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

gtacatcttcccctaatacacatttcctttctatttctttggtttctcatatttttgtgatattaagtgggatgtttgtttcctgacattaggtatggattttttctctgcctgctttaaaactcatattggttgatcatttcttcaccttaaactttcttgacttatttattgcagTTTGTGATGTTCTATGCCTGTGCTCTCGACCCTGAAAATTGTGGTGTGAGATTTGCTAGGGTGCTTGCAGATTTTTTTGTTTGCAGTACTTTTCCACCGC

Basic information

species Vitis vinifera
transcript Vv04s0044g01700.t01
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv04s0044g01700.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: GLYMA09G32870.2 (Glycine max), 3'ss of exon 12
gtacatcttcccctaatacacatttcctttctatttctttggtttctcatatttttgtgatattaagtgggatgtttgtttcctgacattaggtatggattttttctctgcctgctttaaaactcatattggttgatcatttcttcaccttaaactttcttgacttatttattgcagTTTGTGATGTTCTATGCCTGTGCTCTCGACCCTGAAAATTGTGGTGTGAGATTTGCTAGGGTGCTTGCAGATTTTTTTGTTTGCAGTACTTTTCCACCGC
                                                                             ||    |  |  ||   ||   | |||    |   |   ||     |  | ||  |     || | ||| | |||     |  ||  |  ||| ||||||||||||||||||||||| ||||| || |||||||||   |||||||||| |||||| | ||| ||||||||| | ||||   |   | ||  ||| ||  
-----------------------------------------------------------------------------gtactgtttccctaatcattactgtttctattatgtttcttgctggtactgtttctgtgaaatgtgttctcattag----tggtgtttattttgttgcagTTTGTGATGTTCTATGCATGTGCACTGGACCCTGAAGGATGTGGTGTGAAATTTGCGATGGTTCTTGCAGATATGTTTGGAGGTGATGCTAATCCCCCTA

upper sequence: Vv04s0044g01700.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: GLYMA16G21590.2 (Glycine max), 3'ss of exon 10
gtacatcttcccctaatacacatttcctttctatttctttggtttctcatatttttgtgatattaagtgggatgtttgtttcctgacattaggtatggattttttctctgcctgctttaaaactcatattggttgatcatttcttcaccttaaactttcttgacttatttattgcagTTTGTGATGTTCTATGCCTGTGCTCTCGACCCTGAAAATTGTGGTGTGAGATTTGCTAGGGTGCTTGCAGATTTTTTTGTTTGCAGTACTTTTCCACCGC
                                                                    |   |||||   |  | |     | |    | || |  | ||  |  |   |     || |  ||  |  || |  |||      | |  | | | ||  || || |||| ||||||||||||||| ||||| || |||||||||   |||||||||| |||||| | ||| ||||| ||| | ||||  ||   |  |  ||| ||  
--------------------------------------------------------------------gtactgttttgctaatcattactgtttcttacttgtgttatgtttcttgccagtactatttctgtgaaatatgttctcatt----agtggcgtaaatt--ttgtttcagTATGTGATGTTCTATGCATGTGCACTGGACCCTGAAGGATGTGGTGTGAAATTTGCCATGGTTCTTGCTGATATGTTTGGATGTGATGTTAATCCCCCTA

upper sequence: Vv04s0044g01700.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: AT1G30590.1 (Arabidopsis thaliana), 3'ss of exon 10
gtacatcttcccctaatacacatttcctttctatttctttggtttctcatatttttgtgatattaagtgggatgtttgtttcctgacattaggtatggattttttctctgcctgctttaa--aactcat-attggttgatcatttcttcaccttaaactttcttgacttatttattgcagTTTGTGATGTTCTATGCCTGTGCTCTCGACCCTGAAAATTGTGGTGTGAGATTTGCTAGGGTGCTTGCAGATTTTTTTGTTTGCAGTACTTTTCCACCGC
                                                               || |    |    | |  ||| ||||     |  | |||  |    | || ||   |  |  |||| || ||    | || ||||  | ||| |||  ||  ||||   |  |||||||| ||||||||||||| ||  | || || |||||||||||||||||||||||||| ||   |||    ||  | | | | | ||| |        |  |
--------------------------------------------------------------gtaggcatcaaagctatcaccttacatactacaaagttttcattgtaggcttctagcattagttcattatcggcatgtgatgtcttggc-ttagactcactctactttcat-ctgcagTTTCTGATGTTCTATGCATGCTCACTAGATCCTGAAAATTGTGGTGTGAGATTTGCCAGTAAGCTGTTGGACATATATCTCTCCAGCAACACATGTCGAC

upper sequence: Vv04s0044g01700.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: AT2G34750.1 (Arabidopsis thaliana), 3'ss of exon 10
gtacatcttcccctaatacacatttcctttctatttctttggtttctcatatttttgtgatattaagtgggatgtttgtttcctgacattaggtatggattttttctctgcctgctttaaaactcatattggttgatcatttcttcaccttaaactttcttgacttatttattgcagTTTGTGATGTTCTATGCCTGTGCTCTCGACCCTGAAAATTGTGGTGTGAGATTTGCTAGGGTGCTTGCAGATTTTTTTGTTTGCAGTACTTTTCCACCGC
                                                        ||  |   |  | |      | |||      |||| |||   ||| ||          || ||     |||  | |      | |   ||   ||| |||  |||    |||    |||||||| |||| |||||||||||  | || || ||||||||||||||||||| |||||||||   ||| |  ||  ||||| | | ||| |     |      
--------------------------------------------------------gtagt-ccatatagctatcatattttgcataattatgtacatattcttctag-----actctag----catggtcgacatgaaatgtctcggtttatactcactttctatatcatctgcagTTTCTGATATTCTATGCCTGCTCACTGGATCCTGAAAATTGTGGTGTGAAATTTGCTAGTAAGCTAGTGGAGATTTTTCTCTCCAGCAACAAGCATGTAG

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|110687435|gb|EE064841.1|EE064841
EST:     TATCATTTCAGACAACTGTTTTGAATGCATTCAAGTCAAAATTTGCTCAG                         TTTGTGATGTTCTATGCCTGTGCTCTCGACCCTGAAAATTGTGGTGTGAGA
genomic: TATCATTTCAGACAACTGTTTTGAATGCATTCAAGTCAAAATTTGCTCAGgtacatcttc ... tttattgcagTTTGTGATGTTCTATGCCTGTGCTCTCGACCCTGAAAATTGTGGTGTGAGA
EST: gi|110694987|gb|EE072492.1|EE072492
EST:     TATCATTTCAGACAACTGTTTTGAATGCATTCAAGTCAAAATTTGCTCAG                         TTTGTGATGTTCTATGCCTGTGCTCTCGACCCTGAAAATTGTGGTGTGAGA
genomic: TATCATTTCAGACAACTGTTTTGAATGCATTCAAGTCAAAATTTGCTCAGgtacatcttc ... tttattgcagTTTGTGATGTTCTATGCCTGTGCTCTCGACCCTGAAAATTGTGGTGTGAGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctcatattggttgatcatttcttcaccttaaactttcttgacttatttattgcagTTTGTGATGTTCTATGCCTGTGCTCTCGACCCTGAAAATTGTGGTGTGAGATTTGCTAGGGTGCTTGCAGATTTTTTTGTTTGCAGTACTTTTCCACCGC
                                   tcttgac  putative branch site (score: 3)
                                         cttattt  CT-rich tract
                                     ttgacttatttatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacatcttcccctaatacacatttcctttctatttctttggtttctcatatttttgtgatattaagtgggatgtttgtttcctgacattaggtatggattttttctctgcctgctttaaaactcatattggttgatcatttcttcaccttaaactttcttgacttatttattgcagTTTGTGATGTTCTATGCCTGTGCTCTCGACCCTGAAAATTGTGGTGTGAGATTTGCTAGGGTGCTTGCAGATTTTTTTGTTTGCAGTACTTTTCCACCGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGAT