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

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTAGATGGTATGGATGCATTTGCTGTCAAACAAGCTTGCAAATTTGCTAAGCAGCATGCGTTGGAGAAGGGGCCAATAgtaagtttgtattttagtattatcagacgttttgtttttttcccctttggtccttactcatctggcgcattttgtaaatttgctatgagcaatatctagc...

Basic information

species Arabidopsis thaliana
transcript AT1G59900.1
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G59900.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: LOC_Os06g13720.1 (Oryza sativa), 5'ss of exon 3
GTAGATGGTATGGATGCATTTGCTGTCAAACAAGCTTGCAAATTTGCTAAGCAGCATGCGTTGGAGAAGGGGCCAATAgtaagtttgtattttagta---ttatcagacgttt-tgtttttttcccctttggtccttactcatctggcgcattttgtaaatttgctatgagcaatatctagc
|| |||||||||||||   |||| |||||||||||||| |||||||| ||||| |||||  | || || || || || ||||||   | |  |  |     | ||    ||     || |   |   | |||  ||  |     | | ||  |    ||||   ||    | | | |     
GTCGATGGTATGGATGTTCTTGCAGTCAAACAAGCTTGTAAATTTGCCAAGCAACATGCTCTTGAAAATGGACCGATTgtaagtgaatttcctgattgccatttcgactgtgcacattatggacatttctggatctctcaggggttgggctgtgctgaaatacactgctggtagtgtg----

upper sequence: AT1G59900.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: GLYMA02G03080.1 (Glycine max), 5'ss of exon 3
GTAGATGGTATGGATGCATTTGCTGTCAAACAAGCTTGCAAATTTGCTAAGCAGCATGCGTTGGAGAAGGGGCCAATAgtaagtttgtattttagtattatcagacgt-tttgtttttttcccct-----ttggtccttactcatctggcgcattttgtaaatttgctatgagcaatatctagc
|| |||||||||||||   ||||||| |||||||||||||||||||| ||| | ||||| ||| |||| || ||  | || ||||  | ||||  || | | |    |  |||  ||| ||  ||     || ||  ||    ||  |  |   | | |  || | |||  |||   |  ||  
GTTGATGGTATGGATGTTCTTGCTGTTAAACAAGCTTGCAAATTTGCAAAGGAACATGCTTTGAAGAATGGACCCCTTgtgagttgattttttt-tactgttatgtatacttgaatttctcttctaaaaattagttattggcaattggatg---tctattcatctacta-aagcttgacataa-

upper sequence: AT1G59900.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: GLYMA08G40380.1 (Glycine max), 5'ss of exon 3
GTAGATGGTATGGATGCATTTGCTGTCAAACAAGCTTGCAAATTTGCTAAGCAGCATGCGTTGGAGAAGGGGCCAAT----Agtaagtttgtattttagtatta-tcagacgttttg----tttttttcccctttgg-------tccttactcatctggcgcattttg--taaatttgctatgagcaatatctagc----
|||||||| ||||||||  ||||||| ||||||||||| |||||||| ||| ||  ||| ||| |||| || || ||    ||||| ||    | | | |  || | | |  ||||     |||||||  | ||| |       || ||  |  ||||    ||| |   | | ||  ||||    | ||| | |     
GTAGATGGCATGGATGCTCTTGCTGTGAAACAAGCTTGTAAATTTGCAAAGGAGTTTGCTTTGAAGAATGGTCCCATTgtaagtaaattaacctctcatttgtacttatattttttaagaatttttttagcttttaggaatgattcttttattctctgttatattataattgatttctctatcttaattattttgtccag

upper sequence: AT1G59900.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: GLYMA18G17240.1 (Glycine max), 5'ss of exon 3
GTAGATGGTATGGATGCATTTGCTGTCAAACAAGCTTGCAAATTTGCTAAGCAGCATGCGTTGGAGAAGGGGCCAATAgtaagt-------------ttgtattttagtattatcagacgttttgttt---ttttcccctttggtccttactcatctggcgcattttg--taaatttgctatgagcaatatctagc----
|||||||| ||||||||  ||||||| ||||||||||| |||||||| ||| ||  ||| ||  |||| || || || ||||||             || | |  |  ||||     |  || |||||   ||||     |   || ||  |  ||||    |||     | | ||  ||||    | ||| | |     
GTAGATGGCATGGATGCTCTTGCTGTGAAACAAGCTTGTAAATTTGCAAAGGAGTTTGCTTTAAAGAATGGTCCCATTgtaagtaaatttacttcttttttgtacttatatttcttaaatttgtgtttagattttaggaatgattcttttattctctgttatattacaattgatttctctatcttaattattttgtccag

upper sequence: AT1G59900.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: GLYMA01G04470.2 (Glycine max), 5'ss of exon 1
----------------------GTAGATGGTATGGATGCATTTGCTGTCAAACAAGCTTGCAAATTTGCTAAGCAGCATGCGTTGGAGAAGGGGCCAATAgtaagtttgtattttagtattatcagacgttttgtttttttcccctttggtccttactcatctggcgcattttgtaaatttgctatgagcaatatctagc
                      || ||||| |||||||   ||||||| |||||||||||||||||||| ||| | ||||| ||| |||| || |   | || ||||    |||| |   |     |   ||   ||| |   |      |   |  |   |      || || | |||   | ||        |  |||
AGACGAATATTACTTTGTACAGGTTGATGGCATGGATGTTCTTGCTGTTAAACAAGCTTGCAAATTTGCAAAGGAACATGCTTTGAAGAATGGACTCCTTgtgagttaacttttttgctgttatgcatacttgaatttctcttctaaaaattaatcattggcaattagatgttatgaatcacccattcatctgctaaagc

upper sequence: AT1G59900.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: Vv09s0018g01940.t01 (Vitis vinifera), 5'ss of exon 3
GTAGATGGTATGGATGCATTTGCTGTCAAACAAGCTTGCAAATTTGCTAAGCAGCATGCGTTGGAGAAGGGGCCAATAgtaagtttg--tattttagtattatcagacgttttgtttttt----tcccctttggtccttactcatctggcgcattttgtaaatttgctatgagcaatatctagc
||||||||||||||||   ||||||| ||||| || |||| |||||||||| ||||||| ||  | || || || || ||||||||   |||  |  | ||  ||    || | || ||     | || ||||     ||||  | | |   |||    | || | ||||   | |  |||   
GTAGATGGTATGGATGTTCTTGCTGTGAAACAGGCATGCAGATTTGCTAAGGAGCATGCTTTAAAAAATGGACCCATTgtaagtttacttatcctgctgtttcca--ttttgtattcttaaaaattccttttgcaaactactattgttgttgatt----agatcttctatcttctaattctgca

upper sequence: AT1G59900.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: Vv01s0026g00990.t01 (Vitis vinifera), 5'ss of exon 3
GTAGATGGTATGGATGCATTTGCTGTCAAACAAGCTTGCAAATTTGCTAAGCAGCATGCGTTGGAGAAGGGGCCAATAgtaagtttgtattttagtattatcagacgttttgtttttttcccctttggtccttactcatctggcgcattttgtaaatttgctatgagcaatatctagc------
|||||||||||||||||  |||| || ||||| || |||| |||||||||| ||||||| ||  | || || || || ||||||||   || |  |  | |   || |||| | || |      ||| || ||    | ||  |   |  |||| ||||  | | |  |   ||||        
GTAGATGGTATGGATGCTCTTGCGGTGAAACAGGCATGCAGATTTGCTAAGGAGCATGCTTTAAAAAATGGACCCATTgtaagtttac-ttatcctgctgttt-acattttctattctataaaattgttcttt--caaactaccat-tgctgtagatttcatct-actatcttctaattctgca

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|124743059|gb|EH834221.1|EH834221
EST:     CGTTGGAGAAGGGGCCAATA                         ATTCTTGAGATGGACACATACAGGTACCACGGTCACTCCATGTCTGATCCT
genomic: CGTTGGAGAAGGGGCCAATAgtaagtttgt ... ttctatacagATTCTTGAGATGGACACATACAGGTACCACGGTCACTCCATGTCTGATCCT
EST: gi|124941966|gb|EL018273.1|EL018273
EST:     CATGCGTTGGAGAAGGGGCCAATA                         ATTCTTGAGATGGACACATACAGGTACCACGGTCACTCCATGTACTGATCC
genomic: CATGCGTTGGAGAAGGGGCCAATAgtaagtttgt ... ttctatacagATTCTTGAGATGGACACATACAGGTACCACGGTCACTCCATGT-CTGATCC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTAGATGGTATGGATGCATTTGCTGTCAAACAAGCTTGCAAATTTGCTAAGCAGCATGCGTTGGAGAAGGGGCCAATAgtaagtttgtattttagtattatcagacgttttgtttttttcccctttggtccttactcatctggcgcattttgtaaatttgctatgagcaatatctagc

- - - - - - - - - - - - - - - CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tttcccct
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ccttactc