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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tttccaacagtatgcatgtagaacataagctatgaagtgatgcattgtagtttgaattgtgggctcctcactttgcatctgtaactgtactgaaatgtagGTAAATGTGATGTTGAAAGAATTCCCAGAGGATGAATTTGGCCCTGGGATCAATATTAGAGAATACTCTTTCTTTGACAATCCACTAATGCCCAAACAG

Basic information

species Vitis vinifera
transcript Vv02s0087g00740.t01
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv02s0087g00740.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: GLYMA11G09650.1 (Glycine max), 3'ss of exon 8
-tttccaacagtatgcatgtaga-acataagctatgaagtgatgcattgtagtttgaattgtgggctcctcactttgcatctgtaactgtactgaaatgtagGTAAATGTGATGTTGAAAGAATTCCCAGAGGATGAATTTGGCCCTGGGATCAATATTAGAGAATACTCTTTCTTTGACAATCCACTAATGCCCAAACAG
 ||  | |   | |    ||     | |   |  ||     ||  ||   |       ||||  |       ||  || | || || ||||||  | || |||||||||| |||||||||||| |||||||||| || |||||| ||||  |  ||||||| || |||||  |  |||| |||||     | |||  | ||
cttctctatcttttattcgtctctgcctctcccctgtttacata-ataaaaaaacattttgtcagtcttatgctcagc-tatggaaatgtactctattgcagGTAAATGTCATGTTGAAAGAACTCCCAGAGGAAGAGTTTGGCTCTGGAGTAGATATTAGGGAGTACTCAATACTTGATAATCCCTCCCTCCCCTCAGAG

upper sequence: Vv02s0087g00740.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: GLYMA01G35690.1 (Glycine max), 3'ss of exon 10
-----tttccaacagtatgcatgtagaacataagctatgaagtgatgcattgtagtttgaattgtgggctcctcactttgcatctgtaactgtactgaaatgtagGTAAATGTGATGTTGAAAGAATTCCCAGAGGATGAATTTGGCCCTGGGATCAATATTAGAGAATACTCTTTCTTTGACAATCCACTAATGCCCAAACAG
      ||      || |     |    | |    ||   | | |   |   |  | ||  |    | ||  |  ||  ||  | | || ||||||  | |  |||||||||  |||||||||||| |||| ||||| || |||||||| || ||  |||||||||| |||||  |  |||| |||||  |  | |||  | ||
cctatcttttcttcgtctctgcctctcccctgt-ttacataataaaaaaacattttctg--tcactgtcttat-gctcagctacagaaa-tgtactctattacagGTAAATGCCATGTTGAAAGAACTCCCTGAGGAAGAGTTTGGCCCCGGAATAGATATTAGAGAGTACTCAATACTTGATAATCCCATCCTCCCCTCAGAG
















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|56688584|gb|CX126487.1|CX126487
EST:     GGTCTATTACTAGACAACCTTTTCTCTGCCCTTTGGACCATGTATTTGAG                         GTAAATGTGATGTTGAAAGAATTCCCAGAGGATGAATTTGGCCCTGGGATC
genomic: GGTCTATTACTAGACAACCTTTTCTCTGCCCTTTGGACCATGTATTTGAGgtaccttttt ... tgaaatgtagGTAAATGTGATGTTGAAAGAATTCCCAGAGGATGAATTTGGCCCTGGGATC
EST: gi|110360771|gb|EC924133.1|EC924133
EST:     GGTCTATTACTAGACAACCTTTTCTCTGCCCTTTGGACCATGTATTTGAG                         GTAAATGTGATGTTGAAAGAATTCCCAGAGGATGAATTTGGCCCTGGGATC
genomic: GGTCTATTACTAGACAACCTTTTCTCTGCCCTTTGGACCATGTATTTGAGgtaccttttt ... tgaaatgtagGTAAATGTGATGTTGAAAGAATTCCCAGAGGATGAATTTGGCCCTGGGATC
EST: gi|56688689|gb|CX126592.1|CX126592
EST:     GGTCTATTACTAGACAACCTTTTCTCTGCCCTTTGGACCATGTATTTGAG                         GTAAATGTGATGTTGAAAGAATTCCCAGAGGATGAATTTGGCCCTGGGATC
genomic: GGTCTATTACTAGACAACCTTTTCTCTGCCCTTTGGACCATGTATTTGAGgtaccttttt ... tgaaatgtagGTAAATGTGATGTTGAAAGAATTCCCAGAGGATGAATTTGGCCCTGGGATC
EST: gi|56688204|gb|CX126107.1|CX126107
EST:     GGTCTATTACTAGACAACCTTTTCTCTGCCCTTTGGACCATGTATTTGAG                         GTAAATGTGATGTTGAAAGAATTCCCAGAGGATGAATTTGGCCCTGGGATC
genomic: GGTCTATTACTAGACAACCTTTTCTCTGCCCTTTGGACCATGTATTTGAGgtaccttttt ... tgaaatgtagGTAAATGTGATGTTGAAAGAATTCCCAGAGGATGAATTTGGCCCTGGGATC
EST: gi|56688359|gb|CX126262.1|CX126262
EST:     GGTCTATTACTAGACAACCTTTTCTCTGCCCTTTGGACCATGTATTTGAG                         GTAAATGTGATGTTGAAAGAATTCCCAGAGGATGAATTTGGCCCTGGGATC
genomic: GGTCTATTACTAGACAACCTTTTCTCTGCCCTTTGGACCATGTATTTGAGgtaccttttt ... tgaaatgtagGTAAATGTGATGTTGAAAGAATTCCCAGAGGATGAATTTGGCCCTGGGATC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgtagtttgaattgtgggctcctcactttgcatctgtaactgtactgaaatgtagGTAAATGTGATGTTGAAAGAATTCCCAGAGGATGAATTTGGCCCTGGGATCAATATTAGAGAATACTCTTTCTTTGACAATCCACTAATGCCCAAACAG
     tttgaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tttccaacagtatgcatgtagaacataagctatgaagtgatgcattgtagtttgaattgtgggctcctcactttgcatctgtaactgtactgaaatgtagGTAAATGTGATGTTGAAAGAATTCCCAGAGGATGAATTTGGCCCTGGGATCAATATTAGAGAATACTCTTTCTTTGACAATCCACTAATGCCCAAACAG

- tccaaca
- - - - -gtatgca
- - - - - - - - - - -aacataa
- - - - - - - - - - - - - - -ctatgaa
- - - - - - - - - - - - - - - - - - - - tgcattg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - ttgtggg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gcatctg