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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTCAGAAGATCTTGAGAGTGGTTTCAGCTCAGATGTTGAATCCAAGTACAAGAAGATATATGAGGATGATATAAATCCCTTTGCTGCTTTCTCCAAAAAGgttttcattcttgaactcctttgctgaatttgcaattttataacaatttatgtgtcaaacttgaaactaaagcatgattttggatttaaatcattgcttc...

Basic information

species Vitis vinifera
transcript Vv17s0000g03970.t01
intron # 16
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv17s0000g03970.t01 (Vitis vinifera), 5'ss of exon 16
lower sequence: LOC_Os03g50300.1 (Oryza sativa), 5'ss of exon 15
--TTCAGAAGATCTTGAGAGTGGTTTCAGCTCAGATGTTGAATCCAAGTACAAGAAGATATATGAGGATGATATAAATCCCTTTGCTGCTTTCTCCAAAAAGgttttcattcttgaactcctttgctgaatttgcaattttataacaatttatgtgtcaaacttgaaactaaagcatgattttggatttaaatcattgcttc
  | |||||||| |||| |||||||     |||||||||||  | ||||||||||| || ||||||||||| |||||||| ||||||||||| || || |||||    |    |  ||   ||     ||  ||  || | |    | | |||   | | || |  |  |||  |   ||   |                  
TATGCAGAAGATGTTGAAAGTGGTTCT---TCAGATGTTGAGACGAAGTACAAGAAAATGTATGAGGATGACATAAATCCTTTTGCTGCTTTTTCAAAGAAGgtaacaaaatgtttacgttttatgataacgtgttatat-acgttactctatagcttatacatacatttaattccatatccag------------------

upper sequence: Vv17s0000g03970.t01 (Vitis vinifera), 5'ss of exon 16
lower sequence: GRMZM2G011219_T02 (Zea mays), 5'ss of exon 15
--TTCAGAAGATCTTGAGAGTGGTTTCAGCTCAGATGTTGAATCCAAGTACAAGAAGATATATGAGGATGATATAAATCCCTTTGCTGCTTTCTCCAAAAAGgttttcattcttgaactcctttgctgaatt-tgcaattttataacaatttatgtgt-caaacttgaaactaaagcatg-attttggatttaaatcattgcttc---
    |||||||| |||| |||||||     || ||||||||| | ||||||||||| || ||||||||||| ||||| || ||||||||||| || || ||||| | |||||    |||   ||| |  ||     | | |||||||  ||  | |||      ||| |  ||    ||  || ||  ||||   |   ||   |   
TACGCAGAAGATATTGAAAGTGGTTCT---TCTGATGTTGAAGCAAAGTACAAGAAAATGTATGAGGATGACATAAACCCGTTTGCTGCTTTTTCAAAGAAGgtat-cattc----actttattgatagataacatattattataactcttgttctgtatggtattgcatatagtttatttatattttattttcctttctgtacccag

upper sequence: Vv17s0000g03970.t01 (Vitis vinifera), 5'ss of exon 16
lower sequence: GLYMA07G09890.1 (Glycine max), 5'ss of exon 16
TTCAGAAGATCTTGAGAGTGGTTTCAGCTCAGATGTTGAATCCAAGTACAAGAAGATATATGAGGATGATATAAATCCCTTTGCTGCTTTCTCCAAAAAGgttttcattcttgaactcctttgctgaatttgcaattttataacaa--tttatgtgtcaaacttgaaactaaagcatgattttggatttaaatcattgcttc
| | ||||||||||| |||||||||   |||||||||||||| || |||||||||||||||||||||||||||||||| |||||||| ||||| ||||||||       ||||    |  |     ||   |  |||| | ||  |  || |||  | | |  |     |  |  |   |    | |||| ||   ||| | 
TGCTGAAGATCTTGAAAGTGGTTTCGCGTCAGATGTTGAATCTAAATACAAGAAGATATATGAGGATGATATAAATCCTTTTGCTGCATTCTCAAAAAAGgtgacttagcttggctgctgtaatgaaacacgacatttaaaaaatagtttcatgcattataagtttgtatgtattagtgtcacagctttacatg--tgcata

upper sequence: Vv17s0000g03970.t01 (Vitis vinifera), 5'ss of exon 16
lower sequence: GLYMA09G31920.2 (Glycine max), 5'ss of exon 8
TTCAGAAGATCTTGAGAGTGGTTTCAGCTCAGATGTTGAATCCAAGTACAAGAAGATATATGAGGATGATATAAATCCCTTTGCTGCTTTCTCCAAAAAGgttttcattcttgaactcctttgctgaatt--tgca-attttataacaatttatgtgtca-aacttgaaactaaagcatgattttggatttaaatcattgcttc
| | ||||||||||| ||||||||||  |||||||| ||||| || |||||||||||||||||||||||||||||||| |||||||| ||||| ||||||||       ||||  || ||    ||||     ||| |||  | ||   || |||  | | || ||   | ||  |    |  ||| |   || | || ||   
TGCTGAAGATCTTGAAAGTGGTTTCATGTCAGATGTGGAATCTAAATACAAGAAGATATATGAGGATGATATAAATCCTTTTGCTGCATTCTCAAAAAAGgtgacttaacttgg-ctgctgcaatgaaacacagcatattgaaaaatgtttcatgcattataagtttgtattagtgtcacagcttg-acaaaattgatagcg--

upper sequence: Vv17s0000g03970.t01 (Vitis vinifera), 5'ss of exon 16
lower sequence: AT3G18480.1 (Arabidopsis thaliana), 5'ss of exon 16
TTCAGAAGATCTTGAGAGTGGTTTCAGCTCAGATGTTGAATCCAAGTACAAGAAGATATATGAGGATGATATAAATCCCTTTGCTGCTTTCTCCAAAAAGgttttcattcttgaactcctttgctgaatttgcaattttataacaatttatgtgtcaaacttgaaactaaagcatgattttggatttaaatcattgcttc
|   ||||||||||| ||||| |||||||| ||||| ||||| || |||||||| || || || ||||| || || || ||||| || ||||| ||||||||    | |     | ||   |          |||   |   | | ||  |   | ||  || |  ||     ||   | ||  ||| |           
TGTGGAAGATCTTGAAAGTGGATTCAGCTCGGATGTCGAATCAAAATACAAGAAAATTTACGAAGATGACATCAACCCTTTTGCAGCATTCTCGAAAAAGgtaaaaaataaaacattctgctatcatcgacacaagcctt--atatttctttcctaaacattaaccctttcctatttatatgtgtttgatag--------

upper sequence: Vv17s0000g03970.t01 (Vitis vinifera), 5'ss of exon 16
lower sequence: PP1S1_786V6.1 (Physcomitrella patens), 5'ss of exon 16
TTCAGAAGATCTTGAGAGTGGTTTCAGCTCAGATGTTGAATCCAAGTACAAGAAGATATATGAGGATGATATAAATCCCTTTGCTGCTTTCTCCAAAAAGgttttcattcttgaactcctttgctgaatttgcaattttataacaatttatgt-gtcaaacttgaaactaaagcatgattttggatttaaatcattgcttc
    || ||| | ||    ||  |  |    ||||| ||   ||  ||||||||||| ||||| |||||||| ||||| ||| ||||||| || || |||||| | ||||||       |  || ||||  |    | ||| |  |||  | | ||  |      |  |    |     ||||  | | | |  ||   | 
CGGGGAGGATTTGGAATCAGGAATGGGGGGTGATGTAGAGAGCAGATACAAGAAGATGTATGAAGATGATATTAATCCGTTTACTGCTTTTTCAAAGAAGgttgttattcttttcgcaatgcgcagaatcagaccgtctatcagcattggttttgtttacagcacatttcttactcctctttgcgtctcatttttttaat-

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TTCAGAAGATCTTGAGAGTGGTTTCAGCTCAGATGTTGAATCCAAGTACAAGAAGATATATGAGGATGATATAAATCCCTTTGCTGCTTTCTCCAAAAAGgttttcattcttgaactcctttgctgaatttgcaattttataacaatttatgtgtcaaacttgaaactaaagcatgattttggatttaaatcattgcttc

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gaaacta