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'   		11  
 5'  3'   		12  
 5'  3'   		13  
 5'  3'   		14  
 5'  3'   		15  
 5'  3'   		16  
 5'  3'   		17  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTTCTGGAATTTTGATGCTTTGTTCCAGCCTCAGCAGCACCCTGCTCGTGATTCTCATGACACCTTCTTTCTAAAAGgttcaaatcttgaatcctttgtcactaaatttgttgtttaggacagctatttctaggttgcttgttgacatctcaaagaatagataactcttacatttaagacgtaaatctttgaatgtag

Basic information

species Arabidopsis thaliana
transcript AT4G39280.2
intron # 10
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT4G39280.2 (Arabidopsis thaliana), 5'ss of exon 10
lower sequence: GRMZM2G101463_T01 (Zea mays), 5'ss of exon 10
CTTCTGGAATTTTGATGCTTTGTTCCAGCCTCAGCAGCACCCTGCTCGTGATTCTCATGACACCTTCTTTCTAAAAGgttcaaatcttgaatcctttgtcactaaatttgttgtttaggacagctatttctaggttgcttgttgacatctcaaagaatagataactcttacatttaagacgtaaatctttgaatgtag
|||||||||||| |||||  |||| |||||||| ||||| |||||||| ||||| ||||| || || || || ||||||  |  |||   |  || |  ||    ||   |    | |||    |   |||  ||||    |  | || |   ||                                           
CTTCTGGAATTTCGATGCACTGTTTCAGCCTCAACAGCATCCTGCTCGGGATTCACATGATACATTTTTCCTGAAAGgt--atgtctgagacactataccatctcataattgaagttggat--ttggatcttagttgtacatcaa-attttgcag-------------------------------------------

upper sequence: AT4G39280.2 (Arabidopsis thaliana), 5'ss of exon 10
lower sequence: GLYMA11G12530.1 (Glycine max), 5'ss of exon 9
CTTCTGGAATTTTGATGCTTTGTTCCAGCCTCAGCAGCACCCTGCTCGTGATTCTCATGACACCTTCTTTCTAAAAGgttcaaatcttgaatcctttgtcactaaatttgttgtttaggacagctatttctaggttgcttgttgacatctcaaagaatagataactcttacatttaagacgtaaatctttgaatgtag
||||||||| |||||||| ||||||||||| || || ||||| || |||||||| ||||| || |||||| |  || |||       | || ||||  |       ||  | ||        |||| |  |   ||   | ||   || ||  |||| |  | || | || || |                       
CTTCTGGAACTTTGATGCCTTGTTCCAGCCCCAACAACACCCAGCCCGTGATTCACATGATACATTCTTTTTGGAAAgttag-----taaaaccttaatt------ttcatcgt--------gctaatcttgtattatatatttgtat-tctgagaacatgtgacacatatatctgcag-------------------

upper sequence: AT4G39280.2 (Arabidopsis thaliana), 5'ss of exon 10
lower sequence: GLYMA12G04730.1 (Glycine max), 5'ss of exon 9
CTTCTGGAATTTTGATGCTTTGTTCCAGCCTCAGCAGCACCCTGCTCGTGATTCTCATGACACCTTCTTTCTAAAAGgttcaaatcttgaatcctttgtcactaaatttgttgtttaggacagctatttctaggttgcttgttgacatctcaaagaatagataactcttacatttaagacgtaaatctttgaatgtag
||||||||| |||||||| ||||||||||| || || ||||| || |||||||| ||||| || |||||| |  || |||       | || ||||  |   |   ||  | ||        |||| || |   ||   ||||   || ||  |||| |  | || | || || |                       
CTTCTGGAACTTTGATGCCTTGTTCCAGCCCCAACAACACCCAGCCCGTGATTCACATGATACATTCTTTTTGGAAAgttag-----taaaaccttaattgtt---ttcatcgt--------gctaattttgtatt--ctgtttctat-tctgagaacatgtgacacatatatctgcag-------------------

upper sequence: AT4G39280.2 (Arabidopsis thaliana), 5'ss of exon 10
lower sequence: GLYMA17G34950.1 (Glycine max), 5'ss of exon 11
CTTCTGGAATTTTGATGCTTTGTTCCAGCCTCAGCAGCACCCTGCTCGTGATTCTCATGACACCTTCTTTCTAAAAGgttcaaatcttgaatcctttgtcactaaatttgttgtttaggacagctatttctaggttgcttgttgacatctcaaagaatagataactcttacatttaagacgtaaatctttgaatgtag
||||||||| || ||||| ||||||||||| || || ||||| ||||||||||| ||||| || || |||||  ||||||       | || ||||  |   |    || |||          ||| |  ||  ||   ||||   || ||  |||| |  | || | || || |                       
CTTCTGGAACTTCGATGCCTTGTTCCAGCCCCAACAACACCCAGCTCGTGATTCACATGATACATTTTTTCTGGAAGgttag-----taaaaccttgattgtt----ttcttg----------ctaatcttatattctctgtttctat-tctgagaacatgtgacacatatatctgcag-------------------

upper sequence: AT4G39280.2 (Arabidopsis thaliana), 5'ss of exon 10
lower sequence: Vv03s0063g02560.t01 (Vitis vinifera), 5'ss of exon 10
CTTCTGGAATTTTGATGCTTTGTTCCAGCCTCAGCAGCACCCTGCTCGTGATTCTCATGACACCTTCTTTCTAAAAGgttcaa--atcttgaatcctttgtcactaaatttgttgtttaggacagctatttctaggttgcttgttgacatctcaaagaatagataactcttacatttaagacgtaaatctttgaatgtag
||||||||||||||||||  |||||||||| || || ||||||||||||||||| ||||| |||||||| ||  |||||      | |||||   | |  ||| | | |    ||||| | |    | |||   |   |  | ||| | | |  |   | ||                                      
CTTCTGGAATTTTGATGCACTGTTCCAGCCACAACAACACCCTGCTCGTGATTCACATGATACCTTCTTCCTGCAAGgtctgttcaacttgatctcctaatcagtgactgctatgtttggta----ttttttctgacagtcttttggccttttcatttacag--------------------------------------

upper sequence: AT4G39280.2 (Arabidopsis thaliana), 5'ss of exon 10
lower sequence: PP1S358_20V6.1 (Physcomitrella patens), 5'ss of exon 10
CTTCTGGAATTTTGATGCTTTGTTCCAGCCTCAGCAGCACCCTGCTCGTGATTCTCATGACACCTTCTTTCTAAAAGgttcaaatcttgaatccttt--gtcactaaatttgttgtttaggacagctatttctaggttgcttgttgacatctcaaagaatagataactcttac-atttaagacgtaaatctttgaatgtag
|||||||||||| |||||  ||||||||||||| ||||| || || ||||| |||||||||||||| ||  | || |||      |  |   | |||  ||  |||    || ||   ||     ||||| |    |  ||     |||  | | | ||| | ||  | |||   | |  |                    
CTTCTGGAATTTCGATGCACTGTTCCAGCCTCAACAGCATCCAGCCCGTGACTCTCATGACACCTTTTTCTTGAAGGgtgagttgcccgtgacttttaggttgctag---tggtgccgagcttttctattac---ataactca--aacaagtaagataatggctatattttattgtctgcggtac----------------

upper sequence: AT4G39280.2 (Arabidopsis thaliana), 5'ss of exon 10
lower sequence: EFJ23053 (Selaginella moellendorffii), 5'ss of exon 10
CTTCTGGAATTTTGATGCTTTGTTCCAGCCTCAGCAGCACCCTGCTCGTGATTCTCATGACACCTTCTTTCTAAAAGgt---tcaaatcttgaatcctttgtcactaaatttgttgtttaggacagctatttctaggttgcttgttgacatctcaaagaatagataactcttacatttaagacgtaaatctttgaatgtag
|||||||||||| ||||| ||||||||||| |||||||| ||||| || || || || ||||| |||||  ||||| ||   |    || |||    ||| ||| |  ||  ||  | |||                                                                                
CTTCTGGAATTTCGATGCCTTGTTCCAGCCGCAGCAGCATCCTGCCCGGGACTCACACGACACATTCTTCTTAAAAAgtaagtgtgttcgtgatatgtttatcattttatg-gtcatgtag--------------------------------------------------------------------------------

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|164120386|gb|ES088784.1|ES088784
EST:     GCCTCAGCAGCACCCTGCTCGTGATTCTCATGACACCTTCTTTCTAAAAG                         TTCCCTCTACTACAAGAACAC
genomic: GCCTCAGCAGCACCCTGCTCGTGATTCTCATGACACCTTCTTTCTAAAAGgttcaaatct ... ttgaatgtagTTCCCTCTACTACAAGAACAC