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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTGAAGGGACTGGTTTGCTTCGTCTCCATAGTACGTACCGTCATGACCTTAAAATTTACAGCTCTGACGAGGGACGTGTTCAGgtacagatttacgcttttagtagtgaagatgagcatatgatattcaattgttgaacatatactgcaagctttactactcctcactgtttgcaccaaaatatgtgaaagagctcatcgcatagaaaaatgtaaactgatttgcactgttgacag

Basic information

species Arabidopsis thaliana
transcript AT3G01310.1
intron # 19
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G01310.1 (Arabidopsis thaliana), 5'ss of exon 19
lower sequence: GLYMA13G05060.1 (Glycine max), 5'ss of exon 20
GTGAAGGGACTGGTTTGCTTCGTCTCCATAGTACGTACCGTCATGACCTTAAAATTTACAGCTCTGACGAGGGACGTGTTCAGgtacag-----atttacgcttttagtagtga--agatgagcatatgatattca--attgttgaacatatact-gcaagctttactactcctcactgtttgcaccaaaatatgtgaaag-agctcatcgcatagaa--aaatgtaaactgatttg-cactgttgacag-------
| ||||| || ||  | ||||| ||||||||||| ||||||||||| || || |||||||||||||| ||||| ||||| ||||||  |     | ||  |||     || | |  ||| |   |  || | ||||  |||| |    | ||  |   |   |||   | |  |   ||| |   | |   | | | |    |  |  ||   | | |  | |||| | |   |||  ||      | |        
GAGAAGGTACAGGGCTTCTTCGCCTCCATAGTACATACCGTCATGATCTCAAGATTTACAGCTCTGATGAGGGTCGTGTGCAGgtatggcctaaagttgtgctcaccttaatcataagaaggctaagtggttttcattattggttgctacatttttatacattttggaagtgtttgatgtctaggc-attgtttataagcctaatttgtcctttggcatcatatgtgagccattttttcatgacccatattaaacag

upper sequence: AT3G01310.1 (Arabidopsis thaliana), 5'ss of exon 19
lower sequence: GLYMA19G02260.1 (Glycine max), 5'ss of exon 16
GTGAAGGGACTGGTTTGCTTCGTCTCCATAGTACGTACCGTCATGACCTTAAAATTTACAGCTCTGACGAGGGACGTGTTCAGgtacag----atttacgcttttagtagtgaagatgagcata--tgatattca--attgttgaacatatact-gcaagctttactactcctcactgtttgcaccaaaatatgtgaaag---agctcatcgcatagaa--aaatgtaaactgatttg--cactgttgacag-------
| ||||| || ||  | ||||| ||||||||||| ||||||||||| || || |||||||||||||| ||||| ||||| ||||||  |    | ||  |||     || | || |  ||  ||  || | ||||  |||| |    | ||  |   |   |||   | |  |   ||| |   | |  || | |  |||   |  |  ||   | | |  | |||| | |   |||   ||      |          
GAGAAGGTACAGGGCTTCTTCGCCTCCATAGTACATACCGTCATGATCTCAAGATTTACAGCTCTGATGAGGGTCGTGTGCAGgtatggcctaagttgtgctcaccttaataaaaaaaaggctaagtggttttcattattggttgctacatttttatacattttgtaagtgtttgatgtctaggc-agcatgtttataagcctaatttgtcctttggcatcatatgtgagccatttttttcatgacccatgctaaacag

upper sequence: AT3G01310.1 (Arabidopsis thaliana), 5'ss of exon 19
lower sequence: GLYMA09G37610.1 (Glycine max), 5'ss of exon 16
GTGAAGGGACTGGTTTGCTTCGTCTCCATAGTACGTACCGTCATGACCTTAAAATTTACAGCTCTGACGAGGGACGTGTTCAGgtacagatt---------tacgcttttagtagtgaagatgagcatatgatattc--aattgt--tgaacatatactgcaagctttactactcctcactgtttgcaccaaaatatgtgaaagagctcatcgcatagaaaaatgtaaactgatttgcactgttgacag-----------------------------
| ||||| || ||  ||||||| |||||||| || ||||||||||| ||||| || ||||||||||| ||||| ||||| ||||||  |  |         ||  |||   | | | || | ||      ||  | |  | | ||  ||||   | | |||   | ||  || |  | | | |||    | ||    | ||    | |  |  | | | | ||| |      | | |||   || |                                
GAGAAGGTACAGGGCTGCTTCGCCTCCATAGCACATACCGTCATGATCTTAAGATATACAGCTCTGATGAGGGTCGTGTGCAGgtatgggctatgtcatactaaccttcctgcaataaaaaggaagcctcgacttcctgagtggttttgaaagca-attgctccccttgttatt--taattatttatgtctaatgtcgagattatgttgctaacct-gcataatctgtcaaaaatagcatcatttatgaacaatttaatatttggtctctgttaacag

