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

gtatgaaaagctttgagcagtactattgttattttttgtgttcattcccactcctgcatggtctgacaatggattagaaacaaaattattagtttttcttttccaaatgcagGTTTGTTGAGATCATGGCTCCTGTATTTTCTAGAGATGCATGGCGGTGTGTGTGGCATATGCTTCAG

Basic information

species Vitis vinifera
transcript Vv01s0137g00770.t01
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv01s0137g00770.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: GRMZM2G162881_T01 (Zea mays), 3'ss of exon 3
gtatgaaaagctttgagcagtactattgttattttttgtgttcattcccactcctgcatggtctgacaatggattagaaacaaaattattagtttttcttttccaaatgcagGTTTGTTGAGATCATGGCTCCTGTATTTTCTAGAGATGCATGGCGGTGTGTGTGGCATATGCTTCAG
                                  |  | || || ||    |  |  ||  | |    || ||    ||      || ||    | |  | |  | ||||||||||||||| || |||||  ||||||| || || ||||||||||| ||||| ||||||||| |||||
---------------------------------gtaggagtgcaatcat-ttattagattattttcttatcga----aatttctgtttttcacatgtaatctg-atatgcagGTTTGTTGAAATAATGGCAACTGTATTCTCAAGGGATGCATGGCGCTGTGTATGGCATATGATTCAG

upper sequence: Vv01s0137g00770.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: GLYMA18G01710.1 (Glycine max), 3'ss of exon 10
gtatgaaaagctttgagcagtactattgttattttttgtgttcattcccactcctgcatggtctgacaatggattagaaacaaaattattagtttttcttttccaaatgcagGTTTGTTGAGATCATGGCTCCTGTATTTTCTAGAGATGCATGGCGGTGTGTGTGGCATATGCTTCAG
             | || ||  ||  || | | |||     |||||  || |      | || | |||  ||| |  |    |   |  || |   | || |  |||||||||||||||||||| |||||||| || || || |||||||||||||| ||||||||||||||| |||||
------------gtaagtag--ctgctgatgtattta----tcatttacattatc---tagttt-aca--ggactgcatctcattgtgcta-tcactgttatataaatgcagGTTTGTTGAGATTATGGCTCCAGTGTTCTCAAGAGATGCATGGCGCTGTGTGTGGCATATGATTCAG

upper sequence: Vv01s0137g00770.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: GLYMA11G37770.1 (Glycine max), 3'ss of exon 10
gtatgaaaagctttgagcagtactattgttattttttgtgttcattcccactcctgcatggtctgacaatggattagaaacaaaattattagtttttcttttccaaatgcagGTTTGTTGAGATCATGGCTCCTGTATTTTCTAGAGATGCATGGCGGTGTGTGTGGCATATGCTTCAG
                        | |      || ||| || ||    ||   |  || |||| ||||  || |  |    |   |  |||   |  |  | ||||||||||||||||||||| |||||||| || || ||  ||||||||||||| ||||||||||||||| |||||
---------------------gtaagtagctgcttatgtatttatcattacat-tatatagtct-acaa--gactgcatctcattgtgctagcactgttaatacaaatgcagGTTTGTTGAGATTATGGCTCCAGTGTTCTCGCGAGATGCATGGCGCTGTGTGTGGCATATGATTCAG

upper sequence: Vv01s0137g00770.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: GLYMA05G30850.1 (Glycine max), 3'ss of exon 8
gtatgaaaagctttgagcagtactattgttattttttgtgttcattcccactcctgcatggtctgacaatggattagaaacaaaattattagtttttcttttccaaatgcagGTTTGTTGAGATCATGGCTCCTGTATTTTCTAGAGATGCATGGCGGTGTGTGTGGCATATGCTTCAG
   | |  | || | |  || | | || || |||||||       | | |    | |      |   ||||   |     ||  |||             |   | |||||||||||||||||| |||||||| || |||||  || |||||||||| ||||||||||||||| |||||
--gtaagtaactgttaa-agaatttttatttttttttggcaggggtacaatattttcccatctt--taatgagctgattccaccatt------------ctgtaacatgcagGTTTGTTGAGATAATGGCTCCAGTGTTTTCACGAAATGCATGGCGCTGTGTGTGGCATATGATTCAG

upper sequence: Vv01s0137g00770.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: GLYMA08G14050.1 (Glycine max), 3'ss of exon 8
gtatgaaaagctttgagcagtactattgttattttttgtgttcattcccactcctgcatggtctgacaatggattagaaacaaaattattagtttttcttttccaaatgcagGTTTGTTGAGATCATGGCTCCTGTATTTTCTAGAGATGCATGGCGGTGTGTGTGGCATATGCTTCAG
             | || |  ||| ||     ||||| |  |         | |   ||  ||  |   |   ||||         |  |        | |   | |||||||||||||||||| |||||||| || |||||  || |||||||||| ||||||||||||||| |||||
------------gtaagta--actgttacagattttttt--ttgggggggttacaatattttcccatctttagttag--------ctgattccaccattctgtaacatgcagGTTTGTTGAGATTATGGCTCCAGTGTTTTCACGAAATGCATGGCGCTGTGTGTGGCATATGATTCAG

upper sequence: Vv01s0137g00770.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: GLYMA08G14040.1 (Glycine max), 3'ss of exon 10
gtatgaaaagctttgagcagtactattgttattttttgtgttcattcccactcctgcatggtctgacaatggattagaaacaaaattattagtttttcttttccaaatgcagGTTTGTTGAGATCATGGCTCCTGTATTTTCTAGAGATGCATGGCGGTGTGTGTGGCATATGCTTCAG
                           || |   |  || |  |     | |  || ||  ||   | ||         || ||| | |      || | ||    |||||| ||||||||||| |||||||| || |||||  ||||||||||||| ||||| ||||||||| |||||
---------------------------gtaagcatcagt-tgaagcattatttttgtattatccacccat---------accaaactgtatccaattatgttatgcatgcagATTTGTTGAGATTATGGCTCCAGTGTTTTCACGAGATGCATGGCGTTGTGTCTGGCATATGATTCAG

upper sequence: Vv01s0137g00770.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: GLYMA05G30830.1 (Glycine max), 3'ss of exon 10
gtatgaaaagctttgagcagtactattgttattttttgtgttcattcccactcctgcatggtctgacaatggattagaaacaaaattattagtttttcttttccaaatgcagGTTTGTTGAGATCATGGCTCCTGTATTTTCTAGAGATGCATGGCGGTGTGTGTGGCATATGCTTCAG
                           || |   |  || |  |     | |  ||  |  |||  | ||         || ||| | |      || | ||    |||||| ||||||||||| |||||||| || |||||  ||||||||||||  ||||||||||||||| |||||
---------------------------gtaagcatcagt-tgaagcattatttttgtcttatctacccat---------accaaactgtatccaattatgttatgtatgcagATTTGTTGAGATTATGGCTCCAGTGTTTTCACGAGATGCATGGCATTGTGTGTGGCATATGATTCAG

upper sequence: Vv01s0137g00770.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: AT1G13000.2 (Arabidopsis thaliana), 3'ss of exon 10
gtatgaaaagctttgagcagtactattgttattttttgtgttcattcccactcctgcatggtctgacaatggattagaaacaaaattattagtttt-tcttttccaaatgcagGTTTGTTGAGATCATGGCTCCTGTATTTTCTAGAGATGCATGGCGGTGTGTGTGGCATATGCTTCAG---------------------------------
                                     ||    | || ||    | |||      |  || |||   | |||  | | ||  ||   | |  |     | ||||||| | ||||| |||||||| ||||| || |||||||||||||| || |||||||||||| |||||                                 
-------------------------------------gtacgtagtctcaaatgttcattacaaaaacatagatct-atacagtactcttgattccatgtaatattcttacagGTTTATAGAGATTATGGCTCCAGTATTCTCAAGAGATGCATGGCGTTGCGTGTGGCATATGATTCAGAACGATTTGGTTCACGGTTGGGGTCTTGATTTC

upper sequence: Vv01s0137g00770.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: AT1G67850.2 (Arabidopsis thaliana), 3'ss of exon 10
gtatgaaaagctttgagcagtactattgttattttttgtgttcattcccactcctgcatggtctgacaatggattagaaacaaaattattagtttttcttttccaaatgcagGTTTGTTGAGATCATGGCTCCTGTATTTTCTAGAGATGCATGGCGGTGTGTGTGGCATATGCTTCAG
||||| | |      |||  | || ||      ||||| |||  ||    |   |    ||      ||   |  || | | || || |  ||  |||      |||||||| || || ||||||||||||||||||||||| ||| |||| ||||| || ||||||||| || | |||
gtatgtaga------agcctttctttttacccgttttgagttggtttttccctataacagg------aactaaccagtatcgaacttttgtgtcattcaa----aaatgcagATTCGTAGAGATCATGGCTCCTGTATTTTCAAGAAATGCCTGGCGATGCGTGTGGCATGTGATCCAG

upper sequence: Vv01s0137g00770.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: AT3G26440.4 (Arabidopsis thaliana), 3'ss of exon 10
gtatgaaaagctttgagcagtactattgttattttttgtgttcattcccactcctgcatggtctgacaatggattagaaacaaaattattagtttttcttttccaaatgcagGTTTGTTGAGATCATGGCTCCTGTATTTTCTAGAGATGCATGGCGGTGTGTGTGGCATATGCTTCAG---------------------------------
                       ||| | | |  |||||   ||   ||| | |   | |   | | | |   || ||  ||   |||    ||   |  ||||  || ||||||| | ||||| |||||||| || || |||||||| |||||||| ||||||||||||||| |||||                                 
----------------------gtatggatctcatttgt---caaaaccaatacaataagtattcatactctctt-gatcca---ttaagttttgcacggttccttat-cagGTTTATAGAGATTATGGCTCCAGTTTTCTCTAGAGAGGCATGGCGTTGTGTGTGGCATATGATTCAGAATGACTTGGTTCACGGTTGGGGTCTTGACTTT

upper sequence: Vv01s0137g00770.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: AT1G24570.1 (Arabidopsis thaliana), 3'ss of exon 9
gtatgaaaagctttgagcagtactattgttattttttgtgttcattcccactcctgcatggtctgacaatggattagaaacaaaattattagtttttcttttccaaatgcagGTTTGTTGAGATCATGGCTCCTGTATTTTCTAGAGATGCATGGCGGTGTGTGTGGCATATGCTTCAG
                | | |  |      |   | | | |  |   | | |     |     | | |    ||||| |||    ||||     | | |  |  |||  ||| || || ||||| |||||||||||||| || |||||||||||||| || |||||||||||| | |||
----------------gta-tgtttcaaaaaacgtctctatcaaactcaagtttcagacatatttaaacc--attagtaacttcgttatg----tctttaataaaaaaacagATTCGTGGAGATAATGGCTCCTGTATTCTCAAGAGATGCATGGCGCTGCGTGTGGCATATGATCCAG

upper sequence: Vv01s0137g00770.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: PP1S129_53V6.1 (Physcomitrella patens), 3'ss of exon 10
gtatgaaaagctttgagcagtact--attgttattttttgtgttcattcccactcctgcatggt----ctgacaatggattagaaacaaaattattagtttttcttttccaaatgcagGTTTGTTGAGATCATGGCTCCTGTATTTTCTAGAGATGCATGGCGGTGTGTGTGGCATATGCTTCAG
   | | |||  |  | | ||| |   ||  |  ||  ||| ||   | || |   ||   | |     | ||  |   ||||        | |||   || |  |||   | ||||| ||||||||||||||||||||||| |||||  || | |||||||| ||  | ||| | ||  | |||
--gtaataag--tcaacctgtatttagttagtgattcgtgtcttaccttcctcctttggtcgttgaaatttactgtctgttagttgttgggt-atttacttcttgtttaatactgcagATTTGTTGAGATCATGGCTCCTGTGTTTTCACGAAAAGCATGGCGTTGCATCTGGTACATAATACAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atggtctgacaatggattagaaacaaaattattagtttttcttttccaaatgcagGTTTGTTGAGATCATGGCTCCTGTATTTTCTAGAGATGCATGGCGGTGTGTGTGGCATATGCTTCAG
   gtctgac  putative branch site (score: 3)
                               ttagtttttcttttcc  putative PPT
               attagaaacaaaatta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgaaaagctttgagcagtactattgttattttttgtgttcattcccactcctgcatggtctgacaatggattagaaacaaaattattagtttttcttttccaaatgcagGTTTGTTGAGATCATGGCTCCTGTATTTTCTAGAGATGCATGGCGGTGTGTGTGGCATATGCTTCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG