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'   		16  
 5'  3'   		17  
 5'  3'   		18  
 5'  3'   		19  
 5'  3'   		20  
 5'  3'   
21  
 5'  3'   		22  
 5'  3'   		23  
 5'  3'   		24  
 5'  3'   		25  
 5'  3'   		26  
 5'  3'   		27  
 5'  3'   		28  
 5'  3'   		29  
 5'  3'   		30  
 5'  3'   		31  
 5'  3'   		32  
 5'  3'   		33  
 5'  3'   		34  
 5'  3'   		35  
 5'  3'   		36  
 5'  3'   		37  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttgcaaccattttctttcactcttcttttagtgttttgactgtcgttgttttcttctaaattaaatgtagtcaatttcttatggggaaactctcttttgttgttaactttcaatgcagGATGTAATTCCACATATGGCACAGGAATATGGTTTTGAGTATGAGTTGATTACTTACAAATGGCCAACATGGTTGCATAAGCAGAAAGAAAAGCAGCGAA

Basic information

species Vitis vinifera
transcript Vv12s0034g02230.t01
intron # 32
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv12s0034g02230.t01 (Vitis vinifera), 3'ss of exon 32
lower sequence: LOC_Os02g44510.1 (Oryza sativa), 3'ss of exon 11
-------------------------------------------gttgcaaccattttctttcactcttct-tttagtgttttgactgtcgttgttttcttctaaattaaatgtagtcaatttcttatggggaaactctcttttgttgttaactttcaatgcagGATGTAATTCCACATATGGCACAGGAATATGGTTTTGAGTATGAGTTGATTACTTACAAATGGCCAACATGGTTGCATAAGCAGAAAGAAAAGCAGCGAA
                                            |   |    | | | || | |    | |||  ||    ||   | | ||| ||| | | | || | |   |  ||  | |||   |     | |||        |||         |||||||| || || |||||||| ||||||||||| |||||||| ||| |  | || || |||||||||||||||||||| || |||||||| ||||||||||
gtacgtgagctgcctttgcttgagttgagtatttaatgagaagatattagatgtctgcctttagttgagtatttcatgagaagatattagatgtcttcctttgagttgagtaatgagaagatattagatgcctgttgtcta--accaataatccaatggccagGATGTCATACCCCATATGGCCCAGGAATATGGATTTGAGTACGAGCTTGTCACATATAAATGGCCAACATGGTTGCACAAACAGAAAGAGAAGCAGCGAA

upper sequence: Vv12s0034g02230.t01 (Vitis vinifera), 3'ss of exon 32
lower sequence: GRMZM5G846198_T02 (Zea mays), 3'ss of exon 4
gttgcaaccattttctttcactcttcttttagtgttttgactgtcgttgt-tttcttctaaattaaatgtagtcaatttcttatggg-gaaactctcttttgttgttaactttcaatgcagGATGTAATTCCACATATGGCACAGGAATATGGTTTTGAGTATGAGTTGATTACTTACAAATGGCCAACATGGTTGCATAAGCAGAAAGAAAAGCAGCGAA
                                                || | |   |||  ||  |  |  | |||  |||| |   |    ||| |||| |    | |   |    |||||||| || || || ||||| | ||||||||  || ||||||||| |  | || || ||||||||||||||||| || ||||||||||| |||||  | |
------------------------------------------------gtatatgagctacctttgagtttattaatcacttaagattgggtgtctattttctaaccatcccgctgc-cagGATGTCATACCGCACATGGCTCGGGAATATGAATTCGAGTATGAGCTCGTCACATATAAATGGCCAACATGGTTACACAAGCAGAAAGAGAAGCAAAGGA

upper sequence: Vv12s0034g02230.t01 (Vitis vinifera), 3'ss of exon 32
lower sequence: GLYMA08G20020.1 (Glycine max), 3'ss of exon 31
--gttgcaaccattt--tctttcactcttcttttagtgttttgactgtcgttgttttcttctaaattaaatgtagtcaatttcttatggggaaactctcttttgttgttaactttcaatgcagGATGTAATTCCACATATGGCACAGGAATATGGTTTTGAGTATGAGTTGATTACTTACAAATGGCCAACATGGTTGCATAAGCAGAAAGAAAAGCAGCGAA
    | || |||     | | |  |||    |||| |  ||||  | | |    |||    |  | || |   |||    |     |     |||| | ||   |||||  |||   |  |||||| | ||||| || ||||| || |||||||||||||| |  ||  | || || ||||||||||| ||||||||||||||||||||||||||||||||||
gttatacatccacacagtatatgcctcaatgtttattcatttgtatattggaactttaaagtggaatataatgagtttgctcaacttcctcgaactattttgc-ttgttgtcttaacaaacagGATCTGATTCCTCACATGGCTCAAGAATATGGTTTTGAATGCGAACTAATCACCTACAAATGGCCTACATGGTTGCATAAGCAGAAAGAAAAGCAGCGAA

upper sequence: Vv12s0034g02230.t01 (Vitis vinifera), 3'ss of exon 32
lower sequence: GLYMA05G30230.1 (Glycine max), 3'ss of exon 32
gttgcaaccattttctttcactcttcttttagtgttttgactgtcgttgttttcttctaaattaaatgtagtcaatttcttatggggaaactct---cttttgttgttaactttcaatgcagGATGTAATTCCACATATGGCACAGGAATATGGTTTTGAGTATGAGTTGATTACTTACAAATGGCCAACATGGTTGCATAAGCAGAAAGAAAAGCAGCGAA
|||  |   ||   |      | |    |||   |||| | |  | ||  | | ||  ||  ||||        ||   ||     || | |||   |  || | ||| ||||   || |||||  |||||||||| ||||| |  || ||||||||||| |||||  |  | || ||||| ||||| ||||||||||||||||||||||||||||||||||
gttata--tatccacccaagttatatgctta-cattttaatt--catttgtatattggaatgtaaagtagaatgatgagtttgcctgacattctgaaccattttggttgacttaacatacagGACTTAATTCCACACATGGCCCTAGAGTATGGTTTTGAATATGAACTAGTCACGTACAAGTGGCCCACATGGTTGCATAAGCAGAAAGAAAAGCAGCGAA

upper sequence: Vv12s0034g02230.t01 (Vitis vinifera), 3'ss of exon 32
lower sequence: GLYMA08G13400.1 (Glycine max), 3'ss of exon 34
-----gttgcaaccattttctttcactcttcttttagtgttttgactgtcgttgtttt---cttctaaattaaatgtagtcaatttcttatggggaaactctcttttgttgttaactttcaatgcagGATGTAATTCCACATATGGCACAGGAATATGGTTTTGAGTATGAGTTGATTACTTACAAATGGCCAACATGGTTGCATAAGCAGAAAGAAAAGCAGCGAA
      |  | |||    |  |   ||    ||||| |   ||   | | |     ||       |||| || |  |  | | |||    ||          || || | ||| ||||   || |||||  | |||||||| ||||| |  || ||||||||||| |||||  |  | || ||||| ||||| ||||||||||||||||||||||||||||||||||
gttatatatccacccaagttatatgcttacattttaattcattatatattggaacgttaaatggttaaagtaga-atgatgagtttgcc-tgacatcctgaactgttttggttgacttaacatacagGACTTGATTCCACACATGGCCCTAGAGTATGGTTTTGAATATGAACTAGTCACATACAAGTGGCCCACATGGTTGCATAAGCAGAAAGAAAAGCAGCGAA

upper sequence: Vv12s0034g02230.t01 (Vitis vinifera), 3'ss of exon 32
lower sequence: AT1G71220.2 (Arabidopsis thaliana), 3'ss of exon 31
------gttgcaaccattttctttcac-tcttcttttagtgttt-tgactgtcgttgttttcttctaaattaaatgtagtcaatttcttatggggaaactctcttt-tgt-tgttaactttcaa---tgcagGATGTAATTCCACATATGGCACAGGAATATGGTTTTGAGTATGAGTTGATTACTTACAAATGGCCAACATGGTTGCATAAGCAGAAAGAAAAGCAGCGAA
                ||| ||| ||| | | | ||| |||||| |  || |   ||| ||||| |    || ||||   |  | |||| | |  | | |  |||  ||| | |    ||  ||   |||||||||| ||||||||||||||||| |||||    |||||||||||| ||||||| |||||||||||  | ||||||||||| |||||||||||||| ||||
gttggctccttgtttctttgcttccacatatgccttttgtgtttgtatctatatatgtcttcttatct-ctagatgtgaact-tatcttgtagccacattaacttaatgtgtatcgcattctaatcttgcagGATGTGATTCCACATATGGCACAAGAATACAACTTTGAGTATGAGCTGATTACATACAAATGGCCGTCCTGGTTGCATAAACAGAAAGAAAAGCAACGAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aatgtagtcaatttcttatggggaaactctcttttgttgttaactttcaatgcagGATGTAATTCCACATATGGCACAGGAATATGGTTTTGAGTATGAGTTGATTACTTACAAATGGCCAACATGGTTGCATAAGCAGAAAGAAAAGCAGCGAA
                                     tgttaac  putative branch site (score: 2)
                                           ctttc  CT-rich tract
         aatttcttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttgcaaccattttctttcactcttcttttagtgttttgactgtcgttgttttcttctaaattaaatgtagtcaatttcttatggggaaactctcttttgttgttaactttcaatgcagGATGTAATTCCACATATGGCACAGGAATATGGTTTTGAGTATGAGTTGATTACTTACAAATGGCCAACATGGTTGCATAAGCAGAAAGAAAAGCAGCGAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA