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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CACAGACTACATGGTGGATGTTATCTGCAAACGTGCTGAACTTGGTTACAACTACGGTGTCATACTGATTCCAGAAGGTCTGATCGACTTTATTCCTGAGgtgtgttgtcattgtaaaaaaatagaatctactacttttaaaccgattaatataattgttcttcttaactgatgattaattttatttcatgacttctcag

Basic information

species Arabidopsis thaliana
transcript AT1G12000.1
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G12000.1 (Arabidopsis thaliana), 5'ss of exon 9
lower sequence: LOC_Os06g13810.1 (Oryza sativa), 5'ss of exon 9
CACAGACTACATGGTGGATGTTATCTGCAAACGTGCTGAACTTGGTTACAACTACGGTGTCATACTGATTCCAGAAGGTCTGATCGACTTTATTCCTGAGgtgtg----ttgtcattgtaaaaaaatagaatctactacttttaaaccgattaatataattgttcttcttaactgatgattaattttatttcatgacttctcag
||| ||||||||    ||  || ||||||| ||||| ||||||||||||||||| ||||| || || || ||||| |||||||| || || || || ||||| ||    |  |||||        ||      |   ||  ||      | | || | ||| |  |||||  ||                              
CACCGACTACATTACCGACATTGTCTGCAAGCGTGCAGAACTTGGTTACAACTATGGTGTGATCCTTATCCCAGAGGGTCTGATTGATTTCATCCCAGAGgtttgacaatcttcattcacctgtgatttgtgttgtcacgatttgcattactgatttcattctgtttctttcctag----------------------------

upper sequence: AT1G12000.1 (Arabidopsis thaliana), 5'ss of exon 9
lower sequence: GRMZM2G059151_T01 (Zea mays), 5'ss of exon 9
CACAGACTACATGGTGGATGTTATCTGCAAACGTGCTGAACTTGGTTACAACTACGGTGTCATACTGATTCCAGAAGGTCTGATCGACTTTATTCCTGAGgtgtgttgtcattgtaaaaaaatagaatctactacttttaaaccg-attaatataattgttcttcttaactgatgattaattttatttcatgacttctcag
|||| |||||||    ||| | |||||||| ||||| || |||||||||||||| ||||| || || || |||||||| ||||| || || || || ||||| ||      |  | |     ||  |  |  |  | | |  |   |||| |   ||   |||| |    |   |                          
CACAAACTACATTACTGATATCATCTGCAAGCGTGCAGATCTTGGTTACAACTATGGTGTTATCCTTATACCAGAAGGCCTGATTGATTTCATCCCAGAGgtttggcac--tccttatgttctatgactttgtgttgtcagtctatattactgacatcactcttttctttttcag--------------------------

upper sequence: AT1G12000.1 (Arabidopsis thaliana), 5'ss of exon 9
lower sequence: GRMZM2G143862_T01 (Zea mays), 5'ss of exon 2
CACAGACTACATGGTGGATGTTATCTGCAAACGTGCTGAACTTGGTTACAACTACGGTGTCATACTGATTCCAGAAGGTCTGATCGACTTTATTCCTGAGgtgtgttgtcattgtaaaaaaatagaatctactacttttaaaccgattaatataattgttcttcttaactgatgattaattttatttcatgacttctcag
|||| |||||||    ||| | |||||||| ||||| || |||||||||||||| ||||| || || || |||||||| ||||| || || || || ||||| ||     || ||      |  |  |   |        |    | | | |||| |  | |||||   ||| |                          
CACAAACTACATTACTGATATCATCTGCAAGCGTGCAGATCTTGGTTACAACTATGGTGTTATCCTTATACCAGAAGGCCTGATTGATTTCATCCCAGAGgtttgactctat-gttctgtgactgtgttacccgtagaacatattactgacataactccttttctt--ttgaag--------------------------

upper sequence: AT1G12000.1 (Arabidopsis thaliana), 5'ss of exon 9
lower sequence: Vv10s0116g00360.t01 (Vitis vinifera), 5'ss of exon 9
CACAGACTACATGGTGGATGTTATCTGCAAACGTGCTGAACTTGGTTACAACTACGGTGTCATACTGATTCCAGAAGGTCTGATCGACTTTATTCCTGAGgtgtgttgtc-attgtaaaaaaatagaatcta---ctacttttaaaccgatta-atataattgttcttcttaactga--tgattaattttatttcatgacttctcag
 ||||||||||| || |||||| ||||||||||||| ||||||||||||||||| ||||| ||||| ||||||||||| || || || || || |||||||| |  | |  ||| ||| |       || ||   ||  ||||   ||  ||    ||   | | ||| | | |  |  ||  |   ||| ||||| |         
TACAGACTACATTGTTGATGTTGTCTGCAAACGTGCAGAACTTGGTTACAACTATGGTGTTATACTTATTCCAGAAGGCCTTATTGATTTCATACCTGAGgtataatattgattataagacttatttatttaacccttttttttgtcctcttgtgaatgggtatccttttaagcaaacttgtcttgctttttttcaagtt-------

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|124798452|gb|EH888131.1|EH888131
EST:     TACTGATTCCAGAAGGTCTGATCGACTTTATTCCTGAG                         GTCCAAGAGCTCATTGCTGAACTGAATGAAATTCTGGCAAATGAGGTTGTC
genomic: TACTGATTCCAGAAGGTCTGATCGACTTTATTCCTGAGgtgtgttgtc ... gacttctcagGTCCAAGAGCTCATTGCTGAACTGAATGAAATTCTGGCAAATGAGGTTGTC
EST: gi|164119733|gb|ES032715.1|ES032715
EST:     ACTACGGTGTCATACTGATTCCAGAAGGTCTGATCGACTTTATTCCTGAG                         GTCCAAGAGCTCATT
genomic: ACTACGGTGTCATACTGATTCCAGAAGGTCTGATCGACTTTATTCCTGAGgtgtgttgtc ... gacttctcagGTCCAAGAGCTCATT
EST: gi|125044797|gb|EL117066.1|EL117066
EST:     CTGATTCCAGAAGGTCTGATCGACTTTTATTCCTGAG                         GTCCAAGAGCTCATTGCTGAACTGAATGAAATTCTGGCAAATGAGGTTGTC
genomic: CTGATTCCAGAAGGTCTGATCGAC-TTTATTCCTGAGgtgtgttgtc ... gacttctcagGTCCAAGAGCTCATTGCTGAACTGAATGAAATTCTGGCAAATGAGGTTGTC
EST: gi|116438054|gb|EG480646.1|EG480646
EST:     ACTACGGTGTCATACTGATTCCAGAAGGTCTGATCGACTTTATTCCTGAG                         GTCCAAGAGCTCATTGCTGAACTGAATGAAATTCTGGCAAATGAGGTTGTC
genomic: ACTACGGTGTCATACTGATTCCAGAAGGTCTGATCGACTTTATTCCTGAGgtgtgttgtc ... gacttctcagGTCCAAGAGCTCATTGCTGAACTGAATGAAATTCTGGCAAATGAGGTTGTC
EST: gi|125316880|gb|EL330965.1|EL330965
EST:     ACTACGGTGTCATACTGATTCCAGAAGGTCTGATCGACTTTATTCCTGAG                         GTCCAAGAGCT
genomic: ACTACGGTGTCATACTGATTCCAGAAGGTCTGATCGACTTTATTCCTGAGgtgtgttgtc ... gacttctcagGTCCAAGAGCT