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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ACCGTATGCAGAGGTTGAGGTTATGAAGATGTGTATGCCACTTCTTTCGCCTGCTTCTGGAATTATTCAATTTAAGATGTCTGAAGGTCAAGCAATGCAGgtaaaatatgttccatattggaagttttagtatcctatccttggtagagattaagaaatcacattttgtgtag

Basic information

species Vitis vinifera
transcript Vv18s0001g04980.t01
intron # 19
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv18s0001g04980.t01 (Vitis vinifera), 5'ss of exon 19
lower sequence: LOC_Os10g21910.1 (Oryza sativa), 5'ss of exon 15
ACCGTATGCAGAGGTTGAGGTTATGAAGATGTGTATGCCACTTCTTTCGCCTGCTTCTGGAATTATTCAATTTAAGATGTCTGAAGGTCAAGCAATGCAGgtaaaata----tgttccatattggaagttttagtatcc--------------tatccttggtagag--attaagaaatcacattttgtgtag
||| ||||| ||||||||||| ||||||||||||||||| ||  |    || ||||||||  ||||||| |||   ||| |||| |||||||| ||||||||   |||    | || ||   ||  | | || |||| |               ||| ||   |  |  | ||| |  ||   | || || ||
ACCATATGCTGAGGTTGAGGTCATGAAGATGTGTATGCCGCTGTTACTACCAGCTTCTGGTGTTATTCATTTTGTCATGCCTGAGGGTCAAGCCATGCAGgttctatacctctatttcaccctgttattatttgtatgcatcttatttgcatacatcttttacaaggtaactaaaatgtctattcttttgcag

upper sequence: Vv18s0001g04980.t01 (Vitis vinifera), 5'ss of exon 19
lower sequence: GRMZM5G858094_T01 (Zea mays), 5'ss of exon 19
ACCGTATGCAGAGGTTGAGGTTATGAAGATGTGTATGCCACTTCTTTCGCCTGCTTCTGGAATTATTCAATTTAAGATGTCTGAAGGTCAAGCAATGCAGgtaaaat------atgttc------catattggaagttt-tagtatcctatccttggtagagattaagaaatcacattttgtgtag-
||| || || || |||||||||||||||||||| ||||| ||  | || |||||||||||  | ||||| | || ||||||||| || || ||| ||||||| | ||      |||| |         ||||    ||  |   ||  |||     |||    |||  || | | ||||||| |   
ACCATACGCGGAAGTTGAGGTTATGAAGATGTGCATGCCTCTCTTGTCACCTGCTTCTGGTGTCATTCATTGTATGATGTCTGAGGGCCAGGCATTGCAGgttatattcgcacatgtccattccttgcattgtgctttcatcacataatatttcatgtaacatttatcaacttatattttgttttag

upper sequence: Vv18s0001g04980.t01 (Vitis vinifera), 5'ss of exon 19
lower sequence: GLYMA04G11550.1 (Glycine max), 5'ss of exon 18
ACCGTATGCAGAGGTTGAGGTTATGAAGATGTGTATGCCACTTCTTTCGCCTGCTTCTGGAATTATTCAATTTAAGATGTCTGAAGGTCAAGCAATGCAGgtaaaa-----tatgttccatattggaagttttagtatcctatccttggtagagattaagaaatcacat---tttgtgtag
||||||||| || |||||||| ||||| ||||| ||||| |||||||||||||||||||| |||||||| || || ||||||||||||||||||||||||||| |      | | ||||| || ||||||   | | |   |   |||  | |||| |  ||||   ||    || || ||
ACCGTATGCTGAAGTTGAGGTCATGAAAATGTGCATGCCTCTTCTTTCGCCTGCTTCTGGGATTATTCATTTCAAAATGTCTGAAGGTCAAGCAATGCAGgtatatagcattctattccacataggaagtacaattgttgaaa--ttgaaaaagataataaaattgtatcaccttttgcag

upper sequence: Vv18s0001g04980.t01 (Vitis vinifera), 5'ss of exon 19
lower sequence: GLYMA06G11120.1 (Glycine max), 5'ss of exon 18
ACCGTATGCAGAGGTTGAGGTTATGAAGATGTGTATGCCACTTCTTTCGCCTGCTTCTGGAATTATTCAATTTAAGATGTCTGAAGGTCAAGCAATGCAGgtaaaa-----tatgttccatattggaagttttagtatcc-tatccttggtagagattaagaaatcacattttgtgtag
||| ||||| || |||||||| ||||| ||||| ||||| |||||||||||||||||||| |||||||| || || ||||||||||||||||||||||||||| |      | | ||||| |||||||||    || | | |||     |     || ||  | |  || | | || ||
ACCATATGCTGAAGTTGAGGTCATGAAAATGTGCATGCCTCTTCTTTCGCCTGCTTCTGGGATTATTCATTTCAAAATGTCTGAAGGTCAAGCAATGCAGgtatatagcattctattccacattggaagtacaggtgttcatattgaaagagataataaaatagtatcactgtttgcag

upper sequence: Vv18s0001g04980.t01 (Vitis vinifera), 5'ss of exon 19
lower sequence: AT1G36160.1 (Arabidopsis thaliana), 5'ss of exon 18
ACCGTATGCAGAGGTTGAGGTTATGAAGATGTGTATGCCACTTCTTTCGCCTGCTTCTGGAATTATTCAATTTAAGATGTCTGAAGGTCAAGCAATGCAGgtaaaatatgttccatattggaagttttagtatcctatccttggt-agagattaagaaatcacattttgtgtag
 || ||||| || |||||||| ||||||||||| |||||||||||||| |||||||| ||| |||| || ||||| ||||||||||| ||||| ||||||||  | |   || |  |    ||    ||   | || |      | |   |   |   || |  ||||    ||
GCCTTATGCCGAAGTTGAGGTCATGAAGATGTGCATGCCACTTCTTTCACCTGCTTCAGGAGTTATCCATTTTAAAATGTCTGAAGGACAAGCCATGCAGgttcacttcattgctaaacaaaaagcctacagttctgtttaaattgattaacccatccattatttttttcacag

upper sequence: Vv18s0001g04980.t01 (Vitis vinifera), 5'ss of exon 19
lower sequence: AT1G36180.1 (Arabidopsis thaliana), 5'ss of exon 18
ACCGTATGCAGAGGTTGAGGTTATGAAGATGTGTATGCCACTTCTTTCGCCTGCTTCTGGAATTATTCAATTTAAGATGTCTGAAGGTCAAGCAATGCAGgtaaaatat--gttccatattgga-agttttagtatcctatc-cttggtagagattaagaaatcacattttgtgtag---------
 ||||||||||| ||||| || ||||||||||| ||||||||| |||| ||||| || ||| |||| || || ||| |||||||||| ||||| |||||||| ||  |    |||  |  |  | |   || || || ||    || ||||| ||| |  || | |||    | |           
GCCGTATGCAGAAGTTGAAGTCATGAAGATGTGCATGCCACTTATTTCACCTGCGTCAGGAGTTATCCATTTCAAGTTGTCTGAAGGACAAGCCATGCAGgtgaagaaccaattcattgctaaagaaaatttgtttcttacagttttgtagaaattgattaacc-catccgatattttcttgacag

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ACCGTATGCAGAGGTTGAGGTTATGAAGATGTGTATGCCACTTCTTTCGCCTGCTTCTGGAATTATTCAATTTAAGATGTCTGAAGGTCAAGCAATGCAGgtaaaatatgttccatattggaagttttagtatcctatccttggtagagattaagaaatcacattttgtgtag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCAA