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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgattttgtatttctgaggcttgagaagcgtgttatttgcatactcgtgaactataactaatcaggattttaattcttcagGCCGCTGTCGAGGAAGGTATTGTTGTTGGTGGTGGTTGCACTCTGCTTCGTCTTGCTTCCAAGGTTGATGCCATTAAAGCCACGCTTGATAATGATGAAG

Basic information

species Arabidopsis thaliana
transcript AT1G55490.1
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G55490.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: LOC_Os06g02380.1 (Oryza sativa), 3'ss of exon 10
---------------------------------------------------------------gtgattttgtatttctgaggcttgagaagcgtgttatttgcatactcgtgaactataactaatcag--gattttaattcttcagGCCGCTGTCGAGGAAGGTATTGTTGTTGGTGGTGGTTGCACTCTGCTTCGTCTTGCTTCCAAGGTTGATGCCATTAAAGCCACGCTTGATAATGATGAAG
                                                                  |||  |    | ||  |||     ||  || |||   | | ||  ||   |   |    | |   | ||    ||  |||||| ||||| ||||||||||||||||||||||| || |||||||| ||  | || ||  | |  ||||| ||||| || | ||  || || ||||||||  
gttagtctgttgttataactgctttgagatagaaatagattaatgtttgcttcttaaggaagaaaaattaaggtagtttgttgctcactgagt-tgatatcaacgttcttctggctttggatctttaaaccgcttcctctttgtcagGCTGCTGTTGAGGAAGGTATTGTTGTTGGTGGAGGGTGCACTCTTCTGAGACTGGCAGCTAGAGTTGACGCCATCAAGGACAACCTGGAGAATGATGAGC

upper sequence: AT1G55490.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: LOC_Os02g01280.1 (Oryza sativa), 3'ss of exon 10
---------------------------------gtgattttgtatttct-gaggcttgagaagcgtgttatttgcat--actcgtgaactataactaatcaggattttaattcttcagGCCGCTGTCGAGGAAGGTATTGTTGTTGGTGGTGGTTGCACTCTGCTTCGTCTTGCTTCCAAGGTTGATGCCATTAAAGCCACGCTTGATAATGATGAAG
                                  ||   ||| |||    ||| |||  || ||   |    |  ||    | ||    | | ||| |  ||  |  |  |    ||||| ||||| |||||||||||||||||||| ||||| || || ||  | || ||||| || || ||||||||||||| ||  || ||||| ||||||||| 
gtgaatacttctctttgttaatataatttaattttgggattgcattcagagagccttctgatgcacatagagtatatgggtttgttgtttgttacttaatagtttgctc-tgtggcagGCGGCTGTTGAGGAAGGTATTGTTGTTGGAGGTGGCTGTACGCTTTTGCGGCTTGCATCAAAAGTTGATGCCATTATAGAAACACTTGAGAATGATGAAC

upper sequence: AT1G55490.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: GRMZM2G083716_T04 (Zea mays), 3'ss of exon 9
gtgattttgtatttct-gaggcttgagaagc---gtgttatttgc---atactcgtg---------aactataactaatcaggattttaattcttc--agGCCGCTGTCGAGGAAGGTATTGTTGTTGGTGGTGGTTGCACTCTGCTTCGTCTTGCTTCCAAGGTTGATGCCATTAAAGCCACGCTTGATAATGATGAAG
 | | |   || | || |   ||||| |      || || | |||   || ||| |          |  ||| |||||    | || |   |||||  |||| || || ||||||||||||||||||||||| || ||||||||  | || |||||  | || || || ||||| || |  || || || || || ||  
atcactccatactccttgcttcttgaaacattctgtattttctgctgaattctcttctggttacatatgtatcactaaagttgtttctttctcttcacagGCTGCCGTTGAGGAAGGTATTGTTGTTGGTGGAGGGTGCACTCTTTTGCGGCTTGCAGCTAAAGTCGACGCCATCAAGGATACACTGGAGAACGACGAGC

upper sequence: AT1G55490.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: GRMZM2G095252_T02 (Zea mays), 3'ss of exon 4
------------------------------------------------------------gtgattttgtatttctgaggcttgagaagcgtgttatttg-----catactcgtgaactataactaatcaggattttaattcttc--agGCCGCTGTCGAGGAAGGTATTGTTGTTGGTGGTGGTTGCACTCTGCTTCGTCTTGCTTCCAAGGTTGATGCCATTAAAGCCACGCTTGATAATGATGAAG
                                                             |  ||   |   || ||   |  ||    ||  || ||       ||  | || |  |||  ||||    | |  |  |||||   |||| ||||| ||||||||||||||||||||||| || ||||| ||  | || |||||  | || || |||||||| || |  || || || || |||||  
gtaagttgtcggagtaattaaccattttgtgctgccagatttatatttgcttcatgaggaatacttcctttgatcagaacatataggtttgttctagttcaactttattttggttatatatcgctaaaattgctcctttttctttatagGCTGCTGTTGAGGAAGGTATTGTTGTTGGTGGAGGATGCACCCTTTTGCGGCTTGCAGCTAAAGTCGATGCCATCAAGGATACACTGGAGAACGATGAGC

upper sequence: AT1G55490.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: GLYMA08G18760.1 (Glycine max), 3'ss of exon 9
gtgattttgtatttctgaggcttgagaagcgtgttatttgcatactcgtgaactataactaatcaggattttaattcttcagGCCGCTGTCGAGGAAGGTATTGTTGTTGGTGGTGGTTGCACTCTGCTTCGTCTTGCTTCCAAGGTTGATGCCATTAAAGCCACGCTTGATAATGATGAAG
|||   || | ||||  |   ||   |      || || | || ||      || |||   |  ||  | || | | ||||||| ||||| ||||||||||||||||||||||||||||||||||| ||  | ||||| || ||||| ||||| || || |  |  ||||||||||||||||
gtgtccttttctttcccaaagtttttagat---tttttgggattct----gtctgtaagctaatagtttgttgact-ttcagGCAGCTGTAGAGGAAGGTATTGTTGTTGGTGGTGGTTGCACTCTTCTGAGACTTGCATCAAAGGTGGATGCAATCAAGGATAGCCTTGATAATGATGAAG

upper sequence: AT1G55490.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: GLYMA15G40110.1 (Glycine max), 3'ss of exon 9
gtgattttgtatttctgaggcttgagaagcgtgttatttgcatactcgtgaactataactaatcaggattttaattcttcagGCCGCTGTCGAGGAAGGTATTGTTGTTGGTGGTGGTTGCACTCTGCTTCGTCTTGCTTCCAAGGTTGATGCCATTAAAGCCACGCTTGATAATGATGAAG
||    || | ||||  |   ||   |    | ||  ||| || ||  |   || |||   |  ||  | || | | ||||||| ||||| ||||| |||||||| |||||||||||||||||||| ||  | ||||| || ||||| ||  | || || |  |  ||||||||||||||||
gtatccttttctttcccaaagtttttagatttctt--ttgaattctgttt--ctgtaagctaatagtttgttgact-ttcagGCAGCTGTAGAGGAGGGTATTGTAGTTGGTGGTGGTTGCACTCTTCTGAGACTTGCATCAAAGGTGGACACAATCAAGGATAGCCTTGATAATGATGAAG

upper sequence: AT1G55490.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: Vv06s0004g00240.t01 (Vitis vinifera), 3'ss of exon 10
--------------------gtgattttgtatttctgaggcttgagaagcgtgt-tatttgcatactcgtga-actat-aactaatcagga--ttttaat--tcttcagGCCGCTGTCGAGGAAGGTATTGTTGTTGGTGGTGGTTGCACTCTGCTTCGTCTTGCTTCCAAGGTTGATGCCATTAAAGCCACGCTTGATAATGATGAAG
                     ||    || ||| ||      | | |  |  |  |  | ||| |  |   | | ||| || || |  ||   ||| |||  | ||||||| ||||| |||||||| |||||||| |||||||| |||||||| ||  | ||||| || ||||| |||||||| || | |||||||||||||||||| |
gtaatttctttcatgaaattatggcactgaattgctagttgctaatattcaagagtgatggcacagccagaacagtattaagtagtatggcattttcaatgattttcagGCAGCTGTTGAGGAAGGGATTGTTGTAGGTGGTGGGTGCACTCTCCTGAGACTTGCCTCAAAGGTGGATGCCATCAAGGACACGCTTGATAATGATGAGG

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|125282619|gb|EL296704.1|EL296704
EST:     GAGTTGAAGATGCTCTTAATGCAACAAAG                         GCCGCTGTCGAGGAAGGTATTGTTGTTGGTGGTGGTTGCACT
genomic: GAGTTGAAGATGCTCTTAATGCAACAAAGgtgattttgt ... aattcttcagGCCGCTGTCGAGGAAGGTATTGTTGTTGGTGGTGGTTGCACT






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agcgtgttatttgcatactcgtgaactataactaatcaggattttaattcttcagGCCGCTGTCGAGGAAGGTATTGTTGTTGGTGGTGGTTGCACTCTGCTTCGTCTTGCTTCCAAGGTTGATGCCATTAAAGCCACGCTTGATAATGATGAAG
                                               ttcttc  CT-rich tract
                                        attttaattcttca  TA-rich tract