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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...catgtcataaatgaaccaagaaaagagataaggagaaaggaaaggagtgaaaattttgaacccttcttgactgcataatgcatgatgtcatgatttgcagGTGAGCAAAAAAGCTGCAGAATCATTGGCAGATCCTGAAGAGTACCCTAATTTGTTTGAGGACTGGCAGGTTGCTCTTGACATTGAATCTAAAATTTCAG

Basic information

species Vitis vinifera
transcript Vv11s0016g04180.t01
intron # 21
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv11s0016g04180.t01 (Vitis vinifera), 3'ss of exon 21
lower sequence: LOC_Os02g11840.1 (Oryza sativa), 3'ss of exon 12
catgtcataaatgaaccaagaaaagagataaggagaaaggaaaggagtgaaaattttgaacccttcttgactgcataatgcatgatgtcatga--tttgcagGTGAGCAAAAAAGCTGCAGAATCATTGGCAGATCCTGAAGAGTACCCTAATTTGTTTGAGGACTGGCAGGTTGCTCTTGACATTGAATCTAAAATTTCAG
  | | ||      ||  |    | |       |        ||   ||    || | | | |  | || ||   |      | ||| ||| |  |||  |||| | |   ||||| ||||||||||||||||||||||| |||||||| || |||||||| ||||||||  |||||||  |  | ||| ||||  |  |  
--tcttattttcagacttacgcgacactgtttaatttgtaggagctatgtgttttattatctcaccatgccttttttccttctcatgccattatctttatagGTAAACCCCAAAGCAGCAGAATCATTGGCAGATCCTGACGAGTACCCAAACTTGTTTGAAGACTGGCAAATTGCTCTCAATGTAGAAGCTAATGTCGCGC

upper sequence: Vv11s0016g04180.t01 (Vitis vinifera), 3'ss of exon 21
lower sequence: LOC_Os02g11830.2 (Oryza sativa), 3'ss of exon 21
catgtcataaatgaaccaag-aaaagagataaggagaaaggaaaggagtg----aaaattttgaacccttcttgactgcataatgcatgatgtcatgatttgcagGTGAGCAAAAAAGCTGCAGAATCATTGGCAGATCCTGAAGAGTACCCTAATTTGTTTGAGGACTGGCAGGTTGCTCTTGACATTGAATCTAAAATTTCAG
    ||| |  ||  | | |  | |  | | |      |||| |   |||    |  || ||         ||   | |||  | | ||   |  |  |||  |||| | |   ||||| ||||||||||||||||||||  | |||||||| || |||||||| ||||||||  |||||||  |  | ||| ||||  || |  
---ttcagacttgcgctacgcgacactgtttaatttgtaggagatatgtgttttattatcttaccatgccttttttttcattct-cgtgccattttc-tttatagGTAAACCCCAAAGCGGCAGAATCATTGGCAGATCCCAACGAGTACCCAAACTTGTTTGAAGACTGGCAAATTGCTCTCAATGTAGAAGCTAATGTTGCGC

upper sequence: Vv11s0016g04180.t01 (Vitis vinifera), 3'ss of exon 21
lower sequence: LOC_Os06g05180.1 (Oryza sativa), 3'ss of exon 21
--catgtcataaa----tgaaccaagaaaagagataaggagaaagg---aaaggagtgaaaattttgaaccct--tcttgactgcata-atgcatgatgtcatgatttgcagGTGAGCAAAAAAGCTGCAGAATCATTGGCAGATCCTGAAGAGTACCCTAATTTGTTTGAGGACTGGCAGGTTGCTCTTGACATTGAATCTAAAATTTCAG
   || || |||     ||  |  |     |   | |  ||   |     |   ||  || |||||      |  |  ||  |  ||  || |||    || |  | | ||||| |    |||||||||||| ||  |||||||||||   ||||| || ||||| ||||| |||||||||||||| |||    | |||   ||  || |  
gtaatttcttaatcttctgctcttatctttgcattgaaaagtgtgcttccatccagaaaacattttctgttattgttctggttttatctattcatatgttccttctgtacagGTTAATCCAAAAGCTGCAGAGTCTCTGGCAGATCCTTCTGAGTATCCAAATTTATTTGAAGACTGGCAGGTTGCACTTACTGTAGAAAAGAATGTTGCTT

upper sequence: Vv11s0016g04180.t01 (Vitis vinifera), 3'ss of exon 21
lower sequence: GRMZM2G443953_T02 (Zea mays), 3'ss of exon 21
catgtcataaatgaaccaagaaaagagataaggagaaaggaaaggagtgaaaattttgaacccttcttgactgcataatgcatgatgtcatga-tttgcagGTGAGCAAAAAAGCTGCAGAATCATTGGCAGATCCTGAAGAGTACCCTAATTTGTTTGAGGACTGGCAGGTTGCTCTTGACATTGAATCTAAAATTTCAG-------
                   |    ||  |    |    |    |   |  ||  | |   |  ||  ||  | ||| |  | |  | |  ||| |||  ||||||     ||||||||||||||  ||||||||||||  |||||||| ||  |||| |||||||||||| |||||||  |  | ||| |||   || |         
-----------------ttgtgccgatgtgtacactgtgctctgttattcaagctattggcaattgctggtt-catcacccct--ttttgtgacttttaaggtgaattccaaagctgcagAATCTCTGGCAGATCCTGCTGAGTACCCAAACCTGTTCGAGGACTGGCAGATTGCTCTGAATGTAGAAGCTACTGTTGCTCCCAAGAG

upper sequence: Vv11s0016g04180.t01 (Vitis vinifera), 3'ss of exon 21
lower sequence: GRMZM2G443953_T03 (Zea mays), 3'ss of exon 22
-catgtcataaatgaaccaa-gaaaagagataaggagaaaggaaaggagtgaaaattttgaacccttcttgactgcataatgcatgatgtcatga-tttgcagGTGAGCAAAAAAGCTGCAGAATCATTGGCAGATCCTGAAGAGTACCCTAATTTGTTTGAGGACTGGCAGGTTGCTCTTGACATTGAATCTAAAATTTCAG
   | || ||  | |   |  |    ||  |    |    |    |   |  ||  | |   |  ||  ||  | ||| |  | |  | |  ||| |||  ||||||     ||||||||||||||  ||||||||||||  |||||||| ||  |||| |||||||||||| |||||||  |  | ||| |||   || |  
gtttttcgtagtttatttattgtgccgatgtgtacactgtgctctgttattcaagctattggcaattgctggtt-catcacccct--ttttgtgacttttaagGTGAATTCCAAAGCTGCAGAATCTCTGGCAGATCCTGCTGAGTACCCAAACCTGTTCGAGGACTGGCAGATTGCTCTGAATGTAGAAGCTACTGTTGCTC

upper sequence: Vv11s0016g04180.t01 (Vitis vinifera), 3'ss of exon 21
lower sequence: GRMZM2G095348_T02 (Zea mays), 3'ss of exon 20
-catgtcataaatgaaccaagaaaagagat--------aaggagaaaggaaaggagtgaaaattttgaacccttcttgactgcataatgcatgatgtcatgatttgcagGTGAGCAAAAAAGCTGCAGAATCATTGGCAGATCCTGAAGAGTACCCTAATTTGTTTGAGGACTGGCAGGTTGCTCTTGACATTGAATCTAAAATTTCAG
  |  |  | ||||  |  |    ||   |        || | |    |  |  ||  |||| |     |  || |    | | |  |   || |  | || | ||||| | |    |||||||||||| ||  |||||||||||   || || || ||||| ||||| |||||||||||||||||     | |||   |   || |  
gtaatttcttaatgttctcatcttagtcttctttctgaaaagtgtggtgccattagaaaaaaatgcatgctattatcttattctttttttctg-taccttg-tatgcagATTAATCCAAAAGCTGCAGAGTCTCTGGCAGATCCTTCTGAATATCCAAATTTATTTGAAGACTGGCAGGTTGCTCTAACTGTAGAAAAAAGCGTTGCTT

upper sequence: Vv11s0016g04180.t01 (Vitis vinifera), 3'ss of exon 21
lower sequence: GLYMA15G01680.1 (Glycine max), 3'ss of exon 21
catgtcataaatgaaccaagaaaagagataaggagaaaggaaaggagtgaaaattttgaacccttcttg-actgcataatgcatgatgtcatgatttgcagGTGAGCAAAAAAGCTGCAGAATCATTGGCAGATCCTGAAGAGTACCCTAATTTGTTTGAGGACTGGCAGGTTGCTCTTGACATTGAATCTAAAATTTCAG
  |   |  |      |      |        |    || |      | |   |   ||     || || | |  | |  | |  || |  |   |||||||| |    ||||||||| ||||||||||| ||||||||||| || || ||||||||||| || ||||||||||| || |   | |||||||||  |   |
ggtaggagcatcagttctcattcatttgccttgtttgagtagtcttatcatgttgacgagtggctcatggattaaagagagtac-atatattttattgcagGTTAATCCAAAAGCTGCTGAATCATTGGCTGATCCTGAAGAATATCCAAATTTGTTTGAAGATTGGCAGGTTGCACTAGCTGTCGAATCTAAAGCTGTGG

upper sequence: Vv11s0016g04180.t01 (Vitis vinifera), 3'ss of exon 21
lower sequence: GLYMA08G22140.1 (Glycine max), 3'ss of exon 21
------------------------------------------------------------------------------------------------------catgtcataaatgaaccaagaaaagagataaggagaaaggaaaggagtgaaaattttgaacccttcttgactgcataatgcatgatgtcatgatttgcagGTGAGCAAAAAAGCTGCAGAATCATTGGCAGATCCTGAAGAGTACCCTAATTTGTTTGAGGACTGGCAGGTTGCTCTTGACATTGAATCTAAAATTTCAG
                                                                                                      |||  |||       ||  |    | |||    |  | |  |   | || |  |     |    | |  | |     ||  ||  ||| |  ||   ||||| |    |||||| || ||||||||||| |||||||| ||||| |||||||||||||| || ||||| ||||| ||||   |||||||||||  | |||
gtaatgttatatatatatatatatatatatatataatttagcaacggaatagcctgacatttatgttgtgcacatgatactgtgggtaggaacttctgttctcattccattggcctgccctgtcctg-gattcttatcatgctacatattgcatgtgaaataaaaatataaattcttatatttatt-tgttaatatgcacagGTTAATCCAAAAGCCGCCGAATCATTGGCTGATCCTGAGGAGTATCCTAATTTGTTTGATGATTGGCAAGTTGCACTTGCTGTTGAATCTAAAGCTACAG

upper sequence: Vv11s0016g04180.t01 (Vitis vinifera), 3'ss of exon 21
lower sequence: GLYMA07G03890.2 (Glycine max), 3'ss of exon 10
--catgtcataaatgaaccaagaaaagagataaggagaaaggaaaggagtgaaaattttgaacccttcttgactgcataatgcatgatgtcatgatttgcagGTGAGCAAAAAAGCTGCAGAATCATTGGCAGATCCTGAAGAGTACCCTAATTTGTTTGAGGACTGGCAGGTTGCTCTTGACATTGAATCTAAAATTTCAG
  |||  |||       ||  |    | |||    |  | |  |  || || |  |     |    | |  | |     ||  | | ||| |  ||   ||||| |    ||||||||| ||||||||||| |||||||| || || |||||||||||||| || ||||| ||||| || |   |||||||||||  | | |
ctcattccattggcctgccctgtcctg-gattcttatcatgctacagattgcatgtgaaataaaaatataaattcttatattta-gttgttaatatgcacagGTTAATCCAAAAGCTGCTGAATCATTGGCTGATCCTGAGGAATATCCTAATTTGTTTGATGATTGGCAAGTTGCACTAGCTGTTGAATCTAAAGCTACGG

upper sequence: Vv11s0016g04180.t01 (Vitis vinifera), 3'ss of exon 21
lower sequence: GLYMA13G43680.1 (Glycine max), 3'ss of exon 21
-------catgtcataaatgaaccaagaaaagagataaggagaaaggaaaggagtgaaaattttgaacccttcttgactgcataatgcatgatgtcatgatttgcagGTGAGCAAAAAAGCTGCAGAATCATTGGCAGATCCTGAAGAGTACCCTAATTTGTTTGAGGACTGGCAGGTTGCTCTTGACATTGAATCTAAAATTTCAG
         | ||||  ||   ||  |    |  |     |  | |   |  |||||   || || |        || | | || | | | || |  ||  |||||||| |    ||||||||| |||||||||||  |||||||||| || || ||||||||||| || ||||| ||||| || |   | |||||||||  |   |
agcatccgttctcattcatttgccttgtttgggtagtcttatcatgttgacaagtgac--ttatggattaaaga-gagtacgta-tacgt-atattttg--ttgcagGTCAATCCAAAAGCTGCTGAATCATTGGCTAATCCTGAAGAATATCCAAATTTGTTTGAAGATTGGCAAGTTGCACTAGCTGTCGAATCTAAAGCTGTGG

upper sequence: Vv11s0016g04180.t01 (Vitis vinifera), 3'ss of exon 21
lower sequence: AT3G15980.2 (Arabidopsis thaliana), 3'ss of exon 21
catgtcataaatgaaccaagaaaagagataaggagaaaggaaaggagtgaaaattttgaacccttcttgactgcataatgcatgatgtcatgatttgcagGTGAGCAAAAAAGCTGCAGAATCATTGGCAGATCCTGAAGAGTACCCTAATTTGTTTGAGGACTGGCAGGTTGCTCTTGACATTGAATCTAAAATTTCAG
   || ||    | | |           ||  | |  |   |      |||||||     |      || ||  | | ||| |  || | ||   | ||||| |    |||||| || ||||| || || ||||||||||||||| | ||| | |||||||| ||||| |||||||||    ||||| | || | | |||
---gttattttcgcatcttttttttgtttactgtgtcaatga------gaaaatt-----catcatgtggctttaaattgcctt-tgacttgtcat-cagGTTAATCCAAAAGCAGCTGAATCTTTAGCTGATCCTGAAGAGTACTCAAATCTTTTTGAGGATTGGCAAGTTGCTCTTTCTGTTGAAGCGAACACTGCAG

upper sequence: Vv11s0016g04180.t01 (Vitis vinifera), 3'ss of exon 21
lower sequence: PP1S61_1V6.1 (Physcomitrella patens), 3'ss of exon 21
----------------------------------------------------------------------------catgtcataaatgaacc-----aagaaaagagataaggag-aaaggaaaggagtgaaaattttgaac---ccttcttgactgcataatgcatgatgtcatgatttgcagGTGAGCAAAAAAGCTGCAGAATCATTGGCAGATCCTGAAGAGTACCCTAATTTGTTTGAGGACTGGCAGGTTGCTCTTGACATTGAATCTAAAATTTCAG
                                                                                |   | |||  ||     |  ||    ||||||     || ||  | || |       |||||   | ||| | | ||        ||| | ||    || |||| | | | |||| ||||||||||| ||||||||||| ||||| ||||| || ||||||   |||||| |   |||  | |  | |||  | || ||   ||
gtatgtattttttattttttattttttctcaattgtctcattccatagactgctaaaggccattgaattcccaccttgaattggagatgtgcctgtttattaatgttgataagtttcgaaagattgtagagcgctgactgaacactctttcctaaatgttctccttatggt-tctcttttggcagATCAACCAAAAGGCTGCAGAATCTTTGGCAGATCCAGAAGAATACCCCAACTTGTTTTCAGACTGGGAATCTGCGTTAGCTACTGAGGCCAAGATGAAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agtgaaaattttgaacccttcttgactgcataatgcatgatgtcatgatttgcagGTGAGCAAAAAAGCTGCAGAATCATTGGCAGATCCTGAAGAGTACCCTAATTTGTTTGAGGACTGGCAGGTTGCTCTTGACATTGAATCTAAAATTTCAG
                   tcttgac  putative branch site (score: 3)
     aaattttgaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
catgtcataaatgaaccaagaaaagagataaggagaaaggaaaggagtgaaaattttgaacccttcttgactgcataatgcatgatgtcatgatttgcagGTGAGCAAAAAAGCTGCAGAATCATTGGCAGATCCTGAAGAGTACCCTAATTTGTTTGAGGACTGGCAGGTTGCTCTTGACATTGAATCTAAAATTTCAG

catgtca
- - - - aaatgaa
- - - - - - - - -aagaaaa
- - - - - - - - - - - - - - - -ggagaaa
- - - - - - - - - - - - - - - - - gaaagga
- - - - - - - - - - - - - - - - - - - - - - - - gaaaatt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gactgca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gcatgat