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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGTGTGATGGAATATGAAGAGCATGAAAAACGGGCATGGAGTGTTGATTTTTCACGCACAGAACCCTCAAGGCTTGTATCTGGCAGTGATGATTGTAAGgtattgcagaacacttagtatactttaaaccaaatctatcttgattgcttaagtgatctaagataccatgtttaattgctaaaatagaaaaatgaaatgg...

Basic information

species Vitis vinifera
transcript Vv12s0059g01420.t01
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv12s0059g01420.t01 (Vitis vinifera), 5'ss of exon 9
lower sequence: LOC_Os02g53140.1 (Oryza sativa), 5'ss of exon 9
AGTGTGATGGAATATGAAGAGCATGAAAAACGGGCATGGAGTGTTGATTTTTCACGCACAGAACCCTCAAGGCTTGTATCTGGCAGTGATGATTGTAAGgtattgcagaacacttagtatactttaaaccaaatctatcttgattgcttaagtgatctaagataccatgtttaattgctaaaata----gaaaaatgaaatgg------
||||||||||| |||||||| ||||||||  | |||||||||||||||||||| || ||||||||||| | ||| |||||||| ||||||||||| ||||||||    ||     |   |||          | |||  ||  ||  |   |  | | |  | ||  ||  || ||   ||||||     ||| || |  |||      
AGTGTGATGGAGTATGAAGAACATGAAAAGAGAGCATGGAGTGTTGATTTTTCTCGAACAGAACCCTCGATGCTAGTATCTGGGAGTGATGATTGCAAGgtatttgcaaatttcaatggtac----------aactacttttgttattcccgaaagcaagaaaactttgcgtagttctcaaaatacagtaaaacataacttggatatat

upper sequence: Vv12s0059g01420.t01 (Vitis vinifera), 5'ss of exon 9
lower sequence: GRMZM2G126795_T01 (Zea mays), 5'ss of exon 10
AGTGTGATGGAATATGAAGAGCATGAAAAACGGGCATGGAGTGTTGATTTTTCACGCACAGAACCCTCAAGGCTTGTATCTGGCAGTGATGATTGTAAGgtattgcagaacacttagtatactttaaaccaaatctatcttgattgcttaagtgatctaagataccatgtttaattgctaaaatagaaaaatgaaatgg-----
|||||||||||||||||||||||||| ||| | |||||||||||||||||||| || ||||| || |||| ||| |||||||| ||||| ||||| ||||||||    ||   ||| |||  || | | |   ||| | |      || |||  |   ||| |     ||||  |    ||  | ||  |   ||||       
AGTGTGATGGAATATGAAGAGCATGAGAAAAGAGCATGGAGTGTTGATTTTTCTCGAACAGAGCCTTCAATGCTAGTATCTGGGAGTGACGATTGCAAGgtatttggaaa---ttaatattgttcagatccgttctctttctcaaact-aagaaagaaaagct-tggcgttttttcttaaatgttgagtaccaaaatcctaggt

upper sequence: Vv12s0059g01420.t01 (Vitis vinifera), 5'ss of exon 9
lower sequence: GRMZM2G104920_T02 (Zea mays), 5'ss of exon 8
AGTGTGATGGAATATGAAGAGCATGAAAAACGGGCATGGAGTGTTGATTTTTCACGCACAGAACCCTCAAGGCTTGTATCTGGCAGTGATGATTGTAAGgtattgcagaacacttagtatactttaaaccaaatctatcttgattgcttaagtgatctaagataccatgtttaattgctaaaata--gaaaaatgaaatgg------
|||||||||||||||||||||||||| ||  | |||||||||||||||||||| ||||||||  | |||| ||| |||||||| ||||||||||| ||||||||    |    ||| |||  | ||||   | |  ||  | ||| |  || | |   |  | | | || | | || || ||||    |  |   ||||        
AGTGTGATGGAATATGAAGAGCATGAGAAGAGAGCATGGAGTGTTGATTTTTCTCGCACAGACTCTTCAATGCTAGTATCTGGGAGTGATGATTGCAAGgtatttggaag---ttaatat--tgtaaa---attacattctcattccgaaactaagagagaaaagcttggtgattttctcaaatgtcaagtaccaaaatcactttat

upper sequence: Vv12s0059g01420.t01 (Vitis vinifera), 5'ss of exon 9
lower sequence: GRMZM2G126795_T02 (Zea mays), 5'ss of exon 10
AGTGTGATGGAATATGAAGAGCATGAAAAACGGGCATGGAGTGTTGATTTTTCACGCACAGAACCCTCAAGGCTTGTATCTGGCAGTGATGATTGTAAGgtattgcagaacacttagtatactttaaaccaaatctatcttgattgcttaagtgatctaagataccatgtttaattgctaaaatagaaaaatgaaatgg---
|||||||||||||||||||||||||| ||| | |||||||||||||||||||| || ||||| || |||| ||| |||||||| ||||| ||||| ||||||||    ||   ||| |||  || | | |   ||| | |      || |||  |   ||| |     ||||  |    ||  | ||  |   ||||     
AGTGTGATGGAATATGAAGAGCATGAGAAAAGAGCATGGAGTGTTGATTTTTCTCGAACAGAGCCTTCAATGCTAGTATCTGGGAGTGACGATTGCAAGgtatttggaaa---ttaatattgttcagatccgttctctttctcaaact-aagaaagaaaagct-tggcgttttttcttaaatgttgagtaccaaaatcctag

upper sequence: Vv12s0059g01420.t01 (Vitis vinifera), 5'ss of exon 9
lower sequence: GLYMA14G05430.1 (Glycine max), 5'ss of exon 9
AGTGTGATGGAATATGAAGAGCATGAAAAACGGGCATGGAGTGTTGATTTTTCACGCACAGAACCCTCAAGGCTTGTATCTGGCAGTGATGATTGTAAGgtattgcagaacacttagt---atactttaaaccaaatctatcttgattgcttaagtgatctaagataccatgtttaattgctaaaatagaaaaatgaaatgg
||| | ||||||||||||||||||||||| || ||||||||||||||||||||| | ||||| ||||| | |||||||||||| || ||||| ||||||||| |    |||| ||| |   |   |||    ||| | |  ||  | |||||  || || |   ||||  | || || ||  ||    |     |||| |  
AGTTTAATGGAATATGAAGAGCATGAAAAGCGTGCATGGAGTGTTGATTTTTCAAGAACAGACCCCTCTATGCTTGTATCTGGTAGCGATGACTGTAAGgtact-tgaaacatttatttggaagtttttgtgcaagtttccctaaaatgcttctgtaatttccaatac--ttttgaaatgaaaatcatgctttctgaattat

upper sequence: Vv12s0059g01420.t01 (Vitis vinifera), 5'ss of exon 9
lower sequence: GLYMA02G43540.2 (Glycine max), 5'ss of exon 9
AGTGTGATGGAATATGAAGAGCATGAAAAACGGGCATGGAGTGTTGATTTTTCACGCACAGAACCCTCAAGGCTTGTATCTGGCAGTGATGATTGTAAGgtattgcagaacacttagtatactttaaaccaaatctatcttgattgcttaagtgatctaagataccatgtttaattgctaaaatagaaaaatgaaatgg--------
||| | ||||||||||||||||||||||| || ||||||||||| || |||||| | ||||| ||||| | |||||||||||| || ||||| ||||||||| |    ||   || | |   |||   |||  | |  ||  | |||||  || || |   |||   | ||||| ||  ||||| ||    | | ||          
AGTTTAATGGAATATGAAGAGCATGAAAAGCGTGCATGGAGTGTAGACTTTTCAAGAACAGATCCCTCTATGCTTGTATCTGGTAGCGATGACTGTAAGgtactctgaaat--ttggaagtttttgtgccag-tttccctaaaatgcttctgtaatttccaatat--tttttaaatg--aaaat-gatgcttaacatatgtttatta

upper sequence: Vv12s0059g01420.t01 (Vitis vinifera), 5'ss of exon 9
lower sequence: AT2G32950.1 (Arabidopsis thaliana), 5'ss of exon 9
AGTGTGATGGAATATGAAGAGCATGAAAAACGGGCATGGAGTGTTGATTTTTCACGCACAGAACCCTCAAGGCTTGTATCTGGCAGTGATGATTGTAAGgta-----ttgcagaacacttagtat-actttaaaccaaatctatcttgattgcttaagtgatctaagataccatgtttaattgctaaaatagaaaaatgaaatgg
||| | ||||| ||||||||||| |||||||| || ||||||||||| |||||||| |||||||| |||| |||||||||||| ||||| || || ||||||      | || |        ||| || ||  | |  |  |      ||  || |  | |   |  |||| |  ||||  |              || |     
AGTCTTATGGAGTATGAAGAGCACGAAAAACGTGCCTGGAGTGTTGACTTTTCACGAACAGAACCATCAATGCTTGTATCTGGTAGTGACGACTGCAAGgtaaatatctccatattttccgttatcacctttcatctcacattgggctatgtctcatataaaa-agaatactacttttagatatctcctagctcttataa-----

upper sequence: Vv12s0059g01420.t01 (Vitis vinifera), 5'ss of exon 9
lower sequence: PP1S264_64V6.1 (Physcomitrella patens), 5'ss of exon 10
AGTGTGATGGAATATGAAGAGCATGAAAAACGGGCATGGAGTGTTGATTTTTCACGCACAGAACCCTCAAGGCTTGTATCTGGCAGTGATGATTGTAAGgt-----attgcagaacacttagtata---ctttaaac--caaatctat--cttgattgcttaagtgatctaagataccatgtttaattgctaaaatagaaaaatgaaatgg-------------------------------------------
|| || |||||||||||||| || || |||||||| |||||||| ||||||||||| || || ||  | | |||||| || || ||||||||  | |||||     |||  |   ||| |  | |    | | |||    ||| || |  || | ||| ||        ||||  ||| | |||   ||     ||  | || ||||||                                             
AGCGTCATGGAATATGAAGAACACGAGAAACGGGCCTGGAGTGTAGATTTTTCACGAACTGACCCGACTATGCTTGTGTCAGGAAGTGATGACGGCAAGgtgaatgatttgaagtcacgtgatctgtcccctcaaatgataaacctgttactggcttggtttcacagcttaagtaaccgtttttggctgtctgcatttagaa-tgaaatccattgttcgatccattcctaggtttcttatatcgttgtatacag

upper sequence: Vv12s0059g01420.t01 (Vitis vinifera), 5'ss of exon 9
lower sequence: PP1S135_17V6.1 (Physcomitrella patens), 5'ss of exon 9
AGTGTGATGGAATATGAAGAGCATGAAAAACGGGCATGGAGTGTTGATTTTTCACGCACAGAACCCTCAAGGCTTGTATCTGGCAGTGATGATTGTAAGgta--ttgcagaac--------acttagtatactttaaaccaaatctatcttgattgcttaagtgatctaagatacca--tgtttaa---ttgctaaaataga---aaaatgaaatgg-------------------------------
||  | ||||||||||| |||||||||||  |||| |||||||| ||||||||||| || || ||  | | ||| || || || ||||||||| | ||||||   ||  |||         ||||| |     ||  ||   ||     |   ||  | |||   | | | |  |    | |||     || |   |  |     || |||   | |                               
AGCATTATGGAATATGAGGAGCATGAAAAGAGGGCCTGGAGTGTGGATTTTTCACGAACTGATCCGACCATGCTAGTCTCGGGAAGTGATGATGGCAAGgtaacctgttgaaatctggtgaacttaatcactcttgtacttgatgcggttctgtttttcaagctttttcaaactcaggttatttggagttttccgcatcatgtttaatatgcggttgatccgaaatgtttttatgttactgtttgcag

upper sequence: Vv12s0059g01420.t01 (Vitis vinifera), 5'ss of exon 9
lower sequence: PP1S180_148V6.1 (Physcomitrella patens), 5'ss of exon 9
AGTGTGATGGAATATGAAGAGCATGAAAAACGGGCATGGAGTGTTGATTTTTCACGCACAGAACCCTCAAGGCTTGTATCTGGCAGTGATGATTGTAAGgtattgca------gaacacttagtatactttaaaccaaatctatcttgattgcttaagtg-atctaagataccat--gtttaattgctaaaatagaaa-aatgaaatgg-------------------
||||||||||||||||| || |||||||| || || |||||  | |||||||| || ||||| || |||| ||| || ||||| ||||| ||| | |||||   ||        | | |||||  |    | ||||| |   |  || | ||||  |||  |  | | | ||  |  |  |  || |  |    | || ||||  ||                     
AGTGTGATGGAATATGAGGAACATGAAAAGCGTGCTTGGAGCATCGATTTTTCTCGTACAGATCCATCAATGCTGGTTTCTGGAAGTGACGATGGAAAGgtgcagccttagttaagcccttagc-tgtgatgaaccatag--aggtttaatgctgtagtatactttataaacttttgggctggttaccgactctgcaataatgggattactgcgttgacacattgcag

upper sequence: Vv12s0059g01420.t01 (Vitis vinifera), 5'ss of exon 9
lower sequence: PP1S11_401V6.1 (Physcomitrella patens), 5'ss of exon 9
AGTGTGATGGAATATGAAGAGCATGAAAAACGGGCATGGAGTGTTGATTTTTCACGCACAGAACCCTCAAGGCTTGTATCTGGCAGTGATGATTGTAAGgt-attgcagaacacttagtatactttaaaccaaatctatcttgattgcttaagtgatctaagata----ccatgtttaa-ttgctaaaatagaaaaatgaaatgg
||  | ||||||||||| |||||||||||||| || ||||| || ||||| ||||| || || ||  ||| ||| || || |||||||||||  | ||||  | ||      | ||   ||   || ||    ||  ||  |  |  |   |  | | |          | ||| |||  ||  | |  |  |    || |    
AGCATCATGGAATATGAGGAGCATGAAAAACGAGCTTGGAGCGTAGATTTCTCACGGACTGATCCTACAATGCTAGTGTCAGGCAGTGATGACGGCAAGgcgagtgttttggaattgtgatgtgttgaaaatgatgaatgatagtaacgggaaggttttgttgcttaatcgatgcttaggtttttgatgtttatgtttgtag---

upper sequence: Vv12s0059g01420.t01 (Vitis vinifera), 5'ss of exon 9
lower sequence: PP1S86_153V6.2 (Physcomitrella patens), 5'ss of exon 9
AGTGTGATGGAATATGAAGAGCATGAAAAACGGGCATGGAGTGTTGATTTTTCACGCACAGAACCCTCAAGGCTTGTATCTGGCAGTGATGATTGTAAGgta--ttgcagaacacttagtatactttaaaccaa-------atctatcttgattgcttaag------tgatctaagataccatgtttaattgctaaaatagaaaaatgaaatgg------------------------------------------
||  | | ||| |||||||||||||||||  ||||||||||||| ||||||||||| || || ||| | | | | || || || || |||||| | |||||   |||  |||   ||   ||  | | |  |||       ||  | |||  ||    |||      | | ||   |     | |||          ||  |  |  |||  |                                           
AGCATAACGGAGTATGAAGAGCATGAAAAGAGGGCATGGAGTGTGGATTTTTCACGAACTGATCCCACTATGTTAGTCTCGGGAAGCGATGATGGCAAGgtgatttgttgaaatgttgtgattttatcactcaagtaactgatggaccttcgtttgacaaggccccttaaactggaaggtagtttttgggcttctgcatcaaggatcgaagcgaatgtgtagttgatcctgaagctttttgcattgtttcttgcag

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGTGTGATGGAATATGAAGAGCATGAAAAACGGGCATGGAGTGTTGATTTTTCACGCACAGAACCCTCAAGGCTTGTATCTGGCAGTGATGATTGTAAGgtattgcagaacacttagtatactttaaaccaaatctatcttgattgcttaagtgatctaagataccatgtttaattgctaaaatagaaaaatgaaatgg

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gcagaaca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aaccaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gctaaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -agaaaaa