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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATCTCGGCTTGTTGTGAATCAAAACAAAAAGAACCTCTTGGAAAACTGGTTGGCAGAGGATAAGTTAGAATGCAGTGAAGAACTCGGAGACCTTGTCAAAgtaatcttaaaatgaccattttcatttaaagtgtctcctatgggcttctttagtatgctgtaacggtaatattttctgattcag

Basic information

species Arabidopsis thaliana
transcript AT3G11130.1
intron # 12
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G11130.1 (Arabidopsis thaliana), 5'ss of exon 12
lower sequence: LOC_Os11g01380.1 (Oryza sativa), 5'ss of exon 12
ATCTCGGCTTGTTGTGAATCAAAACAAAAAGAACCTCTTGGAAAACTGGTTGGCAGAGGATAAGTTAGAATGCAGTGAAGAACTCGGAGACCTTGTCAAAgtaa------tcttaaaatgaccat---tttcatttaaagtgtctcctatgggcttctttagtatgctgtaacggtaatattttctgattcag--------------------
|||||| |||||||| ||||| |||||||||||||| ||||||||||||||||| || || || || || |||||||||||||| ||||| |||||||| ||||      | ||||  ||    |   || ||  ||  |  | |  ||     |    |  |   ||||  | | | | ||   | ||| |                     
ATCTCGACTTGTTGTCAATCAGAACAAAAAGAACCTTTTGGAAAACTGGTTGGCTGAAGACAAATTGGAGTGCAGTGAAGAACTTGGAGATCTTGTCAAGgtaaaatgggtgttaagttgtttgttgattgcacatatcgattttgttacactgtgtcctgtttgactgt--ctggattgttcattaattgatacctgcactctttggtgtag

upper sequence: AT3G11130.1 (Arabidopsis thaliana), 5'ss of exon 12
lower sequence: LOC_Os12g01390.1 (Oryza sativa), 5'ss of exon 12
ATCTCGGCTTGTTGTGAATCAAAACAAAAAGAACCTCTTGGAAAACTGGTTGGCAGAGGATAAGTTAGAATGCAGTGAAGAACTCGGAGACCTTGTCAAAgtaa------tcttaaaatgaccat---tttcatttaaagtgtctcctatgggcttctttagtatgctgtaacggtaatattttctgattcag--------------------
|||||| |||||||| ||||| |||||||||||||| ||||||||||||||||| || || || || || |||||||||||||| ||||| |||||||| ||||      ||||||  ||    |   || ||  ||  |  | |  ||     |    |  |   ||||  | | | | ||   | ||| |                     
ATCTCGACTTGTTGTCAATCAGAACAAAAAGAACCTTTTGGAAAACTGGTTGGCTGAAGACAAATTGGAGTGCAGTGAAGAACTTGGAGATCTTGTCAAGgtaaaatgggtcttaagttgtttgttgattgcacatatcgattttgttacactgtgtcctgtttgactgt--ctggattgttcattaattgatacctgcactctttggtgtag

upper sequence: AT3G11130.1 (Arabidopsis thaliana), 5'ss of exon 12
lower sequence: GRMZM2G057576_T02 (Zea mays), 5'ss of exon 10
ATCTCGGCTTGTTGTGAATCAAAACAAAAAGAACCTCTTGGAAAACTGGTTGGCAGAGGATAAGTTAGAATGCAGTGAAGAACTCGGAGACCTTGTCAAAgtaa------tcttaaaatgaccattttcattt-aaagtgtctcct---atgggcttctttagtatgctgtaacggtaatattttctgattcag------------
|||||| |||||||| ||||| ||||||||||||||  |||||||||||||||| || || ||  | || |||||||||||||| ||||| |||||||| ||||      || ||   ||    | || |||| |  || | |  |   ||    ||  || || |    || || ||||  |||||  | |              
ATCTCGACTTGTTGTCAATCAGAACAAAAAGAACCTTCTGGAAAACTGGTTGGCTGAAGACAAACTGGAGTGCAGTGAAGAACTAGGAGATCTTGTCAAGgtaagatgggtcctatgctgtttttattgattttactgtattttgttaaattacatttatttgtcttggttatcgctaatcatttcttgtaccctttgatgtatag

upper sequence: AT3G11130.1 (Arabidopsis thaliana), 5'ss of exon 12
lower sequence: GLYMA02G42560.1 (Glycine max), 5'ss of exon 12
ATCTCGGCTTGTTGTGAATCAAAACAAAAAGAACCTCTTGGAAAACTGGTTGGCAGAGGATAAGTTAGAATGCAGTGAAGAACTCGGAGACCTTGTCAAAgtaa-----tcttaaaat---gaccattttcat-ttaaagtgtctcctatgggcttctttagtatgctgtaacggtaatattttct----gattcag-----------------------------------------------------------------------------
 || ||| | |||||||| || ||||| || || || |||||||| |||||||||||||| ||| | ||||||||||| || || ||||| || || || ||         |||||||   ||  | ||  || |||   |||    |||    ||  || |||  || |     ||||  | ||      ||  ||                                                                             
GTCACGGTTGGTTGTGAACCAGAACAAGAAAAATCTGTTGGAAAATTGGTTGGCAGAGGACAAGCTTGAATGCAGTGAGGAGCTAGGAGATCTCGTTAAGgttgggttgcattaaaattttgaaaaattcaatattattttgttatttataactttgctt-gtactctatctttctaattgtctcccaaaaatataggggtactgattctcatctagcctgtttattgtgaaatgttgtattctattaatttttacaagcatgctcccttgtag

upper sequence: AT3G11130.1 (Arabidopsis thaliana), 5'ss of exon 12
lower sequence: GLYMA11G35460.1 (Glycine max), 5'ss of exon 12
ATCTCGGCTTGTTGTGAATCAAAACAAAAAGAACCTCTTGGAAAACTGGTTGGCAGAGGATAAGTTAGAATGCAGTGAAGAACTCGGAGACCTTGTCAAAgtaatcttaaaatgaccattttcatttaaagtgtctcctatgg-------gcttctttagtatgct------gtaacggta-atattttctgattcag--------------------
 || ||||| |||||||| || ||||| || || || ||||| || |||||||||||||| ||| | ||||||||||| || || ||||| ||||| || ||    ||  | | |  |||||  |||    |  ||  ||          |||| || | | ||||      | || |||| || | |  | |||                       
GTCACGGCTGGTTGTGAACCAGAACAAGAAAAATCTTTTGGAGAATTGGTTGGCAGAGGACAAGCTTGAATGCAGTGAGGAGCTAGGAGATCTTGTAAAGgttgggttgcatttataattttgcttttgtttacctaatagtatactactgcttgttgaatttgcttattatgaaatggtatatttgtgttaatttttattaatatgttccattgtag

upper sequence: AT3G11130.1 (Arabidopsis thaliana), 5'ss of exon 12
lower sequence: GLYMA14G06340.2 (Glycine max), 5'ss of exon 12
ATCTCGGCTTGTTGTGAATCAAAACAAAAAGAACCTCTTGGAAAACTGGTTGGCAGAGGATAAGTTAGAATGCAGTGAAGAACTCGGAGACCTTGTCAAAgtaatcttaaaatgaccattttcatttaaagtgtc-tcctatgggcttctttagtatgctgtaacggtaatattttctgattcag---------------------------------------------------------------------------
||| ||| | |||||||| || ||||| || || || |||||||| |||||||||||||| ||| | ||||||||||| || || ||||| || || || ||    ||  | | |   ||   |  |  | | |  | || |    |       | | || || |  |   ||| ||||    |                                                                            
ATCACGGTTGGTTGTGAACCAGAACAAGAAAAATCTGTTGGAAAATTGGTTGGCAGAGGACAAGCTTGAATGCAGTGAGGAGCTAGGAGATCTCGTTAAGgttgggttgcattaaaatttgaaaaattcaatattattctgttatttataactttgtactctatctttctaattgtctgccaaaaatagggtactgattctcatctaacctgtttattgtgaaatgttgtattaacttttacaagcatgctcccttgtag

upper sequence: AT3G11130.1 (Arabidopsis thaliana), 5'ss of exon 12
lower sequence: GLYMA18G02960.1 (Glycine max), 5'ss of exon 12
ATCTCGGCTTGTTGTGAATCAAAACAAAAAGAACCTCTTGGAAAACTGGTTGGCAGAGGATAAGTTAGAATGCAGTGAAGAACTCGGAGACCTTGTCAAAgtaatcttaaaatgaccattttca-----tttaaagtgtctcctatgggcttc---tttagtatgctgtaacggtaatattttctgattcag------------------------------------------------------------------------
 ||  |||| |||||||| || ||||| || || || ||||| || |||||||| ||||||||| | ||||||||||| || || ||||| ||||| || ||    ||  | |    ||||| |     | |||| ||     | |    ||    |||  |    | |||  ||  ||  |  |  |  |                                                                         
GTCAAGGCTGGTTGTGAACCAGAACAAGAAAAATCTTTTGGAGAATTGGTTGGCGGAGGATAAGCTTGAATGCAGTGAGGAGCTAGGAGATCTTGTAAAGgttgggttgcatttgaaattttgaaaaactctaaactgatctgtttattttttgcgtttgtttctttctaattgtt-tacctaatagtataatactgcttgttgaatttgcttattatgaaatggtatatttgtgttaattttgattaatatgttccattgtag

upper sequence: AT3G11130.1 (Arabidopsis thaliana), 5'ss of exon 12
lower sequence: Vv13s0067g01290.t01 (Vitis vinifera), 5'ss of exon 12
ATCTCGGCTTGTTGTGAATCAAAACAAAAAGAACCTCTTGGAAAACTGGTTGGCAGAGGATAAGTTAGAATGCAGTGAAGAACTCGGAGACCTTGTCAAAgt----aat----cttaaaatgaccatttt-----catttaaagtgtctcctatgggctt-----ctttagtatgctgtaacggtaatatttt-ctgattcag-------------------------------------------------------
||| || || ||||||||||| ||||| ||||| || ||||| || ||||| |||||||| ||| | || |||||||| ||||| || || || || || ||    |||     |  | ||||  |||||     || ||||      || | | ||  |      || ||| |  | ||    |  |||  | || ||| |                                                        
ATCACGCCTGGTTGTGAATCAGAACAAGAAGAATCTTTTGGAGAATTGGTTAGCAGAGGACAAGCTGGAGTGCAGTGAGGAACTTGGGGATCTAGTGAAGgtttgaaatgcaattggagatgattattttttgtccacttaagacaattcttgttgggatgctaatttgagtttattttattatttttatcctgctaatttaaatgatttttttttttaaatataattttgacattgaaaaccatgttttttttgtag

upper sequence: AT3G11130.1 (Arabidopsis thaliana), 5'ss of exon 12
lower sequence: PP1S452_30V6.1 (Physcomitrella patens), 5'ss of exon 13
ATCTCGGCTTGTTGTGAATCAAAACAAAAAGAACCTCTTGGAAAACTGGTTGGCAGAGGATAAGTTAGAATGCAGTGAAGAACTCGGAGACCTTGTCAAAgt--aatcttaaaa------tgaccatt---ttcatttaaagtgtctcctatgggcttctttagtatgctgtaacggtaatattttctgattcag-----
 || ||| | ||||| ||||||||||| ||||||||  | || ||||||||||| || || ||  | || |||||||||||||||||||| |||||||| ||   || ||  |       ||| || |   |   | || |    ||  | |   |||      |||     |  | |   |   ||||| ||       
TTCCCGGTTGGTTGTTAATCAAAACAAGAAGAACCTACTTGAGAACTGGTTGGCGGAAGACAAACTCGAGTGCAGTGAAGAACTCGGAGATCTTGTCAAGgtctgatattgtatgcttattgagcagtgcatcagtctagatctactatttttcacttaagagctattgcaaatggatgtcaaggtctgagtctagctga

upper sequence: AT3G11130.1 (Arabidopsis thaliana), 5'ss of exon 12
lower sequence: EFJ13237 (Selaginella moellendorffii), 5'ss of exon 12
ATCTCGGCTTGTTGTGAATCAAAACAAAAAGAACCTCTTGGAAAACTGGTTGGCAGAGGATAAGTTAGAATGCAGTGAAGAACTCGGAGACCTTGTCAAAgtaatcttaaaatgaccattttcatttaaagtgtctcctatgggcttctttagtatgctgtaacggtaatattttctgattcag
 || || || ||||| | ||||||||| || ||||| |||||||| |||||||| || |||||  | || |||||||||||||| || || |||||||| ||   || || |  | | || | | |||   |    |  |  |  || | | | |                             
TTCACGTCTCGTTGTCACTCAAAACAAGAAAAACCTTTTGGAAAATTGGTTGGCTGATGATAAACTCGAGTGCAGTGAAGAACTTGGTGATCTTGTCAAGgt---ctgaacaacatcgttcttagttacc-tactcctgaccgttttttgttgcag----------------------------

upper sequence: AT3G11130.1 (Arabidopsis thaliana), 5'ss of exon 12
lower sequence: EFJ24508 (Selaginella moellendorffii), 5'ss of exon 12
ATCTCGGCTTGTTGTGAATCAAAACAAAAAGAACCTCTTGGAAAACTGGTTGGCAGAGGATAAGTTAGAATGCAGTGAAGAACTCGGAGACCTTGTCAAAgtaatcttaaaatgaccattttcatttaaagtgtctcctatgggcttctttagtatgctgtaacggtaatattttctgattcag
 || || || ||||| | ||||||||| || ||||| ||||| || |||||||| || |||||  | || |||||||||||||| || || |||||||| ||   || || |  | | || | | |||   |    |  |  |  || | | | |                             
TTCACGTCTCGTTGTCACTCAAAACAAGAAAAACCTTTTGGAGAATTGGTTGGCTGATGATAAACTCGAGTGCAGTGAAGAACTTGGTGATCTTGTCAAGgt---ctgaacaacatcgttcttagttacc-tactcctgaccgttttttgttgcag----------------------------

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATCTCGGCTTGTTGTGAATCAAAACAAAAAGAACCTCTTGGAAAACTGGTTGGCAGAGGATAAGTTAGAATGCAGTGAAGAACTCGGAGACCTTGTCAAAgtaatcttaaaatgaccattttcatttaaagtgtctcctatgggcttctttagtatgctgtaacggtaatattttctgattcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAC