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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ACGCAATGTCAAAGTTGCAGACTTTGGACTCAGCAATGTGATGCGTGATGGTCATTTTCTCAAAACAAGCTGTGGAAGTCCAAATTATGCTGCTCCTGAGgtatgggtcaacttgttatataagttgccaatgaacttgtgaataattatgctctgtgtacaatgaaatactgcttgtgcag

Basic information

species Vitis vinifera
transcript Vv08s0040g00720.t01
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv08s0040g00720.t01 (Vitis vinifera), 5'ss of exon 5
lower sequence: LOC_Os05g45420.3 (Oryza sativa), 5'ss of exon 4
ACGCAATGTCAAAGTTGCAGACTTTGGACTCAGCAATGTGATGCGTGATGGTCATTTTCTCAAAACAAGCTGTGGAAGTCCAAATTATGCTGCTCCTGAGgtatgggtc------aacttgttatataagt---tgccaatgaacttgtgaataattatg-ctctgtgtacaatgaaatactgcttgtgcag--------
| ||||||| ||  |||||||||||||  | || ||||| |||||||||||||| ||||| || ||||| ||||| || ||||||||||| || ||||||||||   ||       | |||   ||| | |   |    ||||     | | |  || |  || | | |||  |     | | ||| | ||         
ATGCAATGTTAAGATTGCAGACTTTGGCTTGAGTAATGTTATGCGTGATGGTCACTTTCTGAAGACAAGTTGTGGTAGCCCAAATTATGCAGCACCTGAGgtatttatcttgaatgatttgcattattactccttcttcatgattgcataattgcttctatctttctttacctttttcaattccttttccatttgactag

upper sequence: Vv08s0040g00720.t01 (Vitis vinifera), 5'ss of exon 5
lower sequence: LOC_Os03g17980.2 (Oryza sativa), 5'ss of exon 4
ACGCAATGTCAAAGTTGCAGACTTTGGACTCAGCAATGTGATGCGTGATGGTCATTTTCTCAAAACAAGCTGTGGAAGTCCAAATTATGCTGCTCCTGAGgtatgggtcaacttgttatataagttgccaatgaacttgtgaataattatgctctgtgtacaatgaaatactgcttgtgcag-------------------
    ||||| ||  |||| ||||||||  | || || || |||| |||||| |||||| | || ||||||||||| |||||||| ||||||||||| ||||| |   |    || || | |   |  |    | |||      |  |  | || ||  | |||| |  |  |  |  |  ||                   
GTATAATGTAAAGCTTGCTGACTTTGGTTTGAGTAACGTCATGCATGATGGCCATTTTTTGAAGACAAGCTGTGGGAGTCCAAACTATGCTGCTCCAGAGgttt---ttttttttttttttgtatcactgtgggactatatcttcttgctcctttgcatgcaat-attttttcttattatagtattatggttcctttgcag

upper sequence: Vv08s0040g00720.t01 (Vitis vinifera), 5'ss of exon 5
lower sequence: LOC_Os08g37800.1 (Oryza sativa), 5'ss of exon 4
ACGCAATGTCAAAGTTGCAGACTTTGGACTCAGCAATGTGATGCGTGATGGTCATTTTCTCAAAACAAGCTGTGGAAGTCCAAATTATGCTGCTCCTGAGgtat-------gggtcaacttgttatataagttgccaatgaacttgtgaataat-tatgctctgtgtacaatgaaatactgcttgtgcag
    || || ||  |||| ||||||||  | || ||||| |||| |||||| |||||| | || |||||||| || ||||| |||||||||||||| |||||||       |  |||   ||  |    |  | |        ||      ||| | |  |||   || | |   ||  | | | |||||
GTATAACGTAAAGCTTGCTGACTTTGGTTTGAGTAATGTCATGCATGATGGCCATTTTTTAAAGACAAGCTGCGGGAGTCCGAATTATGCTGCTCCAGAGgtattttttttgtatcactgtgagactatatcttcttgctcctttacatgcaatattttttcttattatagtattatggtccctttgcag

upper sequence: Vv08s0040g00720.t01 (Vitis vinifera), 5'ss of exon 5
lower sequence: GRMZM2G180704_T01 (Zea mays), 5'ss of exon 4
ACGCAATGTCAAAGTTGCAGACTTTGGACTCAGCAATGTGATGCGTGATGGTCATTTTCTCAAAACAAGCTGTGGAAGTCCAAATTATGCTGCTCCTGAGgta------------tgggtcaacttgttatataagttgccaatgaacttgtgaataattatgctctgtgtacaatgaaatactgcttgtgcag--------------------
| ||||||| ||  ||||||| |||||  | || ||||| ||||| |||||||||||||| || ||||| ||||| || ||||||||||||||||||||||||            | ||||||   | |||| |     || || |  |   | ||     |  |   |   |  |      | |   || |||                    
ATGCAATGTTAAGATTGCAGATTTTGGCTTAAGTAATGTTATGCGGGATGGTCATTTTCTGAAGACAAGTTGTGGTAGCCCAAATTATGCTGCTCCTGAGgtaagctttctataataggtcaaa--gatataaagaggacccattagatca-gtatggccgtatttcctacccctttgttggcaggcagtacagtatccttttattttctgcag

upper sequence: Vv08s0040g00720.t01 (Vitis vinifera), 5'ss of exon 5
lower sequence: GRMZM2G107867_T04 (Zea mays), 5'ss of exon 3
ACGCAATGTCAAAGTTGCAGACTTTGGACTCAGCAATGTGATGCGTGATGGTCATTTTCTCAAAACAAGCTGTGGAAGTCCAAATTATGCTGCTCCTGAGgtat--gggtcaacttgttatataagttgccaatgaacttgt-----------gaataattatgctctgtg-tacaatgaaatactgcttgtgcag
    ||||| ||| |||| || ||||| || |||||||| |||| |||||| |||||||| || || |||||||| ||||| || ||||||||||| |||||||     ||   ||| | |  |  ||||  ||  | || |             |  |  ||| |   || ||||  |  |   | ||| |||||
GTATAATGTAAAACTTGCGGATTTTGGTCTGAGCAATGTCATGCATGATGGCCATTTTCTGAAGACTAGCTGTGGGAGTCCGAACTATGCTGCTCCAGAGgtattttattcttattgctgtg-agtttgctgatctatttttttttcctttttagaacaccatgtttcttgatacatagtgagtgttcttttgcag

upper sequence: Vv08s0040g00720.t01 (Vitis vinifera), 5'ss of exon 5
lower sequence: AT5G39440.1 (Arabidopsis thaliana), 5'ss of exon 3
ACGCAATGTCAAAGTTGCAGACTTTGGACTCAGCAATGTGATGCGTGATGGTCATTTTCTCAAAACAAGCTGTGGAAGTCCAAATTATGCTGCTCCTGAGgtatg---ggtcaacttgttatataagttg--ccaatgaacttgtgaata-------attatgctctgtgtacaatgaaatactgcttgtgcag
| ||||  | ||  |||  ||||||||| | || ||||| |||| ||||||||||||| | || || || |||||||| || |||||||||||||| |||||||    | | ||| | || |  |  ||      ||||| |||   |||       | |||    |    |||    ||   |  || |  ||
ATGCAACATAAAGATTGTTGACTTTGGATTGAGTAATGTCATGCATGATGGTCATTTTTTAAAGACTAGTTGTGGAAGCCCTAATTATGCTGCTCCAGAGgtataagagattaacatattcttcatttttatttcatgaatttggatatatatttgaagtatcaattactcacacctgaaacttatttatatag

upper sequence: Vv08s0040g00720.t01 (Vitis vinifera), 5'ss of exon 5
lower sequence: PP1S28_12V6.1 (Physcomitrella patens), 5'ss of exon 3
ACGCAATGTCAAAGTTGCAGACTTTGGACTCAGCAATGTGATGCGTGATGGTCATTTTCTCAAAACAAGCTGTGGAAGTCCAAATTATGCTGCTCCTGAGgtatgggtcaa---cttgttatataagttgccaatgaacttgtgaataattatgctctgtgtacaatgaaatactgcttgtgcag-------------------------------------------------------------------------------
    || |||||  |||| || |||||  |   |||||| ||| | || |||||||| |||||||| ||||||||||||||||||||||||||||| ||||| | | || |   ||  ||   |   ||| || ||   |  |   | ||     | |||  |||      |  |   ||||  |                                                                               
GTCTAACGTCAAGATTGCTGATTTTGGGTTATCCAATGTTATGAGGGACGGTCATTTCCTCAAAACTAGCTGTGGAAGTCCAAATTATGCTGCTCCAGAGgttttgctctatgcctgattgccttgtttgacactgttttaattcgtcatgtgattgtgt-cacatgtttctgttttctgtgttgggtgcctgaaccaagttgtaggttttctgtgcccggacacactcctgcttgttgactgttgatattgttgaacatgcag

upper sequence: Vv08s0040g00720.t01 (Vitis vinifera), 5'ss of exon 5
lower sequence: PP1S7_365V6.1 (Physcomitrella patens), 5'ss of exon 3
ACGCAATGTCAAAGTTGCAGACTTTGGACTCAGCAATGTGATGCGTGATGGTCATTTTCTCAAAACAAGCTGTGGAAGTCCAAATTATGCTGCTCCTGAGgtatgggtcaa---cttgttatataagttgccaatgaacttgtgaataattatgctctgtgtacaatgaaatactgcttgtgcag-------------------
| | || |||||  | || || || |||||   |||| | ||| | |||||||| ||||||||||| || || ||||| || |||||||||||||| ||||| |   || |   ||| |  | ||| |     |  | ||| |   | ||  | || ||| ||  |||   | ||| |  |  |                    
ATGGAACGTCAAGATAGCTGATTTCGGACTGTCCAATATTATGAGGGATGGTCACTTTCTCAAAACTAGTTGCGGAAGCCCCAATTATGCTGCTCCAGAGgttttcctccatgccttttcctttaaat--atgacaaccttctc--tgatactactttgtatatgatgtgcttctgatattaaactttagataaagtatctcag

upper sequence: Vv08s0040g00720.t01 (Vitis vinifera), 5'ss of exon 5
lower sequence: EFJ35371 (Selaginella moellendorffii), 5'ss of exon 3
ACGCAATGTCAAAGTTGCAGACTTTGGACTCAGCAATGTGATGCGTGATGGTCATTTTCTCAAAACAAGCTGTGGAAGTCCAAATTATGCTGCTCCTGAGgtatgggtcaacttgttatataagttgccaatgaacttgtgaataattatgctctgtgtacaatgaaatactgcttgtgcag
  ||||||| ||  |||| ||||||||  | || ||| | ||||| ||||| || ||||| ||||| ||||||||||||||||| ||||| ||||| |||||| |  || ||||  | | |   |    || |   ||     | |                                    
GTGCAATGTGAAGATTGCGGACTTTGGCTTGAGTAATATCATGCGAGATGGACACTTTCTGAAAACGAGCTGTGGAAGTCCAAACTATGCCGCTCCAGAGgtaagcttcgactttcttttttcctctagaaagccttttcctttcag-----------------------------------

upper sequence: Vv08s0040g00720.t01 (Vitis vinifera), 5'ss of exon 5
lower sequence: EFJ16445 (Selaginella moellendorffii), 5'ss of exon 3
ACGCAATGTCAAAGTTGCAGACTTTGGACTCAGCAATGTGATGCGTGATGGTCATTTTCTCAAAACAAGCTGTGGAAGTCCAAATTATGCTGCTCCTGAGgtatgggtcaacttgtta-tataagttgc-caatgaacttgtgaataattatgctctgtgtacaatgaaatactgcttgtgcag
| ||| ||||||  | || || ||||| || |||||  | ||||| || || || ||||| |||||||||||||||||||| || ||||||||||| |||||      ||   | | | ||||||||     ||   || || | |     |  ||| | | |||| | |              
ATGCAGTGTCAAGATAGCGGATTTTGGCCTGAGCAACATTATGCGAGACGGACACTTTCTGAAAACAAGCTGTGGAAGTCCGAACTATGCTGCTCCAGAGgt------cagtatatcagtataagttttgttataggctcgtcattctaagttgtctttct-caatcacag-------------

upper sequence: Vv08s0040g00720.t01 (Vitis vinifera), 5'ss of exon 5
lower sequence: EFJ10631 (Selaginella moellendorffii), 5'ss of exon 4
ACGCAATGTCAAAGTTGCAGACTTTGGACTCAGCAATGTGATGCGTGATGGTCATTTTCTCAAAACAAGCTGTGGAAGTCCAAATTATGCTGCTCCTGAGgtatgggtcaacttgttatataagttgccaatgaacttgtgaataattatgctctgtgtacaatgaaatactgcttgtgcag
  ||||||| ||  |||| ||||||||  | || ||| | ||||| ||||| || ||||| ||||| ||||||||||||||||| ||||| ||||| |||||| |  || || |  | | |   |    || |   ||     | |                                    
GTGCAATGTGAAGATTGCGGACTTTGGCTTAAGTAATATCATGCGAGATGGACACTTTCTGAAAACGAGCTGTGGAAGTCCAAACTATGCCGCTCCAGAGgtaagcttcgacattcttttttcctctagaaagccttttcctttcag-----------------------------------

upper sequence: Vv08s0040g00720.t01 (Vitis vinifera), 5'ss of exon 5
lower sequence: EFJ17922 (Selaginella moellendorffii), 5'ss of exon 3
ACGCAATGTCAAAGTTGCAGACTTTGGACTCAGCAATGTGATGCGTGATGGTCATTTTCTCAAAACAAGCTGTGGAAGTCCAAATTATGCTGCTCCTGAGgtatgggtcaacttgttatataagttgccaatgaacttgtgaataattatgctctgtgtacaatgaaatactgcttgtgcag
| ||| ||||||  | || || ||||| || |||||  | ||||| || ||||| ||||| |||||||||||||||||||| || ||||||||||| |||||  |  |    |    |||    ||| || |   || || | |     |  ||| | | |||| | |              
ATGCAGTGTCAAGATCGCGGATTTTGGCCTGAGCAACATTATGCGAGACGGTCACTTTCTGAAAACAAGCTGTGGAAGTCCGAACTATGCTGCTCCAGAGgtcagtata---tcaggataagttttgtca-taggctcgtcattctaagttgtctttct-caatcacag-------------

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ACGCAATGTCAAAGTTGCAGACTTTGGACTCAGCAATGTGATGCGTGATGGTCATTTTCTCAAAACAAGCTGTGGAAGTCCAAATTATGCTGCTCCTGAGgtatgggtcaacttgttatataagttgccaatgaacttgtgaataattatgctctgtgtacaatgaaatactgcttgtgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT