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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTCTGCAGAGCAACTTAGTGCCCAGATTGGAGAGTTATTTGATGAACCACAGATTTACCGTATTGATCACTATCTGGGAAAGGAACTCGTGCAGAATTTGgtaatacatgtatcataaaaattgtgtctttatttgataaaaaaaaataataataaaatgtttgtctttgtatgccctattttgaaatgtctgctgatttctctccttatgccacttacatttgcag

Basic information

species Vitis vinifera
transcript Vv14s0171g00490.t01
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv14s0171g00490.t01 (Vitis vinifera), 5'ss of exon 6
lower sequence: GLYMA19G24250.2 (Glycine max), 5'ss of exon 6
TTCTGCAGAGCAACTTAGTGCCCAGATTGGAGAGTTATTTGATGAACCACAGATTTACCGTATTGATCACTATCTGGGAAAGGAACTCGTGCAGAATTTGgtaatacatgtatcataaaaattgtgtctttatttgataaaaaaaaataa--taataaaatgtttgtctttgtatgccctattttgaaatgtctgctgatttctctccttatgccacttacatttgcag
 ||||||||| |||| ||| |  |||||||| |||| ||||| |||||||||||||| ||||||||||||||  ||||||||||||| |||||||| ||||||||| ||| || ||| ||  ||  |  || |||| |  |  ||  |    |||| |    |   | |   | |  | ||| |||  |                                        
ATCTGCAGAGGAACTCAGTACTGAGATTGGAAAGTTGTTTGAGGAACCACAGATTTATCGTATTGATCACTACTTGGGAAAGGAACTAGTGCAGAACTTGgtaataaatg-attatacaa--tggcttcttgtttgtttcatgaattttgcctaatgattaatccctttacatttaacttatattggcag---------------------------------------

upper sequence: Vv14s0171g00490.t01 (Vitis vinifera), 5'ss of exon 6
lower sequence: GLYMA16G06850.1 (Glycine max), 5'ss of exon 6
TTCTGCAGAGCAACTTAGTGCCCAGATTGGAGAGTTATTTGATGAACCACAGATTTACCGTATTGATCACTATCTGGGAAAGGAACTCGTGCAGAATTTGgtaatacatgtatcataaaaattgtgtctttatttgataaaaaaaaataa--taataaaatgtttgtctttgtatgccctattttgaaatgtctgctgatttctctccttatgccacttacatttgcag
 ||||||||| |||| ||| |  |||||||| |||| ||||| |||||||||||||| ||||||||||||||  ||||||||||||| |||||||| ||||||||| ||| || ||| || | |  ||||| |||| |  |  |   |    |||| |    |   | |   | |  | ||| |||  |                                        
ATCTGCAGAGGAACTCAGTACTGAGATTGGAAAGTTGTTTGAGGAACCACAGATTTATCGTATTGATCACTACTTGGGAAAGGAACTAGTGCAGAACTTGgtaataaatg-attatacaa-tggcttctttgtttgtttcatgagttttgcctaatgattaatccctttacatttaacttatattggcag---------------------------------------

upper sequence: Vv14s0171g00490.t01 (Vitis vinifera), 5'ss of exon 6
lower sequence: GLYMA19G22690.1 (Glycine max), 5'ss of exon 6
TTCTGCAGAGCAACTTAGTGCCCAGATTGGAGAGTTATTTGATGAACCACAGATTTACCGTATTGATCACTATCTGGGAAAGGAACTCGTGCAGAATTTGgtaatacatg-tatcataaaaattgtgtctttatttgataaaaaaaaataataataaaatgtttgtctttgtatgccctattttgaaatgtctgctgatttctctccttatgccacttacatttgcag
 |||||||||||||| ||| ||||||||||| |||| ||||| ||||| |||||||| || |||||||||||  | ||||||||||| ||||||||| ||||| || ||| |  | ||     | |    ||  ||| |  | |||  |     |||    |   |||   | || | | | ||   |                                        
ATCTGCAGAGCAACTCAGTACCCAGATTGGACAGTTGTTTGAAGAACCCCAGATTTATCGAATTGATCACTACTTAGGAAAGGAACTTGTGCAGAATATGgtagtaaatgattgcttattggctctcatattgcttgcttcataaacttggcc-taa----tccctctccatttgacttgtattaccag---------------------------------------

upper sequence: Vv14s0171g00490.t01 (Vitis vinifera), 5'ss of exon 6
lower sequence: AT3G27300.2 (Arabidopsis thaliana), 5'ss of exon 7
TTCTGCAGAGCAACTTAGTGCCCAGATTGGAGAGTTATTTGATGAACCACAGATTTACCGTATTGATCACTATCTGGGAAAGGAACTCGTGCAGAATTTGgtaatacatgtatcataaaaattgtgtctttatttgataaaaaaaaataataataaaatgtttgtctttgtatgccctattttgaaatgtctgctgatttctctccttatgccacttacatttgcag
 ||||||||||| || ||| | ||||||||||  || ||||| |||||||||||||| ||||||||||||||||||||||| ||  | || || ||  |||||| |||| | |  |   | |  |   ||||||  ||  | | ||||||  ||| ||| |    | ||  || |  || |                                              
ATCTGCAGAGCAGCTGAGTTCTCAGATTGGAGCCTTGTTTGAAGAACCACAGATTTATCGTATTGATCACTATCTGGGAAAAGAGTTAGTTCAAAACATGgtaacacatatttgcttctagtcattagtttatt-aatttagacaaataaagatataatctaacgcatt-cat-cgttagtgcag------------------------------------------

upper sequence: Vv14s0171g00490.t01 (Vitis vinifera), 5'ss of exon 6
lower sequence: AT5G40760.1 (Arabidopsis thaliana), 5'ss of exon 6
TTCTGCAGAGCAACTTAGTGCCCAGATTGGAGAGTTATTTGATGAACCACAGATTTACCGTATTGATCACTATCTGGGAAAGGAACTCGTGCAGAATTTGgtaa--tacatgtatcataaaaattgtgtctttatttgataaaaaaaaataataataaaatgtttgtctttgtatgccctattttgaaatgtctgctgatttctctccttatgccacttacatttgcag
 |||||||||||||| ||| | |||||||||||||||||||||||| ||||||| || ||||| || || ||||| || |||||| | || || ||  ||||||  | | | | |  |||    |   || | | |   |      | |  || |   | | |||    | ||        |   |                                           
ATCTGCAGAGCAACTGAGTTCTCAGATTGGAGAGTTATTTGATGAATCACAGATCTATCGTATAGACCATTATCTTGGGAAGGAATTAGTTCAAAACATGgtaacctgcttctctattaatgtctaaatcatcaatctctttctttagactatcagtgattattttatctcgtgcatttcttgcag-------------------------------------------

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|30299156|gb|CB975950.1|CB975950
EST:     AGATTTACCGTATTGATCACTACCTGGGAAAGGAACTCGTGCAGAATTTG                         TTGGTACTTCGTTTTGCAAATCGCATGTTTTTGCCCCTCTGGAACCGTGAC
genomic: AGATTTACCGTATTGATCACTATCTGGGAAAGGAACTCGTGCAGAATTTGgtaatacatg ... acatttgcagTTGGTACTTCGTTTTGCAAATCGCATGTTTTTGCCCCTCTGGAACCGTGAC
EST: gi|110686452|gb|EE064108.1|EE064108
EST:     GATTTACCGTATTGATCCCTATCTGGGAACAGGA-CTCGTGCACAATTTG                         TTGGTTCTTCGTTTTGCAAATCGCATGATTTTGCCCCT
genomic: GATTTACCGTATTGATCACTATCTGGGAA-AGGAACTCGTGCAGAATTTGgtaatacatg ... acatttgcagTTGGTACTTCGTTTTGCAAATCGCATGTTTTTGCCCCT
EST: gi|161717585|gb|FC065623.1|FC065623
EST:     AGATTTACCGTATTGATCACTACCTGGGAAAGGAACTCGTGCAGAATTTG                         TTGGTACTTCGTTTTGCAA-TCGCATGTTTTTGCCCCTCTGGAAC
genomic: AGATTTACCGTATTGATCACTATCTGGGAAAGGAACTCGTGCAGAATTTGgtaatacatg ... acatttgcagTTGGTACTTCGTTTTGCAAATCGCATGTTTTTGCCCCTCTGGAAC
EST: gi|110364929|gb|EC928538.1|EC928538
EST:     AGATTTACCGTATTGATCACTACCTGGGAAAGGAACTCGTGCAGAATTTG                         TTGGTACTTCGTTTTGCAAATCGCATGTTTTTGCCCCTCTGGAACCGTGAC
genomic: AGATTTACCGTATTGATCACTATCTGGGAAAGGAACTCGTGCAGAATTTGgtaatacatg ... acatttgcagTTGGTACTTCGTTTTGCAAATCGCATGTTTTTGCCCCTCTGGAACCGTGAC
EST: gi|161719304|gb|FC068268.1|FC068268
EST:     AGATTTACCGTATTGATCACTACCTGGGAAAGGAACTCGTGCAGAATTTG                         TTGGTACTTCGTTTTGCAAATCGCATGTTTTTGCCCCTCTGG
genomic: AGATTTACCGTATTGATCACTATCTGGGAAAGGAACTCGTGCAGAATTTGgtaatacatg ... acatttgcagTTGGTACTTCGTTTTGCAAATCGCATGTTTTTGCCCCTCTGG
EST: gi|110372969|gb|EC937167.1|EC937167
EST:     AGATTTACCGTATTGATCACTACCTGGGAAAGGAACTCGTGCAGAATTTG                         TTGGTACTTCGTTTTGCAAATCGCATGTTTTTGCCCCTCTGGAACCGTGAC
genomic: AGATTTACCGTATTGATCACTATCTGGGAAAGGAACTCGTGCAGAATTTGgtaatacatg ... acatttgcagTTGGTACTTCGTTTTGCAAATCGCATGTTTTTGCCCCTCTGGAACCGTGAC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TTCTGCAGAGCAACTTAGTGCCCAGATTGGAGAGTTATTTGATGAACCACAGATTTACCGTATTGATCACTATCTGGGAAAGGAACTCGTGCAGAATTTGgtaatacatgtatcataaaaattgtgtctttatttgataaaaaaaaataataataaaatgtttgtctttgtatgccctattttgaaatgtctgctgatttctctccttatgccacttacatttgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAA