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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cacttgaattattatgcacacatggaagcatccgttctcttattgttatatctaaatttttctctattggttgtacaattcaaactatccatctcatcagTTGCCTGGACAACAGCAGATGCAGTTTTCTCAGACAATGGGGCACCAGCAATTTCAGAGTCGGCAGCTGCCTTCTGGACATGTCCAGCATGGCATGGGTC

Basic information

species Vitis vinifera
transcript Vv09s0054g00970.t01
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv09s0054g00970.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: GLYMA13G45020.1 (Glycine max), 3'ss of exon 2
cacttgaattattatgcacacatggaagcatccgttctcttattgttatatctaaatttttctctattggttgtacaattcaaactatccatc-tcatcagTTGCCTGGACAACAGCAGATGCAGTTTTCTCAGACAATGGGGCACCAGCAATTTCAGAGTCGGCAGCTGCCTTCTGGACATGTCCAGCATGGCATGGGTC
         || |||   ||  |  | | ||  || || ||  |||| |||||   || |  ||| ||  |||       ||| ||  |  || |||||||||||  |||||||| |||||||| ||||||||  || | |||||||||||||||||| || ||||||||||||| |||||||| ||||||||||| ||||
--------gtaatattttcaagtt-atgtattagtgctatt--tgttgtatct---ttctattctcttttttgggggtaacaagcttgctttcatcatcagTTGCACGGACAACATCAGATGCAATTTTCTCAACCACTTGGGCACCAGCAATTTCAGGGTAGGCAGCTGCCTTCAGGACATGTTCAGCATGGCATTGGTC

upper sequence: Vv09s0054g00970.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: GLYMA12G31400.1 (Glycine max), 3'ss of exon 2
---cacttgaattattatgcacacatggaagcatccgttctcttattgttatatctaaatttttctctattggttgta-caattcaaactatccatctcatcagTTGCCTGGACAACAGCAGATGCAGTTTTCTCAGACAATGGGGCACCAGCAATTTCAGAGTCGGCAGCTGCCTTCTGGACATGTCCAGCATGGCATGGGTC
   ||| | ||||   | | | | ||  ||  |   || || ||  |  ||| | | |||| |  | | ||||| ||| |||       |       ||||||||||| ||||||||| |||||||| ||||||||  || | ||||| || ||||||||| || ||||| ||||||| |||||||| ||||||||||| ||||
ggacacattaattgccaagtagaaattaaatta---gtgctatttgttgtatctttcaattctctttt-ttggtggtaacaagcttgcttgctttcatcatcagTTGCATGGACAACATCAGATGCAATTTTCTCAACCACTTGGGCATCAACAATTTCAGGGTAGGCAGTTGCCTTCAGGACATGTTCAGCATGGCATTGGTC


















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttatatctaaatttttctctattggttgtacaattcaaactatccatctcatcagTTGCCTGGACAACAGCAGATGCAGTTTTCTCAGACAATGGGGCACCAGCAATTTCAGAGTCGGCAGCTGCCTTCTGGACATGTCCAGCATGGCATGGGTC
    atctaaa  putative branch site (score: 3)
                                          tccatctc  putative PPT
       taaatttttctctatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cacttgaattattatgcacacatggaagcatccgttctcttattgttatatctaaatttttctctattggttgtacaattcaaactatccatctcatcagTTGCCTGGACAACAGCAGATGCAGTTTTCTCAGACAATGGGGCACCAGCAATTTCAGAGTCGGCAGCTGCCTTCTGGACATGTCCAGCATGGCATGGGTC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC
cacttga
- - - - - - - - cacacat
- - - - - - - - - - - - - -gcatccg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tcaaact