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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTTGCCTTCCTCAAGTCAAGAAAAGGATTTGTTCGCATAGCCATGGAGATGGGACGGCCCTTGGTTCCAGTTTTCTGCTTTGGTCAGgtatttgttttcttccccaccaggtatttggccatctgcatagccgactgggtctagcctgatttttcagttgtgtctattttacatttgttaatttcaa...

Basic information

species Vitis vinifera
transcript Vv04s0044g01940.t01
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv04s0044g01940.t01 (Vitis vinifera), 5'ss of exon 6
lower sequence: GLYMA16G21960.2 (Glycine max), 5'ss of exon 6
GTTGCCTTCCTCAAGTCAAGAAAAGGATTTGTTCGCATAGCCATGGAGATGGGACGGCCCTTGGTTCCAGTTTTCTGCTTTGGTCAGgtatttgttttcttccccaccaggtatttggccatctgcatagccgactgggtctagcctgatttttcagttgtgtctattttacatttgttaatttcaa-
 ||||||| || || ||||| | ||||||||| |||||||| ||||||| ||||   ||| |||||||||||||||||||||||||||||||| ||| |||  |||       | |   | |  | | |    ||      |   ||||||      |  |  ||     | |||  | || |  || 
ATTGCCTTTCTTAAATCAAGGAGAGGATTTGTCCGCATAGCAATGGAGAAGGGAAAACCCCTGGTTCCAGTTTTCTGCTTTGGTCAGgtatttattt-cttgtccatttatcttatattcttaaggaaaaatcacgcaccatttgctgattccaagatattagctgcagaaaattcttaaactaaaat

upper sequence: Vv04s0044g01940.t01 (Vitis vinifera), 5'ss of exon 6
lower sequence: GLYMA09G32790.1 (Glycine max), 5'ss of exon 6
GTTGCCTTCCTCAAGTCAAGAAAAGGATTTGTTCGCATAGCCATGGAGATGGGACGGCCCTTGGTTCCAGTTTTCTGCTTTGGTCAGgtatttgttttcttccccaccaggtatt-tggccatctgcatagccgactgggtctagcctgatttttcagttgtgtctattttacatttgttaatttcaa---
 ||||||  || ||  ||||||  |||||||| |||||||| |||||||  |||   ||| |||||||||||||||||||||||||||||||| |||  |  ||    |  | || |    |     | | |   | |  | | || ||| |      ||   |  |    | |  ||||||  | ||   
ATTGCCTATCTTAAAGCAAGAAGGGGATTTGTCCGCATAGCAATGGAGAAAGGAAAACCCCTGGTTCCAGTTTTCTGCTTTGGTCAGgtatttctttattgtccatgtatattttattcttaaggaaaaatcttgccgcattttgc-tgactcccagattagctgcag---aaaactgttaaactaaaatg

upper sequence: Vv04s0044g01940.t01 (Vitis vinifera), 5'ss of exon 6
lower sequence: GLYMA01G36010.1 (Glycine max), 5'ss of exon 3
GTTGCCTTCCTCAAGTCAAGAAAAGGATTTGTTCGCATAGCCATGGAGATGGGACGGCCCTTGGTTCCAGTTTTCTGCTTTGGTCAGgtatttgttttcttccccaccaggtatttggccat--ctgcatagccgactgggtctagcctgatttttcagttgtgtctattttacatttgttaatttcaa
 |||| ||||| ||| |||||| ||||||||| ||| |||| |||| ||  ||    || ||||||||||| ||||||||||||||||||||| ||| |      | ||| | |  |   |    |  | |  |   ||    | |  |   | |       | |||   |  |||    | || ||  
ATTGCTTTCCTTAAGGCAAGAAGAGGATTTGTCCGCGTAGCAATGGTGAAAGGCAAACCTTTGGTTCCAGTCTTCTGCTTTGGTCAGgtatttatttccgatggaatcagatttcagtttacaattcaacaatcatttgtaatttgtttctctctctctacatttcttcctctcatactctgatatc--

upper sequence: Vv04s0044g01940.t01 (Vitis vinifera), 5'ss of exon 6
lower sequence: GLYMA16G21970.1 (Glycine max), 5'ss of exon 6
GTTGCCTTCCTCAAGTCAAGAAAAGGATTTGTTCGCATAGCCATGGAGATGGGACGGCCCTTGGTTCCAGTTTTCTGCTTTGGTCAGgtatttgttttcttccccaccaggtatt--tggccatctgcatagccg-actgggtctagcctgatttttcagttgtgtctattttacatttgttaatttcaa
 ||||||| || |||  ||||| ||||||||| ||||||||  || | ||||| |  ||| | |||||||||||||||||||| ||||||||| ||        |   |    ||  |   | | |   ||     ||   || ||     |  || || | ||  ||   ||| | |  | |  |||  
ATTGCCTTTCTTAAGCAAAGAAGAGGATTTGTCCGCATAGCATTGCAAATGGGCCTACCCCTTGTTCCAGTTTTCTGCTTTGGCCAGgtatttcttgagcagagctgtattctttaattttcttttatttaattataccatgtatatatccaacttgcaatcgttgctggcttaaaat-atcagcttc--

upper sequence: Vv04s0044g01940.t01 (Vitis vinifera), 5'ss of exon 6
lower sequence: AT3G51520.1 (Arabidopsis thaliana), 5'ss of exon 5
GTTGCCTTCCTCAAGTCAAGAAAAGGATTTGTTCGCATAGCCATGGAGATGGGACGGCCCTTGGTTCCAGTTTTCTGCTTTGGTCAGgtatttgtttt--cttccccaccaggtatttggccatctgcatagccgactgggtctagcctgatttttcagttgtgtctattttacatttgt-taatttcaa--------------------------------------------------------
  || ||||||       |||| ||||||||| ||||||||||||||   |||  | ||  |||||||||| ||||||||||||||||||   |       || | ||| | || ||  ||  |||   |||  | ||   | || |   |  | |||      ||  ||   ||      | |||  ||                                                        
AATGTCTTCCTTTCAAGGAGAAGAGGATTTGTGCGCATAGCCATGGAACAGGGGAGCCCTCTGGTTCCAGTATTCTGCTTTGGTCAGgtaggggaaaagagttgctcacaaagtgttatgc--tctatgtagttgtctttatgtacctgaaactctcaaactaatcagttggtcagaaacgtgattcgaattttgtaccgtttctgcattccagttttacgtttcatatgtgcgtttcttttgcag

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|110410772|gb|EC976464.1|EC976464
EST:     TAGCCATGGAGATGGGACGGCCCTTGGTTCCAGTTTTCTGCTTTGGTCAG                         TCTCGCGTCTATAAGTGGTGGAAACCTGGTGGGAACTTGTACCTGCAATTT
genomic: TAGCCATGGAGATGGGACGGCCCTTGGTTCCAGTTTTCTGCTTTGGTCAGgtatttgttt ... tgtactacagTCTCGCGTCTATAAGTGGTGGAAACCTGGTGGGAACTTGTACCTGCAATTT
EST: gi|110718650|gb|EE095723.1|EE095723
EST:     ACCCATGGAGATGGGAAGGCCCTTTGGTTCCA-TTTTCTGCTTTGGTCAG                         TCTCCCGTCCTATAA-TGGTGGAAACCTGG
genomic: AGCCATGGAGATGGGACGGCCCTT-GGTTCCAGTTTTCTGCTTTGGTCAGgtatttgttt ... tgtactacagTCTCGCGTC-TATAAGTGGTGGAAACCTGG
EST: gi|110405821|gb|EC971375.1|EC971375
EST:     TAGCCATGGAGATGGGACGGCCCTTAGTTCCAGTTTTCTGCTTTGGTCAG                         TCTCACGTCTATAAGTGGTGGAAACCTGGTGGGAACTTGTACCTGCAATTT
genomic: TAGCCATGGAGATGGGACGGCCCTTGGTTCCAGTTTTCTGCTTTGGTCAGgtatttgttt ... tgtactacagTCTCGCGTCTATAAGTGGTGGAAACCTGGTGGGAACTTGTACCTGCAATTT
EST: gi|110715904|gb|EE094489.1|EE094489
EST:     TAGCCATGGAGATGGGACGGCCCTTGGTTCCAGTTTTCTGCTTTGGTCAG                         TCTCACGTCTATAAGTGGTGGAAACCTGGTGGGAACTTGTACCTGCAATTT
genomic: TAGCCATGGAGATGGGACGGCCCTTGGTTCCAGTTTTCTGCTTTGGTCAGgtatttgttt ... tgtactacagTCTCGCGTCTATAAGTGGTGGAAACCTGGTGGGAACTTGTACCTGCAATTT
EST: gi|30131047|gb|CB916386.1|CB916386
EST:     TAGCCATGGAGATGGGACGGCCCTTGGTTCCAGTTTTCTGCTTTGGTCAG                         TCTCGCGTCTATAAGTGGTGGAAACCTGGTGGGAACTTGTACCTGCAATTT
genomic: TAGCCATGGAGATGGGACGGCCCTTGGTTCCAGTTTTCTGCTTTGGTCAGgtatttgttt ... tgtactacagTCTCGCGTCTATAAGTGGTGGAAACCTGGTGGGAACTTGTACCTGCAATTT
EST: gi|156739053|gb|EV243166.1|EV243166
EST:     TAGCCATGGAGATGGGACGGCCCTTGGTTCCAGTTTTCTGCTTTGGTCAG                         TCTCGCGTCTATAAGTGGTGGAAACCTGGTGGGAACTTGTACCTGCAATTT
genomic: TAGCCATGGAGATGGGACGGCCCTTGGTTCCAGTTTTCTGCTTTGGTCAGgtatttgttt ... tgtactacagTCTCGCGTCTATAAGTGGTGGAAACCTGGTGGGAACTTGTACCTGCAATTT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTTGCCTTCCTCAAGTCAAGAAAAGGATTTGTTCGCATAGCCATGGAGATGGGACGGCCCTTGGTTCCAGTTTTCTGCTTTGGTCAGgtatttgttttcttccccaccaggtatttggccatctgcatagccgactgggtctagcctgatttttcagttgtgtctattttacatttgttaatttcaa

- - - - - - - - - - - - - - - - - - - -  CATGGA
- - - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - - - - - - - - - - -  GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ccccacc