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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGAGCTTGGTATTGGAATAGTAGCATATAGCCCTCTTGGTCGTGGATTCTTTGGTGGGAAGGCAGTTGTGGAGAGCTTGCCCACTCAGAGTATCCTGgtcagtaactatagataaaaatttagtaatttgaatataggttcttctccgtctgagttttttttacttcttttgatgggcaaagaacatcgatcatttttttagcattggaatcagttatttaaattcatactgacattcctgccacag

Basic information

species Vitis vinifera
transcript Vv05s0020g04130.t01
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv05s0020g04130.t01 (Vitis vinifera), 5'ss of exon 5
lower sequence: GRMZM5G813143_T02 (Zea mays), 5'ss of exon 5
AGAGCTTGGTATTGGAATAGTAGCATATAGCCCTCTTGGTCGTGGATTCTTTGGTGGGAAGGCAGTTGTGGAGAGCTTGCCCACTCAGAGTATCCTGgtcagtaactatagataaaaatttagtaatttgaatataggttcttctccgtctgagttttttttacttcttttgatgggcaaagaacatcgatcatttttttagcattggaatcagttatttaaattcatactgacattcctgccacag
 ||||||||||||||||||||  |||||||||| ||||| ||||| ||||||| ||| | ||||| ||| ||  |  | ||  |  | ||| |  |||| | | |  ||  | |  |   || ||||||   || ||     |    ||  || | | || |   |       || |    |||||| |    |||||  | |  |                                         
GGAGCTTGGTATTGGAATAGTTCCATATAGCCCACTTGGCCGTGGCTTCTTTGCTGGCAGGGCAGCTGTAGAACGTGTTCCATCAGAAAGTCTATTGgtaaatgaa-atttacactatcgtaataattttc-tacagtaatgttattgttagactatgttgtgtat------gtgtgtgtggaacatgg----tttttaaaacggtatg--------------------------------------

upper sequence: Vv05s0020g04130.t01 (Vitis vinifera), 5'ss of exon 5
lower sequence: GLYMA10G38900.1 (Glycine max), 5'ss of exon 5
AGAGCTTGGTATTGGAATAGTAGCATATAGCCCTCTTGGTCGTGGATTCTTTGGTGGGAAGGCAGTTGTGGAGAGCTTGCCCACTCAGAGTATCCTGgtca-gtaactatagataaaaatttagtaatttgaatataggttcttctccgtctgagttttttttacttcttttgatgggcaaagaacatcgatcatttttttagcattggaatcagttatttaaattcatactgacattcctgccacag
| | ||||| ||||||||||| |||||||| |||||||||||||| || ||||  || |||||||| || ||||  ||||| | ||||||  | ||||| | | | |||  |  ||     | |||  |    |  || || |  |  |||| | |       |  |   |       || |  |||  | |  || | ||      |   |    |||| || ||  |  ||   || |||  ||||
ACAACTTGGGATTGGAATAGTGGCATATAGTCCTCTTGGTCGTGGCTTTTTTGCAGGAAAGGCAGTGGTAGAGACTTTGCCTAGTCAGAGCTTGCTGgtaatgcagctagtgtcaa----cttgtagctct--tccagattatgatg-gtctaaataacaccaatataggtcat---acatatcacactgttagttctatttctgcagtggttgtctattgaattttct--tgttgtttctgtgacag

upper sequence: Vv05s0020g04130.t01 (Vitis vinifera), 5'ss of exon 5
lower sequence: GLYMA10G38890.2 (Glycine max), 5'ss of exon 5
AGAGCTTGGTATTGGAATAGTAGCATATAGCCCTCTTGGTCGTGGATTCTTTGGTGGGAAGGCAGTTGTGGAGAGCTTGCCCACTCAGAGTATCCTGgtcagtaactatagataaaaatttagtaatttgaatataggttcttctccgtctgag--ttttttttacttcttttgatgggcaaagaacatcgatcatttttttagc-att---ggaatca----gttatttaaattcatactgac--attcctgccacag--------------------------------
 || ||||| ||||||||||| ||||||||||||||||||| ||| || || |  ||||||||||  || ||||  ||||| | ||||||    |||||  ||| |||  ||        ||||||    | |  |||||    |   | ||     ||||  ||   ||| | |     |||     | | |||  |||  | | |||    | ||||     || | |    |   ||| |   ||||||||                                     
GGAACTTGGGATTGGAATAGTGGCATATAGCCCTCTTGGTCATGGCTTTTTCGCAGGGAAGGCAGCGGTAGAGACTTTGCCTAGTCAGAGCGCACTGgtatgtagctagtgac-------tagtaaaccaatttcaggtttgcatgaatttgtagccttttcctataacttgtcaaaataaaattgactggttcaaatttcaaaccatttgtaggatcatatgattgtgttggataggactaatctattcctgcagggattgtctattgaattttgatgtttctgatacag

upper sequence: Vv05s0020g04130.t01 (Vitis vinifera), 5'ss of exon 5
lower sequence: PP1S158_112V6.2 (Physcomitrella patens), 5'ss of exon 6
AGAGCTTGGTATTGGAATAGTAGCATATAGCCCTCTTGGTCGTGGATTCTTTGGTGGGAAGGCAGTTGTGGAGAG-CTTGCCCACTCAGAGTATCCTGgtcagtaactatagataaaaatttagtaatttgaatataggttcttctccgtctgagttttttttacttcttttgatgggcaaagaacatcgatcatttttttagcattggaatcagttatttaaattcatactgacattcctgccacag
 |||||||| |||||||||||  | |||||||||||||| || ||||||||   |||||| || || || ||||  || |   |   ||| ||||  | |  |||| | |   | ||   ||   ||  ||    ||       ||   |       |||||  |||  |||     ||| |||    |  |   | || |||   |  |      | ||     || |  | |              
GGAGCTTGGAATTGGAATAGTGCCCTATAGCCCTCTTGGGCGAGGATTCTTCTCTGGGAAAGCCGTCGTTGAGAAACTGGAAGAGCAAGACTATC--GATTCgtaagtct---tcaattcttcacaacctgctattaataaggcctttattctttcatttttaccttgattttgaaagcacagattgac--ttgctcttatagtggtaaatgtgaatgtt--ggctcctgatcag-------------

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|33409014|gb|CF214641.1|CF214641
EST:     TCTTTGGTGGGAAGGCAGTTGTGGAGAGCTTGCCCACTCAGAGTATCCTG                         ACTATGCATCCAAGGTTCACTGGAGAGAATTTAGAGAAGAACAAACTTATA
genomic: TCTTTGGTGGGAAGGCAGTTGTGGAGAGCTTGCCCACTCAGAGTATCCTGgtcagtaact ... cctgccacagACTATGCATCCAAGGTTCACTGGAGAGAATTTAGAGAAGAACAAACTTATA
EST: gi|30254580|gb|CB971325.1|CB971325
EST:     TCTTTGGTGGGAAGGCAGTTGTGGAGAGCTTGCCCACTCAGAGTATCCTG                         ACTATGCATCCAAGGTTCACTGGAGAGAATTTAGAGAAGAACAAACTTATA
genomic: TCTTTGGTGGGAAGGCAGTTGTGGAGAGCTTGCCCACTCAGAGTATCCTGgtcagtaact ... cctgccacagACTATGCATCCAAGGTTCACTGGAGAGAATTTAGAGAAGAACAAACTTATA
EST: gi|33408926|gb|CF214553.1|CF214553
EST:     TCTTTGGTGGGAAGGCAGTTGTGGAGAGCTTGCCCACTCAGAGTATCCTG                         ACTATGCATCCAAGGTTCACTGGAGAGAATTTAGAGAAGAACAAACTTATA
genomic: TCTTTGGTGGGAAGGCAGTTGTGGAGAGCTTGCCCACTCAGAGTATCCTGgtcagtaact ... cctgccacagACTATGCATCCAAGGTTCACTGGAGAGAATTTAGAGAAGAACAAACTTATA
EST: gi|110414170|gb|EC979996.1|EC979996
EST:     TCTTTGGTGGGAAGGCAGTTGTGGAGAGCTTGCCCACTCAGAGTATCCTG                         ACTATGCATCCAAGGTTCACTGGAGAGAATTTAGAGAAGAACAAACTTATA
genomic: TCTTTGGTGGGAAGGCAGTTGTGGAGAGCTTGCCCACTCAGAGTATCCTGgtcagtaact ... cctgccacagACTATGCATCCAAGGTTCACTGGAGAGAATTTAGAGAAGAACAAACTTATA
EST: gi|32458980|gb|CD800154.1|CD800154
EST:     TCTTTGGTGGGAAGGCAGTTGTGGAGAGCTTGCCCACTCAGAGTATCCTG                         ACTATGCATCCAAGGTTCACTGGAGAGAATTTAGAGAAGAACAAACTTATA
genomic: TCTTTGGTGGGAAGGCAGTTGTGGAGAGCTTGCCCACTCAGAGTATCCTGgtcagtaact ... cctgccacagACTATGCATCCAAGGTTCACTGGAGAGAATTTAGAGAAGAACAAACTTATA
EST: gi|30254582|gb|CB971327.1|CB971327
EST:     TCTTTGGTGGGAAGGCAGTTGTGGAGAGCTTGCCCACTCAGAGTATCCTG                         ACTATGCATCCAAGGTTCACTGGAGAGAATTTAGAGAAGAACAAACTTATA
genomic: TCTTTGGTGGGAAGGCAGTTGTGGAGAGCTTGCCCACTCAGAGTATCCTGgtcagtaact ... cctgccacagACTATGCATCCAAGGTTCACTGGAGAGAATTTAGAGAAGAACAAACTTATA
EST: gi|46918219|gb|CN547548.1|CN547548
EST:     TCTTTGGTGGGAAGGCAGTTGTGGAGAGCTTGCCCACTCAGAGTATCCTG                         ACTATGCATCCAAGGTTCACTGGAGAGAATTTAGAGAAGAACAAACTTATA
genomic: TCTTTGGTGGGAAGGCAGTTGTGGAGAGCTTGCCCACTCAGAGTATCCTGgtcagtaact ... cctgccacagACTATGCATCCAAGGTTCACTGGAGAGAATTTAGAGAAGAACAAACTTATA
EST: gi|33407206|gb|CF212833.1|CF212833
EST:     TCTTTGGTGGGAAGGCAGTTGTGGAGAGCTTGCCCACTCAGAGTATCCTG                         ACTATGCATCCAAGGTTCACTGGAGAGAATTTAGAGAAGAACAAACTTATA
genomic: TCTTTGGTGGGAAGGCAGTTGTGGAGAGCTTGCCCACTCAGAGTATCCTGgtcagtaact ... cctgccacagACTATGCATCCAAGGTTCACTGGAGAGAATTTAGAGAAGAACAAACTTATA
EST: gi|33406858|gb|CF212485.1|CF212485
EST:     TCTTTGGTGGGAAGGCAGTTGTGGAGAGCTTGCCCACTCAGAGTATCCTG                         ACTATGCATCCAAGGTTCACTGGAGAGAATTTAGAGAAGAACAAACTTATA
genomic: TCTTTGGTGGGAAGGCAGTTGTGGAGAGCTTGCCCACTCAGAGTATCCTGgtcagtaact ... cctgccacagACTATGCATCCAAGGTTCACTGGAGAGAATTTAGAGAAGAACAAACTTATA
EST: gi|33406944|gb|CF212571.1|CF212571
EST:     TCTTTGGTGGGAAGGCAGTTGTGGAGAGCTTGCCCACTCAGAGTATCCTG                         ACTATGCATCCAAGGTTCACTGGAGAGAATTT
genomic: TCTTTGGTGGGAAGGCAGTTGTGGAGAGCTTGCCCACTCAGAGTATCCTGgtcagtaact ... cctgccacagACTATGCATCCAAGGTTCACTGGAGAGAATTT
EST: gi|110373812|gb|EC938182.1|EC938182
EST:     TCTTTGGTGGGAAGGCAGTTGTGGAGAGCTTGCCCACTCAGAGTATCCTG                         ACTATGCATCCAAGGTTCACTGGAGAGAATTTAGAGAAGAACAAACTTATA
genomic: TCTTTGGTGGGAAGGCAGTTGTGGAGAGCTTGCCCACTCAGAGTATCCTGgtcagtaact ... cctgccacagACTATGCATCCAAGGTTCACTGGAGAGAATTTAGAGAAGAACAAACTTATA
EST: gi|30254500|gb|CB971245.1|CB971245
EST:     TCTTTGGTGGGAAGGCAGTTGTGGAGAGCTTGCCCACTCAGAGTATCCTG                         ACTATGCATCCAAGGTTCACTGGAGAGAATTTAGAGAAGAACAAACTTATA
genomic: TCTTTGGTGGGAAGGCAGTTGTGGAGAGCTTGCCCACTCAGAGTATCCTGgtcagtaact ... cctgccacagACTATGCATCCAAGGTTCACTGGAGAGAATTTAGAGAAGAACAAACTTATA
EST: gi|110374215|gb|EC938843.1|EC938843
EST:     TCTTTGGTGGGAAGGCAGTTGTGGAGAGCTTGCCCACTCAGAGTATCCTG                         ACTATGCATCCAAGGTTCACTGGAGAGAATTTAGAGAAGAACAAACTTATA
genomic: TCTTTGGTGGGAAGGCAGTTGTGGAGAGCTTGCCCACTCAGAGTATCCTGgtcagtaact ... cctgccacagACTATGCATCCAAGGTTCACTGGAGAGAATTTAGAGAAGAACAAACTTATA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGAGCTTGGTATTGGAATAGTAGCATATAGCCCTCTTGGTCGTGGATTCTTTGGTGGGAAGGCAGTTGTGGAGAGCTTGCCCACTCAGAGTATCCTGgtcagtaactatagataaaaatttagtaatttgaatataggttcttctccgtctgagttttttttacttcttttgatgggcaaagaacatcgatcatttttttagcattggaatcagttatttaaattcatactgacattcctgccacag

- - - - - - - - - - - - - - - - - - - - - - - - -  TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT