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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ggatgcacaattgtagaagatatgaacctttaacttgtatacttacattactactgattattttgctctgacaagtgaggcattgattttatcattgcagGAGTGGAATTGCTTACATATCAAATGTTGCAGTTCGGGAGACATTCAGGCGCAAGGGGATAGCCAAAAGGCTTATAGTAAAGGCAGAGGCTCAAGCTAGA

Basic information

species Vitis vinifera
transcript Vv13s0019g04360.t01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv13s0019g04360.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA20G32020.2 (Glycine max), 3'ss of exon 2
ggatgcacaattgtagaagatatgaacctttaacttgtatacttacattactactgattattttgctctgacaagtgaggcattgattttatc-----attgcagGAGTGGAATTGCTTACATATCAAATGTTGCAGTTCGGGAGACATTCAGGCGCAAGGGGATAGCCAAAAGGCTTATAGTAAAGGCAGAGGCTCAAGCTAGA
   | ||      |    ||     |  || |   | ||| |||   |||  |||||| | ||||  ||||    ||     ||   ||  ||     | || |||| ||||||||| |||||||||||||| ||||| || || | ||| ||||| ||||| ||||| |||    |  | | |||||||||  | |||||||||
---tacatggccatgttggagtatgatattcatggtttatgcttcactta--actgatgaatttgtgctgatggctgtaattttttcttcttcaaaatactgtagGACTGGAATTGCATACATATCAAATGTGGCAGTCCGAGAAAAATTTAGGCGGAAGGGAATAGCTAAACACTTGGTTGCAAAGGCAGAATCACAAGCTAGA
















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|18459514|gb|BM437792.1|BM437792
EST:     GATACTGTTGCTGATTTTCTACCAAGGAAAGGCCCGCTTCGCCAAAGAAG                         GAGTGGAATTGCTTACATATCAAATGTTGCAGTTCGGGAGACATTCAGGCG
genomic: GATACTGTTGCTGATTTTCTACCAAGGAAAGGCCCGCTTCGCCAAAGAAGgtgagtttgg ... atcattgcagGAGTGGAATTGCTTACATATCAAATGTTGCAGTTCGGGAGACATTCAGGCG
EST: gi|32249196|gb|CD715015.1|CD715015
EST:     GATACTGTTGCTGATTTTCTACCAAGGAAAGGCCCGCTTCGCCAAAGAAG                         GAGTGGAATTGCTTACATATCANATGTTGCAGTTCGGGAGACATTCANGCG
genomic: GATACTGTTGCTGATTTTCTACCAAGGAAAGGCCCGCTTCGCCAAAGAAGgtgagtttgg ... atcattgcagGAGTGGAATTGCTTACATATCAAATGTTGCAGTTCGGGAGACATTCAGGCG
EST: gi|32248451|gb|CD714270.1|CD714270
EST:     GATACTGTTGCTGATTTTCTACCAAGGAAAGGCCCGCTTCGCCAAAGAAG                         GAGTGGAATTGCTTACATATCAAATGTTGCAGTTCGGG
genomic: GATACTGTTGCTGATTTTCTACCAAGGAAAGGCCCGCTTCGCCAAAGAAGgtgagtttgg ... atcattgcagGAGTGGAATTGCTTACATATCAAATGTTGCAGTTCGGG
EST: gi|110409888|gb|EC975562.1|EC975562
EST:     GATACTGTTGCTGATTTTCTACCAAGGAAAGGCCCGCTTCGCCAAAGAAG                         GAGTGGAATTGCTTACATATCAAATGTTGCAGTTCGGGAGACATTCAGGCG
genomic: GATACTGTTGCTGATTTTCTACCAAGGAAAGGCCCGCTTCGCCAAAGAAGgtgagtttgg ... atcattgcagGAGTGGAATTGCTTACATATCAAATGTTGCAGTTCGGGAGACATTCAGGCG
EST: gi|110401396|gb|EC968006.1|EC968006
EST:     GATACTGTTGCTGATTTTCTACCAAGGAAAGGCCCGCTTCGCCAAAGAAG                         GAGTGGAATTGCTTACATATCAAATGTTGCAGTTCGGGAGACATTCAGGCG
genomic: GATACTGTTGCTGATTTTCTACCAAGGAAAGGCCCGCTTCGCCAAAGAAGgtgagtttgg ... atcattgcagGAGTGGAATTGCTTACATATCAAATGTTGCAGTTCGGGAGACATTCAGGCG
EST: gi|26258286|gb|CA809349.1|CA809349
EST:     GATACTGTTGCGGATTTTCTACCAAGGAAAGGCCCGCTTCGCCAAAGAAG                         GAGTGGAATTGCTTACATATCAAATGTTGCAGTTCGGGAGACATTCAGGCG
genomic: GATACTGTTGCTGATTTTCTACCAAGGAAAGGCCCGCTTCGCCAAAGAAGgtgagtttgg ... atcattgcagGAGTGGAATTGCTTACATATCAAATGTTGCAGTTCGGGAGACATTCAGGCG
EST: gi|349825461|gb|FQ419378.1|FQ419378
EST:     GATACTGTTGCTGATTTTCTACCAAGGAAAGGCCCGCTTCGCCAAAGAAG                         GAGTGGAATTGCTTACATATCATATGTTGCAGTTCGGGAGACATTCAAGCG
genomic: GATACTGTTGCTGATTTTCTACCAAGGAAAGGCCCGCTTCGCCAAAGAAGgtgagtttgg ... atcattgcagGAGTGGAATTGCTTACATATCAAATGTTGCAGTTCGGGAGACATTCAGGCG
EST: gi|30322468|gb|CD005730.1|CD005730
EST:     GATACTGTTGCTGATTTTCTACCAAGGAAAGGCCCGCTTCGCCAAAGAAG                         GAGTGGAATTGCTTACATATCAAATGT
genomic: GATACTGTTGCTGATTTTCTACCAAGGAAAGGCCCGCTTCGCCAAAGAAGgtgagtttgg ... atcattgcagGAGTGGAATTGCTTACATATCAAATGT
EST: gi|34549279|gb|CF517511.1|CF517511
EST:     GATACTGTTGCTGATTTTCTACCAAGGAAAGGCCCGCTTCGCCAAAGAAG                         GAGTGGAATTGCTTACATATCAAATGTTGCAGTTCGGGAGACATTCAGGCG
genomic: GATACTGTTGCTGATTTTCTACCAAGGAAAGGCCCGCTTCGCCAAAGAAGgtgagtttgg ... atcattgcagGAGTGGAATTGCTTACATATCAAATGTTGCAGTTCGGGAGACATTCAGGCG
EST: gi|32269110|gb|CD718269.1|CD718269
EST:     GATACTGTTGCTGATTTTCTACCAAGGAAAGGCCCGCTTCGCCAAAGAAG                         GAGTGGAATTGCTTACATATCANATGTTGC
genomic: GATACTGTTGCTGATTTTCTACCAAGGAAAGGCCCGCTTCGCCAAAGAAGgtgagtttgg ... atcattgcagGAGTGGAATTGCTTACATATCAAATGTTGC
EST: gi|351046898|gb|FQ454508.1|FQ454508
EST:     GATACTGTTGCTGATTTTCTACCAAGGAAAGGCCCGCTTCGCCAAAGAAG                         GAGTGGAATTGCTTACATATCANATGTTGCAGTTCGGGAGACATTCAGGCG
genomic: GATACTGTTGCTGATTTTCTACCAAGGAAAGGCCCGCTTCGCCAAAGAAGgtgagtttgg ... atcattgcagGAGTGGAATTGCTTACATATCAAATGTTGCAGTTCGGGAGACATTCAGGCG
EST: gi|32269034|gb|CD718193.1|CD718193
EST:     GATACTGTTGCTGATTTTCTACCAAGGAAAGGCCCGCTTCGCCAAAGAAG                         GAGTGGAATTGCTTACATATCANATGTTGCAGTTCGGGAG
genomic: GATACTGTTGCTGATTTTCTACCAAGGAAAGGCCCGCTTCGCCAAAGAAGgtgagtttgg ... atcattgcagGAGTGGAATTGCTTACATATCAAATGTTGCAGTTCGGGAG
EST: gi|26257461|gb|CA808524.1|CA808524
EST:     GATACTGTTGCCGATTTTCTACCAAGGAAAGGCCCGCTTCGCCAAAGAAG                         GAGTGGAATTGCTTACATATCAAATGTTGCAGTTCGGGAGACATTCAGGCG
genomic: GATACTGTTGCTGATTTTCTACCAAGGAAAGGCCCGCTTCGCCAAAGAAGgtgagtttgg ... atcattgcagGAGTGGAATTGCTTACATATCAAATGTTGCAGTTCGGGAGACATTCAGGCG
EST: gi|110701724|gb|EE079624.1|EE079624
EST:     GATACTGTTGCTGATTTTCTACCAAGGAAAGGCCCGCTTCGCCAAAGAAG                         GAGTGGAATTGCTTACATATCAAATGTTGCAGTTCGGGAGACATTCAGGCG
genomic: GATACTGTTGCTGATTTTCTACCAAGGAAAGGCCCGCTTCGCCAAAGAAGgtgagtttgg ... atcattgcagGAGTGGAATTGCTTACATATCAAATGTTGCAGTTCGGGAGACATTCAGGCG
EST: gi|32249014|gb|CD714833.1|CD714833
EST:     GATACTGTTGCTGATTTTCTACCAAGGAAAGGCCCGCTTCGCCAAAGAAG                         GAGTGGAATTGCTTACATATCANATGTTGCAGTTCG
genomic: GATACTGTTGCTGATTTTCTACCAAGGAAAGGCCCGCTTCGCCAAAGAAGgtgagtttgg ... atcattgcagGAGTGGAATTGCTTACATATCAAATGTTGCAGTTCG
EST: gi|30322577|gb|CD005839.1|CD005839
EST:     GATACTGTTGCTGATTTTCTACCAAGGAAAGGCCCGCTTCGCCANAGAAG                         GAGTGGAATTGCTTACATATCANATGTTGCAGTTCGGG
genomic: GATACTGTTGCTGATTTTCTACCAAGGAAAGGCCCGCTTCGCCAAAGAAGgtgagtttgg ... atcattgcagGAGTGGAATTGCTTACATATCAAATGTTGCAGTTCGGG
EST: gi|351036439|gb|FQ457152.1|FQ457152
EST:     GATACTGTTGCTGATTTTCTACCAAGGAAAGGCCCGCTTCGCCAAAGAAG                         GAGTGGAATTGCCTACATATCANATGTTGCAGTTCGGGAGACATTCAGGCG
genomic: GATACTGTTGCTGATTTTCTACCAAGGAAAGGCCCGCTTCGCCAAAGAAGgtgagtttgg ... atcattgcagGAGTGGAATTGCTTACATATCAAATGTTGCAGTTCGGGAGACATTCAGGCG
EST: gi|110708111|gb|EE085280.1|EE085280
EST:     GATACTGTTGCTGATTTTCTACCAAGGAAAGGCCCGCTTCGCCAAAGAAG                         GAGTGGAATTGCTTACATATCAAATGTTGCAGTTCGGGAGACATTCAGGCG
genomic: GATACTGTTGCTGATTTTCTACCAAGGAAAGGCCCGCTTCGCCAAAGAAGgtgagtttgg ... atcattgcagGAGTGGAATTGCTTACATATCAAATGTTGCAGTTCGGGAGACATTCAGGCG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cattactactgattattttgctctgacaagtgaggcattgattttatcattgcagGAGTGGAATTGCTTACATATCAAATGTTGCAGTTCGGGAGACATTCAGGCGCAAGGGGATAGCCAAAAGGCTTATAGTAAAGGCAGAGGCTCAAGCTAGA
                                         ttttatc  CT-rich tract
                                    attgattttatcatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ggatgcacaattgtagaagatatgaacctttaacttgtatacttacattactactgattattttgctctgacaagtgaggcattgattttatcattgcagGAGTGGAATTGCTTACATATCAAATGTTGCAGTTCGGGAGACATTCAGGCGCAAGGGGATAGCCAAAAGGCTTATAGTAAAGGCAGAGGCTCAAGCTAGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAAGCT
ggatgca
- - - - - - - - - - tatgaac
- - - - - - - - - - - - - - - - - - - - - - - - - ctactga