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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGTGTTTGCCTGGTTGATGCATTGGGCAATCGTACAATGCGGCCCTGTCTCTCAAGTGCTGTTAAGATTCAGgtgcatgcttcttttctggttttctttcttgtcacttaaatagtttaggctccaagtctttcttttcatacagttttcttattaagatgagcatacatggagtcttattattgttttgtcccttgcag

Basic information

species Vitis vinifera
transcript Vv18s0001g12750.t01
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv18s0001g12750.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: GLYMA17G37040.1 (Glycine max), 5'ss of exon 3
TGTGTTTGCCTGGTTGATGCATTGGGCAATCGTACAATGCGGCCCTGTCTCTCAAGTGCTGTTAAGATTCAGgtgcatgcttcttttctggttttctttcttgtcacttaaatagtttaggctccaagtctttcttttcatacagttttcttattaagatgagcatacatggagtcttattattgttttgtcccttgcag-
 |||||||  |||||||||  ||||| || ||||| ||||||||||||||||||| |||||| ||  ||||||| ||||| ||| |  ||  |    |   ||    |||  | |  | |     || |            ||||||              |  ||   |  ||| | |  |||  | |||   |||||| 
-GTGTTTGTTTGGTTGATGACTTGGGAAACCGTACCATGCGGCCCTGTCTCTCAAATGCTGTGAAAGTTCAGGtacatgcctctgtagtgtctcaaatatatgcgtgttatttggggtggaacataaatag--------gcacagtt-------------aaatat-tgttaagtttgacaattactctgttttttgcagg

upper sequence: Vv18s0001g12750.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: GLYMA04G03290.1 (Glycine max), 5'ss of exon 3
TGTGTTTGCCTGGTTGATGCATTGGGCAATCGTACAATGCGGCCCTGTCTCTCAAGTGCTGTTAAGATTCAGgtgcatgcttcttttctggttttctttcttgtcacttaaatagtttaggctccaagtctttcttttcatacagttttcttattaagatgagcatacatggagtcttattattgttttgtcccttg-cag
||||||||| |||| ||||   |||| || ||||||||||||||||||||||||| |||||| ||  ||||||| |    |    |||   |   |  | |  ||| ||    ||  |||| |   | |     | |    |  |   || | ||       |     ||| | |||   | || |||| |   ||| |||
TGTGTTTGCTTGGTAGATGACATGGGTAACCGTACAATGCGGCCCTGTCTCTCAAATGCTGTCAAAGTTCAGgtac---ttctaattcatatacaccctttcttcattttttgaggctaggttaggaattacgatgtctgaattgaagtcatgtttgtgcctgatattatgtattctctctctttttttcttttttggcag

upper sequence: Vv18s0001g12750.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: GLYMA14G07980.2 (Glycine max), 5'ss of exon 3
TGTGTTTGCCTGGTTGATGCATTGGGCAATCGTACAATGCGGCCCTGTCTCTCAAGTGCTGTTAAGATTCAGgtgcatgcttcttttctggttttctttcttgtcacttaaatagtttaggctccaagtctttcttttcatacagttttcttattaagatgagcatacatggagtcttattattgttttgtcccttgcag
||||||||  |||||||||  ||||| || ||||| ||||| ||||||||||| | |||||| ||  ||||||||||||  | | || ||| |          |       | |||| |   |  |     ||  |  ||   | | |  || ||                                             
TGTGTTTGTTTGGTTGATGACTTGGGAAACCGTACCATGCGACCCTGTCTCTCTAATGCTGTGAAAGTTCAGgtgcatgactatgttttgggtggaacataaatag---ggacagttaaatattaagtgagtttgtgacaattactctgttttttgcag-----------------------------------------

upper sequence: Vv18s0001g12750.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: AT1G19600.1 (Arabidopsis thaliana), 5'ss of exon 3
TGTGTTTGCCTGGTTGATGCATTGGGCAATCGTACAATGCGGCCCTGTCTCTCAAGTGCTGTTAAGATTCAGgtgcatgcttctt-ttctggttttctttcttgtcac-ttaaatagtttaggctccaagtctttcttttcatacagttttcttattaagatgagcatacatggagtcttattattgttttgtcccttgcag
||||||||| |||||||||  |  || ||||| |||||||| || |||||||| |||||||| |||||||||||   || ||||  || |  |    | | | || |  || ||| | || | |    ||      |  | | |    |||||  || ||                                          
TGTGTTTGCTTGGTTGATGACTCTGGTAATCGAACAATGCGACCATGTCTCTCGAGTGCTGTGAAGATTCAGgtttgtgtttctaatttttttgggatatatagttatattgaattggtttgtcagtgagaaaggatggtaaaaactatttctctttcag------------------------------------------

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|161712186|gb|FC061558.1|FC061558
EST:     TGGGCAATCGTACAATGCGGCCCTGTCTCTCAAGTGCTGTTAAGATTCAG                         GCAGAGGAATTAACTAAAGAGGATTTTAAAGGGGTAAAG
genomic: TGGGCAATCGTACAATGCGGCCCTGTCTCTCAAGTGCTGTTAAGATTCAGgtgcatgctt ... tcccttgcagGCAGAGGAATTAACTAAAGAGGATTTTAAAGGGGTAAAG
EST: gi|30125650|gb|CB910989.1|CB910989
EST:     TGGGCAATCGTACAATGCGGCCCTGTCTCTCAAGTGCTGTTAAGATTCAG                         GCAGAGGAATTAACTAAAG
genomic: TGGGCAATCGTACAATGCGGCCCTGTCTCTCAAGTGCTGTTAAGATTCAGgtgcatgctt ... tcccttgcagGCAGAGGAATTAACTAAAG
EST: gi|161714080|gb|FC064381.1|FC064381
EST:     TGGGCAATCGTACAATGCGGCCCTGTCTCTCAAGTGCTGTTAAGATTCAG                         GCAGAGGAATTAACTAAAGAGGATTTTAAAGGGGTAAAG
genomic: TGGGCAATCGTACAATGCGGCCCTGTCTCTCAAGTGCTGTTAAGATTCAGgtgcatgctt ... tcccttgcagGCAGAGGAATTAACTAAAGAGGATTTTAAAGGGGTAAAG
EST: gi|110697937|gb|EE075379.1|EE075379
EST:     TGGGCAATCGTACAATGCGGCCCTGTCTCTCAAGTGCTGTTAAGATTCAG                         GCAGAGGAATTAACTAAGGAGGATTTTAAAGGGGTAAAG
genomic: TGGGCAATCGTACAATGCGGCCCTGTCTCTCAAGTGCTGTTAAGATTCAGgtgcatgctt ... tcccttgcagGCAGAGGAATTAACTAAAGAGGATTTTAAAGGGGTAAAG
EST: gi|161716110|gb|FC069483.1|FC069483
EST:     TGGGCAATCGTACAATGCGGCCCTGTCTCTCAAGTGCTGTTAAGATTCAG                         GCAGAGGAATTAACTAAAGAGGATTTTAAAGGGGTAAAG
genomic: TGGGCAATCGTACAATGCGGCCCTGTCTCTCAAGTGCTGTTAAGATTCAGgtgcatgctt ... tcccttgcagGCAGAGGAATTAACTAAAGAGGATTTTAAAGGGGTAAAG
EST: gi|110718647|gb|EE095720.1|EE095720
EST:     TGGGCAATCGTACAATGCGGCCCTGTCTCTCAAGTGCTGTTAAGATTCAG                         GCAGAGGAATTAACTAAAGAGGATTTTAAAGGGGTAAAG
genomic: TGGGCAATCGTACAATGCGGCCCTGTCTCTCAAGTGCTGTTAAGATTCAGgtgcatgctt ... tcccttgcagGCAGAGGAATTAACTAAAGAGGATTTTAAAGGGGTAAAG
EST: gi|161714866|gb|FC063017.1|FC063017
EST:     TGGGCAATCGTACAATGCGGCCCTGTCTCTCAAGTGCTGTTAAGATTCAG                         GCAGAGGAATTAACTAAAGAGGATTTTAAAGGGGTAAAG
genomic: TGGGCAATCGTACAATGCGGCCCTGTCTCTCAAGTGCTGTTAAGATTCAGgtgcatgctt ... tcccttgcagGCAGAGGAATTAACTAAAGAGGATTTTAAAGGGGTAAAG
EST: gi|110697939|gb|EE075381.1|EE075381
EST:     TGGGCAATCGTACAATGCGGCCCTGTCTCTCAAGTGCTGTTAAGATTCAG                         GCAGAGGAATTAACTAAGGAGGATTTTAAAGGGGTAAAG
genomic: TGGGCAATCGTACAATGCGGCCCTGTCTCTCAAGTGCTGTTAAGATTCAGgtgcatgctt ... tcccttgcagGCAGAGGAATTAACTAAAGAGGATTTTAAAGGGGTAAAG
EST: gi|110701299|gb|EE078705.1|EE078705
EST:     TGGGCAATCGTACAATGCGGCCCTGTCTCTCAAGTGCTGTTAAGATTCAG                         GCAGAGGAATTAACTAAGGAGGATTTTAAAGGGGTAAAG
genomic: TGGGCAATCGTACAATGCGGCCCTGTCTCTCAAGTGCTGTTAAGATTCAGgtgcatgctt ... tcccttgcagGCAGAGGAATTAACTAAAGAGGATTTTAAAGGGGTAAAG
EST: gi|110684947|gb|EE062806.1|EE062806
EST:     TGGGCAATCGTACAATGCGGCCCTGTCTCTCAAGTGCTGTTAAGATTCAG                         GCAGAGGAATTAACTAAAGAGGATTTTAAAGGGGTAAAG
genomic: TGGGCAATCGTACAATGCGGCCCTGTCTCTCAAGTGCTGTTAAGATTCAGgtgcatgctt ... tcccttgcagGCAGAGGAATTAACTAAAGAGGATTTTAAAGGGGTAAAG
EST: gi|110699416|gb|EE076394.1|EE076394
EST:     TGGGCAATCGTACAATGCGGCCCTGTCTCTCAAGTGCTGTTAAGATTCAG                         GCAGAGGAATTAACTAAAGAGGATTTTAAAGGGGTAAAG
genomic: TGGGCAATCGTACAATGCGGCCCTGTCTCTCAAGTGCTGTTAAGATTCAGgtgcatgctt ... tcccttgcagGCAGAGGAATTAACTAAAGAGGATTTTAAAGGGGTAAAG
EST: gi|110718530|gb|EE095467.1|EE095467
EST:     TGGGCAATCGTACAATGCGGCCCTGTCTCTCAAGTGCTGTTAAGATTCAG                         GCAGAGGAATTAACTAAAGAGGATTTTAAGGGGGTAAAG
genomic: TGGGCAATCGTACAATGCGGCCCTGTCTCTCAAGTGCTGTTAAGATTCAGgtgcatgctt ... tcccttgcagGCAGAGGAATTAACTAAAGAGGATTTTAAAGGGGTAAAG
EST: gi|161717418|gb|FC067550.1|FC067550
EST:     TGGGCAATCGTACAATGCGGCCCTGTCTCTCAAGTGCTGTTAAGATTCAA                         GCAGAGGAATTAACTAAAGAGGATTTTAAAGGGGTAAAG
genomic: TGGGCAATCGTACAATGCGGCCCTGTCTCTCAAGTGCTGTTAAGATTCAGgtgcatgctt ... tcccttgcagGCAGAGGAATTAACTAAAGAGGATTTTAAAGGGGTAAAG
EST: gi|110719756|gb|EE095160.1|EE095160
EST:     TGGGCAATCGTACAATGCGGCCCTGTCTCTCAAGTGCTGTTAAGATTCAG                         GCAGAGGAATTAACTAAAGAGGATTTTAAAGGGGTAAAG
genomic: TGGGCAATCGTACAATGCGGCCCTGTCTCTCAAGTGCTGTTAAGATTCAGgtgcatgctt ... tcccttgcagGCAGAGGAATTAACTAAAGAGGATTTTAAAGGGGTAAAG
EST: gi|33401764|gb|CF207391.1|CF207391
EST:     TGGGCAATCGTACAATGCGGCCCTGTCTCTCAAGTGCTGTTAAGATTCAG                         GCAGAGGAATTAACTAAAGAGGATTTTAAAGGGGTAAAG
genomic: TGGGCAATCGTACAATGCGGCCCTGTCTCTCAAGTGCTGTTAAGATTCAGgtgcatgctt ... tcccttgcagGCAGAGGAATTAACTAAAGAGGATTTTAAAGGGGTAAAG
EST: gi|110710884|gb|EE087453.1|EE087453
EST:     TGGGCAATCGTACAATGCGGCCCTGTCTCTCAAGTGCTGTTAAGATTCAA                         GCAGAGGAATTAACTAAAGAGGATTTTAAAGGGGTAAAG
genomic: TGGGCAATCGTACAATGCGGCCCTGTCTCTCAAGTGCTGTTAAGATTCAGgtgcatgctt ... tcccttgcagGCAGAGGAATTAACTAAAGAGGATTTTAAAGGGGTAAAG
EST: gi|161709889|gb|FC060207.1|FC060207
EST:     TGGGCAATCGTACAATGCGGCCCTGTCTCTCAAGTGCTGTTAAGATTCAG                         GCAGAGGAATTAACTAAAGAGGAATTTTAAAGGGGTAAAG
genomic: TGGGCAATCGTACAATGCGGCCCTGTCTCTCAAGTGCTGTTAAGATTCAGgtgcatgctt ... tcccttgcagGCAGAGGAATTAACTAAAGAGGA-TTTTAAAGGGGTAAAG
EST: gi|30126585|gb|CB911924.1|CB911924
EST:     TGGGCAATCGTACAATGCGGCCCTGTCTCTCAAGTGCTGTTAAGATTCAG                         GCAGAGGAATTAACTAAAGAGGATTT
genomic: TGGGCAATCGTACAATGCGGCCCTGTCTCTCAAGTGCTGTTAAGATTCAGgtgcatgctt ... tcccttgcagGCAGAGGAATTAACTAAAGAGGATTT
EST: gi|110697936|gb|EE075378.1|EE075378
EST:     TGGGCAATCGTACAATGCGGCCCTGTCTCTCAAGTGCTGTTAAGATTCAG                         GCAGAGGAATTAACTAAGGAGGATTTTAAAGGGGTAAAG
genomic: TGGGCAATCGTACAATGCGGCCCTGTCTCTCAAGTGCTGTTAAGATTCAGgtgcatgctt ... tcccttgcagGCAGAGGAATTAACTAAAGAGGATTTTAAAGGGGTAAAG
EST: gi|110720579|gb|EE096626.1|EE096626
EST:     TGGGCAATCGTACAATGCGGCCCTGTCTCTCAAGTGCTGTTAAGATTCAG                         GCAGAGGAATTAACTAAAGAGGATTTTAAAGGGGTAAAG
genomic: TGGGCAATCGTACAATGCGGCCCTGTCTCTCAAGTGCTGTTAAGATTCAGgtgcatgctt ... tcccttgcagGCAGAGGAATTAACTAAAGAGGATTTTAAAGGGGTAAAG
EST: gi|71868003|gb|DT017058.1|DT017058
EST:     TGGGCAATCGTACAATGCGGCCCTGTCTCTCAAGTGCTGTTAAGATTCAG                         GCAGAGGAATTAACTAAAGAGGATTTTAAAGGGGTAAAG
genomic: TGGGCAATCGTACAATGCGGCCCTGTCTCTCAAGTGCTGTTAAGATTCAGgtgcatgctt ... tcccttgcagGCAGAGGAATTAACTAAAGAGGATTTTAAAGGGGTAAAG
EST: gi|110698651|gb|EE076389.1|EE076389
EST:     TGGGCAATCGTACAATGCGGCCCTGTCTCTCAAGTGCTGTTAAGATTCAG                         GCAGAGGAATTAACTAAAGAGGATTTTAAAGGGGTAAAG
genomic: TGGGCAATCGTACAATGCGGCCCTGTCTCTCAAGTGCTGTTAAGATTCAGgtgcatgctt ... tcccttgcagGCAGAGGAATTAACTAAAGAGGATTTTAAAGGGGTAAAG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGTGTTTGCCTGGTTGATGCATTGGGCAATCGTACAATGCGGCCCTGTCTCTCAAGTGCTGTTAAGATTCAGgtgcatgcttcttttctggttttctttcttgtcacttaaatagtttaggctccaagtctttcttttcatacagttttcttattaagatgagcatacatggagtcttattattgttttgtcccttgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGTT