgatttatagtcctgctcactttgaacattggtacctttaacaaaagctagagtttgcattctacttttct--ttcagTTGGATGATGTAATTGATCTAGTGATTCCAAGAGGCAGCAACAAACTTGTCACTCAGATCAAGAGTTCCACTAAAATTCCTGTCCTGGGTCATGCAG

upper sequence: AT3G55610.2 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: Vv13s0019g02360.t01 (Vitis vinifera), 3'ss of exon 12
-----------------gtaagcagatagatacatatgaatggcaagtccccagaagtgattagcttttttcacttatactggaacccaccatttacatttt-tggtacagCTTGATGACGTTATTGATCTTGTGATCCCAAGAGGCAGCAACAAGCTTGTTTCTCAAATAAAAAACTCGACGAAAATCCCAGTGCTAGGCCATGCTG
                 | | |   || ||||  ||  ||        |      | || |     |     |   ||  |   || ||  ||||   |||| || | ||||||||||| || || || ||||| ||||||||||||||||| || |||||||||||||||||  | || || ||||| || || || ||||||||||
gtgagctgatgtgctgagaatgatcattgatagttaaaaacatttgaactttcagaatggt-gatatgaaaaatggatgttcacactcagtatttttgttttgtgctccagCTTGATGATGTGATCGACCTTGTAATCCCAAGAGGCAGCAATAAACTTGTTTCTCAAATAAAGGATTCAACAAAAATTCCTGTTCTGGGCCATGCTG

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|86042495|gb|DR338250.1|DR338250
EST:     AACTCATAGGACTTGTGACCTCAAGAGAGGAGATTCCTGATTTGCTCAAG                         CTTGATGACGTTATTGATCTTGTGATCCCAAGAGGCAGCAACAAGCTTGTT
genomic: AACTCATAGGACTTGTGACCTCAAGAGAGGAGATTCCTGATTTGCTCAAGgtaagcagat ... tttggtacagCTTGATGACGTTATTGATCTTGTGATCCCAAGAGGCAGCAACAAGCTTGTT
EST: gi|86042492|gb|DR338247.1|DR338247
EST:     AACTCATAGGACTTGTGACCTCAAGAGAGGAGATTCCTGATTTGCTCAAG                         CTTGATGACGTTATTGATCTTGTGATCCCAAGAGGCAGCAACAAGGCTTGT
genomic: AACTCATAGGACTTGTGACCTCAAGAGAGGAGATTCCTGATTTGCTCAAGgtaagcagat ... tttggtacagCTTGATGACGTTATTGATCTTGTGATCCCAAGAGGCAGCAACAAG-CTTGT
EST: gi|86042493|gb|DR338248.1|DR338248
EST:     AACTCATAGGACTTGTGACCTCAAGAGAGGAGATTCCTGATTTGCTCAAG                         CTTGATGACGTTATTGATCTTGTGATCCCAAGAGGCAGCAACAAGCTTGTT
genomic: AACTCATAGGACTTGTGACCTCAAGAGAGGAGATTCCTGATTTGCTCAAGgtaagcagat ... tttggtacagCTTGATGACGTTATTGATCTTGTGATCCCAAGAGGCAGCAACAAGCTTGTT
EST: gi|124970824|gb|EL044633.1|EL044633
EST:     ACTCATAGGACTTGTGACCTCAAGAGAGGAGATTCCTGATTTAGCTCAAG                         CTTGATGACGTTATTG
genomic: ACTCATAGGACTTGTGACCTCAAGAGAGGAGATTCCTGATTT-GCTCAAGgtaagcagat ... tttggtacagCTTGATGACGTTATTG
EST: gi|86042496|gb|DR338251.1|DR338251
EST:     AACTCATAGGACTTGTGACCTCAAGAGAGGAGATTCCTGATTTGCTCAAG                         CTTGATGACGTTATTGATCTTGTGATCCCAAGAGGCAGCAACAAGCTTGTT
genomic: AACTCATAGGACTTGTGACCTCAAGAGAGGAGATTCCTGATTTGCTCAAGgtaagcagat ... tttggtacagCTTGATGACGTTATTGATCTTGTGATCCCAAGAGGCAGCAACAAGCTTGTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agtgattagcttttttcacttatactggaacccaccatttacatttttggtacagCTTGATGACGTTATTGATCTTGTGATCCCAAGAGGCAGCAACAAGCTTGTTTCTCAAATAAAAAACTCGACGAAAATCCCAGTGCTAGGCCATGCTG
                                         cattttt  CT-rich tract
          ttttttcacttata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagcagatagatacatatgaatggcaagtccccagaagtgattagcttttttcacttatactggaacccaccatttacatttttggtacagCTTGATGACGTTATTGATCTTGTGATCCCAAGAGGCAGCAACAAGCTTGTTTCTCAAATAAAAAACTCGACGAAAATCCCAGTGCTAGGCCATGCTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG