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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gaactgttttaacaacctcaaaggtagcttcatattttcttctcttttttaagcattttatttttgttttgttttgttttgttttgttttatttttgcagCCATTGCTGTTCGAGATAAGCTTGAGTCACTGTGTAGGGAATTACAACGTCAGAACAAATTGCTAATG

Basic information

species Vitis vinifera
transcript Vv13s0019g03960.t01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv13s0019g03960.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA20G31830.1 (Glycine max), 3'ss of exon 5
-gaact---gttttaacaacctcaaaggtagcttcatattttcttctcttttttaagcatttt-atttttgttttgttttgttttgttttgt-tttatttttgcagCCATTGCTGTTCGAGATAAGCTTGAGTCACTGTGTAGGGAATTACAACGTCAGAACAAATTGCTAATG
   |||    ||||   || || |||      |  ||     | |||  | | ||| ||  || ||  |  || |  | | ||  || |||  ||| |||||| |||  |||| || ||||||||||||||||||||||| || || |||||||| || || ||| |||| |||
aagactcacatttttgtaatcttaaa------taaatgacagcatctaatctgtaaccacattgatgctaattcttgtctattgagtgttgcctttctttttgtagCTCTTGCCGTCCGAGATAAGCTTGAGTCACTGTGCAGAGAGTTACAACGCCAAAATAAAATGCTGATG

upper sequence: Vv13s0019g03960.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: AT5G50840.2 (Arabidopsis thaliana), 3'ss of exon 3
---gaactgttttaacaacctcaaaggtagcttcatattttcttctcttttttaagcattttatttttgttttgttttgttttgttttgttttatttttgcagCCATTGCTGTTCGAGATAAGCTTGAGTCACTGTGTAGGGAATTACAACGTCAGAACAAATTGCTAATG
     |   | | || ||   ||||  ||| ||  | ||  ||||    ||| | ||      ||| |  | |||  |  |   | ||||||| |    | ||| ||| ||||||| || |||||||| ||||| ||||| || |||||||||||||||||| || |||||
gtaataggatatcaataaaaccaaac-tagttttgtgttaccttcatcgtttaatgc------tttatagtctgtactcatcattattgtttt-taaccgtagCTATTACTGTTCGTGACAAGCTTGAATCACTTTGTAGAGAGTTACAACGTCAGAACAAAATGTTAATG
















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|352782197|gb|FQ470099.1|FQ470099
EST:     TCTGGAATTCTCTTTGAAATATCAACAGGTTATAGCAGAAAGAGATACGG                         CCATTGCTGTTCGAGATAAGCTTGAGTCACTGTGTAGGGAATTACAACGTC
genomic: TCTGGAATTCTCTTTGAAATATCAACAGGTTATAGCAGAAAGAGATACGGgtaagtagaa ... atttttgcagCCATTGCTGTTCGAGATAAGCTTGAGTCACTGTGTAGGGAATTACAACGTC
EST: gi|351029666|gb|FQ427506.1|FQ427506
EST:     TCTGGAATTCTCTTTGAAATATCAACAGGTTATAGCAGAAAGAGATACGG                         CCATTGCTGTTCGAGATAAGCTTGAGTCACTGTGTAGGGAATTACAACGTC
genomic: TCTGGAATTCTCTTTGAAATATCAACAGGTTATAGCAGAAAGAGATACGGgtaagtagaa ... atttttgcagCCATTGCTGTTCGAGATAAGCTTGAGTCACTGTGTAGGGAATTACAACGTC
EST: gi|351025048|gb|FQ433465.1|FQ433465
EST:     TCTGGAATTCTCTTTGAAATATCAACAGGTTATAGCAGAAAGAGATACGG                         CCATTGCTGTTCGAGATAAGCTTGAGTCACTGTGTAGGGAATTACAACGTC
genomic: TCTGGAATTCTCTTTGAAATATCAACAGGTTATAGCAGAAAGAGATACGGgtaagtagaa ... atttttgcagCCATTGCTGTTCGAGATAAGCTTGAGTCACTGTGTAGGGAATTACAACGTC
EST: gi|110711711|gb|EE088504.1|EE088504
EST:     TCTGGAATTCTCTTTGAAATATCAACAGGTTATAGCAGAAAGAGATACGG                         CCATTGCTGTTCGAGATAAGCTTGAGTCACTGTGTANGGAATTACAACGTC
genomic: TCTGGAATTCTCTTTGAAATATCAACAGGTTATAGCAGAAAGAGATACGGgtaagtagaa ... atttttgcagCCATTGCTGTTCGAGATAAGCTTGAGTCACTGTGTAGGGAATTACAACGTC
EST: gi|30255027|gb|CB971474.1|CB971474
EST:     TCTGGAATTCTCTTTGAAATATCAACAGGTTATAGCAGAAAGAGATACGG                         CCATTGCTGTTCGAGATAAGCTTGAGTCACTGTGTAGGGAATTACAACGTC
genomic: TCTGGAATTCTCTTTGAAATATCAACAGGTTATAGCAGAAAGAGATACGGgtaagtagaa ... atttttgcagCCATTGCTGTTCGAGATAAGCTTGAGTCACTGTGTAGGGAATTACAACGTC
EST: gi|352769260|gb|FQ471409.1|FQ471409
EST:     TCTGGAATTCTCTTTGAAATATCAACAGGTTATAGCAGAGAGAGATACGG                         CCATTGCTGTTCGAGATAAGCTTGAGTCACTGTGTAGGGAATTACAACGTC
genomic: TCTGGAATTCTCTTTGAAATATCAACAGGTTATAGCAGAAAGAGATACGGgtaagtagaa ... atttttgcagCCATTGCTGTTCGAGATAAGCTTGAGTCACTGTGTAGGGAATTACAACGTC
EST: gi|110713047|gb|EE088636.1|EE088636
EST:     TCTGGAATTCTCTTTGAAATATCAACAGGTTATAGCAGAAAGAGATACGG                         CCATTGCTGTTCGAGATAAGCTTGAGTCACTGTGTANGGAATTA-AACGTC
genomic: TCTGGAATTCTCTTTGAAATATCAACAGGTTATAGCAGAAAGAGATACGGgtaagtagaa ... atttttgcagCCATTGCTGTTCGAGATAAGCTTGAGTCACTGTGTAGGGAATTACAACGTC
EST: gi|351023970|gb|FQ423393.1|FQ423393
EST:     TCTGGAATTCTCTTTGAAATATCAACAGGTTATAGCAGAAAGAGATACGG                         CCATTGCTGTTCGAGATAAGCTTGAGTCACTGTGTAGGGAATTACAACGTC
genomic: TCTGGAATTCTCTTTGAAATATCAACAGGTTATAGCAGAAAGAGATACGGgtaagtagaa ... atttttgcagCCATTGCTGTTCGAGATAAGCTTGAGTCACTGTGTAGGGAATTACAACGTC
EST: gi|30254970|gb|CB971417.1|CB971417
EST:     TCTGGAATTCTCTTTGAAATATCAACAGGTTATAGCAGAAAGAGATACGG                         CCATTGCTGTTCGAGATAAGCTTGAGTCACTGTGTAGGGAATTACAACGTC
genomic: TCTGGAATTCTCTTTGAAATATCAACAGGTTATAGCAGAAAGAGATACGGgtaagtagaa ... atttttgcagCCATTGCTGTTCGAGATAAGCTTGAGTCACTGTGTAGGGAATTACAACGTC
EST: gi|351029504|gb|FQ436898.1|FQ436898
EST:     TCTGGAATTCTCTTTGAAATATCAACAGGTTATAGCAGAAAGAGATACGG                         CCATTGCTGTTCCAGATAAGCT
genomic: TCTGGAATTCTCTTTGAAATATCAACAGGTTATAGCAGAAAGAGATACGGgtaagtagaa ... atttttgcagCCATTGCTGTTCGAGATAAGCT
EST: gi|110721939|gb|EE097735.1|EE097735
EST:     TCTGGAATTCTCTTTGAAATATCAACAGGTTATAGCAGAAAGAGATACGG                         CCATTGCTGTTCGAGATAAGCTTGAGTCACTGTGTAGGGAATTACAACGTC
genomic: TCTGGAATTCTCTTTGAAATATCAACAGGTTATAGCAGAAAGAGATACGGgtaagtagaa ... atttttgcagCCATTGCTGTTCGAGATAAGCTTGAGTCACTGTGTAGGGAATTACAACGTC
EST: gi|110711601|gb|EE088266.1|EE088266
EST:     TCTGGAATTCTCTTTGAAATATCAACAGGTTATAGCAGAAAGAGATACGG                         CCATTGCTGTTCGAGATAAGCTTGAGTCACTGTGTAGGNAATTACAACGTC
genomic: TCTGGAATTCTCTTTGAAATATCAACAGGTTATAGCAGAAAGAGATACGGgtaagtagaa ... atttttgcagCCATTGCTGTTCGAGATAAGCTTGAGTCACTGTGTAGGGAATTACAACGTC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttttaagcattttatttttgttttgttttgttttgttttgttttatttttgcagCCATTGCTGTTCGAGATAAGCTTGAGTCACTGTGTAGGGAATTACAACGTCAGAACAAATTGCTAATG
                                    ttttgttttattttt  CT-rich tract
         attttatttttgtttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gaactgttttaacaacctcaaaggtagcttcatattttcttctcttttttaagcattttatttttgttttgttttgttttgttttgttttatttttgcagCCATTGCTGTTCGAGATAAGCTTGAGTCACTGTGTAGGGAATTACAACGTCAGAACAAATTGCTAATG

- - - - - - caacctc
- - - - - - - - - -aaaggta
- - - - - - - - - - - - - - - - - - - - - - - - ttaagca