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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtattgtaatcataactctagccttcatttcttgatttcatctctgatgatctgtaattgatgcttctttgccacctaaaacatcatacccattttgttagGAACAACATTGACAAGAGGGAGGCACTTGAGAACTTGGATCTCATTCTCCTATGCCTTGATGAGATTGTTGATGGAGG

Basic information

species Vitis vinifera
transcript Vv09s0002g01710.t01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv09s0002g01710.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA07G01000.1 (Glycine max), 3'ss of exon 3
gtattgtaatcataactctagccttcatttcttgatttcatctctgatgatctgtaattgatgcttctttgccacctaaaacatcatacccattttgttagGAACAACATTGACAAGAGGGAGGCACTTGAGAACTTGGATCTCATTCTCCTATGCCTTGATGAGATTGTTGATGGAGG
     ||| |  |   | ||   ||  | ||| ||||| |   ||||||     | | ||||  | || ||     ||   |    ||  | ||||   |||| |||  ||||||| || |||||||||||||||||||||||||||||| | || ||||| |||||||||||||||||
-----gtatttttggttgta--tttgctatctggatttaaaacctgatgcgtctttactgatcatgctctgt-gtttattcctctgtatgccttttac-agGAGCAATGTTGACAAAAGAGAGGCACTTGAGAACTTGGATCTCATTCTCTTGTGTCTTGACGAGATTGTTGATGGAGG

upper sequence: Vv09s0002g01710.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA08G20370.1 (Glycine max), 3'ss of exon 3
gtattgtaatcataactctagccttcatttcttgatttcatctctgatgatctgtaattgatgcttctttgccacctaaaacatcatacccattttgttagGAACAACATTGACAAGAGGGAGGCACTTGAGAACTTGGATCTCATTCTCCTATGCCTTGATGAGATTGTTGATGGAGG
            ||  | | |   | || ||||||||| |   ||||||  |  | | ||||  | || ||     |         ||     |||  |||||  ||  ||||||| || ||||||||||||||||| |||||||||||||| || ||||| |||||||||||||||||
-----------gtatttttggttgt-atatcttgatttaaaacctgatgtgcctttactgatcatgctctgtgtgtt---------tattgccttttatagGAGTAATGTTGACAAAAGAGAGGCACTTGAGAACTTAGATCTCATTCTCCTGTGTCTTGACGAGATTGTTGATGGAGG

upper sequence: Vv09s0002g01710.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA13G42470.1 (Glycine max), 3'ss of exon 3
gtattgtaatcataactctagccttcatttcttgatttcatctctgatgatctgtaattgatgcttctttgccacctaaaacatcatacccattttgtt---agGAACAACATTGACAAGAGGGAGGCACTTGAGAACTTGGATCTCATTCTCCTATGCCTTGATGAGATTGTTGATGGAGG
||||| ||     || | |    |     | || | || |  |    |  |||  |  | |||||||||         | |  |  |     |    ||   ||||||||  ||||||| || ||||| || || |||||||| ||||||||  ||||||||||||||||||||||||||||
gtattttaggtcgaattttgctatctggattttaaatttagatgcacttttcttca--tcatgcttcttctgtcttgtatattttttttttgtgccatttacagGAACAATGTTGACAAAAGAGAGGCGCTGGAAAACTTGGACCTCATTCTTTTATGCCTTGATGAGATTGTTGATGGAGG

upper sequence: Vv09s0002g01710.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA15G02910.1 (Glycine max), 3'ss of exon 4
gtattgtaatcataactctagccttcatttcttgatttcatctctgatgatctgtaattgatgcttctttgccacctaaaacatcatacccattttgttagGAACAACATTGACAAGAGGGAGGCACTTGAGAACTTGGATCTCATTCTCCTATGCCTTGATGAGATTGTTGATGGAGG
                                                                                          | ||||   ||||||||  ||||||| || |||||||| || |||||||| ||||||||  |||||||||||||||||||||  ||   
---------------------------------------------------------------------------------------gtgccttttac-aggaacaatgttgacaaaagAGAGGCACTGGAAAACTTGGACCTCATTCTTTTATGCCTTGATGAGATTGTTGGAGG---

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|110729434|gb|EE105385.1|EE105385
EST:     TTAGCCACAGTTCTTCAGGGCTTCTCCGATGCAGTTGCCCTTCTCCTCAG                         GAACAACATTGACAAGAGGGAGGCACTTGAGAACTTGGATCTCATTCTCCT
genomic: TTAGCCACAGTTCTTCAGGGCTTCTCCGATGCAGTTGCCCTTCTCCTCAGgtattgtaat ... attttgttagGAACAACATTGACAAGAGGGAGGCACTTGAGAACTTGGATCTCATTCTCCT
EST: gi|110689128|gb|EE065079.1|EE065079
EST:     TTAGCCACAGTTCTTCAGGGCTTCTCCGATGCAGTTGCCCTTCTCCTCAG                         GAACAACATTGACAAGAGGGAGGCACTTGAGAACTTGGATCTCATTCTCCT
genomic: TTAGCCACAGTTCTTCAGGGCTTCTCCGATGCAGTTGCCCTTCTCCTCAGgtattgtaat ... attttgttagGAACAACATTGACAAGAGGGAGGCACTTGAGAACTTGGATCTCATTCTCCT
EST: gi|71882963|gb|DT032018.1|DT032018
EST:     TTAGCCACAGTTCTTCAGGGCTTCTCCGATGCAGTTGCCCTTCTCCTCAG                         GAACAACATTGACAAGAGGGAGGCACTTGAGAACTTGGATCTCATTCTCCT
genomic: TTAGCCACAGTTCTTCAGGGCTTCTCCGATGCAGTTGCCCTTCTCCTCAGgtattgtaat ... attttgttagGAACAACATTGACAAGAGGGAGGCACTTGAGAACTTGGATCTCATTCTCCT
EST: gi|110715702|gb|EE094055.1|EE094055
EST:     TTAGCCACAGTTCTTCAGGGCTTCTCCGATGCAGTTGCCCTTCTCCTCAG                         GAACAACATTGACAAGAGGGAGGCACTTGAGAACTTGGATCTCATTCTCCT
genomic: TTAGCCACAGTTCTTCAGGGCTTCTCCGATGCAGTTGCCCTTCTCCTCAGgtattgtaat ... attttgttagGAACAACATTGACAAGAGGGAGGCACTTGAGAACTTGGATCTCATTCTCCT
EST: gi|30298228|gb|CB975022.1|CB975022
EST:     TTAGCCACAGTTCTTCAGGGCTTCTCTGATGCAGTTGCCCTTCTCCTCAG                         GAACAACATTGACAAGAGGGAGGCACTTGAGAACTTGGATCTCATTCTCCT
genomic: TTAGCCACAGTTCTTCAGGGCTTCTCCGATGCAGTTGCCCTTCTCCTCAGgtattgtaat ... attttgttagGAACAACATTGACAAGAGGGAGGCACTTGAGAACTTGGATCTCATTCTCCT
EST: gi|110376897|gb|EC941971.1|EC941971
EST:     TTAGCCACAGTTCTTCAGGGCTTCTCCGATGCAGTTGCCCTTCTCCTCAG                         GAACAACATTGACAAGAGGGAGGCACTTGAGAACTTGGATCTCATTCTCCT
genomic: TTAGCCACAGTTCTTCAGGGCTTCTCCGATGCAGTTGCCCTTCTCCTCAGgtattgtaat ... attttgttagGAACAACATTGACAAGAGGGAGGCACTTGAGAACTTGGATCTCATTCTCCT
EST: gi|110694240|gb|EE071171.1|EE071171
EST:     TTAGCCACAGTTCTTCAGGGCTTCTCCGATGCAGTTGCCCTTCTCCTCAG                         GAACAACATTGACAAGAGGGAGGCACTTGAGAACTTGGATCTCATTCTCCT
genomic: TTAGCCACAGTTCTTCAGGGCTTCTCCGATGCAGTTGCCCTTCTCCTCAGgtattgtaat ... attttgttagGAACAACATTGACAAGAGGGAGGCACTTGAGAACTTGGATCTCATTCTCCT
EST: gi|32460975|gb|CD802149.1|CD802149
EST:     TTAGCCACAGTTCTTCAGGGCTTCTCTGATGCAGTTGCCCTTCTCCTCAG                         GAACAGCATTGACAAGAGGGAGGCACTTGAGAACTTGGATCTCATTCTCCT
genomic: TTAGCCACAGTTCTTCAGGGCTTCTCCGATGCAGTTGCCCTTCTCCTCAGgtattgtaat ... attttgttagGAACAACATTGACAAGAGGGAGGCACTTGAGAACTTGGATCTCATTCTCCT
EST: gi|77583199|gb|DV220638.1|DV220638
EST:     TTAGCCACAGTTCTTCAGGGCTTCTCTGATGCAGTTGCCCTTCTCCTCAG                         GAACAACATTGACAAGAGGGAGGCACTTGAGAACTTGGATCTCATTCTCCT
genomic: TTAGCCACAGTTCTTCAGGGCTTCTCCGATGCAGTTGCCCTTCTCCTCAGgtattgtaat ... attttgttagGAACAACATTGACAAGAGGGAGGCACTTGAGAACTTGGATCTCATTCTCCT
EST: gi|110723706|gb|EE101328.1|EE101328
EST:     TTAGCCACAGTTCTTCAGGGCTTCTCCGATGCAGTTGCCCTTCTCCTCAG                         GAACAACATTGACAAGAGGGAGGCACTTGAGAACTTGGATCTCATTCTCCT
genomic: TTAGCCACAGTTCTTCAGGGCTTCTCCGATGCAGTTGCCCTTCTCCTCAGgtattgtaat ... attttgttagGAACAACATTGACAAGAGGGAGGCACTTGAGAACTTGGATCTCATTCTCCT
EST: gi|71875897|gb|DT024952.1|DT024952
EST:     TTAGCCACAGTTCTTCAGGGCTTCTCCGATGCAGTTGCCCTTCTCCTCAG                         GAACAACATTGACAAGAGGGAGGCACTTGAGAACTTGGATCTCATTCTCCT
genomic: TTAGCCACAGTTCTTCAGGGCTTCTCCGATGCAGTTGCCCTTCTCCTCAGgtattgtaat ... attttgttagGAACAACATTGACAAGAGGGAGGCACTTGAGAACTTGGATCTCATTCTCCT
EST: gi|71873249|gb|DT022304.1|DT022304
EST:     TTAGCCACAGTTCTTCAGGGCTTCTCTGATGCAGTTGCCCTTCTCCTCAG                         GAACAACATTGACAAGAGGGAGGCACTTGAGAACTTGGATCTCATTCTCCT
genomic: TTAGCCACAGTTCTTCAGGGCTTCTCCGATGCAGTTGCCCTTCTCCTCAGgtattgtaat ... attttgttagGAACAACATTGACAAGAGGGAGGCACTTGAGAACTTGGATCTCATTCTCCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atgatctgtaattgatgcttctttgccacctaaaacatcatacccattttgttagGAACAACATTGACAAGAGGGAGGCACTTGAGAACTTGGATCTCATTCTCCTATGCCTTGATGAGATTGTTGATGGAGG
                           acctaaa  putative branch site (score: 3)
                                          cccatttt  putative PPT
                                             attttgtta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtattgtaatcataactctagccttcatttcttgatttcatctctgatgatctgtaattgatgcttctttgccacctaaaacatcatacccattttgttagGAACAACATTGACAAGAGGGAGGCACTTGAGAACTTGGATCTCATTCTCCTATGCCTTGATGAGATTGTTGATGGAGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGG