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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgaactattgagtcctgatcttaatagcctacaattcaagcaagttatactagtaggtatgcttggagtgctgctaattttctgttcactttgattgtagGATGGGATTGAAGAATGCCGAAAACTATGTGGTGGCCATGGTTACCTATGTAGTAGTGGGCTTCCCGAGTTATTTGCCGTGTATGTCCCTGCCTGTACAT

Basic information

species Vitis vinifera
transcript Vv00s0389g00020.t01
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv00s0389g00020.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: LOC_Os06g01390.1 (Oryza sativa), 3'ss of exon 8
tgaactattgagtcctgat-cttaatag--cctacaattcaagcaagttatactagtaggtatgcttggagtgctgctaatttt-----ctgttcactttgattgtagGATGGGATTGAAGAATGCCGAAAACTATGTGGTGGCCATGGTTACCTATGTAGTAGTGGGCTTCCCGAGTTATTTGCCGTGTATGTCCCTGCCTGTACAT
        |||||    |  | ||   |  || ||| |  |  ||  |||||  |  ||  |       | |  |  |  || |     |||||   ||| | || ||||||| |||||||||||||||||||| |||||||| |||||||||||    || || |||||||| || || |||||  | ||||| ||||| || || |
--------tgagtttacacgcatagctggtccaacagtctagccagtttatataacgagtgaattacacaattttcattgttctcaaacctgtttttttttaatgcagGATGGAATTGAAGAATGCCGAAAACTCTGTGGTGGACATGGTTACCTGAACAGCAGCGGGCTTCCTGAATTGTTTGCTATCTATGTTCCTGCTTGCACTT

upper sequence: Vv00s0389g00020.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GRMZM2G052389_T02 (Zea mays), 3'ss of exon 8
tgaactattgagtcctgatcttaatagcctacaattcaagcaagttatactagtaggtatgcttggagtgctgctaattttctg-----ttcactttgatt-gtagGATGGGATTGAAGAATGCCGAAAACTATGTGGTGGCCATGGTTACCTATGTAGTAGTGGGCTTCCCGAGTTATTTGCCGTGTATGTCCCTGCCTGTACAT
     || |  || ||| |||  || | |||      |   |  | |    || |   ||           || |  ||    |     ||| || || || | ||||||  ||||||||||||||||| || |||||||| ||||||||| |    || ||||||||||| ||||| ||||| || ||||| || || || || |
----gtagtaggttctggtct-gatggtctagtcactatatatataaacaaaggacacatttacaatccattgttgtttaaggggagatttctctctgttttgcagGATGCAATTGAAGAATGCCGAAAGCTCTGTGGTGGACATGGTTACTTGAACAGCAGTGGGCTTCCTGAGTTGTTTGCGGTCTATGTTCCCGCTTGCACTT

upper sequence: Vv00s0389g00020.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GRMZM2G052389_T01 (Zea mays), 3'ss of exon 8
tgaactattgagtcctgatcttaatagcctacaattcaagcaagttatactagtaggtatgcttggagtgctgctaattttctg-----ttcactttgatt-gtagGATGGGATTGAAGAATGCCGAAAACTATGTGGTGGCCATGGTTACCTATGTAGTAGTGGGCTTCCCGAGTTATTTGCCGTGTATGTCCCTGCCTGTACAT
     || |  || ||| |||  || | |||      |   |  | |    || |   ||           || |  ||    |     ||| || || || | ||||||  ||||||||||||||||| || |||||||| ||||||||| |    || ||||||||||| ||||| ||||| || ||||| || || || || |
-----tagtaggttctggtct-gatggtctagtcactatatatataaacaaaggacacatttacaatccattgttgtttaaggggagatttctctctgttttgcagGATGCAATTGAAGAATGCCGAAAGCTCTGTGGTGGACATGGTTACTTGAACAGCAGTGGGCTTCCTGAGTTGTTTGCGGTCTATGTTCCCGCTTGCACTT

upper sequence: Vv00s0389g00020.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA14G14990.1 (Glycine max), 3'ss of exon 7
----tgaactattgagtcctgatcttaatagcctacaattcaagcaagttatactagtaggtatgcttggagtgctgctaattttctgttcactttgattgt-agGATGGGATTGAAGAATGCCGAAAACTATGTGGTGGCCATGGTTACCTATGTAGTAGTGGGCTTCCCGAGTTATTTGCCGTGTATGTCCCTGCCTGTACAT
    | ||    |||    || |  |  |  | |    | | |  |   | |   | |  | ||  |||  || |   ||| |||   || ||||  |||   ||||||| |||||||||||||| |||||||||||||| ||||||||||| ||||| ||||| || || ||||||||||| || ||||| |||||||| || |
catttaaatggatgaag--tgtttctgttgtcgtt--gtgctattatcctttgtaactctgaat-tttgatgttcaattaagtttaaattaacttcaatttccagGATGGAATTGAAGAATGCCGTAAACTATGTGGTGGTCATGGTTACCTTTGTAGCAGTGGTCTCCCTGAGTTATTTGCTGTTTATGTTCCTGCCTGCACGT

upper sequence: Vv00s0389g00020.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA11G03800.1 (Glycine max), 3'ss of exon 8
----tgaactattgagtcctgatcttaatagcctacaattcaagcaagttatactagtaggtatgcttggagtgctgctaattttctgttcactttgattgt-agGATGGGATTGAAGAATGCCGAAAACTATGTGGTGGCCATGGTTACCTATGTAGTAGTGGGCTTCCCGAGTTATTTGCCGTGTATGTCCCTGCCTGTACAT
    | ||    |||    || |  |  |  | |    | | |  |   | |   | |  | ||  |||  || |   ||| |||   || ||||  |||   ||||||| |||||||||||||| |||||||||||||| ||||||||||| ||||| ||||| || || ||||||||||| || ||||| |||||||| || |
catttaaatggatgaag--tgtttctgctgtcgtt--gtgctattatcctttgtaactctgaat-tttgatgttcaattaagtttaaattaacttcaatttccagGATGGAATTGAAGAATGCCGTAAACTATGTGGTGGTCATGGTTACCTTTGTAGCAGTGGTCTCCCTGAGTTATTTGCTGTTTATGTTCCTGCCTGCACGT

upper sequence: Vv00s0389g00020.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA01G41600.1 (Glycine max), 3'ss of exon 8
--tgaact--attgagtcctgatcttaatagcctacaattcaagcaagttatactagtaggtatgcttggagtgctgctaattttctgttcactttgattgt-agGATGGGATTGAAGAATGCCGAAAACTATGTGGTGGCCATGGTTACCTATGTAGTAGTGGGCTTCCCGAGTTATTTGCCGTGTATGTCCCTGCCTGTACAT
  | ||||  ||  |||  |  | ||       | | |||     |   | |   | |  | |   ||   || | | |||  ||   || ||||  |||   ||||||| |||||||||||||| ||||||||||| || ||||||||||| ||||| ||||| || || ||||||||||| || ||||| |||||||| || |
atttaactggatgaagtatttctgttgtggttgtgctatt-----atcctttgtaactctgaactttttatgttcagttaaagttaaattaacttcaatttccagGATGGAATTGAAGAATGCCGTAAACTATGTGGCGGTCATGGTTACCTTTGTAGCAGTGGTCTCCCTGAGTTATTTGCTGTTTATGTTCCTGCCTGCACGT

upper sequence: Vv00s0389g00020.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA05G04940.1 (Glycine max), 3'ss of exon 8
tgaactattgagtcctgatcttaatagcctacaattcaagcaagttatactagtaggta--tgcttggagtgctgctaattttctgttcactttgatt-gtagGATGGGATTGAAGAATGCCGAAAACTATGTGGTGGCCATGGTTACCTATGTAGTAGTGGGCTTCCCGAGTTATTTGCCGTGTATGTCCCTGCCTGTACAT
   |   ||| |     ||    ||    ||  || | |  |  |  |  |     | |  | |||  | | ||   || ||    || | ||  ||| | ||||||| ||||| |||||||| |||||||||||||||||||||||||| || || ||||| || || ||||||||||| || ||  | ||| |||| ||||
---atcgttgtgcttatattactattttatagtatcctattacatggtgttcacttgcaacttcttttaattctttgaagttcacattaaattaaatttgcagGATGGAATTGAGGAATGCCGCAAACTATGTGGTGGCCATGGTTACCTTTGCAGCAGTGGTCTCCCTGAGTTATTTGCAGTCTACATTCCTACCTGCACAT

upper sequence: Vv00s0389g00020.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA17G15320.1 (Glycine max), 3'ss of exon 9
tgaactattgagtcctgatcttaatagcctacaat-tcaagcaagttatactagtaggtatgctt-ggagtgctgctaattttctgttcactttgatt-gtagGATGGGATTGAAGAATGCCGAAAACTATGTGGTGGCCATGGTTACCTATGTAGTAGTGGGCTTCCCGAGTTATTTGCCGTGTATGTCCCTGCCTGTACAT
    || ||    |    |  || || ||||  || |   |     | | | | |    || ||| | ||| |   | |  ||  ||| ||||  ||| | ||||||| ||||| |||||||| |||||||| ||||||||||||||||| || || ||||| || || ||||||||||| || ||  | ||| |||| ||||
---gcttttattactattttatagtatcctattatatggtgttcactttgcaacttttaattctttgaagttcaaattaaattaagtttacttaaatttgcagGATGGAATTGAGGAATGCCGCAAACTATGCGGTGGCCATGGTTACCTTTGCAGCAGTGGTCTGCCTGAGTTATTTGCAGTCTACATTCCTTCCTGCACAT

upper sequence: Vv00s0389g00020.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: AT2G35690.1 (Arabidopsis thaliana), 3'ss of exon 7
tgaactattgagtcctgatcttaatagcctacaattcaagcaagttatactagtaggtatgcttggagtgctgctaattttctgttcactttgattgta-gGATGGGATTGAAGAATGCCGAAAACTATGTGGTGGCCATGGTTACCTATGTAGTAGTGGGCTTCCCGAGTTATTTGCCGTGTATGTCCCTGCCTGTACAT
                       ||    |  |||   | |   ||| | ||    | ||  |   ||     ||   ||| | ||    ||| ||  | |||||||||||||||||| || ||  |||||||||| ||||| ||| | ||  ||||||||||||| || || ||||| || ||||| ||||| || ||||
---------------------gtatgctttcaaatcttaacttattaaaataagttgaatattatcagctaaactgtgttttttttgttgttggttaaaagGATGGGATTGAAGAATGTCGTAAGTTATGTGGTGGACATGGATACTTGTGGTGTAGTGGGCTTCCTGAATTGTTTGCTGTATATGTTCCTGCTTGCACAT

upper sequence: Vv00s0389g00020.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: AT4G16760.2 (Arabidopsis thaliana), 3'ss of exon 8
-----------------------------------------------------------tgaactattga--gtcctgatcttaatagcctacaattcaagcaagttatactagtaggtatgcttggagt--gctgctaattttctgttcact-ttgattgtagGATGGGATTGAAGAATGCCGAAAACTATGTGGTGGCCATGGTTACCTATGTAGTAGTGGGCTTCCCGAGTTATTTGCCGTGTATGTCCCTGCCTGTACAT
                                                           |||       |  |  |  || ||   ||  |            |  | |  | | |||| |  || ||||       | |  ||  |   ||| |||  || ||||||| ||||||||||| || ||  |||||||||| ||||| ||| | ||  | |||||||| |||||| | ||||| || ||||| |||||||| ||||
gtaagttccagagctgatcctttatactcactagactagattgattggtttcgtttctctgaggatccaactgctcacatgttggaagtttgttccctccttgacat-tgtttggaggtgtatttagagttgaaaattcagcttaagggtactattgggtgcagGATGGCATTGAAGAATGTCGTAAGTTATGTGGTGGACATGGATACTTGTGGTGCAGTGGGCTCCCCGAGCTGTTTGCTGTATATGTTCCTGCCTGCACAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatactagtaggtatgcttggagtgctgctaattttctgttcactttgattgtagGATGGGATTGAAGAATGCCGAAAACTATGTGGTGGCCATGGTTACCTATGTAGTAGTGGGCTTCCCGAGTTATTTGCCGTGTATGTCCCTGCCTGTACAT
                                ttttctgttcacttt  CT-rich tract
                             taattttct  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgaactattgagtcctgatcttaatagcctacaattcaagcaagttatactagtaggtatgcttggagtgctgctaattttctgttcactttgattgtagGATGGGATTGAAGAATGCCGAAAACTATGTGGTGGCCATGGTTACCTATGTAGTAGTGGGCTTCCCGAGTTATTTGCCGTGTATGTCCCTGCCTGTACAT

- - - - - - -cctgatc
- - - - - - - - - - - - - gcctaca
- - - - - - - - - - - - - - - - - -tcaagca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - gtatgct
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ctgctaa