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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...agaacttaagtttcagaacagtcttaaaggccaacactgtcataaatcacttgagtaaatgggaaggaaacttgtcagtattgatttttatgaacagcagGGTGTGAAGTGTACAACTTGGGAACTGGGAAAGGAACTTCAGTTTTGGAGATGGTTGCAGCATTTGAGAAGGCATCTGGAAAG

Basic information

species Vitis vinifera
transcript Vv02s0025g01560.t01
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv02s0025g01560.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GRMZM2G138410_T01 (Zea mays), 3'ss of exon 6
-------agaacttaagtttcagaacagtcttaaaggccaacactgtcataaatcacttgagtaaatgggaaggaaacttgt--cagtattgatttttatgaacagcagGGTGTGAAGTGTACAACTTGGGAACTGGGAAAGGAACTTCAGTTTTGGAGATGGTTGCAGCATTTGAGAAGGCATCTGGAAAG
        ||||  |  ||   | |||   |   | ||  | |  |||| ||   ||   |     ||     ||| |||||  ||   || | | || |     ||||| |||||||  |||||| | ||||| || |||||||| ||||| |||||||| ||    |||||||||||||| |||||||||
tttttgttgaac--agtttcttgtaca---tatgatgctcataaagtcagaacgtacagtaagttttgtagttgaatcttgttccaaatttaactgttctt----gcagGATGTGAAGCATACAACCTTGGAACCGGAAAAGGAACATCAGTGTTGGAGATAGTCAATGCATTTGAGAAGGCTTCTGGAAAG

upper sequence: Vv02s0025g01560.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA11G01940.4 (Glycine max), 3'ss of exon 6
-----------------------------agaacttaagtttcagaacagtcttaaaggccaacactgtcataaatcacttgagtaaatgggaaggaaacttgtcagtattgatttttatga--acagcagGGTGTGAAGTGTACAACTTGGGAACTGGGAAAGGAACTTCAGTTTTGGAGATGGTTGCAGCATTTGAGAAGGCATCTGGAAAG-----------------
                             |  | |||| | |   |    |  | |   |  |  | || | |      | || |  || |     ||| ||     | || ||||| |||       |||| ||||| || || ||| ||||||| || || ||||| ||||||||||||||||||  ||| ||||||| |||||||||||||                 
gtatcattctaaaattttcttcatcttctattatttaactatgccagttctggtgatttctgaagcagtgacattgtggt-gaatttatagtggtaaaatttt---attttaattttcatggtgtttacagGTTGTGAGGTTTATAACCTGGGAACAGGAAAGGGAACATCAGTTTTGGAGATGGTTCGAGCTTTTGAGATGGCATCTGGAAAGGTGAATAGAATAATGTA

upper sequence: Vv02s0025g01560.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA11G01940.3 (Glycine max), 3'ss of exon 6
-----------------------------agaacttaagtttcagaacagtcttaaaggccaacactgtcataaatcacttgagtaaatgggaaggaaacttgtcagtattgatttttatgaa--cagcagGGTGTGAAGTGTACAACTTGGGAACTGGGAAAGGAACTTCAGTTTTGGAGATGGTTGCAGCATTTGAGAAGGCATCTGGAAAG
                             |  | |||| | |   |    |  | |   |  |  | || | |      | || |  || |     ||| ||     | || ||||| |||       |||| ||||| || || ||| ||||||| || || ||||| ||||||||||||||||||  ||| ||||||| |||||||||||||
gtatcattctaaaattttcttcatcttctattatttaactatgccagttctggtgatttctgaagcagtgacattgtggt-gaatttatagtggtaaaatttt---attttaattttcatggtgtttacagGTTGTGAGGTTTATAACCTGGGAACAGGAAAGGGAACATCAGTTTTGGAGATGGTTCGAGCTTTTGAGATGGCATCTGGAAAG

upper sequence: Vv02s0025g01560.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA01G43540.1 (Glycine max), 3'ss of exon 6
----------------------------agaacttaagtttcagaacagtcttaaaggccaacactgtcataaatcacttgagtaaatgggaaggaaacttgtcagtattgatttttatg----aacagcagGGTGTGAAGTGTACAACTTGGGAACTGGGAAAGGAACTTCAGTTTTGGAGATGGTTGCAGCATTTGAGAAGGCATCTGGAAAG
                               | |||| | |   | |  |  | |   |  | || || | ||     |  | |   |       ||| || |     || ||||| |||    |    |||| ||||| || || ||| ||||||| || || ||||| ||||||||||||||||||  ||| ||||| | |||||||||||||
gtattattctaaagttttctttatcttctatatttaactctgtcagctctggtgatttctgaaacagtgacaatgtggt-aaatttgtattggtaaaatttatt----ttaattttcatggtgtatttacagGTTGTGAGGTTTATAACCTGGGAACAGGAAAGGGAACATCAGTTTTGGAGATGGTTAGAGCTTTTGAAATGGCATCTGGAAAG

upper sequence: Vv02s0025g01560.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA08G02690.2 (Glycine max), 3'ss of exon 6
agaacttaagtttcagaacagtcttaaaggccaacactgtcataaatcacttgagtaaatgggaaggaaacttgtcagtattgatttttatgaaca---gcagGGTGTGAAGTGTACAACTTGGGAACTGGGAAAGGAACTTCAGTTTTGGAGATGGTTGCAGCATTTGAGAAGGCATCTGGAAAG-----------------
  |   | | ||    ||| | | | |   ||   | ||| ||||     |   ||       |    |  |||  |  |||   |  | |   ||   ||||| ||||| || || ||||||||||| || || ||||| |||||||||||||||||    || |||||  |||| |||||||||                 
-aagtatgatttatgtaaccgacctcatcacc--tagtgtgataaggttttgttgtcgtcatcatattactttggtaaaattttgtactgtttgcatatgcagGTTGTGAGGTTTATAACTTGGGAACAGGAAAGGGAACATCAGTTTTGGAGATGGTAAACGCTTTTGAACAGGCCTCTGGAAAGGTAACAGACTTATAGCT

upper sequence: Vv02s0025g01560.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA08G02690.1 (Glycine max), 3'ss of exon 6
agaacttaagtttcagaacagtcttaaaggccaacactgtcataaatcacttgagtaaatgggaaggaaacttgtcagtattgatttttatgaaca---gcagGGTGTGAAGTGTACAACTTGGGAACTGGGAAAGGAACTTCAGTTTTGGAGATGGTTGCAGCATTTGAGAAGGCATCTGGAAAG
  |   | | ||    ||| | | | |   ||   | ||| ||||     |   ||       |    |  |||  |  |||   |  | |   ||   ||||| ||||| || || ||||||||||| || || ||||| |||||||||||||||||    || |||||  |||| |||||||||
-aagtatgatttatgtaaccgacctcatcacc--tagtgtgataaggttttgttgtcgtcatcatattactttggtaaaattttgtactgtttgcatatgcagGTTGTGAGGTTTATAACTTGGGAACAGGAAAGGGAACATCAGTTTTGGAGATGGTAAACGCTTTTGAACAGGCCTCTGGAAAG

upper sequence: Vv02s0025g01560.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: AT1G64440.1 (Arabidopsis thaliana), 3'ss of exon 6
--------agaacttaagtttcagaacagtcttaaaggc-caacactgtcataaatcacttgagtaaatggg-aaggaaacttgtcagtattgatttttatgaacagcagGGTGTGAAGTGTACAACTTGGGAACTGGGAAAGGAACTTCAGTTTTGGAGATGGTTGCAGCATTTGAGAAGGCATCTGGAAAG
              |   ||||| ||    || |  | | | ||| |  ||||   | |||   || |     |||   |  |||| |  |||  | || ||      ||| ||||| || |||||| ||||||| || ||||||||  |||| |||||||||||||  ||||||||||| || ||||||| |
gtatgcttttcttcttcttttcataagtacctcattgtctcgacaata-catat-ccgcttatttatacaaacaagctcaactgtctgatttggctgttgtgc----tagGTTGTGAGGTATACAACCTGGGAACCGGAAAAGGAACAACAGTGTTGGAGATGGTTGATGCATTTGAGAAAGCTTCTGGAATG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atcacttgagtaaatgggaaggaaacttgtcagtattgatttttatgaacagcagGGTGTGAAGTGTACAACTTGGGAACTGGGAAAGGAACTTCAGTTTTGGAGATGGTTGCAGCATTTGAGAAGGCATCTGGAAAG
                                 tattgat  putative branch site (score: 3)
                                       tttttat  CT-rich tract
                                 tattgatttttatgaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
agaacttaagtttcagaacagtcttaaaggccaacactgtcataaatcacttgagtaaatgggaaggaaacttgtcagtattgatttttatgaacagcagGGTGTGAAGTGTACAACTTGGGAACTGGGAAAGGAACTTCAGTTTTGGAGATGGTTGCAGCATTTGAGAAGGCATCTGGAAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATG
- - - - - - -cagaaca
- - - - - - - - - - - - - - - ccaacac
- - - - - - - - - - - - - - - - - - - - - -aaatcac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aaggaaa