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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cctcaaccttgctatttgtgttatttgctgccttcatatggccagacaccattcacatgggcattgtaattgattttgatcttcccttttgcattcacagGCAGCTCAGGATGGAGTTGACATAGTAAGCTTGTCAATCACTCCCAACAGGCGTCCCCCTGGAATTGCAACTTTTTTTAATCCCATAGATATGGCCTTGC

Basic information

species Vitis vinifera
transcript Vv10s0092g00170.t01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv10s0092g00170.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA05G30460.1 (Glycine max), 3'ss of exon 5
cctcaaccttgctatttgtgttatttgctgccttcatatggccagacaccattcaca--tgggcat---tgtaattgattttgatcttcccttttgcattcacagGCAGCTCAGGATGGAGTTGACATAGTAAGCTTGTCAATCACTCCCAACAGGCGTCCCCCTGGAATTGCAACTTTTTTTAATCCCATAGATATGGCCTTGC
     ||  |    | |    || || |    |   | |  | | |    || | ||  |   |||   ||  || | || |  | |   |  |||  || |||||||||||||||||| ||||||||| || |||||||||||||||| || ||||||||  |||| || |||||||| || ||||| ||||||||||| ||||
--gttactgtaaagtgtaaagtactttcaaaatctgttta-ctaaattatatccccaattttacatctatggcatggcttatagtataatcaattg--tttacagGCAGCTCAGGATGGGGTTGACATAATATGCTTGTCAATCACTCCTAATAGGCGTCCTTCTGGCATCGCAACTTTCTTCAATCCAATAGATATGGCATTGC

upper sequence: Vv10s0092g00170.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA08G13590.1 (Glycine max), 3'ss of exon 5
cctcaaccttgctatttgtgttatttgctgccttcatatggccagacaccattcaca--tgggcatt---gtaattgattttgatcttcccttttgcattcacagGCAGCTCAGGATGGAGTTGACATAGTAAGCTTGTCAATCACTCCCAACAGGCGTCCCCCTGGAATTGCAACTTTTTTTAATCCCATAGATATGGCCTTGC
    |   |   |   ||| ||  || |    |     |  | | |    || ||||  |   ||||   |  || | || |  | |   |  |||  || |||||||||||||||| | ||||||||| || |||||||||||||||| || ||||||||  |||| ||||||||||| || ||||| ||||||||||| ||||
--atactttccttgcatgtcttcctttcaaaatctgctta-ctaaattgtatccacaattttacatttacggtatggcttatagtataatcaattg--tttacagGCAGCTCAGGATAGGGTTGACATAATATGCTTGTCAATCACTCCTAATAGGCGTCCTTCTGGTATTGCAACTTTCTTCAATCCAATAGATATGGCATTGC

upper sequence: Vv10s0092g00170.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA09G09850.1 (Glycine max), 3'ss of exon 5
--cctcaaccttgctatttgtg--ttatttgctgccttcatatggccagacaccattcacatgggcattgtaattgattttgatcttcccttttgcattcacagGCAGCTCAGGATGGAGTTGACATAGTAAGCTTGTCAATCACTCCCAACAGGCGTCCCCCTGGAATTGCAACTTTTTTTAATCCCATAGATATGGCCTTGC
    |      || || | |||  ||   |||         |     | |   ||| ||  |  || |||    | |   | ||  |     |    ||  ||||||||||||||||| ||||||||| |||||||||| || |||||||| || ||||| |||||  ||||||| || || || || ||||| ||||| ||||
agagttgtaagtgatagtggtgatttccatgcatgtccttcacaataaaattgcatccaattttgctttgcctgtaacactaatagtg----tgatgtttgcagGCAGCTCAGGATGGGGTTGACATAATAAGCTTGTCTATTACTCCCAATAGACGTCCTCCTGGTGTTGCAACCTTCTTCAACCCAATAGACATGGCTTTGC

upper sequence: Vv10s0092g00170.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA15G21920.1 (Glycine max), 3'ss of exon 5
-----------------------cctcaaccttgctatttgtgttatttgc-tgcct-tcatatggccagaca--ccattcacatgggcattgtaattgattttgatcttccctt--------ttgcat------tcacagGCAGCTCAGGATGGAGTTGACATAGTAAGCTTGTCAATCACTCCCAACAGGCGTCCCCCTGGAATTGCAACTTTTTTTAATCCCATAGATATGGCCTTGC
                            || ||| | |     | |||| | || |  | |||||    | ||  | ||| |  |   | ||| | |  |||||  | ||||  |        | | ||      |  ||||||||||||||||| ||||||||| ||||||||||||| ||||| || || ||||| |||||  |||||||||| || || || ||||| ||||| ||| 
gtacattttcaatttttggacaagtgatacattgttgtgcaaataatttacatgtcagtgatatgatatgtcagtctatttatctaaac-ttgcactaaattttacttttcctgtaagactaatagtatgatgttttgcagGCAGCTCAGGATGGGGTTGACATAATAAGCTTGTCAATTACTCCTAATAGACGTCCTCCTGGTGTTGCAACTTTCTTCAACCCAATAGACATGGCTTTGA

upper sequence: Vv10s0092g00170.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: AT1G30600.1 (Arabidopsis thaliana), 3'ss of exon 5
cctcaaccttgctatttgtgttatttgctgccttcatatggccagacaccattcacatgggcattgtaattgattttgatcttcccttttgcattcacagGCAGCTCAGGATGGAGTTGACATAGTAAGCTTGTCAATCACTCCCAACAGGCGTCCCCCTGGAATTGCAACTTTTTTTAATCCCATAGATATGGCCTTGC
        |  |||    ||||| ||         | |     | | ||  ||    |     |||  || | | | ||| ||  ||||||||      ||| ||||| ||||||||||||||| ||| ||| |||||||| || || || ||||| ||||| || || || || ||||| || || |||||||| ||||
-------gtaactaaaaatgttacttttgtaacagaaactttgataaacagtttttcttatgtttgacatggttatggatgttttcttttgca------gGCGGCTCAAGATGGAGTTGACATAATAAACTTATCAATCACACCAAATAGACGTCCTCCTGGTATCGCTACGTTCTTTAACCCAATCGATATGGCATTGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acaccattcacatgggcattgtaattgattttgatcttcccttttgcattcacagGCAGCTCAGGATGGAGTTGACATAGTAAGCTTGTCAATCACTCCCAACAGGCGTCCCCCTGGAATTGCAACTTTTTTTAATCCCATAGATATGGCCTTGC
                            ttttgat  putative branch site (score: 4)
                                  tcttcccttttgcatt  CT-rich tract
                 attgtaattgatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cctcaaccttgctatttgtgttatttgctgccttcatatggccagacaccattcacatgggcattgtaattgattttgatcttcccttttgcattcacagGCAGCTCAGGATGGAGTTGACATAGTAAGCTTGTCAATCACTCCCAACAGGCGTCCCCCTGGAATTGCAACTTTTTTTAATCCCATAGATATGGCCTTGC

cctcaac
- - - -cttgcta
- - - - - - - - - - - - - - -gccttca
- - - - - - - - - - - - - - - - - - - - -ccagaca
- - - - - - - - - - - - - - - - - - - - - - - - ccattca
- - - - - - - - - - - - - - - - - - - - - - - - - - - -catgggc