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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGTATTTTTATTTCAAGCTCAGGAGATCAAGCCCATTCAATGAGTGGAAATGgtactcccttgttcttctaccctgcatttcttacagaaaaattgaatgcttgaatgcaagtttactgatcctggtttggcttaggttctaacgttttacc...

Basic information

species Vitis vinifera
transcript Vv13s0084g00660.t01
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv13s0084g00660.t01 (Vitis vinifera), 5'ss of exon 9
lower sequence: GLYMA10G44270.1 (Glycine max), 5'ss of exon 7
GGTATTTTTATTTCAAGCTCAGGAGATCAAGCCCATTCAATGAGTGGAAATGgtactcccttgttcttctaccctgcatttcttacagaaaaattga-atgcttgaatgcaagtt----tactgatcctggtttggcttaggttctaacgttttacc--------------------------------------------------------------------------
|| || ||||| |||| |||||| |||||||| ||||||||||||||||||||||  |   | |||||  |   |  |||  || || ||   || | ||   ||     ||  |    |  |  |  | || |   ||| ||| || |   |||                                                                            
GGAATCTTTATATCAAACTCAGGTGATCAAGCACATTCAATGAGTGGAAATGgtatcctgct-ttcttaaatattttattcattccacaagttttaatatcaatgtccataaaatgtagtgttattatttgtgtctgttatgttgtaccaaattatttcaggaatgttttaacttttaatttctcctgttatatgatatatgagataataaaaaactatgttgttttacag

upper sequence: Vv13s0084g00660.t01 (Vitis vinifera), 5'ss of exon 9
lower sequence: GLYMA20G39050.2 (Glycine max), 5'ss of exon 7
GGTATTTTTATTTCAAGCTCAGGAGATCAAGCCCATTCAATGAGTGGAAATGgtactcccttgttcttctaccctgcatttcttacagaaaaattgaatgcttgaatgcaagtttactgatcctggtttggcttaggt-tctaacgttttacc--------------------------------------------------------------------
|| ||  |||| |||| |||||| |||||||| |||||||||||||||||||||| ||| |  |||||  |   |  |||  || || ||   || |||      ||| |   | |    |  |||| |   ||  || | | | ||| ||||                                                                    
GGAATCATTATATCAAACTCAGGTGATCAAGCACATTCAATGAGTGGAAATGgta-tccttctttcttaaatattttattcattccacaagtttt-aatatcaatatg-accataaaaagtagtggtattatttgtgtctgttatgttgtaccaaactatttcaggaatgttttcatttctcctgttatatgagataataaataactatgttgttttatag
















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|156737550|gb|EV241663.1|EV241663
EST:     TATTTTTATTTCAAGCTCAGGAGATCAAGCCCATTCAATGAGTGGAAATG                         GGGCCATGGCATTTGATGTAGAATATGCTAGGTGGCTGGAAGAGCAGAACC
genomic: TATTTTTATTTCAAGCTCAGGAGATCAAGCCCATTCAATGAGTGGAAATGgtactccctt ... cttctgtcagGGGCCATGGCATTTGATGTAGAATATGCTAGGTGGCTGGAAGAGCAGAACC
EST: gi|110687850|gb|EE065730.1|EE065730
EST:     TATTTTTATTTCAAGCTCAGGAGATCAAGCCCATTCAATGAGTGGAAATG                         GGGCCATGGCATTTGATGTAGAATATGCTAGGTGGCTGGAAGAGCAGAACC
genomic: TATTTTTATTTCAAGCTCAGGAGATCAAGCCCATTCAATGAGTGGAAATGgtactccctt ... cttctgtcagGGGCCATGGCATTTGATGTAGAATATGCTAGGTGGCTGGAAGAGCAGAACC
EST: gi|30301282|gb|CB978076.1|CB978076
EST:     TATTTTTATTTCAAGCTCAGGAGATCAAGCCCATTCAATGAGTGGAAATG                         GGGCCATGGCATTTGATGTAGAATATGCTAGGTGGCTGGAAGAGCAGAACC
genomic: TATTTTTATTTCAAGCTCAGGAGATCAAGCCCATTCAATGAGTGGAAATGgtactccctt ... cttctgtcagGGGCCATGGCATTTGATGTAGAATATGCTAGGTGGCTGGAAGAGCAGAACC
EST: gi|110685242|gb|EE063437.1|EE063437
EST:     TATTTTTATTTCAAGCTCAGGAGATCAAGCCCATTCAATGAGTGGAAATG                         GGGCCATGGCATTTGATGTAGAATATGCTAGGTGGCTGGAAGAGCAGAACC
genomic: TATTTTTATTTCAAGCTCAGGAGATCAAGCCCATTCAATGAGTGGAAATGgtactccctt ... cttctgtcagGGGCCATGGCATTTGATGTAGAATATGCTAGGTGGCTGGAAGAGCAGAACC
EST: gi|77583990|gb|DV221036.1|DV221036
EST:     TATTTTTATTTCAAGCTCAGGAGATCAAGCCCATTCAATGAGTGGAAATG                         GGGCCATGGCATTTGATGTAGAATATGCTAGGTGGCTGGAAGAGCAGAACC
genomic: TATTTTTATTTCAAGCTCAGGAGATCAAGCCCATTCAATGAGTGGAAATGgtactccctt ... cttctgtcagGGGCCATGGCATTTGATGTAGAATATGCTAGGTGGCTGGAAGAGCAGAACC
EST: gi|110383071|gb|EC947420.1|EC947420
EST:     TATTTTTATTTCAAGCTCAGGAGATCAAGCCCATTCAATGAGTGGAAATG                         GGGCCATGGCATTTGATGTAGAATATGCTAGGTGGCTGGAAGAGCAGAACC
genomic: TATTTTTATTTCAAGCTCAGGAGATCAAGCCCATTCAATGAGTGGAAATGgtactccctt ... cttctgtcagGGGCCATGGCATTTGATGTAGAATATGCTAGGTGGCTGGAAGAGCAGAACC
EST: gi|110428204|gb|EC994669.1|EC994669
EST:     TATTTTTATTTCAAGCTCAGGAGATCAAGCCCATTCAATGAGTGGAAATG                         GGGCCATGGCATTTGATGTAGAATATGCTAGGTGGCTGGAAGAGCAGAACC
genomic: TATTTTTATTTCAAGCTCAGGAGATCAAGCCCATTCAATGAGTGGAAATGgtactccctt ... cttctgtcagGGGCCATGGCATTTGATGTAGAATATGCTAGGTGGCTGGAAGAGCAGAACC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGTATTTTTATTTCAAGCTCAGGAGATCAAGCCCATTCAATGAGTGGAAATGgtactcccttgttcttctaccctgcatttcttacagaaaaattgaatgcttgaatgcaagtttactgatcctggtttggcttaggttctaacgttttacc

- - - - - -  CAAGCT
- - - - - - -  AGCTCA
- - - - - - - - - - AGGAGA
- - - - - - - - - -  GGAGAT
- - - - - - - - - - - GAGATC
- - - - - - - - - - -  AGATCA
- - - - - - - - - - - - - - - - - - - - - AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - agaaaaa