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

ACTTCTGACATGCTGCATACGTCCAAGCAGCATCTTTGGCCCTGGCGATAAGTTGTTGGTTCCGTCTTTGGTTAATGCTGCAAGGGCTGGGAAATCCAAGgcaagcatgttctctatccctgttaatcatcattttggcatcttcttcatgtatttttcctcatgatattcaatttcaatttaagactatgatttgaatt...

Basic information

species Vitis vinifera
transcript Vv04s0008g02200.t01
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv04s0008g02200.t01 (Vitis vinifera), 5'ss of exon 5
lower sequence: LOC_Os03g29170.2 (Oryza sativa), 5'ss of exon 4
ACTTCTGACATGCTGCATACGTCCAAGCAGCATCTTTGGCCCTGGCGATAAGTTGTTGGTTCCGTCTTTGGTTAATGCTGCAAGGGCTGGGAAATCCAAGgcaagcatgttctctatccctgttaa--tcatcattttggcatcttcttcatgtatttttcctcatg-----atattcaatt---tcaatttaagactat--gatttgaatt-----------------------------------------------------------------------------------
 ||||| || || || ||||| ||||| ||||| ||||||||||| |||||| |  ||||||| ||| |||||| |||||||||||| || || || |||| ||| |||   |  ||  |||| ||  |    ||  | |  |    ||||| | |  ||   ||||     || || |  |     | || || | | |  |||  ||||                                                                                    
GCTTCTTACTTGTTGTATACGCCCAAGTAGCATTTTTGGCCCTGGTGATAAGCTACTGGTTCCTTCTCTGGTTACTGCTGCAAGGGCAGGAAAGTCTAAGgtaagaatggcttgcatgtctgtaaacattggtatgctaggtttgatttcatttctcgttgtccatgttcacatgttgatatggactatttcaatattgtaggatcagaatgctatttataagtagcaaaaataatattgaacaaactaacacttgaattacttttttatgcttgttccaaaatttcatcgctag

upper sequence: Vv04s0008g02200.t01 (Vitis vinifera), 5'ss of exon 5
lower sequence: GRMZM2G149224_T03 (Zea mays), 5'ss of exon 4
ACTTCTGACATGCTGCATACGTCCAAGCAGCATCTTTGGCCCTGGCGATAAGTTGTTGGTTCCGTCTTTGGTTAATGCTGCAAGGGCTGGGAAATCCAAGgcaagcatgttctctatccctgttaatcatcattttggcatcttcttcatgtatttttcctcatgatattcaatttcaatttaagactatgattt--gaatt--
 ||||| |||||||| ||||| ||||| ||||| ||||||||||| |||||| |  ||||||| |||||||||  |||||||||||| ||||| ||||| | ||| ||   ||  || | ||    | |  ||  | |  |||  |  ||||   | || |  ||||   || |    ||| |  ||| | ||||    |||  
GCTTCTTACATGCTGTATACGCCCAAGTAGCATTTTTGGCCCTGGTGATAAGCTAATGGTTCCATCTTTGGTTGCTGCTGCAAGGGCAGGGAAGTCCAAAgtaagaatag-ctacatgcatggacttaagtatgctag--tctagtaaatgttggtgtcttggtgat-cacactgcatattgacaactctcatttatagattca

upper sequence: Vv04s0008g02200.t01 (Vitis vinifera), 5'ss of exon 5
lower sequence: AT1G47290.1 (Arabidopsis thaliana), 5'ss of exon 5
ACTTCTGACATGCTGCATACGTCCAAGCAGCATCTTTGGCCCTGGCGATAAGTTGTTGGTTCCGTCTTTGGTTAATGCTGCAAGGGCTGGGAAATCCAAGgcaagcatgttctctatccctgttaatcatcattttggcatcttcttcatg-tatttttcctcatgatattcaatttcaatttaagactatgatttgaatt------
||| || || || ||||||||||| |||||||| ||||| ||||| ||||| ||  ||||||| ||  | |||| |||||| |||||||||||||||||||    |   |    | ||  ||||  | |||  ||||||  |||||  ||| ||| | |  || |  |   | |||    | |          |||  | |      
ACTACTCACTTGTTGCATACGTCCTAGCAGCATATTTGGTCCTGGTGATAAATTAATGGTTCCATCGCTTGTTACTGCTGCCAGGGCTGGGAAATCCAAGgttgcc---tctattttctttgtt--ttatctctttggc--cttctaaatgctatctattttccttgtgacctattatgctctggtctctccttttttagtgatgtt

upper sequence: Vv04s0008g02200.t01 (Vitis vinifera), 5'ss of exon 5
lower sequence: AT2G26260.2 (Arabidopsis thaliana), 5'ss of exon 4
ACTTCTGACATGCTGCATACGTCCAAGCAGCATCTTTGGCCCTGGCGATAAGTTGTTGGTTCCGTCTTTGGTTAATGCTGCAAGGGCTGGGAAATCCAAGgcaagcatgttctctatccctgttaatcatcattttggcatcttcttcatgtatttttcctcatgatattcaatttcaatttaagactatgatttga-att-
||| || || || ||||||||||||||||| || ||||| || || ||||  || |||||||||||  | |||  |||||| |||||||||||||| ||||   |  |||| ||| |   |     |  |   |     || | ||   ||  ||  |  | |   | || |  ||   | |       |   |||| | | 
ACTACTCACTTGTTGCATACGTCCAAGCAGTATTTTTGGTCCCGGTGATAGATTATTGGTTCCGTCGCTTGTTGCTGCTGCTAGGGCTGGGAAATCTAAGgttggattgttttctttgtttaccgtt--ttgctcctctatgtgctgtctgccttcctttttaccttttttacctttcctcttctctcttctcttgatactt

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|37185871|gb|CF605224.1|CF605224
EST:     AGTTGTTGGTTCCGTCTTTGGTTAATGCTGCAAGGGCTGGGAAATCCAAG                         TTCATCATTGGTGATGGCAATAACATGTATGATTTCACTTATGTTGAAAAT
genomic: AGTTGTTGGTTCCGTCTTTGGTTAATGCTGCAAGGGCTGGGAAATCCAAGgcaagcatgt ... aacaatgcagTTCATCATTGGTGATGGCAATAACATGTATGATTTCACTTATGTTGAAAAT
EST: gi|161711002|gb|FC060357.1|FC060357
EST:     AGTTGTTGGTTCCGTCTTTGGTTAATGCTGCAAGGGCTGGGAAATCCAAG                         TTCATCATTGGTGATGGCAATAACATGTA
genomic: AGTTGTTGGTTCCGTCTTTGGTTAATGCTGCAAGGGCTGGGAAATCCAAGgcaagcatgt ... aacaatgcagTTCATCATTGGTGATGGCAATAACATGTA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ACTTCTGACATGCTGCATACGTCCAAGCAGCATCTTTGGCCCTGGCGATAAGTTGTTGGTTCCGTCTTTGGTTAATGCTGCAAGGGCTGGGAAATCCAAGgcaagcatgttctctatccctgttaatcatcattttggcatcttcttcatgtatttttcctcatgatattcaatttcaatttaagactatgatttgaatt

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctatccc