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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtattgcaatttgctttttcattgttttttgtttcaaatcctttagtcttatgtcactgttggagataattttctcttcctttccctgtcctttcttttcttctgtgtgtggggcagGGTCAATGGAATCCAGAGGATTTATTGGAGTTGCTGCAGAGCCCACCTTTTCGCCAACAAGTAGATTCATTTACTTAT

Basic information

species Vitis vinifera
transcript Vv11s0065g00450.t01
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv11s0065g00450.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: GLYMA08G03080.1 (Glycine max), 3'ss of exon 11
gtattgcaatttgctttttcattgttttttgtttcaaatcctttagtcttatgtcactgttggagat-aattttctcttcctttccctgtcctttcttttcttctgtgtgtggggcagGGTCAATGGAATCCAGAGGATTTATTGGAGTTGCTGCAGAGCCCACCTTTTCGCCAACAAGTAGATTCATTTACTTAT
                                                  ||| || ||| |    | | ||||    | |||||  |  |   |   | |     | | ||  | ||||| |||||  |||||| ||  ||||||||||| |||||||||||||||| || || ||||||||||| |||||||||
----------------------------------------------gtacatgacaatgtggtgtttgagttttagtattctttcatttacagattcatgcaatattctttgatgtagGGTGAATGGTCTCCAGAAGAGATATTGGAGTTGTTGCAGAGCCCACCTTTCCGTCAGCAAGTAGATTCGTTTACTTAT

upper sequence: Vv11s0065g00450.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: GLYMA05G36490.2 (Glycine max), 3'ss of exon 11
gtattgcaatttgctttttcattgttttttgtttcaaatcctttagtcttatgtcactgttggagataa-ttttctcttcctttccctgtcctttcttttcttctgtgtgtggggcagGGTCAATGGAATCCAGAGGATTTATTGGAGTTGCTGCAGAGCCCACCTTTTCGCCAACAAGTAGATTCATTTACTTAT
                                                 ||||||| ||| |    ||| ||||    | |||||  |  |   |   | |     | | ||  | ||||| |||||  |||||| ||  ||||||||||| |||||||||||||||| || || ||||||||||| |||||||||
----------------------------------------------gtatatgtcaatgtggagattaagttttagtattctttcatttacagattcatgcaatattctttgatgtagGGTAAATGGTCTCCAGAAGAGATATTGGAGTTGTTGCAGAGCCCACCTTTCCGTCAGCAAGTAGATTCGTTTACTTAT

upper sequence: Vv11s0065g00450.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: AT2G26590.1 (Arabidopsis thaliana), 3'ss of exon 10
gtattgcaatttgctttttcattgttttttgtttcaaatcctttagtcttatgtcactgttggagataattttctcttcctttccctgtcctttcttttcttctgtgtgtggggcagGGTCAATGGAATCCAGAGGATTTATTGGAGTTGCTGCAGAGCCCACCTTTTCGCCAACAAGTAGATTCATTTACTTAT
               ||   |  | ||   |   |||    || |    || |     | |    | | |  ||   | |    |    ||      |  |    |   |    |||||||| |  |   |||| ||| || |||||||| |||||||||| |||||||| |||||||||||| ||||||| |||
--------------gttgctaaagcttaaagaa-caagagattgaaagctaagctgaggctaatcacattggtcatgtaccagactaacccaaaggctaatctaatcaatca--cagGGTCATTCTAGGGCAGAAGATATACTGGAGTTGTTGCAGAGCCCTCCTTTTCGTCAACAAGTAGATGCATTTACCTAT

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|110702756|gb|EE079004.1|EE079004
EST:     TGATTGAGACATTACCAATGGAACAACGTTTAGCCTCTTACTTACCTGAG                         GGTCAATGGAATCCAGAGGATTTATTGGAGTTGCTGCAGAGCCCACCTTTT
genomic: TGATTGAGACATTACCAATGGAACAACGTTTAGCCTCTTACTTACCTGAGgtattgcaat ... tgtggggcagGGTCAATGGAATCCAGAGGATTTATTGGAGTTGCTGCAGAGCCCACCTTTT
EST: gi|110395278|gb|EC960936.1|EC960936
EST:     TGATTGAGACATTACCAATGGAACAACGTTTAGCCTCTTACTTACCTGAG                         GGTCAATGGAATCCAGAGGATTTATTGGAGTTGCTGCAGAGCCCACCTTTT
genomic: TGATTGAGACATTACCAATGGAACAACGTTTAGCCTCTTACTTACCTGAGgtattgcaat ... tgtggggcagGGTCAATGGAATCCAGAGGATTTATTGGAGTTGCTGCAGAGCCCACCTTTT
EST: gi|18459586|gb|BM437864.1|BM437864
EST:     TGATTGAGACATTACCAATGGAACAACGTTTAGCCTCTTACTTACCTGAG                         GGTCAATGGAATCCAGAGGATTTATTGGAGTTGCTGCAGAGCCCACCTTTT
genomic: TGATTGAGACATTACCAATGGAACAACGTTTAGCCTCTTACTTACCTGAGgtattgcaat ... tgtggggcagGGTCAATGGAATCCAGAGGATTTATTGGAGTTGCTGCAGAGCCCACCTTTT
EST: gi|33405732|gb|CF211359.1|CF211359
EST:     TGATTGAGACATTACCAATGGAACAACGTTTAGCCTCTTACTTACCTGAG                         GGTCAATGGAATCCAGAGGATTTATTGNAGTTGCTGCAGAGCCCACCTTTT
genomic: TGATTGAGACATTACCAATGGAACAACGTTTAGCCTCTTACTTACCTGAGgtattgcaat ... tgtggggcagGGTCAATGGAATCCAGAGGATTTATTGGAGTTGCTGCAGAGCCCACCTTTT
EST: gi|110391622|gb|EC956610.1|EC956610
EST:     TGATTGAGACATTACCAATGGAACAACGTTTAGCCTCTTACTTACCTGAG                         GGTCAATGGAATCCAGAGGATTTATTGGAGTTGCTGCAGAGCCCACCTTTT
genomic: TGATTGAGACATTACCAATGGAACAACGTTTAGCCTCTTACTTACCTGAGgtattgcaat ... tgtggggcagGGTCAATGGAATCCAGAGGATTTATTGGAGTTGCTGCAGAGCCCACCTTTT
EST: gi|351028718|gb|FQ433148.1|FQ433148
EST:     TGATTGAGACATTACCAATGGAACAACGTTTAGCCTCTTACTTACCTGAG                         GGTCAATGGAATCCAGAGGATTTATTGGA
genomic: TGATTGAGACATTACCAATGGAACAACGTTTAGCCTCTTACTTACCTGAGgtattgcaat ... tgtggggcagGGTCAATGGAATCCAGAGGATTTATTGGA
EST: gi|22011495|gb|BQ796529.1|BQ796529
EST:     TGATTGAGACATTACCAATGGAACAACGTTTAGCCTCTTACTTACCTGAG                         GGTCAATGGAATCCAGAGGATTTATTGGAGTTGCT
genomic: TGATTGAGACATTACCAATGGAACAACGTTTAGCCTCTTACTTACCTGAGgtattgcaat ... tgtggggcagGGTCAATGGAATCCAGAGGATTTATTGGAGTTGCT
EST: gi|110377829|gb|EC942921.1|EC942921
EST:     TGATTGAGACATTACCAATGGAACAACGTTTAGCCTCTTACTTACCTGAG                         GGTCAATGGAATCCAGAGGATTTATTGGAGTTGCTGCAGAGCCCACCTTTT
genomic: TGATTGAGACATTACCAATGGAACAACGTTTAGCCTCTTACTTACCTGAGgtattgcaat ... tgtggggcagGGTCAATGGAATCCAGAGGATTTATTGGAGTTGCTGCAGAGCCCACCTTTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gagataattttctcttcctttccctgtcctttcttttcttctgtgtgtggggcagGGTCAATGGAATCCAGAGGATTTATTGGAGTTGCTGCAGAGCCCACCTTTTCGCCAACAAGTAGATTCATTTACTTAT
       ttttctcttcctttcc  CT-rich tract
     aattttct  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtattgcaatttgctttttcattgttttttgtttcaaatcctttagtcttatgtcactgttggagataattttctcttcctttccctgtcctttcttttcttctgtgtgtggggcagGGTCAATGGAATCCAGAGGATTTATTGGAGTTGCTGCAGAGCCCACCTTTTCGCCAACAAGTAGATTCATTTACTTAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG