Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGTGATTGTGCATAATAACGAGGTTGTCGCTAGCTGCCACAATATGGTTTTGAAATATACTGACCCAACTGCACATGCTGAAGTCACTGCCATTAGAGAGgtaagaaaagagtattacgcttgaatctcttgaaacgttgcaaaaaccggttttctgatgatgatttgaatccattgtgaatgtgcag

Basic information

species Arabidopsis thaliana
transcript AT5G28050.2
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G28050.2 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: LOC_Os07g14150.5 (Oryza sativa), 5'ss of exon 2
GGTGATTGTGCATAATAACGAGGTTGTCGCTAGCTGCCACAATATGGTTTTGAAATATACTGACCCAACTGCACATGCTGAAGTCACTGCCATTAGAGAGgtaagaaaagagtattacgcttgaat-ctcttgaaacgttgcaaaaaccggttttctgatgatgatttgaatccattgtgaatgtgcag-----------------------------------------------------------------
 ||  |||| | |||| | || || || |  |||||||| || |||||| ||||  ||||||| |||||||||||||||||||| ||||| || |||||||| | |        |||    | | | ||| | || | ||     |   |  | | || |     ||||   |  ||| |  |||  |                                                                  
AGTCGTTGTCCGTAATGATGAAGTAGTAGTCAGCTGCCATAACATGGTTCTGAAGCATACTGATCCAACTGCACATGCTGAAGTGACTGCAATAAGAGAGgtgaaatgctttatttatctgtcactgctcgtaaatcatttgttcatgagaatatgtg-tatccgtttgggccttttgcg--tgttaaacttcgaattgtttaccacaccattttcggatagctactcacattgtcgttctgttaaattttcag

upper sequence: AT5G28050.2 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: LOC_Os03g61810.1 (Oryza sativa), 5'ss of exon 3
GGTGATTGTGCATAATAACGAGGTTGTCGCTAGCTGCCACAATATGGTTTTGAAATATACTGACCCAACTGCACATGCTGAAGTCACTGCCATTAGAGAGgtaa---gaaaagagtattacgcttgaatctcttgaaacgttgcaaaaaccggttttctgatgatgatttgaatccattgtgaatgtgcag-----------
 ||  |||| | |||| | ||| | || | ||| ||||| || ||||||||| | || ||||| |||||||| ||||||||||| ||||| || ||||||||||   |    | ||| |  |  |  | |   |  |  ||    |         ||  | ||||  || | || | ||   | ||  |             
AGTTGTTGTCCGTAATGATGAGATAGTAGTTAGTTGCCATAACATGGTTTTGGATTACACTGATCCAACTGCGCATGCTGAAGTAACTGCAATAAGAGAGgtaacttgccctgtgtactgtggct--accagctacatggtgtttactctttacatttcgttgatacttagcattctttagtagtggcctcatctctgctga

upper sequence: AT5G28050.2 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: GRMZM2G082924_T01 (Zea mays), 5'ss of exon 3
GGTGATTGTGCATAATAACGAGGTTGTCGCTAGCTGCCACAATATGGTTTTGAAATATACTGACCCAACTGCACATGCTGAAGTCACTGCCATTAGAGAGgtaagaaa--agagtattacgcttgaatctcttgaaacgttgcaaaa--accggttttctgatgatgatttgaatccattgtgaatgtgcag------------------------------------------------
 ||  | || | |||| | || || || | ||||||||| || |||||| ||||  | |||||||| ||||| ||||||||||| ||||| |||||||||||||   |   ||    |||  ||     ||||   || | | ||||  | |  |  | | ||     |||| |  |  | |    ||  |                                                 
AGTTGTCGTCCGTAATGATGAAGTGGTTGTTAGCTGCCATAACATGGTTCTGAAGCACACTGACCCTACTGCGCATGCTGAAGTAACTGCAATTAGAGAGgtaaattacctgaaggctaccattagcagtctt---acttagtaaaattatcattactttaatctctttttgcaatctgtctagcagttaatttcattatttgatatgtgcttgatggtctctgtatgcccatattttag

upper sequence: AT5G28050.2 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: GRMZM5G840909_T01 (Zea mays), 5'ss of exon 3
GGTGATTGTGCATAATAACGAGGTTGTCGCTAGCTGCCACAATATGGTTTTGAAATATACTGACCCAACTGCACATGCTGAAGTCACTGCCATTAGAGAGgtaagaaaa------gagtattacgcttgaatctcttgaaacgttgcaaaaaccggttttctgatgatg-atttgaatccattgtgaatgtgcag--------------------------------------------------------
 ||  |||| |||||| | || ||  | | ||||||||| || |||||||||||  | ||||| |||||||| ||||||||||| ||||| || ||||||||| ||         || |    | || |  |     |   | |   || |   ||     |||  ||  | |||  | |    |  |||    |                                                        
AGTTGTTGTCCATAATGATGAAGTAATAGTTAGCTGCCATAACATGGTTTTGAAGAACACTGATCCAACTGCGCATGCTGAAGTAACTGCGATAAGAGAGgtaggatgctctgttgactgcctctctagcttgcaccggggcatcttaatatgtggacccttgaccatccagttggttactccttccatgctttggtgttagtaccacattcagcatgtaaatagtcaaatgttacattcatcttttacag

upper sequence: AT5G28050.2 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: GRMZM2G008216_T04 (Zea mays), 5'ss of exon 1
GGTGATTGTGCATAATAACGAGGTTGTCGCTAGCTGCCACAATATGGTTTTGAAATATACTGACCCAACTGCACATGCTGAAGTCACTGCCATTAGAGAGgtaag--aaaagagtattacgcttg--aatctctt---gaaacgttgcaa-------aaaccggttttctgatgatgat-----ttgaatccattgtgaa-tgtgcag------------------------------
 ||  | ||   |||| |||| || || |  |||||||| || |||||| ||||  | |||||||| ||||| ||||||||||| ||||| |||||||||||||   |   ||    |||  ||   | |  ||    | ||  |||  |        | |  ||| | | ||  |  |     || | |||||| |    ||||  |                              
AGTTGTCGTCTGTAATGACGAAGTAGTAGTCAGCTGCCATAACATGGTTCTGAAGCACACTGACCCTACTGCGCATGCTGAAGTAACTGCAATTAGAGAGgtaaattacctgaaggctaccattagcagttgctctaaggaaaattgtcattactttgatctcgttctgtaatcttcctggcagttaattccattatttgctgtgtggtttgatggttgatgtatgtccatattttag

upper sequence: AT5G28050.2 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: GRMZM5G840909_T02 (Zea mays), 5'ss of exon 3
GGTGATTGTGCATAATAACGAGGTTGTCGCTAGCTGCCACAATATGGTTTTGAAATATACTGACCCAACTGCACATGCTGAAGTCACTGCCATTAGAGAGgtaaga------aaagagtattacgcttgaatctcttgaaacgttgcaaaaaccggttttctgatgatg-atttgaatccattgtgaatgtgcag-----
 ||  |||| |||||| | || ||  | | ||||||||| || |||||||||||  | ||||| |||||||| ||||||||||| ||||| || ||||||||| ||         || |    | || |  |     |   | |   || |   ||     |||  ||  | |||  | |    |  |||    |     
AGTTGTTGTCCATAATGATGAAGTAATAGTTAGCTGCCATAACATGGTTTTGAAGAACACTGATCCAACTGCGCATGCTGAAGTAACTGCGATAAGAGAGgtaggatgctctgttgactgcctctctagcttgcaccggggcatcttaatatgtggacccttgaccatccagttggttactccttccatgctttggtgtt

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|125259041|gb|EL273126.1|EL273126
EST:     TGAAATATACTGACCCAACTGCACATGCTGAAGTCACTGCCATTAGAGAG                         GCATGTAAGAAACTTAAACAAAATCGAGTTATCAGAAT
genomic: TGAAATATACTGACCCAACTGCACATGCTGAAGTCACTGCCATTAGAGAGgtaagaaaag ... gaatgtgcagGCATGTAAGAAACTTAA-CAAAATCGAGTTATCAGAAT
EST: gi|301501150|gb|HO206690.1|HO206690
EST:     TGAAATATACTGACCCAACTGCACATGCTGAAGTCACTGCCATTAGAGAG                         GCATGTAAGAAACTTAACAAAATCGAGTTATCAGAATGCGAGATTTACGCA
genomic: TGAAATATACTGACCCAACTGCACATGCTGAAGTCACTGCCATTAGAGAGgtaagaaaag ... gaatgtgcagGCATGTAAGAAACTTAACAAAATCGAGTTATCAGAATGCGAGATTTACGCA
EST: gi|301502126|gb|HO207666.1|HO207666
EST:     AATATACTGACCCAACTGCACATGCTGAAGTCACTGCCATTAGAGAG                         GCATGTAAGAAACTTAACAAAATCGAGTTATCAGAATGCGAGATTTACGCA
genomic: AATATACTGACCCAACTGCACATGCTGAAGTCACTGCCATTAGAGAGgtaagaaaag ... gaatgtgcagGCATGTAAGAAACTTAACAAAATCGAGTTATCAGAATGCGAGATTTACGCA
EST: gi|124884110|gb|EH963012.1|EH963012
EST:     TACTGACCCAACTGCACATGCTGAAGTCACTGCCATTAGAGAG                         GCATGCAAGAAACTTAACAAAATCGAGTTATCAGAATGCGAGAT
genomic: TACTGACCCAACTGCACATGCTGAAGTCACTGCCATTAGAGAGgtaagaaaag ... gaatgtgcagGCATGTAAGAAACTTAACAAAATCGAGTTATCAGAATGCGAGAT
EST: gi|125126733|gb|EL171800.1|EL171800
EST:     TGCTGAAGTCACTGCCATTAGAGAG                         GCATGTAAGAAACTTAACAAAATCGAGTTATCAGAATGCGAGATTTACGCA
genomic: TGCTGAAGTCACTGCCATTAGAGAGgtaagaaaag ... gaatgtgcagGCATGTAAGAAACTTAACAAAATCGAGTTATCAGAATGCGAGATTTACGCA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGTGATTGTGCATAATAACGAGGTTGTCGCTAGCTGCCACAATATGGTTTTGAAATATACTGACCCAACTGCACATGCTGAAGTCACTGCCATTAGAGAGgtaagaaaagagtattacgcttgaatctcttgaaacgttgcaaaaaccggttttctgatgatgatttgaatccattgtgaatgtgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGAAG