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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtcagtatgcttgttaagttggtgggcctttttttgtttctgtgcccaggttgattcttaaaccctttcctttacaacttgcagAAGGAGGAGGAGAAGCCGAAGGAGAGAGAGAAGGGGAAGTCACGCAACATAGATCATTTTATGGAGGAGCTGAAGCATGAGCAAGAGATGAGGGAGAGAC

Basic information

species Vitis vinifera
transcript Vv04s0008g06810.t01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv04s0008g06810.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA16G15820.1 (Glycine max), 3'ss of exon 1
gtcagtatgcttgttaagttggtgggc-ctttttttgtttctgtgcccaggttgattct----taaaccctttcctttacaacttgcagAAGGAGGAGGAGAAGCCGAAGGAGAGAGAGAAGGGGAAGTCACGCAACATAGATCATTTTATGGAGGAGCTGAAGCATGAGCAAGAGATGAGGGAGAGAC
||| ||||     ||||     ||  | ||  |||| |||    |  ||  |  || |     |||    | |   ||  |  ||| |||| |||||||| ||||| ||||||| |||||| ||||||||| | ||||| |||||||||||||||||||| |||||||||||||||||||||||||| |
gtctgtatctcaattaaagcattgacctctgattttattttccagttcaaatgtatccagatgtaatgtttgtttgttgtactttgtagAAAGAGGAGGAAAAGCCAAAGGAGAAAGAGAAAGGGAAGTCAAGAAACATTGATCATTTTATGGAGGAGCTAAAGCATGAGCAAGAGATGAGGGAGAGGC

upper sequence: Vv04s0008g06810.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA08G34030.2 (Glycine max), 3'ss of exon 5
gtcagtatgcttgttaagttggtgggc-ctttttttgtttctgtgcccaggttgattct----taaaccctttcctttacaacttgcagAAGGAGGAGGAGAAGCCGAAGGAGAGAGAGAAGGGGAAGTCACGCAACATAGATCATTTTATGGAGGAGCTGAAGCATGAGCAAGAGATGAGGGAGAGAC
||| ||||     || |     ||  | ||  |||| |||    |  | | |  || |     |||    | |   ||  |  ||| |||| |||||||| ||||  ||||||| |||||| |||||| || | ||||| |||||||||||||||||||| |||||||||||||||||||||||||| |
gtctgtatctcaattgaagctttgacctctgattttattttgcagttctgatgtatccagatgtaatgtttgtttgttgtactttgtagAAAGAGGAGGAAAAGCTAAAGGAGAAAGAGAAAGGGAAGGCAAGAAACATTGATCATTTTATGGAGGAGCTAAAGCATGAGCAAGAGATGAGGGAGAGGC

upper sequence: Vv04s0008g06810.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: AT5G10800.1 (Arabidopsis thaliana), 3'ss of exon 4
-------------------gtcagtatgct-tgttaagttggtgggcctttttttgtttctgtgcccaggttgattcttaaaccctttcctttacaacttgcagAAGGAGGAGGAGAAGCCGAAGGAGAGAGAGAAGGGGAAGTCACGCAACATAGATCATTTTATGGAGGAGCTGAAGCATGAGCAAGAGATGAGGGAGAGAC
                    |||||||  | | |||   ||||    | |  |||       ||       ||||| |||   |  ||  |   |   ||  ||| ||| || ||||   | |||||||  || ||||| ||| | || ||||||||||||||| |||||||||| |||| ||| ||||| || || || || |
gtcagtagttagagaccatatcagtattttatattattctggt---tcctgatttaaagtaatggtttaactgattattagtacaatttttcctc--tttctagAGGGATGAAGAGAGATCAAAGGAGATGGAAAAGGGAAAGACTCGAAACATAGATCATTTTGTGGAGGAGCTCAAGCGTGAACAAGAAATAAGAGAAAGGC

upper sequence: Vv04s0008g06810.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: EFJ16538 (Selaginella moellendorffii), 3'ss of exon 3
gtcagtatgcttgttaagttggtgggcctttttttgtttctgtgcccaggttgattcttaaaccctttcc--tttacaacttgc---agAAGGAGGAGGAGAAGCCGAAGGAGAGAGAGAAGGGGAAGTCACGCAACATAGATCATTTTATGGAGGAGCTGAAGCATGAGCAAGAGATGAGGGAGAGAC
       | | |||| |  |    ||  |||  |   |    ||   ||  | |||||   | |   ||   ||| ||  || |   ||||||| || |||||  | ||||| | |||    || || || |||||||||||| |||||||||| ||||||||  | || ||||| ||||||||||  |
------gtacatgttga--ttacaggtttttgataaatgaactgaagagcctcattctcttatcaactcaaatttgcacgttactttagAAGGATGAAGAGAAAGCCAAGGAAAAAGATCGTGGCAAATCCCGCAACATAGATAATTTTATGGAAGAGCTGAAAAAAGAACAAGAAATGAGGGAGAAGC

upper sequence: Vv04s0008g06810.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: EFJ32251 (Selaginella moellendorffii), 3'ss of exon 3
gtcagtatgcttgttaagttggtgggcctttttttgtttctgtgcccaggttgattcttaaaccctttcc--tttacaacttgc---agAAGGAGGAGGAGAAGCCGAAGGAGAGAGAGAAGGGGAAGTCACGCAACATAGATCATTTTATGGAGGAGCTGAAGCATGAGCAAGAGATGAGGGAGAGAC
       | | |||| |  |    ||  |||  |   |    ||   ||  | |||||   | |   ||   ||| ||  || |   ||||||| || |||||  | ||||| | |||    || ||  | |||||||||||| |||||||||| ||||||||  | || ||||| ||||||||||  |
------gtacatgttga--ttacaggtttttgataaatgaactgaagagcctcattctcttatcaactcaaatttgcacgttactttagAAGGATGAAGAGAAAGCCAAGGAAAAAGATCGTGGCAAACCCCGCAACATAGATAATTTTATGGAAGAGCTGAAAAAAGAACAAGAAATGAGGGAGAAGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttttttgtttctgtgcccaggttgattcttaaaccctttcctttacaacttgcagAAGGAGGAGGAGAAGCCGAAGGAGAGAGAGAAGGGGAAGTCACGCAACATAGATCATTTTATGGAGGAGCTGAAGCATGAGCAAGAGATGAGGGAGAGAC
                   ggttgat  putative branch site (score: 5)
                                 ccctttcctttac  putative PPT
                        attcttaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtcagtatgcttgttaagttggtgggcctttttttgtttctgtgcccaggttgattcttaaaccctttcctttacaacttgcagAAGGAGGAGGAGAAGCCGAAGGAGAGAGAGAAGGGGAAGTCACGCAACATAGATCATTTTATGGAGGAGCTGAAGCATGAGCAAGAGATGAGGGAGAGAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGATCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG