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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gggtaagtatcttactcttttgtttttcttaagatcctataaaaagttctgaacttgtatattattcatttctaatgtatttatattgcaaatattttagGTACCCCAATTTGAAGAGTGTGCGAGAACTGATTTACAAGAGGGGCTATGGAAAGTTGAACAAGCAGAGAACTGCCTTGACCGACAACTCCATTGTGGAA

Basic information

species Vitis vinifera
transcript Vv09s0054g00090.t01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv09s0054g00090.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: LOC_Os04g51630.3 (Oryza sativa), 3'ss of exon 4
------gggtaagtatcttactcttttgtttttcttaagatcctataaaaagttctgaacttgtatattattcatttctaatgtatttatattgcaaatattttagGTACCCCAATTTGAAGAGTGTGCGAGAACTGATTTACAAGAGGGGCTATGGAAAGTTGAACAAGCAGAGAACTGCCTTGACCGACAACTCCATTGTGGAA
         | | |    ||   | |    |   | |||  ||||   |     ||  | |||  ||||  || ||  || |  |||  |  | |  || |||||||||||| |||||||||||||| || ||| |||| ||||||||||||||||||||| | |||||||| ||||   |  | ||  |||||    |  | || 
attttaatttgaattgtctagggtctgaaatagttcaagcccctaatga-----ctagagttgattattgatc-ttcttactagattagtgattcttatgttttagGTACCCAAATTTGAAGAGTGTCCGTGAATTGATCTACAAGAGGGGCTATGGAAAGCTCAACAAGCAAAGAATCCCTCTTACAAACAACAAAGTCATCGAG

upper sequence: Vv09s0054g00090.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GRMZM2G094051_T03 (Zea mays), 3'ss of exon 5
gggtaagtatcttactcttttgtttttcttaagatcctataaaaagttctgaacttgtatattattcatttctaatg----tatttatattgcaaatatt--ttagGTACCCCAATTTGAAGAGTGTGCGAGAACTGATTTACAAGAGGGGCTATGGAAAGTTGAACAAGCAGAGAACTGCCTTGACCGACAACTCCATTGTGGAA
    ||  ||    |          |     || ||||  |     |  |    | ||   | ||    |||| |||    || | |  | |||||| ||  |||||||||| || |||||||||||  | ||  |||| ||||||||||||||||||||| ||||||||||||| |   |  || || |||||    |  | || 
-aaaaaacataaagcagacagtgcctggagtagttcctgca-----tcttagcttggtgactcatctgcttctgatgaccttactaaagtggcaaatcttgtttagGTACCCAAACTTGAAGAGTGTCAGGGAGTTGATCTACAAGAGGGGCTATGGAAAGCTGAACAAGCAGAGGATCCCTCTGTCCAACAACCAAGTCATCGAG

upper sequence: Vv09s0054g00090.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GRMZM2G344279_T01 (Zea mays), 3'ss of exon 5
gggtaagtatcttactcttttgtttttcttaagatcctataaaaagttctgaacttgtatattattcatttctaatg----tatttatattgcaaatatt--ttagGTACCCCAATTTGAAGAGTGTGCGAGAACTGATTTACAAGAGGGGCTATGGAAAGTTGAACAAGCAGAGAACTGCCTTGACCGACAACTCCATTGTGGAA
 |  ||     | |  | |    | |     || ||||  |     |  |    | ||   | ||    |||  |||    || | |  | |||||| ||  |||||||||| || ||||| |||||  | ||  |||| ||||||||||||||||||||  ||||||||||||| |   |  || || |||||    |  | || 
-gaaaaaagcataaagcatactgtctggagtagttcctgca-----tcttagcttggtgactcatctgcttccgatgaccttactaacgtggcaaatcttgtttagGTACCCAAACTTGAACAGTGTCAGGGAGTTGATCTACAAGAGGGGCTATGGAAATCTGAACAAGCAGAGGATCCCTCTGTCCAACAACCAAGTCATCGAG

upper sequence: Vv09s0054g00090.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GRMZM5G868433_T02 (Zea mays), 3'ss of exon 5
gggtaagtatcttactcttttgtttttcttaagatcctataaaaagttctgaacttgtatattattcatttctaatgtatttatattgcaaatat------tttagGTACCCCAATTTGAAGAGTGTGCGAGAACTGATTTACAAGAGGGGCTATGGAAAGTTGAACAAGCAGAGAACTGCCTTGACCGACAACTCCATTGTGGAA
     |  |  || ||    |       |   ||     | |     |||   ||||   | |      |||| |||   ||      |  ||||      ||||||||||| || |||||||||||  | ||  |||| |||||||||||||| |||||  ||||||||||||| |   |  || |  |||||    |  | || 
-----aaaacattgctacaataggagagtctggaggtagttactgcatctttgcttggtgact-ccagcttctcatgaccttgctaaactgatatatcttgtttagGTACCCGAACTTGAAGAGTGTCAGGGAGTTGATCTACAAGAGGGGCTACGGAAAACTGAACAAGCAGAGGATCCCTCTGTCTAACAACCAAGTCATCGAG

upper sequence: Vv09s0054g00090.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA15G18170.2 (Glycine max), 3'ss of exon 5
gggtaagtatcttactcttttgtttttcttaagatcctataaaaagttctgaacttgtatattattcatttctaatgtatttatatt-gcaaat--attttagGTACCCCAATTTGAAGAGTGTGCGAGAACTGATTTACAAGAGGGGCTATGGAAAGTTGAACAAGCAGAGAACTGCCTTGACCGACAACTCCATTGTGGAA
                        |   | ||  | | |  | |     |    | ||  ||||       |     | || ||||| ||||||  | || |||||||| ||||||||||||||  ||||| |||| ||||||||||||||||||||  | ||||||||||||| ||| ||||| |||||||| ||| | |||
-----------------------gtaagtgaaagttcaactacattgattctcatggttcattacctgcaccatggttcttaatatttgcaaatccacttcagGTACCCTAATTTGAAGAGTGTTAGAGAATTGATCTACAAGAGGGGCTATGGAAAAGTTAACAAGCAGAGAATTGCTTTGACAGACAACTCTATTATTGAA

upper sequence: Vv09s0054g00090.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA09G06860.1 (Glycine max), 3'ss of exon 5
gggtaagtatcttactcttttgtttttcttaagatcctataaaaagttctgaacttgtatattattcatttctaatgtatttatattgcaaatattttagGTACCCCAATTTGAAGAGTGTGCGAGAACTGATTTACAAGAGGGGCTATGGAAAGTTGAACAAGCAGAGAACTGCCTTGACCGACAACTCCATTGTGGAA
      |||  | |   ||         | |   || |||     ||||   || || |    |    ||  |||| | |  | ||       | || |||||||| ||||||||||||||   |||| |||| ||||||||||||||||||||  | ||||||||||||| |||||| |  |||||||| ||||| |||
------gtaagtgaaagttcaacgacattgattgtcatatg----gttcattacctgcac--cacgggttcttaatatttgcaaatc-----cacttcagGTACCCTAATTTGAAGAGTGTAAAAGAATTGATCTACAAGAGGGGCTATGGAAAAGTTAACAAGCAGAGAATTGCCTTAAATGACAACTCTATTGTTGAA

upper sequence: Vv09s0054g00090.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA08G23750.2 (Glycine max), 3'ss of exon 5
gggtaagtatcttactcttttgtttttcttaagatcctataaaaagttctgaacttgtatattattcatttctaatgtatttatattgcaaatattttagGTACCCCAATTTGAAGAGTGTGCGAGAACTGATTTACAAGAGGGGCTATGGAAAGTTGAACAAGCAGAGAACTGCCTTGACCGACAACTCCATTGTGGAA
               | | ||   || | |   || || ||   | || |||   |   | ||  | | | ||||||    |    |||   | |||||| ||||| ||| | ||||||||| ||||||| ||||||||||| || ||||||||| | ||||||||||| |||||  | || |||||||||||  | || 
--------------gtatgtttacttccctgccatact-tatttaattatgattataggtttttataactgctaatgagacttc--tgcttttgttttagATACCCAAATCTTAAGAGTGTGAGAGAACTTATTTACAAGAGAGGGTATGGAAAGCTAAACAAGCAGAGGACTGCTCTAACTGACAACTCCATCATTGAG

upper sequence: Vv09s0054g00090.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA07G02270.1 (Glycine max), 3'ss of exon 5
gggtaagtatcttactcttttgtttttcttaagatcctataaaaagttctgaacttgtatattattcatttctaatgtatttatattgcaaatattttagGTACCCCAATTTGAAGAGTGTGCGAGAACTGATTTACAAGAGGGGCTATGGAAAGTTGAACAAGCAGAGAACTGCCTTGACCGACAACTCCATTGTGGAA
      |||| | |  |||||  || |||||    | |||  |||    |    |  | |||| || | |  |||||    |    |||   | || ||| ||||| ||| | ||||||||| ||||||| ||||||||||| || ||||||||| | |  |||||||| |||||  | || |||||||| ||  | || 
------gtatgtcaa-cttttccttgtctta----cttatttaaa----tacgatgatttatt-tttactgttaatgagacttc--tgcttttgttctagATACCCAAATCTCAAGAGTGTGAGAGAACTTATTTACAAGAGAGGGTATGGAAAGCTAATGAAGCAGAGGACTGCTCTAACTGACAACTCTATCATTGAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gttctgaacttgtatattattcatttctaatgtatttatattgcaaatattttagGTACCCCAATTTGAAGAGTGTGCGAGAACTGATTTACAAGAGGGGCTATGGAAAGTTGAACAAGCAGAGAACTGCCTTGACCGACAACTCCATTGTGGAA
                        ttctaat  putative branch site (score: 2)
            tatattattcatttct  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gggtaagtatcttactcttttgtttttcttaagatcctataaaaagttctgaacttgtatattattcatttctaatgtatttatattgcaaatattttagGTACCCCAATTTGAAGAGTGTGCGAGAACTGATTTACAAGAGGGGCTATGGAAAGTTGAACAAGCAGAGAACTGCCTTGACCGACAACTCCATTGTGGAA

- - - - - - - - - - - - - - - - - - - ataaaaa