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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TAATCGGATACCTGAAGCTGCTTTAATGGCACGATCTTACCTTCCAAGCAAGGTTCCAGAGATAATCACGATTTGGAGAAATGACCTCAACAAGgttattcttctgattatttcattttgttttccatgaagcactttggttagtaaatcatatccgagatagagagaggacaacaaatgatgatgaatgtgat...

Basic information

species Vitis vinifera
transcript Vv11s0016g04180.t01
intron # 21
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv11s0016g04180.t01 (Vitis vinifera), 5'ss of exon 21
lower sequence: LOC_Os06g05180.1 (Oryza sativa), 5'ss of exon 21
TAATCGGATACCTGAAGCTGCTTTAATGGCACGATCTTACCTTCCAAGCAAGGTTCCAGAGATAATCACGATTTGGAGAAATGACCTCAACAAGgttattcttctgattatttcattttgttttccatgaagcactttggtt------agtaaatcatatccgagatagagagaggacaacaaatgatgatgaatgtgat------
 ||||| |||||||||||||| ||||||||||| ||||| ||||| ||||| ||| | |||||| |  | || ||||||||||||||||  || || |||  |     |  | |  ||   ||| |||  |  | | || ||      || |||   | || |  || |     |    |   ||    |||    |  |      
CAATCGTATACCTGAAGCTGCGTTAATGGCACGTTCTTATCTTCCCAGCAAAGTTTCTGAGATAGTAGCAATATGGAGAAATGACCTCAGTAAAgtaatttcttaatcttctgctcttatctttgcattgaaaagtgtgcttccatccagaaaacattttctgttattgttctggttttatctattcatatgttccttctgtacag

upper sequence: Vv11s0016g04180.t01 (Vitis vinifera), 5'ss of exon 21
lower sequence: GRMZM2G443953_T03 (Zea mays), 5'ss of exon 22
TAATCGGATACCTGAAGCTGCTTTAATGGCACGATCTTACCTTCCAAGCAAGGTTCCAGAGATAATCACGATTTGGAGAAATGACCTCAACAAGgttattcttctgattatttcattttgttttccatgaagcactttggttagtaaatcatatccgag-atagagagaggacaacaaatgatgatgaatgtgat-
|||||| || || ||||| ||  | |||||||||||||||||||||||||| ||| | || ||  || | || |||| ||| |||||| | ||||| ||  | || |  | ||  || | |   |         |||    |   |  ||| ||      ||  |  || || | |   |  | ||     | |  
TAATCGTATTCCAGAAGCAGCACTGATGGCACGATCTTACCTTCCAAGCAAAGTTTCTGATATTGTCTCAATATGGAAAAAGGACCTCCAAAAGgt-atcttcctaacgaattttttctctgcccttgttcttccttccaatcacacttcacattttcccatgcaatgaaga-atctgtttctaattctcttaagc

upper sequence: Vv11s0016g04180.t01 (Vitis vinifera), 5'ss of exon 21
lower sequence: GRMZM2G095348_T02 (Zea mays), 5'ss of exon 20
TAATCGGATACCTGAAGCTGCTTTAATGGCACGATCTTACCTTCCAAGCAAGGTTCCAGAGATAATCACGATTTGGAGAAATGACCTCAACAAGgttattcttc----tgattatttcattttgttttccatgaagcactttg--gttagtaaatcatatccgagatagagagaggacaacaaatgatgatgaatgtgat-
||  || ||||||||||||||  ||||||| ||||| || ||||| ||||| || ||||| ||| |  | ||||||||||| |||||||  || || |||  |     |  | || | | | |  ||||    |||     ||   |||| |||  ||    |  ||      |             |      | ||   
TAGCCGTATACCTGAAGCTGCACTAATGGCGCGATCGTATCTTCCTAGCAAAGTACCAGAAATAGTAGCAATTTGGAGAAACGACCTCAGTAAAgtaatttcttaatgttctcatcttagtcttctttctgaaaagtgtggtgccattagaaaaaaatgcatgctattatcttattctttttttctgtaccttgtatgcag

upper sequence: Vv11s0016g04180.t01 (Vitis vinifera), 5'ss of exon 21
lower sequence: GLYMA13G43680.1 (Glycine max), 5'ss of exon 21
TAATCGGATACCTGAAGCTGCTTTAATGGCACGATCTTACCTTCCAAGCAAGGTTCCAGAGATAATCACGATTTGGAGAAATGACCTCAACAAGgttattcttctgattatttcattttgttttccatgaagcactttggttagtaaatcatatccgagatagagagaggacaacaaatgatgatgaatgtgat---
 ||||| || || || || ||||||||||| |||||||| || ||||| |||||  |||||||| |  | ||||||||||| |||||||| ||||| |||  |||||||     |  | || ||   | | |   |    ||  |   |  || |   |     || |  | |  |   ||   |||||        
CAATCGAATTCCAGAGGCAGCTTTAATGGCTCGATCTTATCTCCCAAGTAAGGTCTCAGAGATAGTGGCAATTTGGAGAAAAGACCTCAATAAGgtaatt--tctgattcaggtagatggtatttacttatgt-ttgaacttcctgttttttacctttgtgcatgatattatataatgggaatctgaatcctccaca

upper sequence: Vv11s0016g04180.t01 (Vitis vinifera), 5'ss of exon 21
lower sequence: GLYMA15G01680.1 (Glycine max), 5'ss of exon 21
TAATCGGATACCTGAAGCTGCTTTAATGGCACGATCTTACCTTCCAAGCAAGGTTCCAGAGATAATCACGATTTGGAGAAATGACCTCAACAAGgttattcttctgattatttcattttgttttccatgaagcactttggttagtaaatcatatccgagatagagagaggacaacaaatgatgatgaatgtgat---
 ||||| || || || || ||||||||||| |||||||| || ||||| |||||  |||||||| |  | ||||||||||| |||||||| ||||| |||  |||||||     |  | || ||   | | |   |    ||  |   |  || |   |     || |  | |  |   ||   |||||    |   
CAATCGAATTCCGGAGGCAGCTTTAATGGCTCGATCTTATCTCCCAAGTAAGGTCTCAGAGATAGTGGCAATTTGGAGAAAAGACCTCAATAAGgtaatt--tctgattcaggtagatggtatttacttatgt-ttgaacttcctgttttttacctttgtgcatgatattatattatgcgaatctgaattctctaca

upper sequence: Vv11s0016g04180.t01 (Vitis vinifera), 5'ss of exon 21
lower sequence: GLYMA08G22140.1 (Glycine max), 5'ss of exon 21
TAATCGGATACCTGAAGCTGCTTTAATGGCACGATCTTACCTTCCAAGCAAGGTTCCAGAGATAATCACGATTTGGAGAAATGACCTCAACAAGgttattct---tctgattatttcattttgttttccatgaagcactttggttagtaaatcatatccgagatagagagaggacaacaaatgatgatgaatgtgat--------------------------------------------------------------------------------------------------
 |||||||| || || |||||||||||||| ||||| || || |||||||||||  |||||||| |  | ||||||||||| || ||||  ||||| ||  |   | |   ||| |   | | | |   ||  ||||    |  |||     ||| |  |   |  | |    ||      |    |    |||  |                                                                                                  
CAATCGGATTCCAGAGGCTGCTTTAATGGCTCGATCCTATCTCCCAAGCAAGGTCTCAGAGATAGTGGCAATTTGGAGAAAAGATCTCAGTAAGgtaatgttatatatatatatatatatatatatataatttagcaacg-gaatagcctgacatttatgttgtgcacatgatactgtgggtaggaacttctgttctcattccattggcctgccctgtcctggattcttatcatgctacatattgcatgtgaaataaaaatataaattcttatatttatttgttaatatgcacag

upper sequence: Vv11s0016g04180.t01 (Vitis vinifera), 5'ss of exon 21
lower sequence: GLYMA07G03890.2 (Glycine max), 5'ss of exon 10
TAATCGGATACCTGAAGCTGCTTTAATGGCACGATCTTACCTTCCAAGCAAGGTTCCAGAGATAATCACGATTTGGAGAAATGACCTCAACAAGgttattc----ttctgat-tatttcattttgttttccatgaagcactttggttagtaaatcatatccgagatagagagaggacaacaaatgatgatgaatgtgat
 |||||||| || || |||||||||||||| ||||| || || |||||||||||  |||||||| |  | ||||||||||| || ||||  ||||| |||     ||||||| ||| |   | | | |      |   || |   |||||||   |    |  || |   |   |    || |||||  |    |    
CAATCGGATTCCAGAGGCTGCTTTAATGGCTCGATCCTATCTCCCAAGCAAGGTCTCAGAGATAGTGGCAATTTGGAGAAAAGATCTCAGTAAGgtaatttgttattctgatatatatatgtatatatatacatacatacataatttagtaatggaatagcctgacatttatgtggtg-cacatgatactttggg----

upper sequence: Vv11s0016g04180.t01 (Vitis vinifera), 5'ss of exon 21
lower sequence: AT3G15980.2 (Arabidopsis thaliana), 5'ss of exon 21
TAATCGGATACCTGAAGCTGCTTTAATGGCACGATCTTACCTTCCAAGCAAGGTTCCAGAGATAATCACGATTTGGAGAAATGACCTCAACAAGgttattcttctgattatttcattttgttttccatgaagcactttggttagtaaatcatatccgagatagagagaggacaacaaatgatgatgaatgtgat
||| |||||||| ||||||||| | |||||||| ||||| ||||||||||| ||| | |||||| |  |  | |||||  | || |||| |||||||||| |||  ||  |||  |||||||| |  ||       |   | || ||||       | |      |   | |    | |  | || |       
TAACCGGATACCAGAAGCTGCTCTGATGGCACGTTCTTATCTTCCAAGCAAAGTTTCGGAGATAGTAGCTCTATGGAGGGAAGATCTCAGCAAGgttatt-ttcgcatctttt--ttttgtttactgtg-------tcaatgagaaaattcatcatgtggctttaaattgcctttgacttgtcatcag------

upper sequence: Vv11s0016g04180.t01 (Vitis vinifera), 5'ss of exon 21
lower sequence: AT1G79990.1 (Arabidopsis thaliana), 5'ss of exon 25
TAATCGGATACCTGAAGCTGCTTTAATGGCACGATCTTACCTTCCAAGCAAGGTTCCAGAGATAATCACGATTTGGAGAAATGACCTCAACAAGgttattcttctgattatttcattttgttttccatgaagc-----actttggttagtaaatcatatccgagatagagagaggacaacaaatgatgatgaatgtgat
|||||| ||||||||||| ||| | |||||  |||| |||||||||||||||||  | || ||| |  |  | |||||||| ||  | | |||||||| |  |      ||   ||     ||   ||  |       || |||  |  | |   ||||||   ||          |  |     ||  || || |   
TAATCGAATACCTGAAGCCGCTCTGATGGCGAGATCGTACCTTCCAAGCAAGGTCTCCGAAATAGTGGCATTGTGGAGAAACGATTTGACCAAGgttagtggtagacacatccgatgcaccttgtgattgaatttcaaaccttgcctgttgag--atatccacaatttttcttcatcctctgtcaatc-tggatatag-

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TAATCGGATACCTGAAGCTGCTTTAATGGCACGATCTTACCTTCCAAGCAAGGTTCCAGAGATAATCACGATTTGGAGAAATGACCTCAACAAGgttattcttctgattatttcattttgttttccatgaagcactttggttagtaaatcatatccgagatagagagaggacaacaaatgatgatgaatgtgat

- - - - - - - - - - - - - - - - - - - - - -  AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tagagag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aggacaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - atgatgaa