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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttgaactaataattttcattctttttatgctgtagaattttaattaatgcatattttgatgttatttttcttacaatatgcatcttctctttccatttagGCAGCAGCATCAATTAAAGATGGAAAGCGGATCCTTTTCCGGTTTGATAGAGCAGCCTTTTCTTTCAAATTTTTGCCATTTAAGGTTCCATATCCAGTGC

Basic information

species Vitis vinifera
transcript Vv06s0004g01220.t01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv06s0004g01220.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: LOC_Os07g28790.1 (Oryza sativa), 3'ss of exon 4
--ttgaactaataattttcattctttttatgctgtagaattttaattaatgcatattttgatgt-tatttttcttacaatatgcatcttctctttccatttagGCAGCAGCATCAATTAAAGATGGAAAGCGGATCCTTTTCCGGTTTGATAGAGCAGCCTTTTCTTTCAAATTTTTGCCATTTAAGGTTCCATATCCAGTGC
   |   | | ||| ||  |||  |  ||     || | || || |   |  | | | |  |   |   ||| | |  | ||  || |    | | |    |||||| |||| | ||| |||| |||||||| || ||||| || |||||  ||||||| ||    ||||| ||||||||||||||||||||||| |||||||
tactagtcaactaacttcgattactgctagttgctaaatttatagtgcttttacaatgttctacatgactttatgatgagatttatttaaaatatac---cagGCAGAAGCAACTATTGAAGACGGAAAGCGCATTCTTTTTCGTTTTGACCGAGCAGCATTCAACTTCAAGTTTTTGCCATTTAAGGTTCCATACCCAGTGC

upper sequence: Vv06s0004g01220.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GRMZM2G171871_T01 (Zea mays), 3'ss of exon 4
ttgaac-taataattttcattctttttatgctgtagaattttaattaatgcatattttgatgttatttttcttacaata---tgcatcttctctttccatttagGCAGCAGCATCAATTAAAGATGGAAAGCGGATCCTTTTCCGGTTTGATAGAGCAGCCTTTTCTTTCAAATTTTTGCCATTTAAGGTTCCATATCCAGTGC
|| |   |||  |  |  || |||||  |||  |||   ||    || |  | ||||   | |||   | |||||||||   ||  |  |     |  |  ||||||| |||| | ||||| ||||||||||| || |||||||| |||||  ||||||| ||| | ||||| ||| |||||||||| |||||||| |||||||
ttaactgtaaagaaataaatccttttattgccttagcgatt--gctactttaaatttc--ttttacaatacttacaataaggtgttttgtgaaaataaaactagGCAGAAGCAACTATTAAGGATGGAAAGCGCATACTTTTCCGTTTTGACCGAGCAGCATTTGCCTTCAAGTTTCTGCCATTTAAAGTTCCATACCCAGTGC

upper sequence: Vv06s0004g01220.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA10G44120.1 (Glycine max), 3'ss of exon 5
ttgaactaataattttcattctttttatgctgtagaattttaattaatgcatattttgatgttatttttcttacaatatgcatcttctctttccatttagGCAGCAGCATCAATTAAAGATGGAAAGCGGATCCTTTTCCGGTTTGATAGAGCAGCCTTTTCTTTCAAATTTTTGCCATTTAAGGTTCCATATCCAGTGC
                                                     ||| | | || |  |||||    | |   |||| ||  |  |   ||||||||||||||||| ||||||||||  | ||||||||  ||||||| ||||| || |||||||| |||||| | |||||||| ||||| |||||||| |
----------------------------------------------------gtttagttattgtagttcttgtttt-tatgtctt-tcaatttacacagGCAGCAGCATCAATTGAAGATGGAAAAAGAATCCTTTTTAGGTTTGACAGAGCTGCTTTTTCTTTTAAATTTCTTCCATTTAAAGTTCCGTATCCAGTTC

upper sequence: Vv06s0004g01220.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA20G38820.2 (Glycine max), 3'ss of exon 3
ttgaactaataattttcattctttttatgctgtag--aattttaattaatgcatattttgatgttatttttcttacaatatgcatcttctctttccatttagGCAGCAGCATCAATTAAAGATGGAAAGCGGATCCTTTTCCGGTTTGATAGAGCAGCCTTTTCTTTCAAATTTTTGCCATTTAAGGTTCCATATCCAGTGC
     | | |||  ||  ||  | || | |   ||   || |   |  ||  |  ||| | |||| |  |||||    | |   |||| |  ||  |   ||||||||||||||||| ||||||||||  | ||||||||  ||||||| ||||| ||||||||||| |||||| | ||||| || ||||| |||||||| |
agagcccagtaacattgtttgatcttgtacctgagcccatatagttggatagaggtttagttgttgtagttcttgtttt-tatgtcttttaattt-acacagGCAGCAGCATCAATTGAAGATGGAAAAAGAATCCTTTTTAGGTTTGACAGAGCTGCCTTTTCTTTTAAATTTCTTCCATTCAAAGTTCCGTATCCAGTTC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aatgcatattttgatgttatttttcttacaatatgcatcttctctttccatttagGCAGCAGCATCAATTAAAGATGGAAAGCGGATCCTTTTCCGGTTTGATAGAGCAGCCTTTTCTTTCAAATTTTTGCCATTTAAGGTTCCATATCCAGTGC
                      ttcttac  putative branch site (score: 2)
                                   catcttctctttccat  putative PPT
     atattttgatgttatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttgaactaataattttcattctttttatgctgtagaattttaattaatgcatattttgatgttatttttcttacaatatgcatcttctctttccatttagGCAGCAGCATCAATTAAAGATGGAAAGCGGATCCTTTTCCGGTTTGATAGAGCAGCCTTTTCTTTCAAATTTTTGCCATTTAAGGTTCCATATCCAGTGC

- -aactaat
- - - - - - - - - - - - -tatgctg
- - - - - - - - - - - - - - - - - - - - - - -aatgcat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tatgcat