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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGAAGACTTCCTTTTTGAGTCATCTGACGGCAGGCGCTACCTCAACTTTACTTTTGGTTGTCCACTTGTGGAGACCGTAGTTGACAAGTTGACAGTCAAAgtaggtctagcactattattctgattcatatggtaattatttgatttctccttactttttgcttcagtgatctcatctaagattttgtctcag

Basic information

species Vitis vinifera
transcript Vv13s0019g04410.t01
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv13s0019g04410.t01 (Vitis vinifera), 5'ss of exon 5
lower sequence: GLYMA10G35450.1 (Glycine max), 5'ss of exon 5
GGAAGACTTCCTTTTTGAGTCATCTGACGGCAGGCGCTACCTCAACTTTACTTTTGGTTGTCCACTTGTGGAGACCGTAGTTGACAAGTTGACAGTCAAAgtaggtctagcactatta-ttctgattcatatggtaattatttgatttctccttact----ttttgcttcagtgatctcatctaag-attttgtctcag
| |||||||||||||||||||  | || |||||  | |||||||| |||||||||||||| || ||||| ||||| || |||||||||||||  || ||||| ||| |   | |||||  |   | |  |     || |  ||   |   |  || |     |||  || |    |||  |  ||  |||   | ||||
GCAAGACTTCCTTTTTGAGTCTCCGGATGGCAGAAGATACCTCAATTTTACTTTTGGTTGCCCTCTTGTCGAGACAGTGGTTGACAAGTTGATTGTAAAAgtgggtttgttattattaactgaaaattgtgcatcaactgcttctgtatgcaatagtggaggtttaatttacccttcttgttgaaccattaaatttcag

upper sequence: Vv13s0019g04410.t01 (Vitis vinifera), 5'ss of exon 5
lower sequence: GLYMA20G32070.1 (Glycine max), 5'ss of exon 5
GGAAGACTTCCTTTTTGAGTCATCTGACGGCAGGCGCTACCTCAACTTTACTTTTGGTTGTCCACTTGTGGAGACCGTAGTTGACAAGTTGACAGTCAAAgtaggtctagcactattattctgattcatatggta-attatttgatttctccttactttttgcttcagtgatctcatctaagattttgtctcag--------------
| ||||||| |||||||||||  | || |||||  | |||||||| |||||||||||||| || ||||| ||||| || |||||||||||||  || ||||| ||| |   | |||||  ||||    | || |  ||| ||| |  |     |   |         | | | | || ||   || |   | |               
GCAAGACTTTCTTTTTGAGTCTCCAGATGGCAGAAGATACCTCAATTTTACTTTTGGTTGCCCTCTTGTTGAGACAGTGGTTGACAAGTTGATTGTAAAAgtgggtttgttattattaa-ctgaaaattgtgctccattgtttcaactgcttctgtatgcaatagtggaggtttaatttacccttcttgttgaaccattaaatttcag
















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|71865487|gb|DT014542.1|DT014542
EST:     CTTTTGGTTGTCCACTTGTGGAGACCGTAGTTGACAAGTTGACAGTCAAA                         GTGGTGCTGCCAGAGGGATCGAAAGAACCTTCTGCTGTGGTTCCTTTCCCA
genomic: CTTTTGGTTGTCCACTTGTGGAGACCGTAGTTGACAAGTTGACAGTCAAAgtaggtctag ... tttgtctcagGTGGTGCTGCCAGAGGGATCGAAAGAACCTTCTGCTGTGGTTCCTTTCCCA
EST: gi|351015486|gb|FQ447315.1|FQ447315
EST:     CTTTTGGTTGTCCACTTGTGGAGACCGTAGTTGACAAGTTGACAGTCAAA                         GTGGTGCTGCCAGAGGGATCGAAAGAACCTTCTGCTGTGGTTCCTTTCCCA
genomic: CTTTTGGTTGTCCACTTGTGGAGACCGTAGTTGACAAGTTGACAGTCAAAgtaggtctag ... tttgtctcagGTGGTGCTGCCAGAGGGATCGAAAGAACCTTCTGCTGTGGTTCCTTTCCCA
EST: gi|71881801|gb|DT030856.1|DT030856
EST:     CTTTTGGTTGTCCACTTGTGGAGACCGTAGTTGACAAGTTGACAGTCAAA                         GTGGTGCTGCCAGAGGGATCGAAAGAACCTTCTGCTGTGGTTCCTTTCCCA
genomic: CTTTTGGTTGTCCACTTGTGGAGACCGTAGTTGACAAGTTGACAGTCAAAgtaggtctag ... tttgtctcagGTGGTGCTGCCAGAGGGATCGAAAGAACCTTCTGCTGTGGTTCCTTTCCCA
EST: gi|37187617|gb|CF606970.1|CF606970
EST:     CTTTTGGTTGTCCACTTGTGGAGACCGTAGTTGACAAGTTGACAGTCAAA                         GTGGTGCTGCCAGAGGGATCGAAAGAACCTTCTGCTGTGGTTCCTTTCCCA
genomic: CTTTTGGTTGTCCACTTGTGGAGACCGTAGTTGACAAGTTGACAGTCAAAgtaggtctag ... tttgtctcagGTGGTGCTGCCAGAGGGATCGAAAGAACCTTCTGCTGTGGTTCCTTTCCCA
EST: gi|349824067|gb|FQ417454.1|FQ417454
EST:     CTTTTGGTTGTCCACTTGTGGAGACCGTAGTTGACAAGTTGACAGTCAAA                         GTGGTGCTGCCAGAGGGATCGAAAGAACCTTCTGCTGTGGTTCCTTTCCCA
genomic: CTTTTGGTTGTCCACTTGTGGAGACCGTAGTTGACAAGTTGACAGTCAAAgtaggtctag ... tttgtctcagGTGGTGCTGCCAGAGGGATCGAAAGAACCTTCTGCTGTGGTTCCTTTCCCA
EST: gi|351031867|gb|FQ460124.1|FQ460124
EST:     CTTTTGGTTGTCCACTTGTGGAGACCGTAGTTGACAAGTTGACAGTCAAA                         GTGGTGCTGCCAGAGGGATCGAAAGAACCTTCTGCTGTGGTTCCTTTCCCA
genomic: CTTTTGGTTGTCCACTTGTGGAGACCGTAGTTGACAAGTTGACAGTCAAAgtaggtctag ... tttgtctcagGTGGTGCTGCCAGAGGGATCGAAAGAACCTTCTGCTGTGGTTCCTTTCCCA
EST: gi|352790365|gb|FQ478005.1|FQ478005
EST:     CTTTTGGTTGTCCACTTGTGGAGACCGTAGTTGACAAGTTGACAGTCAAA                         GTGGTGCTGCCAGAGGGATCGAAAGAACCTTCTGCTGTGGTTCCTTTCCCA
genomic: CTTTTGGTTGTCCACTTGTGGAGACCGTAGTTGACAAGTTGACAGTCAAAgtaggtctag ... tttgtctcagGTGGTGCTGCCAGAGGGATCGAAAGAACCTTCTGCTGTGGTTCCTTTCCCA
EST: gi|349812777|gb|FQ410419.1|FQ410419
EST:     CTTTTGGTTGTCCACTTGTGGAGACCGTAGTTGACAAGTTGACAGTCAAA                         GTGGTGCTGTCAGAGGGATCGAAAGAACCTTCTGCTGTGGTTCCTTTCCCA
genomic: CTTTTGGTTGTCCACTTGTGGAGACCGTAGTTGACAAGTTGACAGTCAAAgtaggtctag ... tttgtctcagGTGGTGCTGCCAGAGGGATCGAAAGAACCTTCTGCTGTGGTTCCTTTCCCA
EST: gi|349816667|gb|FQ404914.1|FQ404914
EST:     CTTTTGGTTGTCCACTTGTGGAGACCGTAGTTGACAAGTTGACAGTCAAA                         GTGGTGCTGCCAGAGGGATCGAAAGAACCTTCTGCTGTGGTTCCTTTCCCA
genomic: CTTTTGGTTGTCCACTTGTGGAGACCGTAGTTGACAAGTTGACAGTCAAAgtaggtctag ... tttgtctcagGTGGTGCTGCCAGAGGGATCGAAAGAACCTTCTGCTGTGGTTCCTTTCCCA
EST: gi|77585403|gb|DV221793.1|DV221793
EST:     CTTTTGGTTGTCCACTTGTGGAGACCGTAGTTGACAAGTTGACAGTCAAA                         GTGGTGCTGCCAGAGGGAT
genomic: CTTTTGGTTGTCCACTTGTGGAGACCGTAGTTGACAAGTTGACAGTCAAAgtaggtctag ... tttgtctcagGTGGTGCTGCCAGAGGGAT
EST: gi|51052013|gb|CO819346.1|CO819346
EST:     CTTTTGGTTGTCCACTTGTGGAGACCGTAGTTGACAAGTTGACAGTCAAA                         GTGGTGCTGCCAGAGGGATCGAAAGAACCTTCTGCTGTGGTTCCTTTCCCA
genomic: CTTTTGGTTGTCCACTTGTGGAGACCGTAGTTGACAAGTTGACAGTCAAAgtaggtctag ... tttgtctcagGTGGTGCTGCCAGAGGGATCGAAAGAACCTTCTGCTGTGGTTCCTTTCCCA
EST: gi|351051855|gb|FQ455269.1|FQ455269
EST:     CTTTTGGTTGTCCACTTGTGGAGACCGTAGTTGACAAGTTGACAGTCAAA                         GTGGTGCTGCCAGAGGGATCGAAAGAACCTTCTGCTGTGGTTCCTTTCCCA
genomic: CTTTTGGTTGTCCACTTGTGGAGACCGTAGTTGACAAGTTGACAGTCAAAgtaggtctag ... tttgtctcagGTGGTGCTGCCAGAGGGATCGAAAGAACCTTCTGCTGTGGTTCCTTTCCCA
EST: gi|351045790|gb|FQ440975.1|FQ440975
EST:     CTTTTGGTTGTCCACTTGTGGAGACCGTAGTTGACAAGTTGACAGTCAAA                         GTGGTGCTGCCAGAGGGATCGAAAGAACCTTCTGCTGTGGTTCCTTTCCCA
genomic: CTTTTGGTTGTCCACTTGTGGAGACCGTAGTTGACAAGTTGACAGTCAAAgtaggtctag ... tttgtctcagGTGGTGCTGCCAGAGGGATCGAAAGAACCTTCTGCTGTGGTTCCTTTCCCA
EST: gi|349811345|gb|FQ407571.1|FQ407571
EST:     CTTTTGGTTGTCCACTTGTGGAGACCGTAGTTGACAAGTTGACAGTCAAA                         GTGGTGCTGTCAGAGGGATCGAAAGAACCTTCTGCTGTGGTTCCTTTCCCA
genomic: CTTTTGGTTGTCCACTTGTGGAGACCGTAGTTGACAAGTTGACAGTCAAAgtaggtctag ... tttgtctcagGTGGTGCTGCCAGAGGGATCGAAAGAACCTTCTGCTGTGGTTCCTTTCCCA
EST: gi|351048526|gb|FQ448800.1|FQ448800
EST:     CTTTTGGTTGTCCACTTGTGGAGACCGTAGTTGACAAGTTGACAGTCAAA                         GTGGTGCTGCCAGAGGGATCGAAAGAACCTTCTGCTGTGGTTCCTTTCCCA
genomic: CTTTTGGTTGTCCACTTGTGGAGACCGTAGTTGACAAGTTGACAGTCAAAgtaggtctag ... tttgtctcagGTGGTGCTGCCAGAGGGATCGAAAGAACCTTCTGCTGTGGTTCCTTTCCCA
EST: gi|351053182|gb|FQ455639.1|FQ455639
EST:     CTTTTGGTTGTCCACTTGTGGAGACCGTAGTTGACAAGTTGACAGTCAAA                         GTGGTGCTGCCAGAGGGATCGAAAGAACCTTCTGCTGTGGTTCCTTTCCCA
genomic: CTTTTGGTTGTCCACTTGTGGAGACCGTAGTTGACAAGTTGACAGTCAAAgtaggtctag ... tttgtctcagGTGGTGCTGCCAGAGGGATCGAAAGAACCTTCTGCTGTGGTTCCTTTCCCA
EST: gi|349807244|gb|FQ401236.1|FQ401236
EST:     CTTTTGGTTGTCCACTTGTGGAGACCGTAGTTGACAAGTTGACAGTCAAA                         GTGGTGCTGCCAGAGGGATCGAAAGAACCTTCTGCTGTGGTTCCTTTCCCA
genomic: CTTTTGGTTGTCCACTTGTGGAGACCGTAGTTGACAAGTTGACAGTCAAAgtaggtctag ... tttgtctcagGTGGTGCTGCCAGAGGGATCGAAAGAACCTTCTGCTGTGGTTCCTTTCCCA
EST: gi|110414535|gb|EC980369.1|EC980369
EST:     CTTTTGGTTGTCCACTTGTGGAGACCGTAGTTGACAAGTTGACAGTCAAA                         GTGGTGCTGCCAGAGGGATCGAAAGAACCTTCTGCTGTGGTTCCTTTCCCA
genomic: CTTTTGGTTGTCCACTTGTGGAGACCGTAGTTGACAAGTTGACAGTCAAAgtaggtctag ... tttgtctcagGTGGTGCTGCCAGAGGGATCGAAAGAACCTTCTGCTGTGGTTCCTTTCCCA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGAAGACTTCCTTTTTGAGTCATCTGACGGCAGGCGCTACCTCAACTTTACTTTTGGTTGTCCACTTGTGGAGACCGTAGTTGACAAGTTGACAGTCAAAgtaggtctagcactattattctgattcatatggtaattatttgatttctccttactttttgcttcagtgatctcatctaagattttgtctcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA