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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgtaatttaaggataaaattttctatgctttctctattcttttgatatgaagttgcaaacttcaaacttcaactctgacatcttgcttgctgaataacagAAATACAGGCAGCTGGGAGTACATATGGAACATATTTCCGTGTTACGACATATGGAGAATCTCATGGAGGTGGTGTTGGTTGCATAATTGATGGATGTCC

Basic information

species Vitis vinifera
transcript Vv13s0019g04190.t01
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv13s0019g04190.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: LOC_Os03g14990.1 (Oryza sativa), 3'ss of exon 1
--tgtaatttaaggataaaattttctatgctttctctattcttttgatatgaagttgcaaacttcaaacttcaactctgacatcttgcttgctgaataacagAAATACAGGCAGCTGGGAGTACATATGGAACATATTTCCGTGTTACGACATATGGAGAATCTCATGGAGGTGGTGTTGGTTGCATAATTGATGGATGTCC
  |  | | |    ||    |  | |    |   | | |||| ||   | || |  | ||      || |  | |  |  | || ||     |||| ||||||  |  ||||  |||  | |  || ||| |  || ||||  ||| | || |||||||| ||||||||||| |||||||||||| ||||   |||||| ||
aatagagtatttaaatctgctactttgcattacttttgttctattagaaggatggcgaaaggacttaattaaatccgttgc-tcctgaaatttgaa-aacagAGGTGAAGGCGTCTGCAAATGTATTTGGGAACTACTTCCAGGTTGCAACTTATGGAGAGTCTCATGGAGGCGGTGTTGGTTGCGTAATCAGTGGATGCCC

upper sequence: Vv13s0019g04190.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA20G31980.1 (Glycine max), 3'ss of exon 1
tgtaatttaaggataaaattttctatgctttctctattcttttgatatgaagttgcaa-acttcaaacttcaactctgacatcttgcttgctgaataacagAAATACAGGCAGCTGGGAGTACATATGGAACATATTTCCGTGTTACGACATATGGAGAATCTCATGGAGGTGGTGTTGGTTGCATAATTGATGGATGTCC
  |  ||   |    |  |    ||    |     |||||      ||| | |||  | |  ||    || ||||     |   || |||    || ||||| |||||||| ||||||||||| |||||||   | || |||||||| |||||||| ||||| |||||||| |||||||||||  | ||||||||||||||
cttggttcttgtgccagttacattacatgtcaagaattctaaattaatggaattgagatagctcggtttttaacttaatgacactg-ttgacatattacagACATACAGGCGGCTGGGAGTACCTATGGAAATCACTTTCGTGTTACAACATATGGGGAATCACATGGAGGAGGTGTTGGTTGTGTTATTGATGGATGTCC

upper sequence: Vv13s0019g04190.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA10G35560.1 (Glycine max), 3'ss of exon 1
tgtaatttaaggataaaattttctatgctttctctattcttttgatatgaagttgcaa-acttcaaacttcaactctgacatcttgcttgctgaataacagAAATACAGGCAGCTGGGAGTACATATGGAACATATTTCCGTGTTACGACATATGGAGAATCTCATGGAGGTGGTGTTGGTTGCATAATTGATGGATGTCC
  |  ||        |  |    ||    ||    |||||      ||| | |||  | |  ||    || |||| |   |   || |||    || ||||| |||| ||| ||||||||||  |||||||   | || |||||| | |||||||||||||| |||||||| ||||||||||| || ||||||||||||||
attggttctcatgccagttacattacatgttaagaattctaaattaatggaattgagatagctcggtttttaactttctgagactg-ttgacatattacagAGATACGGGCTGCTGGGAGTATCTATGGAAATCACTTTCGTGTTTCAACATATGGAGAATCGCATGGAGGAGGTGTTGGTTGTATTATTGATGGATGTCC

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|352790897|gb|FQ477345.1|FQ477345
EST:     TTTTCCCTCCGTCCGCTACGCGATCCGTCCGACGCATCGTCGTACTCTCG                         AAATACAGGCAGCTGGGAGTACATATGGAACATATTTCCGTGTTACGACAT
genomic: TTTTCCCTCCGTCCGCTACGCGATCCGTCCGACGCATCGTCGTACTCTCGgtttgtctcc ... tgaataacagAAATACAGGCAGCTGGGAGTACATATGGAACATATTTCCGTGTTACGACAT
EST: gi|71880899|gb|DT029954.1|DT029954
EST:     TTTTCCCTCCGTCCGCTACGCGATCCGTCCGACGCATCGTCGTACTCTCG                         AAATACAGGCAGCTGGGAGTACATATGGAACATATTTCCGTGTTACGACAT
genomic: TTTTCCCTCCGTCCGCTACGCGATCCGTCCGACGCATCGTCGTACTCTCGgtttgtctcc ... tgaataacagAAATACAGGCAGCTGGGAGTACATATGGAACATATTTCCGTGTTACGACAT
EST: gi|71877721|gb|DT026776.1|DT026776
EST:     TTTTCCCTCCGTCCGCTACGCGATCCGTCCGACGCATCGTCGTACTCTCG                         AAATACAGGCAGCTGGGAGTACATATGGAACATATTTCCGTGTTACGACAT
genomic: TTTTCCCTCCGTCCGCTACGCGATCCGTCCGACGCATCGTCGTACTCTCGgtttgtctcc ... tgaataacagAAATACAGGCAGCTGGGAGTACATATGGAACATATTTCCGTGTTACGACAT
EST: gi|71863219|gb|DT012274.1|DT012274
EST:     TTTTCCCTCCGTCCGCTACGCGATCCGTCCGACGCATCGTCGTACTCTCG                         AAATACAGGCAGCTGGGAGTACATATGGAACATATTTCCGTGTTACGACAT
genomic: TTTTCCCTCCGTCCGCTACGCGATCCGTCCGACGCATCGTCGTACTCTCGgtttgtctcc ... tgaataacagAAATACAGGCAGCTGGGAGTACATATGGAACATATTTCCGTGTTACGACAT
EST: gi|352778035|gb|FQ467088.1|FQ467088
EST:     TTTTCCCTCCGTCCGCTACGCGATCCGTCCGACGCATCGTCGTACTCTCG                         AAATACAGGCAGCTGGGAGTACATATGGAACATATTTCCGTGTTACGACAT
genomic: TTTTCCCTCCGTCCGCTACGCGATCCGTCCGACGCATCGTCGTACTCTCGgtttgtctcc ... tgaataacagAAATACAGGCAGCTGGGAGTACATATGGAACATATTTCCGTGTTACGACAT
EST: gi|71855293|gb|DT004348.1|DT004348
EST:     TTTTCCCTCCGTCCGCTACGCGATCCGTCCGACGCATCGTCGTACTCTCG                         AAATACAGGCAGCTGGGAGTACATATGGAACATATTTCCGTGTTACGACAT
genomic: TTTTCCCTCCGTCCGCTACGCGATCCGTCCGACGCATCGTCGTACTCTCGgtttgtctcc ... tgaataacagAAATACAGGCAGCTGGGAGTACATATGGAACATATTTCCGTGTTACGACAT
EST: gi|71861705|gb|DT010760.1|DT010760
EST:     TTTTCCCTCCGTCCGCTACGCGATCCGTCCGACGCATCGTCGTACTCTCG                         AAATACAGGCAGCTGGGAGTACATATGGAACATATTTCCGTGTTACGACAT
genomic: TTTTCCCTCCGTCCGCTACGCGATCCGTCCGACGCATCGTCGTACTCTCGgtttgtctcc ... tgaataacagAAATACAGGCAGCTGGGAGTACATATGGAACATATTTCCGTGTTACGACAT
EST: gi|71879200|gb|DT028255.1|DT028255
EST:     TTTTCCCTCCGTCCGCTACGCGATCCGTCCGACGCATCGTCGTACTCTCG                         AAATACAGGCAGCTGGGAGTACATATGGAACATATTTCCGTGTTACGACAT
genomic: TTTTCCCTCCGTCCGCTACGCGATCCGTCCGACGCATCGTCGTACTCTCGgtttgtctcc ... tgaataacagAAATACAGGCAGCTGGGAGTACATATGGAACATATTTCCGTGTTACGACAT
EST: gi|71880874|gb|DT029929.1|DT029929
EST:     TTTTCCCTCCGTCCGCTACGCGATCCGTCCGACGCATCGTCGTACTCTCG                         AAATACAGGCAGCTGGGAGTACATATGGAACATATTTCCGTGTTACGACAT
genomic: TTTTCCCTCCGTCCGCTACGCGATCCGTCCGACGCATCGTCGTACTCTCGgtttgtctcc ... tgaataacagAAATACAGGCAGCTGGGAGTACATATGGAACATATTTCCGTGTTACGACAT
EST: gi|352776661|gb|FQ465459.1|FQ465459
EST:     TTTTCCCTCCGTCCGCTACGCGATCCGTCCGACGCATCGTCGTACTCTCG                         AAATACAGGCAGCTGGGAGTACATATGGAACATATTTCCGTGTTACGACAT
genomic: TTTTCCCTCCGTCCGCTACGCGATCCGTCCGACGCATCGTCGTACTCTCGgtttgtctcc ... tgaataacagAAATACAGGCAGCTGGGAGTACATATGGAACATATTTCCGTGTTACGACAT
EST: gi|352785537|gb|FQ475540.1|FQ475540
EST:     TTTTCCCTCCGTCCGCTACGCGATCCGTCCGACGCATCGTCGTACTCTCG                         AAATACAGGCAGCTGGGAGTACATATGGAACATATTTCCGTGTTACGGCAT
genomic: TTTTCCCTCCGTCCGCTACGCGATCCGTCCGACGCATCGTCGTACTCTCGgtttgtctcc ... tgaataacagAAATACAGGCAGCTGGGAGTACATATGGAACATATTTCCGTGTTACGACAT
EST: gi|352777956|gb|FQ467009.1|FQ467009
EST:     TTTTCCCTCCGTCCGCTACGCGATCCGTCCGACGCATCGTCGTACTCTCG                         AAATACAGGCAGCTGGGAGTACATATGGAACATATTTCCGTGTTACGACAT
genomic: TTTTCCCTCCGTCCGCTACGCGATCCGTCCGACGCATCGTCGTACTCTCGgtttgtctcc ... tgaataacagAAATACAGGCAGCTGGGAGTACATATGGAACATATTTCCGTGTTACGACAT
EST: gi|352785449|gb|FQ477663.1|FQ477663
EST:     TTTTCCCTCCGTCCGCTACGCGATCCGTCCGACGCATCGTCGTACTCTCG                         AAATACAGGCAGCTGGGAGTACATATGGAACATATTTCCGTGTTACGACAT
genomic: TTTTCCCTCCGTCCGCTACGCGATCCGTCCGACGCATCGTCGTACTCTCGgtttgtctcc ... tgaataacagAAATACAGGCAGCTGGGAGTACATATGGAACATATTTCCGTGTTACGACAT
EST: gi|351024445|gb|FQ426254.1|FQ426254
EST:     TTTTCCCTCCGTCCGCTACGCGATCCGTCCGACGCATCGTCGTACTCTCG                         AAATACAGGCAGCTGGGAGTACATATGGAACATATTTCCGTGTTACGACAT
genomic: TTTTCCCTCCGTCCGCTACGCGATCCGTCCGACGCATCGTCGTACTCTCGgtttgtctcc ... tgaataacagAAATACAGGCAGCTGGGAGTACATATGGAACATATTTCCGTGTTACGACAT
EST: gi|352778092|gb|FQ467145.1|FQ467145
EST:     TTTTCCCTCCGTCCGCTACGCGATCCGTCCGACGCATCGTCGTACTCTCG                         AAATACAGGCAGCTGGGAGTACATATGGAACATATTTCCGTGTTACGACAT
genomic: TTTTCCCTCCGTCCGCTACGCGATCCGTCCGACGCATCGTCGTACTCTCGgtttgtctcc ... tgaataacagAAATACAGGCAGCTGGGAGTACATATGGAACATATTTCCGTGTTACGACAT
EST: gi|352763986|gb|FQ467556.1|FQ467556
EST:     TTTTCCCTCCGTCCGCTACGCGATCCGTCCGACGCATCGTCGTACTCTCG                         AAATACAGGCAGCTGGGAGTACATATGGAACATATTTCCGTGTTACGACAT
genomic: TTTTCCCTCCGTCCGCTACGCGATCCGTCCGACGCATCGTCGTACTCTCGgtttgtctcc ... tgaataacagAAATACAGGCAGCTGGGAGTACATATGGAACATATTTCCGTGTTACGACAT
EST: gi|352768213|gb|FQ467352.1|FQ467352
EST:     TTTTCCCTCCGTCCGCTACGCGATCCGTCCGACGCATCGTCGTACTCTCG                         AAATACAGGCAGCTGGGAGTACATATGGAACATATTTCCGTGTTACGACAT
genomic: TTTTCCCTCCGTCCGCTACGCGATCCGTCCGACGCATCGTCGTACTCTCGgtttgtctcc ... tgaataacagAAATACAGGCAGCTGGGAGTACATATGGAACATATTTCCGTGTTACGACAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatgaagttgcaaacttcaaacttcaactctgacatcttgcttgctgaataacagAAATACAGGCAGCTGGGAGTACATATGGAACATATTTCCGTGTTACGACATATGGAGAATCTCATGGAGGTGGTGTTGGTTGCATAATTGATGGATGTCC
                           ctctgac  putative branch site (score: 3)
                                             tgaataa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgtaatttaaggataaaattttctatgctttctctattcttttgatatgaagttgcaaacttcaaacttcaactctgacatcttgcttgctgaataacagAAATACAGGCAGCTGGGAGTACATATGGAACATATTTCCGTGTTACGACATATGGAGAATCTCATGGAGGTGGTGTTGGTTGCATAATTGATGGATGTCC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GATGGA
- - - - - ggataaa
- - - - - - - - - - - ctatgct
- - - - - - - - - - - - - - - - - - - - - - - - - - -tgcaaac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tcaaact
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -caactct