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

AGGTTGGGACAGAGCAAACCCATTTACAATGCATTTAAGGCTATTCGAGAATCTCCAGACTGGAATTCATTGAGCGAAGCTCGTCAACGATTAGTTGAAGgcaagtaattataatcggagcataagaaggaacacaatttgttctttcctttccagtttttttttgtataagaggaatcgttttatattttcaatgctcagagatatgtgctaatatagtttccatgtgttttcag

Basic information

species Arabidopsis thaliana
transcript AT5G10540.1
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G10540.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: Vv06s0061g01070.t01 (Vitis vinifera), 5'ss of exon 3
AGGTTGGGACAGAGCAAACCCATTTACAATGCATTTAAGGCTATTCGAGAATCTCCAGACTGGAATTCATTGAGCGAAGCTCGTCAACGATTAGTTGAAGgcaagt-aattataatcggagcataagaaggaacacaatttgttctttcctttccagtttttttttgtataagaggaatcgttttatattttcaatgctcagagatatgtgctaatatagtttccatgtgttttcag
|||||||| || |||||||||||||| |||||||| |  ||||||||||||||| |||| ||| |  |  |||  || |||||| | ||  | || |||||  ||| ||   |  | | |  |||||| |      ||||| |            | || || ||| |       ||||| |  || | | | | | |  ||| ||||                             
AGGTTGGGCCAAAGCAAACCCATTTATAATGCATTCAGAGCTATTCGAGAATCTTCAGATTGGGAAGCTCTGAATGATGCTCGTAAGCGCATTGTGGAAGgttagttaaacttgtttgcattataagaggt--tgtaatttttgagaagaaaagtaattgttcttttt-------gaatc-tcataaaatatgagtacatagatatatag---------------------------

upper sequence: AT5G10540.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: Vv00s0211g00060.t01 (Vitis vinifera), 5'ss of exon 3
AGGTTGGGACAGAGCAAACCCATTTACAATGCATTTAAGGCTATTCGAGAATCTCCAGACTGGAATTCATTGAGCGAAGCTCGTCAACGATTAGTTGAAGgcaagtaattataatcggagcataagaaggaacacaatttgttctttcctttccagtttttttttgtataagaggaatcgttttatattttcaatgctcagagatatgtgctaatatagtttccatgtgttttcag
|||||||| || |||||||||||||| ||||||||||| ||||||| ||||||||| || ||| |  || |||| || ||||   ||||  |||| ||  |  ||||  ||   | | |      |||         |   ||  |||| |   |||  ||     |||   ||||| | |  ||||||   ||  || | | ||                               
AGGTTGGGGCAAAGCAAACCCATTTATAATGCATTTAAAGCTATTCAAGAATCTCCTGAGTGGCAAACACTGAGTGATGCTCAGAAACGTATAGTGGACTgtgagta--tacttttgtaatg---gaaattttttgttcattttgttccatgtgagtggttaaccttatggcaggaaac-tgatatattacgaaaactaaaatatt------------------------------
















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|116452131|gb|EG494723.1|EG494723
EST:     CATTGAGCGAAGCTCGTCAACGATTAGTTGAAG                         TCCAAATAAAGGAGGCGGTTCTGAGTGGTATTGCTCTTGAAGATGATAAGA
genomic: CATTGAGCGAAGCTCGTCAACGATTAGTTGAAGgcaagtaatt ... gtgttttcagCCCAAATAAAGGAGGCGGTTCTGAGTGGTATTGCTCTTGAAGATGATAAGA
EST: gi|164063100|gb|ES144823.1|ES144823
EST:     ATCTCCAGACTGGAATTCATTGAGCGAAGCTCGTCAACGAT-AGTTGAAG                         CCCAAATAAAGGAGGCGGTTC
genomic: ATCTCCAGACTGGAATTCATTGAGCGAAGCTCGTCAACGATTAGTTGAAGgcaagtaatt ... gtgttttcagCCCAAATAAAGGAGGCGGTTC
EST: gi|116476837|gb|EG519429.1|EG519429
EST:     ATCTCCAGACTGGAATTCATTGAGCGAAGCTCGTCAACGATTAGTTGAAG                         CCCAAATAAAGGAGGCGGTTCTGAGTGGTATTGCTCTTGAAGATGATAAGA
genomic: ATCTCCAGACTGGAATTCATTGAGCGAAGCTCGTCAACGATTAGTTGAAGgcaagtaatt ... gtgttttcagCCCAAATAAAGGAGGCGGTTCTGAGTGGTATTGCTCTTGAAGATGATAAGA
EST: gi|116452130|gb|EG494722.1|EG494722
EST:     ATCTCCAGACTGGAATTCATTGAGCGAAGCTCGTCAACGATTAGTTGAAG                         TCCAAATAAAGGAGGCGGTTCTGAGTGGTATTGCTCTTGAAGATGATAAGA
genomic: ATCTCCAGACTGGAATTCATTGAGCGAAGCTCGTCAACGATTAGTTGAAGgcaagtaatt ... gtgttttcagCCCAAATAAAGGAGGCGGTTCTGAGTGGTATTGCTCTTGAAGATGATAAGA
EST: gi|116452113|gb|EG494705.1|EG494705
EST:     ATCTCCAGACTGGAATTCATTGAGCGAAGCTCGTCAACGATTAGTTGAAG                         CCCAAATAAAGGAGGCGGTTCTGAGTGGTATTGCTCTTGAAGATGATAAGA
genomic: ATCTCCAGACTGGAATTCATTGAGCGAAGCTCGTCAACGATTAGTTGAAGgcaagtaatt ... gtgttttcagCCCAAATAAAGGAGGCGGTTCTGAGTGGTATTGCTCTTGAAGATGATAAGA
EST: gi|116452116|gb|EG494708.1|EG494708
EST:     GACTGGAATTCATTGAGCGAAGCTCGTCAACGATTAGTTGAAG                         CCCAAATAAAGGAGGCGGTTCTGAGTGGTATTGCTCTTGAAGATGATAAGA
genomic: GACTGGAATTCATTGAGCGAAGCTCGTCAACGATTAGTTGAAGgcaagtaatt ... gtgttttcagCCCAAATAAAGGAGGCGGTTCTGAGTGGTATTGCTCTTGAAGATGATAAGA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGGTTGGGACAGAGCAAACCCATTTACAATGCATTTAAGGCTATTCGAGAATCTCCAGACTGGAATTCATTGAGCGAAGCTCGTCAACGATTAGTTGAAGgcaagtaattataatcggagcataagaaggaacacaatttgttctttcctttccagtttttttttgtataagaggaatcgttttatattttcaatgctcagagatatgtgctaatatagtttccatgtgttttcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG