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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagggagcttgggagctgcacttctgcaatctgactgcttttgttcttgtaattgatctaaatttatttatgttatcttatgcagTGTTATGGGATATACCTTACTTCTCAATTTGATTGAGTACAAGACACTTGTAATGCGTGGAGACTTTCAACGTGCAAGTGAAATTTTACCTTTGATTCCT

Basic information

species Vitis vinifera
transcript Vv11s0016g04180.t01
intron # 16
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv11s0016g04180.t01 (Vitis vinifera), 3'ss of exon 16
lower sequence: LOC_Os06g05180.1 (Oryza sativa), 3'ss of exon 16
gtgagggagcttgggagctgcacttctgcaat-ctgactgcttttgttcttgtaattgatc--taaatttatttatgttatcttatgcagTGTTATGGGATATACCTTACTTCTCAATTTGATTGAGTACAAGACACTTGTAATGCGTGGAGACTTTCAACGTGCAAGTGAAATTTTACCTTTGATTCCT
              | |       |    ||| ||| |||||| |  ||| ||  |  ||   | || | |  ||| ||   |  |||||||| ||||| || || |||||||| | |||||||||||||||||||||||| |||||||| ||  || ||||||||| ||| |||||||| |  || || 
--------------gtgtgttttcttgataatactgcctgcttattgtctggtgttgaattcttgaactaacatatttttcttgttgcagTGTCATGGGGTACACATTACTTCTTAGTTTGATTGAGTACAAGACACTTGTGATGCGTGGGGATATTGAACGTGCAAATGATATTTTACCATCCATACCA

upper sequence: Vv11s0016g04180.t01 (Vitis vinifera), 3'ss of exon 16
lower sequence: LOC_Os02g11830.2 (Oryza sativa), 3'ss of exon 16
gtgagggagcttgggagctgcacttctgcaatctgactgc-ttttgttcttgtaattga--tctaaatttatttatgttatctta-tgcagTGTTATGGGATATACCTTACTTCTCAATTTGATTGAGTACAAGACACTTGTAATGCGTGGAGACTTTCAACGTGCAAGTGAAATTTTACCTTTGATTCCT
           || |   ||    ||||  |||  |     ||  |       |||  |  ||| |  |||  | |||| ||||| ||||||||| |||| ||||| ||||| || | | |||||||||| || |||||||||||||||||||||||  | |||||||  |   ||||||| |  || || 
----------gtgagtcttggttgtctggtatcgtatcatattcggaagccacaatgaacttctgaggttaact-tgttttcttactgcagTGTTGTGGGGTATACTTTACTCCTTACTATGATTGAGTATAAAACACTTGTAATGCGTGGAGACTTCGATCGTGCAAACGCTCTTTTACCATCTATACCA

upper sequence: Vv11s0016g04180.t01 (Vitis vinifera), 3'ss of exon 16
lower sequence: LOC_Os02g11840.1 (Oryza sativa), 3'ss of exon 7
gtgagggagcttgggagctgcacttctgcaatctgactgc-ttttgttcttgtaattga--tctaaatttatttatgttatctta-tgcagTGTTATGGGATATACCTTACTTCTCAATTTGATTGAGTACAAGACACTTGTAATGCGTGGAGACTTTCAACGTGCAAGTGAAATTTTACCTTTGATTCCT
           || |   ||    ||||  ||   |     || ||       |||  |  ||| |  |||  | |||| ||||| ||||||||| |||| ||||| ||||| || |   |||||||||| || |||||||||||||||||||||||  | |||||||  |   ||||||| |  || || 
----------gtgagtcttggttgtctggtattgtatcatattctgaagccacaatgaacttctgaggttaact-tgttttcttactgcagTGTTGTGGGGTATACTTTACTCCTTACCATGATTGAGTATAAAACACTTGTAATGCGTGGAGACTTCGATCGTGCAAACGCTCTTTTACCATCTATACCA

upper sequence: Vv11s0016g04180.t01 (Vitis vinifera), 3'ss of exon 16
lower sequence: GRMZM2G095348_T01 (Zea mays), 3'ss of exon 16
gtgagggagcttgggagctgcacttctgcaatctgactgcttttgttcttgtaattgatctaaatttatttatgttatcttatgcagTGTTATGGGATATACCTTACTTCTCAATTTGATTGAGTACAAGACACTTGTAATGCGTGGAGACTTTCAACGTGCAAGTGAAATTTTACCTTTGATTCCT
||| |    ||    | |     |||     | |     | | || | ||  ||||  | | |  | |  |||      | || |||| | || || || || |||||||| | |||||||||||||||||| ||||| |||||||| || ||  ||| ||||| |||||||||| | |  || || 
gtgcgctttctctaaaacaatgtttcctttcttttgtaacatctgctgtt--aatttctgtga-ctaacatataa-gcttgatacagTATCATTGGGTACACATTACTTCTGAGTTTGATTGAGTACAAGACCCTTGTGATGCGTGGGGATTTGGAACATGCAAATGAAATTTTATCATCCATACCA

upper sequence: Vv11s0016g04180.t01 (Vitis vinifera), 3'ss of exon 16
lower sequence: GRMZM2G443953_T03 (Zea mays), 3'ss of exon 17
gtgag-ggagcttgggagctgcacttctg-caatctgactgcttttgttcttgtaat-tgatctaaatttatttatgttatcttatgcagTGTTATGGGATATACCTTACTTCTCAATTTGATTGAGTACAAGACACTTGTAATGCGTGGAGACTTTCAACGTGCAAGTGAAATTTTACCTTTGATTCCT
|| ||  |      | |     |||||||    ||| ||    | |||| |||   | |||    ||||| |||||         | ||||||  |||| ||||| ||||| |||| ||||||||||||||| |||||||| |||||||| || ||  ||| ||| | |   |||||||| |  || || 
gtaagcagcatgcagcatacctacttctgatcttcttacatgatgtgtttttgggttatgacaacaatttttttat---------tacagTGTGGTGGGTTATACTTTACTACTCAGTTTGATTGAGTACAAAACACTTGTGATGCGTGGGGATTTGGAACATGCGAATATTATTTTACCATCCATACCA

upper sequence: Vv11s0016g04180.t01 (Vitis vinifera), 3'ss of exon 16
lower sequence: GRMZM2G124886_T01 (Zea mays), 3'ss of exon 16
gtgagggagcttgggagctgcacttctgcaatctgactgcttttgttcttgtaattgatctaaatttatttatgttatcttatgcagTGTTATGGGATATACCTTACTTCTCAATTTGATTGAGTACAAGACACTTGTAATGCGTGGAGACTTTCAACGTGCAAGTGAAATTTTACCTTTGATTCCT
    | ||| |   || ||      |   ||| | |||  |  | ||  |  |   | |||     || |    || | |  ||||||||| |||| ||||| ||||| || | |||||| ||||| || ||||||||||||||||| || ||| | ||||||| |||  ||||| | |  || || 
----gtgagtt---gatctttgtcacctaaatttcacttgtagtttttgtacacaagttctgtggctaatgtacttttttattgcagTGTTGTGGGGTATACTTTACTCCTTAGTTTGATCGAGTATAAAACACTTGTAATGCGTGGGGATTTTGATCGTGCAAATGATGTTTTATCATCTATACCA

upper sequence: Vv11s0016g04180.t01 (Vitis vinifera), 3'ss of exon 16
lower sequence: GRMZM2G086015_T01 (Zea mays), 3'ss of exon 1
gtgagggagcttgggagctgcacttctgcaatctgactgcttttgttcttgtaattgatctaaatttatttatgttatcttatgcagTGTTATGGGATATACCTTACTTCTCAATTTGATTGAGTACAAGACACTTGTAATGCGTGGAGACTTTCAACGTGCAAGTGAAATTTTACCTTTGATTCCT
||  |    || |  | |    ||||       |    || | ||||  | |   ||| ||||        |  |    |  | |||||| || || || || |||||||| | |||||||||||||||||| ||||| |||||||| || ||  | | |||||   |||||||| | |  || || 
gtatgttttctcgaaaacaatgcttcctttcctttgtagcatctgttaatttctctga-ctaa-------caaatagcttggtacagTGTCATTGGGTACACATTACTTCTGAGTTTGATTGAGTACAAGACCCTTGTGATGCGTGGGGATTTGGATCATGCAAACAAAATTTTATCATCCATACCA

upper sequence: Vv11s0016g04180.t01 (Vitis vinifera), 3'ss of exon 16
lower sequence: GRMZM2G000645_T01 (Zea mays), 3'ss of exon 16
gtgagggagcttgggagctgcacttctgcaatctgactgcttttgttcttgtaattgatctaaatttatttatgttatcttatgcagTGTTATGGGATATACCTTACTTCTCAATTTGATTGAGTACAAGACACTTGTAATGCGTGGAGACTTTCAACGTGCAAGTGAAATTTTACCTTTGATTCCT
||  |    || |  | |    ||||       |    || | ||||  | |   ||| ||||        |  |    |  | |||||| || || || || |||||||| | |||||||||||||||||| ||||| |||||||| || ||  | | |||||   |||||||| | |  || |||
gtatgttttctcgaaaacaatgcttcctttcctttgtagcatctgttaatttctctga-ctaa-------caaatagcttggtacagTGTCATTGGGTACACATTACTTCTGAGTTTGATTGAGTACAAGACCCTTGTGATGCGTGGGGATTTGGATCATGCAAACAAAATTTTATCATCCATACCT

upper sequence: Vv11s0016g04180.t01 (Vitis vinifera), 3'ss of exon 16
lower sequence: GRMZM2G448913_T01 (Zea mays), 3'ss of exon 5
gtgagggagcttgggagctgcacttctgcaatctgactgcttttgttcttgtaattgatctaaatttatttatgttatcttatgcagTGTTATGGGATATACCTTACTTCTCAATTTGATTGAGTACAAGACACTTGTAATGCGTGGAGACTTTCAACGTGCAAGTGAAATTTTACCTTTGATTCCT
||  |    || |  | |    ||||       |    || | | ||  | |   ||| ||||        |  |    |  | |||||| || || || || |||||||| | |||||||||||||||||| ||||| |||||||| || ||  | | |||||   |||||||| | |  || || 
gtatgttttctcgaaaacaatgcttcctttcctttgtagcatctattaatttctctga-ctaa-------caaatagcttggtacagTGTCATTGGGTACACATTACTTCTGAGTTTGATTGAGTACAAGACCCTTGTGATGCGTGGGGATTTGGATCATGCAAACAAAATTTTATCATCCATACCA

upper sequence: Vv11s0016g04180.t01 (Vitis vinifera), 3'ss of exon 16
lower sequence: GRMZM2G141587_T02 (Zea mays), 3'ss of exon 16
gtgagggagcttgggagctgcacttctgcaatctgactgcttttgttcttgtaattgatcta-aatttatttatgttatcttatgcagTGTTATGGGATATACCTTACTTCTCAATTTGATTGAGTACAAGACACTTGTAATGCGTGGAGACTTTCAACGTGCAAGTGAAATTTTACCTTTGATTCCT
    | ||| |    | ||    | ||  | ||    ||   || ||  |  |   | |||     | || ||  ||||  | ||||||||| |||| ||||| ||||| || | |||||| || || || ||||||||||||||||| || ||  | || || | |||  ||||| | |  || || 
----gtgagttc---atctttgttactaaattccacttgtagtt-tttgtacacaagttctgtggctaatgtaccttattat-tgcagTGTTGTGGGGTATACTTTACTCCTTAGTTTGATCGAATATAAAACACTTGTAATGCGTGGGGATTTCGATCGCGCGAATGATGTTTTATCATCTATACCA

upper sequence: Vv11s0016g04180.t01 (Vitis vinifera), 3'ss of exon 16
lower sequence: GLYMA08G22140.1 (Glycine max), 3'ss of exon 16
gtgagggagcttgggagctgcacttctgcaatctgactgcttttgttcttgtaattgatctaaatttatttatgttatcttatgcagTGTTATGGGATATACCTTACTTCTCAATTTGATTGAGTACAAGACACTTGTAATGCGTGGAGACTTTCAACGTGCAAGTGAAATTTTACCTTTGATTCCT
|| || |       |   |||| |      ||   |    | |   |   |||||    || | | | |||    | | |||  ||||||||||||||| ||  ||||| | | ||||||||| |||||||||||||| |||||||| || ||  || | || | ||||||| |||| |  ||||||
gtaagtggatcaatggtttgcatt------attcaaaatatctcaatgcagtaatc---ctgattattttttaactgttttactcagTGTTATGGGATACACGCTACTTTTAAGTTTGATTGAATACAAGACACTTGTCATGCGTGGTGATTTGGAAAGGGCCAATGAAATTCTACCATCAATTCCT

upper sequence: Vv11s0016g04180.t01 (Vitis vinifera), 3'ss of exon 16
lower sequence: GLYMA15G01680.1 (Glycine max), 3'ss of exon 16
gtgagggagcttgggagctgcacttctgcaatct---gactgcttttgttcttgtaattgatctaaatttatttatgttatcttatgcagTGTTATGGGATATACCTTACTTCTCAATTTGATTGAGTACAAGACACTTGTAATGCGTGGAGACTTTCAACGTGCAAGTGAAATTTTACCTTTGATTCCT
|| || ||   |      || | |  |  ||  |    | |||  |  |  |    |||  |||   |||||  ||  | | ||   ||||||||||||||| ||  | ||| | |  ||||||||||||||||||||||| |||||||| || ||  || | || | ||| ||| | || |  || || 
gtaagtgaaacttctgcttggattattcaaagttttaaattgcaataatcttgactatttttctg--tttatcaat--tgtttttctcagTGTTATGGGATACACACTGCTTTTAAGCTTGATTGAGTACAAGACACTTGTGATGCGTGGTGATTTGGAAAGGGCCAATGATATTCTGCCATCAATCCCC

upper sequence: Vv11s0016g04180.t01 (Vitis vinifera), 3'ss of exon 16
lower sequence: GLYMA13G43680.2 (Glycine max), 3'ss of exon 16
gtgagggagcttgggagctgcacttctgcaatctgactgcttttgttcttgtaattgatctaaatttatttat--gttatcttatgcagTGTTATGGGATATACCTTACTTCTCAATTTGATTGAGTACAAGACACTTGTAATGCGTGGAGACTTTCAACGTGCAAGTGAAATTTTACCTTTGATTCCT
|| || ||   |      || | |  |  ||  |      |   ||  |  | | |  | |   | | |||||   || | ||   ||||||||||||||| ||  | ||| | |  ||||||||||||||||||||||| |||||||| || ||  || | || | ||||||| |||| |  || || 
gtaagtgaaacttctgcttggattattcaaagttttaaattgcagtaatcttgactacttt---tctgtttatcaattttttttctcagTGTTATGGGATACACACTGCTTTTAAGCTTGATTGAGTACAAGACACTTGTGATGCGTGGTGATTTGGAAAGGGCCAATGAAATTCTACCATCAATCCCC

upper sequence: Vv11s0016g04180.t01 (Vitis vinifera), 3'ss of exon 16
lower sequence: AT1G79990.1 (Arabidopsis thaliana), 3'ss of exon 20
gtgagggagcttgggagctgcacttctgcaatctgactgcttttgttcttgtaattgatctaaatttatttatgttatcttat-gcagTGTTATGGGATATACCTTACTTCTCAATTTGATTGAGTACAAGACACTTGTAATGCGTGGAGACTTTCAACGTGCAAGTGAAATTTTACCTTTGATTCCT
    |  |||   |  | |  |||  |   ||    ||     |||| |||||| | |   |  | | | |    | | | ||  ||||||||| ||||| || |||||| | | |||||||||||||||||| ||||| ||||||||||| ||  |||  || | |||| | |||||||  ||||||
----gtaagc--agatgttttactgttatgatt--gctaacaatgtt-ttgtaacttactgacttctgtgtccactttatgattacagTGTTATTGGATACACTTTACTTTTAAGTTTGATTGAGTACAAGACTCTTGTGATGCGTGGAGATTTGGAACAGGCTAATGAAGTCTTACCTTCAATTCCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctgactgcttttgttcttgtaattgatctaaatttatttatgttatcttatgcagTGTTATGGGATATACCTTACTTCTCAATTTGATTGAGTACAAGACACTTGTAATGCGTGGAGACTTTCAACGTGCAAGTGAAATTTTACCTTTGATTCCT
                         atctaaa  putative branch site (score: 3)
                                          ttatctt  putative PPT
                ttgtaattgatctaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagggagcttgggagctgcacttctgcaatctgactgcttttgttcttgtaattgatctaaatttatttatgttatcttatgcagTGTTATGGGATATACCTTACTTCTCAATTTGATTGAGTACAAGACACTTGTAATGCGTGGAGACTTTCAACGTGCAAGTGAAATTTTACCTTTGATTCCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA