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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaaaaaccaaagttgaagtccatatttttacacactcagttttctgttgttgaatctaaaactgtaaaatctcattttttacagGTTTTGTGCTCGGCTTGGAAGGATGATGGAACAATTGTCTTTTCTGGAGGCTGTGACAAGCAAGTGAAGATGTGGCCTTTGCTGTCTGGTGGTCAACCAG

Basic information

species Vitis vinifera
transcript Vv09s0002g09150.t01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv09s0002g09150.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: LOC_Os08g07960.2 (Oryza sativa), 3'ss of exon 4
gtaaaaaaccaaagttg-----aagtccatatttttaca-cactcagtttt--ctgttgttgaatctaaaactgtaa--aatctcattttttacagGTTTTGTGCTCGGCTTGGAAGGATGATGGAACAATTGTCTTTTCTGGAGGCTGTGACAAGCAAGTGAAGATGTGGCCTTTGCTGTCTGGTGGTCAACCAG
|||  |   |||  ||      ||| ||| |||   | |     |||| ||   | |  | | || ||      | |   || |  ||| |  |||||  | || || |||||||||||||||||||| | ||| || |||||||||||||| || ||||| || ||||||||| || |||||||||| ||  |  
gtatgatctcaatatttctctcaagaccacattcacataatgtacagtattgattttcctagtatttagtgtgctcattgatttgttttctatcagGTCCTCTGTTCAGCTTGGAAGGATGATGGAACTACTGTGTTCTCTGGAGGCTGTGATAAACAAGTAAAAATGTGGCCTCTGTTGTCTGGTGGGCAGGCTC

upper sequence: Vv09s0002g09150.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: LOC_Os01g44394.1 (Oryza sativa), 3'ss of exon 3
-----------------------------------gtaaaaaaccaaagttgaagtccatatttttacacactcagttttctgttgttgaatctaaaactgtaaaatctcattttttacagGTTTTGTGCTCGGCTTGGAAGGATGATGGAACAATTGTCTTTTCTGGAGGCTGTGACAAGCAAGTGAAGATGTGGCCTTTGCTGTCTGGTGGTCAACCAG
                                   |      |   | || |||      |||| | ||| ||   ||| |     ||||     |    ||      | ||||  | |||||  |||||||||| |||||||||||||| || | ||| ||||| ||||| ||||| || ||  | |||||||||||  |||| || ||||| || ||  
gtactgcggcccttccatatagtttgctcccattagctcgttatagatgtggaatcttcgatttctgcactctgtatttccctgcattgacatctagttggt------tgatttcatgcagGTGCTGTGCTCGGCATGGAAGGATGATGGGACTACTGTTTTTTCGGGAGGTTGTGATAAACAGATTAAGATGTGGCCGCTGCTCTCCGGTGGGCAGCCCA

upper sequence: Vv09s0002g09150.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GRMZM2G058498_T01 (Zea mays), 3'ss of exon 4
gtaaaaaaccaaagttg--------aagtccatattttta---------cacactcagttttctgttgtt-gaatctaaaactgtaa--aatctcattttttacagGTTTTGTGCTCGGCTTGGAAGGATGATGGAACAATTGTCTTTTCTGGAGGCTGTGACAAGCAAGTGAAGATGTGGCCTTTGCTGTCTGGTGGTCAACCAG
|||  |    |  |||         | ||  |||| |||           | | |   ||   ||| ||| | ||||   |   | |   || |  ||  ||  ||||| | |||||||||||||||||||||||||| | |||||| |||||||||||||||||||| || || ||||||||| | ||||| ||||| || ||  
gtatgatcttagtgttttctgggatatgttaatatatttgattgggcggtagattgtcttccatgtagtttgtatctggtatcctcattgatttgtttccttttagGTTCTCTGCTCGGCTTGGAAGGATGATGGAACTACTGTCTTCTCTGGAGGCTGTGACAAGCAGGTCAAAATGTGGCCTCTTCTGTCAGGTGGGCAGCCTC

upper sequence: Vv09s0002g09150.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GRMZM2G180815_T01 (Zea mays), 3'ss of exon 3
---------------------------------------------------------gtaaaaaaccaaagttgaagtccatatttttacacactcagttttctgttgttgaatctaaaactgtaaaatctcattttttacagGTTTTGTGCTCGGCTTGGAAGGATGATGGAACAATTGTCTTTTCTGGAGGCTGTGACAAGCAAGTGAAGATGTGGCCTTTGCTGTCTGGTGGTCAACCAG
                                                           | |  | |  | |     || | || | |     ||  |   |||||    || ||  |  |||     | |  |||  | |||||  |||||||||||||||||||||||||    | ||| || || ||||||||||| ||||| || || ||||||||  |||| || ||||  || ||  
gtattgtgattgtcttagcacttttttcacccagaagtgattcgtcttagcatttgctcatattagctgattatggatctagatgtctttgttctaggccctctgtatgcgactcacaggctg----gttttgtttcgtgcagGTGCTGTGCTCGGCTTGGAAGGATGATGGGTTGACTGTTTTCTCAGGAGGCTGTGATAAGCAGGTTAAAATGTGGCCCCTGCTCTCAGGTGCCCAGCCCA

upper sequence: Vv09s0002g09150.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA08G19260.1 (Glycine max), 3'ss of exon 3
-gtaaaaaaccaaagttg---aagtccatatttttac---acactcagttttctgttgttgaa----tctaaaactgtaaa---atctcattttttacagGTTTTGTGCTCGGCTTGGAAGGATGATGGAACAATTGTCTTTTCTGGAGGCTGTGACAAGCAAGTGAAGATGTGGCCTTTGCTGTCTGGTGGTCAACCAG
 ||   |   |    |      | || |  || |  |   ||| | |  |||   | ||| |       ||||    ||||   || |   |||  | |||||||||||||  | |||||||||||||| |||| |||||| ||||| || ||||||||||||||||||||||||||| || | ||||| || |||||| 
tgttggatttcgtgatcttgccaatctaccttgtaccaaaacagtgaacttttaatagtttatatgccataaattcataaatgtatatttctttgcatagGTTTTGTGCTCTACATGGAAGGATGATGGCACAACTGTCTTCTCTGGTGGATGTGACAAGCAAGTGAAGATGTGGCCTCTGTTATCTGGAGGCCAACCAA

upper sequence: Vv09s0002g09150.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA15G05740.1 (Glycine max), 3'ss of exon 3
-------gtaaaaaaccaaagttgaagtccat-atttttacacactcagttttctgttgttga-atct---aaaactgtaaaatctcattttttac--agGTTTTGTGCTCGGCTTGGAAGGATGATGGAACAATTGTCTTTTCTGGAGGCTGTGACAAGCAAGTGAAGATGTGGCCTTTGCTGTCTGGTGGTCAACCAG
        |           | |||  | | |  |  | | ||| | |  |||   | |||   ||||   |||    |||  | |  || ||| |  |||||||||||||  | |||||||||||||| || | ||| || ||||| || ||||| ||||||||||||||||||||| || | ||||| || |||||| 
ctattggatttcgtgatcttgctgatctgcgttgtcctgaaacagtgaacttttaatagtttttatctcataaattcataatgtatatttctttgcgtagGTTTTGTGCTCTACATGGAAGGATGATGGCACGACTGTATTCTCTGGTGGATGTGATAAGCAAGTGAAGATGTGGCCTCTGTTATCTGGAGGCCAACCAA

upper sequence: Vv09s0002g09150.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: AT1G15850.1 (Arabidopsis thaliana), 3'ss of exon 3
---gtaaaaaaccaaagttgaagtccatatttttacacactcagttttctgttgttgaatctaaaactgtaaaatctcattttttacagGTTTTGTGCTCGGCTTGGAAGGATGATGGAACAATTGTCTTTTCTGGAGGCTGTGACAAGCAAGTGAAGATGTGGCCTTTGCTGTCTGGTGGTCAACCAG
    ||   |||     |   |||  || | |   |   ||   || ||| |  |  |||   ||      |  | || | |  |  |||||||||| || |||||||| ||||||||||| |  |||||| | ||||| ||||| ||||| |  || |||||||| ||| ||||||||| ||||||| 
gtaatatgcaactgctttctgagtttatgtgtcctcctgct---ttctctttgctcaaattctaatgaaagatttttcttgtggttaagGTTTTGTGTTCTGCTTGGAAAGATGATGGAACCACAGTCTTTACCGGAGGATGTGATAAGCAGGCAAAAATGTGGCCATTGTTGTCTGGTGCTCAACCAT

upper sequence: Vv09s0002g09150.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: AT1G80670.1 (Arabidopsis thaliana), 3'ss of exon 4
gtaaaaaaccaaagttgaagtccatatttttacacactcagttttctgttgttgaatctaaaac---tgtaaaatctcattttttacagGTTTTGTGCTCGGCTTGGAAGGATGATGGAACAATTGTCTTTTCTGGAGGCTGTGACAAGCAAGTGAAGATGTGGCCTTTGCTGTCTGGTGGTCAACCAG
|||| |   ||   ||    | | ||| ||  |    |   | || ||   |||||||| |  |   |      | || | | ||  ||||||| || || |||||||| ||||||||||| |  ||||||   || || ||||| |||||||  || |||||||| ||| |||||||||||||||| |
gtaatatgtcattcttc---ttcttatcttacctttttttttcttttgcctttgaatctgatgcatatacgtcctttcttgtgttgaagGTTTTATGTTCTGCTTGGAAAGATGATGGAACCACAGTCTTTAGCGGTGGATGTGATAAGCAAGCAAAAATGTGGCCCTTGTTGTCTGGTGGTCAACCTG

upper sequence: Vv09s0002g09150.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: EFJ10886 (Selaginella moellendorffii), 3'ss of exon 3
-------------------gtaaaaaaccaaagttga---agtccatatttttacacactcagttttctgttg--ttgaatctaaaactgtaaaatctcattttttacagGTTTTGTGCTCGGCTTGGAAGGATGATGGAACAATTGTCTTTTCTGGAGGCTGTGACAAGCAAGTGAAGATGTGGCCTTTGCTGTCTGGTGGTCAACCAG
                   | ||||||   |  | ||     || |  |||||  | | |   | ||   |||  | ||     || || |    || | |||||  ||||| |||||||||||||||||||||||||| || | |||||| || ||||| || || || || || |||||||||||| |    || ||    ||  |||
gtaagtcttttacatgctcgaaaaaaaaggatctagacttgttctaagtttttcaagattggatatttccttggctcgagagctaagctttcttttcgcttttttctcagGTATTGTGCTCGGCTTGGAAGGATGATGGCACGACTGTCTTCTCAGGAGGATGCGATAAACAGGTCAAGATGTGGCCTCTTTCATCCGGAAACCAGTCAG

upper sequence: Vv09s0002g09150.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: EFJ25923 (Selaginella moellendorffii), 3'ss of exon 3
-------------------gtaaaaaaccaaagttga---agtccatatttttacacactcagttttctgttg--ttgaatctaaaactgtaaaatctcattttttacagGTTTTGTGCTCGGCTTGGAAGGATGATGGAACAATTGTCTTTTCTGGAGGCTGTGACAAGCAAGTGAAGATGTGGCCTTTGCTGTCTGGTGGTCAACCAG
                   | ||||||   |  | ||     || |  |||||  | | |   ||||   |||  | ||     || || |    || | |||||  ||||| |||||||||||||||||||||||||| || | |||||| || ||||| || || || || || |||||||||||| |    || ||   |||  |||
gtaagtcttttacatgctcgaaaaaaaaggatctagacttgttctaagtttttcaagattggatttttccttgactcgagagctaagctttcttttcgcttttttctcagGTATTGTGCTCGGCTTGGAAGGATGATGGCACGACTGTCTTCTCAGGAGGATGCGATAAACAGGTCAAGATGTGGCCTCTTTCATCCGGAAATCAGTCAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acacactcagttttctgttgttgaatctaaaactgtaaaatctcattttttacagGTTTTGTGCTCGGCTTGGAAGGATGATGGAACAATTGTCTTTTCTGGAGGCTGTGACAAGCAAGTGAAGATGTGGCCTTTGCTGTCTGGTGGTCAACCAG
                        atctaaa  putative branch site (score: 3)
                                        tctcatttttt  putative PPT
                                   taaaatctcatttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaaaaaccaaagttgaagtccatatttttacacactcagttttctgttgttgaatctaaaactgtaaaatctcattttttacagGTTTTGTGCTCGGCTTGGAAGGATGATGGAACAATTGTCTTTTCTGGAGGCTGTGACAAGCAAGTGAAGATGTGGCCTTTGCTGTCTGGTGGTCAACCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG