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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTGTTATATATAGCAACAACAAGAAGCTATTATACAGCAACGTGAATCTGAAAGAAGTTAGTCATATGTGTCCCTTCAACTCTGCTGCTTTTCCAGACAGgtaaactatatttttcctctgttattttcctttgggatcaaagtacattgtggtgaaatctggctctacttctcttccattggcag

Basic information

species Arabidopsis thaliana
transcript AT4G21100.1
intron # 16
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT4G21100.1 (Arabidopsis thaliana), 5'ss of exon 16
lower sequence: GRMZM2G402002_T01 (Zea mays), 5'ss of exon 16
CTGTTATATATAGCAACAACAAGAAGCTATTATACAGCAACGTGAATCTGAAAGAAGTTAGTCATATGTGTCCCTTCAACTCTGCTGCTTTTCCAGACAGgtaaactatatttttcctctgttattttcctttgggatcaaagtacattgtggtgaaatctggctctacttct--cttccattggcag----------------
|||| || ||||||| ||| ||||||||  | |||||||| || ||| ||||||| |||| ||||||||| || |||||  | || ||||||||||||||||    | |    |  ||   || | || |  ||| || |       ||   ||     |||  | |||||     ||    ||  |                 
CTGTCATCTATAGCAGCAATAAGAAGCTTCTCTACAGCAATGTCAATTTGAAAGAGGTTAATCATATGTGCCCTTTCAATACAGCCGCTTTTCCAGACAGgt---ttgttccctctctagatt-tgttgcaatggaattacttagtctttgagtacctcctgtatgtacttgggaattgggatgatatatcaatttgtttgaat

upper sequence: AT4G21100.1 (Arabidopsis thaliana), 5'ss of exon 16
lower sequence: GRMZM2G430027_T01 (Zea mays), 5'ss of exon 4
CTGTTATATATAGCAACAACAAGAAGCTATTATACAGCAACGTGAATCTGAAAGAAGTTAGTCATATGTGTCCCTTCAACTCTGCTGCTTTTCCAGACAGgtaaactatatttttcctctgttattttcctttgggatcaaagt----acattgtggtgaaatctggctctacttctcttccattggcag--------------
|||| || ||||||| ||| ||||||||  | || ||||| || ||| ||||||| |||| ||||||||| || |||||  | || ||||||||||||||||    | |    |  ||   || || | |  ||| ||  ||||    |  ||   || || | |  |     |   ||   ||||| |               
CTGTCATCTATAGCAGCAATAAGAAGCTTCTCTATAGCAATGTAAATTTGAAAGAGGTTAATCATATGTGCCCTTTCAATACAGCCGCTTTTCCAGACAGgt---ttgttccctctctagatt-ttgtgcaatggaattgaagtcttcaactttgagtcaagtatctcctgtatgtactggaattgggattatgtatcaatttg

upper sequence: AT4G21100.1 (Arabidopsis thaliana), 5'ss of exon 16
lower sequence: GLYMA08G13680.1 (Glycine max), 5'ss of exon 16
CTGTTATATATAGCAACAACAAGAAGCTATTATACAGCAACGTGAATCTGAAAGAAGTTAGTCATATGTGTCCCTTCAACTCTGCTGCTTTTCCAGACAGgtaaactatatttttcctctgttattttcctttgggatcaaagtacattgtggtgaaatc--tggctctacttctcttccattggcag----------------------------------------------
|||| || ||||| |  ||||| ||  || | || || || ||||||||||| ||||| ||||| |||||||| ||||| |||||||||||||||||||||||   |    |||     | | | || |    |   |  |  ||     | |||   |   ||| |||  | |  ||  ||    |                                               
CTGTAATTTATAGTAGTAACAAAAAATTACTTTATAGTAATGTGAATCTGAAGGAAGTGAGTCACATGTGTCCTTTCAATTCTGCTGCTTTTCCAGACAGgtatcttggtctttgttagtttgacttactagagttgtttacatatccccttgtgctgttcttggatcttgtacaatttaatgtaaaatcttttactggtgatgacactcatctactgttaataactgaaacag

upper sequence: AT4G21100.1 (Arabidopsis thaliana), 5'ss of exon 16
lower sequence: GLYMA05G30530.1 (Glycine max), 5'ss of exon 16
CTGTTATATATAGCAACAACAAGAAGCTATTATACAGCAACGTGAATCTGAAAGAAGTTAGTCATATGTGTCCCTTCAACTCTGCTGCTTTTCCAGACAGgtaaactatatttttcctctgttattttcctttggg-atcaaagtacattgtggtgaaatc--tggctctacttctcttccattggcag----------------------------------------------
|||| || || || |  ||||| ||  || | || || || ||||||||||| ||||| ||||| |||||||| ||||| |||||||||||||||||||||||  |||| |  || ||   ||   || ||   |  ||  |  ||     | |||   |   ||| |||  | |  ||  ||    |                                               
CTGTGATTTACAGTAGTAACAAAAAATTACTTTATAGTAATGTGAATCTGAAGGAAGTGAGTCACATGTGTCCTTTCAATTCTGCTGCTTTTCCAGACAGgtat-ctatgtcattgctagtttgacttactagagttattgacatatccccttgtgctgttcttggatcttgtacaatttaatataaaatcctttactggtgatggtactcatctacttttaataacttaaacag

