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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatcacatcaagtccccttactctgtcttattcaacaaatgagtttcttggttaatgctttaagcaaaacgctctacagGTACCCAATTTATGGTGGCATGCAAGACTGGAATTACATATATGGGGGATGCTTTGAATTGACTCTGGAAATAAGCGACAACAAGTGGCCTAAAGCCTCA

Basic information

species Arabidopsis thaliana
transcript AT1G71696.1
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G71696.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: LOC_Os06g05240.1 (Oryza sativa), 3'ss of exon 10
-----------gtatcacatcaagtccccttactctgtcttattcaacaaatgagtttcttggttaatgct-----ttaagcaa---aacgctctac--------------agGTACCCAATTTATGGTGGCATGCAAGACTGGAATTACATATATGGGGGATGCTTTGAATTGACTCTGGAAATAAGCGACAACAAGTGGCCTAAAGCCTCA
           || |   || |   | |||||   | | || |    || || |     || |||  ||||     | | || |   | |  ||||               ||||| ||||| |||||||| |||||||||||||| || ||| |||| || |||||||| || || |||||||| || |||   || ||||| || ||  | 
gtataaaactagttttgtattattgctccttatcattttttttatttcatatcaaacattttgttgctgctacttttcatgctaactagcaatctatgcttttttgtgttgagGTATCCAATCTATGGTGGGATGCAAGACTGGAACTATATACATGGAGGTTGCTTTGAGTTAACCCTGGAAATTAGTGACGTAAAATGGCCAAAGGCAGCT

upper sequence: AT1G71696.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GRMZM2G106683_T02 (Zea mays), 3'ss of exon 10
------------------------gtatcacatcaagtccccttactct--gtcttattcaacaaatgagtttcttggttaatgctttaagcaa----aacgctc----tacagGTACCCAATTTATGGTGGCATGCAAGACTGGAATTACATATATGGGGGATGCTTTGAATTGACTCTGGAAATAAGCGACAACAAGTGGCCTAAAGCCTCA
                           ||| || |  |  ||||  |||  ||  ||   |     ||  | | |||| |  ||  | || |||    |  |||     | |||||||||||| |||||||| ||||| |||||||| || ||| |||| || |||||||| || |||||||| || || ||||  |||||||| |||||    
gtaaacgaacaatagcaagttcatacttcatatgagatttcctttatctaggtactaggtaggttgtgtatgtgttggctt-tgaatcaaacaacatcattgcttgtggtccagGTACCCAATATATGGTGGTATGCAGGACTGGAACTATATACATGGAGGCTGCTTTGAGTTAACTCTGGAGATTAGTGACACAAAGTGGCCAAAAGCAGAT

upper sequence: AT1G71696.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: Vv18s0157g00050.t01 (Vitis vinifera), 3'ss of exon 10
-------------gtatcaca-tcaagtcccctta-----ctctgtcttattcaacaaatgagtttcttggttaatgctttaagcaaaacgct-ctacagGTACCCAATTTATGGTGGCATGCAAGACTGGAATTACATATATGGGGGATGCTTTGAATTGACTCTGGAAATAAGCGACAACAAGTGGCCTAAAGCCTCA
              | | ||| ||||||      |      ||| | || |||     ||    |  || |  | ||||| ||| |||||  | || ||||||||| || ||||||||||||||||| ||||| || ||| |||| || || ||||||||||| ||||| || || |||||||||||||||||  |    
cggttatttttttttttaacaatcaagttgttaaaagtacttctcttttcttctttttattttctgtttagcaattgcttcaagaaaaacttttctgcagGTACCCCATATATGGTGGCATGCAAGATTGGAACTATATACATGGTGGCTGTTTTGAATTGACACTGGAGATCAGTGACAACAAGTGGCCTAACACTATT

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|124777828|gb|EH867771.1|EH867771
EST:     GGAGCATCCTG                         GTACCCAATTTATGGTGGCATGCAAGACTGGAATTACATATATGGGG-ATG
genomic: GGAGCATCCTGgtatcacatc ... cgctctacagGTACCCAATTTATGGTGGCATGCAAGACTGGAATTACATATATGGGGGATG






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtcttattcaacaaatgagtttcttggttaatgctttaagcaaaacgctctacagGTACCCAATTTATGGTGGCATGCAAGACTGGAATTACATATATGGGGGATGCTTTGAATTGACTCTGGAAATAAGCGACAACAAGTGGCCTAAAGCCTCA
                         ggttaat  putative branch site (score: 4)
         aacaaat  TA-rich tract