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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TCTGAAAGGATCGAAACTTTCAGCAAACGTTTTCAATATACTCTTCAACCTTAATAAGTTCATGGCATTTGAAACACGTGACCCATTTCTCATTCGCCAGgtaagtttggcttaccagtggagtttttatagcactcaagagggaaaaaaataacaaagaatatgacttcttttaactgctaaaggcagtttgtagtagttcggattgaggcaattagaacaagtataattctctttcattgctgtag

Basic information

species Arabidopsis thaliana
transcript AT1G03960.1
intron # 11
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G03960.2 (Arabidopsis thaliana), 5'ss of exon 11
lower sequence: LOC_Os10g33680.1 (Oryza sativa), 5'ss of exon 11
TCTGAAAGGATCGAAACTTTCAGCAAACGTTTTCAATATACTCTTCAACCTTAATAAGTTCATGGCATTTGAAACACGTGACCCATTTCTCATTCGCCAGgtaagtttggcttacca--gtggagtttttatagcactcaagagggaaaaaaataacaaagaatatgacttcttttaactgctaaaggcagtttgtagtagttcggattgaggcaattagaacaagtataattctctttcattgctgtag
  | ||| | |  ||||| ||||  ||  | ||||| || || ||||| || || || || |||||||||||||| ||||| ||||| |||||||||||||| |      |||       |  ||   | |   ||||    |   |   |||||||||     || |  |||||| | | |                                                                    
CTTAAAACGGTGTAAACTCTCAGGGAATATATTCAACATCCTATTCAATCTCAACAAATTTATGGCATTTGAAACTCGTGATCCATTCCTCATTCGCCAGgtgatcacaacttcttgccataaagcagtgaattcact-gttaatcatctaaataacaagttggatca--tctttttatttcag------------------------------------------------------------------

upper sequence: AT1G03960.2 (Arabidopsis thaliana), 5'ss of exon 11
lower sequence: GRMZM2G148323_T01 (Zea mays), 5'ss of exon 11
TCTGAAAGGATCGAAACTTTCAGCAAACGTTTTCAATATACTCTTCAACCTTAATAAGTTCATGGCATTTGAAACACGTGACCCATTTCTCATTCGCCAGgtaagtttggcttaccagtggagtttttata-gcactcaag-agggaaaaaaataacaaagaatatgacttcttttaactgctaaaggcagtttgtagtagttcggattgaggcaattagaacaagtataattctctttcattgctgtag
  | ||| | |  ||||| |||| |||| | |||||||| || ||||| || || |||||||||||||||||||| ||||| ||||| |||||||||||||| | | |        | |  | |||  ||  ||   |||| |   |   ||||||      | |||  |  || ||                                                                         
CTTAAAACGGTGTAAACTCTCAGGAAACATATTCAATATTCTTTTCAATCTCAACAAGTTCATGGCATTTGAAACTCGTGATCCATTCCTCATTCGCCAGgtgattataatcc-ttaataaactttagatttgctgccaagtattaagttaaataattggcta-atgtttaattgtag------------------------------------------------------------------------

upper sequence: AT1G03960.2 (Arabidopsis thaliana), 5'ss of exon 11
lower sequence: Vv07s0005g03730.t01 (Vitis vinifera), 5'ss of exon 12
TCTGAAAGGATCGAAACTTTCAGCAAACGTTTTCAATATACTCTTCAACCTTAATAAGTTCATGGCATTTGAAACACGTGACCCATTTCTCATTCGCCAGgtaagtttggcttaccagtggagtttttatagcactcaagagggaaaaaaataacaaagaatatgacttcttttaactgctaaaggcagtttgtagtagttcggattgaggcaattagaacaagtataattctctttcattgctgtag
  |||| ||||  |||||||| | ||| ||||||||||| || ||||| ||||||||||||||||| |||||||| ||||| |||||||| || |||||||||| ||   | |     | | ||  |  ||| | ||||          | |  |||    |||    |   || |    || ||    ||   | | |     |||  |||||  ||                              
CTTGAAGGGATGCAAACTTTCTGGAAATGTTTTCAATATTCTTTTCAATCTTAATAAGTTCATGGCTTTTGAAACTCGTGATCCATTTCTAATACGCCAGgtaaattcaacatttttatag-gtgctcctagtaatcaa--------tcattgccaagttgtattttattcctttagcattatagt--attcccattggcatttattt-ggcaagcag------------------------------

upper sequence: AT1G03960.2 (Arabidopsis thaliana), 5'ss of exon 11
lower sequence: PP1S34_411V6.1 (Physcomitrella patens), 5'ss of exon 11
TCTGAAAGGATCGAAACTTTCAGCAAACGTTTTCAATATACTCTTCAACCTTAATAAGTTCATGGCATTTGAAACACGTGACCCATTTCTCATTCGCCAGgtaagtttggcttaccagtggagtttttatagcactcaagagggaaaaaaataacaaagaatatgacttcttttaactgctaaaggcagtttgtagtagttcggattgaggcaattagaacaagtataattctctttcattgctgtag
 |||||  | |  ||| | || |  ||  |||||||||| ||||||||||| || |||||| | |||||||| || |||||||| ||||||||||| ||||||   ||   ||||   |   |      | |   ||||     |      | | ||||    ||  | |  || | |  | |      | || | ||  ||  |||                                         
CCTGAAGCGGTGTAAATTATCTGGGAATTTTTTCAATATTCTCTTCAACCTGAACAAGTTCGTAGCATTTGAGACTCGTGACCCTTTTCTCATTCGTCAGgta---ttacattactcatatcgaaaacctggatttcaattcttagttgg-tcataaagcgagtg--tccagttcattattcacaat--tatgaactaaatcttattt----------------------------------------

upper sequence: AT1G03960.2 (Arabidopsis thaliana), 5'ss of exon 11
lower sequence: PP1S147_62V6.2 (Physcomitrella patens), 5'ss of exon 11
TCTGAAAGGATCGAAACTTTCAGCAAACGTTTTCAATATACTCTTCAACCTTAATAAGTTCATGGCATTTGAAACACGTGACCCATTTCTCATTCGCCAGgtaagtttggcttaccagtggagttttta---tagcactca------agagggaaaaaaataacaaagaatat-gacttcttttaactgctaaaggcagtttgtagtagttcggattgaggcaattagaacaagtataattctctttcattgctgtag
| ||||  |||  ||| | || |  ||| | ||||||||||||||||| || ||||||||| | || ||||| || |||||||| || ||||| || ||||||  || | | |   | |  || | | |   || || |||      |      | |   ||  |   || |  |    ||||  ||   || |    |                                                           
TTTGAAGCGATGTAAATTGTCTGGGAACTTCTTCAATATACTCTTCAATCTCAATAAGTTCGTTGCTTTTGAGACTCGTGACCCCTTCCTCATCCGTCAGgtat-ttcgtcctcttattcaagatctcagcatatcagtcatcttctaagcttgatattgtagtacgaaaaacaggtccctttcgacgtttataaattgcc---------------------------------------------------------

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|124753077|gb|EH843207.1|EH843207
EST:     TTAATAAGTTCATGGCATTTGAAGCACGTGACCCATTTCTCATTCGCCAG                         GAACGGGAAGA
genomic: TTAATAAGTTCATGGCATTTGAAACACGTGACCCATTTCTCATTCGCCAGgtaagtttgg ... attgctgtagGAACGGGAAGA
EST: gi|86085050|gb|DR380809.1|DR380809
EST:     TTAATAAGTTCATGGCATTTGAAACACGTGACCCATTTCTCATTCGCCAG                         GAACGGGAAGATCCAAATTTGACAGAGTGGGATCGATTTGCTCAGAGAGAG
genomic: TTAATAAGTTCATGGCATTTGAAACACGTGACCCATTTCTCATTCGCCAGgtaagtttgg ... attgctgtagGAACGGGAAGATCCAAATTTGACAGAGTGGGATCGATTTGCTCAGAGAGAG