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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tttcatagaaactgggactttggggcctcaatttgcttgaaatatcttgagattttttgttgtggaaacttaattagcttttgggattccaaatttgaagCCGGGAGATGTTTAATAAATGGCAAGCTCAGCGATGGTGGGGAGAGAATTATGACCGGATCATGGAGCTGTACAATGTCCAGAGATTCAACCGCCAAGCT

Basic information

species Vitis vinifera
transcript Vv02s0033g00590.t01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv02s0033g00590.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA16G17590.1 (Glycine max), 3'ss of exon 1
---tttcatag-aaactgggactttggggcctcaatttgcttgaaatatcttgagattttttgttgtggaaacttaattagcttttgggattccaaatttgaagCCGGGAGATGTTTAATAAATGGCAAGCTCAGCGATGGTGGGGAGAGAATTATGACCGGATCATGGAGCTGTACAATGTCCAGAGATTCAACCGCCAAGCT
    |  |||  ||||   |  | ||||   |  | ||  |   ||  |  | |    | | |  |   | ||| |   |    || | |||   |||||||||||| ||||||||||||||||||||||||||  |||||||||| |||||||| ||| | |||||||| || ||||| ||||||||||| ||    ||||||
aatataaatattaaacaaagcatatgggatttttagtttttgagaacttaattat-cctgtaggagcaaagactga--caatacttagcattt-gaatttgaagCCGAGAGATGTTTAATAAATGGCAAGCTCAAAGATGGTGGGGTGAGAATTACGACAGAATCATGGAACTTTACAACGTCCAGAGATTTAATAAACAAGCT

upper sequence: Vv02s0033g00590.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA16G08070.1 (Glycine max), 3'ss of exon 3
---tttcatag-aaactgggactttggggcctcaatttgcttgaaatatcttgagattttttgttgtggaaacttaattagcttttgggattccaaatttgaagCCGGGAGATGTTTAATAAATGGCAAGCTCAGCGATGGTGGGGAGAGAATTATGACCGGATCATGGAGCTGTACAATGTCCAGAGATTCAACCGCCAAGCT
    |  |||  ||||   |  | ||||   |  | ||  |   ||  |  | |    | | |  |   | ||| |   |    || | |||   |||||||||||| ||||||||||||||||||||||||||  |||||||||| |||||||| ||| | |||||||| || ||||| ||||||||||| ||    ||||||
catataaatattaaacaaagcatatgggatttttagtttttgagaacttaattat-cctgtaggagcaaagactga--caatacttagcattt-gaatttgaagCCGAGAGATGTTTAATAAATGGCAAGCTCAAAGATGGTGGGGTGAGAATTACGACAGAATCATGGAACTTTACAACGTCCAGAGATTTAATAAACAAGCT

upper sequence: Vv02s0033g00590.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA01G35180.1 (Glycine max), 3'ss of exon 1
-tttcatagaaactg--ggactttggggcctcaatttgcttgaaatatcttgagattttttgttgtggaaacttaattagcttttgggattccaaatttgaagCCGGGAGATGTTTAATAAATGGCAAGCTCAGCGATGGTGGGGAGAGAATTATGACCGGATCATGGAGCTGTACAATGTCCAGAGATTCAACCGCCAAGCT
  || ||  | ||     |  | | ||   |  | ||| |  |||  |     |     | |  |   | ||| |   |    |  | |||  ||||||||||||| ||||| ||| | || |||||||||||   ||||||||| |||||||||||| | |||||||| || ||||| || ||||||||||| || ||||||
tctttattcagaccattagtatataggaattttagttgttgaaaaagttaattgtccagtaggagcaaagactga--caatactaagcattt-aaatttgaagCCGAGAGATTTTTGACAAGTGGCAAGCTCAAAAATGGTGGGGTGAGAATTATGACAGAATCATGGAACTTTACAACGTGCAGAGATTCAATCGACAAGCT

upper sequence: Vv02s0033g00590.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA09G34600.1 (Glycine max), 3'ss of exon 3
-tttcatagaaactgg--gactttggggcctcaatttgcttgaaatatcttgagattttttgttgtggaaacttaattagcttttgggattccaaatttgaagCCGGGAGATGTTTAATAAATGGCAAGCTCAGCGATGGTGGGGAGAGAATTATGACCGGATCATGGAGCTGTACAATGTCCAGAGATTCAACCGCCAAGCT
  || || || ||     |  | || |   |  | ||| |  |||  |           | |  |   | |||||  ||    || | |||  | ||||||||||| ||||| ||  | || |||||||||||   ||||||||| |||||||||||| | |||||||| || ||||| || ||||||||||| || ||||||
tctttattgagaccatttgtatatgagaattttagttgttgaaaaagttaattatccagtaggagcaaagactta--taatagttagcattt-acatttgaagCCGAGAGATTTTCGACAAGTGGCAAGCTCAAAAATGGTGGGGTGAGAATTATGACAGAATCATGGAACTTTACAACGTGCAGAGATTCAATCGACAAGCT

upper sequence: Vv02s0033g00590.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: AT1G31880.1 (Arabidopsis thaliana), 3'ss of exon 4
tttcatagaaactgggactttggggcctcaatttgcttgaaatatcttgagattttttgttgtggaaacttaattagcttttgggattccaaatttgaagCCGGGAGATGTTTAATAAATGGCAAGCTCAGCGATGGTGGGGAGAGAATTATGACCGGATCATGGAGCTGTACAATGTCCAGAGATTCAACCGCCAAGCT
    ||   ||||    |        ||| || |  |      ||     | |      |     |||    |  |  |  | |  |      ||  |||||| ||||||||| |||| ||||||||||| || |||||||| ||||| ||||||  |||| | ||||| |||||||| |||||||| ||||||||||||
--gtatttgaactact-caaaacaatctctatatcttcatggcattcaacgctgaaacatgagataaaaactaacaattacttgtgtcttgttttgaaagCCGAGAGATGTTTGATAAGTGGCAAGCTCAACGGTGGTGGGGTGAGAACTATGACAAGATCGTTGAGCTTTACAATGTACAGAGATTTAACCGCCAAGCT

upper sequence: Vv02s0033g00590.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: AT2G21030.1 (Arabidopsis thaliana), 3'ss of exon 1
-tttcatagaaactgggactttggggcctcaatttgcttgaaatatcttgagattttttgttgtg-gaaacttaattagcttttgggattccaaatttgaagCCGGGAGATGTTTAATAAATGGCAAGCTCAGCGATGGTGGGGAGAGAATTATGACCGGATCATGGAGCTGTACAATGTCCAGAGATTCAACCGCCAAGCT
 | |  ||   |||   |         ||| || |  |    | ||    || |      |      |||  |||  |    ||| | |      ||  |||||| |||||||  ||||| ||||||||||| ||  ||||||| ||||| ||||||  |||| | ||||| |||||||| |||||||| ||||||||||||
gtattttaactactcaaaac----aatctctatatcttcatgacattcaaagctggaacatgagataaaaactaaccattacttgtg-tcttgttttgaaagCCGAGAGATGTACAATAAGTGGCAAGCTCAACGGCGGTGGGGTGAGAACTATGACAAGATCGTTGAGCTTTACAATGTACAGAGATTTAACCGCCAAGCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttgagattttttgttgtggaaacttaattagcttttgggattccaaatttgaagCCGGGAGATGTTTAATAAATGGCAAGCTCAGCGATGGTGGGGAGAGAATTATGACCGGATCATGGAGCTGTACAATGTCCAGAGATTCAACCGCCAAGCT
                      acttaat  putative branch site (score: 4)
                    aaacttaatta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tttcatagaaactgggactttggggcctcaatttgcttgaaatatcttgagattttttgttgtggaaacttaattagcttttgggattccaaatttgaagCCGGGAGATGTTTAATAAATGGCAAGCTCAGCGATGGTGGGGAGAGAATTATGACCGGATCATGGAGCTGTACAATGTCCAGAGATTCAACCGCCAAGCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT
- - atagaaa
- - - - - - - - - - - - gcctcaa
- - - - - - - - - - - - - - - - -tgcttga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ttttggg