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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AAGACCTATCACCAATTGGCTTTGGGCAGCCGGTTGTCACCCGTTTGGACCATTCTCAAACGTCTCCCTGATCAGTCAAATGCTTCAAGATGTTGCACTGgtgagtccaatcataatgatttctgaatagaaactagcattaaaatccttctgaatcttgtgagatatgatattttatatttgcag

Basic information

species Arabidopsis thaliana
transcript AT4G16180.2
intron # 12
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT4G16180.2 (Arabidopsis thaliana), 5'ss of exon 12
lower sequence: LOC_Os03g19690.1 (Oryza sativa), 5'ss of exon 12
AAGACCTATCACCAATTGGCTTTGGGCAGCCGGTTGTCACCCGTTTGGACCATTCTCAAACGTCTCCCTGATCAGTCAAATGCTTCAAGATGTTGCACTGgtgagtccaatcataatgattt---------ctgaatagaaactagcattaaaatccttctgaatcttgtga-gatatgatattttatatttgcag------
||||||| |    |||||| | ||||| || || || || || ||||||||||||||||||  |||   |||||||||||| ||||| ||||||||||||||  ||      || ||| |||         ||||| | |||  | ||||   || | || || |     |   ||   ||     | |  ||         
AAGACCTGTTGTGAATTGGTTGTGGGCTGCTGGATGCCATCCCTTTGGACCATTCTCAAACTCCTCTAAGATCAGTCAAATCCTTCAGGATGTTGCACTGgtatgttatccaatgatgcttttcctttctcctgaacataaa--aacatttttatgcatcagagtgagacgtcaatggaatgcacaaaacatgttcatgcat

upper sequence: AT4G16180.2 (Arabidopsis thaliana), 5'ss of exon 12
lower sequence: GRMZM2G135968_T01 (Zea mays), 5'ss of exon 12
AAGACCTATCACCAATTGGCTTTGGGCAGCCGGTTGTCACCCGTTTGGACCATTCTCAAACGTCTCCCTGATCAGTCAAATGCTTCAAGATGTTGCACTGgtgagtccaatcataatgatttctgaatagaaactagcattaaaatccttctgaatcttgtgagatatg---atattttatatttgcag-----------
||||| | |    || ||||| ||||| || || ||||| ||||||||||||||||| |||  ||| | |||||||||||| ||||| ||||| |||||||| |    |   | ||  |||| |  ||    |  |    || |||   |  | |    | |||  | |   ||  |  ||  |   |            
AAGACATGTAGTGAACTGGCTGTGGGCTGCAGGCTGTCATCCGTTTGGACCATTCTCGAACTCCTCACAGATCAGTCAAATTCTTCAGGATGTAGCACTGgtaatgttatcaacaacaatttttttatttctatgatatgtacaatgagtaggcagggagcgagggaggtcaatgctcaatgctcctatgtcgaagtgca

upper sequence: AT4G16180.2 (Arabidopsis thaliana), 5'ss of exon 12
lower sequence: GRMZM2G101893_T01 (Zea mays), 5'ss of exon 1
AAGACCTATCACCAATTGGCTTTGGGCAGCCGGTTGTCACCCGTTTGGACCATTCTCAAACGTCTCCCTGATCAGTCAAATGCTTCAAGATGTTGCACTGgtgagtccaatcataatgatttctgaatagaaactagcat-taaaatccttctgaatcttgtgagatatgatattttatatttgcag---------------
||||| | |    || ||||| ||||| || || ||||| ||||||||| ||||||  |||  ||||| |||||||||||| ||||| ||||| ||||| || |    |   | ||   ||| | | |   |  |   || || |||   |  | |    | |||  | |  | |     | ||  |               
AAGACATGTAGTGAAATGGCTGTGGGCTGCAGGCTGTCATCCGTTTGGAACATTCTTGAACTCCTCCCAGATCAGTCAAATTCTTCAGGATGTAGCACTAgtaatgttatcaacaacatttttttatttcta--tgatatgtacaatgagtaggcagggagagagggaggtcaatgctcctatgtcgaagtgcagcttaaag

upper sequence: AT4G16180.2 (Arabidopsis thaliana), 5'ss of exon 12
lower sequence: GLYMA07G36720.1 (Glycine max), 5'ss of exon 6
AAGACCTATCACCAATTGGCTTTGGGCAGCCGGTTGTCACCCGTTTGGACCATTCTCAAACGTCTCCCTGATCAGTCAAATGCTTCAAGATGTTGCACTGgtgagtccaatcataatgatttctgaatagaaactagcattaaaatccttctgaatcttgtgagatatgatattttatatttgcag
 || ||| |    |||||||||||||| || |||||||| || |||||||||||||| ||    || |  |||||||||||||| |||||||||||  |||||| | |  ||  ||| ||  |  ||     | |   ||| |   |     | || |    |   |   | || | | ||  |||
GAGGCCTGTTGTGAATTGGCTTTGGGCTGCTGGTTGTCATCCATTTGGACCATTCTCTAATACATCTCACATCAGTCAAATGCTCCAAGATGTTGCTTTGgtgaatgctctctcaat-atgccaaaacg---atttttattta--ccaagaggtatttctcaaatcagttttttgtttgttgacag

upper sequence: AT4G16180.2 (Arabidopsis thaliana), 5'ss of exon 12
lower sequence: GLYMA17G03880.1 (Glycine max), 5'ss of exon 6
AAGACCTATCACCAATTGGCTTTGGGCAGCCGGTTGTCACCCGTTTGGACCATTCTCAAACGTCTCCCTGATCAGTCAAATGCTTCAAGATGTTGCACTGgtgagtccaatcataatgatttctgaatagaaactagc-attaaaatccttctgaatcttgtgagatatgatattttatatttgcag
 || ||  |    |||||||||||||| || |||||||| || |||||||||||||| ||    || |  |||||||||||||| | |||||||||  |||||| | |  ||  ||| ||  |  |||      ||   |  || |       | || |    |   |   | || | | |   |||
GAGGCCCGTTGTGAATTGGCTTTGGGCTGCTGGTTGTCATCCATTTGGACCATTCTCTAATACATCTCACATCAGTCAAATGCTCCTAGATGTTGCTTTGgtgaatgctctctcaat-atgccaaaatgctttttatttaccaagag------gtatttctcaaatcagctttttgtttgtcgacag

upper sequence: AT4G16180.2 (Arabidopsis thaliana), 5'ss of exon 12
lower sequence: Vv05s0077g00820.t01 (Vitis vinifera), 5'ss of exon 12
AAGACCTATCACCAATTGGCTTTGGGCAGCCGGTTGTCACCCGTTTGGACCATTCTCAAACGTCTCCCTGATCAGTCAAATGCTTCAAGATGTTGCACTGgtgagtccaatcataatgatt-------tctgaatagaaact---agcattaaaatccttctgaatcttgt-gagatatgatattttatatttgcag---
|||||| |||   |||||||| ||| |||| |||||||| ||||||||||||||||| ||    |||| ||||||||||||||| || ||||||||  |||| | |||||| ||  |  ||       |||| ||| |||     |  || | ||||    | |   |  |  || ||  | |  | | |  |  |    
AAGACCGATCGTGAATTGGCTCTGGTCAGCTGGTTGTCATCCGTTTGGACCATTCTCCAATACTTCCCAGATCAGTCAAATGCTCCAGGATGTTGCCTTGgtaattccaatgatgttctttgcttaattctgcataaaaatattaaaaatgataatcaaggttagcttcattaaggtagcaaaagtcacaacttaaaagc

upper sequence: AT4G16180.2 (Arabidopsis thaliana), 5'ss of exon 12
lower sequence: Vv05s0077g00250.t01 (Vitis vinifera), 5'ss of exon 7
AAGACCTATCACCAATTGGCTTTGGGCAGCCGGTTGTCACCCGTTTGGACCATTCTCAAACGTCTCCCTGATCAGTCAAATGCTTCAAGATGTTGCACTGgtgagtccaatcataatgatttctgaat---------agaaactagcattaa-aatccttctgaatcttgt-gagatatgatattttatatttgcag---
|||| | |||   |||||||| ||| |||| |||||||| || |||||||||||||| ||    |||| ||| ||||||||||| || ||||||||  |||| | |||||| ||  |  ||||| |||         | | | ||  | | | ||||    | |   |  |  || ||  | |  | | |  |  |    
AAGATCGATCGTGAATTGGCTCTGGTCAGCTGGTTGTCATCCATTTGGACCATTCTCCAATACTTCCCAGATGAGTCAAATGCTCCAGGATGTTGCCTTGgtaattccaatgatgttcttttcttaattctgcataaaaatattaaaaatgataatcaaggttagcttcattaaggtagcaaaagtcacaacttaaaagc

Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|116426967|gb|EG469559.1|EG469559
EST:     CATTCTCAAACGTCTCCCTGATCAGTCAAATGCTTCAAGATGTTGCACTG                         AGGAATACTATTTATGCTCGGGTTGATTTTGCTCTACGCAAAATCCGTGAA
genomic: CATTCTCAAACGTCTCCCTGATCAGTCAAATGCTTCAAGATGTTGCACTGgtgagtccaa ... atatttgcagAGGAATACTATTTATGCTCGGGTTGATTCTGCTCTACGCAAAATCCGTGAA
EST: gi|116426969|gb|EG469561.1|EG469561
EST:     CATTTTCAAACGTCTCCCTGATCAGTCAAATGCTTCAAGATGTTGCACTG                         AGGAATACTATTTATGCTCGGGTTGATTCTGCTCTACGCAAAATCCGTGAA
genomic: CATTCTCAAACGTCTCCCTGATCAGTCAAATGCTTCAAGATGTTGCACTGgtgagtccaa ... atatttgcagAGGAATACTATTTATGCTCGGGTTGATTCTGCTCTACGCAAAATCCGTGAA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AAGACCTATCACCAATTGGCTTTGGGCAGCCGGTTGTCACCCGTTTGGACCATTCTCAAACGTCTCCCTGATCAGTCAAATGCTTCAAGATGTTGCACTGgtgagtccaatcataatgatttctgaatagaaactagcattaaaatccttctgaatcttgtgagatatgatattttatatttgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG