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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttttgtatatttttatcagatctttatcctcttcttgatttttttatgtgtgtgtatatatatgtgatgtttttaaggtatatatttttacataattcagGTTTAGAGGTGGGTGGTGAGATGAACTTAGCCGCAGGTATCCAAGTGGCTCAATTGGCTCTTAAGCATCGACAAAACAAAAAGCAGCAACAAAGGATCAT

Basic information

species Vitis vinifera
transcript Vv04s0023g03620.t01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv04s0023g03620.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA16G23590.1 (Glycine max), 3'ss of exon 3
----ttttgtatatttttat-cagatct-ttatcctcttcttgatttttttatgtgtgtgtatatatatgtgatgtttttaaggtatatatttttacataattcagGTTTAGAGGTGGGTGGTGAGATGAACTTAGCCGCAGGTATCCAAGTGGCTCAATTGGCTCTTAAGCATCGACAAAACAAAAAGCAGCAACAAAGGATCAT
        ||  ||| |||| | ||  | |||        | |||| || |||   |||   | |  || ||   ||||   | | | | ||||    ||  | |||  ||||  | ||||||||||||||| |||| || || || || || || |||||||||||||||||||| || ||||| |||||||| |||||||| ||
agttggcagtgcattgttattctgacatgttagttatggttggattcttctattcttgtaagtgttgatttg---ttttcctgttttttgttttc---tatgttagGACTAGAAATAGGTGGTGAGATGAACCTAGCTGCTGGCATTCAGGTTGCGCAATTGGCTCTTAAGCATCGGCAGAACAAGAAGCAGCAGCAAAGGATTAT

upper sequence: Vv04s0023g03620.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA11G08290.1 (Glycine max), 3'ss of exon 3
ttttgtatatttttatcagatctttatcctcttcttgatttttt-tatgtgtgtgtatatatatgtgatgtttttaaggtatatatttttacataattcagGTTTAGAGGTGGGTGGTGAGATGAACTTAGCCGCAGGTATCCAAGTGGCTCAATTGGCTCTTAAGCATCGACAAAACAAAAAGCAGCAACAAAGGATCAT
|  || ||||| || |   || ||  |    || | |||| ||| | | ||| | | | || |  |||  |  ||  | | | | ||||| |  |||| |||  ||||  | ||||||||||||||| |||| || || || || ||||| |||||||||||||||||||| ||||| |||||||| || || ||||| ||
tgctgcatattcttctaccatgtt-gtgtcattgtggattctttctttttgtttttttttaaaaatgagttcattttgtttttttttttttcccaatttagGACTAGATATAGGTGGTGAGATGAACCTAGCTGCTGGCATTCAGGTGGCACAATTGGCTCTTAAGCATCGGCAAAATAAAAAGCAACAGCAGAGGATTAT

upper sequence: Vv04s0023g03620.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA02G05250.2 (Glycine max), 3'ss of exon 3
ttttgtatatttttatcagatctttatcctcttcttgatttttttatgtgtgtgtatatatatgtgatgtttttaaggtatatatttttacataattcagGTTTAGAGGTGGGTGGTGAGATGAACTTAGCCGCAGGTATCCAAGTGGCTCAATTGGCTCTTAAGCATCGACAAAACAAAAAGCAGCAACAAAGGATCAT------
   ||||   || |         ||||       | ||||||| |||   |||   |  |  ||   |||||||    | | | || || | ||  | |||  ||||  | || |||||||||||  |||| || || || || || || |||||||||||||||||||| || ||||| |||||||| |||||||| ||      
---tgtactgttattctgacatgttattaatggttggatttttctattcttgt---tggagttgatttgtttttccttttttttttgtttcctatgttaggactagAAATAGGCGGTGAGATGAATCTAGCTGCTGGCATTCAGGTTGCACAATTGGCTCTTAAGCATCGGCAGAACAAGAAGCAGCAGCAAAGGATTATTGTCTT

upper sequence: Vv04s0023g03620.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA02G05250.1 (Glycine max), 3'ss of exon 3
-ttttgtatatttttat-cagatct-ttatcctcttcttgatttttttatgtgtgtgtatatatatgtgatgtttttaaggtatatatttttacataattcagGTTTAGAGGTGGGTGGTGAGATGAACTTAGCCGCAGGTATCCAAGTGGCTCAATTGGCTCTTAAGCATCGACAAAACAAAAAGCAGCAACAAAGGATCAT
     || || | |||| | ||  | ||||       | ||||||| |||   |||   |  |  ||   |||||||    | | | || || | ||  | |||  ||||  | || |||||||||||  |||| || || || || || || |||||||||||||||||||| || ||||| |||||||| |||||||| ||
tggcagtgtactgttattctgacatgttattaatggttggatttttctattcttgt---tggagttgatttgtttttccttttttttttgtttcctatgttagGACTAGAAATAGGCGGTGAGATGAATCTAGCTGCTGGCATTCAGGTTGCACAATTGGCTCTTAAGCATCGGCAGAACAAGAAGCAGCAGCAAAGGATTAT

upper sequence: Vv04s0023g03620.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA01G36990.1 (Glycine max), 3'ss of exon 3
-------ttttgtatatttttatcagatctt-tatcctcttcttgatttttttatgtgtgtgtatatatatgtgatgtttttaaggtatatatttttacataattcagGTTTAGAGGTGGGTGGTGAGATGAACTTAGCCGCAGGTATCCAAGTGGCTCAATTGGCTCTTAAGCATCGACAAAACAAAAAGCAGCAACAAAGGATCAT
       |  || ||||| || |   || || | || |  | ||  ||||||| | ||     ||   |   |  ||||||||       | ||||| | ||||| |||  ||||  | ||||||||||||||| |||| || || || || || || ||| |||||||||||||||| ||||| ||||| || || || ||||| ||
acatgtttgctgcatattcttctaccatattgtgtcatagtgtttttttttttttttgaaaa-atgagttcattttgttttta-------tttttttccctaatttagGGCTAGATATAGGTGGTGAGATGAACCTAGCTGCTGGCATTCAGGTTGCACAACTGGCTCTTAAGCATCGGCAAAATAAAAAACAACAGCAGAGGATTAT

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|110724206|gb|EE099841.1|EE099841
EST:     TTTGGTCACTCCCACAAGCGATCTCGGCAAGATCTTGGCGTGCATGCACG                         GTTTAGAGGTGGGTGGTGAGATGAACTTAGCCGCAGGTATCCAAGTGGCTC
genomic: TTTGGTCACTCCCACAAGCGATCTCGGCAAGATCTTGGCGTGCATGCACGgtatgttcat ... cataattcagGTTTAGAGGTGGGTGGTGAGATGAACTTAGCCGCAGGTATCCAAGTGGCTC
EST: gi|110718273|gb|EE094914.1|EE094914
EST:     TTTGGTCACTCCCACAAGCGGTCTCGGCAAGATCTTGGCGTGCATGCACG                         GTTTAGAGGTGGGTGGTGAGATGAACTTAGCCGCAGGTATCCAAGTGGCTC
genomic: TTTGGTCACTCCCACAAGCGATCTCGGCAAGATCTTGGCGTGCATGCACGgtatgttcat ... cataattcagGTTTAGAGGTGGGTGGTGAGATGAACTTAGCCGCAGGTATCCAAGTGGCTC
EST: gi|71865268|gb|DT014323.1|DT014323
EST:     TTTGGTCACTCCCACAAGCGATCTCGGCAAGATCTTGGCGTGCATGCACG                         GTTTAGAGGTGGGTGGTGAGATGAACTTAGCCGCAGGTATCCAAGTGGCTC
genomic: TTTGGTCACTCCCACAAGCGATCTCGGCAAGATCTTGGCGTGCATGCACGgtatgttcat ... cataattcagGTTTAGAGGTGGGTGGTGAGATGAACTTAGCCGCAGGTATCCAAGTGGCTC
EST: gi|37185661|gb|CF605014.1|CF605014
EST:     TTTGGTCACTCCCACAAGCGATCTCGGCAAGATCTTGGCGTGCATGCACG                         GTTTAGAGGTGGGTGGTGAGATGAACTTAGCCGCAGGTATCCAAGTGGCTC
genomic: TTTGGTCACTCCCACAAGCGATCTCGGCAAGATCTTGGCGTGCATGCACGgtatgttcat ... cataattcagGTTTAGAGGTGGGTGGTGAGATGAACTTAGCCGCAGGTATCCAAGTGGCTC
EST: gi|110723511|gb|EE100909.1|EE100909
EST:     TTTGGTCACTCCCACAAGCGATCTCGGCAAGATCTTGGCGTGCATGCACG                         GTTTAGAGGTGGGTGGTGAGATGAACTTAGCCGCAGGTATCCAAGTGGCTC
genomic: TTTGGTCACTCCCACAAGCGATCTCGGCAAGATCTTGGCGTGCATGCACGgtatgttcat ... cataattcagGTTTAGAGGTGGGTGGTGAGATGAACTTAGCCGCAGGTATCCAAGTGGCTC
EST: gi|37188389|gb|CF607738.1|CF607738
EST:     TTTGGTCACTCCCACAAGCGATCTCGGCAAGATCTTGGCGTGCATGCACG                         GTTTAGAGGTGGGTGGTGAGATGAACTTAGCCGCAGGTATCCAAGTGGCTC
genomic: TTTGGTCACTCCCACAAGCGATCTCGGCAAGATCTTGGCGTGCATGCACGgtatgttcat ... cataattcagGTTTAGAGGTGGGTGGTGAGATGAACTTAGCCGCAGGTATCCAAGTGGCTC
EST: gi|110702751|gb|EE079006.1|EE079006
EST:     TTTGGTCACTCCCACAAGCGATCTCGGCAAGATCTTGGCGTGCATGCACG                         GTTTAGAGGTGGGTGGTGAGATGAACTTAGCTGCAGGTATCCAAGTGGCTC
genomic: TTTGGTCACTCCCACAAGCGATCTCGGCAAGATCTTGGCGTGCATGCACGgtatgttcat ... cataattcagGTTTAGAGGTGGGTGGTGAGATGAACTTAGCCGCAGGTATCCAAGTGGCTC
EST: gi|110687737|gb|EE065489.1|EE065489
EST:     TTTGGTCACTCCCACAAGCGATCTCGGCAAGATCTTGGCGTGCATGCACG                         GTTTAGAGGTGGGTGGTGAGATGAACTTAGCCGCAGGTATCCAAGTGGCTC
genomic: TTTGGTCACTCCCACAAGCGATCTCGGCAAGATCTTGGCGTGCATGCACGgtatgttcat ... cataattcagGTTTAGAGGTGGGTGGTGAGATGAACTTAGCCGCAGGTATCCAAGTGGCTC
EST: gi|110689406|gb|EE065602.1|EE065602
EST:     TTTGGTCACTCCCACAAGCGATCTCGGCAAGATCTTGGCGTGCATGCACG                         GTTTAGAGGTGGGTGGTGAGATGAACTTAGCCGCAGGTATCCAAGTGGCTC
genomic: TTTGGTCACTCCCACAAGCGATCTCGGCAAGATCTTGGCGTGCATGCACGgtatgttcat ... cataattcagGTTTAGAGGTGGGTGGTGAGATGAACTTAGCCGCAGGTATCCAAGTGGCTC
EST: gi|110730475|gb|EE107599.1|EE107599
EST:     TTTGGTCACTCCCACAAGCGATCTCGGCAAGATCTTGGCGTGCATGCACG                         GTTTAGAGGTGGGTGGTGAGATGAACTTAGCCGCAGGTATCCAAGTGGCTC
genomic: TTTGGTCACTCCCACAAGCGATCTCGGCAAGATCTTGGCGTGCATGCACGgtatgttcat ... cataattcagGTTTAGAGGTGGGTGGTGAGATGAACTTAGCCGCAGGTATCCAAGTGGCTC
EST: gi|71864038|gb|DT013093.1|DT013093
EST:     TTTGGTCACTCCCACAAGCGATCTCGGCAAGATCTTGGCGTGCATGCACG                         GTTTAGAGGTGGGTGGTGAGATGAACTTAGCCGCAGGTATCCAAGTGGCTC
genomic: TTTGGTCACTCCCACAAGCGATCTCGGCAAGATCTTGGCGTGCATGCACGgtatgttcat ... cataattcagGTTTAGAGGTGGGTGGTGAGATGAACTTAGCCGCAGGTATCCAAGTGGCTC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atgtgtgtgtatatatatgtgatgtttttaaggtatatatttttacataattcagGTTTAGAGGTGGGTGGTGAGATGAACTTAGCCGCAGGTATCCAAGTGGCTCAATTGGCTCTTAAGCATCGACAAAACAAAAAGCAGCAACAAAGGATCAT
                                       tttttac  CT-rich tract
         tatatatatgtgatgt  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttttgtatatttttatcagatctttatcctcttcttgatttttttatgtgtgtgtatatatatgtgatgtttttaaggtatatatttttacataattcagGTTTAGAGGTGGGTGGTGAGATGAACTTAGCCGCAGGTATCCAAGTGGCTCAATTGGCTCTTAAGCATCGACAAAACAAAAAGCAGCAACAAAGGATCAT

- - - - - - - - - - - - - -cctcttc
- - - - - - - - - - - - - - - - - - - - - - - -gtgtgtg