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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...agcaagtttctgttctattaaatggcatagaagtttgtcatatcttagctggttttgcatcattaagaatttctgaaatctctgttatttgtatgatcagCCTTGCTTAGGTGGGGATTCCAAGACCCTGATGTTTGTCAACATCTCTCCCGACCCATCTTCAGTTGGTGAGTCCCTATGCTCTCTTAGGTTTGCTGCCA

Basic information

species Vitis vinifera
transcript Vv00s0532g00020.t01
intron # 16
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv00s0532g00020.t01 (Vitis vinifera), 3'ss of exon 16
lower sequence: LOC_Os04g53760.2 (Oryza sativa), 3'ss of exon 16
agcaagtttct-gttctattaaatggca---tagaagtttgtcatatcttagctggttttgcatcattaagaatttctgaaatctctgttatttgtatgatcagCCTTGCTTAGGTGGGGATTCCAAGACCCTGATGTTTGTCAACATCTCTCCCGACCCATCTTCAGTTGGTGAGTCCCTATGCTCTCTTAGGTTTGCTGCCA
 |  |||  || || | | |  |||| |    | ||   ||  ||  || |  |  ||| | | |||     |||||| | |||       ||| |||   ||||||||| | || || |||||||| || ||||||||||||||||| ||||| ||  |||| || ||||| ||| |  | || || || ||||| ||| | |
-gtgagtgacttgtgcaaatggatggtaatacaaaaacctgcaatccctgaatttattt-gaaacat-----atttcttatatcaac----tttctattg-cagCCTTGCCTTGGAGGTGATTCCAAAACGCTGATGTTTGTCAACATTTCTCCGGAGGCATCATCCGTTGGGGAGACGATTTGTTCACTGAGGTTCGCTTCAA

upper sequence: Vv00s0532g00020.t01 (Vitis vinifera), 3'ss of exon 16
lower sequence: GLYMA13G32450.1 (Glycine max), 3'ss of exon 15
-------------agcaagtttctgttct--attaaatggcatagaagtttgtcatat--cttagctggttttgcatcattaagaatttctgaaatctctgttatttgtatgatcagCCTTGCTTAGGTGGGGATTCCAAGACCCTGATGTTTGTCAACATCTCTCCCGACCCATCTTCAGTTGGTGAGTCCCTATGCTCTCTTAGGTTTGCTGCCA
              | || |||   |||   ||| ||    |      |||| |||||   | || |   |   |   | |   |||||      | |  ||| | |  ||   ||||| ||  | |||||||||||||| ||  |||||||||| |||||||| || || |||||||||  ||| ||||| || ||||||||| ||||||||||  
gtatgataagctatgaaaatttgcattcctcattcaaaattaacttgctttgacatatacttcagatacatgaaccaaacttgtaatttgc----ttttggttgtatccattggcagCCATGTCTTGGTGGGGATTCCAAAACTTTGATGTTTGTGAACATCTCACCTGATCCATCTTCAACTGGAGAGTCACTTTGCTCTCTTCGGTTTGCTGCTG

upper sequence: Vv00s0532g00020.t01 (Vitis vinifera), 3'ss of exon 16
lower sequence: GLYMA15G06880.1 (Glycine max), 3'ss of exon 16
---agcaagtttctgttctatt-aaatggcatagaagtttgtcatatcttagctggttttgcatcattaagaatttctgaaatctctgttatttgtatg---atcagCCTTGCTTAGGTGGGGATTCCAAGACCCTGATGTTTGTCAACATCTCTCCCGACCCATCTTCAGTTGGTGAGTCCCTATGCTCTCTTAGGTTTGCTGCCA
    ||||   | ||    |||   ||  | |     |||||  ||| ||   |  ||  |    || ||  |    || ||| |   |   ||||||      ||||| ||  | |||||||||||||| ||  |||||||||| |||||||| || || |||||||||  ||| ||||| || ||||||||| | ||||| ||  
gtatgcaaagctatgcaaaatttgcatttcgtttccatttgtt-tattttcattacttcagttatatgaaccaaacttgtaatttgcttatgttgtatccgtggcagCCATGTCTTGGTGGGGATTCCAAAACTTTGATGTTTGTGAACATCTCACCTGATCCATCTTCAACTGGAGAGTCACTTTGCTCTCTTCGATTTGCCGCTG

upper sequence: Vv00s0532g00020.t01 (Vitis vinifera), 3'ss of exon 16
lower sequence: GLYMA07G30580.1 (Glycine max), 3'ss of exon 15
-agcaagtttctgt-tctattaaatggcatagaagtttgtc-atatcttagctggttttgcatcattaagaatttctgaaatctctgttatttgtatgatcagCCTTGCTTAGGTGGGGATTCCAAGACCCTGATGTTTGTCAACATCTCTCCCGACCCATCTTCAGTTGGTGAGTCCCTATGCTCTCTTAGGTTTGCTGCCA
    ||  |  | | | | || |    |  |||  || ||  | |  ||   |    |||      |||   | | |  ||  | | || | || |||  ||||| |   | |||||||| ||||| ||  ||||||||||||||||||| || || | |||||||| ||| || || |||||||||||  | ||||| ||||
gcttaaactattatatttgttgatcaccgaagatcttagtttacaatttgcatttacttgttcttctaatgctcttt--aacttatattgtatgcatgg-cagCCATATCTTGGTGGGGACTCCAAAACGTTGATGTTTGTCAACATCTCACCTGATCAATCTTCAGCTGGCGAATCACTATGCTCTCTACGCTTTGCAGCCA

upper sequence: Vv00s0532g00020.t01 (Vitis vinifera), 3'ss of exon 16
lower sequence: AT4G05190.1 (Arabidopsis thaliana), 3'ss of exon 16
---agcaagtttctgttctattaaatggcatagaagtttgtcatatcttagctggttttgcatcattaagaatttctgaaatctctgttatttgtatgatcagCCTTGCTTAGGTGGGGATTCCAAGACCCTGATGTTTGTCAACATCTCTCCCGACCCATCTTCAGTTGGTGAGTCCCTATGCTCTCTTAGGTTTGCTGCCA
   ||  |   | | | ||  | |||      | |  |  || | ||| | || | | |   | |||||| |       ||||  | |||        | ||||| || ||||| ||||| || |||||| | |||||||| ||||| || || || |||||||||  ||| ||||| |||||||||||| |||||||||| |
gttagataacatttttacttctgaatcattatgcaaataatc-tgtct-atctagctctttctaattaagga------gaatcattttta--------aacagCCATGTTTAGGAGGGGACTCAAAGACCTTAATGTTTGTGAACATATCACCTGATCCATCTTCAACTGGAGAGTCTCTATGCTCTCTTCGGTTTGCTGCTA

upper sequence: Vv00s0532g00020.t01 (Vitis vinifera), 3'ss of exon 16
lower sequence: PP1S87_179V6.1 (Physcomitrella patens), 3'ss of exon 15
agcaagtttctgttctattaaa-tggcata-gaagtttgtcatatct-tagctggttttgcatcattaagaatttctgaaatctctgttatttgtatgatcagCCTTGCTTAGGTGGGGATTCCAAGACCCTGATGTTTGTCAACATCTCTCCCGACCCATCTTCAGTTGGTGAGTCCCTATGCTCTCTTAGGTTTGCTGCCA
     ||  | |   | ||| | |||  |  |     ||    | ||   ||  |  ||  |   |||||  || ||||| |     ||  |||     |||||||||  | || || ||||| |||||| |||||||||||||||||||||| ||       ||  |   ||| ||  | || ||||| || || ||||| |
---gtgtgaccgccgttttacactggtttctgtgacatgctgcagctactgcaagcattcgagatttaagtgttcctgaatttgtactttgttgctgtttcagCCTTGTCTCGGAGGAGATTCGAAGACCTTGATGTTTGTCAACATCTCTCCTGATATGAAGTCTTTGAATGAATCATTGTGTTCTCTCAGATTCGCTGCTA

upper sequence: Vv00s0532g00020.t01 (Vitis vinifera), 3'ss of exon 16
lower sequence: PP1S80_62V6.1 (Physcomitrella patens), 3'ss of exon 15
---------------------------------------------------------------------agcaagtttctgttctattaaatggcataga---agtttgtcatatcttagctggttttgcatcattaa--gaatttctgaaatctctgttatttgtatgat-cagCCTTGCTTAGGTGGGGATTCCAAGACCCTGATGTTTGTCAACATCTCTCCCGACCCATCTTCAGTTGGTGAGTCCCTATGCTCTCTTAGGTTTGCTGCCA
                                                                      |  | |   | |  ||||  |   | |  |   |||  || | |   |   |  | ||   ||  | |  ||     ||   || |||  | ||   || | ||||||||| |||| || ||||| |||||| ||||||||||||||||||| || ||       ||  |   ||||||| | |||||||| || || || ||||
gtaaggcttctgaatgatgtgcgaatcggtcatcactatcgttctaatgcaaagtatataaataaacatgggtattgcatctaatattgcactccctgaattgagtgcgttaaaatattattattgttatttctcttactgacaacttgctgtcactgacaatttactgtttcagCCTTGCCTAGGGGGAGATTCAAAGACCTTGATGTTTGTCAACATCTCGCCTGATATGAAATCCTTGAATGAGTCCTTGTGCTCTCTCAGATTCGCAGCCA

upper sequence: Vv00s0532g00020.t01 (Vitis vinifera), 3'ss of exon 16
lower sequence: EFJ35821 (Selaginella moellendorffii), 3'ss of exon 15
agcaagtttctgttctattaaatggcatagaagtttgtcatatcttagctgg--ttttgcat-cattaag-aatttctgaaatctctgttatttgtatgatcagCCTTGCTTAGGTGGGGATTCCAAGACCCTGATGTTTGTCAACATCTCTCCCGACCCATCTTCAGTTGGTGAGTCCCTATGCTCTCTTAGGTTTGCTGCCA
        |          | ||||| | | | ||||   |  ||||||  |  | ||  ||  | | ||  |  | |     | || || ||  | |   ||||||||||||||||| ||||| ||||| |||||||| ||||||||| | |||||  |      ||| | ||                              
-------gtaaacaaagagatatggctttggactttga-gttgcttagcgaggatcttatatgtactgagCGAGATTTTCTTCCCCTTTTTTTCATCTTG-CAGCCTTGCTTAGGTGGAGATTCGAAGACGCTGATGTTCGTCAACATCGCCCCCGAGGC----CAAGTCGCTGC-----------------------------

upper sequence: Vv00s0532g00020.t01 (Vitis vinifera), 3'ss of exon 16
lower sequence: EFJ36382 (Selaginella moellendorffii), 3'ss of exon 15
---agcaagtttctgttctattaaatggcatagaagtttgtcatatcttagctgg--ttttgcat-cattaag-aatttctgaaatctctgttatttgtatgatcagCCTTGCTTAGGTGGGGATTCCAAGACCCTGATGTTTGTCAACATCTCTCCCGACCCATCTTCAGTTGGTGAGTCCCTATGCTCTCTTAGGTTTGCTGCCA
   | |||      |   ||| | ||||| | | | ||||   |  ||||||  |  | ||  ||  | | ||  |  | |     | || || ||| | |   ||||||||||||||||| ||||| ||||| |||||||| ||||||||| | |||||  |      ||| | ||                              
gtaaacaaagagagga--tatgatatggctttggactttga-gttgcttagcgaggatcttatatgtactgagCGAGATTTTCTTCCCCTTTTTTTTATCTTG-CAGCCTTGCTTAGGTGGAGATTCGAAGACGCTGATGTTCGTCAACATCGCCCCCGAGGC----CAAGTCGCTGC-----------------------------


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tagctggttttgcatcattaagaatttctgaaatctctgttatttgtatgatcagCCTTGCTTAGGTGGGGATTCCAAGACCCTGATGTTTGTCAACATCTCTCCCGACCCATCTTCAGTTGGTGAGTCCCTATGCTCTCTTAGGTTTGCTGCCA
             atcattaagaattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
agcaagtttctgttctattaaatggcatagaagtttgtcatatcttagctggttttgcatcattaagaatttctgaaatctctgttatttgtatgatcagCCTTGCTTAGGTGGGGATTCCAAGACCCTGATGTTTGTCAACATCTCTCCCGACCCATCTTCAGTTGGTGAGTCCCTATGCTCTCTTAGGTTTGCTGCCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - aatggca
- - - - - - - - - - - - - - - - - - - - - - -tagctgg
- - - - - - - - - - - - - - - - - - - - - - - - - - - -tgcatca