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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atctcaaagctgcttggattaatttttgatagaatttattttaccagaatgtcgttttttcttgggttttgttaatctaaactcttccaaggacattcagGGAGGAAATATTCTGATTGGTGGGTCCACTGTAGAATCTGAGGGAAATTTTGTGCAGCCAACAATCGTTGAGATTTCTCCAAATGCCTCTGTAGTTAAGG

Basic information

species Vitis vinifera
transcript Vv11s0016g00900.t01
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv11s0016g00900.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: GLYMA09G08150.1 (Glycine max), 3'ss of exon 10
---------------------------------------------------------------------------atctcaaagctgcttggattaatttttgatagaatttattttaccagaatgtcgttt-tttcttgggttttgttaatctaaactcttccaaggacattcagGGAGGAAATATTCTGATTGGTGGGTCCACTGTAGAATCTGAGGGAAATTTTGTGCAGCCAACAATCGTTGAGATTTCTCCAAATGCCTCTGTAGTTAAGG
                                                                            |  |  ||  |  |     |  ||||  |   |  |||   ||      |  | || | |  || ||   | |||| ||     | |   |   || |||||||| || || || |  ||||| ||     |||| || |  ||||||||||| || |||||||| ||||||||||||||| ||||  |||||||||| |
gcatggttcattttactctttttctagttaagttaaatatttaggggatgtaaccttccatttcatgtctgtaattttgctcagtaggatatgcaagctttttctcatacatataccacggattggatgcttgtcttctgtgtagagataatttacttgatactctgattat-cagGGAGGGAAAATCCTAACCGGTGGATCTGTATTAGAGTCGGGAGGAAATTTTGTACAACCAACAATTGTTGAGATTTCTCCAGATGCTCCTGTAGTTAAAG

upper sequence: Vv11s0016g00900.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: GLYMA15G19670.1 (Glycine max), 3'ss of exon 10
--------------------------------------------------------------------------atctcaaagctgcttggattaatttttgatagaatttattttaccagaatgtcgttt-tttcttgggttttgttaatctaaactcttccaaggacattcagGGAGGAAATATTCTGATTGGTGGGTCCACTGTAGAATCTGAGGGAAATTTTGTGCAGCCAACAATCGTTGAGATTTCTCCAAATGCCTCTGTAGTTAAGG
                                                                           |  |  ||     |        ||||| |   |  |||   |       |  | || | |  || ||   | |||| ||     | |   |   || |||||||| || || || |  ||||| ||     |||| || |  ||||||||||| || |||||||| ||||||||||||||  ||||  |||||||||| |
gtatgtttcatttcactattttctagttatgttaaatatttaggggatgtaaccttccatttcatatctgtaattttgctcagtaagatatgcaggcttttgctcatacatatacaatggattggatgcttgtattctgtgtagagataatttacttgatactctgattat-cagGGAGGGAAGATCCTAACAGGTGGATCTGTATTAGAGTCAGCAGGAAATTTTGTACAACCAACAATTGTTGAGATTTCTCCCGATGCTCCTGTAGTTAAAG
















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|349820814|gb|FQ404199.1|FQ404199
EST:     GTGCTTCGAAGGAGAACTTTGAGAAGTGCATTGAGATCATAAAATTTCAG                         GGAGGAAATATTCTGATTGGTGGGTCCACTGTAGAATCTGAGGGAAATTTT
genomic: GTGCTTCGAAGGAGAACTTTGAGAAGGGCATTGAGATCATAAAATTTCAGgcatgtatct ... ggacattcagGGAGGAAATATTCTGATTGGTGGGTCCACTGTAGAATCTGAGGGAAATTTT
EST: gi|33405776|gb|CF211403.1|CF211403
EST:     GTGCTTCGAAGGAGAACTTTGAGAAGGGCATTGAGATCATAAAATTTCAG                         GGAGGAAATATTCTGATTGGTGGGTCCACTGTAGAATCTGAGGGAAATTTT
genomic: GTGCTTCGAAGGAGAACTTTGAGAAGGGCATTGAGATCATAAAATTTCAGgcatgtatct ... ggacattcagGGAGGAAATATTCTGATTGGTGGGTCCACTGTAGAATCTGAGGGAAATTTT
EST: gi|351015872|gb|FQ431827.1|FQ431827
EST:     GTGCTTCGAAGGAGAACTTTGAGAAGTGCATTGAGATCATAAAATTTCAG                         GGAGGAAATATTCTGATTGGTGGGTCCACTGTAGAATCTGAGGGAAATTTT
genomic: GTGCTTCGAAGGAGAACTTTGAGAAGGGCATTGAGATCATAAAATTTCAGgcatgtatct ... ggacattcagGGAGGAAATATTCTGATTGGTGGGTCCACTGTAGAATCTGAGGGAAATTTT
EST: gi|349816247|gb|FQ403743.1|FQ403743
EST:     GTGCTTCGAAGGAGAACTTTGAGAAGCGCATTGAGATCATAAAATTTCAG                         GGAGGAAATATTCTGATTGGTGGGTCCACTGTAGAATCTGAGGGAAATTTT
genomic: GTGCTTCGAAGGAGAACTTTGAGAAGGGCATTGAGATCATAAAATTTCAGgcatgtatct ... ggacattcagGGAGGAAATATTCTGATTGGTGGGTCCACTGTAGAATCTGAGGGAAATTTT
EST: gi|349819677|gb|FQ402614.1|FQ402614
EST:     GTGCTTCGAAGGAGAACTTTGAGAAGTGCATTGAGATCATAAAATTTCAG                         GGAGGAGATATTCTGATTGGTGGGTCCACTGTAGAATCTGAGGGAAATTTT
genomic: GTGCTTCGAAGGAGAACTTTGAGAAGGGCATTGAGATCATAAAATTTCAGgcatgtatct ... ggacattcagGGAGGAAATATTCTGATTGGTGGGTCCACTGTAGAATCTGAGGGAAATTTT
EST: gi|351019460|gb|FQ429595.1|FQ429595
EST:     GTGCTTCGAAGGAGAACTTTGAGAAGTGCATTGAGATCATAAAATTTCAG                         GGAGGAGATATTCTGATTGGTGGGTCCACTGTAGAATCTGAGGGAAATTTT
genomic: GTGCTTCGAAGGAGAACTTTGAGAAGGGCATTGAGATCATAAAATTTCAGgcatgtatct ... ggacattcagGGAGGAAATATTCTGATTGGTGGGTCCACTGTAGAATCTGAGGGAAATTTT
EST: gi|349817443|gb|FQ405447.1|FQ405447
EST:     GTGCTTCGAAGGAGAACTTTGAGAAGTGCATTGAGATCATAAAATTTCAG                         GGAGGAGATATTCTGATTGGTGGGTCCACTGTAGAATCTGAGGGAAATTTT
genomic: GTGCTTCGAAGGAGAACTTTGAGAAGGGCATTGAGATCATAAAATTTCAGgcatgtatct ... ggacattcagGGAGGAAATATTCTGATTGGTGGGTCCACTGTAGAATCTGAGGGAAATTTT
EST: gi|349808691|gb|FQ405835.1|FQ405835
EST:     GTGCTTCGAAGGAGAACTTTGAGAAGTGCATTGAGATCATAAAATTTCAG                         GGAGGAAATATTCTGATTGGTGGGTCCACTGTAGAATCTGAGGGAAATTTT
genomic: GTGCTTCGAAGGAGAACTTTGAGAAGGGCATTGAGATCATAAAATTTCAGgcatgtatct ... ggacattcagGGAGGAAATATTCTGATTGGTGGGTCCACTGTAGAATCTGAGGGAAATTTT
EST: gi|351027458|gb|FQ444707.1|FQ444707
EST:     GTGCTTCGAAGGAGAACTTTGAGAAGTGCATTGAGATCATAAAATTTCAG                         GGAGGAAATATTCTGATTGGTGGGTCCACTGTAGAATCTGAGGGAAATTTT
genomic: GTGCTTCGAAGGAGAACTTTGAGAAGGGCATTGAGATCATAAAATTTCAGgcatgtatct ... ggacattcagGGAGGAAATATTCTGATTGGTGGGTCCACTGTAGAATCTGAGGGAAATTTT
EST: gi|349817851|gb|FQ407840.1|FQ407840
EST:     GTGCTTCGAAGGAGAACTTTGAGAAGTGCATTGAGATCATAAAATTTCAG                         GGAGGAGATATTCTGATTGGTGGGTCCACTGTAGAATCTGAGGGAAATTTT
genomic: GTGCTTCGAAGGAGAACTTTGAGAAGGGCATTGAGATCATAAAATTTCAGgcatgtatct ... ggacattcagGGAGGAAATATTCTGATTGGTGGGTCCACTGTAGAATCTGAGGGAAATTTT
EST: gi|351033661|gb|FQ462191.1|FQ462191
EST:     GTGCTTCGAAGGAGAACTTTGAGAAGTGCATTGAGATCATAAAATTTCAG                         GGAGGAGATATTCTGATTGGTGGGTCCACTGTAGAATCTGAGGGAAATTTT
genomic: GTGCTTCGAAGGAGAACTTTGAGAAGGGCATTGAGATCATAAAATTTCAGgcatgtatct ... ggacattcagGGAGGAAATATTCTGATTGGTGGGTCCACTGTAGAATCTGAGGGAAATTTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agaatgtcgttttttcttgggttttgttaatctaaactcttccaaggacattcagGGAGGAAATATTCTGATTGGTGGGTCCACTGTAGAATCTGAGGGAAATTTTGTGCAGCCAACAATCGTTGAGATTTCTCCAAATGCCTCTGTAGTTAAGG
                             atctaaa  putative branch site (score: 3)
                     ttttgttaatctaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atctcaaagctgcttggattaatttttgatagaatttattttaccagaatgtcgttttttcttgggttttgttaatctaaactcttccaaggacattcagGGAGGAAATATTCTGATTGGTGGGTCCACTGTAGAATCTGAGGGAAATTTTGTGCAGCCAACAATCGTTGAGATTTCTCCAAATGCCTCTGTAGTTAAGG

- - - - - tgcttgg
- - - - - - - - - - - - - - - - - - - - - accagaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctcttcc