Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTATGGTGAGGTTGTTGCAGTGACAGGTGATGGGACAAATGATGCACCAGCTTTGCATGAGGCTGACATTGGGCTTGCCATGGGCATAGCTGGAACAGAGgtttgcttatccgaccatcttatgtactagtcatctgtttttactgcccttatctgttgtctttcttcttggttgcacagttattttttagttttttgat...

Basic information

species Vitis vinifera
transcript Vv08s0007g08960.t01
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv08s0007g08960.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: LOC_Os12g04220.1 (Oryza sativa), 5'ss of exon 4
GTATGGTGAGGTTGTTGCAGTGACAGGTGATGGGACAAATGATGCACCAGCTTTGCATGAGGCTGACATTGGGCTTGCCATGGGCATAGCTGGAACAGAGgtttgcttatccgaccatcttatgtactagtcatctgtttttactgcccttatctgttgtctttcttcttggttgcaca-gttattttttagtttt-ttgat--------------------------------------------------------------------
|| || |||||| ||| | |||||||||||||| ||||||||||| || || || || || || || ||||||||||| |||||||| || |||||||||||    ||  |    ||  | |     ||   |  |    | | |   | |       |||     | | ||  | | | || | | || | | ||  |||                                                                     
GTTTGATGAGGTGGTTTCTGTGACAGGTGATGGTACAAATGATGCTCCTGCATTACACGAAGCAGATATTGGGCTTGCTATGGGCATTGCAGGAACAGAGgtactgtttcctatgcagttcaaaacttatgaacgtagcatcaatagacattaaaaaagtcagatatttaggacgaatatgtcagtattcactcttactgaattaagttgatcctgataatccatttttcatcttctgaaatggagtaattttgtcttgtatttgtgcag

upper sequence: Vv08s0007g08960.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: LOC_Os11g04460.1 (Oryza sativa), 5'ss of exon 4
GTATGGTGAGGTTGTTGCAGTGACAGGTGATGGGACAAATGATGCACCAGCTTTGCATGAGGCTGACATTGGGCTTGCCATGGGCATAGCTGGAACAGAGgtttgcttatccgaccatcttatgtactagtcatctgtttttactgcccttatctgttgtctttcttcttggttgcaca-gttattttttagtttt-ttgat-----------------------------------------------------------------------------------------
|| || |||||| ||| | |||||||||||||| ||||||||||| || || || || || || || || |||||||| |||||||| || |||||||||||    ||  |    ||  | |     ||   || |    | | |   | |       |||     | | ||    | | || | | || | | ||  |||                                                                                          
GTTTGATGAGGTGGTTTCTGTGACAGGTGATGGTACAAATGATGCTCCTGCATTACACGAAGCAGATATCGGGCTTGCTATGGGCATTGCAGGAACAGAGgtactgtttcctatgcagttcaaaacttatggatgtagcatcaatagacattaaaaaagtcagatatttaggacaaatatgtcagtattcattcttactgaaataagttgaccctgataacccattttggatactttgtattttctttttcatcttctgaaatggagtaattttgtcttttatttgtgcag

upper sequence: Vv08s0007g08960.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: LOC_Os01g71240.1 (Oryza sativa), 5'ss of exon 4
GTATGGTGAGGTTGTTGCAGTGACAGGTGATGGGACAAATGATGCACCAGCTTTGCATGAGGCTGACATTGGGCTTGCCATGGGCATAGCTGGAACAGAGgtttgcttatccgaccatcttatgtactagtcatctgtttttact---gcccttatctgttgtctttcttcttggttgcacagttattttttagttttttgat
||     ||||| || || ||||| || || || || || || || || ||  |||| ||||| ||||| || || ||||||||||| ||||||||||||||| |     |  |||  | | |    |  | |  |||||| |||   | |    ||   |  ||||    |||  |       ||      | | ||||   
GTTCAACGAGGTGGTGGCGGTGACCGGCGACGGCACCAACGACGCGCCGGCGCTGCACGAGGCCGACATCGGCCTCGCCATGGGCATCGCTGGAACAGAGgttcgtactacttacctccgtttcaggttataagatgttttgactttggtcaaagtcaaattgctttaagtttgactaagtttgtagaaaaaaatatttt---

upper sequence: Vv08s0007g08960.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: GRMZM2G104730_T02 (Zea mays), 5'ss of exon 5
GTATGGTGAGGTTGTTGCAGTGACAGGTGATGGGACAAATGATGCACCAGCTTTGCATGAGGCTGACATTGGGCTTGCCATGGGCATAGCTGGAACAGAGgt--ttgct-tatccgaccat--cttatgtactagtcat-----------ctgtttttactgcccttatctgttg-----tctttcttcttggttgcacagttattttttagttttttgat----------------------------------------------------
||   | ||||| ||||| |||||||| ||||| || ||||| || ||||| |||||||| || || ||||||||||| ||||||||||| |||||||||||  |  || || |   | ||  ||  ||| ||     |           |   ||  |  ||| | |   | |      || |   |     |||||  |  ||  |    ||     ||                                                    
GTTCAGGGAGGTGGTTGCTGTGACAGGCGATGGTACCAATGACGCTCCAGCATTGCATGAAGCAGATATTGGGCTTGCAATGGGCATAGCAGGAACAGAGgtactaactatacctcgcaatttctactgttcttactgtgaatgtaaaaacctcttgcaaggccatcagaagctaagaactcctcacttgcaattgcaaggccatcatgcccttcggcaattctgtgcgtcccttgaaaagataaataacagtataagcttacatacttgcag

upper sequence: Vv08s0007g08960.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: GRMZM2G357620_T01 (Zea mays), 5'ss of exon 4
GTATGGTGAGGTTGTTGCAGTGACAGGTGATGGGACAAATGATGCACCAGCTTTGCATGAGGCTGACATTGGGCTTGCCATGGGCATAGCTGGAACAGAGgt--ttgcttatccgaccatctta-tgtactagtcatctgtttttactgcccttatctgt-tgtctttcttcttggttgcacagttattt-tttagttttttgat
|| | | ||||| ||||| ||||||||||| || || |||||||| ||||| |||||||| || || || || ||||| ||||||||||| |||||||||||  | | ||||     |   ||  |  |  | | |   |  |  |  |    |  || | ||  |      |||||  || | | |  |   ||||  |||   
GTTTCGCGAGGTGGTTGCTGTGACAGGTGACGGCACGAATGATGCTCCAGCGTTGCATGAAGCAGATATCGGCCTTGCTATGGGCATAGCAGGAACAGAGgtactggattattatgtcgcattggttcatgaatgacagggatacataggttgtgactctatgattcgagagttggt--caaaataacctacctagtaattt---

upper sequence: Vv08s0007g08960.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: GRMZM2G028812_T01 (Zea mays), 5'ss of exon 4
GTATGGTGAGGTTGTTGCAGTGACAGGTGATGGGACAAATGATGCACCAGCTTTGCATGAGGCTGACATTGGGCTTGCCATGGGCATAGCTGGAACAGAGgtttgcttatccgaccatcttatg--tactagtcatctgtttttactgcccttatctgttgtctttcttcttggttgca-cagttattttttagttttttgat
||     || || || || ||||| || || || || || || || || || ||||| ||||| ||||| || || ||||||||||| || |||||||||||||| |          |  ||    | ||       ||| ||| ||| |   | | |        ||||  |  |||| ||  |  |  | ||         
GTTCAACGAAGTGGTGGCGGTGACCGGCGACGGCACCAACGACGCGCCGGCGTTGCACGAGGCCGACATCGGCCTCGCCATGGGCATTGCAGGAACAGAGgtttgttgtagtagtagtagtacccttgctcacgccatgtctttcctggcgacaaccg--------cttcacgcctgcaacaacttctggtcag---------

upper sequence: Vv08s0007g08960.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: GLYMA10G15800.1 (Glycine max), 5'ss of exon 4
GTATGGTGAGGTTGTTGCAGTGACAGGTGATGGGACAAATGATGCACCAGCTTTGCATGAGGCTGACATTGGGCTTGCCATGGGCATAGCTGGAACAGAGgtttgcttatccgaccatcttatgtactagtcatctgtttttactgcccttatctgttgtctttcttcttggttgcacagttattttttagttttttgat--
|| |||||||||||| || || || |||||||| || |||||||| || ||  |||||||| | |||||||||||||| ||||||||||||||||||||||||||       ||     |||  ||      |||||    || | |   || | |||   | |  | ||  ||||  ||||  ||   |  || || |   
GTTTGGTGAGGTTGTAGCTGTTACTGGTGATGGAACCAATGATGCTCCTGCACTGCATGAGTCAGACATTGGGCTTGCTATGGGCATAGCTGGAACAGAGgtttgtgcccatgattgatttac-tatggtgtatctgacggtattacgtgtagcagttcattgtactgttt-ttgcttagttgcttggcatcttgtttaaga

upper sequence: Vv08s0007g08960.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: GLYMA02G32780.1 (Glycine max), 5'ss of exon 4
GTATGGTGAGGTTGTTGCAGTGACAGGTGATGGGACAAATGATGCACCAGCTTTGCATGAGGCTGACATTGGGCTTGCCATGGGCATAGCTGGAACAGAGgtttgcttatccgaccatcttatgtactagtcatctgtttttactgcccttatctgttgtctttcttcttggttgcacagttattttttagttttttgat--
|| |||||||||||| || || || |||||||| || |||||||| || ||  |||||||| | |||||||||||||| ||||||||| ||||||| ||||||||       ||     |||  ||       |||| |  || |     || | ||| | | |  | ||  ||||   |||  ||   |  || ||  |  
GTTTGGTGAGGTTGTAGCTGTTACTGGTGATGGAACCAATGATGCTCCTGCACTGCATGAGTCAGACATTGGGCTTGCTATGGGCATATCTGGAACTGAGgtttgtgcccatgatttgtttac-tatggtgtgtctgatggtattaagtgtagcagttctttgtactgttt-ttgctttgttgcttggcatcttgttttttc

upper sequence: Vv08s0007g08960.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: GLYMA03G29010.1 (Glycine max), 5'ss of exon 5
GTATGGTGAGGTTGTTGCAGTGACAGGTGATGGGACAAATGATGCACCAGCTTTGCATGAGGCTGACATTGGGCTTGCCATGGGCATAGCTGGAACAGAGgtttgcttatccgaccatcttatgtactagtcat--ctgtttttactgcccttatctgttgtctttcttcttggttgcacagttattttttagttttttgat
||  |||||||||||||| || || || ||||| || |||||||| || ||  ||| |||||| |||||||| ||||| ||||||||||| ||||| ||||||||  | ||       ||  | |  || |  |  | |||   | |    |||  | |  |  |||| ||   ||      | |  | | || | ||    
GTTCGGTGAGGTTGTTGCTGTTACTGGCGATGGAACTAATGATGCCCCTGCACTGCGTGAGGCAGACATTGGACTTGCAATGGGCATAGCAGGAACTGAGgtttgtatctcttgtgtactattatgataattctgacagttacgagttgttttagttttgttaattctcctgcattatgttttaagatataaggtgttat--

upper sequence: Vv08s0007g08960.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: GLYMA19G31770.1 (Glycine max), 5'ss of exon 2
GTATGGTGAGGTTGTTGCAGTGACAGGTGATGGGACAAATGATGCACCAGCTTTGCATGAGGCTGACATTGGGCTTGCCATGGGCATAGCTGGAACAGAGgtttgcttatccgaccatcttatgtacta-gtcatctgtttttactgcccttatctgttgtctttcttcttggttgcacagttattttttagttttttgat--------
|| ||||||||||||||| || || |||||||| || |||||||| || ||  ||   ||||| |||||||| ||||| ||||||||||| ||||| ||||||||  ||||      |||| | ||||| |  |  | |      |     ||    | || ||   |  | ||   ||| |||| ||  || | |  |          
GTTTGGTGAGGTTGTTGCTGTTACTGGTGATGGAACTAATGATGCTCCTGCACTGTGCGAGGCAGACATTGGACTTGCAATGGGCATAGCAGGAACTGAGgtttg--tatc------tcttgtttactacgataattctggcagttaagtgtacgcttagttttgtataatagtcctaca-ttatgttaaagatataaggcgttagcgt

upper sequence: Vv08s0007g08960.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: AT3G57330.1 (Arabidopsis thaliana), 5'ss of exon 4
GTATGGTGAGGTTGTTGCAGTGACAGGTGATGGGACAAATGATGCACCAGCTTTGCATGAGGCTGACATTGGGCTTGCCATGGGCATAGCTGGAACAGAGgtttgctt--atccgaccatcttatgtactagtcatctgtttttactgcccttatctgttgtctttcttcttggttgcacagttattttttagttttttgat
    || ||||| ||||||||||| || ||||| ||||||||||| || || |||||||||||||||||||| ||||||||||| |||||||||||||||||   |||   | |  |  | |||   | |  | |  |  || ||    |  | |    | | ||      |    ||  |   |      ||         
AATGGGAGAGGTAGTTGCAGTGACTGGGGATGGAACAAATGATGCTCCTGCATTGCATGAGGCTGACATTGGACTTGCCATGGGAATAGCTGGAACAGAGgtagcctttggttctcctctgttactgagttattaaatcattgtaaaatcgatgttctctatgttaaaaactc-ccgcgtatacaacacacag---------

upper sequence: Vv08s0007g08960.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: AT2G41560.1 (Arabidopsis thaliana), 5'ss of exon 4
GTATGGTGAGGTTGTTGCAGTGACAGGTGATGGGACAAATGATGCACCAGCTTTGCATGAGGCTGACATTGGGCTTGCCATGGGCATAGCTGGAACAGAGgtttgcttatccgaccatcttatgtactagtcatctgtttttactgcccttatctgttgtctttcttcttggttgcacagttattttttagttttttgat
   ||| ||||| |||||||||||||| ||||||||||| ||||| || || ||||||||||| |||||||| || || ||||| |||||||||||||||||  |||         ||  | |||  || |  | || ||  | |      ||||   |  |  | | || |||     | || ||     | |   |  
AATTGGAGAGGTAGTTGCAGTGACAGGGGATGGGACAAACGATGCCCCTGCGTTGCATGAGGCAGACATTGGACTAGCAATGGGAATAGCTGGAACAGAGgtaagcta---tagttattctctgt--tattggtttggtt--aataaaaaaatctcgagattaacattttcgtttggt-gctaattcccgatatgcag--

upper sequence: Vv08s0007g08960.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: PP1S37_351V6.1 (Physcomitrella patens), 5'ss of exon 6
GTATGGTGAGGTTGTTGCAGTGACAGGTGATGGGACAAATGATGCACCAGCTTTGCATGAGGCTGACATTGGGCTTGCCATGGGCATAGCTGGAACAGAGgtttgc-ttatccgaccatcttatgt--actagtcatctgttttt--actgcccttatctgttgtctttcttcttggttgcacagttattttttagttttttgat
 |  || || || || || |||||||||||||| || |||||||| || |||||||||||  ||||||| ||  | || |||||||| || || ||||||||  |  || |   ||  ||| | ||  |  |||  |  |    |  |  | | | |||      |  | ||| ||  || | | | | |  | | |        
ATTGGGAGAAGTGGTGGCCGTGACAGGTGATGGCACCAATGATGCTCCTGCTTTGCATGAATCTGACATCGGAATGGCGATGGGCATTGCGGGTACAGAGgtacgtatttttttacggtctgaagtgaaacagttgtggggccatggatagtcttgatcaac--ccgctgttcatgtctgtataataagtcgtcaatggcag---

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTATGGTGAGGTTGTTGCAGTGACAGGTGATGGGACAAATGATGCACCAGCTTTGCATGAGGCTGACATTGGGCTTGCCATGGGCATAGCTGGAACAGAGgtttgcttatccgaccatcttatgtactagtcatctgtttttactgcccttatctgttgtctttcttcttggttgcacagttattttttagttttttgat

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA