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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AAGAACAGCTTTGAACAACTCTGTATAAACTATGCAAATGAGAGGCTGCAACAGCATTTCAATCGTCATCTACTTAAACTCGAACAGGAGgtatgcatctaaactctatttataccattggagttgttggtcattcatgacacgagtatacagaagctttctgaaaattttatcttgattaaaaaatgca...

Basic information

species Vitis vinifera
transcript Vv19s0014g03640.t01
intron # 15
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv19s0014g03640.t01 (Vitis vinifera), 5'ss of exon 15
lower sequence: GLYMA12G34780.1 (Glycine max), 5'ss of exon 17
AAGAACAGCTTTGAACAACTCTGTATAAACTATGCAAATGAGAGGCTGCAACAGCATTTCAATCGTCATCTACTTAAACTCGAACAGGAGgtatgcatcta-----aactctatttataccattggagttgttggtcattcatgacacgagtatacagaagctttctgaaaattttatcttgattaaaaaatgca-
|| ||||||||||||||| | |||||||||||||| ||||||||||| ||||| ||||||||||| |||||  ||||||| || ||||||||  ||| |||     | || || ||  | ||    | ||||  ||      | | || | |   ||| |  ||| |     ||| |  ||| |    |  |  | 
AATAACAGCTTTGAACAATTTTGTATAAACTATGCCAATGAGAGGCTTCAACAACATTTCAATCGGCATCTGTTTAAACTTGAGCAGGAGgtcagcaactatgttaagctttaatttgaacac-aaaattgtcagtg---tgtaatacaattc--caggaattttatttgtgtttaagattgctgggtattttgat

upper sequence: Vv19s0014g03640.t01 (Vitis vinifera), 5'ss of exon 15
lower sequence: GLYMA13G35790.1 (Glycine max), 5'ss of exon 16
AAGAACAGCTTTGAACAACTCTGTATAAACTATGCAAATGAGAGGCTGCAACAGCATTTCAATCGTCATCTACTTAAACTCGAACAGGAGgtatgcatcta-----aactctatttataccattggagttgttggtcattcatgacacgagtatacagaagctttctgaaaattt--tatcttgattaaaaaatgca
|| ||||||||||||||| | |||||||||||||| ||||||||||| ||||| ||||||||||| |||||  ||||||| || ||||||||  ||| |||     | || || ||  | ||| | | || |  ||      | | ||   |     | | |||| |  ||||     |  ||  ||     ||   
AATAACAGCTTTGAACAATTTTGTATAAACTATGCCAATGAGAGGCTTCAACAACATTTCAATCGGCATCTGTTTAAACTTGAGCAGGAGgtcggcaactatgttaatctttaatttgaacat-gaaattttcagtg---tgtaatacttatg-gtggtatctttatacaaatccaggaatttagtttgtgtatt--

upper sequence: Vv19s0014g03640.t01 (Vitis vinifera), 5'ss of exon 15
lower sequence: GLYMA06G39740.1 (Glycine max), 5'ss of exon 15
AAGAACAGCTTTGAACAACTCTGTATAAACTATGCAAATGAGAGGCTGCAACAGCATTTCAATCGTCATCTACTTAAACTCGAACAGGAGgtatgcatctaaactc--tatttataccattggagttgttggtcattcatgacacgagtatacagaagctttctgaaaattttatcttgattaaaaaatgca
|| ||||||||||||||  | | |||||| ||||| ||||||||| | ||||| ||||| ||||| |||||| ||||||| || ||||||||  | | | |   |   | || |||    |||   | ||| |      || |   | | |  |  |  |     || ||   |     || ||    |   
AAAAACAGCTTTGAACAGTTTTATATAAATTATGCCAATGAGAGGATTCAACAACATTTTAATCGGCATCTATTTAAACTTGAGCAGGAGgtcagtaaccatgttaaatgttaatattgctgggtattttgatgccaattgcctttaatttgaatgaaatagtgtaatatacaaatacaataaagcctta--

upper sequence: Vv19s0014g03640.t01 (Vitis vinifera), 5'ss of exon 15
lower sequence: GLYMA12G22300.1 (Glycine max), 5'ss of exon 15
AAGAACAGCTTTGAACAACTCTGTATAAACTATGCAAATGAGAGGCTGCAACAGCATTTCAATCGTCATCTACTTAAACTCGAACAGGAGgtatgcatctaaactctat--ttataccattggagttgttggtcattcatgacacgagtatacagaagctttctgaaaattttatcttgattaaaaaatgca
|| ||||||||||||||  | | |||||| ||||| ||||||||| | ||||| ||||| ||||| |||||  ||||||| || ||||||||  | | |||   | | |  | |||    | |   | ||| |      |  |   | | |  | ||    | ||| |   ||   |  |||          
AAAAACAGCTTTGAACAGTTTTATATAAATTATGCCAATGAGAGGATTCAACAACATTTTAATCGGCATCTGTTTAAACTTGAGCAGGAGgtcagtaactatgttatgtgttaatattgcttggtattttgatgccaatttcctttaatttgaaaaaatagtgtgatataattccatcaattttgtttct--

upper sequence: Vv19s0014g03640.t01 (Vitis vinifera), 5'ss of exon 15
lower sequence: AT4G27370.1 (Arabidopsis thaliana), 5'ss of exon 13
AAGAACAGCTTTGAACAACTCTGTATAAACTATGCAAATGAGAGGCTGCAACAGCATTTCAATCGTCATCTACTTAAACTCGAACAGGAGgtatgcatctaaactctatttataccattggagttgttggtcattcatgacacga------gtatacagaagctttctgaaaattttatcttg---attaaaaaatgca--------------
 | || || || |||||| | || ||||||||||||||||| || ||||| || |||||||| || |||||| ||||||| ||||| |||||   | ||| |    |   | |        | |   ||   ||   | || | |      ||  ||   |  | ||  | || | | | |||   |||||  || | |              
GATAATAGTTTCGAACAATTTTGCATAAACTATGCAAATGAAAGACTGCAGCAACATTTCAACCGACATCTATTTAAACTTGAACAAGAGgtgatcttcttactcttgactcttgagcctcattatatgaagatgtgtaactctacttctggtcaactacacatatcaaataaatgtgtattgtctattaatgaaagtatcttcgctgttcag

upper sequence: Vv19s0014g03640.t01 (Vitis vinifera), 5'ss of exon 15
lower sequence: PP1S228_18V6.1 (Physcomitrella patens), 5'ss of exon 14
AAGAACAGCTTTGAACAACTCTGTATAAACTATGCAAATGAGAGGCTGCAACAGCATTTCAATCGTCATCTACTTAAACTCGAACAGGAGgtatgcatctaaactctatttataccattggagttgttggtcattcatgacacgagtatacagaagctttctgaaaattttatcttgattaaaaaatgca---------------------------------------------------------------------------------
|| ||||| ||||| ||| | |||||||| ||||| ||||| ||| ||||||| |||||||||||||||||  | || || || || ||||||   |     |   |  |||   |  ||   |  ||     |||   ||      ||   | |  | ||| |   |   |   | |  |  |  ||                                                                                   
AAAAACAGTTTTGAGCAATTATGTATAAATTATGCGAATGAAAGGTTGCAACAACATTTCAATCGTCATCTGTTCAAGCTTGAGCAAGAGgta-atacgaggatgattgttacggccatgttatctttccctgttcgc-acgtactgattttgtaattctcttatcttcccactgtcac-agcatctgtgtacttctcccattccggactcagtcacgaaatgctacgccgaacgattaacagaggtcggctttttgcgtgaatttttcag

upper sequence: Vv19s0014g03640.t01 (Vitis vinifera), 5'ss of exon 15
lower sequence: PP1S104_215V6.1 (Physcomitrella patens), 5'ss of exon 14
AAGAACAGCTTTGAACAACTCTGTATAAACTATGCAAATGAGAGGCTGCAACAGCATTTCAATCGTCATCTACTTAAACTCGAACAGGAGgtatgcatctaa--actctatttataccattgga-gttgttggtcattcatgacacgagtatacagaagctttctgaaaattttatcttgattaaaaaatgca---------------------------------------------------------------------------------
|  || || ||||| ||||| ||||||||||||||||||||||||||||| ||||||||||| ||||||||  |||| |||||||| || ||| |  |  |   |   ||  |||     |  |  | | |||   ||| |   |      |  || |  || |     ||||      |   |     |||                                                                                  
AGAAATAGTTTTGAGCAACTGTGTATAAACTATGCAAATGAGAGGCTGCAGCAGCATTTCAACCGTCATCTTTTTAAGCTCGAACAAGAAgtacgtttaaagggaacttagatatgttggtaaatatagctggcttttctttttatttacgtcaagcacgttacattggatttgggtgaggacagctcttgcttttctcttacttactgcggcgaccgttttctaacggattctaaatgttcacatcttatggcttcttgtgataattatttag

upper sequence: Vv19s0014g03640.t01 (Vitis vinifera), 5'ss of exon 15
lower sequence: PP1S199_21V6.1 (Physcomitrella patens), 5'ss of exon 14
AAGAACAGCTTTGAACAACTCTGTATAAACTATGCAAATGAGAGGCTGCAACAGCATTTCAATCGTCATCTACTTAAACTCGAACAGGAGgtatgcatct--aaactctatttataccattgga-gttgttggtcattcatgacacgagt---atacagaagctttctgaaaattttatcttgattaaaaaatgca-------------------------------------------------------------------------
|  || || || || ||||| ||||||||||||||||||||||||||||| || |||||||| ||||| ||  |||| || || || || |||||  |    |||   ||  || |    | ||  | | |     ||| | | |  | |   |||| | |  |      | |||   || |   |      | |                                                                          
AGAAATAGTTTCGAGCAACTTTGTATAAACTATGCAAATGAGAGGCTGCAGCAACATTTCAACCGTCACCTTTTTAAGCTTGAGCAAGAAgtatgtgttatgaaagcttagatacagtgatagatatagctatcttttccttaaattaatgttatactggaattgaacccagattagctccttgctgtttccttccgtttttgtggcattcattctacaccagcttgcaaaatacttattctgttcgggttgctttgatgatcatgcag

upper sequence: Vv19s0014g03640.t01 (Vitis vinifera), 5'ss of exon 15
lower sequence: PP1S174_120V6.1 (Physcomitrella patens), 5'ss of exon 14
AAGAACAGCTTTGAACAACTCTGTATAAACTATGCAAATGAGAGGCTGCAACAGCATTTCAATCGTCATCTACTTAAACTCGAACAGGAGgtatgcatcta---aactctatttatacca--ttggagttgttggtcattcatgacacg--agtatacagaagctttctgaaaattttatcttgattaaaaaatgca--------------------------------------------------------------------
|||||||| ||||| ||  | || |||||||||||||| || ||| ||||||| ||||||||||| |||||  |||| || || || ||||||  ||   |   || | | |  | || |   |    || | |||| || | |       |  || |  | | || |   |||||  || ||  | |     |||                                                                     
AAGAACAGTTTTGAGCAGTTATGCATAAACTATGCAAACGAAAGGTTGCAACAACATTTCAATCGCCATCTGTTTAAGCTTGAGCAAGAGgtacacaaaaagctaattatttgcaaactagtctttctttctgggtcttttaggttgttgtacgattccaatgtttccctgaaattcgatttttttcatctcttgcgtctgaatggatcttggagtagaattatgcaactgatagagtacgactttggctgtgacaaatttacag

upper sequence: Vv19s0014g03640.t01 (Vitis vinifera), 5'ss of exon 15
lower sequence: EFJ05534 (Selaginella moellendorffii), 5'ss of exon 13
AAGAACAGCTTTGAACAACTCTGTATAAACTATGCAAATGAGAGGCTGCAACAGCATTTCAATCGTCATCTACTTAAACTCGAACAGGAGgtatgcatctaaactctatttataccattggagttgttggtcattcatgacacgagtatacagaagctttctgaaaattttatcttgattaaaaaatgca
|| ||||| || || || || || ||||||||||||||||||||||| ||||||  ||||||||  || ||  | ||| | || ||||| ||| ||   |     |||||   |  ||| |  |  ||  |  ||| |        | | |  |   |||  |                           
AACAACAGTTTCGAGCAGCTGTGCATAAACTATGCAAATGAGAGGCTTCAACAGTTTTTCAATCACCACCTCTTCAAAATTGAGCAGGACgtaagctcat-----ctattataatgatttggatctttattttttctttcttttttttttctca---ttttag---------------------------

upper sequence: Vv19s0014g03640.t01 (Vitis vinifera), 5'ss of exon 15
lower sequence: EFJ25955 (Selaginella moellendorffii), 5'ss of exon 13
AAGAACAGCTTTGAACAACTCTGTATAAACTATGCAAATGAGAGGCTGCAACAGCATTTCAATCGTCATCTACTTAAACTCGAACAGGAGgtatgcatctaaactctatttataccattggagttgttggtcattcatgacacgagtatacagaagctttctgaaaattttatcttgattaaaaaatgca
|| ||||| || || || || || ||||||||||||||||||||||| ||||||  ||||||||  || ||  | ||| | || ||||| ||| ||   |     || ||   |  ||| |  |  ||  |  ||| |        | | |  |   |||  |                           
AACAACAGTTTCGAGCAGCTGTGCATAAACTATGCAAATGAGAGGCTTCAACAGTTTTTCAATCACCACCTCTTCAAAATTGAGCAGGACgtaagctcat-----ctgttataatgatttggatctttattttttctttctttttcttttctca---ttttag---------------------------

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AAGAACAGCTTTGAACAACTCTGTATAAACTATGCAAATGAGAGGCTGCAACAGCATTTCAATCGTCATCTACTTAAACTCGAACAGGAGgtatgcatctaaactctatttataccattggagttgttggtcattcatgacacgagtatacagaagctttctgaaaattttatcttgattaaaaaatgca

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -atacagaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gaaaatt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aaaaaat