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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttagaagcctattgtattggaagaacatattagcatcaggttgtgccatctcatgattcaaaaaaatgttttctaatattctgactattttgatctacagGTATGAAGATGCTTTTAACAGATTCATTGATGAGATTAATTCAGTTGCTGCATATGATTGGTGGGAAGGGTCAGTACACAGCATACTTTCAGTGCTTGCA

Basic information

species Vitis vinifera
transcript Vv02s0012g00460.t01
intron # 15
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv02s0012g00460.t01 (Vitis vinifera), 3'ss of exon 15
lower sequence: LOC_Os04g10380.1 (Oryza sativa), 3'ss of exon 15
-ttagaagcctat-tgtattggaagaacatattagcatcaggttgtgccatctcatgattcaaaaaaatgttttctaatattctgactattttgatctacagGTATGAAGATGCTTTTAACAGATTCATTGATGAGATTAATTCAGTTGCTGCATATGATTGGTGGGAAGGGTCAGTACACAGCATACTTTCAGTGCTTGCA
        | ||| | | |  ||||||  |    |  ||     ||    | |    ||||      ||   |  || | || | ||| ||||  |   ||| |||||||||||||||||| | || || |||||||| ||||  || |||||||| || ||||||||||| ||  |||| || ||||||||||| ||||||
aactatgtcatatatatttccgaagaatgttcatgtctccatcagtattttgtttgtattccttgccataggtgata-tcttgttactttttttttgc-cagATATGAAGATGCTTTTAACCGTTTTATCGATGAGATCAATTTGGTGGCTGCATACGAGTGGTGGGAAGGATCTATACATAGTATACTTTCAGTACTTGCA

upper sequence: Vv02s0012g00460.t01 (Vitis vinifera), 3'ss of exon 15
lower sequence: GRMZM2G015291_T01 (Zea mays), 3'ss of exon 7
ttagaagcctattgtattggaagaacatattagcatcaggttgtgccatctcatgattcaaaaaaatgttttctaa-tattctgactattttgatctacagGTATGAAGATGCTTTTAACAGATTCATTGATGAGATTAATTCAGTTGCTGCATATGATTGGTGGGAAGGGTCAGTACACAGCATACTTTCAGTGCTTGCA
     |  |||   |   | ||  |  ||||  |   ||          ||  |||   | | | |    |   || ||  ||   | ||||    | ||| |||||||||||||| ||| | || ||||||||||| ||||  || ||||||||||| ||||||||||| ||  |||| || |||||||| || ||||| 
-atctattctaacttgaggaaatgatttattttcccaagtacagaatgacttgtgagaaatacagaaacatcagaactaagctctgtttttttcctttcagTTATGAAGATGCTTTCAACCGTTTTATTGATGAGATCAATTTGGTGGCTGCATATGAGTGGTGGGAAGGATCTATACATAGTATACTTTCTGTTCTTGCG

upper sequence: Vv02s0012g00460.t01 (Vitis vinifera), 3'ss of exon 15
lower sequence: GLYMA11G04290.1 (Glycine max), 3'ss of exon 15
ttagaagcctattgtattggaagaacatattagcatcaggttgtgccatctcatgattcaaaaaaatgttttctaat---attctgactattttgatctacagGTATGAAGATGCTTTTAACAGATTCATTGATGAGATTAATTCAGTTGCTGCATATGATTGGTGGGAAGGGTCAGTACACAGCATACTTTCAGTGCTTGCA
    |||| ||   | || |  ||| | |   |  |    || |   |  ||   |   | ||   || |||  | |   |||    |     ||   | ||||||||| ||||||||||| ||||| |||||||| || || || ||||||||||||||||||||||| || ||||| ||||| |||||||||||  |||||
---aaagcttaagctgttaggtgaaaacacatgactggctttatattacttctctaacaataattgtgattttaagttagatttaatcctaactgtgatgcagGTATGAGGATGCTTTTAATAGATTTATTGATGAAATCAACTCGGTTGCTGCATATGATTGGTGGGAGGGATCAGTGCACAGTATACTTTCAGTTGTTGCA

upper sequence: Vv02s0012g00460.t01 (Vitis vinifera), 3'ss of exon 15
lower sequence: GLYMA01G41140.1 (Glycine max), 3'ss of exon 15
-------ttagaagcctattgtattgga--agaacatattagcatcaggttgtgccatc-tcatgattcaaaaaaatgttttctaatattctgactattttgatctacagGTATGAAGATGCTTTTAACAGATTCATTGATGAGATTAATTCAGTTGCTGCATATGATTGGTGGGAAGGGTCAGTACACAGCATACTTTCAGTGCTTGCA
         | || | ||   | ||||   | |||| || |    |   |    | ||  |  |||||  ||   |  |||  | |||        | | ||||   ||||||||| ||||||||||| || || |||||||| || || || ||||||||||||||||||||||| || ||||| ||||| |||||||| ||  |||||
tactattccaaaaccttaagctgttgggtgaaaacacatgactgacttctctaacaataattgtgattttaagttagatttgatcata--------actgtgat--gcagGTATGAGGATGCTTTTAATAGGTTTATTGATGAAATCAACTCGGTTGCTGCATATGATTGGTGGGAGGGATCAGTGCACAGTATACTTTCTGTTGTTGCA

upper sequence: Vv02s0012g00460.t01 (Vitis vinifera), 3'ss of exon 15
lower sequence: AT5G47020.1 (Arabidopsis thaliana), 3'ss of exon 16
ttagaagcctattgtattggaagaacatattagcatcaggttgtgccatctcatgattcaaaaaaatgttttctaata-ttctgactattt-tgatctacagGTATGAAGATGCTTTTAACAGATTCATTGATGAGATTAATTCAGTTGCTGCATATGATTGGTGGGAAGGGTCAGTACACAGCATACTTTCAGTGCTTGCA
       | |||  | || |   | ||   |  ||||    | || | || | | |||| ||   ||||   || ||| |||||   |||| ||||   |||||| ||||||||||||||||| || ||| |||| || || ||    || ||||||||||||||||||||||| || |||||||| |||||||| ||||||
-cgttttcttatactctttgcttatcaatgtgacatcgtcctttggc-tcactttattccaaggcatgtccactcatagttctggacatttctgattcgcagGTACGAAGATGCTTTTAACAGCTTTATTAATGAAATAAACTCTACCGCAGCATATGATTGGTGGGAAGGGTCTGTGCACAGCATTCTTTCAGTTCTTGCA

upper sequence: Vv02s0012g00460.t01 (Vitis vinifera), 3'ss of exon 15
lower sequence: EFJ14465 (Selaginella moellendorffii), 3'ss of exon 15
ttagaagcctattgtattggaagaacatattagcatcaggttgtgccatctcatgattcaaaaaaatgttttctaatattctgactatt----ttgatctacagGTATGAAGATGCTTTTAACAGATTCATTGATGAGATTAATTCAGTTGCTGCATATGATTGGTGGGAAGGGTCAGTACACAGCATACTTTCAGTGCTTGCA
                                                     |   |  || |  |    |  ||| | ||| | | |    ||  | |||||||| ||||| ||||| ||||||||| |||||||||| ||||   |||| || ||  | |||||||||||||| ||  |||||||||| |   |   ||||
----------------------------------------------------gtacgttgaatacttcaccttcaatttactgtcgactaagtttcttgtacagGTACGAAGACGCTTTCAACAGATTCGTTGATGAGATCAATTGCCTTGCAGCGTACCAGTGGTGGGAAGGGTCTGTGTACAGCATACTGTGCTTTGCTGCA

upper sequence: Vv02s0012g00460.t01 (Vitis vinifera), 3'ss of exon 15
lower sequence: EFJ26064 (Selaginella moellendorffii), 3'ss of exon 15
ttagaagcctattgtattggaagaacatattagcatcaggttgtgccatctcatgattcaaaaaaatgttttctaatattctgactatt----ttgatctacagGTATGAAGATGCTTTTAACAGATTCATTGATGAGATTAATTCAGTTGCTGCATATGATTGGTGGGAAGGGTCAGTACACAGCATACTTTCAGTGCTTGCA
                                                     |   |  || |  |  | |  ||| | ||| | | |    ||  | |||||||| ||||| ||||| ||||||||| |||||||||| ||||   |||| || ||  | |||||||||||||| ||  |||||||||| |   |   ||||
----------------------------------------------------gtacgttgaatacttcatcttcaatttactgtcgactaagtttcttgtacagGTACGAAGACGCTTTCAACAGATTCGTTGATGAGATCAATTGCCTTGCAGCGTACCAGTGGTGGGAAGGGTCTGTGTACAGCATACTGTGCTTTGCTGCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ccatctcatgattcaaaaaaatgttttctaatattctgactattttgatctacagGTATGAAGATGCTTTTAACAGATTCATTGATGAGATTAATTCAGTTGCTGCATATGATTGGTGGGAAGGGTCAGTACACAGCATACTTTCAGTGCTTGCA
                                       ctatttt  CT-rich tract
       atgattcaaaaaaatg  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttagaagcctattgtattggaagaacatattagcatcaggttgtgccatctcatgattcaaaaaaatgttttctaatattctgactattttgatctacagGTATGAAGATGCTTTTAACAGATTCATTGATGAGATTAATTCAGTTGCTGCATATGATTGGTGGGAAGGGTCAGTACACAGCATACTTTCAGTGCTTGCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - -cctattg
- - - - - - - - - ggaagaa
- - - - - - - - - - - - - - - -agcatca
- - - - - - - - - - - - - - - - - - - ggttgtg
- - - - - - - - - - - - - - - - - - - - - - -ccatctc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aaaaaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ttctgac