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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gcgagtcttcctcagcatttcgcactttttctctttgcaaatctgtgtttctgtgaagtaactgttttgttaattccattgtgcagATTATCCCCGAGAAGAATCGGAGAGAGATCTCCAAGTACCTCTTCCAAG

Basic information

species Vitis vinifera
transcript Vv16s0050g01160.t01
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv16s0050g01160.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: LOC_Os02g34460.1 (Oryza sativa), 3'ss of exon 1
--gcgagtcttcctcagcatttcgcactttttctctttgcaaatc-----tgtgtttctgtgaagtaactgttttgttaattccattgtgc-agATTATCCCCGAGAAGAATCGGAGAGAGATCTCCAAGTACCTCTTCCAAG
   ||  |||    |   | |       |    ||  | ||| ||     ||  |    | |  |    |||  ||||  ||   || ||  |||| |||||| ||||||| ||||  ||||||| |||||||||||||||||
gtacgcatctgagcccaaaatcaatgtgtcccgtcggttcaattcgttggtgaatactggcgctgatgttgtggtgtttttttttttctgttagATCATCCCCAAGAAGAACCGGAATGAGATCTGCAAGTACCTCTTCCAAG
















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|51051467|gb|CO819071.1|CO819071
EST:     CACCGCAG-CATG                         A-TAT-CCCGAG-AGAATCGGAGAGAGAT-TCCAAGTACCTC-TCCAAG
genomic: CACCGCAGCCATGgcgagtcttc ... cattgtgcagATTATCCCCGAGAAGAATCGGAGAGAGATCTCCAAGTACCTCTTCCAAG
EST: gi|110377465|gb|EC942530.1|EC942530
EST:     TAGCCCTTGCCCTTGCGTGCCTTCTCTCTCGCAACTTCACCGCAGCCATG                         ATTATCCCCGAGAAGAATCGGAGAGAGATCTCCAAGTACCTCTTCCAAG
genomic: TAGCCCTTGCCCTTGCGTGCCTTCTCTCTCGCAACTTCACCGCAGCCATGgcgagtcttc ... cattgtgcagATTATCCCCGAGAAGAATCGGAGAGAGATCTCCAAGTACCTCTTCCAAG
EST: gi|110715571|gb|EE093772.1|EE093772
EST:     CTCTCTCGCAACTTCACCGCAGCCATG                         ATTATCCCCGAGAAGAATCGGAGAGAGATCTCCAAGTACCTCTTCCAAG
genomic: CTCTCTCGCAACTTCACCGCAGCCATGgcgagtcttc ... cattgtgcagATTATCCCCGAGAAGAATCGGAGAGAGATCTCCAAGTACCTCTTCCAAG
EST: gi|110700496|gb|EE078604.1|EE078604
EST:     TAGCCCTTGCCCTTGCGTGCCTTCTCTCTCGCAACTTCACCGCAGCCATG                         ATTATCCCCGAGAAGAATCGGAGAGAGATCTCCAAGTACCTCTTCCAAG
genomic: TAGCCCTTGCCCTTGCGTGCCTTCTCTCTCGCAACTTCACCGCAGCCATGgcgagtcttc ... cattgtgcagATTATCCCCGAGAAGAATCGGAGAGAGATCTCCAAGTACCTCTTCCAAG
EST: gi|71868077|gb|DT017132.1|DT017132
EST:     TAGCCCTTGCCCTTGCGTGCCTTCTCTCTCGCAACTTCACCGCAGCCATG                         ATTATCCCCGAGAAGAATCGGAGAGAGATCTCCAAGTACCTCTTCCAAG
genomic: TAGCCCTTGCCCTTGCGTGCCTTCTCTCTCGCAACTTCACCGCAGCCATGgcgagtcttc ... cattgtgcagATTATCCCCGAGAAGAATCGGAGAGAGATCTCCAAGTACCTCTTCCAAG
EST: gi|110702044|gb|EE080304.1|EE080304
EST:     CGTGCCTTCTCTCTCGCAACTTCACCGCAGCCATG                         ATTATCCCCGAGAAGAATCGGAGAGAGATCTCCAAGTACCTCTTCCAAG
genomic: CGTGCCTTCTCTCTCGCAACTTCACCGCAGCCATGgcgagtcttc ... cattgtgcagATTATCCCCGAGAAGAATCGGAGAGAGATCTCCAAGTACCTCTTCCAAG
EST: gi|110703760|gb|EE080890.1|EE080890
EST:     TAGCCCTTGCCCTTGCGTGCCTTCTCTCTCGCAACTTCACCGCAGCCATG                         ATTATCCCCGAGAAGAATCGGAGAGAGATCTCCAAGTACCTCTTCCAAG
genomic: TAGCCCTTGCCCTTGCGTGCCTTCTCTCTCGCAACTTCACCGCAGCCATGgcgagtcttc ... cattgtgcagATTATCCCCGAGAAGAATCGGAGAGAGATCTCCAAGTACCTCTTCCAAG
EST: gi|110398785|gb|EC965259.1|EC965259
EST:     TAGCCCTTGCCCTTGCGTGCCTTCTCTCTCGCAACTTCACCGCAGCCATG                         ATTATCCCCGAGAAGAATCGGAGAGAGATCTCCAAGTACCTCTTCCAAG
genomic: TAGCCCTTGCCCTTGCGTGCCTTCTCTCTCGCAACTTCACCGCAGCCATGgcgagtcttc ... cattgtgcagATTATCCCCGAGAAGAATCGGAGAGAGATCTCCAAGTACCTCTTCCAAG
EST: gi|110360451|gb|EC923562.1|EC923562
EST:     CAACTTCACCGCAGCCATG                         ATTATCCCCGAGAAGAATCGGAGAGAGATCTCCAAGTACCTCTTCCAAG
genomic: CAACTTCACCGCAGCCATGgcgagtcttc ... cattgtgcagATTATCCCCGAGAAGAATCGGAGAGAGATCTCCAAGTACCTCTTCCAAG
EST: gi|110692204|gb|EE071178.1|EE071178
EST:     AGCCCTTGCCCTTGCGTGCCTTCTCTCTCGCAACTTCACCGCAGCCATG                         ATTATCCCCGAGAAGAATCGGAGAGAGATCTCCAAGTACCTCTTCCAAG
genomic: AGCCCTTGCCCTTGCGTGCCTTCTCTCTCGCAACTTCACCGCAGCCATGgcgagtcttc ... cattgtgcagATTATCCCCGAGAAGAATCGGAGAGAGATCTCCAAGTACCTCTTCCAAG
EST: gi|110723368|gb|EE100598.1|EE100598
EST:     TAGCCCTTGCCCTTGCGTGCCTTCTCTCTCGCAACTTCACCGCAGCCATG                         ATTATCCCCGAGAAGAATCGGAGAGAGATCTCCAAGTACCTCTTCCAAG
genomic: TAGCCCTTGCCCTTGCGTGCCTTCTCTCTCGCAACTTCACCGCAGCCATGgcgagtcttc ... cattgtgcagATTATCCCCGAGAAGAATCGGAGAGAGATCTCCAAGTACCTCTTCCAAG
EST: gi|87584250|gb|DY473484.1|DY473484
EST:     CTCGCAACTTCACCGCAGCCATG                         ATTATCCCCGAGAAGAATCGGAGAGAGATCTCCAAGTACCTCTTCCAAG
genomic: CTCGCAACTTCACCGCAGCCATGgcgagtcttc ... cattgtgcagATTATCCCCGAGAAGAATCGGAGAGAGATCTCCAAGTACCTCTTCCAAG
EST: gi|30320459|gb|CD003721.1|CD003721
EST:     CTCGCAACTTCACCGCAGCCATG                         ATTATCCCCGAGAAGAATCGGAGAGAGATCTCCAAGTACCTCTTCCAAG
genomic: CTCGCAACTTCACCGCAGCCATGgcgagtcttc ... cattgtgcagATTATCCCCGAGAAGAATCGGAGAGAGATCTCCAAGTACCTCTTCCAAG
EST: gi|29781884|gb|CB346698.2|CB346698
EST:     TAGCCCTTGCCCTTGCGTGCCTTCTCTCTCGCAACTTCACCGCAGCCATG                         ATTATCCCCGAGAAGAATCGGAGAGAGATCTCCAAGTACCTCTTCCAAG
genomic: TAGCCCTTGCCCTTGCGTGCCTTCTCTCTCGCAACTTCACCGCAGCCATGgcgagtcttc ... cattgtgcagATTATCCCCGAGAAGAATCGGAGAGAGATCTCCAAGTACCTCTTCCAAG
EST: gi|18458561|gb|BM436839.1|BM436839
EST:     CTCGCAACTTCACCGCAGCCATG                         ATTATCCCCGAGAAGAATCGGAGAGAGATCTCCAAGTACCTCTTCCAAG
genomic: CTCGCAACTTCACCGCAGCCATGgcgagtcttc ... cattgtgcagATTATCCCCGAGAAGAATCGGAGAGAGATCTCCAAGTACCTCTTCCAAG
EST: gi|110722253|gb|EE098322.1|EE098322
EST:     TAGCCCTTGCCCTTGCGTGCCTTCTCTCTCGCAACTTCACCGCAGCCATG                         ATTATCCCCGAGAAGAATCGGAGAGAGATCTCCAAGTACCTCTTCCAAG
genomic: TAGCCCTTGCCCTTGCGTGCCTTCTCTCTCGCAACTTCACCGCAGCCATGgcgagtcttc ... cattgtgcagATTATCCCCGAGAAGAATCGGAGAGAGATCTCCAAGTACCTCTTCCAAG
EST: gi|32268119|gb|CD717278.1|CD717278
EST:     TAGCCCTTGCCCTTGCGTGCCTTCTCTCTCGCAACTTCACCGCAGCCATG                         ATTATCCCCGAGAAGAATCGGAGAGAGATCTCCAAGTACCTCTTCCAAG
genomic: TAGCCCTTGCCCTTGCGTGCCTTCTCTCTCGCAACTTCACCGCAGCCATGgcgagtcttc ... cattgtgcagATTATCCCCGAGAAGAATCGGAGAGAGATCTCCAAGTACCTCTTCCAAG
EST: gi|110401412|gb|EC968022.1|EC968022
EST:     CGCAACTTCACCGCAGCCATG                         ATTATCCCCGAGAAGAATCGGAGAGAGATCTCCAAGTACCTCTTCCAAG
genomic: CGCAACTTCACCGCAGCCATGgcgagtcttc ... cattgtgcagATTATCCCCGAGAAGAATCGGAGAGAGATCTCCAAGTACCTCTTCCAAG
EST: gi|37189321|gb|CF608670.1|CF608670
EST:     TAGCCCTTGCCCTTGCGTGCCTTCTCTCTCGCAACTTCACCGCAGCCATG                         ATTATCCCCGAGAAGAATCGGAGAGAGATCTCCAAGTACCTCTTCCAAG
genomic: TAGCCCTTGCCCTTGCGTGCCTTCTCTCTCGCAACTTCACCGCAGCCATGgcgagtcttc ... cattgtgcagATTATCCCCGAGAAGAATCGGAGAGAGATCTCCAAGTACCTCTTCCAAG
EST: gi|110692508|gb|EE071834.1|EE071834
EST:     CTTCTCTCTCGCAACTTCACCGCAGCCATG                         ATTATCCCCGAGAAGAATCGGAGAGAGATCTCCAAGTACCTCTTCCAAG
genomic: CTTCTCTCTCGCAACTTCACCGCAGCCATGgcgagtcttc ... cattgtgcagATTATCCCCGAGAAGAATCGGAGAGAGATCTCCAAGTACCTCTTCCAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tctttgcaaatctgtgtttctgtgaagtaactgttttgttaattccattgtgcagATTATCCCCGAGAAGAATCGGAGAGAGATCTCCAAGTACCTCTTCCAAG
                                          ttccatt  CT-rich tract
                                 ttttgttaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gcgagtcttcctcagcatttcgcactttttctctttgcaaatctgtgtttctgtgaagtaactgttttgttaattccattgtgcagATTATCCCCGAGAAGAATCGGAGAGAGATCTCCAAGTACCTCTTCCAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATC