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'   		10  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CCCTGTGTATTTCAATGAACCAATATCATCCCTCCAAAAATGTTTTGAAGACTTGGAGTATTCGTATCTTTTGGACCGAGCATATGAACATGGAAAATCTgtaagtgacaccaaagtctcttacttatcttgtacattactacattctgtttatcttatattgacttaaagcctattggataatcag

Basic information

species Arabidopsis thaliana
transcript AT4G22540.3
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT4G22540.1 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: GRMZM5G875564_T03 (Zea mays), 5'ss of exon 4
CCCTGTGTATTTCAATGAACCAATATCATCCCTCCAAAAATGTTTTGAAGACTTGGAGTATTCGTATCTTTTGGACCGAGCATATGAACATGG----AAAATCTgtaagtgacaccaaagtctc------ttacttatcttgtacattactacattctgtttatcttatattgacttaa---agcctattggataatcag-------------------------
 || || || || || |||||| ||||||| || |||||||| ||||| |||||||||||||| ||| | ||||| || |||||||||  |||    ||  | | |   |  |  |||| || |      | |   ||  | |   |||  || |||  | ||   | |||| | |  |     |   |   |||||                            
TCCAGTTTACTTTAACGAACCATTATCATCTCTTCAAAAATGCTTTGAGGACTTGGAGTATTCTTATTTGTTGGATCGTGCATATGAATGTGGCCTAAAGgtatttttcttgctacaaattcgcacttgataatcaattatttgagttagaaccttcactgtaaggtttattaagtagatttgactcgtgaaataattccgcagttattatgcttctgaattcag

upper sequence: AT4G22540.1 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: GRMZM5G875564_T01 (Zea mays), 5'ss of exon 5
CCCTGTGTATTTCAATGAACCAATATCATCCCTCCAAAAATGTTTTGAAGACTTGGAGTATTCGTATCTTTTGGACCGAGCATATGAACATGG----AAAATCTgtaagtgacaccaaagtctc------ttacttatcttgtacattactacattctgtttatcttatattgacttaa---agcctattggataatcag
 || || || || || |||||| ||||||| || |||||||| ||||| |||||||||||||| ||| | ||||| || |||||||||  |||    ||  | | |   |  |  |||| || |      | |   ||  | |   |||  || |||  | ||   | |||| | |  |     |   |   |||||   
TCCAGTTTACTTTAACGAACCATTATCATCTCTTCAAAAATGCTTTGAGGACTTGGAGTATTCTTATTTGTTGGATCGTGCATATGAATGTGGCCTAAAGgtatttttcttgctacaaattcgcacttgataatcaattatttgagttagaaccttcactgtaaggtttattaagtagatttgactcgtgaaataattcc

upper sequence: AT4G22540.1 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: GRMZM2G402653_T03 (Zea mays), 5'ss of exon 3
CCCTGTGTATTTCAATGAACCAATATCATCCCTCCAAAAATGTTTTGAAGACTTGGAGTATTCGTATCTTTTGGACCGAGCATATGAACATGGAAAATCTgtaag-tgacaccaaagtctcttacttatcttgtacattactacattctgtttatcttatattgac-ttaaagcctattggataatcag--------------
 || || || |||||||||||| | |||||||| || || || ||||| || ||||||||||| || || ||||| |  |||||| |||||||||||   ||||| | ||    |  ||| | || |  |   |     |  | |||   | |   ||  ||       | ||  || || |  ||||               
TCCAGTTTACTTCAATGAACCACTCTCATCCCTTCAGAAGTGCTTTGAGGATTTGGAGTATTCATACCTCTTGGATCAGGCATATCAACATGGAAAAGTGgtaagatcacttttacatctttaacattgcacatgtccgagga-atttcatctgctttccatgagtgccatagattaatgaa--atcatttccaatccatttt

upper sequence: AT4G22540.1 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: GLYMA17G14820.1 (Glycine max), 5'ss of exon 5
CCCTGTGTATTTCAATGAACCAATATCATCCCTCCAAAAATGTTTTGAAGACTTGGAGTATTCGTATCTTTTGGACCGAGCATATGAACATGGAAAATCTgtaagtgacaccaaagtctcttacttatcttgtacattactacattctgtttatcttatattgacttaaagcc--tattggataatcag------------
 ||||| || || ||||| ||||||||||| || || ||||||||||| ||||||||||| || | |||| |||| ||||| |||||  |||||||||| |||||  | ||     | ||||  || |  | | || | || | | | ||  |    |||   | || ||     | ||||   ||               
TCCTGTATACTTTAATGAGCCAATATCATCTCTTCAGAAATGTTTTGAGGACTTGGAGTACTCTTTTCTTCTGGATCGAGCTTATGAGTATGGAAAATCAgtaagatatacatctttatcttgattgtgctattcacttct-cttgcagtgaaaacaatacaaatttcaaagtagtgttggtacatgtccttttattctgt

upper sequence: AT4G22540.1 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: GLYMA05G04340.2 (Glycine max), 5'ss of exon 5
CCCTGTGTATTTCAATGAACCAATATCATCCCTCCAAAAATGTTTTGAAGACTTGGAGTATTCGTATCTTTTGGACCGAGCATATGAACATGGAAAATCTgtaagtgacaccaaagtctcttacttatcttgtacattactacattctgtttatcttatattgacttaaagcctattggataatcag---------------
 ||||| || || ||||| ||||||||||| || || ||||||||||| ||||| ||||| || | |||| |||| ||||| |||||  ||||||||||||||||  | ||       ||||  || | || |   ||  |      || | | |    |   | || ||   |   ||   | ||                
TCCTGTATACTTTAATGAGCCAATATCATCTCTTCAGAAATGTTTTGAGGACTTTGAGTACTCTTTTCTTCTGGATCGAGCTTATGAGTATGGAAAATCTgtaagatatacatcttgatcttgattgtgttttttttttttttgccttggtaaccaacaa--aatttcaaaagtggggggggaccatttctttttttttttt

upper sequence: AT4G22540.1 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: GLYMA01G41940.1 (Glycine max), 5'ss of exon 4
CCCTGTGTATTTCAATGAACCAATATCATCCCTCCAAAAATGTTTTGAAGACTTGGAGTATTCGTATCTTTTGGACCGAGCATATGAACATGGAAAATCTgtaagtgacaccaaagtctcttacttatcttgtacattactacattctgtttatcttatattgacttaaagcctattggataatcag--------------
||| || || || ||||| || ||||||||||| |||||||||| ||| ||||||||||| || |||||| |||| | ||| |||||  | |||||||| |||||  | ||      |||||  ||||      ||    |   |   || ||    |||   | ||||| |   |     | |                 
CCCGGTATACTTTAATGAGCCGATATCATCCCTACAAAAATGTTGTGAGGACTTGGAGTACTCTTATCTTCTGGATCAAGCTTATGAGTACGGAAAATCAgtaagatatacatcttgctcttgtttatgcctctcacctgtgt-tgaagtgtaatcaatacaaatttaaaactcgtattgaagttgaatgcccacattttc

upper sequence: AT4G22540.1 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: GLYMA11G03420.2 (Glycine max), 5'ss of exon 6
CCCTGTGTATTTCAATGAACCAATATCATCCCTCCAAAAATGTTTTGAAGACTTGGAGTATTCGTATCTTTTGGACCGAGCATATGAACATGGAAAATCTgtaagtgacacca--aagtctcttacttatcttgtacattactacattctgttt---atcttatattgacttaaagcctattggataatcag---------
||| || || || ||||| || ||||||||||| ||||| |||| ||| ||||||||||| || |||||| |||| | ||| |||||  | |||||||| |||||  ||| |   | | |||| ||   | ||  |    | |  || |   ||   | ||  ||||||  |  |    |    ||  |||          
CCCGGTATACTTTAATGAGCCGATATCATCCCTACAAAAGTGTTGTGAGGACTTGGAGTACTCTTATCTTCTGGATCAAGCTTATGAGTACGGAAAATCAgtaagatacatctttatgcctctcaccagtgttcaattgcaatcaatacaaatttaaaactcgtattgaagttgaatg-accacattttcaaaagcacctc

upper sequence: AT4G22540.1 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: Vv02s0154g00250.t01 (Vitis vinifera), 5'ss of exon 3
CCCTGTGTATTTCAATGAACCAATATCATCCCTCCAAAAATGTTTTGAAGACTTGGAGTATTCGTATCTTTTGGACCGAGCATATGAACATGGAAAATCTgtaagtgacaccaaagtctcttact---tatcttgtacattactacattctgtttatcttatattgac-ttaaagcctattggataatcag----------
|||||| ||||| ||||| |||||||||||||| || ||||||||||| ||||||||||| || ||||||||||| |||||||||||| |||||||| | ||| |  | | |    |||||||||   |  |||  | ||   |  | |    || |  | | | |   ||    | ||||     |   |          
CCCTGTTTATTTTAATGAGCCAATATCATCCCTTCAGAAATGTTTTGAGGACTTGGAGTACTCTTATCTTTTGGATCGAGCATATGAATATGGAAAAGCGgtatgc-atatctttatctcttactctctccctttgatataggtgtacttgcattgttctttttggttatttctccttattatgctacatgcttgtctata

upper sequence: AT4G22540.1 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: Vv02s0154g00240.t01 (Vitis vinifera), 5'ss of exon 5
CCCTGTGTATTTCAATGAACCAATATCATCCCTCCAAAAATGTTTTGAAGACTTGGAGTATTCGTATCTTTTGGACCGAGCATATGAACATGGAAAATCTgtaagtgacaccaaagtctcttact---tatcttgtacattactacattctgtttatcttatattgac-ttaaagcctattggataatcag----------
|||||| ||||| ||||| |||||||||||||| || ||||||||||| ||||||||||| || ||||||||||| ||||| |||||| |||||||| | ||| |  | | |    |||||||||   |  |||  | ||   |  | |    || |  | | | |   ||    | ||||     |   |          
CCCTGTTTATTTTAATGAGCCAATATCATCCCTTCAGAAATGTTTTGAGGACTTGGAGTACTCTTATCTTTTGGATCGAGCGTATGAATATGGAAAAGCGgtatgc-atatctttatctcttactctctccctttgatataggtgtacttgcattgttctttttggttatttctccttattatgctacatgcttgtctata

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|164141356|gb|ES079431.1|ES079431
EST:     GTATTCGTATCTTTTGGACCGAGCATATGAACATGGAAAATCT                         GGGAATGGTCTCTTAAGAGCCTTAAATGTTGCTGCTTTTGCGGTCTCTGGA
genomic: GTATTCGTATCTTTTGGACCGAGCATATGAACATGGAAAATCTgtaagtgaca ... ggataatcagGGGAATGGTCTCTTAAGAGCCTTAAATGTTGCTGCTTTTGCGGTCTCTGGA




















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CCCTGTGTATTTCAATGAACCAATATCATCCCTCCAAAAATGTTTTGAAGACTTGGAGTATTCGTATCTTTTGGACCGAGCATATGAACATGGAAAATCTgtaagtgacaccaaagtctcttacttatcttgtacattactacattctgtttatcttatattgacttaaagcctattggataatcag

- - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA