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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...acggtcatgggtagtatggaagataaaccttgttgaccttccattgtaaaaattttaggcaagttttttactttccattattcatttttaataattgcagGAAAAACAAAAGATTAAAGTAAAAGAGAAATTTGACAAGTGCGTTAAAGAGAAGCTGTTGGAGTTCTGTGACGTTCTTGACATATCAATTGCCAAAACTA

Basic information

species Vitis vinifera
transcript Vv19s0015g00430.t01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv19s0015g00430.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA18G08630.1 (Glycine max), 3'ss of exon 5
--------------------------------------------------------------acggtcat-gggtagtatggaagataaacc---ttgttgaccttccattgtaaaaattttaggcaagtttttt----actttccattattcatttttaataattgcagGAAAAACAAAAGATTAAAGTAAAAGAGAAATTTGACAAGTGCGTTAAAGAGAAGCTGTTGGAGTTCTGTGACGTTCTTGACATATCAATTGCCAAAACTA-
                                                              ||  |||| ||||  | | |     ||      ||  |||  |     | |    |||  || |     | |     |  ||| |   | ||  | |  | | |||||||||| |||| ||||||||||||||| ||| ||||||||||   |||||||||| |  ||||||||||||| || |||||| || |||||||||   | | 
taattattacccttatatattaagagaattggtgctcataaaatgcaactatatcatactttacaatcatagggttttgttggtagcaagttcttttactgatttcttgcttttctgattgaagtccttcatctgccaaaggttctaaagtccaaatattgttactgcaggAAAAGCAAATGATTAAAGTAAAAGAAAAACTTGACAAGTGTAATAAAGAGAAGTTACTGGAGTTCTGTGATGTGCTTGACTTAACAATTGCCAGGCCAAC

upper sequence: Vv19s0015g00430.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA08G44120.2 (Glycine max), 3'ss of exon 5
---------------------------------------------------------------acggtcat-gggtagtatggaagataaacc---ttgttgaccttccattgtaaaaattttaggcaagttttttact----ttccattattcatttttaataattgcagGAAAAACAAAAGATTAAAGTAAAAGAGAAATTTGACAAGTGCGTTAAAGAGAAGCTGTTGGAGTTCTGTGACGTTCTTGACATATCAATTGCCAAAACTA
                                                               ||   ||| ||||  | |  |   | |      ||  |||  |    || |    |||  || |   | | |  |     ||| |   | ||  | |  | | |||||||||| |||| ||||||||||||||| ||| ||||||||||   |||||||||| |  |||| |||||||| || ||||||||| |||||  |||  | |
gtaattataacctttatatataaagaaaattggtactcataacatgcaactatatcatatgttacaaccatagggttttgtttatagtgagttcttttactgatttcttgtttttctgattgaagtcctttgtctgccaaaggttctaaagtccaaatattgttactgcagGAAAAGCAAATGATTAAAGTAAAAGAAAAACTTGACAAGTGTAATAAAGAGAAGTTACTGGAATTCTGTGATGTGCTTGACATAACAATTAACAAGGCAA

upper sequence: Vv19s0015g00430.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA08G44130.1 (Glycine max), 3'ss of exon 5
-------------------------------------------------------------acggtcat-gggtagtatggaagataaacc---ttgttgaccttccattgtaaaaattttaggc----aagttttttactttccattattcatttttaataattgcagGAAAAACAAAAGATTAAAGTAAAAGAGAAATTTGACAAGTGCGTTAAAGAGAAGCTGTTGGAGTTCTGTGACGTTCTTGACATATCAATTGCCAAAACTA
                                                             ||  |||| ||||  | | ||   |||      ||  |||  |     | |    |||  || |    |  |  |  | |||| |   | ||  | |  | | |||||||||| |||| ||||||||||||||| ||| ||||||||||   |||||||||| |  |||| |||||||| || ||||||||| |||||  |||  | |
gtaattattacctttgtatattaagagttacaataattattacctttgtatattaagagttacaatcatagggttttgttgatagtaagttcttttactgatttcttgcttttctgattgaagtccttcatctgctgaagtttctaacgtccaaatattgttactgcagGAAAAGCAAAGGATTAAAGTAAAAGAAAAACTTGACAAGTGTAATAAAGAGAAGTTACTGGAATTCTGTGATGTGCTTGACATAACAATTAACAAGGCAA

upper sequence: Vv19s0015g00430.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA18G08640.1 (Glycine max), 3'ss of exon 5
--------------------------------------------------------------acggtcat-gggtagtatggaagataaacc---ttgttgaccttccattgtaaaaattttaggcaagttttttact-----ttccattattcatttttaataattgcagGAAAAACAAAAGATTAAAGTAAAAGAGAAATTTGACAAGTGCGTTAAAGAGAAGCTGTTGGAGTTCTGTGACGTTCTTGACATATCAATTGCCAAAACTA-
                                                              ||  |||| ||||  | |  |   |        ||  |||  ||   || |   |  || | |    || | | |      ||| |  || ||  | |  | | |||||||||| |||| ||||||||||||||| ||| ||||||||||   |||||||||| |  |||| |||||||| || ||||||||| |||||  |||  | | 
taattataacctttatatattaagaaatttgtgactcataagatgcaactatataatacgttacaatcatagggttttgtttatagtgggttcttttactgatttttgcttttctga--ttgaagtcctttgtctgccaaaggttctaaaatccaaatattgttactgcaggAAAAGCAAATGATTAAAGTAAAAGAAAAACTTGACAAGTGTAATAAAGAGAAGTTACTGGAATTCTGTGATGTGCTTGACATAACAATTAACAAGGCAAC

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|26261738|gb|CA812801.1|CA812801
EST:     TTAAGAATAATATATCCCGGTTTTCTGGCTTTGTGTGGCATGAGAACGAG                         GAAAAACAAAAGATTAAAGTAAAAGAGAAATTTGACAAGTGCGTTAAAGAG
genomic: TTAAGAATAATATATCCCGGTTTTCTGGCTTTGTGTGGCATGAGAACGAGgtaaaaaaag ... ataattgcagGAAAAACAAAAGATTAAAGTAAAAGAGAAATTTGACAAGTGCGTTAAAGAG
EST: gi|351031373|gb|FQ445398.1|FQ445398
EST:     TTAAGAATAATATATCCCGATTTTCTGGCTTTGTGTGGCATGAGAACGAG                         GAAAAACAAAAGATTAAAGTAAAAGAGAAATTTGACAAGTGCGTTAAAGAG
genomic: TTAAGAATAATATATCCCGGTTTTCTGGCTTTGTGTGGCATGAGAACGAGgtaaaaaaag ... ataattgcagGAAAAACAAAAGATTAAAGTAAAAGAGAAATTTGACAAGTGCGTTAAAGAG
EST: gi|110686557|gb|EE064333.1|EE064333
EST:     TTAAGAATAATATATCCCGGTTTTCTGGCTTTGTGTGGCATGAGAACGAG                         GAAAAACAAAAGATTAAAGTAAAAGAGAAATTTGACAAGTGCGTTAAAGAG
genomic: TTAAGAATAATATATCCCGGTTTTCTGGCTTTGTGTGGCATGAGAACGAGgtaaaaaaag ... ataattgcagGAAAAACAAAAGATTAAAGTAAAAGAGAAATTTGACAAGTGCGTTAAAGAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtaaaaattttaggcaagttttttactttccattattcatttttaataattgcagGAAAAACAAAAGATTAAAGTAAAAGAGAAATTTGACAAGTGCGTTAAAGAGAAGCTGTTGGAGTTCTGTGACGTTCTTGACATATCAATTGCCAAAACTA
                                        ttttaat  putative branch site (score: 3)
               aagttttttactttcc  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
acggtcatgggtagtatggaagataaaccttgttgaccttccattgtaaaaattttaggcaagttttttactttccattattcatttttaataattgcagGAAAAACAAAAGATTAAAGTAAAAGAGAAATTTGACAAGTGCGTTAAAGAGAAGCTGTTGGAGTTCTGTGACGTTCTTGACATATCAATTGCCAAAACTA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGGAG
- ggtcatg
- - - - - - - - - - -gataaac
- - - - - - - - - - - - - - cttgttg
- - - - - - - - - - - - - - - - - - ccttcca
- - - - - - - - - - - - - - - - - - - - - - -gtaaaaa