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

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTTTGACATGCTTAGAAGACAATCTCTCCGCCCTGACTGCATCAAGATGTTTGTCCTTGATGAAGCTGATGAAATGCTCTCCCGTGGTTTCAAGGATCAGgtttgttatcttcttcaaagtttgaatctaccctctgtggttatctctgatattgacttggttttgtgttgttttctggtgaatttgcag

Basic information

species Arabidopsis thaliana
transcript AT1G54270.2
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G54270.2 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: GLYMA08G20300.2 (Glycine max), 5'ss of exon 4
TTTTGACATGCTTAGAAGACAATCTCTCCGCCCTGACTGCATCAAGATGTTTGTCCTTGATGAAGCTGATGAAATGCTCTCCCGTGGTTTCAAGGATCAGgtttgttatcttcttcaaagtttgaatctaccctctgtggttatctctgatattgacttggttttgtgttgttttctggtgaatttgcag-------------
 |||||||||||  | || || ||||| ||||| || ||||| |||||||||||  | ||||| |||||||||||||| || ||||||||||||||||||||||||| | ||  | |        || |  | | | | ||   | || || |   ||||||| | |||  | | || ||  | |  |               
GTTTGACATGCTGCGGAGGCAGTCTCTTCGCCCAGATTGCATAAAGATGTTTGTTTTGGATGAGGCTGATGAAATGCTTTCACGTGGTTTCAAGGATCAGgtttgttgttttgattagttcccacattt-tcatatttagtg--cactaatttattcttggttgtctgtcctatacttgttgactatcctacttcttgtgttg

upper sequence: AT1G54270.2 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: GLYMA07G00950.1 (Glycine max), 5'ss of exon 4
TTTTGACATGCTTAGAAGACAATCTCTCCGCCCTGACTGCATCAAGATGTTTGTCCTTGATGAAGCTGATGAAATGCTCTCCCGTGGTTTCAAGGATCAGgtttgttatctt--cttcaaagttt--gaatctaccctctgtggttatctctgata--ttgacttggttttgtgttgttttctggtgaatttgcag----
 |||||||||||  | || || ||||| ||||| || ||||| |||||||||||  | ||||| |||||||||||||| || |||||||| |||||||||||||||||| ||   | | | ||||    || ||          |||||  || |    || | |    ||||    | | ||      | ||  |    
GTTTGACATGCTGCGGAGGCAGTCTCTTCGCCCAGATTGCATAAAGATGTTTGTTTTGGATGAGGCTGATGAAATGCTTTCACGTGGTTTTAAGGATCAGgtttgttattttgattaccatgttttcatatttagtgcactaatttatccttggttgtctgtcctatacttgttgactatcctatctcttatgttggtaa

upper sequence: AT1G54270.2 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: GLYMA15G03020.1 (Glycine max), 5'ss of exon 4
TTTTGACATGCTTAGAAGACAATCTCTCCGCCCTGACTGCATCAAGATGTTTGTCCTTGATGAAGCTGATGAAATGCTCTCCCGTGGTTTCAAGGATCAGgtttgttatcttcttcaaagtttgaatctaccctctgtggt-tatctctgatattgacttggttttgtgttgttttctggtgaat-ttgcag-------------------------------------------------------------------------------------------
 |||||||||||  ||||||||||||| ||||| ||   ||| || ||||||||  | ||||| |||||||||||||| || |||||||||||||| ||||||||  ||  | ||| | ||||      |  || ||   | | | |||  |  |    ||   |       || | |  || || ||| |                                                                                            
GTTTGACATGCTACGAAGACAATCTCTTCGCCCAGATCACATAAAAATGTTTGTTTTGGATGAGGCTGATGAAATGCTTTCACGTGGTTTCAAGGACCAGgtttg--atggttttccatgttttgtctaaaactttgaattgtttttcttttccttgagtgtcatctaaacattctttcatgcatgttgaaataattctttatttaaaacctgtgtgctagatgaagtcatcttgtgttagatagatagctaacagtttatatttttcgtgcatgaaatgcag

upper sequence: AT1G54270.2 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: GLYMA17G06110.1 (Glycine max), 5'ss of exon 4
TTTTGACATGCTTAGAAGACAATCTCTCCGCCCTGACTGCATCAAGATGTTTGTCCTTGATGAAGCTGATGAAATGCTCTCCCGTGGTTTCAAGGATCAGgtttgttatcttcttcaaa---gtttgaatctaccctctgtggttatctctgatatt----gacttggttttgtgttgttttctggtgaatttgcag---
 ||||| |||||  |  |||| || || |  || |||  |||||||||||||||  | ||||| |||||||||||||| ||||| |||||||||||||||||   || ||   |   ||    |||    ||   | || |  ||||  || ||| |    |  || | |  ||  ||  | |   ||  | || |    
GTTTGATATGCTGCGCCGACAGTCACTTCAGCCAGACCACATCAAGATGTTTGTATTGGATGAGGCTGATGAAATGCTTTCCCGAGGTTTCAAGGATCAGgtaccttttcaattcacaactcatttagtacttttcactttaattattactaatactttatgtttttgataagtaatgcctacacttgtctatggatttt

upper sequence: AT1G54270.2 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: GLYMA15G18760.3 (Glycine max), 5'ss of exon 4
TTTTGACATGCTTAGAAGACAATCTCTCCGCCCTGACTGCATCAAGATGTTTGTCCTTGATGAAGCTGATGAAATGCTCTCCCGTGGTTTCAAGGATCAGgtttgtt----atcttcttcaaagtttgaatctaccctctgtggtt--atctctgatattgacttggttttgtgttgttttctggtgaatttgcag----
 ||||| |||||  | ||||| || || || || |||| |||||||||||||||  | ||||| |||||||||||||| ||||||||||| || |||||||||  ||    ||| | |||    | | |||  |   |   || ||  || |||  | |    |  ||  ||       ||   ||   |||| |     
ATTTGATATGCTGCGCAGACAGTCACTTCGGCCAGACTACATCAAGATGTTTGTATTGGATGAGGCTGATGAAATGCTTTCCCGTGGTTTTAAAGATCAGgttctttctaaatcatattccttttgttaatgaagaattactgattggatttcttgtttatgatatgtaatgccccacgtttctgtatttttgtacattg

upper sequence: AT1G54270.2 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: GLYMA13G16570.1 (Glycine max), 5'ss of exon 4
TTTTGACATGCTTAGAAGACAATCTCTCCGCCCTGACTGCATCAAGATGTTTGTCCTTGATGAAGCTGATGAAATGCTCTCCCGTGGTTTCAAGGATCAGgt--ttgttatcttcttcaaagtttgaatctaccctctgtggttatctctgatattgac-ttggttttgtgttgttttctggtgaatttgcag-------
 ||||| |||||  | ||||| || || |  || ||   |||||||||||||||  | ||||| |||||||||||||| ||||| ||||| |||||||||||  || | |  ||  | |    |  | | |    |   |  |||    | |||   ||  | || |   | | ||||    |  || || |        
GTTTGATATGCTGCGCAGACAGTCACTTCTGCCAGATCACATCAAGATGTTTGTATTGGATGAGGCTGATGAAATGCTTTCCCGAGGTTTTAAGGATCAGgtacttttcactttaattattactaaatttttttgttgttttttacaagtaatacctacacttgtctacggatttttttaaattgatgtgtaaacgttcg

upper sequence: AT1G54270.2 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: GLYMA09G07530.3 (Glycine max), 5'ss of exon 4
TTTTGACATGCTTAGAAGACAATCTCTCCGCCCTGACTGCATCAAGATGTTTGTCCTTGATGAAGCTGATGAAATGCTCTCCCGTGGTTTCAAGGATCAGgtttgttatcttcttcaaagtttgaatctaccctctgtggtta-tctctga---tattgacttggttttgtgttgtt------ttctggtgaatttgcag--
 ||||| |||||  | ||||| || || || || ||||  ||||||||||||||  | ||||| |||||||||||||| ||||||||||| || ||||||||  | | | |  |||| | | |   | |    | | |  ||| |  |||    | |||  || | | |||  ||        ||   ||   |||| |   
ATTTGATATGCTGCGCAGACAGTCACTTCGGCCAGACTATATCAAGATGTTTGTATTGGATGAGGCTGATGAAATGCTTTCCCGTGGTTTTAAAGATCAGgt--gctttttaattcatattctttttgttaattttataattactgactggacttgttgtttttgatatgtaatgcccacacgtttctgtatttttgtacat

upper sequence: AT1G54270.2 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: GLYMA13G42360.1 (Glycine max), 5'ss of exon 4
TTTTGACATGCTTAGAAGACAATCTCTCCGCCCTGACTGCATCAAGATGTTTGTCCTTGATGAAGCTGATGAAATGCTCTCCCGTGGTTTCAAGGATCAGgtttgtta--tcttcttcaaagtttgaa---tctaccctctgtggttatctctgatattgacttggttttgtgttgttttctggtgaat-ttgcag----
 |||||||||||  | ||||| ||||| || || ||   ||| |||||||||||  | ||||| |||||||||||||| || |||||||||||||| |||||||| |   | | | |    |||| ||   |  |     | |  ||   ||||||       ||   |      ||| | |  || || || |      
ATTTGACATGCTACGGAGACAGTCTCTTCGTCCAGATCACATAAAGATGTTTGTTTTGGATGAGGCTGATGAAATGCTTTCTCGTGGTTTCAAGGACCAGgtttgatggttttccatgtttgtttaaaacattgaattgtttttttttcttctgattcctgactgtcatctaaacgttctttcatgcatgttaccaatat

upper sequence: AT1G54270.2 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: GLYMA06G05580.1 (Glycine max), 5'ss of exon 4
TTTTGACATGCTTAGAAGACAATCTCTCCGCCCTGACTGCATCAAGATGTTTGTCCTTGATGAAGCTGATGAAATGCTCTCCCGTGGTTTCAAGGATCAGgtttgttatcttcttcaaagt------ttgaatctaccctctgtggttatctctg-atattgacttgg---ttttgtgttgttttctggt-gaatttgcag
 |||||||||||  | ||||||||| | ||||||||   ||||| |||||||||  | ||||| || ||||| |||||||| || |||||||||||||||||    |   ||    |   |      ||  ||   |    |    || | | || || ||| |||     |  | | | ||||| |  | |||||| || 
ATTTGACATGCTGTGCAGACAATCTTTGCGCCCTGATAACATCAGGATGTTTGTATTGGATGAGGCAGATGAGATGCTCTCTCGAGGTTTCAAGGATCAGgtcctctcattttcctatgctgctctcttttattggcttcattctattgtttgtggattttggcttaaaaatactatttagttttttatttgaattttca-

upper sequence: AT1G54270.2 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: GLYMA04G05580.1 (Glycine max), 5'ss of exon 4
TTTTGACATGCTTAGAAGACAATCTCTCCGCCCTGACTGCATCAAGATGTTTGTCCTTGATGAAGCTGATGAAATGCTCTCCCGTGGTTTCAAGGATCAGgtttgttatcttcttcaaagtttgaatctaccctctg--tggttatctctgatattgacttgg--ttttgtgttgttttctggtgaatttgcag-------
 |||||||||||  | || |||||  | ||| ||||   ||||| |||||||||  | ||||| || ||||| |||||||| || |||||||||||||||||    |   || | | | |||    |||    | ||  |  || | |    | |||  ||||  |    | |||  ||      ||| |  ||       
ATTTGACATGCTGCGCAGGCAATCATTGCGCTCTGATAACATCAGGATGTTTGTATTGGATGAGGCAGATGAGATGCTCTCTCGAGGTTTCAAGGATCAGgtcctct-cattttcccatgttgctctcttttatttgcttcattctattgtttgttgtgttggaatacgattttggcttaaaaataatatttagtgttttt

upper sequence: AT1G54270.2 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: Vv04s0008g01000.t01 (Vitis vinifera), 5'ss of exon 3
TTTTGACATGCTTAGAAGACAATCTCTCCGCCCTGACTGCATCAAGATGTTTGTCCTTGATGAAGCTGATGAAATGCTCTCCCGTGGTTTCAAGGATCAGgtttgttatct-tcttcaaagtttgaatctaccctctgtggttatctctgatattgact-----tggttttgtgttgttttctggtgaatttgcag----
|||||||||| |  | || ||||| || || ||||| | ||| |||||||||||  | |||||||| ||||||||||| || || |||||||||||||||||   |  | |  |||     | |  ||||      |||| |  |  ||  || |  ||     ||    | || |||| || | |   | |   |    
TTTTGACATGTTGCGCAGGCAATCACTTCGTCCTGATTACATTAAGATGTTTGTGTTAGATGAAGCAGATGAAATGCTTTCACGAGGTTTCAAGGATCAGgtccttcctttgcctttgctctgtatatctttttgttgtgctgtttgctactactctctataactgtcagtatgatgttgtcagatttttgtctggatat

upper sequence: AT1G54270.2 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: Vv11s0016g01920.t01 (Vitis vinifera), 5'ss of exon 3
TTTTGACATGCTTAGAAGACAATCTCTCCGCCCTGACTGCATCAAGATGTTTGTCCTTGATGAAGCTGATGAAATGCTCTCCCGTGGTTTCAAGGATCAGgtttgttatcttcttcaaagtttgaatctaccctctgtggttatctctgatattgacttggttttgtgttgttttctggtgaatttgcag-----------
 |||||||||||  ||||||| || || || ||||| | ||| || ||||||||  | |||||||| |||||||||||||| || |||||||||||||||||   || |      | || |       ||   | |    || | |   | | |  |       ||   | || | | |  | | ||              
ATTTGACATGCTGCGAAGACAGTCCCTTCGTCCTGATTACATTAAAATGTTTGTGTTGGATGAAGCAGATGAAATGCTCTCTCGAGGTTTCAAGGATCAGgtc-attcttaaaccctaaatccattcttattgttttcacttttgtggcaaaatttccatcaactgcaatattcttttgacagtatgagtatatgatgcat

upper sequence: AT1G54270.2 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: Vv09s0002g01760.t01 (Vitis vinifera), 5'ss of exon 4
TTTTGACATGCTTAGAAGACAATCTCTCCGCCCTGACTGCATCAAGATGTTTGTCCTTGATGAAGCTGATGAAATGCTCTCCCGTGGTTTCAAGGATCAGgtttgttatcttct-tcaaagtttgaatctaccctctgtggttatctctgatattgacttggttttgtgttgttttctggtga--atttgcag----------------------------------------------------------------------------------------------------
 ||||||||| |  | ||||| || || ||||| || | ||| |||||||||||  | ||||| |||||||||||||| || || ||||||||||||||||| |||| | || | ||   ||||   | |||    |||  |  | |   ||| |  | ||||   |     | || || | |   || | ||                                                                                                    
GTTTGACATGTTGCGGAGACAGTCACTTCGCCCAGATTACATTAAGATGTTTGTATTGGATGAGGCTGATGAAATGCTTTCACGAGGTTTCAAGGATCAGgtctgttctattatatctctgtttc--tttactagttgtaatatttttgcatactt-catggtgaagaacattattttgctaattgttagaagttcatgctcattgcttattgctggatttttcaatatgtgcaagttttgactggctttgttgtttttctgataattcattaattttttttgctgctgtcag

upper sequence: AT1G54270.2 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: Vv04s0008g00980.t01 (Vitis vinifera), 5'ss of exon 1
TTTTGACATGCTTAGAAGACAATCTCTCCGCCCTGACTGCATCAAGATGTTTGTCCTTGATGAAGCTGATGAAATGCTCTCCCGTGGTTTCAAGGATCAGgtttgttatcttcttcaaagtttgaatctaccctctgtggttatctctgatattgacttggttttgtgttgttttctggtgaatttgcag
      || ||| ||  |    |||||||   |||||| ||||||||||||||| || ||||| |||||||||||||||||  | || || ||||||||||| | ||||||   ||          | |        |  || |  |  | | |    || |  |   ||||||||| |      |||||
------CACGCTGAGGCGGGGCTCTCTCCATGCTGACTCCATCAAGATGTTTGTTCTGGATGAGGCTGATGAAATGCTCTCTAGAGGCTTTAAGGATCAGgtct-ttatctagctcttgtccgtgttttcataagaatttttgtagccaaaact--tgtgttcctaaattgttttcttgc----ctgcag

upper sequence: AT1G54270.2 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: EFJ16567 (Selaginella moellendorffii), 5'ss of exon 3
TTTTGACATGCTTAGAAGACAATCTCTCCGCCCTGACTGCATCAAGATGTTTGTCCTTGATGAAGCTGATGAAATGCTCTCCCGTGGTTTCAAGGATCAGgtttgttatcttcttcaaagtttgaatctaccctctgtggttatctctgatattgacttggttttgtgttgttttctggtgaatttgcag
 |  || ||||| ||  | |   | || || || |||| |||||||||||||||||| || || || || || ||||| ||||| ||||||||||| |||||  | |          |||    || ||   || | |    | | |||    || ||||    ||||| |                   
CTACGATATGCTCAGGCGTCGCGCGCTGCGGCCGGACTACATCAAGATGTTTGTCCTGGACGAGGCGGACGAGATGCTGTCCCGCGGTTTCAAGGACCAGgtaaggtg--------gaagg--aaagctggtctatataaccacc-ctgcctgtgccttg----tgtgtcgcag----------------

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|163980587|gb|EL987789.1|EL987789
EST:     CTGATGAAATGCTCTCCCGTGGTTTCAAGGATCAG                         ATCTATGACATATTCCAGCTTCTCCCACCAAAGATTCAGGTTGGAGTGTTC
genomic: CTGATGAAATGCTCTCCCGTGGTTTCAAGGATCAGgtttgttatc ... gaatttgcagATCTATGACATATTCCAGCTTCTCCCACCAAAGATTCAGGTTGGAGTGTTC
EST: gi|125082358|gb|EL143274.1|EL143274
EST:     TTGTCCTTGATGAAGCTGATGAAATGCTCTCCCGTGG-TTCAAGGATCAG                         ATCTATGACATATTCCAGCTTCTCCCACCAAAGATTC
genomic: TTGTCCTTGATGAAGCTGATGAAATGCTCTCCCGTGGTTTCAAGGATCAGgtttgttatc ... gaatttgcagATCTATGACATATTCCAGCTTCTCCCACCAAAGATTC
EST: gi|125052397|gb|EL124200.1|EL124200
EST:     TTGTCCTTGATGAAGCTGATGAAATGCTCTCCCGTGGTTTCAAGGATCAG                         ATCTATGACATATT
genomic: TTGTCCTTGATGAAGCTGATGAAATGCTCTCCCGTGGTTTCAAGGATCAGgtttgttatc ... gaatttgcagATCTATGACATATT
EST: gi|125305970|gb|EL320055.1|EL320055
EST:     TTGTCCTTGATGAAGCTGATGAAATGCTCTCCCGTGGTTTCAAGGATCAG                         ATCTATGACATATTCCAGCTTCTCCCACCAAAGATT
genomic: TTGTCCTTGATGAAGCTGATGAAATGCTCTCCCGTGGTTTCAAGGATCAGgtttgttatc ... gaatttgcagATCTATGACATATTCCAGCTTCTCCCACCAAAGATT
EST: gi|125267915|gb|EL282000.1|EL282000
EST:     TTGTCCTTGATGAAGCTGATGAAATGCTCTCCCGTGGTTTCAAGGATCAG                         ATCTATGACATATTCC
genomic: TTGTCCTTGATGAAGCTGATGAAATGCTCTCCCGTGGTTTCAAGGATCAGgtttgttatc ... gaatttgcagATCTATGACATATTCC
EST: gi|125287338|gb|EL301423.1|EL301423
EST:     TTGTCCTTGATGAAGCTGATGAAATGCTCTCCCGTGGTTTCAAGGATCAG                         ATCTATGACATATTCCAGCTTCTCCCACCAAAGATTCAGG
genomic: TTGTCCTTGATGAAGCTGATGAAATGCTCTCCCGTGGTTTCAAGGATCAGgtttgttatc ... gaatttgcagATCTATGACATATTCCAGCTTCTCCCACCAAAGATTCAGG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TTTTGACATGCTTAGAAGACAATCTCTCCGCCCTGACTGCATCAAGATGTTTGTCCTTGATGAAGCTGATGAAATGCTCTCCCGTGGTTTCAAGGATCAGgtttgttatcttcttcaaagtttgaatctaccctctgtggttatctctgatattgacttggttttgtgttgttttctggtgaatttgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT