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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTGTATTCAAATCTTGATGGCAACAGATCTCATGTAGTAAATACCGCATGGGCTATGCTGGCTCTCATTGATGCTGGGCAGgtacacatcatattttactacatgtttgctaatgttgaagagggactcagtttttgttgtgtttatagtcagtttcctttttatagaattgttatcgtgc...

Basic information

species Vitis vinifera
transcript Vv11s0065g00640.t01
intron # 17
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv11s0065g00640.t01 (Vitis vinifera), 5'ss of exon 17
lower sequence: GLYMA01G00430.1 (Glycine max), 5'ss of exon 17
GTGTATTCAAATCTTGATGGCAACAGATCTCATGTAGTAAATACCGCATGGGCTATGCTGGCTCTCATTGATGCTGGGCAGgtacacatcatattttactacatgtttgctaatgttgaagagggactcagtttttgttgt-gtttatagtcagtttcctttttatagaattgttatcgtgc------
|||||||||||||| || |||||||| |||||||| || || || |  ||||||||| ||||||||||||||||||| ||||||     || | ||||||   | |||| |||||  | |    |       |||| || | |   |    || |||    ||||  |   ||||    |        
GTGTATTCAAATCTGGAAGGCAACAGGTCTCATGTGGTCAACACTGGGTGGGCTATGTTGGCTCTCATTGATGCTGGACAGgtatga--caaagtttact---tttttg-taatgcagtattatgttgattattttattattgcacagcaccaatttttcattta-gggtctgtttggataaacttca

upper sequence: Vv11s0065g00640.t01 (Vitis vinifera), 5'ss of exon 17
lower sequence: AT2G07050.1 (Arabidopsis thaliana), 5'ss of exon 16
GTGTATTCAAATCTTGATGGCAACAGATCTCATGTAGTAAATACCGCATGGGCTATGCTGGCTCTCATTGATGCTGGGCAGgt----------------acacatcatattttactacat-gtttgctaatgttgaagagggactcagtttt-tgttgtgtttatagtcagtttcctttttatagaattgttatcgtgc-------
|| |||||||| |||||||||||||||||||| || || ||||| |||||||||||||| || ||||||| ||||||||| ||                | || |  || || | | ||| ||     || |  |  |     |||| | || |  | | | | |   || || |  ||||||    |||||   || |       
GTCTATTCAAACCTTGATGGCAACAGATCTCACGTCGTGAATACAGCATGGGCTATGCTCGCACTCATTGGTGCTGGGCAAgtgagtaaattccttaagaaactttgtacttcagttcatcgtgctgcaaggcggggggattgctcattcttgtcctctctctctttccatttacaattttatctctttgtttgtgttcttattag
















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|32265187|gb|CD716776.1|CD716776
EST:     ATGTAGTAAATACCGCATGGGCTATGCTGGCTCTCATTGATGCTGGGCAG                         GCTGAGAGAGACCCAACACCATTGCACAGAGCAGCACGAGTATTGATAAAT
genomic: ATGTAGTAAATACCGCATGGGCTATGCTGGCTCTCATTGATGCTGGGCAGgtacacatca ... tttgatgcagGCTGAGAGAGACCCAACACCATTGCACAGAGCAGCACGAGTATTGATAAAT
EST: gi|18458985|gb|BM437263.1|BM437263
EST:     ATGTAGTAAATACCGCATGGGCTATGCTGGCTCTCATTGATGCTGGGCAG                         GCTGAGAGAGACCCAACACCATTGCACAGAGCAGCACGAGTATTGATAAAT
genomic: ATGTAGTAAATACCGCATGGGCTATGCTGGCTCTCATTGATGCTGGGCAGgtacacatca ... tttgatgcagGCTGAGAGAGACCCAACACCATTGCACAGAGCAGCACGAGTATTGATAAAT
EST: gi|161717232|gb|FC067238.1|FC067238
EST:     ATGTAGTAAATACCGCATGGGCTATGCTGGCTCTCATTGATGCTGGGCAG                         GCTGAGAGAGACCTCA-CACCATTGCACAGAGCAGCACGAGTATTGATAAA
genomic: ATGTAGTAAATACCGCATGGGCTATGCTGGCTCTCATTGATGCTGGGCAGgtacacatca ... tttgatgcagGCTGAGAGAGACC-CAACACCATTGCACAGAGCAGCACGAGTATTGATAAA
EST: gi|30299701|gb|CB976495.1|CB976495
EST:     ATGTAGTAAATACCGCATGGGCTATGCTGGCTCTCATTGATGCTGGGCAG                         GCTGAGAGAGACCCAACACCATTGCACAGAGCAGCACGAGTATTGATAAAT
genomic: ATGTAGTAAATACCGCATGGGCTATGCTGGCTCTCATTGATGCTGGGCAGgtacacatca ... tttgatgcagGCTGAGAGAGACCCAACACCATTGCACAGAGCAGCACGAGTATTGATAAAT
EST: gi|110391126|gb|EC956083.1|EC956083
EST:     ATGTAGTAAATACCGCATGGGCTATGCTGGCTCTCATTGATGCTGGGCAG                         GCTGAGAGAGACCCAACACCATTGCACAGAGCAGCACGAGTATTGATAAAT
genomic: ATGTAGTAAATACCGCATGGGCTATGCTGGCTCTCATTGATGCTGGGCAGgtacacatca ... tttgatgcagGCTGAGAGAGACCCAACACCATTGCACAGAGCAGCACGAGTATTGATAAAT
EST: gi|32270024|gb|CD719183.1|CD719183
EST:     ATGTAGTAAATACCGCATGGGCTATGCTGGCTCTCATTGATGCTGGGCAG                         GCTGAGAGAGACCCAACACCATTGCACAGAGCAGCACGAGTATTGATAAAT
genomic: ATGTAGTAAATACCGCATGGGCTATGCTGGCTCTCATTGATGCTGGGCAGgtacacatca ... tttgatgcagGCTGAGAGAGACCCAACACCATTGCACAGAGCAGCACGAGTATTGATAAAT
EST: gi|34543141|gb|CF511373.1|CF511373
EST:     ATGTAGTAAATACCGCATGGGCTATGCTGGCTCTCATTGATGCTGGGCAG                         GCTGAGAGAGACCCAACACCATTGCACAGAGCAGCACGAGTATTGATAAAT
genomic: ATGTAGTAAATACCGCATGGGCTATGCTGGCTCTCATTGATGCTGGGCAGgtacacatca ... tttgatgcagGCTGAGAGAGACCCAACACCATTGCACAGAGCAGCACGAGTATTGATAAAT
EST: gi|30320591|gb|CD003853.1|CD003853
EST:     ATGTAGTAAATACCGCATGGGCTATGCTGGCTCTCATTGATGCTGGGCAG                         GCTGAGAGAGACCCAACACCATTGCACAGAGCAGCACGAGTATTGATAAAT
genomic: ATGTAGTAAATACCGCATGGGCTATGCTGGCTCTCATTGATGCTGGGCAGgtacacatca ... tttgatgcagGCTGAGAGAGACCCAACACCATTGCACAGAGCAGCACGAGTATTGATAAAT
EST: gi|352785395|gb|FQ477609.1|FQ477609
EST:     ATGTAGTAAATACCGCATGGGCTATGCTGGCTCTCATTGATGCTGGGCAG                         GCTGAGAGAGACCCAACACCATTGCACAGAGCAGCACGAGTATTGATAAAT
genomic: ATGTAGTAAATACCGCATGGGCTATGCTGGCTCTCATTGATGCTGGGCAGgtacacatca ... tttgatgcagGCTGAGAGAGACCCAACACCATTGCACAGAGCAGCACGAGTATTGATAAAT
EST: gi|34543224|gb|CF511456.1|CF511456
EST:     ATGTAGTAAATACCGCATGGGCTATGCTGGCTCTCATTGATGCTGGGCAG                         GCTGAGAGAGACCCAACACCATTGCACAGAGCAGCACGAGTATTGATAAAT
genomic: ATGTAGTAAATACCGCATGGGCTATGCTGGCTCTCATTGATGCTGGGCAGgtacacatca ... tttgatgcagGCTGAGAGAGACCCAACACCATTGCACAGAGCAGCACGAGTATTGATAAAT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTGTATTCAAATCTTGATGGCAACAGATCTCATGTAGTAAATACCGCATGGGCTATGCTGGCTCTCATTGATGCTGGGCAGgtacacatcatattttactacatgtttgctaatgttgaagagggactcagtttttgttgtgtttatagtcagtttcctttttatagaattgttatcgtgc

- - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gaagaggg