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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aatgagtttgcttttatagaacttgaaaggaaaaaccaattaaatgaaaaatggtgcttagtatttatgaattataaccagcaattttctttggcagcagTGCGAAATGGATGCCGGGGTGAAGCATGCTGTGGTGGTGAAAGTTATGGGTCGAACTGGATCAAGGGGTCAGGTGACACAGGTGAGAGTGAAGTTTTTGG

Basic information

species Vitis vinifera
transcript Vv08s0007g07210.t01
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv08s0007g07210.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: LOC_Os10g27174.1 (Oryza sativa), 3'ss of exon 1
aatgagtttgcttttatagaacttgaaaggaaaaaccaattaaatgaaa-aatggtgcttagtatt---tatgaattataaccagcaattt-tctttggcagcagTGCGAAATGGATGCCGGGGTGAAGCATGCTGTGGTGGTGAAAGTTATGGGTCGAACTGGATCAAGGGGTCAGGTGACACAGGTGAGAGTGAAGTTTTTGG-----
          || | |||    |||||| ||     | ||| ||| |     || || || ||||     || | || |  |   |  | | |  ||       ||||   |||||| ||  ||| || | ||| || |||||||| || ||||| || || || || |||||||||||||| ||||| |||||||||||  | |     
----cacgaactgtaata----ttgaaatgactg--cgattgaattacctgctgctggtttgtatagaacatcagttttgcctgactgtatatgcttcctgcttgtgcagCATGGATACCCAGGTCAAACTTGCCGTCGTGGTGAAGGTGATGGGCCGCACCGGCTCCAGGGGTCAGGTGACCCAGGTCAGAGTGAAGTTCCTCGACGAC

upper sequence: Vv08s0007g07210.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GRMZM2G455828_T01 (Zea mays), 3'ss of exon 1
-aatgagtttgcttttatagaacttgaaaggaaaaaccaattaaatgaaaaatggtgcttagtatttatgaattataaccagcaattttctttggcagcagTGCGAAATGGATGCCGGGGTGAAGCATGCTGTGGTGGTGAAAGTTATGGGTCGAACTGGATCAAGGGGTCAGGTGACACAGGTGAGAGTGAAGTTTTTGG-----
  |  ||         ||   ||     ||  ||||  || ||  |||  ||  |    | ||     |  ||||    ||     ||||| |      | |||   |||||  ||  |||||||| |||||| |||||||| || |||||  | || || || |||||||||||||| ||||| ||||||||||||||||     
ccagtagcaacaaaccatgtgacagtgcagttaaaatgaactatgtgatcaa-agcatatggttcaccttgattactgacaaatgctttctat-----taatgcagCATGGACACCCAGGTGAAGCTTGCTGTTGTGGTGAAGGTGATGGGCAGGACCGGCTCCAGGGGTCAGGTGACCCAGGTCAGAGTGAAGTTTTTGGATGAC

upper sequence: Vv08s0007g07210.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GRMZM2G124143_T03 (Zea mays), 3'ss of exon 1
-----aatgagtttgcttttatagaacttgaaaggaaaaaccaattaaatgaaaaatggtgcttagtatttatgaattataaccagcaattttctttggcagcagTGCGAAATGGATGCCGGGGTGAAGCATGCTGTGGTGGTGAAAGTTATGGGTCGAACTGGATCAAGGGGTCAGGTGACACAGGTGAGAGTGAAGTTTTTGG-----
         |||||    ||  |     |||   ||  |||    | ||  ||       || |  |     |   | | |||   ||| |   ||   ||  |||||   |||||  ||   ||||||| |||||| |||||||| || |||||  | || || || ||||||||||| || ||||| ||||||||||| ||||     
ttgtttgccagtttctacttcaaagctgtgatttgaggaactttgtgaacaaagg-----gcctgattcacct---tgacaactgacaaatgctttctaca--agtgcagTATGGACACCCAAGTGAAGCTTGCTGTTGTGGTGAAGGTGATGGGAAGGACCGGCTCCAGGGGTCAGGTTACCCAGGTCAGAGTGAAGTTCTTGGATGAC

upper sequence: Vv08s0007g07210.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GRMZM2G030293_T02 (Zea mays), 3'ss of exon 1
--aatgagtttgcttttatagaacttgaaaggaaaaaccaattaaatgaaaaatggtgcttagtatttatgaattataaccagcaattttctttggcagcagTGCGAAATGGATGCCGGGGTGAAGCATGCTGTGGTGGTGAAAGTTATGGGTCGAACTGGATCAAGGGGTCAGGTGACACAGGTGAGAGTGAAGTTTTTGG-----
  ||| |||      | ||   ||     ||   |||  ||  |   ||| || |    | | |     |||    ||||    || |   ||  |   || |||   |||||  ||   ||||||| |||||| ||||| || || |||||  | || || || |||||||||||||| ||||| ||||||||||| ||||     
ccaat-agtaccaaatcatgtgacagtgcagttgaaatgaaccatgcgaacaaagcaaatgattcaccttga----taacttataaatgctttctgt--caatgcagCATGGACACCCAAGTGAAGCTTGCTGTTGTGGTAAAGGTGATGGGCAGGACCGGCTCCAGGGGTCAGGTGACCCAGGTCAGAGTGAAGTTCTTGGATGAC

upper sequence: Vv08s0007g07210.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA03G36420.1 (Glycine max), 3'ss of exon 1
aatgagtttgcttttatagaacttgaaaggaaaaaccaattaa--atgaaaaatggtgcttagt-atttatgaattataaccagcaattttctttggcagcagTGCGAAATGGATGCCGGGGTGAAGCATGCTGTGGTGGTGAAAGTTATGGGTCGAACTGGATCAAGGGGTCAGGTGACACAGGTGAGAGTGAAGTTTTTGG-----
       ||  |  |     |  ||  | |   | |  |||||   |||   ||    |  | |  |||   | ||  | |    || | |   | |     |  |   |||||  |   ||||||||||||| | || || |||||||||||||| |||||||| || || |||||||| ||||| ||||||||||||||||     
-------ttattcctgatttatctgtgatgctga-ctgattaactgtgatgcattaaacgcaattgttttccactttcatctcataactgttgattgtgtttgatcagGATGGAGTCTCAGGTGAAGCATGCTCTTGTTGTCAAAGTTATGGGTCGTACTGGATCCAGAGGACAGGTGACTCAGGTTAGAGTGAAGTTTTTGGATGAT

upper sequence: Vv08s0007g07210.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA13G37600.1 (Glycine max), 3'ss of exon 2
aatgagtttgcttttatagaacttgaaaggaaaaaccaattaaatgaaaaatggtgcttagtatttatgaattataaccagcaattttctttggcagcagTGCGAAATGGATGCCGGGGTGAAGCATGCTGTGGTGGTGAAAGTTATGGGTCGAACTGGATCAAGGGGTCAGGTGACACAGGTGAGAGTGAAGTTTTTGG-----
    |  ||||  | | |    |     |   |||   | | || | ||  | || |  | |  |||       |||| |  |    |  || |     | ||   |||||  |   ||||||||| ||  | || || |||||||||||||| ||||| || ||||| |||||||| ||||| ||||||||||||||||     
---tatgttgccct-acacttttctgttgtccaaatggaatgaaagcaatgttgtccacaatccttactccacttaac-attatgaatgctttgtgtttgagcagGATGGAATCTCAGGTGAAGCACGCCCTTGTTGTCAAAGTTATGGGTCGTACTGGGTCTAGGGGGCAGGTGACTCAGGTTAGAGTGAAGTTTTTGGATGAT

upper sequence: Vv08s0007g07210.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA19G39070.1 (Glycine max), 3'ss of exon 1
----aatgagtttgctt-ttatag-aacttgaaaggaaaaaccaattaaatgaaaaatggtgcttagtatttatga-attataaccagcaattttctttggcagcagTGCGAAATGGATGCCGGGGTGAAGCATGCTGTGGTGGTGAAAGTTATGGGTCGAACTGGATCAAGGGGTCAGGTGACACAGGTGAGAGTGAAGTTTTTGG--
     |    ||| | | | |  |  ||     ||     |   ||||||   ||  | ||  |    ||| ||   || | |||     ||| | ||||        ||   |||||  |   ||||||||| ||  | || || |||||||||||||| |||||||| || || || ||||| ||||| ||||||||||||||||  
gtgatacatatttacctgtcacggtgaccaattagctgtgatgcattaaacccaa--ttgttttccacattcatctcataaaaactgttgattgtgtttga-------gCAGGATGGAGTCTCAGGTGAAGCACGCACTTGTTGTCAAAGTTATGGGTCGTACTGGATCCAGAGGACAAGTGACCCAGGTTAGAGTGAAGTTTTTGGAT

upper sequence: Vv08s0007g07210.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA03G36580.1 (Glycine max), 3'ss of exon 1
aatgagtttgcttt-tatagaacttgaa--aggaaaaaccaattaaatgaaaaatggtgcttagtatttatgaattataaccagcaattttctttggcagcagTGCGAAATGGATGCCGGGGTGAAGCATGCTGTGGTGGTGAAAGTTATGGGTCGAACTGGATCAAGGGGTCAGGTGACACAGGTGAGAGTGAAGTTTTTGG-----
  ||  ||||     | |    | |||   |      |   ||| | | || |    || ||   | ||     | |||||      |||  ||  |     | ||   |||||  |   ||||||||| ||  | || || ||||| |||||||| |||||||| || || |||||||| ||||| |||||||||||| |||     
--tgcatttggaagatgttattcctgatttatctgtcattgattcattaaacacatttgttttccactttcatctcataac----ggtttgatt--gtgtttgagcagGATGGAGTCTCAGGTGAAGCACGCACTTGTTGTCAAAGTAATGGGTCGTACTGGATCCAGAGGACAGGTGACCCAGGTTAGAGTGAAGTTTCTGGATGAT

upper sequence: Vv08s0007g07210.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA19G39250.1 (Glycine max), 3'ss of exon 1
----aatgagtttgctt-ttat-agaacttgaaaggaaaaaccaattaaatgaaaaatggtgcttagtatttatga-attataaccagcaattttctttggcagcagTGCGAAATGGATGCCGGGGTGAAGCATGCTGTGGTGGTGAAAGTTATGGGTCGAACTGGATCAAGGGGTCAGGTGACACAGGTGAGAGTGAAGTTTTTGG--
     |    ||| | | | |  || ||     ||     |   ||||||   ||  | ||  |    ||| ||   || |||||     ||| | |||   |||||      |||||  |   ||||||||| ||  | || || |||||||||||||| |||||||| || || || || || ||||| |||||||| |||||||  
gtgatacatatttacctgtcacgaggaccgattagctgtgatgcattaaacccaa--ttgttttccacattcatctcataataactgttgattgtgttt--tagCAG-----GATGGAGTCTCAGGTGAAGCACGCACTTGTTGTCAAAGTTATGGGTCGTACTGGATCCAGAGGACAAGTAACCCAGGTTAGAGTGAAATTTTTGGAT

upper sequence: Vv08s0007g07210.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA19G39250.2 (Glycine max), 3'ss of exon 1
-aatgagtttgctt-ttat-agaacttgaaaggaaaaaccaattaaatgaaaaatggtgcttagtatttatga-attataaccagcaattttctttggcagcagTGCGAAATGGATGCCGGGGTGAAGCATGCTGTGGTGGTGAAAGTTATGGGTCGAACTGGATCAAGGGGTCAGGTGACACAGGTGAGAGTGAAGTTTTTGG-----
  |    ||| | | | |  || ||     ||     |   ||||||   ||  | ||  |    ||| ||   || |||||     ||| | |||   |||||      |||||  |   ||||||||| ||  | || || |||||||||||||| |||||||| || || || || || ||||| |||||||| |||||||     
atacatatttacctgtcacgaggaccgattagctgtgatgcattaaacccaa--ttgttttccacattcatctcataataactgttgattgtgttt--tagcag-

upper sequence: Vv08s0007g07210.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: AT3G10090.1 (Arabidopsis thaliana), 3'ss of exon 1
aatgagtttgcttttatagaacttgaaaggaaaaaccaattaaatgaaaaatggtgcttagtatttatgaattataaccagcaattttctttggcagcagTGCGAAATGGATGCCGGGGTGAAGCATGCTGTGGTGGTGAAAGTTATGGGTCGAACTGGATCAAGGGGTCAGGTGACACAGGTGAGAGTGAAGTTTTTGG-----
  |       |||   |  ||  ||||    ||  |   ||   | |  | |    |||  | | ||  | ||     | | |  ||| | |          |  ||||||| |   | | ||||| ||||| || |||||||| |||||  | ||||||||||||||||| ||||| ||||| |||||||||||    |     
--tatacagtcttgattcaaatgtgaac---aattctctttttctaaggattttcacttcttttgtaaaatttggtctctgaatgtttttgttttgttgaatcagAATGGATTCTCAGATCAAGCACGCTGTTGTAGTGAAAGTGATGGGAAGGACTGGATCAAGGGGTCAAGTGACTCAGGTTAGAGTGAAGTTCACTGACTCG

upper sequence: Vv08s0007g07210.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: AT5G03850.1 (Arabidopsis thaliana), 3'ss of exon 1
-aatgagtttgcttttatagaacttgaaaggaaaaaccaattaaatgaaaaatggtgcttagtatttatgaattataaccagcaattttctttggcagcagTGCGAAATGGATGCCGGGGTGAAGCATGCTGTGGTGGTGAAAGTTATGGGTCGAACTGGATCAAGGGGTCAGGTGACACAGGTGAGAGTGAAGTTTTTGG-----
   | |  ||| ||   |   || |||||      ||  |||   |    | |  || ||  | |||     | |          ||||  |||   | |   |  ||||||| |   | | ||||| ||||||||||| || || |||||| | ||||| |||||||||||||| || |||||  |||||||||||   |     
ctgtaaagttgattgcttt--acatgaaactgtgtactgattgtgtatgcatt--tgattgatgttttaatgtgaattttcatggttttggttgattgaat--cagAATGGATTCTCAGATCAAGCACGCTGTGGTGGTTAAGGTCATGGGTAGGACTGGTTCAAGGGGTCAGGTTACTCAGGTTCGAGTGAAGTTTACCGACTCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gaaaaatggtgcttagtatttatgaattataaccagcaattttctttggcagcagTGCGAAATGGATGCCGGGGTGAAGCATGCTGTGGTGGTGAAAGTTATGGGTCGAACTGGATCAAGGGGTCAGGTGACACAGGTGAGAGTGAAGTTTTTGG
                          ttataac  putative branch site (score: 2)
                                       ttttcttt  putative PPT
            ttagtatttatgaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aatgagtttgcttttatagaacttgaaaggaaaaaccaattaaatgaaaaatggtgcttagtatttatgaattataaccagcaattttctttggcagcagTGCGAAATGGATGCCGGGGTGAAGCATGCTGTGGTGGTGAAAGTTATGGGTCGAACTGGATCAAGGGGTCAGGTGACACAGGTGAGAGTGAAGTTTTTGG

- - - - - - - - - - - - -aaaggaa
- - - - - - - - - - - - - - - - aaaccaa
- - - - - - - - - - - - - - - - - - - - - - tgaaaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - tgcttag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ataacca