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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...attaacaacatggtgcaattttatttaacattactattaatgattttttggcaccgtttgtattttcttgttgttgaaaatatcaattactgacctgcagCACTCCTATGTAAGATTGCGGCTTTGAGATCATTTTCTCTGGACAAATTACACTACTGGAGAGAGAGTGCATCTGGCATGAGCAGTCTGGCTTATTTTCT

Basic information

species Vitis vinifera
transcript Vv08s0040g01620.t01
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv08s0040g01620.t01 (Vitis vinifera), 3'ss of exon 12
lower sequence: LOC_Os06g51460.1 (Oryza sativa), 3'ss of exon 11
------------------------------------------attaacaacat--ggtgcaattttatttaacattactattaatgattttttggcaccgtttgtattttcttgttgttgaaaatatcaattactgacctgcagCACTCCTATGTAAGATTGCGGCTTTGAGATCATTTTCTCTGGACAAATTACACTACTGGAGAGAGAGTGCATCTGGCATGAGCAGTCTGGCTTATTTTCT
                                          || ||  |  |   | | |||  | ||||  || |    ||||||     |        | |||       | |  | |   |   |  || | |  |||||| || || || |||||||  ||  |||||||||| |||||||| ||  ||||||||||||| ||||| |||||||| ||||||    |||| || ||  |
gtaagtttctcagcccatcctggaaaggagtcttttttatccatgaattattttcagagaaataatgttta-tataatacgtaatgagaaaataa-gtaagtagtaaaaataaggtaataagcgtgggatatattaat-tgcagCTCTGCTGTGCAAGATTGGAGCGCTGAGATCATTCTCTCTGGAGAAGATACACTACTGGAGGGAGAGAGCATCTGGAATGAGCTCGTTGGCGTACTTCAT

upper sequence: Vv08s0040g01620.t01 (Vitis vinifera), 3'ss of exon 12
lower sequence: GLYMA13G20750.1 (Glycine max), 3'ss of exon 10
--attaacaacatggtgcaattttatttaacattactattaatgattttttggcaccgtttgtattttcttgttgttgaaaatatcaattactgacctgcagCACTCCTATGTAAGATTGCGGCTTTGAGATCATTTTCTCTGGACAAATTACACTACTGGAGAGAGAGTGCATCTGGCATGAGCAGTCTGGCTTATTTTCT
   |||  || | |    ||||||  ||    || | | ||||  ||  ||         |||||    || ||     |   ||  ||| |  |  ||||||  | || || |||||||| ||  | ||| ||||||||||||| |||||||| |||||||| |||||||||||||| || || ||||||||| ||||| |
tccttagaaagaagacaaaattttgattttttttcccactaatttttcattaagttaagctgtataagtttcttccctcattcat--attgcacatttgcagCTTTACTTTGCAAGATTGCAGCACTCAGAGCATTTTCTCTGGATAAATTACAATACTGGAGGGAGAGTGCATCTGGAATTAGTAGTCTGGCTCATTTTTT

upper sequence: Vv08s0040g01620.t01 (Vitis vinifera), 3'ss of exon 12
lower sequence: GLYMA10G06550.1 (Glycine max), 3'ss of exon 10
attaacaacatggtgcaatttt-atttaacattactattaatgattttttggcaccgtttgtattttcttgttgttgaaaatatcaattactgacctgcagCACTCCTATGTAAGATTGCGGCTTTGAGATCATTTTCTCTGGACAAATTACACTACTGGAGAGAGAGTGCATCTGGCATGAGCAGTCTGGCTTATTTTCT
 |||  || | |    |||||| ||||    ||   | |||   ||  ||    |      | | |   |||  |     |||   ||| |  |  ||||||  | || || |||||||| ||  | ||| ||||||||||||| |||||||| |||||||| ||||||||||| || || |||||||||||| ||||  |
cttataaagaagacaaaattttgatttgtttttttcactaaattttcatttaagctaagctt-tatgtgtgtcttccctcatacgtattgcacatttgcagCTTTACTTTGCAAGATTGCAGCACTCAGAGCATTTTCTCTGGATAAATTACAATACTGGAGGGAGAGTGCATCAGGAATTAGCAGTCTGGCTCATTTCTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttttggcaccgtttgtattttcttgttgttgaaaatatcaattactgacctgcagCACTCCTATGTAAGATTGCGGCTTTGAGATCATTTTCTCTGGACAAATTACACTACTGGAGAGAGAGTGCATCTGGCATGAGCAGTCTGGCTTATTTTCT
                                          tactgac  putative branch site (score: 1)
                            ttgaaaatatcaatta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
attaacaacatggtgcaattttatttaacattactattaatgattttttggcaccgtttgtattttcttgttgttgaaaatatcaattactgacctgcagCACTCCTATGTAAGATTGCGGCTTTGAGATCATTTTCTCTGGACAAATTACACTACTGGAGAGAGAGTGCATCTGGCATGAGCAGTCTGGCTTATTTTCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCAG
- - -caacatg
- - - - - - - - - - - - - - - - - - - - - - - - -ggcaccg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gaaaata