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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATTGGAGGAGCAAGTGAGACAGAAGTTAGTGAAAAGAAAGATAGAGTAACGGATGCTCTAAATGCCACTAAAGCAGCCGTAGAGGAGGGTATTGTTCCAGgtataatctatcccaaatctaaaacaaaatttggttgaatcccttaagaaaattgcgtgagaagagaattatattactttgtgtgtattacag

Basic information

species Arabidopsis thaliana
transcript AT2G33210.1
intron # 13
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT2G33210.1 (Arabidopsis thaliana), 5'ss of exon 13
lower sequence: LOC_Os03g04970.1 (Oryza sativa), 5'ss of exon 14
ATTGGAGGAGCAAGTGAGACAGAAGTTAGTGAAAAGAAAGATAGAGTAACGGATGCTCTAAATGCCACTAAAGCAGCCGTAGAGGAGGGTATTGTTCCAGgtataatctatc-ccaaatctaaaacaaaatttg--gttgaatcccttaagaaaattgcgtgagaagagaattatattactttgtgtgtattacag
||||| ||||| |||||  | || ||| |||| ||||| |||||||| || ||||| |||||||| || ||||| || ||||||||||||||||| |||||||   | | ||  |    |||    |   | ||  ||| | |      || | ||  |    | |||| || ||||    || |   |     ||
ATTGGTGGAGCTAGTGAAGCGGAGGTTGGTGAGAAGAAGGATAGAGTGACTGATGCACTAAATGCTACCAAAGCTGCTGTAGAGGAGGGTATTGTACCAGgtactgtatgtcatcgctgctattttattttctgcagtttactattagcagcatatcaccattgcagagcatcatatctgattctaatttacgtag

upper sequence: AT2G33210.1 (Arabidopsis thaliana), 5'ss of exon 13
lower sequence: LOC_Os10g32550.1 (Oryza sativa), 5'ss of exon 14
ATTGGAGGAGCAAGTGAGACAGAAGTTAGTGAAAAGAAAGATAGAGTAACGGATGCTCTAAATGCCACTAAAGCAGCCGTAGAGGAGGGTATTGTTCCAGgtata-atctatcccaaatctaaaacaaaatttggttgaatcccttaagaaaattgcgtgagaag-----agaattatattactttgtgtgtat-tacag---------------------------
|| |||||||| |||||  | |||||| |||| ||||| |||||||| || |||||  | |||||||||||||| || || || ||||||||||| ||||||||  |  |   |||  ||   |      |||   |   |       | ||  | | ||   ||     |   ||  |||| | ||      | | | |                           
ATCGGAGGAGCCAGTGAAGCTGAAGTTGGTGAGAAGAAGGATAGAGTGACAGATGCATTGAATGCCACTAAAGCTGCTGTGGAAGAGGGTATTGTACCAGgtatgcagttgctccacttcagtagatttctttcaatatgttttccttgtaatgtacttgttcagtttgcatctttgcattattatgcccaagtatgctgacatgacatctttgcattacaatacag

upper sequence: AT2G33210.1 (Arabidopsis thaliana), 5'ss of exon 13
lower sequence: GRMZM2G111477_T02 (Zea mays), 5'ss of exon 2
ATTGGAGGAGCAAGTGAGACAGAAGTTAGTGAAAAGAAAGATAGAGTAACGGATGCTCTAAATGCCACTAAAGCAGCCGTAGAGGAGGGTATTGTTCCAGg-----tataatct----atcccaaatctaaaacaaaatttggttgaatcccttaagaaaattgcgtgagaagagaattatattac-tttgtgtgtattacag-
||||| ||||| || ||  |||||||| |||| ||||| |||||||| || ||||| || ||||| |||||||| || || || ||||||||||| |||||     ||| || |    ||   |  |  |    |   |   | ||| | ||||      ||| |    ||      |  | || | |  || ||  | | || 
ATTGGGGGAGCTAGCGAAGCAGAAGTTGGTGAGAAGAAGGATAGAGTGACAGATGCACTGAATGCTACTAAAGCTGCTGTTGAAGAGGGTATTGTACCAGgtaatgtatcatttgaatatttgatgttcacgggatgttcatgctgatttcctttgtgttattcctactgatc----tcctgttgcatcagtatgcctgatagt

upper sequence: AT2G33210.1 (Arabidopsis thaliana), 5'ss of exon 13
lower sequence: GRMZM2G111477_T01 (Zea mays), 5'ss of exon 2
ATTGGAGGAGCAAGTGAGACAGAAGTTAGTGAAAAGAAAGATAGAGTAACGGATGCTCTAAATGCCACTAAAGCAGCCGTAGAGGAGGGTATTGTTCCAGgta-----taatct----atcccaaatctaaaacaaaatttggttgaatcccttaagaaaattgcgtgagaagagaattatattac-tttgtgtgtattacag----------------------
||||| ||||| || ||  |||||||| |||| ||||| |||||||| || ||||| || ||||| |||||||| || || || ||||||||||| |||||||     | || |    ||   |  |  |    |   |   | ||| | ||||      ||| |    ||      |  | || | |  || ||  | | ||                      
ATTGGGGGAGCTAGCGAAGCAGAAGTTGGTGAGAAGAAGGATAGAGTGACAGATGCACTGAATGCTACTAAAGCTGCTGTTGAAGAGGGTATTGTACCAGgtaatgtatcatttgaatatttgatgttcacgggatgttcatgctgatttcctttgtgttattcctactgatc----tcctgttgcatcagtatgcctgatagtcatctttaattgtatatgcag

upper sequence: AT2G33210.1 (Arabidopsis thaliana), 5'ss of exon 13
lower sequence: GRMZM2G416120_T01 (Zea mays), 5'ss of exon 13
ATTGGAGGAGCAAGTGAGACAGAAGTTAGTGAAAAGAAAGATAGAGTAACGGATGCTCTAAATGCCACTAAAGCAGCCGTAGAGGAGGGTATTGTTCCAGgta-taatctatcccaaatctaaaacaaaa------tttggttgaatcccttaagaaaattgcgtgagaagaga---attatattact--ttgtgtgtattacag-------------------------------------------------------
||||||||||| || ||  |||||||| |||| ||||| |||||||| || ||||| || ||||| |||||||| || || || ||||| ||||| ||||||| |     |    |||| | |             |||      ||  | |  |  | ||||       ||      ||  || | |  ||||||   |||                                                          
ATTGGAGGAGCCAGCGAAGCAGAAGTTGGTGAGAAGAAGGATAGAGTGACAGATGCACTGAATGCTACTAAAGCTGCTGTTGAAGAGGGCATTGTACCAGgtaatgtatcaattaaaatttcatggggggggggtgtttatgctgatttcctgtgttatttgctcctactgattcctgttgcatcagtatttgtgttagttattcctgatttcctgttgcgtcagtatgcccgggagtcaatctttaattgtgtatgcag

upper sequence: AT2G33210.1 (Arabidopsis thaliana), 5'ss of exon 13
lower sequence: GLYMA10G33680.1 (Glycine max), 5'ss of exon 14
ATTGGAGGAGCAAGTGAGACAGAAGTTAGTGAAAAGAAAGATAGAGTAACGGATGCTCTAAATGCCACTAAAGCAGCCGTAGAGGAGGGTATTGTTCCAGgtataatctatcccaaatctaaaacaaaatttggttgaatcccttaagaaaattgcgtgagaagagaattatattactttgtgtgtattacag
||||||||||| |||||| | |||||| |||| ||||| |||||||| || |||||  ||||||| || || ||||| ||||||||||| || || ||||||| | | |   |     |      |   || | |  ||| |  |       ||   | | |   ||  | |  | |||||||          
ATTGGAGGAGCCAGTGAGGCTGAAGTTGGTGAGAAGAAGGATAGAGTGACAGATGCCTTAAATGCAACCAAGGCAGCTGTAGAGGAGGGCATAGTACCAGgtagattattagcactggcagttgtatgcttagttctaattctatgttg---ttcaatcaaatttgatgtgttgtgctttgtgcag-------

upper sequence: AT2G33210.1 (Arabidopsis thaliana), 5'ss of exon 13
lower sequence: GLYMA20G33910.1 (Glycine max), 5'ss of exon 14
ATTGGAGGAGCAAGTGAGACAGAAGTTAGTGAAAAGAAAGATAGAGTAACGGATGCTCTAAATGCCACTAAAGCAGCCGTAGAGGAGGGTATTGTTCCAGgtataatctatcccaaatctaaaacaaaatttggttgaatcccttaagaaaattgcgtgagaagagaattatattactttgtgtgtattacag
||||||||||| |||||| | |||||| |||| ||||| |||||||| || |||||  ||||||| || || ||||| ||||||||||| || || || |||| | | | |  ||  |  |     |   |  |||  |   ||  |     ||   | | |   ||  | |  | ||||| |          
ATTGGAGGAGCCAGTGAGGCTGAAGTTGGTGAGAAGAAGGATAGAGTGACAGATGCCTTAAATGCAACCAAGGCAGCTGTAGAGGAGGGCATAGTACCTGgtagattat-tagcacttgcagttgtatgctgagttctaattct--acgtcgttcaatcaaatttgatgtgttgtgctttgcgcag-------

upper sequence: AT2G33210.1 (Arabidopsis thaliana), 5'ss of exon 13
lower sequence: GLYMA20G19980.1 (Glycine max), 5'ss of exon 14
ATTGGAGGAGCAAGTGAGACAGAAGTTAGTGAAAAGAAAGATAGAGTAACGGATGCTCTAAATGCCACTAAAGCAGCCGTAGAGGAGGGTATTGTTCCAGgtataatctatcccaaatctaaaacaaaatttggttgaatcccttaagaaaattgcgtgagaagagaattatattactttgtgtgtattacag
||||||||||| |||||  | |||||| |||| ||||| |||||||| || |||||  ||||||| ||||| || || ||||||||||| || || || |||| ||| |    ||| ||||| |      ||   ||  |   || | ||  |    | |||   || ||  |||  ||   |   | |  ||
ATTGGAGGAGCCAGTGAAGCTGAAGTTGGTGAGAAGAAGGATAGAGTGACTGATGCATTAAATGCAACTAAGGCTGCTGTAGAGGAGGGCATAGTGCCTGgtaaaatat----caactctaacag-----ttcaatggttagttttacaatctcaaatcagatccgactttaatttgttctcgc--actgtag

upper sequence: AT2G33210.1 (Arabidopsis thaliana), 5'ss of exon 13
lower sequence: GLYMA10G25630.1 (Glycine max), 5'ss of exon 14
ATTGGAGGAGCAAGTGAGACAGAAGTTAGTGAAAAGAAAGATAGAGTAACGGATGCTCTAAATGCCACTAAAGCAGCCGTAGAGGAGGGTATTGTTCCAGgtataatctatcccaaatctaaaacaaaatttggttgaatcccttaagaaaattgcgtgagaagagaattatattactttgtgtgtattacag
||||||||||| |||||  | |||||| |||| ||||| |||||||| || |||||  ||||||| ||||| || || |||||||| || |||||  |||||| |||         ||| |    || | ||   ||  |   || | ||  |    | |||   ||  |||| |   || |  | ||| |||
ATTGGAGGAGCCAGTGAAGCTGAAGTTGGTGAGAAGAAGGATAGAGTGACAGATGCCTTAAATGCAACTAAGGCTGCTGTAGAGGAAGGCATTGTATCAGgtaaaat---------atcaatgctaatagttcaatggttagttttacaatctcaaatcagatccga-ctataatttgttct-cgcattgcag

upper sequence: AT2G33210.1 (Arabidopsis thaliana), 5'ss of exon 13
lower sequence: Vv05s0051g00340.t01 (Vitis vinifera), 5'ss of exon 14
ATTGGAGGAGCAAGTGAGACAGAAGTTAGTGAAAAGAAAGATAGAGTAACGGATGCTCTAAATGCCACTAAAGCAGCCGTAGAGGAGGGTATTGTTCCAGgtataatctatcccaaatctaaaacaaaatttggttgaatcccttaagaaaattgcgtgagaagagaattatattactttgtgtgtattacag
|| |||||||| |||||  | ||||||||||| ||||||||||| || || |||||||||||||| ||||| ||||| ||||| || || ||||| |||||||   | | |      | |  |       ||||||  |   || ||    | |   ||   | |   | |||  | ||| | |   || |||
ATAGGAGGAGCTAGTGAAGCTGAAGTTAGTGAGAAGAAAGATAGGGTTACAGATGCTCTAAATGCTACTAAGGCAGCTGTAGAAGAAGGAATTGTACCAGgtaagcttttt----ggtttgcattttcccttggtt--actactcaaccggagt---tggacaaatcttcataa-aatttatat---ttgcag

upper sequence: AT2G33210.1 (Arabidopsis thaliana), 5'ss of exon 13
lower sequence: PP1S52_245V6.1 (Physcomitrella patens), 5'ss of exon 14
ATTGGAGGAGCAAGTGAGACAGAAGTTAGTGAAAAGAAAGATAGAGTAACGGATGCTCTAAATGCCACTAAAGCAGCCGTAGAGGAGGGTATTGTTCCAGgtataatctatcccaaatctaaaacaaaatttg-gttg-aatcccttaagaaaattgcgtgagaagagaattata--ttactttgtgtgtattacag----
|| ||||||||||| ||    || || ||||||||||||||| | || || ||||| || ||||| |||||||| || || |||||||| ||||| || ||||| || | ||  |  | | ||     | ||| ||||  |||| |      | |||  |   ||     | | |  ||| |||       | |       
ATCGGAGGAGCAAGCGAAGTTGAGGTGAGTGAAAAGAAAGATCGTGTTACTGATGCACTGAATGCTACTAAAGCTGCTGTCGAGGAGGGGATTGTACCTGgtatgat-tgtcgaacttttgaattttgacttgcgttgtgatccttcgcatcagttgttttgaaatccgttaagaagttagtttaaaaacgtgatcaatat

upper sequence: AT2G33210.1 (Arabidopsis thaliana), 5'ss of exon 13
lower sequence: PP1S149_289V6.1 (Physcomitrella patens), 5'ss of exon 13
ATTGGAGGAGCAAGTGAGACAGAAGTTAGTGAAAAGAAAGATAGAGTAACGGATGCTCTAAATGCCACTAAAGCAGCCGTAGAGGAGGGTATTGTTCCAGgtat---------aatctatcccaaatctaaaaca-aaatttg-gttgaatcccttaagaaaattgcgtgagaagagaattatattactttgtgtgtattacag
|| |||||||| |||||    || || |  || ||||||||  | ||||| |||||  | || ||||||||||| || || ||||||||||||||||| |||||         |||| |       | | | |   |||  || || |  | | || |   | | || |   | ||    ||| ||| | | | || ||| |  
ATCGGAGGAGCTAGTGAAGTCGAGGTAAACGAGAAGAAAGACCGTGTAACTGATGCATTGAACGCCACTAAAGCTGCTGTTGAGGAGGGTATTGTTCCTGgtatgtccgacaaaatcaacgttttgtgtgatatgtaaacgtgtgtaggtttctttgaattagtggcatctcatgaatggtat-ttagtgtat-tggattgc--

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATTGGAGGAGCAAGTGAGACAGAAGTTAGTGAAAAGAAAGATAGAGTAACGGATGCTCTAAATGCCACTAAAGCAGCCGTAGAGGAGGGTATTGTTCCAGgtataatctatcccaaatctaaaacaaaatttggttgaatcccttaagaaaattgcgtgagaagagaattatattactttgtgtgtattacag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAG