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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAAGCTATACCAGTGGAGAAGCTTGTGAACATCCAAATTCCTCCAACACTGAAGAAGCAACTAGTTGATGATTGTGAATTCATTACTCATCTGGGCCAGgtagttatattctaaattcatcacggggcctcaatttttcaccttatcagacgatacatgaatttttttttggaatcgagttgctatatgataatttata...

Basic information

species Vitis vinifera
transcript Vv18s0001g09710.t01
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv18s0001g09710.t01 (Vitis vinifera), 5'ss of exon 6
lower sequence: GLYMA06G04620.1 (Glycine max), 5'ss of exon 6
GAAGCTATACCAG---TGGAGAAGCTTGTGAACATCCAAATTCCTCCAACACTGAAGAAGCAACTAGTTGATGATTGTGAATTCATTACTCATCTGGGCCAGgtagttatattctaaattcatcacggggcctcaatttttcaccttatcagacgatacatgaatttttttttggaatcgagttgctatatga----taatttata--------------------------------------------------------------------------
  | ||  |   |   | || |||||||| ||||| ||||||||||||||||| ||||| ||| |||||||||||||||| || ||||| ||||| ||| ||||||| ||||  |   ||||  |       | |||||   |    ||   || || | | |  |||| ||| | | |  |||| |||   |    || ||| |                                                                           
--ACCTGCAGTTGATCTTGAAAAGCTTGTCAACATTCAAATTCCTCCAACACTAAAGAAACAATTAGTTGATGATTGTGAGTTTATTACCCATCTCGGCAAGgtagtgatatcatc--ttcaatatattaatttaatttacgaag--attgcacaatgcctca--ttttctttaggagcatgttgatattctagatgtagtttgttagttgttacagaacacagttttactttgaaaaagtcattttcaaattgttgaatttatgtttttccatctgcag

upper sequence: Vv18s0001g09710.t01 (Vitis vinifera), 5'ss of exon 6
lower sequence: GLYMA04G04530.1 (Glycine max), 5'ss of exon 5
----GAAGCTATACCAGTGGAGAAGCTTGTGAACATCCAAATTCCTCCAACACTGAAGAAGCAACTAGTTGATGATTGTGAATTCATTACTCATCTGGGCCAGgtagttatattctaaattcatcacggggcctcaatttttcaccttatcagacgatacatgaatttttttttggaatcgagttgctatatga----taatttata-----------------------------------------------------------------------
    | || |   || |   | |||||||| ||||| ||||||||||||||||| ||||| ||| |||||||||||||||| || ||||| ||||| ||| ||||||  ||||  |   ||||  |       | |||||   |    || |  | || | | |  |||| ||| | | | ||||| |||   |    ||  ||                                                                          
ACCTGCAGTTGATCCTG---ACAAGCTTGTTAACATTCAAATTCCTCCAACACTAAAGAAACAATTAGTTGATGATTGTGAGTTTATTACCCATCTCGGCAAGgtagcgatataatc--ttcaatatattaatttaatttacgaag--attactcaatgcctta--ttttctttaggagcaagttgatattccagatgtagcttgctaattgttacagaacacagttttacttccaaaaagtcattttcaagttgaatttatgttttgtcctctgcag
















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|71859464|gb|DT008519.1|DT008519
EST:     TGAAGAAGCAACTAGTTGATGATTGTGAATTCATTACTCATCTGGGCCAG                         CTTGTTAGACTGCCTCGAGCTCCAACTGTTGACAAAATATTGAAGAAGTAT
genomic: TGAAGAAGCAACTAGTTGATGATTGTGAATTCATTACTCATCTGGGCCAGgtagttatat ... cttcttgcagCTTATTAGACTGCCTCGAGCTCCAACTGTTGACAAAATATTGAAGAAGTAT
EST: gi|27584092|gb|CB006787.1|CB006787
EST:     TGAAGAAGCAACTAGTTGATGATTGTGAATTCATTACTCATCTGGGCCAG                         CTTGTTAGACTGCCTCGAGCTCCAACTGTTGACAAAATATTGAAGAAGTAT
genomic: TGAAGAAGCAACTAGTTGATGATTGTGAATTCATTACTCATCTGGGCCAGgtagttatat ... cttcttgcagCTTATTAGACTGCCTCGAGCTCCAACTGTTGACAAAATATTGAAGAAGTAT
EST: gi|30303537|gb|CB980331.1|CB980331
EST:     TGAAGAAGCAACTAGTTGATGATTGTGAATTCATTACTCATCTGGGCCAG                         CTTGTTAGACTGCCTCGAGCTCCAACTGTTGACAAAATATTGAAGAAGTAT
genomic: TGAAGAAGCAACTAGTTGATGATTGTGAATTCATTACTCATCTGGGCCAGgtagttatat ... cttcttgcagCTTATTAGACTGCCTCGAGCTCCAACTGTTGACAAAATATTGAAGAAGTAT
EST: gi|71877948|gb|DT027003.1|DT027003
EST:     TGAAGAAGCAACTAGTTGATGATTGTGAATTCATTACTCATCTGGGCCAG                         CTTGTTAGACTGCCTCGAGCTCCAACTGTTGACAAAATATTGA
genomic: TGAAGAAGCAACTAGTTGATGATTGTGAATTCATTACTCATCTGGGCCAGgtagttatat ... cttcttgcagCTTATTAGACTGCCTCGAGCTCCAACTGTTGACAAAATATTGA
EST: gi|30133633|gb|CB918972.1|CB918972
EST:     TGAAGAAGCAACTAGTTGATGATTGTGAATTCATTACTCATCTGGGCCAG                         CTTGTTAGACTGCCTCGAGCTCCAACTGTTGACAAAATATTGAAGAAGTAT
genomic: TGAAGAAGCAACTAGTTGATGATTGTGAATTCATTACTCATCTGGGCCAGgtagttatat ... cttcttgcagCTTATTAGACTGCCTCGAGCTCCAACTGTTGACAAAATATTGAAGAAGTAT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GAAGCTATACCAGTGGAGAAGCTTGTGAACATCCAAATTCCTCCAACACTGAAGAAGCAACTAGTTGATGATTGTGAATTCATTACTCATCTGGGCCAGgtagttatattctaaattcatcacggggcctcaatttttcaccttatcagacgatacatgaatttttttttggaatcgagttgctatatgataatttata

- - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA