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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TATTCGTAGGCGTGCTCTTGATTTATTATATGGGATGTGTGATGTGTCAAATGCAAAGGATATAGTCGAAGAGTTGCTGCAGgtaagtctttgaccttactttatattaatatttcttgatttttagtctccttatgatttgtgaagtttaacagaaaggaaggattaagttgtgtagtgtttaagcttacatggaagctaaaaatatattgcag

Basic information

species Arabidopsis thaliana
transcript AT5G22770.1
intron # 11
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G22770.2 (Arabidopsis thaliana), 5'ss of exon 12
lower sequence: LOC_Os03g02150.2 (Oryza sativa), 5'ss of exon 11
TATTCGTAGGCGTGCTCTTGATTTATTATATGGGATGTGTGATGTGTCAAATGCAAAGGATATAGTCGAAGAGTTGCTGCAGgtaagt--ctttgaccttactttatattaat--atttcttgatttttagtctccttatgatttgtgaagt-ttaacagaaaggaaggattaagttgtgtagtgtttaagcttacatggaagctaaaaatatattgcag
|||| | ||||| ||||||||| | |||||||| |||||||||||  | ||||||||||| || ||||| |||||  ||||||||  |    ||||  |     | | | ||   |    |  | ||  |      ||  |   ||| |  | |  |    |      | |   ||| |||      ||||  ||  |   | ||     | | |  |||
TATTAGAAGGCGGGCTCTTGATCTGTTATATGGTATGTGTGATGTTACGAATGCAAAGGAAATTGTCGAGGAGTTATTGCAGgtatataatattgaaatagtggtctctcaaatgaaaaataaacttcgaaaaatattgaggcatgttatttgtcgatgtcatctgttggtcttgttatgtgaatcctaagactagttattatct-----tgtttctcag

upper sequence: AT5G22770.2 (Arabidopsis thaliana), 5'ss of exon 12
lower sequence: GRMZM2G137236_T01 (Zea mays), 5'ss of exon 12
TATTCGTAGGCGTGCTCTTGATTTATTATATGGGATGTGTGATGTGTCAAATGCAAAGGATATAGTCGAAGAGTTGCTGCAGgtaagtctttgaccttactttatattaatatttcttgatttttagtctccttatgatttgtgaagtttaacagaaaggaaggattaagttgtgtagtgtttaagcttacatggaagctaaaaatatattgcag
 ||| | ||  | |||||||||||||||||||| |||||||||||  |||| || ||||| || || || |||||| ||||||||| |  |                   | ||        | || | |  ||      ||| |   |||      | |                                                       
CATTAGGAGAAGGGCTCTTGATTTATTATATGGCATGTGTGATGTTACAAACGCGAAGGAAATTGTGGAGGAGTTGTTGCAGgtaactactcttttgaggggggggggggtcttaaccacactgtactattttttattcatgtcattcttactttctaag-------------------------------------------------------

upper sequence: AT5G22770.2 (Arabidopsis thaliana), 5'ss of exon 12
lower sequence: GRMZM2G700148_T01 (Zea mays), 5'ss of exon 11
TATTCGTAGGCGTGCTCTTGATTTATTATATGGGATGTGTGATGTGTCAAATGCAAAGGATATAGTCGAAGAGTTGCTGCAGgtaagtctttgaccttactttatattaatatttcttga--tttttagtctccttatgatttgtgaagtttaacagaaaggaaggattaagttgtgtagtgtttaagcttacatggaagctaaaaatatattgcag
 ||| |  || | |||||||||||||||||||| |||||||||||  |||| || || || || || || |||||| |||||||||    || | |||  | | | |   |       |    | |||  | |  |||  | |      || |    |         |  | |  || |   | |   ||||| |                      
CATTAGACGGAGGGCTCTTGATTTATTATATGGCATGTGTGATGTTACAAACGCGAAAGAAATTGTTGAGGAGTTGTTGCAGgtaa----ttaatctttgtgtgtgtgtgtggggggggggggtcttaaccgcactatactattgtttattcatgtcattcctgctttctaatattgaatcctcttttcttacctcag-------------------

upper sequence: AT5G22770.2 (Arabidopsis thaliana), 5'ss of exon 12
lower sequence: GLYMA17G05410.1 (Glycine max), 5'ss of exon 11
---TATTCGTAGGCGTGCTCTTGATTTATTATATGGGATGTGTGATGTGTCAAATGCAAAGGATATAGTCGAAGAGTTGCTGCAGgta---agtc---tttgaccttactt----tatattaatatttctt------gatttttagtctccttatgat-------ttgtgaagt--ttaacagaaaggaaggattaagttgtgtagtgtttaagcttacatggaagctaaaaatatattgcag-----------
   |||||| ||||||||||| |||||  | ||||| ||||||||||| |||||||||||||||||||| |||||  | |||||||||   ||     |  || || | |      || | || || || |       |    ||  | | |    |        |  || |    | |||| ||   |   | | |      || |   |      |||       ||       ||| ||            
CAGTATTCGGAGGCGTGCTCTAGATTTGCTTTATGGCATGTGTGATGTTTCAAATGCAAAGGATATAGTTGAAGAACTACTGCAGgtatagagctaggtccgaactaattcatgcaatttgaaaatctcattaaagtaaaccctacccccttcccaacagcaacctcatggaacaataaacaaaataaagaaaatgaaccagctattacctggatacacaaaatgattagtttgcaattccaacttttttgtag

upper sequence: AT5G22770.2 (Arabidopsis thaliana), 5'ss of exon 12
lower sequence: GLYMA12G30520.1 (Glycine max), 5'ss of exon 11
TATTCGTAGGCGTGCTCTTGATTTATTATATGGGATGTGTGATGTGTCAAATGCAAAGGATATAGTCGAAGAGTTGCTGCAGgtaag--tctttgaccttactttatattaatatttcttgattt--ttag-----------tctccttatga--------tttgtgaagt--ttaacagaaaggaaggattaagttgtgtagtgtttaagcttacatggaagctaaaaatatattgcag------------
|||||| ||||||||||| |||||  | ||||| |||||||| || |||||||||||||||||||| |||||  | ||||||||| |   ||  | ||  |||   |  | | ||||    || |  |||            |||||||   |         |  || |    | |||| ||   |   | | |      || |   |     ||||       ||      |||| ||             
TATTCGGAGGCGTGCTCTAGATTTGCTTTATGGCATGTGTGACGTTTCAAATGCAAAGGATATAGTTGAAGAACTACTGCAGgtatggagctaggtccaaactaattcatgaaatttgaaaatctcattaaagtaaaccgtatctccttcccaacagaaacctcatggaacaataaacaaaagaaagaaaatgaaccagctattacctgga--tacacaatgattagtttgctattccaactgtttttgtag

upper sequence: AT5G22770.2 (Arabidopsis thaliana), 5'ss of exon 12
lower sequence: Vv06s0061g01170.t01 (Vitis vinifera), 5'ss of exon 11
TATTCGTAGGCGTGCTCTTGATTTATTATATGGGATGTGTGATGTGTCAAATGCAAAGGATATAGTCGAAGAGTTGCTGCAGgta----agtctttga------ccttactttatattaatatttcttgatttttagtctccttatgatttgtgaa-gtttaac--agaaag----gaaggattaagttgtgtagtgtttaagcttacatggaa----gctaaaaatatattgcag--------
|||  | || || || |||||| |  | ||||| ||||||||| | |||||||||||||| || || ||||| || |||||||||    | | || ||         ||  ||   |||| |||          |  |||   |   |||| | || |||  ||  ||||||    | || | |   |  | | |||   ||    ||| || |     | |  || ||||  | |        
TATAAGGAGACGAGCACTTGATCTGCTTTATGGTATGTGTGATATTTCAAATGCAAAGGACATTGTTGAAGAATTACTGCAGgtacacaaatattggaagaaaatagtaacttggtttaaaattctcgatcaaatcttctatattcaattttttaatgttgcaccaagaaagtgcagtagaaatttttcatctggtgcaaaacaaaacaagggatcataccactaacatatgtctgtttttcag

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TATTCGTAGGCGTGCTCTTGATTTATTATATGGGATGTGTGATGTGTCAAATGCAAAGGATATAGTCGAAGAGTTGCTGCAGgtaagtctttgaccttactttatattaatatttcttgatttttagtctccttatgatttgtgaagtttaacagaaaggaaggattaagttgtgtagtgtttaagcttacatggaagctaaaaatatattgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG