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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGTTTAGTGAAGTTTTTGTACACCAACTTATTCATACCATAGAGTTTGTCCTTGGAGCAGTCTCTAATACAGCTTCATACTTACGTTTATGGGCCCTCAGgtaggcaggaacaacctgaagttatttcatatggcatgctgagctaaaatgtgcactgctaaaatgcatggtagaaagccaaagttatgtctatagaata...

Basic information

species Vitis vinifera
transcript Vv18s0001g13410.t01
intron # 16
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv18s0001g13410.t01 (Vitis vinifera), 5'ss of exon 16
lower sequence: LOC_Os03g14690.1 (Oryza sativa), 5'ss of exon 16
AGTTTAGTGAAGTTTTTGTACACCAACTTATTCATACCATAGAGTTTGTCCTTGGAGCAGTCTCTAATACAGCTTCATACTTACGTTTATGGGCCCTCAGgtaggcaggaacaacctgaa-------gttatttcatatggcatgc--------tgagctaaaatgtgcactgctaaaatgca-tggtagaaagccaaagttatgtctatagaata---------------
|||| |||||||||||||| |||||  | || || || || |||||||| ||||| |||||||| |||||||| |||||  | ||| | ||||| ||||||||       |||  | | |        ||| ||   |  || |          | | |  |  | ||  ||   | |||||| |  | |  |||||    ||  || ||  |||                
AGTTCAGTGAAGTTTTTGTTCACCAGTTGATCCACACAATTGAGTTTGTTCTTGGGGCAGTCTCAAATACAGCCTCATATCTTCGTCTCTGGGCTCTCAGgtacttctagacattcagcatcaccgcattactttgaacagccttactccctcatcatcccacttttgatctataacaatgcactccttgttagccactaata-atcgattaaattgtattctttatacag

upper sequence: Vv18s0001g13410.t01 (Vitis vinifera), 5'ss of exon 16
lower sequence: GRMZM2G058910_T01 (Zea mays), 5'ss of exon 16
AGTTTAGTGAAGTTTTTGTACACCAACTTATTCATACCATAGAGTTTGTCCTTGGAGCAGTCTCTAATACAGCTTCATACTTACGTTTATGGGCCCTCAGgtag-gcaggaacaacctgaagttat-ttcatatggcatgctgagctaaaatgtgcactgctaaaatgcatggtagaaagccaa---agttatgtctat-agaata----------------------------------------------------------------
||||  ||||||||||||| |||||||| ||||| || ||||| ||||| || || |||||||| || || ||||||||| | ||| | ||||| || |||||  ||      || | | |  | | || | |  || |         | |    ||    |    ||  |||  | |  | ||   |  || ||  ||  || |                                                                 
AGTTCGGTGAAGTTTTTGTTCACCAACTGATTCACACGATAGAATTTGTTCTGGGTGCAGTCTCAAACACCGCTTCATACCTTCGTCTTTGGGCTCTGAGgtaatgctattttaagcagtatctttatttacacagcctcacctatgcacagtcccatacttcctttgtttggctgcaccctaatccacataggtgcattggagtgcagccaaacaagtcattttattacctcactggctactaacgtgctactgatattctcctttcag

upper sequence: Vv18s0001g13410.t01 (Vitis vinifera), 5'ss of exon 16
lower sequence: GLYMA06G03040.1 (Glycine max), 5'ss of exon 16
AGTTTAGTGAAGTTTTTGTACACCAACTTATTCATACCATAGAGTTTGTCCTTGGAGCAGTCTCTAATACAGCTTCATACTTACGTTTATGGGCCCTCAGgtaggcag---gaacaacctgaagttatttcata-----tggcatgctgagctaaaatgtgcactgctaaaatgcatggtagaaagccaaagttatgtctatagaata
| || || || |||||||| ||||||||||| ||||| ||||| ||||| |||||||| || ||||| || ||||| ||  |||||||||||||||||||||||| ||    ||     ||| | ||||   |      | || |  ||      |||    | |  ||  ||| ||  | |    || |  |     ||  |     
ACTTCAGCGAGGTTTTTGTGCACCAACTTATACATACAATAGAATTTGTGCTTGGAGCTGTTTCTAACACGGCTTCGTATCTACGTTTATGGGCCCTCAGgtaggtagttgaaagcgtttgatgctattctttgaatttttgctttttggttatgaataaaaatt--tagcatggata-tgggcttcctatttccccccttca-----

upper sequence: Vv18s0001g13410.t01 (Vitis vinifera), 5'ss of exon 16
lower sequence: GLYMA04G03010.1 (Glycine max), 5'ss of exon 17
-AGTTTAGTGAAGTTTTTGTACACCAACTTATTCATACCATAGAGTTTGTCCTTGGAGCAGTCTCTAATACAGCTTCATACTTACGTTTATGGGCCCTCAGgtaggcaggaacaacctgaagttatttcatatggcatgctgagctaaaatgtgcactgctaaaatgcatggtagaaagccaaagttatgtctatagaata----
 | || || || |||||||| ||||||||||| ||||| ||||| ||||| |||||||| || ||||| || || || |   ||||||| ||||||||||| |      |    |   ||   | |    | | |  |   |   | |||    ||    ||| ||  ||    |     |    ||    |  |  ||||    
GACTTCAGCGAGGTTTTTGTGCACCAACTTATACATACAATAGAATTTGTGCTTGGAGCTGTTTCTAACACGGCATCGTCTCTACGTTTGTGGGCCCTCAgttgaaagcgtttgatgcgactctctgaatttttgtttttggtaatgaaa---acaaaattaacattgatat--gggcttcctgtttccccccttcaaataggtg

upper sequence: Vv18s0001g13410.t01 (Vitis vinifera), 5'ss of exon 16
lower sequence: AT4G39080.1 (Arabidopsis thaliana), 5'ss of exon 16
AGTTTAGTGAAGTTTTTGTACACCAACTTATTCATACCATAGAGTTTGTCCTTGGAGCAGTCTCTAATACAGCTTCATACTTACGTTTATGGGCCCTCAGgtaggcaggaacaacctgaagttatttcatatggcatgctgagctaaaatgtgcactgctaaaatgcatggtagaaagccaaagttatgtctatagaata
| || || ||  | ||||| || || || ||||| |||||||||||||| |||||||| || || || || ||||| ||| | ||| ||||||| |||||||| | || |  |    |||| |||   | |||   | |  | |  | |   |      ||| || |||  |       ||                   
AATTCAGCGAGATATTTGTGCATCAGCTGATTCACACCATAGAGTTTGTGCTTGGAGCTGTTTCCAACACCGCTTCTTACCTGCGTCTATGGGCTCTCAGgtatg-agtagta----gaagctat---acatgaattacataacctatactcgtggc-ttaatatccattcttttgtttcag------------------

upper sequence: Vv18s0001g13410.t01 (Vitis vinifera), 5'ss of exon 16
lower sequence: PP1S296_62V6.1 (Physcomitrella patens), 5'ss of exon 15
AGTTTAGTGAAGTTTTTGTACACCAACTTATTCATACCATAGAGTTTGTCCTTGGAGCAGTCTCTAATACAGCTTCATACTTACGTTTATGGGCCCTCAGgtaggc-----aggaacaacc-tgaagttatttcatatggcatgc--tgagctaa--------aatgtgc--ac-tgctaaaatgcatggtagaaagccaaagttatgtctatagaata-------------------------------------------
||||||||||||||||||| |||||| | ||||| || || ||||||||  |     | || || || || ||||| ||  | ||  | ||||| ||||||||        |||        | |  || || ||| | | | |   || |||||        || |||   || || |   |      | | |||        | | || | |   |                                            
AGTTTAGTGAAGTTTTTGTGCACCAAATGATTCACACTATTGAGTTTGTGTTGAATTCTGTATCCAACACTGCTTCCTATCTGCGGCTGTGGGCGCTCAGgtaattctcttaggtgttgttattactttgttccatttagaaagtcttgtgctaactctttttaacgtgttgacgtggtgttaccagctgcaaaaaaattgttctgtatcgacatggttcatgctctctcgactgatcttttctaggacttttggcctgcag

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGTTTAGTGAAGTTTTTGTACACCAACTTATTCATACCATAGAGTTTGTCCTTGGAGCAGTCTCTAATACAGCTTCATACTTACGTTTATGGGCCCTCAGgtaggcaggaacaacctgaagttatttcatatggcatgctgagctaaaatgtgcactgctaaaatgcatggtagaaagccaaagttatgtctatagaata

- - - - - - - - - - - - - - - - - - - - - - - - -  TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aggaaca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gctaaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gtagaaa