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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATGGGTGAGGAATATTGTTGTGCCAAGCTTCACTTGGTAGATCTTGCTGGATCTGAAAGAGCTAAACGAACAGGTTCAGGCGGTGTTCGATTAAAAGAAGgttggaaaaactaagcatcctatttttaatcctcttgagaacgttaactgacattcttctttcttctctgaaacag

Basic information

species Arabidopsis thaliana
transcript AT3G50240.1
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G50240.1 (Arabidopsis thaliana), 5'ss of exon 5
lower sequence: LOC_Os09g02650.1 (Oryza sativa), 5'ss of exon 5
ATGGGTGAGGAATATTGTTGTGCCAAGCTTCACTTGGTAGATCTTGCTGGATCTGAAAGAGCTAAACGAACAGGTTCAGGCGGTGTTCGATTAAAAGAAGgttggaaaaactaagcatcctatttttaatcctcttgagaacgttaactgacattcttctttcttctctgaaacag--------------------------------------
|||  ||| || |||   |||||||| || ||||| ||||||||||||||||| ||| | |||||| |||| ||||| |  ||  |||| || || ||||||       |||  ||||  |  || |  ||    |||   | | | |  |||| | ||||   |   |||||||                                       
ATGAATGAAGACTATCTCTGTGCCAAACTCCACTTAGTAGATCTTGCTGGATCAGAACGTGCTAAAAGAACTGGTTCTGATGGCCTTCGGTTTAAGGAAGgt-------acttggcatgttgcttgt--tctatctgaatccctaatcaaacatccatcttgtct---tgaaacaagatactccgtataatttatttatgtatcatgtcatcag

upper sequence: AT3G50240.1 (Arabidopsis thaliana), 5'ss of exon 5
lower sequence: GRMZM2G026218_T02 (Zea mays), 5'ss of exon 5
ATGGGTGAGGAATATTGTTGTGCCAAGCTTCACTTGGTAGATCTTGCTGGATCTGAAAGAGCTAAACGAACAGGTTCAGGCGGTGTTCGATTAAAAGAAGgt-----------tggaaaaactaagcatcctatttttaatcctcttgagaacgttaactgacattcttctttcttctctgaaacag---
|||  ||| || |||   |||||||| || ||||| ||||||||||||||||| ||| | |||||  |||| |||||||  ||  | || || || ||||||           | |     | || |  | ||   |   |  |  |    | |  || | | |  ||  ||| | ||  |  |||    
ATGAATGAAGACTATCTCTGTGCCAAACTACACTTAGTAGATCTTGCTGGATCAGAACGGGCTAAGAGAACTGGTTCAGATGGCCTGCGCTTCAAGGAAGgtatgcttgcttcttgtctgtccaaac-ccttagcctatgtatttatttctatgccaaattaaaggctattttatacttcgtgacattag

upper sequence: AT3G50240.1 (Arabidopsis thaliana), 5'ss of exon 5
lower sequence: GLYMA05G15750.1 (Glycine max), 5'ss of exon 5
ATGGGTGAGGAATATTGTTGTGCCAAGCTTCACTTGGTAGATCTTGCTGGATCTGAAAGAGCTAAACGAACAGGTTCAGGCGGTGTTCGATTAAAAGAAGgttggaaaaac-taagcatcctatttttaatcctcttgagaacgttaactgacattcttc--tttcttctctgaaacag---------------------------------------------------------
|||||||| |||||   ||  || ||||| || ||||||||||| |||||||||||| |||||||| |||||||||| |  |||||||| || |||||||||||| ||  | | |  | | |   | ||||  |  ||| |  ||  |||    ||      |  | | || |||| |                                                          
ATGGGTGAAGAATACCTTTCAGCAAAGCTCCATTTGGTAGATCTAGCTGGATCTGAACGAGCTAAAAGAACAGGTTCTGATGGTGTTCGTTTGAAAGAAGgttggtaatgcatgattaacttgaatataatgataatgaca-tgtatacttttgtttcaaaataccatgtcagaaatactgtttaaataattgaaactgataatgacaaagatttaatgactttgttttataatag

upper sequence: AT3G50240.1 (Arabidopsis thaliana), 5'ss of exon 5
lower sequence: GLYMA17G18540.1 (Glycine max), 5'ss of exon 1
ATGGGTGAGGAATATTGTTGTGCCAAGCTTCACTTGGTAGATCTTGCTGGATCTGAAAGAGCTAAACGAACAGGTTCAGGCGGTGTTCGATTAAAAGAAGgttggaaaaac-taagcatcctatttttaatcctcttgagaacgttaactgacattcttctttctt---ctctgaaacag-----------------------------------------------
|||||||| |||||   ||  || ||||| || ||||||||||| |||||||||||| |||||||| |||||||||| |  |||||||| || ||||||||| || || || | |  | | |   |  |||  | |  | |   ||   | | | |  | | ||     | |||   ||                                                
ATGGGTGAAGAATACCTTTCAGCAAAGCTCCATTTGGTAGATCTAGCTGGATCTGAACGAGCTAAAAGAACAGGTTCTGATGGTGTTCGTTTGAAAGAAGgtcggtaatacatgattaacttgaatacaatgatatgtatacttttgtttcaaaatactgtgtcagaaacgctgtttcaataattgaaaatgataatggcaaggatttaatgacttttttttaatag

upper sequence: AT3G50240.1 (Arabidopsis thaliana), 5'ss of exon 5
lower sequence: Vv07s0031g00130.t01 (Vitis vinifera), 5'ss of exon 5
ATGGGTGAGGAATATTGTTGTGCCAAGCTTCACTTGGTAGATCTTGCTGGATCTGAAAGAGCTAAACGAACAGGTTCAGGCGGTGTTCGATTAAAAGAAGgttggaaaaactaagcatcctatttttaatcctcttgagaacgttaactgacattcttctttcttctctgaaacag-----------------------------
||||||||||| ||||   |||| |||||||| |||||||||||||||||||||||| |||||||| |||||||||| |  ||  |||| || |||||||||  | |  | ||     | | || |     ||||| |     ||  |   ||||||| ||     | | ||  |                              
ATGGGTGAGGAGTATTTAAGTGCAAAGCTTCATTTGGTAGATCTTGCTGGATCTGAACGAGCTAAAAGAACAGGTTCTGATGGCCTTCGTTTCAAAGAAGgtaagtagtagtataagccttcttat-----ctctttaatgaatt--ccatcattctttttgagcatataaatgatgaaaataagtttcccccctaatttttcag

upper sequence: AT3G50240.1 (Arabidopsis thaliana), 5'ss of exon 5
lower sequence: PP1S80_21V6.1 (Physcomitrella patens), 5'ss of exon 5
ATG-GGTGAGGAATATTGTTGTGCCAAGCTTCACTTGGTAGATCTTGCTGGATCTGAAAGAGCTAAACGAACAGGTTCAGGCGGTGTTCGATTAAAAGAAGgttggaaaaactaagcatcctatttttaatc---ctcttgagaacgttaactgacattcttctttcttctctg-aaacag--------------------
 ||   |||||| ||||  ||||| ||||| |||||||| ||||| || ||||| ||||| ||||||||||| ||  |||  ||  | ||||| |||||||||     ||  ||    |    ||| || ||   |  ||      | |   |||   |||   ||| | |||   ||||                     
-TGCAATGAGGATTATTTGTGTGCGAAGCTGCACTTGGTGGATCTAGCGGGATCAGAAAGGGCTAAACGAACTGGAGCAGATGGACTACGATTCAAAGAAGgtaatccaatttatttgttaattttctattcactcatttcctggagctgtttgatggtctgagttcctgtctttgaacatccacgtatatgaaactgatg

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATGGGTGAGGAATATTGTTGTGCCAAGCTTCACTTGGTAGATCTTGCTGGATCTGAAAGAGCTAAACGAACAGGTTCAGGCGGTGTTCGATTAAAAGAAGgttggaaaaactaagcatcctatttttaatcctcttgagaacgttaactgacattcttctttcttctctgaaacag

- - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG