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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ACATTTGCAATTTTGTCTGGAGTTCACAGTTTGGTTGTCTGTTTTCTGAAGAGGTTGAGAGGAAAGGATGATGgtatggcatctcaactctacaactggcatttcatataatttatccattttaagataaccatgttctgtttctttacag

Basic information

species Vitis vinifera
transcript Vv19s0090g01590.t01
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv19s0090g01590.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: GLYMA02G46620.1 (Glycine max), 5'ss of exon 3
ACATTTGCAATTTTGTCTGGAGTTCACAGTTTGGTTGTCTGTTTTCTGAAGAGGTTGAGAGGAAAGGATGATGgtatggcatctcaactctacaactgg-cattt---catataatttatccattttaagataaccatgttctgtttc-tttacag
||||||||| |||||||||||||||| ||||||||||| ||  |  |||| ||| | |||||||| ||||||||||||     | |  | || || | | || ||   | | ||| | |||    |   |  |      |||| || | ||| |||
ACATTTGCAGTTTTGTCTGGAGTTCATAGTTTGGTTGTTTGCATCTTGAAAAGGCTTAGAGGAAAAGATGATGgtatgaatatttagttgtaaaatttgtcacttttgcttttaagtgatcttcctctggtaatgtgaattcttttgcatttgcag

upper sequence: Vv19s0090g01590.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: GLYMA14G02050.1 (Glycine max), 5'ss of exon 3
ACATTTGCAATTTTGTCTGGAGTTCACAGTTTGGTTGTCTGTTTTCTGAAGAGGTTGAGAGGAAAGGATGATGgtatggcatctcaactctacaactggcatttcatataatttatccattttaagataaccatgt----tctgtttc-tttacag
||||||||| |||||||||||||||| ||||||||||| ||  |  |||| ||  | |||||||| ||||||||||||     | || | || ||   |    |  |    ||||   || ||    |    ||||    ||| || | | | |||
ACATTTGCAGTTTTGTCTGGAGTTCATAGTTTGGTTGTTTGCATCTTGAAAAGACTTAGAGGAAAAGATGATGgtatgaatatttaattataaaatgtgtcacttttgctttttagtgatcttcctctggtaatgtgaattcttttgcatctgcag

upper sequence: Vv19s0090g01590.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: GLYMA18G09940.1 (Glycine max), 5'ss of exon 3
ACATTTGCAATTTTGTCTGGAGTTCACAGTTTGGTTGTCTGTTTTCTGAAGAGGTTGAGAGGAAAGGATGATGgtatggcatctcaactctacaactggcatttcatataatttatccattttaagataaccatgttct-----gtttctttacag-------------------
|||||||||||||| || |||||| | ||||||||||||||  |  ||   ||  |  |||||||||||||||||||   || |  | | |  |    |  ||| | | || ||| |   | |||| ||        ||     |||  ||   |                    
ACATTTGCAATTTTATCCGGAGTTGATAGTTTGGTTGTCTGCATATTGGGAAGACTTCGAGGAAAGGATGATGgtataaaatatttaatttcaatgatgtgtttgacaaaacttaaca--tataagttagttggaagctaaaaagttagttggaaactattaatgaaaagaaaga

upper sequence: Vv19s0090g01590.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: GLYMA0121S00230.1 (Glycine max), 5'ss of exon 2
ACATTTGCAATTTTGTCTGGAGTTCACAGTTTGGTTGTCTGTTTTCTGAAGAGGTTGAGAGGAAAGGATGATGgtatggcatctcaactctacaactggcatttcatataatttatccattttaagataaccatgttctgtttcttta-cag-----------------------
|||||||||||||| || |||||| | ||||||||||||||  |  ||   ||  |  |||||||||||||||||||   || |  | | |  |    |  ||| | | || ||| |   | |||| ||        ||      |||  ||                       
ACATTTGCAATTTTATCCGGAGTTGATAGTTTGGTTGTCTGCATATTGGGAAGACTTCGAGGAAAGGATGATGgtataaaatatttaatttcaatgatgtgtttgacaaaacttaaca--tataagttagttggaagctaaaaagttagtaggaaactattaatgaaaagaaaga

upper sequence: Vv19s0090g01590.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: GLYMA18G09780.1 (Glycine max), 5'ss of exon 4
ACATTTGCAATTTTGTCTGGAGTTCACAGTTTGGTTGTCTGTTTTCTGAAGAGGTTGAGAGGAAAGGATGATGgtatggcatctcaactctacaactggcatttcatataatttatccattttaagataaccatgttct-----gtttctttacag-------------------
|||||||||||||| || |||||| | ||||||||||||||  |  ||   ||  | ||||||||||||||||||||   || |  | | |  |    |  ||| | | || ||| |   | |||| |||       ||     |||  ||   |                    
ACATTTGCAATTTTATCCGGAGTTGATAGTTTGGTTGTCTGCATATTGGGAAGACTTAGAGGAAAGGATGATGgtataaaatatttaatttcaatgatgtgtttgacaaaacttaaca--tataagttaattggaagctaaaaagttagttggaaactattaatgaaaagaaaga

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|26262978|gb|CA814041.1|CA814041
EST:     TCACAGTTTGGTTGTCTGTTTTCTGAAGAGGTTGAGAGGAAAGGATGATG                         TTGTGAATGCTGGAGTAGCTGGGTGTTGCACTGGTCTCGCATTAAGTTTTC
genomic: TCACAGTTTGGTTGTCTGTTTTCTGAAGAGGTTGAGAGGAAAGGATGATGgtatggcatc ... ttctttacagTTGTGAATGCTGGAGTAGCTGGGTGTTGCACTGGTCTCGCATTAAGTTTTC
EST: gi|71875197|gb|DT024252.1|DT024252
EST:     TCACAGTTTGGTTGTCTGTTTTCTGAAGAGGTTGAGAGGAAAGGATGATG                         TTGTGAATGCTGGAGTAGCTGGGTGTTGCACTGGTCTCGCATTAAGTTTTC
genomic: TCACAGTTTGGTTGTCTGTTTTCTGAAGAGGTTGAGAGGAAAGGATGATGgtatggcatc ... ttctttacagTTGTGAATGCTGGAGTAGCTGGGTGTTGCACTGGTCTCGCATTAAGTTTTC
EST: gi|34549393|gb|CF517625.1|CF517625
EST:     TCACAGTTTGGTTGTCTGTTTTCTGAAGAGGTTGAGAGGAAAGGATGATG                         TTGTGAATGCTGGAGTAGCTGGGTGTTGCACTGGTCTCGCATTAAGTTTTC
genomic: TCACAGTTTGGTTGTCTGTTTTCTGAAGAGGTTGAGAGGAAAGGATGATGgtatggcatc ... ttctttacagTTGTGAATGCTGGAGTAGCTGGGTGTTGCACTGGTCTCGCATTAAGTTTTC
EST: gi|71876494|gb|DT025549.1|DT025549
EST:     TCACAGTTTGGTTGTCTGTTTTCTGAAGAGGTTGAGAGGAAAGGATGATG                         TTGTGAATGCTGGAGTAGCTGGGTGTTGCACTGGTCTCGCATTAAGTTTTC
genomic: TCACAGTTTGGTTGTCTGTTTTCTGAAGAGGTTGAGAGGAAAGGATGATGgtatggcatc ... ttctttacagTTGTGAATGCTGGAGTAGCTGGGTGTTGCACTGGTCTCGCATTAAGTTTTC
EST: gi|51050247|gb|CO818453.1|CO818453
EST:     TCACAGTTTGGTTGTCTGTTTTCTGAAGAGGTTGAGAGGAAAGGATGATG                         TTGTGAATGCTGGAGTAGCTGGGTGTTGCACTGGTCTCGCATTAAGTTTTC
genomic: TCACAGTTTGGTTGTCTGTTTTCTGAAGAGGTTGAGAGGAAAGGATGATGgtatggcatc ... ttctttacagTTGTGAATGCTGGAGTAGCTGGGTGTTGCACTGGTCTCGCATTAAGTTTTC
EST: gi|28961283|gb|CB340652.1|CB340652
EST:     TCACAGTTTGGTTGTCTGTTTTCTGAAGAGGTTGAGAGGAAAGGATGATG                         TTGTGAATGCTGGAGTAGCTGGGTGTTGCACTGGTCTCGCATTAAGTTTTC
genomic: TCACAGTTTGGTTGTCTGTTTTCTGAAGAGGTTGAGAGGAAAGGATGATGgtatggcatc ... ttctttacagTTGTGAATGCTGGAGTAGCTGGGTGTTGCACTGGTCTCGCATTAAGTTTTC
EST: gi|28961109|gb|CB340563.1|CB340563
EST:     TCACAGTTTGGTTGTCTGTTTTCTGAAGAGGTTGAGAGGAAAGGATGATG                         TTGTGAATGCTGGAGTAGCTGGGTGTTGCACTGGTCTCGCATTAAGTTTTC
genomic: TCACAGTTTGGTTGTCTGTTTTCTGAAGAGGTTGAGAGGAAAGGATGATGgtatggcatc ... ttctttacagTTGTGAATGCTGGAGTAGCTGGGTGTTGCACTGGTCTCGCATTAAGTTTTC
EST: gi|351041236|gb|FQ444213.1|FQ444213
EST:     TCACAGTTTGGTTGTCTGTTTTCTGAAGAGGTTGAGAGGAAAGGATGATG                         TTGTGAATGCTGGAGTAGCTGGGTGTTGCACTGGTCTCGCATTAAGTTTTC
genomic: TCACAGTTTGGTTGTCTGTTTTCTGAAGAGGTTGAGAGGAAAGGATGATGgtatggcatc ... ttctttacagTTGTGAATGCTGGAGTAGCTGGGTGTTGCACTGGTCTCGCATTAAGTTTTC
EST: gi|110720822|gb|EE097079.1|EE097079
EST:     TCACAGTTTGGTTGTCTGTTTTCTGAAGAGGTTGAGAGGAAAGGATGATG                         TTGTGAATGCTGGAGTAGCTGGGTGTTGCACTGGTCTCGCATTAAGTTTTC
genomic: TCACAGTTTGGTTGTCTGTTTTCTGAAGAGGTTGAGAGGAAAGGATGATGgtatggcatc ... ttctttacagTTGTGAATGCTGGAGTAGCTGGGTGTTGCACTGGTCTCGCATTAAGTTTTC
EST: gi|351023175|gb|FQ432558.1|FQ432558
EST:     TCACAGTTTGGTTGTCTGTTTTCTGAAGAGGTTGAGAGGAAAGGATGATG                         TTGTGAATGCTGGAGTAGCTGGGTGTTGCACTGGTCTCGCATTAAGTTTTC
genomic: TCACAGTTTGGTTGTCTGTTTTCTGAAGAGGTTGAGAGGAAAGGATGATGgtatggcatc ... ttctttacagTTGTGAATGCTGGAGTAGCTGGGTGTTGCACTGGTCTCGCATTAAGTTTTC
EST: gi|26266858|gb|CA817921.1|CA817921
EST:     TCACAGTTTGGTTGTCTGTTTTCTGAAGAGG-TGAGAGGAAAGGATGATG                         TTGTGAATGCTGGAGTAGCTGGGTGTTGCACTGGTCTCGCATTAAGTTTTC
genomic: TCACAGTTTGGTTGTCTGTTTTCTGAAGAGGTTGAGAGGAAAGGATGATGgtatggcatc ... ttctttacagTTGTGAATGCTGGAGTAGCTGGGTGTTGCACTGGTCTCGCATTAAGTTTTC
EST: gi|351029437|gb|FQ436831.1|FQ436831
EST:     TCACAGTTTGGTTGTCTGTTTTCTGAAGAGGTTGAGAGGAAAGGATGATG                         TTGTGAATGCTGGAGTAGCTGGGTGTTGCACTGGTCTCGCATTAAGTTTTC
genomic: TCACAGTTTGGTTGTCTGTTTTCTGAAGAGGTTGAGAGGAAAGGATGATGgtatggcatc ... ttctttacagTTGTGAATGCTGGAGTAGCTGGGTGTTGCACTGGTCTCGCATTAAGTTTTC
EST: gi|110714518|gb|EE091519.1|EE091519
EST:     AAGAGGTTGAGAGGAAAGGATGATG                         TTGTGAATGCTGGAGTAGCTGGGTGTTGCACTGGTCTCGCATTAAGTTTTC
genomic: AAGAGGTTGAGAGGAAAGGATGATGgtatggcatc ... ttctttacagTTGTGAATGCTGGAGTAGCTGGGTGTTGCACTGGTCTCGCATTAAGTTTTC
EST: gi|71867379|gb|DT016434.1|DT016434
EST:     TCACAGTTTGGTTGTCTGTTTTCTGAAGAGGTTGAGAGGAAAGGATGATG                         TTGTGAATGCTGGAGTAGCTGGGTGTTGCACTGGTCTCGCATTAAGTTTTC
genomic: TCACAGTTTGGTTGTCTGTTTTCTGAAGAGGTTGAGAGGAAAGGATGATGgtatggcatc ... ttctttacagTTGTGAATGCTGGAGTAGCTGGGTGTTGCACTGGTCTCGCATTAAGTTTTC
EST: gi|26262072|gb|CA813135.1|CA813135
EST:     TCACAGTTTGGTTGTCTGTTTTCTGAAGAGGTTGAGAGGAAAGGATGATG                         TTGTGAATGCTGGAGTAGCTGGGTGTNGCACTGGTCTCGCATTAAGTTTTC
genomic: TCACAGTTTGGTTGTCTGTTTTCTGAAGAGGTTGAGAGGAAAGGATGATGgtatggcatc ... ttctttacagTTGTGAATGCTGGAGTAGCTGGGTGTTGCACTGGTCTCGCATTAAGTTTTC
EST: gi|33408488|gb|CF214115.1|CF214115
EST:     TCACAGTTTGGTTGTCTGTTTTCTGAAGAGGTTGAGAGGAAAGGATGATG                         TTGTGAATGCTGGAGTAGCTGGGTGTTGCACTGGTCTCGCATTAAGTTTTC
genomic: TCACAGTTTGGTTGTCTGTTTTCTGAAGAGGTTGAGAGGAAAGGATGATGgtatggcatc ... ttctttacagTTGTGAATGCTGGAGTAGCTGGGTGTTGCACTGGTCTCGCATTAAGTTTTC
EST: gi|26261889|gb|CA812952.1|CA812952
EST:     TCACAGTTTGGTTGTCTGTTTTCTGAAGAGGTTGAGAGGAAAGGATGATG                         TTGTGAATGCTGGAGTAGCTGGGTGTTGCACTGGTCTCGCATTAAGTTTTC
genomic: TCACAGTTTGGTTGTCTGTTTTCTGAAGAGGTTGAGAGGAAAGGATGATGgtatggcatc ... ttctttacagTTGTGAATGCTGGAGTAGCTGGGTGTTGCACTGGTCTCGCATTAAGTTTTC
EST: gi|34549479|gb|CF517711.1|CF517711
EST:     TCACAGTTTGGTTGTCTGTTTTCTGAAGAGGTTGAGAGGAAAGGATGATG                         TTGTGAATGCTGGAGTAGCTGGGTGTTGCACTGGTCTCGCATTAAGTTTTC
genomic: TCACAGTTTGGTTGTCTGTTTTCTGAAGAGGTTGAGAGGAAAGGATGATGgtatggcatc ... ttctttacagTTGTGAATGCTGGAGTAGCTGGGTGTTGCACTGGTCTCGCATTAAGTTTTC
EST: gi|33410548|gb|CF216175.1|CF216175
EST:     TCACAGTTTGGTTGTCTGTTTTCTGAAGAGGTTGAGAGGAAAGGATGATG                         TTGTGAATGCTGGAGTAGCTGGGTGTTGCACTGGTCTCGCATTAAGTTTTC
genomic: TCACAGTTTGGTTGTCTGTTTTCTGAAGAGGTTGAGAGGAAAGGATGATGgtatggcatc ... ttctttacagTTGTGAATGCTGGAGTAGCTGGGTGTTGCACTGGTCTCGCATTAAGTTTTC
EST: gi|351023375|gb|FQ432758.1|FQ432758
EST:     TCACAGTTTGGTTGTCTGTTTTCTGAAGAGGTTGAGAGGAAAGGATGATG                         TTGTGAATGCTGGAGTAGCTGGGTGTTGCACTGGTCTCGCATTAAGTTTTC
genomic: TCACAGTTTGGTTGTCTGTTTTCTGAAGAGGTTGAGAGGAAAGGATGATGgtatggcatc ... ttctttacagTTGTGAATGCTGGAGTAGCTGGGTGTTGCACTGGTCTCGCATTAAGTTTTC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ACATTTGCAATTTTGTCTGGAGTTCACAGTTTGGTTGTCTGTTTTCTGAAGAGGTTGAGAGGAAAGGATGATGgtatggcatctcaactctacaactggcatttcatataatttatccattttaagataaccatgttctgtttctttacag

- - - - - - - - - - - - - - - - - - - - - -  CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG