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

gtgccctattcattggttacaattttacttgtttatgccttttcatggataatgttgtattgcctggtagtgtatcttatgtcctcatccattgcctcgtcttcaatagGAGGATTTTCCACATAATGCTCACCATAGGGAGATAGCAATCTCAATAAGCAATTATACCCTGAAGCATGGCGATGCAGGATTGGTAATTGTTGGGGGGA

Basic information

species Vitis vinifera
transcript Vv04s0023g02750.t01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv04s0023g02750.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA11G07720.1 (Glycine max), 3'ss of exon 3
gtgccctattcattggttacaattttacttgtttatgccttttcatggataatgttgtattgcctggtagtgtatcttatgtcctcatccattgcctcgtcttcaatagGAGGATTTTCCACATAATGCTCACCATAGGGAGATAGCAATCTCAATAAGCAATTATACCCTGAAGCATGGCGATGCAGGATTGGTAATTGTTGGGGGGA
                     ||  |  |   || | |  | | ||   |  | |||||||   |  | ||  | ||||    || || | ||   | ||  | | |||||||||||||||||||||||||||||||||||  | |||||||| |||||||||||||| || |||||||| ||| |||||||| ||||||| || || |
-------------------gtatgatgttcagttgtactatatgatcc-tgttattgtattaggtt-tggttgagctta----ctaattcttttagtggttgtta-tagGAGGATTTTCCACATAATGCTCACCATAGGGAAGTTGCAATCTCTATAAGCAATTATACTCTAAAGCATGGAGATACAGGATTGATAATTGTCGGTGGCA

upper sequence: Vv04s0023g02750.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA01G37580.1 (Glycine max), 3'ss of exon 3
gtgccctattcattggttacaattttacttgtttatgccttttcatggataatgttgtattgcc-tggtagtgtatcttatgtcctcatccattgcctcgtcttcaatagGAGGATTTTCCACATAATGCTCACCATAGGGAGATAGCAATCTCAATAAGCAATTATACCCTGAAGCATGGCGATGCAGGATTGGTAATTGTTGGGGGGA
                              || |     |||   || |  || |  |  ||   |  || |   |    |   || || | ||   |  |  | | |||||||||||||||||||||||||||||||||||  | |||||||| |||||||||||||| || |||||||| ||| |||||||  ||||||| || || |
------------------------------gtatgatgttttagctgtactatatgatcctgttattatattaggttgagttcactaattctttaagtgattgtta-tagGAGGATTTTCCACATAATGCTCACCATAGGGAAGTTGCAATCTCTATAAGCAATTATACTCTAAAGCATGGAGATACAGGATTAATAATTGTCGGTGGCA

upper sequence: Vv04s0023g02750.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: AT3G51050.1 (Arabidopsis thaliana), 3'ss of exon 3
gtgccctattcattggttacaattttacttgtttatgccttttcatggataatgttgtattgcctggtagtgt--atcttatgtcctcatccattgcctcgtctt-caatagGAGGATTTTCCACATAATGCTCACCATAGGGAGATAGCAATCTCAATAAGCAATTATACCCTGAAGCATGGCGATGCAGGATTGGTAATTGTTGGGGGGA
         |  ||   | |    ||  |||| ||    | | |||  | | | |    | |    ||||| |  ||  |   |   | | | ||   | ||      | |||||||||| ||||||||||| |||||||| ||||||||||| || ||||||||||| ||  |||||||||| ||| | || ||||| |||||||| ||  
--------gtttttatcttcttcgttctttgtctaacgttctgcataaa-agtttgtcttggttcagtagtattgattctccttttgcttacctttgttggtggaatgacagGAGGATTTCCCACATAATGCACACCATAGAGAGATAGCAATTTCGATAAGCAATTACACATTGAAGCATGGTGATACGGGTTTGGTTATTGTTGGTGGAC

upper sequence: Vv04s0023g02750.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: PP1S11_162V6.1 (Physcomitrella patens), 3'ss of exon 3
-----------------------------------------------------------------gtgccctattcattggttacaattttacttgtttatgcctttt-catggataatgttgtattgcctggta-gtgtat----cttatgtcctcat--ccattgcc-tcgtcttcaatagGAGGATTTTCCACATAATGCTCACCATAGGGAGATAGCAATCTCAATAAGCAATTATACCCTGAAGCATGGCGATGCAGGATTGGTAATTGTTGGGGGGA
                                                                   |       | | |  |   | |  ||   || |   |||   ||| | |||    ||| || |||  | ||  ||    | || | ||| ||      ||   |  | ||  | |||| || || ||||||  | ||||||| |  ||  |||| || |||||||||||||||||| |||||||||| ||  | ||| | || ||||| ||||| |
gtttgcacttgttaatatacctcgttttcttgtattttcaatttgtttttctaccataactttttacgatgcgggcgtcgtcttgcagtgcaccaattaaactcttcgacatcggtaacag-gtactgtctgcaatgtcaattgcacctacgcccttatagtagctgatgttttgtttgacagGATGACTTCCCACATGGTTCTCACCACAAAGAAGTAGCCATTTCAATAAGCAATTATACCTTGAAGCATGGAGACACCGGACTAGTCATTGTGGGGGGAA

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|161719161|gb|FC069357.1|FC069357
EST:     TAATGTGTTTCGATCACAACCTCAAAAAGCTATGGGAAGCAAATCTACAG                         GAGGATTTTCCACATAATGCTCACCATAGGGAGATAGCAATCTCAATAAGC
genomic: TAATGTGTTTCGATCACAACCTCAACAAGCTATGGGAAGCAAATCTACAGgtgccctatt ... tcttcaatagGAGGATTTTCCACATAATGCTCACCATAGGGAGATAGCAATCTCAATAAGC
EST: gi|352769223|gb|FQ471372.1|FQ471372
EST:     TAATGTGTTTCGATCACAACCTCAACAAGCTATGGGAAGCAAATCTACAG                         GAGGATTTTCCACATAATGCTCACCATAGGGAGATAGCAATCTCAATAAGC
genomic: TAATGTGTTTCGATCACAACCTCAACAAGCTATGGGAAGCAAATCTACAGgtgccctatt ... tcttcaatagGAGGATTTTCCACATAATGCTCACCATAGGGAGATAGCAATCTCAATAAGC
EST: gi|161712184|gb|FC061556.1|FC061556
EST:     TAATGTGTTTCGATCACAACCTCAAAAAGCTATGGGAAGCAAATCTACAG                         GAGGATTTTCCACATAATGCTCACCATAGGGAGATAGCAATCTCAATAAGC
genomic: TAATGTGTTTCGATCACAACCTCAACAAGCTATGGGAAGCAAATCTACAGgtgccctatt ... tcttcaatagGAGGATTTTCCACATAATGCTCACCATAGGGAGATAGCAATCTCAATAAGC
EST: gi|352767961|gb|FQ466170.1|FQ466170
EST:     TAATGTGTTTCGATCACAACCTCAACAAGCTATGGGAAGCAAATCTACAG                         GAGGATTTTCCACATAATGCTCACCATAGGGAGATAGCAATCTCAATAAGC
genomic: TAATGTGTTTCGATCACAACCTCAACAAGCTATGGGAAGCAAATCTACAGgtgccctatt ... tcttcaatagGAGGATTTTCCACATAATGCTCACCATAGGGAGATAGCAATCTCAATAAGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgtattgcctggtagtgtatcttatgtcctcatccattgcctcgtcttcaatagGAGGATTTTCCACATAATGCTCACCATAGGGAGATAGCAATCTCAATAAGCAATTATACCCTGAAGCATGGCGATGCAGGATTGGTAATTGTTGGGGGGA
                                        cctcgtcttc  CT-rich tract
                  tatcttat  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgccctattcattggttacaattttacttgtttatgccttttcatggataatgttgtattgcctggtagtgtatcttatgtcctcatccattgcctcgtcttcaatagGAGGATTTTCCACATAATGCTCACCATAGGGAGATAGCAATCTCAATAAGCAATTATACCCTGAAGCATGGCGATGCAGGATTGGTAATTGTTGGGGGGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC