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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGAAGTTCAATGTTAACCGAGTGGATAACATGGTTATTCAAGCTATCTTCATGCTTGACACGCTTGATAAGGATATCAATTCCTTTGCCATGAGAGTCAGgtttgttttgtgcttttccctttcagattgtgtgttttcctcgagaaaattggtagctgaactgtttataatgttattacag

Basic information

species Arabidopsis thaliana
transcript AT1G56110.1
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G56110.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: LOC_Os07g46720.2 (Oryza sativa), 5'ss of exon 3
TGAAGTTCAATGTTAACCGAGTGGATAACATGGTTATTCAAGCTATCTTCATGCTTGACACGCTTGATAAGGATATCAATTCCTTTGCCATGAGAGTCAGgtttgttttgtgcttttccct----ttcagattgtgtgttt-----tcctcgagaaaattggtagctgaactgtttataatgttattacag---------
| ||||||||||| ||||| |||||||||||||| |||||||| || ||  || | || || |||||||||||||||||||||||  |||||||||| |||||||||     ||||| | |    | ||  ||   |||||     |  |     | |||  ||| ||   ||  |  ||| | || ||           
TTAAGTTCAATGTGAACCGTGTGGATAACATGGTAATTCAAGCGATTTTTTTGTTGGATACACTTGATAAGGATATCAATTCCTTCTCCATGAGAGTGAGgtttgttgccatcttttgcttaatttacatgttcattgtttagtgatttttatttagatttttagatgttgtgactggaatttaatcacctcaattatgt

upper sequence: AT1G56110.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: LOC_Os03g22880.1 (Oryza sativa), 5'ss of exon 3
TGAAGTTCAATGTTAACCGAGTGGATAACATGGTTATTCAAGCTATCTTCATGCTTGACACGCTTGATAAGGATATCAATTCCTTTGCCATGAGAGTCAGgtttgttttgtgcttttccctttcagattg----------tgtgttttcctcgagaaaattggtagctgaactgtttata-atgttattacag-------
||||||||||||| ||||| || || |||||||| ||||| ||||||||| || | || || ||||| ||||| |||||||| ||  |||||||||| |||| || ||| | |||     |||  | ||           | | ||||  | | | | ||   |   ||  || || ||  |    |  |  |       
TGAAGTTCAATGTGAACCGCGTTGACAACATGGTGATTCAGGCTATCTTCCTGTTGGATACACTTGACAAGGACATCAATTCTTTCTCCATGAGAGTGAGgtctggtttcttcttccgtgttttgggttaatatgatgcatttttttttgttgtggacatgcatgattgttctattgattcaccacacaatggtgtttgg

upper sequence: AT1G56110.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: GRMZM2G110233_T01 (Zea mays), 5'ss of exon 3
TGAAGTTCAATGTTAACCGAGTGGATAACATGGTTATTCAAGCTATCTTCATGCTTGACACGCTTGATAAGGATATCAATTCCTTTGCCATGAGAGTCAGgt-ttgtt-ttgtgcttttccctttcagattgtgtgt--tttcctcgagaaaattggtagctgaactgtttataa------tgttattacag--------------------------------------------------------------------------
||||||||||||| || || || ||||||||||| || ||||| || ||  |||| || || ||||| ||||| |||||||||||  |||||||||||||||  |||  |||| | | | |   |   ||||| | |  ||  ||    | ||  |  |   |   | ||||||       || | | | ||                                                                          
TGAAGTTCAATGTGAATCGTGTTGATAACATGGTGATCCAAGCAATATTTCTGCTGGATACACTTGACAAGGACATCAATTCCTTCTCCATGAGAGTCAGgtactgtccttgttcatgttctcatataattgtttatggttaacttcttataagcgtaataggccgtatttatagacagtctgctctgatagaaaactctgataatatgaatatgcaaatattccttattatgattatttattgctttctcaataaaacattgcag

upper sequence: AT1G56110.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: GRMZM2G144995_T01 (Zea mays), 5'ss of exon 3
TGAAGTTCAATGTTAACCGAGTGGATAACATGGTTATTCAAGCTATCTTCATGCTTGACACGCTTGATAAGGATATCAATTCCTTTGCCATGAGAGTCAGgtttgttttgtgcttttccctttcagattgt-gtgttttcctcgagaaaattggtagctgaactgtttataatgttattacag------------------------------------------------------
||||||||||||| || || || || |||||||| || || || |||||  |  | || |||||||| ||||| |||||||||||  ||||||||||||||| ||||   || | | |  |  | | || | ||   ||     |||    |  |||       | || | | | ||| |  |                                                      
TGAAGTTCAATGTGAATCGTGTTGACAACATGGTGATCCAGGCAATCTTTCTATTGGATACGCTTGACAAGGACATCAATTCCTTCTCCATGAGAGTCAGgtctgttgcttgttctcctataactgtttattgtcaattttctaagaggcatcataggcagggagctt-tgaggatatgaatgtgccaatatgcccttggtatgattatttactgttttctcaataaaacactgcag

upper sequence: AT1G56110.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: GLYMA05G03150.1 (Glycine max), 5'ss of exon 3
TGAAGTTCAATGTTAACCGAGTGGATAACATGGTTATTCAAGCTATCTTCATGCTTGACACGCTTGATAAGGATATCAATTCCTTTGCCATGAGAGTCAGgt---------------------------ttgttttgtgcttttccctttcag-attgtgtgttttcctcgagaaaattggtagctg-aactgtttataatgttattacag-----------------
||||||| ||||||||||| || || |||||||||||||||||||||||| | ||||| || ||||| |||||||| ||||| ||  |||||||||||||||                           |  || |    |||||   ||||  ||  | ||||||| | ||||| ||||  | ||| ||   || ||     ||||                     
TGAAGTTTAATGTTAACCGTGTAGACAACATGGTTATTCAAGCTATCTTCCTTCTTGATACACTTGACAAGGATATTAATTCATTCTCCATGAGAGTCAGgtagtatgtctcaaatttgaatgctcaattaattatagaattttcttattcaatataatttgttttctttgagaacattgtgaactggaagaattcatttctctatttgctttgtcaattatgtgcag

upper sequence: AT1G56110.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: GLYMA17G13770.1 (Glycine max), 5'ss of exon 3
TGAAGTTCAATGTTAACCGAGTGGATAACATGGTTATTCAAGCTATCTTCATGCTTGACACGCTTGATAAGGATATCAATTCCTTTGCCATGAGAGTCAGgtt---tgttttgtgctt---ttccctttcagattgtgtgttttcctcgagaaaattggtagctgaactgtttataatgttattacag------------------------------------------
||||||| ||||||||||| || || |||||||||||||||||||||||| | ||||| || ||||| |||||| | ||||| ||  |||||||||||||||    |||||     ||   | | |  | |  ||     ||||| | |  |||||   | | |   |  || | ||  ||  || |                                           
TGAAGTTTAATGTTAACCGTGTTGACAACATGGTTATTCAAGCTATCTTCCTTCTTGATACACTTGACAAGGATGTTAATTCGTTCTCCATGAGAGTCAGgtagtatgtttcaacattggatgctcaattaattttaaaattttcatggtcaaaataatttgttc--cctttgagaaaatttgtaaactggaaggattcatgtaacttttggcttgtcaattatgtgcag

upper sequence: AT1G56110.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: GLYMA07G11560.1 (Glycine max), 5'ss of exon 3
TGAAGTTCAATGTTAACCGAGTGGATAACATGGTTATTCAAGCTATCTTCATGCTTGACACGCTTGATAAGGATATCAATTCCTTTGCCATGAGAGTCAGgt---ttgtttt-----gtgcttttccctttcagattgtgtgttttcctcgagaaaattggtagctgaactgtttataatgttattacag------------------------------------------
|||| |||||||||||||| || || |||||||| |||||||| || ||| | ||||| || |||||||||||||| ||||| ||  |||||||||||||||   |||| ||     |||  |   |   | ||  | |   ||||| |     |||| | |  ||   |  || |  |  |||||| |                                           
TGAAATTCAATGTTAACCGTGTTGACAACATGGTCATTCAAGCAATTTTCCTTCTTGATACACTTGATAAGGATATTAATTCATTCTCCATGAGAGTCAGgtagtttgtgttcaacagtgaatactctaataagtctata-attttcatactctaaatagttttctt--cctttaaggaaattattaaactcgaaagagttcaattctctgctattcatcaattgtatgcag

upper sequence: AT1G56110.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: Vv17s0000g01720.t01 (Vitis vinifera), 5'ss of exon 3
TGAAGTTCAATGTTAACCGAGTGGATAACATGGTTATTCAAGCTATCTTCATGCTTGACACGCTTGATAAGGATATCAATTCCTTTGCCATGAGAGTCAGgtttgttttgtgcttttccctttcagattgtgtgttttcctcgagaaaattggtagctgaactgtttataatgttattacag-------------------
||||||||||||| ||| |||| ||||| ||||| ||||| || |||||| | || || || |||||||| ||||||||||||||  |||||||||||||||||||| | |  | |||     || |   ||| |||       |  |  |   | | ||  | | |    | ||  | | |                   
TGAAGTTCAATGTGAACAGAGTCGATAATATGGTCATTCAGGCCATCTTCCTTCTCGATACTCTTGATAAAGATATCAATTCCTTCTCCATGAGAGTCAGgtttgttat-taatattcgtccacaaaccttgtctttggtgattgttatcttcaatccgacatatattatttattccttcggagctaatccactggtcctg

upper sequence: AT1G56110.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: PP1S88_119V6.1 (Physcomitrella patens), 5'ss of exon 3
TGAAGTTCAATGTTAACCGAGTGGATAACATGGTTATTCAAGCTATCTTCATGCTTGACACGCTTGATAAGGATATCAATTCCTTTGCCATGAGAGTCAGgtttgttttgtgcttttccctttcagattgtgtgttttcctcgagaaaattggtagctgaactgtttataatgttattacag-------------------------------------------------------------------
| |||||||||||||||||||| ||||||||| | ||||||   |||  | || | || || ||||| |||||  ||||  | ||   |||| | ||| |||  |||| ||      ||| |||  | |  |  |||   |    | | ||| || |  | | |    | |     ||  |                                                                    
TTAAGTTCAATGTTAACCGAGTAGATAACATGATCATTCAAAGCATCAGCTTGTTGGATACCCTTGACAAGGACGTCAACACGTTCTGCATGCGGGTCCGgtgagtttcgtttacccccccttcttacttcgcttttgtgtgattatatttgatatcccagcagaggctgagagatttgtaagcatggtctgtgtgatacgtatctcggattgtagtgtgctaaattatgtttgcaacatatcgtgcag

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|47829863|gb|CK119547.1|CK119547
EST:     ATGCTTGACACGCTTGATAAGGATATCAATTCCTTTGCCATGAGAGTCAG                         GGAATGGTATTCGTGGCACTTCCCCGAACTAGTGAAGATAGTCAATGACAA
genomic: ATGCTTGACACGCTTGATAAGGATATCAATTCCTTTGCCATGAGAGTCAGgtttgttttg ... gttattacagGGAATGGTATTCGTGGCACTTCCCCGAACTAGTGAAGATAGTCAATGACAA
EST: gi|124972846|gb|EL046515.1|EL046515
EST:     CTTGACACGCTTGATAAGGATATCAATTCCTTTGCCATGAGAGTCAG                         GGAATGGTATTCGTGGCACTTCCCCGAACTAGTGAAGATAGTCAATGACAA
genomic: CTTGACACGCTTGATAAGGATATCAATTCCTTTGCCATGAGAGTCAGgtttgttttg ... gttattacagGGAATGGTATTCGTGGCACTTCCCCGAACTAGTGAAGATAGTCAATGACAA
EST: gi|116482901|gb|EG525493.1|EG525493
EST:     ATGCTTGACACGCTTGATAAGGATATCAATTCCTTTGCCATGGGAGTCAG                         GGAATGGTATTCGTGGCACTTCCCCGAACTAGTGAAGATAGTCAATGACAA
genomic: ATGCTTGACACGCTTGATAAGGATATCAATTCCTTTGCCATGAGAGTCAGgtttgttttg ... gttattacagGGAATGGTATTCGTGGCACTTCCCCGAACTAGTGAAGATAGTCAATGACAA