upper sequence: AT4G21100.1 (Arabidopsis thaliana), 5'ss of exon 16
lower sequence: GLYMA12G08330.1 (Glycine max), 5'ss of exon 3
CTGTTATATATAGCAACAACAAGAAGCTATTATACAGCAACGTGAATCTGAAAGAAGTTAGTCATATGTGTCCCTTCAACTCTGCTGCTTTTCCAGACAGgtaaactatatttttcctctgttattttcct---ttgggatcaaagtacattgtggtg-----aaatctggctctacttct--------cttccattggcag--------------------------------
|||| || ||||| |  ||||| ||  || | || || || ||||||||||| ||||| ||||| |||||||| ||||| |||||||||||||||||||||||   |    |||     | | | || |     |||    || |   | ||||| ||       |||| |  | | || |        |||  | |||                                   
CTGTAATTTATAGTAGTAACAAAAAATTACTTTATAGTAATGTGAATCTGAAGGAAGTGAGTCACATGTGTCCTTTCAATTCTGCTGCTTTTCCAGACAGgtatcttggtctttgttagtttgacttactagagttgtttacatatccccttgtgctgttcttggatcttgtacaatttattgtaaaatcttttactggtgatgacactcatctactgttaataactgaaacag

upper sequence: AT4G21100.1 (Arabidopsis thaliana), 5'ss of exon 16
lower sequence: Vv10s0003g04360.t01 (Vitis vinifera), 5'ss of exon 16
CTGTTATATATAGCAACAACAAGAAGCTATTATACAGCAACGTGAATCTGAAAGAAGTTAGTCATATGTGTCCCTTCAACTCTGCTGCTTTTCCAGACAGgtaaactatatt--tttcctctgttattttcctttgggat--------------caaagtacat-tgtggtgaaatctggctctacttctcttccattggcag
| || || || ||||  |||||||||||| | |||||||| || ||| |||||||||| || || ||||| || ||||| ||||||||||||||||| |||||   | |  |   ||    ||||  |||   ||    |              ||| |||    ||||     ||   |    | |||  ||||| ||    
CGGTGATTTACAGCAGTAACAAGAAGCTACTCTACAGCAATGTTAATTTGAAAGAAGTCAGCCACATGTGCCCTTTCAATTCTGCTGCTTTTCCAGATAGgtaccttttgctgcctttacttgttgcttttacttattgttctttactttcttccaacgtatgcatgtgaaatcatacagaaaaaattcatttccaatga---

upper sequence: AT4G21100.1 (Arabidopsis thaliana), 5'ss of exon 16
lower sequence: EFJ30457 (Selaginella moellendorffii), 5'ss of exon 16
CTGTTATATATAGCAACAACAAGAAGCTATTATACAGCAACGTGAATCTGAAAGAAGTTAGTCATATGTGTCCCTTCAACTCTGCTGCTTTTCCAGACAGgtaaacta-tatttttcctctgttattttcctttgggatcaaagtacattgtggtgaaatctggctctacttctcttccattggcag
| || || || || | ||||||||||||  | |||||||||||||||||||| || || | |||||||||||| |||||||||||  ||||||| |||||||    |  || || || | ||| |  |   ||    | |||  |    | ||  | |||| |                        
CGGTCATTTACAGTAGCAACAAGAAGCTGCTTTACAGCAACGTGAATCTGAAGGAGGTGAATCATATGTGTCCTTTCAACTCTGCATCTTTTCCCGACAGgtctgtttctagttctcttttgtgagctctatt----aacaagcttttgtttgtcgtaatcag------------------------

upper sequence: AT4G21100.1 (Arabidopsis thaliana), 5'ss of exon 16
lower sequence: EFJ23079 (Selaginella moellendorffii), 5'ss of exon 16
CTGTTATATATAGCAACAACAAGAAGCTATTATACAGCAACGTGAATCTGAAAGAAGTTAGTCATATGTGTCCCTTCAACTCTGCTGCTTTTCCAGACAGgtaaacta-tatttttcctctgttattttcctttgggatcaaagtacattgtggtgaaatctggctctacttctcttccattggcag
| || || || || | ||||||||||||  | |||||||||||||||||||| || || | ||| |||||||| |||||||||||  ||||||| |||||||    |  || || || | ||| |  |   ||    | |||  |    | ||  | |||| |                        
CGGTCATTTACAGTAGCAACAAGAAGCTGCTTTACAGCAACGTGAATCTGAAGGAGGTGAATCACATGTGTCCTTTCAACTCTGCATCTTTTCCCGACAGgtctgtttctagttctcttttgtgagctctatt----aacaagcttttgtttgtcgtaatcag------------------------

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CTGTTATATATAGCAACAACAAGAAGCTATTATACAGCAACGTGAATCTGAAAGAAGTTAGTCATATGTGTCCCTTCAACTCTGCTGCTTTTCCAGACAGgtaaactatatttttcctctgttattttcctttgggatcaaagtacattgtggtgaaatctggctctacttctcttccattggcag

- - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGCT