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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagcttcatatttcttctatataaatggactagctctttgacattttttcattggaattctggataataagtgctggaaatttattgacactggtacatcacagTGTGTTTGCCTGGTTGATGCATTGGGCAATCGTACAATGCGGCCCTGTCTCTCAAGTGCTGTTAAGATTCAG

Basic information

species Vitis vinifera
transcript Vv18s0001g12750.t01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv18s0001g12750.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA17G37040.1 (Glycine max), 3'ss of exon 2
gtgagcttcatatttcttctatataaatggactagctctttgacattttttcattgg-aattctggataataagtgctggaaatttattgacactg--gtacatcacagTGTGTTTGCCTGGTTGATGCATTGGGCAATCGTACAATGCGGCCCTGTCTCTCAAGTGCTGTTAAGATTCAG-
         |  | |     |  ||  |    |   ||       || |||||||   || | |       ||  | || |||| ||   ||      ||   ||||||||||||||  |||||||||  ||||| || ||||| ||||||||||||||||||| |||||| ||  ||||| 
---------agttataaggaaggtatttaagttttgtcccaagttttatttcattaataaatgttttgtgcaaaagttg-aaatgtaacaacttgactgtttgtcacagtGTGTTTGTTTGGTTGATGACTTGGGAAACCGTACCATGCGGCCCTGTCTCTCAAATGCTGTGAAAGTTCAGG

upper sequence: Vv18s0001g12750.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA04G03290.1 (Glycine max), 3'ss of exon 2
gtgagcttcatatttcttctatataaatggactagctctttgacattttttcattggaattctggataataagtgctggaaatttattgacactggtacatcacagTGTGTTTGCCTGGTTGATGCATTGGGCAATCGTACAATGCGGCCCTGTCTCTCAAGTGCTGTTAAGATTCAG
                     ||  |    || |  | | | |  |  ||  ||   | |   | || | |      |  |||  |||  | |||     |   ||||||||||| |||| ||||   |||| || ||||||||||||||||||||||||| |||||| ||  |||||
--------------------gtaccagcacacaatgtatgtaat-tcattctatcatattatagtatgacataacaagttaatggatttgctctg---tgtactagTGTGTTTGCTTGGTAGATGACATGGGTAACCGTACAATGCGGCCCTGTCTCTCAAATGCTGTCAAAGTTCAG

upper sequence: Vv18s0001g12750.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA14G07980.1 (Glycine max), 3'ss of exon 3
gtgagcttcatatttcttctatataaatggactagctctttgacattttttcattgg-aattctggataataagtgctggaaatttattgac--actggtacatcacagTGTGTTTGCCTGGTTGATGCATTGGGCAATCGTACAATGCGGCCCTGTCTCTCAAGTGCTGTTAAGATTCAG
         |  | |     |  ||  |    | | || |  |  |  |||||||   || | |     | ||  | ||||||| ||   ||  |   ||   ||||||||||||||  |||||||||  ||||| || ||||| ||||| ||||||||||| | |||||| ||  |||||
--------tagctataaggaaggtatttaagtttggtcctaaaattcatttcattaataaatgttttgcacaaaag-tggaaatgtaacaacttaaatgtttgtcacagTGTGTTTGTTTGGTTGATGACTTGGGAAACCGTACCATGCGACCCTGTCTCTCTAATGCTGTGAAAGTTCAG

upper sequence: Vv18s0001g12750.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: AT1G19600.1 (Arabidopsis thaliana), 3'ss of exon 2
gtgagcttcatatttcttctatataaatggactagctctttgacattttttcattggaattctggataataagtgctggaaatttattgacactggtacatcacagTGTGTTTGCCTGGTTGATGCATTGGGCAATCGTACAATGCGGCCCTGTCTCTCAAGTGCTGTTAAGATTCAG
                     | |   | | | | || ||  |  ||  ||| |    |||  | | | |  ||  ||       ||||    || | | |   ||||||||||| |||||||||  |  || ||||| |||||||| || |||||||| |||||||| |||||||||
--------------------gtctgttttgtcaaactgttaaattttgcttcttccttattgggaagagttggttttg-------attggtgttgtttcttt-tagTGTGTTTGCTTGGTTGATGACTCTGGTAATCGAACAATGCGACCATGTCTCTCGAGTGCTGTGAAGATTCAG

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:     GTGGAGTGAACCTTTCAGCATTGAGGATAAAGAAGGGGCCAACAGCTCAG                         TGTGTTTGCCTGGTTGATGCATTGGGCAATCGTACAATGCGGCCCTGTCTC
genomic: GTGGAGTGAACCTTTCAGCATTGAGGATAAAGAAGGGGCCAACAGCTCAGgtgagcttca ... tacatcacagTGTGTTTGCCTGGTTGATGCATTGGGCAATCGTACAATGCGGCCCTGTCTC
EST: gi|30125650|gb|CB910989.1|CB910989
EST:     GTGGAGTGAACCTTTCAGCATTGAGGATAAAGAAGGGGCCAACAGCTCAG                         TGTGTTTGCCTGGTTGATGCATTGGGCAATCGTACAATGCGGCCCTGTCTC
genomic: GTGGAGTGAACCTTTCAGCATTGAGGATAAAGAAGGGGCCAACAGCTCAGgtgagcttca ... tacatcacagTGTGTTTGCCTGGTTGATGCATTGGGCAATCGTACAATGCGGCCCTGTCTC
EST: gi|161714080|gb|FC064381.1|FC064381
EST:     GTGGAGTGAACCTTTCAGCATTGAGGATAAAGAAGGGGCCAACAGCTCAG                         TGTGTTTGCCTGGTTGATGCATTGGGCAATCGTACAATGCGGCCCTGTCTC
genomic: GTGGAGTGAACCTTTCAGCATTGAGGATAAAGAAGGGGCCAACAGCTCAGgtgagcttca ... tacatcacagTGTGTTTGCCTGGTTGATGCATTGGGCAATCGTACAATGCGGCCCTGTCTC
EST: gi|110697937|gb|EE075379.1|EE075379
EST:     GTGGAGTGAACCTTTCAGCATTGAGGATAAAGAAGGGGCCAACAGCTCAG                         TGTGTTTGCCTGGTTGATGCATTGGGCAATCGTACAATGCGGCCCTGTCTC
genomic: GTGGAGTGAACCTTTCAGCATTGAGGATAAAGAAGGGGCCAACAGCTCAGgtgagcttca ... tacatcacagTGTGTTTGCCTGGTTGATGCATTGGGCAATCGTACAATGCGGCCCTGTCTC
EST: gi|161716110|gb|FC069483.1|FC069483
EST:     GTGGAGTGAACCTTTCAGCATTGAGGATAAAGAAGGGGCCAACAGCTCAG                         TGTGTTTGCCTGGTTGATGCATTGGGCAATCGTACAATGCGGCCCTGTCTC
genomic: GTGGAGTGAACCTTTCAGCATTGAGGATAAAGAAGGGGCCAACAGCTCAGgtgagcttca ... tacatcacagTGTGTTTGCCTGGTTGATGCATTGGGCAATCGTACAATGCGGCCCTGTCTC
EST: gi|110718647|gb|EE095720.1|EE095720
EST:     GTGGAGTGAACCTTTCAGCATTGAGGATAAAGAAGGGGCCAACAGCTCAG                         TGTGTTTGCCTGGTTGATGCATTGGGCAATCGTACAATGCGGCCCTGTCTC
genomic: GTGGAGTGAACCTTTCAGCATTGAGGATAAAGAAGGGGCCAACAGCTCAGgtgagcttca ... tacatcacagTGTGTTTGCCTGGTTGATGCATTGGGCAATCGTACAATGCGGCCCTGTCTC
EST: gi|161714866|gb|FC063017.1|FC063017
EST:     GTGGAGTGAACCTTTCAGCATTGAGGATAAAGAAGGGGCCAACAGCTCAG                         TGTGTTTGCCTGGTTGATGCATTGGGCAATCGTACAATGCGGCCCTGTCTC
genomic: GTGGAGTGAACCTTTCAGCATTGAGGATAAAGAAGGGGCCAACAGCTCAGgtgagcttca ... tacatcacagTGTGTTTGCCTGGTTGATGCATTGGGCAATCGTACAATGCGGCCCTGTCTC
EST: gi|71859911|gb|DT008966.1|DT008966
EST:     GTGGAGTGAACCTTTCAGCATTGAGGATAAAGAAGGGGCCAACAGCTCAG                         TGTGTTTGCCTGGTTGATGCATTGGGCAATCGTACAATGCGGCCCTGTCTC
genomic: GTGGAGTGAACCTTTCAGCATTGAGGATAAAGAAGGGGCCAACAGCTCAGgtgagcttca ... tacatcacagTGTGTTTGCCTGGTTGATGCATTGGGCAATCGTACAATGCGGCCCTGTCTC
EST: gi|110697939|gb|EE075381.1|EE075381
EST:     GTGGAGTGAACCTTTCAGCATTGAGGATAAAGAAGGGGCCAACAGCTCAG                         TGTGTTTGCCTGGTTGATGCATTGGGCAATCGTACAATGCGGCCCTGTCTC
genomic: GTGGAGTGAACCTTTCAGCATTGAGGATAAAGAAGGGGCCAACAGCTCAGgtgagcttca ... tacatcacagTGTGTTTGCCTGGTTGATGCATTGGGCAATCGTACAATGCGGCCCTGTCTC
EST: gi|110701299|gb|EE078705.1|EE078705
EST:     GTGGAGTGAACCTTTCAGCATTGAGGATAAAGAAGGGGCCAACAGCTCAG                         TGTGTTTGCCTGGTTGATGCATTGGGCAATCGTACAATGCGGCCCTGTCTC
genomic: GTGGAGTGAACCTTTCAGCATTGAGGATAAAGAAGGGGCCAACAGCTCAGgtgagcttca ... tacatcacagTGTGTTTGCCTGGTTGATGCATTGGGCAATCGTACAATGCGGCCCTGTCTC
EST: gi|110684947|gb|EE062806.1|EE062806
EST:     GTGGAGTGAACCTTTCAGCATTGAGGATAAAGAAGGGGCCAACAGCTCAG                         TGTGTTTGCCTGGTTGATGCATTGGGCAATCGTACAATGCGGCCCTGTCTC
genomic: GTGGAGTGAACCTTTCAGCATTGAGGATAAAGAAGGGGCCAACAGCTCAGgtgagcttca ... tacatcacagTGTGTTTGCCTGGTTGATGCATTGGGCAATCGTACAATGCGGCCCTGTCTC
EST: gi|110699416|gb|EE076394.1|EE076394
EST:     GTGGAGTGAACCTTTCAGCATTGAGGATAAAGAAGGGGCCAACAGCTCAG                         TGTGTTTGCCTGGTTGATGCATTGGGCAATCGTACAATGCGGCCCTGTCTC
genomic: GTGGAGTGAACCTTTCAGCATTGAGGATAAAGAAGGGGCCAACAGCTCAGgtgagcttca ... tacatcacagTGTGTTTGCCTGGTTGATGCATTGGGCAATCGTACAATGCGGCCCTGTCTC
EST: gi|294966810|gb|GW837829.1|GW837829
EST:     GTGGAGTGAACCTTTCAGCATTGAGGATAAAGAAGGGGCCAACAGCTCAG                         TGTGTTTGCCTGGTTGATGCATTGGGCAATCGTACAATGCGGCCCTGTCTC
genomic: GTGGAGTGAACCTTTCAGCATTGAGGATAAAGAAGGGGCCAACAGCTCAGgtgagcttca ... tacatcacagTGTGTTTGCCTGGTTGATGCATTGGGCAATCGTACAATGCGGCCCTGTCTC
EST: gi|161708249|gb|FC057005.1|FC057005
EST:     GTGGAGTGAACCTTTCAGCATTGAGGATAAAGAAAGGGCCAACAGCTCAG                         TGTGTTTGCCTGGTTGAT
genomic: GTGGAGTGAACCTTTCAGCATTGAGGATAAAGAAGGGGCCAACAGCTCAGgtgagcttca ... tacatcacagTGTGTTTGCCTGGTTGAT
EST: gi|110718530|gb|EE095467.1|EE095467
EST:     GTGGAGTGAACCTTTCAGCATTGAGGATAAAGAAGGGGCCAACAGCTCAG                         TGTGTTTGCCTGGTTGATGCATTGGGCAATCGTACAATGCGGCCCTGTCTC
genomic: GTGGAGTGAACCTTTCAGCATTGAGGATAAAGAAGGGGCCAACAGCTCAGgtgagcttca ... tacatcacagTGTGTTTGCCTGGTTGATGCATTGGGCAATCGTACAATGCGGCCCTGTCTC
EST: gi|161717418|gb|FC067550.1|FC067550
EST:     GTGGAGTGAACCTTTCAGCATTGAGGATAAAGAAGGGGCCAACAGCTCAG                         TGTGTTTGCCTGGTTGATGCATTGGGCAATCGTACAATGCGGCCCTGTCTC
genomic: GTGGAGTGAACCTTTCAGCATTGAGGATAAAGAAGGGGCCAACAGCTCAGgtgagcttca ... tacatcacagTGTGTTTGCCTGGTTGATGCATTGGGCAATCGTACAATGCGGCCCTGTCTC
EST: gi|37188269|gb|CF607618.1|CF607618
EST:     GTGGAGTGAACCTTTCAGCATTGAGGATAAAGAAGGGGCCAACAGCTCAG                         TGTGTTTGCCTGGTTGATGCATTGGGCAATCGTACAATGCGGCCCTGTCTC
genomic: GTGGAGTGAACCTTTCAGCATTGAGGATAAAGAAGGGGCCAACAGCTCAGgtgagcttca ... tacatcacagTGTGTTTGCCTGGTTGATGCATTGGGCAATCGTACAATGCGGCCCTGTCTC
EST: gi|110719756|gb|EE095160.1|EE095160
EST:     GTGGAGTGAACCTTTCAGCATTGAGGATAAAGAAGGGGCCAACAGCTCAG                         TGTGTTTGCCTGGTTGATGCATTGGGCAATCGTACAATGCGGCCCTGTCTC
genomic: GTGGAGTGAACCTTTCAGCATTGAGGATAAAGAAGGGGCCAACAGCTCAGgtgagcttca ... tacatcacagTGTGTTTGCCTGGTTGATGCATTGGGCAATCGTACAATGCGGCCCTGTCTC
EST: gi|110710884|gb|EE087453.1|EE087453
EST:     GTGGAGTGAACCTTTCAGCATTGAGGATAAAGAAGGGGCCAACAGCTCAG                         TGTGTTTGCCTGGTTGATGCATTGGGCAATCGTACAATGCGGCCCTGTCTC
genomic: GTGGAGTGAACCTTTCAGCATTGAGGATAAAGAAGGGGCCAACAGCTCAGgtgagcttca ... tacatcacagTGTGTTTGCCTGGTTGATGCATTGGGCAATCGTACAATGCGGCCCTGTCTC
EST: gi|161709889|gb|FC060207.1|FC060207
EST:     GTGGAGTGAACCTTTCAGCATTGAGGATAAAGAAGGGGCCAACAGCTCAG                         TGTGTTTGCCTGGTTGATGCATTGGGCAATCGTACAATGCGGCCCTGTCTC
genomic: GTGGAGTGAACCTTTCAGCATTGAGGATAAAGAAGGGGCCAACAGCTCAGgtgagcttca ... tacatcacagTGTGTTTGCCTGGTTGATGCATTGGGCAATCGTACAATGCGGCCCTGTCTC
EST: gi|30126585|gb|CB911924.1|CB911924
EST:     GTGGAGTGAACCTTTCAGCATTGAGGATAAAGAAGGGGCCAACAGCTCAG                         TGTGTTTGCCTGGTTGATGCATTGGGCAATCGTACAATGCGGCCCTGTCTC
genomic: GTGGAGTGAACCTTTCAGCATTGAGGATAAAGAAGGGGCCAACAGCTCAGgtgagcttca ... tacatcacagTGTGTTTGCCTGGTTGATGCATTGGGCAATCGTACAATGCGGCCCTGTCTC
EST: gi|110697936|gb|EE075378.1|EE075378
EST:     GTGGAGTGAACCTTTCAGCATTGAGGATAAAGAAGGGGCCAACAGCTCAG                         TGTGTTTGCCTGGTTGATGCATTGGGCAATCGTACAATGCGGCCCTGTCTC
genomic: GTGGAGTGAACCTTTCAGCATTGAGGATAAAGAAGGGGCCAACAGCTCAGgtgagcttca ... tacatcacagTGTGTTTGCCTGGTTGATGCATTGGGCAATCGTACAATGCGGCCCTGTCTC
EST: gi|110720579|gb|EE096626.1|EE096626
EST:     GTGGAGTGAACCTTTCAGCATTGAGGATAAAGAAGGGGCCAACAGCTCAG                         TGTGTTTGCCTGGTTGATGCATTGGGCAATCGTACAATGCGGCCCTGTCTC
genomic: GTGGAGTGAACCTTTCAGCATTGAGGATAAAGAAGGGGCCAACAGCTCAGgtgagcttca ... tacatcacagTGTGTTTGCCTGGTTGATGCATTGGGCAATCGTACAATGCGGCCCTGTCTC
EST: gi|71868003|gb|DT017058.1|DT017058
EST:     GTGGAGTGAACCTTTCAGCATTGAGGATAAAGAAGGGGCCAACAGCTCAG                         TGTGTTTGCCTGGTTGATGCATTGGGCAATCGTACAATGCGGCCCTGTCTC
genomic: GTGGAGTGAACCTTTCAGCATTGAGGATAAAGAAGGGGCCAACAGCTCAGgtgagcttca ... tacatcacagTGTGTTTGCCTGGTTGATGCATTGGGCAATCGTACAATGCGGCCCTGTCTC
EST: gi|352774042|gb|FQ474565.1|FQ474565
EST:     GTGGAGTGAACCTTTCAGCATTGAGGATAAAGAAGGGGCCCACAGCTCAG                         TGTGTTTGCCTGGTTGATGCATTGGGCAATCGTACCATGCGGCCCTGTCTC
genomic: GTGGAGTGAACCTTTCAGCATTGAGGATAAAGAAGGGGCCAACAGCTCAGgtgagcttca ... tacatcacagTGTGTTTGCCTGGTTGATGCATTGGGCAATCGTACAATGCGGCCCTGTCTC
EST: gi|110698651|gb|EE076389.1|EE076389
EST:     GTGGAGTGAACCTTTCAGCATTGAGGATAAAGAAGGGGCCAACAGCTCAG                         TGTGTTTGCCTGGTTGATGCATTGGGCAATCGTACAATGCGGCCCTGTCTC
genomic: GTGGAGTGAACCTTTCAGCATTGAGGATAAAGAAGGGGCCAACAGCTCAGgtgagcttca ... tacatcacagTGTGTTTGCCTGGTTGATGCATTGGGCAATCGTACAATGCGGCCCTGTCTC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cattggaattctggataataagtgctggaaatttattgacactggtacatcacagTGTGTTTGCCTGGTTGATGCATTGGGCAATCGTACAATGCGGCCCTGTCTCTCAAGTGCTGTTAAGATTCAG
                                 tattgac  putative branch site (score: 2)
                            aaatttattga  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagcttcatatttcttctatataaatggactagctctttgacattttttcattggaattctggataataagtgctggaaatttattgacactggtacatcacagTGTGTTTGCCTGGTTGATGCATTGGGCAATCGTACAATGCGGCCCTGTCTCTCAAGTGCTGTTAAGATTCAG

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