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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TCCCTCAAAAACATTGATAACCCCTGTTCAGTGCAAAAATTTGTGGAGGCAATTCAAGATGGAGACAGAGTACAGTGTAACTCAGGCCATTGCTGCTCAGgcatgatatcatatatttaactacttttagcattctttatatcaatttccagttatttttttgttcccctgaaatatgagaaccagcttgggctggatat...

Basic information

species Vitis vinifera
transcript Vv09s0002g02200.t01
intron # 20
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv09s0002g02200.t01 (Vitis vinifera), 5'ss of exon 20
lower sequence: GRMZM5G873287_T01 (Zea mays), 5'ss of exon 2
TCCCTCAAAAACATTGATAACCCCTGTTCAGTGCAAAAATTTGTGGAGGCAATTCAAGATGGAGACAGAGTACAGTGTAACTCAGGCCATTGCTGCTCAGgcatgatatcatat--atttaactactt--ttagcattctttatatcaatttccagttatttttttgtt----cccctgaaatatgagaaccagcttgggctggatat--------------------------------------------------------------------------
       || || || || |||||||| ||||||||||||||||||||||||||||||   || || || || |  || ||||| ||| | |||||||||| ||     ||| |  |||  || | ||   |   ||   |  |||  |   |  ||   |||  | |      ||||  | | ||   |  |       ||    ||                                                                          
CGAGGAGAAGACTTTAATTACCCCTGTGCAGTGCAAAAATTTGTGGAGGCAATTCAAGGCTGAAACTGAATATACAGTGACTCAAGCCTTAGCTGCTCAGgtatctccacatttccattccaccagttaactgatatgtgtgctattgacaccttgtggatttcatctcaaaatccctctattttgtttattactcaatactcatgattttcttgggaagtgggactggttcacttaattagagacgatctatctgctaaacattactgttgccttgatcag

upper sequence: Vv09s0002g02200.t01 (Vitis vinifera), 5'ss of exon 20
lower sequence: AC196426.3_FGT007 (Zea mays), 5'ss of exon 19
TCCCTCAAAAACATTGATAACCCCTGTTCAGTGCAAAAATTTGTGGAGGCAATTCAAGATGGAGACAGAGTACAGTGTAACTCAGGCCATTGCTGCTCAGgcatgatatcatat--atttaactactt--ttagcattctttat-atcaatttccagttatttttttgtt-cccctgaaatatgagaaccagcttgggctggatat----------------------------------------------------------------------------
|      || || || || |||||||| |||||||||||||||||||||||||||||    || || || || |  || ||||| ||||| |||||||||| ||     | | |  |||  || | ||   |   ||    |||   ||  ||   | | |  |||      ||||  | | ||   |  |  |  |  |   |                                                                              
TGAGGAGAAGACTTTAATTACCCCTGTGCAGTGCAAAAATTTGTGGAGGCAATTCAAAGCTGAAACTGAATATACAGTCACTCAAGCCATAGCTGCTCAGgtatctccacgtttccattccaccagttaactgatatgtggtattgacaccttgtggatgtcatttcaaaatccctctattttgtttattacttatgattttttgggaagtgggaatgacccacttaaataaatattaaagtttgagaagatctatctgctaattactgttgccttgatcag

upper sequence: Vv09s0002g02200.t01 (Vitis vinifera), 5'ss of exon 20
lower sequence: GLYMA08G20610.1 (Glycine max), 5'ss of exon 20
TCCCTCAAAAACATTGATAACCCCTGTTCAGTGCAAAAATTTGTGGAGGCAATTCAAGATGGAGACAGAGTACAGTGTAACTCAGGCCATTGCTGCTCAGgcatgatatcatatatt-taactacttttagcattctttatatcaatttccagttatttttttgttcccctgaaatatgagaaccagcttgggctggatat
  |||| ||||||||||| || ||||| ||||||||   ||||||||||||||||||||  |||||||||||||||||  ||||||||||| |||| ||||||||||  ||||  || | |  || |||   |||  || |   ||     |    |||  |   |    | | ||||       |  ||  |        
ATCCTCTAAAACATTGATTACACCTGTCCAGTGCAAGTCTTTGTGGAGGCAATTCAAGACAGAGACAGAGTACAGTGTCTCTCAGGCCATTTCTGCACAGgcatgatg-cataagttatcaagacatttga-atttcttgttggaa-----aacattttactaactgatgtaatatattctttttattttcag--------

upper sequence: Vv09s0002g02200.t01 (Vitis vinifera), 5'ss of exon 20
lower sequence: GLYMA07G01230.1 (Glycine max), 5'ss of exon 20
TCCCTCAAAAACATTGATAACCCCTGTTCAGTGCAAAAATTTGTGGAGGCAATTCAAGATGGAGACAGAGTACAGTGTAACTCAGGCCATTGCTGCTCAGgcatgatatcatatatt-taactacttttagcattctttatatcaatt-tccagttatttttttgttcccctgaaatatgagaaccagcttgggctggatat
  |||| ||||||||||| || ||||| ||||||||   ||||||||||||||||||||  |||||||||||||||||  ||||||||||| |||| ||||||||||  |||| ||| | |  || |||    |||||  |   ||   |     |||||||   |     || |||||      | |  |   | |     
ATCCTCTAAAACATTGATTACACCTGTCCAGTGCAAGTCTTTGTGGAGGCAATTCAAGACAGAGACAGAGTACAGTGTCTCTCAGGCCATTTCTGCACAGgcatgatg-cataaattatcaagacatttgaatttcttgttggaaaacatattactatttttacttattgatgtaatatattcttctgtattttcag-----

upper sequence: Vv09s0002g02200.t01 (Vitis vinifera), 5'ss of exon 20
lower sequence: GLYMA13G42650.1 (Glycine max), 5'ss of exon 21
TCCCTCAAAAACATTGATAACCCCTGTTCAGTGCAAAAATTTGTGGAGGCAATTCAAGATGGAGACAGAGTACAGTGTAACTCAGGCCATTGCTGCTCAGgcatgatatcatatatttaactacttttagcattctttatatcaatttccagttatttttttgttcccctgaaatatgagaaccagcttgggctggatat---
 ||||| ||||||||||| || ||||| || ||||||   ||||||||||||||||||||||||||||| || |||||  ||||||||||| |||| |||| || || |  | |     | || |||||  ||| |  |  |   | |     ||      | |  |  ||||| || | ||  |   |       |||    
ACCCTCTAAAACATTGATCACACCTGTCCAATGCAAATCCTTGTGGAGGCAATTCAAGATGGAGACAGAATATAGTGTCTCTCAGGCCATTTCTGCACAGgtataatgttctgtcc---attatttttatgattttcaaggttcctctatttataggaaaatctatcattgaaaaattataagaaatataattcctataaatt

upper sequence: Vv09s0002g02200.t01 (Vitis vinifera), 5'ss of exon 20
lower sequence: GLYMA15G02780.1 (Glycine max), 5'ss of exon 20
-----TCCCTCAAAAACATTGATAACCCCTGTTCAGTGCAAAAATTTGTGGAGGCAATTCAAGATGGAGACAGAGTACAGTGTAACTCAGGCCATTGCTGCTCAGgcatgatatcatatatttaactacttttagcattctttatatcaatttccagttatttttttgttcccctgaaatatgagaaccagcttgggctggatat
      ||||| ||||||||||| || || || ||||| |||   ||||||||||||||||||||||||||||| ||  ||||  ||||||||||| |||| |||||||||| |  ||||    | |  |||||  ||| |      |||  | |   ||||| |  |     ||   ||   | ||  |               
GTACCGCCCTCTAAAACATTGATCACACCCGTCCAGTGTAAATCCTTGTGGAGGCAATTCAAGATGGAGACAGAATATTGTgtctctcaggccatttctgcacaggcatgatgttctatac---attgtttttataatttt------caaggttcctctatttataggaaaatctattattgaaaaatta---------------

Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|30127826|gb|CB913165.1|CB913165
EST:     AATTCAAGATGGAGACAGAGTACAGTGTAACTCAGGCCATTGCTGCTCAG                         GAAGCCAACAAGCGTAATAACAACTGGTTACCACCTCCATGGGCAATTGTT
genomic: AATTCAAGATGGAGACAGAGTACAGTGTAACTCAGGCCATTGCTGCTCAGgcatgatatc ... caattatcagGAAGCCAACAAGCGTAATAACAACTGGTTACCACCTCCATGGGCAATTGTT
EST: gi|87583837|gb|DY473232.1|DY473232
EST:     AATTCAAGATGGAGACAGAGTACAGTGTAACTCAGGCCATTGCTGCTCAG                         GAAGCCAACAAGCGTAATAACAACTGGTTACCACCTCCATGGGCAATTGTT
genomic: AATTCAAGATGGAGACAGAGTACAGTGTAACTCAGGCCATTGCTGCTCAGgcatgatatc ... caattatcagGAAGCCAACAAGCGTAATAACAACTGGTTACCACCTCCATGGGCAATTGTT
EST: gi|161721258|gb|FC070023.1|FC070023
EST:     AATTCAAGATGGAGACAGAGTACAGTGTAACTCAGGCCATTGCTGCTCAG                         GAAGCCAACAAGCGTAATAACAACTGGTTACCACCTCCATGGGCAATTGTT
genomic: AATTCAAGATGGAGACAGAGTACAGTGTAACTCAGGCCATTGCTGCTCAGgcatgatatc ... caattatcagGAAGCCAACAAGCGTAATAACAACTGGTTACCACCTCCATGGGCAATTGTT
EST: gi|110375865|gb|EC940885.1|EC940885
EST:     AATTCAAGATGGAGACAGAGTACAGTGTAACTCAGGCCATTGCTGCTCAG                         GAAGCCAACAAGCGTAATAACAACTGGTTACCACCTCCATGGGCAATTGTT
genomic: AATTCAAGATGGAGACAGAGTACAGTGTAACTCAGGCCATTGCTGCTCAGgcatgatatc ... caattatcagGAAGCCAACAAGCGTAATAACAACTGGTTACCACCTCCATGGGCAATTGTT
EST: gi|30134459|gb|CB919797.1|CB919797
EST:     GTACAGTGTAACTCAGGCCATTGCTGCTCAG                         GAAGCCAACAAGCGTAATAACAACTGGTTACCACCTCCATGGGCAATTGTT
genomic: GTACAGTGTAACTCAGGCCATTGCTGCTCAGgcatgatatc ... caattatcagGAAGCCAACAAGCGTAATAACAACTGGTTACCACCTCCATGGGCAATTGTT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TCCCTCAAAAACATTGATAACCCCTGTTCAGTGCAAAAATTTGTGGAGGCAATTCAAGATGGAGACAGAGTACAGTGTAACTCAGGCCATTGCTGCTCAGgcatgatatcatatatttaactacttttagcattctttatatcaatttccagttatttttttgttcccctgaaatatgagaaccagcttgggctggatat

- - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - -  GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ttcccct
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -atgagaa