upper sequence: AT3G01310.1 (Arabidopsis thaliana), 5'ss of exon 19
lower sequence: GLYMA18G49000.1 (Glycine max), 5'ss of exon 18
GTGAAGGGACTGGTTTGCTTCGTCTCCATAGTACGTACCGTCATGACCTTAAAATTTACAGCTCTGACGAGGGACGTGTTCAGgtacagatt---------tacgcttttagtagtgaagatgagcatatgatattc--aattgttgaacatata-ctgcaagctttactactcctcactgtttgcaccaaaatatgtgaaagagctcatcgcatagaaaa---atgtaaactgatttgcactgttgacag-------------------------
| ||||| || ||  ||||||| |||||||| || ||||| ||||| ||||| || ||||||||||| ||||| ||||| ||||||  |  |         ||  |||   | | | || | ||     |||  | |  | | |||    |   |  ||    | ||  ||   || | | |||    | ||   || ||    | |  |  | | || ||    |  ||| | || |    | |  | |                          
GAGAAGGTACAGGGCTGCTTCGCCTCCATAGCACATACCGCCATGATCTTAAGATATACAGCTCTGATGAGGGTCGTGTGCAGgtatgggctatgttacactaaccttcctgcaatcaaaaggaatccttgacttcctgagtggttttgaaagcagttgttctccttgttat--ctaattatttatgtctaatattgagattatgttgctaacctggataatctgtcaaaaataatatcatttatgaagaattttatatttgatctgtgttaacag

upper sequence: AT3G01310.1 (Arabidopsis thaliana), 5'ss of exon 19
lower sequence: Vv14s0066g02540.t01 (Vitis vinifera), 5'ss of exon 18
GTGAAGGGACTGGTTTGCTTCGTCTCCATAGTACGTACCGTCATGACCTTAAAATTTACAGCTCTGACGAGGGACGTGTTCAGgtacagatttacgcttttagtagtgaagatgagcatatgatattcaattgttgaacatatactgcaagctttactactcctcactgtttgcaccaaaatatgtgaaagagctcatcgcatagaaaaatgtaaactgatttgcactgttgacag
||||||| |||||  ||||||| || |||||||| || |||||||| || |||||||||||||| || ||||| ||||| |||||||||  |||  | | |                  || ||  |   |||||  |  |   |  ||||| ||   | |   | | ||      || | | ||| |   | ||  ||                                     
GTGAAGGCACTGGCCTGCTTCGCCTTCATAGTACTTATCGTCATGATCTAAAAATTTACAGCTCAGATGAGGGTCGTGTACAGgtacagccttaatcatctg----------------cataatccttggttgtttcatctgccccccaagcctttggagtgtgc-cagtggaaggcatagt-tgttatcca-cttttcctg----------------------------------

upper sequence: AT3G01310.1 (Arabidopsis thaliana), 5'ss of exon 19
lower sequence: PP1S112_67V6.1 (Physcomitrella patens), 5'ss of exon 18
GTGAAGGGACTGGTTTGCTTCGTCTCCATAGTACGTACCGTCATGACCTTAAAATTTACAGCTCTGACGAGGGACGTGTTCAGgtacagatttacgcttttagtagtgaagatgagcatatgatattcaattgttgaacatatactgcaa-gctttactactcctcactgtttgcaccaaaatatgtgaaagagctcatcgcatagaaaaatgtaaactgatttgcactgttgacag
| || |||||||||||||| || ||||||||||| || || |||||| | ||||| ||||| || ||||| ||  | || ||||||   || | | |||  |  | |||  |   |   ||  | ||   ||       |  || ||||| ||  | | | |  |   | ||| |   |   |   |                                                  
GAGAGGGGACTGGTTTGCTGCGACTCCATAGTACTTATCGGCATGACTTGAAAATCTACAGTTCCGACGAAGGGAGGGTGCAGgta---atatcctcttcaaagattgacaacatggtcatagt-tttggttaacatgga-gtattgcaatgcacttcca-tatttgtttttttccttagggttcctag------------------------------------------------

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTGAAGGGACTGGTTTGCTTCGTCTCCATAGTACGTACCGTCATGACCTTAAAATTTACAGCTCTGACGAGGGACGTGTTCAGgtacagatttacgcttttagtagtgaagatgagcatatgatattcaattgttgaacatatactgcaagctttactactcctcactgtttgcaccaaaatatgtgaaagagctcatcgcatagaaaaatgtaaactgatttgcactgttgacag

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