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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TCCTGGAGATCCAAAGCTTGGAGAAGGTAAGCCTGAAAACCAAAATCATGCTATAATCTTCACACGTGGGGAAGCTATTCAAACTATTGATATGAATCAGgtgagtctttgcacattgttttctttccaagtatcttgtgtgatttcggtttagtttcataaactgttgctataaaaacctggttttcagtagattatca...

Basic information

species Vitis vinifera
transcript Vv17s0000g10010.t01
intron # 30
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv17s0000g10010.t01 (Vitis vinifera), 5'ss of exon 30
lower sequence: GRMZM2G326643_T03 (Zea mays), 5'ss of exon 35
TCCTGGAGATCCAAAGCTTGGAGAAGGTAAGCCTGAAAACCAAAATCATGCTATAATCTTCACACGTGGGGAAGCTATTCAAACTATTGATATGAATCAGgtgagtctttgcacattgttttctttc-caagtatcttgtgtgatttcggtttagtttcataaactgttgctata-aaaacctggttttcagtagattatca---
 |||||  | || |||||||| ||||| || ||||| |||||||| ||||| ||||||||||| || || || ||  |||| || || ||||||||||||||     ||  |||    |   |  || ||   |  |  |    |  |  |    ||         |   | | | ||||  | |||| | |||  ||  ||   
GCCTGGGAACCCCAAGCTTGGTGAAGGCAAACCTGAGAACCAAAACCATGCCATAATCTTCACTCGAGGAGATGCAGTTCAGACGATCGATATGAATCAGgt-----ttaacaccccctgccccctcacacacacatgctaaagtaaccttcccattggtagcttcgcctccacacaaaatgtagtttactgtattttcacaaac

upper sequence: Vv17s0000g10010.t01 (Vitis vinifera), 5'ss of exon 30
lower sequence: GLYMA04G36710.1 (Glycine max), 5'ss of exon 13
TCCTGGAGATCCAAAGCTTGGAGAAGGTAAGCCTGAAAACCAAAATCATGCTATAATCTTCACACGTGGGGAAGCTATTCAAACTATTGATATGAATCAGgtgagtctttgcacattgttttctttccaagtatcttgtgtgatttcggtttagtttcataaactgttgctataaaaacctggttttcagtagattatca----
|||||||||||| |||||||| ||||| ||||||||||||||||| ||||| || |||||||| ||||| |||||| ||||||||||||| |||||||||||||   | ||     | |  || ||    ||  ||| | |  || | || | ||   |     | ||| ||| | ||  || |||||| |    ||  |    
TCCTGGAGATCCTAAGCTTGGGGAAGGAAAGCCTGAAAACCAAAACCATGCCATCATCTTCACTCGTGGTGAAGCTGTTCAAACTATTGACATGAATCAGgtgaagatatgtctcatatggtcattt---gttccttttctctttgccgtct-gtaatacctttttttgttattacaagatgcttttcattgtgctacaatgga

upper sequence: Vv17s0000g10010.t01 (Vitis vinifera), 5'ss of exon 30
lower sequence: GLYMA06G18220.1 (Glycine max), 5'ss of exon 16
TCCTGGAGATCCAAAGCTTGGAGAAGGTAAGCCTGAAAACCAAAATCATGCTATAATCTTCACACGTGGGGAAGCTATTCAAACTATTGATATGAATCAGgtgagtctttg---cacattgttttctttccaagtatcttgtgtgatttcggtttagtttcataaactgttgctata----aaaacctggttttcagtagattatca
|||||||||||| |||||||| ||||| ||||||||||||||||| ||||| ||| | ||||| ||||| |||||| ||||||||||||| |||||||||||||   | ||   || || ||  | | | |   |    | ||  || | | | ||  ||  |    | || |||      | |   ||   | || | ||      
TCCTGGAGATCCTAAGCTTGGGGAAGGAAAGCCTGAAAACCAAAACCATGCAATAGTTTTCACTCGTGGTGAAGCTGTTCAAACTATTGACATGAATCAGgtgaagatatgtctcatatggtcatttgttctttttctctttgccatct-gttataccttttttggttattactaggtgctatacattgtgctacaatgga------

upper sequence: Vv17s0000g10010.t01 (Vitis vinifera), 5'ss of exon 30
lower sequence: AT2G36850.1 (Arabidopsis thaliana), 5'ss of exon 36
TCCTGGAGATCCAAAGCTTGGAGAAGGTAAGCCTGAAAACCAAAATCATGCTATAATCTTCACACGTGGGGAAGCTATTCAAACTATTGATATGAATCAGgtgagtctttgca-cattgttttctttccaagtatcttgtgtgatttcggtttagtttcataaactgttgctataa-aaacctggttttcagtagattatca
||| |||||||| || ||||| ||||| |||||||| || ||||||||||||||  | || || || || |||||||| || || || ||||||||||||||   || |  |  | ||||  | ||||     || |  ||| |||    || ||        ||||  | ||    ||||| |   | ||   |      |
TCCCGGAGATCCTAAACTTGGTGAAGGGAAGCCTGAGAATCAAAATCATGCTATCGTGTTTACGCGGGGAGAAGCTATCCAGACCATAGATATGAATCAGgtttttcctcacttctttgtcatgtttcggcacatttc-tgt-attgacattaagagagtcgtactgcggataagctaaacccgtcatgcatgtggccgata

upper sequence: Vv17s0000g10010.t01 (Vitis vinifera), 5'ss of exon 30
lower sequence: PP1S13_132V6.1 (Physcomitrella patens), 5'ss of exon 35
TCCTGGAGATCCAAAGCTTGGAGAAGGTAAGCCTGAAAACCAAAATCATGCTATAATCTTCACACGTGGGGAAGCTATTCAAACTATTGATATGAATCAGgtgagtctttgcacattgttttctttccaagtatc-ttgtgtg---atttcggtttagtttcataaactgttgctataaaaacctggttttcag--tagattatca---------------------------------------------------------------------------------------
 ||||||||    |  || ||||| || ||||||||||||||||| ||||| ||  | || || ||||| || || |||||||||||||| ||||| |||||   ||  |     |     ||| ||    | ||  ||| |    || |   | ||  |  ||| |    || | ||    | | ||    |   | |  |  |                                                                                        
GCCTGGAGAAGTTATTCTGGGAGAGGGCAAGCCTGAAAACCAAAACCATGCAATTGTATTTACTCGTGGAGAGGCCATTCAAACTATTGACATGAACCAGgtacatccctctctctctagctctctctctctctcgctgtatatatatatatatatatatatatatatatatgttttagttcctttgtgacaaacttggggtggcgatttgttcgaacacctgcacagtagttacacagtttttcgttgatgagaagtgtcatcatatttcggagcacgttgcattgacgcag

upper sequence: Vv17s0000g10010.t01 (Vitis vinifera), 5'ss of exon 30
lower sequence: PP1S160_88V6.1 (Physcomitrella patens), 5'ss of exon 36
TCCTGGAGATCCAAAGCTTGGAGAAGGTAAGCCTGAAAACCAAAATCATGCTATAATCTTCACACGTGGGGAAGCTATTCAAACTATTGATATGAATCAGgtgagtctttgcacattgttttctttccaagtatcttgtgtgatttcggtttagtttcataaactgttgctataaaaacctggttttcagtagattatca
 |||||       || || |||||||| || || ||||| |||||||||||||| || || |  |||||||| ||  ||||||| ||||||||||| |||||           | ||  ||| || |  | |    |        | | | ||| | | |      |  ||      |   | | | |  || ||| || 
CCCTGGGCCGTTTAAACTCGGAGAAGGAAAACCAGAAAATCAAAATCATGCTATCATATTTAGTCGTGGGGATGCAGTTCAAACCATTGATATGAACCAGgtttcatgcgcttcttttcttttttcctcattcctctcctccggattgttctagatgcgtccttcttaacttatgttaagggctgtactataaattttct

upper sequence: Vv17s0000g10010.t01 (Vitis vinifera), 5'ss of exon 30
lower sequence: PP1S67_70V6.1 (Physcomitrella patens), 5'ss of exon 31
TCCTGGAGATCCAAAGCTTGGAGAAGGTAAGCCTGAAAACCAAAATCATGCTATAATCTTCACACGTGGGGAAGCTATTCAAACTATTGATATGAATCAGgtgagtctttgcacattgttttctttccaagtatcttgtgtgatttcggtttagtttcataaactgttgctataaaaacctggttttcagtagattatca--
||||||       || |||||||| || || || || |||||||||||||| || || ||||  || ||||| ||| ||||||||||||||||||| |||||  |        | ||  |   | |||        | |||   | |   | | |||         ||    ||||    |  || ||   | ||       
TCCTGGGCCATTTAAACTTGGAGAGGGAAAACCAGAGAACCAAAATCATGCCATTATATTCAGTCGGGGGGATGCTGTTCAAACTATTGATATGAACCAGgtttgatgcccttcttttctccttgtcctcactctctttgtagatgcatctaaatttttctctggattatggtaaattttt--ttctctaaacatcgatggg

upper sequence: Vv17s0000g10010.t01 (Vitis vinifera), 5'ss of exon 30
lower sequence: PP1S88_136V6.1 (Physcomitrella patens), 5'ss of exon 34
TCCTGGAGATCCAAAGCTTGGAGAAGGTAAGCCTGAAAACCAAAATCATGCTATAATCTTCACACGTGGGGAAGCTATTCAAACTATTGATATGAATCAGgtgagtctttgcacattgt--tttc----tttccaagtatcttgt-gtgatttcggtttag--tttcataaactgttgct-ataaaaacctggttttcagtagattatca---------------------
 || |||||    |||||||| ||||| || || || || ||||||||||| ||||| ||||| ||||| ||    || ||||||||||| |||||||||||  || ||      |     ||||    |||  || ||    ||    |  | |  ||||  | |  ||   |||  || |   |  | |||  |||  |    |   |                     
CCCCGGAGACGTTAAGCTTGGTGAAGGAAAACCCGAGAATCAAAATCATGCAATAATTTTCACGCGTGGAGATTGCATCCAAACTATTGACATGAATCAGgtttgttttaaggtttcaaaatttcagggtttagaaatacaaagttaaaaacttgagttagggtgttctagtgtgtgcctgactgatgcttggaattctattcgctgaaagtcatcttccgattgttttag

upper sequence: Vv17s0000g10010.t01 (Vitis vinifera), 5'ss of exon 30
lower sequence: PP1S145_49V6.1 (Physcomitrella patens), 5'ss of exon 34
TCCTGGAGATCCAAAGCTTGGAGAAGGTAAGCCTGAAAACCAAAATCATGCTATAATCTTCACACGTGGGGAAGCTATTCAAACTATTGATATGAATCAGgtgagtct---ttgcacattgttttctttc---caagtatcttgt--gtgatttcggtttagttt---cataaactgttgctataaaaacctggttttcagtagattatca-----------------------------------------------------------
 || |||||   ||   | || || || ||||||||||| ||||| ||||| || || || || |||||||||||  |||| |||||||| |||||||||||  ||||   ||||  |    | |   |    ||| ||| |||   |   | ||  || |  |    ||| || |  || | |  | |  |    | ||| |  | |  |                                                           
GCCCGGAGAAGTAATTTTAGGGGAGGGCAAGCCTGAAAATCAAAACCATGCGATTATTTTTACTCGTGGGGAAGCCCTTCAGACTATTGACATGAATCAGgtttgtctaccttgcgaaggactctgcgtggtgcaactattttgatagctctctcctttcaaatcaaacatgaattagtggtttttatattttacctgcagaatttcagtagagtttgaacgttggtgggatttgacgtcatatttgtggataccctctcattgatgcag

upper sequence: Vv17s0000g10010.t01 (Vitis vinifera), 5'ss of exon 30
lower sequence: EFJ05083 (Selaginella moellendorffii), 5'ss of exon 35
TCCTGGAGATCCAAAGCTTGGAGAAGGTAAGCCTGAAAACCAAAATCATGCTATAATCTTCACACGTGGGGAAGCTATTCAAACTATTGATATGAATCAGgtgagtctttgcacattgttttctttccaagtatcttgtgtgatttcggtttagtttcataaactgttgctataaaaacctggttttcagtagattatca
 || ||| ||||||| ||||||||||| ||||||||||| ||||||||||| || || || || ||||| || || || ||||| || |||||||| |||||    |||||||  ||  |||  |  ||    |    | | |||| |                                                    
ACCGGGAAATCCAAAACTTGGAGAAGGCAAGCCTGAAAATCAAAATCATGCGATTATTTTTACCCGTGGAGATGCAATACAAACCATAGATATGAACCAGgtactactttgca--ttcattttctcacagacttaccattttattttgcag-------------------------------------------------

upper sequence: Vv17s0000g10010.t01 (Vitis vinifera), 5'ss of exon 30
lower sequence: EFJ07568 (Selaginella moellendorffii), 5'ss of exon 35
TCCTGGAGATCCAAAGCTTGGAGAAGGTAAGCCTGAAAACCAAAATCATGCTATAATCTTCACACGTGGGGAAGCTATTCAAACTATTGATATGAATCAGgtgagtctttgcacattgttttctttccaagtatcttgtgtgatttcggtttagtttcataaactgttgctataaaaacctggttttcagtagattatca
 || ||| ||||||| ||||||||||| ||||||||||| ||||||||||| || || || || ||||| || || || ||||| || |||||||| |||||    |||||||  ||  |||  |  ||    |    | | | || |                                                    
ACCGGGAAATCCAAAACTTGGAGAAGGCAAGCCTGAAAATCAAAATCATGCGATTATTTTTACCCGTGGAGATGCAATACAAACCATAGATATGAACCAGgtactactttgca--ttcattttctcacagacttaccattttactttgcag-------------------------------------------------

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TCCTGGAGATCCAAAGCTTGGAGAAGGTAAGCCTGAAAACCAAAATCATGCTATAATCTTCACACGTGGGGAAGCTATTCAAACTATTGATATGAATCAGgtgagtctttgcacattgttttctttccaagtatcttgtgtgatttcggtttagtttcataaactgttgctataaaaacctggttttcagtagattatca

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ataaaaa