Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   		7  
 5'  3'   		8  
 5'  3'   		9  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CGGCTAGGACATGCAACTGCATCTTAATAGTTCTTGATGCCATAAAACCAATTACTCACAAGCGTCTCATTGAAAAAGAGCTCGAAGGATTCGGAATAAGgtatagattgtttatataacaacctttatacactgtatatttgatcgtttctggtagatagtctgactcgatcatggactgttgctatgtag

Basic information

species Arabidopsis thaliana
transcript AT4G39520.1
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT4G39520.1 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: GRMZM2G158021_T01 (Zea mays), 5'ss of exon 6
CGGCTAGGACATGCAACTGCATCTTAATAGTTCTTGATGCCATAAAACCAATTACTCACAAGCGTCTCATTGAAAAAGAGCTCGAAGGATTCGGAATAAGgtatagattgtttatataacaacctttatacactgtatatttgatcgtttctggtagatagtctgac--tcgatcatg----gactgttgctatgtag-----
| ||||||||||||||    || || || ||||||||||||||||||||||| |||||||||||||| ||||| || ||||| |||||||| || || |||||    || |||| ||    || | |     |  ||    ||  ||   || ||| | ||  || |  ||  || |     ||   || || ||        
CAGCTAGGACATGCAATGTTATTTTGATTGTTCTTGATGCCATAAAACCAATAACTCACAAGCGTCTTATTGAGAAGGAGCTTGAAGGATTTGGCATTAGgtaagtcttctttacattcatacttctgctggcgctag---tgtacgaaacttgtacacagcttggccatcagtccttttgtgatctttcctttgctcccaat

upper sequence: AT4G39520.1 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: GLYMA06G15180.2 (Glycine max), 5'ss of exon 6
CGGCTAGGACATGCAACTGCATCTTAATAGTTCTTGATGCCATAAAACCAATTACTCACAAGCGTCTCATTGAAAAAGAGCTCGAAGGATTCGGAATAAGgtatagattgtttatataacaacc-tttatacactgtatatttgatcgtttctggtagatagtctgactcgatcatggactgttgctatgtag--------
| || ||||||||||| ||||| || || || |||||||| ||||| ||||| |||||||||||||| || ||||||||||| || ||||| || |||||||| || |    | || |   |   |||      | ||| ||   ||     |  |      ||| |      || ||     |  ||  |          
CTGCAAGGACATGCAATTGCATTTTGATTGTCCTTGATGCAATAAAGCCAATAACTCACAAGCGTCTTATAGAAAAAGAGCTAGAGGGATTTGGTATAAGgta-aggtaacatgtaaattgattatttgctatttttatgttacgtcaccaatattctgatttctaaacaaggcaggggtctcttataattgtttaccact

upper sequence: AT4G39520.1 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: GLYMA04G39690.1 (Glycine max), 5'ss of exon 6
CGGCTAGGACATGCAACTGCATCTTAATAGTTCTTGATGCCATAAAACCAATTACTCACAAGCGTCTCATTGAAAAAGAGCTCGAAGGATTCGGAATAAGgtat------agattgtttatataacaacctttat---acactgtatatttgatcgtttctggtagatagtctgactcgatcatggactgttgctatgtag
| || || |||||||| ||||| || || || |||||||| || || ||||| ||||| |||||||| || ||||||||||| || ||||| || ||||||||       | |||| |||| |  | |  |||||   |   |    || |  |  ||||||    |      |      || |  | | ||      | |
CTGCAAGAACATGCAATTGCATTTTGATTGTCCTTGATGCAATTAAGCCAATAACTCATAAGCGTCTTATCGAAAAAGAGCTAGAGGGATTTGGTATAAGgtaacatgtaatattgattatttg-ctatttttatgttatgttaccaatattctgatttctgaacaaggcaagggtctcctcttataattttttcccattg

upper sequence: AT4G39520.1 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: Vv07s0031g01620.t01 (Vitis vinifera), 5'ss of exon 6
CGGCTAGGACATGCAACTGCATCTTAATAGTTCTTGATGCCATAAAACCAATTACTCACAAGCGTCTCATTGAAAAAGAGCTCGAAGGATTCGGAATAAGgtatagattgtttatataacaacctttatacactgtatatttgatcgtttctggtagatagtct-----gactcgatcatggactgttgctatgtag----------
| ||||| |||||||| ||||| || || ||||||||||| ||||| |||||||||||||||||||| || || ||||||||||| ||||| || |||||||  |  ||| |||||    ||  |   |   || | | ||||  |  |||||||  ||  | |      |    ||   |  | | | |||  |            
CTGCTAGAACATGCAATTGCATTTTGATTGTTCTTGATGCAATAAAGCCAATTACTCACAAGCGTCTGATAGAGAAAGAGCTCGAGGGATTTGGCATAAGgt--aagttggttatacttgaaatt---tgtgctctctctttg--cagttctggttcatttttttggggaaaggtatagcgtccagcttctacctgaaaaacccctt

upper sequence: AT4G39520.1 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: EFJ09453 (Selaginella moellendorffii), 5'ss of exon 6
CGGCTAGGACATGCAACTGCATCTTAATAGTTCTTGATGCCATAAAACCAATTACTCACAAGCGTCTCATTGAAAAAGAGCTCGAAGGATTCGGAATAAGgta----tagattgtttatataacaacctttatacactgtatatttgatcgtttctggtagatagtctgactcgatcatggactgttgctatgtag------
                                                  ||||| |||||| | ||||| || ||||||||||||||||| ||||||||| |    |   ||| ||   | |    || | |   |  |   |  ||  || | || | | |  || | ||| || | | ||          ||       
--------------------------------------------------ATTACACACAAGAGGCTCATCGAGAAAGAGCTCGAAGGATTTGGAATAAGGCAAGCTTGCTTTGCTTTCTTGATTCTCTCTCTCTTCATTGCCTAAGAATgtctgtgttcgttt-tcaggctcaataaagaaccaccaaatcttacgttcag

upper sequence: AT4G39520.1 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: EFJ34569 (Selaginella moellendorffii), 5'ss of exon 5
CGGCTAGGACATGCAACTGCATCTTAATAGTTCTTGATGCCATAAAACCAATTACTCACAAGCGTCTCATTGAAAAAGAGCTCGAAGGATTCGGAATAAGgtatagattgtttatataacaacctttatacactgtatatttgatcgtttctggtagatagtctgactcgatcatggactgttgctatgtag
                                                               | ||||| || ||||||||||||||||| ||||||||| | || ||| ||      |   ||| || | || | | |||  || || |    | ||        ||| |    | ||    | ||  ||
--------------------------------------------------------------AGGCTCATCGAGAAAGAGCTCGAAGGATTTGGAATAAGGCA-AGCTTGCTTT----GCTTTCTTGATTCTCTTTCTCTTT--TCATTGCCTAAAAATGTCTCTGTTCgttttcaggct----caataaag

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|47830368|gb|CK120052.1|CK120052
EST:     ATTACTCACAAGCGTCTCATTGAAAAAGAGCTCGAAGGATTCGGAATAAG                         GTTGAACAAGGAGCCACCAAATTTAACATTTAGGAAAAAAGACAAAGGTGG
genomic: ATTACTCACAAGCGTCTCATTGAAAAAGAGCTCGAAGGATTCGGAATAAGgtatagattg ... tgctatgtagGTTGAACAAGGAGCCACCAAATTTAACATTTAGGAAAAAAGACAAAGGTGG
EST: gi|124755238|gb|EH845368.1|EH845368
EST:     CGAAGGATTCGGAATAAG                         GTTGAACAAGGAGCCACCAAATTTAACATTTAGG-AAAAAGACAAAGGTGG
genomic: CGAAGGATTCGGAATAAGgtatagattg ... tgctatgtagGTTGAACAAGGAGCCACCAAATTTAACATTTAGGAAAAAAGACAAAGGTGG
EST: gi|164126634|gb|ES046317.1|ES046317
EST:     ATTACTCACAAGCGTCTCATTGAAAAAGAGCTCGAAGGATTCGGAATAAG                         GTTGAACAAGGAGCCACCA
genomic: ATTACTCACAAGCGTCTCATTGAAAAAGAGCTCGAAGGATTCGGAATAAGgtatagattg ... tgctatgtagGTTGAACAAGGAGCCACCA
EST: gi|124795030|gb|EH884709.1|EH884709
EST:     ATTACTCACAAGCGTCTCATTGAAAAAGAGCTCGAAGGATTCGGAATAAG                         GTTGAACAAGGAGCCACCAAATTTAACATTTAGGAAAAAAGACAAAGG
genomic: ATTACTCACAAGCGTCTCATTGAAAAAGAGCTCGAAGGATTCGGAATAAGgtatagattg ... tgctatgtagGTTGAACAAGGAGCCACCAAATTTAACATTTAGGAAAAAAGACAAAGG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CGGCTAGGACATGCAACTGCATCTTAATAGTTCTTGATGCCATAAAACCAATTACTCACAAGCGTCTCATTGAAAAAGAGCTCGAAGGATTCGGAATAAGgtatagattgtttatataacaacctttatacactgtatatttgatcgtttctggtagatagtctgactcgatcatggactgttgctatgtag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCT