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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ataaaaataaaaataaaaaatctggattcttgacaactgtactgtgcatgaaggaaatgtattatgtcacaaaaacttaactacttggagttttttgcagACATTTCAGAATAAAAAACTTGCTCATGCTGTCAAGGAGTCTACTCTTGACAGTCTTATCACTGAGCTTTTGCTTTGGCTTTTGGATGAAAGGGTTCCTC

Basic information

species Vitis vinifera
transcript Vv00s0652g00030.t01
intron # 15
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv00s0652g00030.t01 (Vitis vinifera), 3'ss of exon 15
lower sequence: LOC_Os01g60040.2 (Oryza sativa), 3'ss of exon 43
ataaaaataaaaataaaaaatctggattcttgacaactgtactgtgcatgaaggaaatgtattatgtcacaaaaacttaactacttggagttttttgcagACATTTCAGAATAAAAAACTTGCTCATGCTGTCAAGGAGTCTACTCTTGACAGTCTTATCACTGAGCTTTTGCTTTGGCTTTTGGATGAAAGGGTTCCTC
                       |  |  |||   ||| |  | | | |        ||| |  | |||     | |||  ||  | |  | | || ||||| || ||||  |||   |||||||||||||| ||||||  |||||| || |  |||||||| |||||  | |||||||| || ||||||||||||||||
-----------------------gtttgtttgtgtactcttttctccttttgctctttgtttggt-tcaatgttatttatgta--taggctgtatttcagACTTTCCAGATCAAACGTCTTGCTCATGCTGTGAAGGAGGGTACTCTAGATAACCTTATCACAGAGCTACTACTTTGGCTCTTAGATGAAAGGGTTCCTC

upper sequence: Vv00s0652g00030.t01 (Vitis vinifera), 3'ss of exon 15
lower sequence: GRMZM2G068755_T01 (Zea mays), 3'ss of exon 44
ataaaaataaaaataaaaaatctggattcttgacaactgtactgtgcatgaaggaaatgtattatgtcacaaaaacttaactacttggagttttttg-cagACATTTCAGAATAAAAAACTTGCTCATGCTGTCAAGGAGTCTACTCTTGACAGTCTTATCACTGAGCTTTTGCTTTGGCTTTTGGATGAAAGGGTTCCTC
             | | |  | || |||||   |      | | |  ||| | ||    | || | |  |  |||        |||||  | ||||| |||||||||||||  |||   |||||||||||||| ||||||  ||| |||||||  ||||| || ||| |  | ||||||||||| ||||||||||||||||
----------gtttgacatgtttgtattct-acccttcacattttttatggaaga----ttttgtttatctgaaat-------cttgggctattttgacagACATTTCAGATCAAACGTCTTGCTCATGCTGTGAAGGAGGGTACCCTTGACAACCTTATTACGGAGTTACTTCTTTGGCTTTTAGATGAAAGGGTTCCTC

upper sequence: Vv00s0652g00030.t01 (Vitis vinifera), 3'ss of exon 15
lower sequence: GRMZM2G009849_T02 (Zea mays), 3'ss of exon 26
ataaaaataaaaataaaaaatctggattcttgacaactgtactgtgcatgaaggaaatgtattatgtcacaaaaacttaactacttggagttttttgcagACATTTCAGAATAAAAAACTTGCTCATGCTGTCAAGGAGTCTACTCTTGACAGTCTTATCACTGAGCTTTTGCTTTGGCTTTTGGATGAAAGGGTTCCTC
             |   | || |   |  ||| |  || |||| |   |   | | || |  | | ||  |||   |   ||| || ||        |||||||||||||  |||   |||||||||||||| ||||||  ||| |||||||  ||||| || ||| |  | |||||||| || ||||||||||||||||
------------gtttgacatgtttttgtttggcc-ctttacttttt-tatggcagattttgtttatctgaaatcttgggctattttga--------cagACATTTCAGATCAAACGTCTTGCTCATGCTGTGAAGGAGGGTACCCTTGACAACCTTATTACGGAGTTACTTCTTTGGCTCTTAGATGAAAGGGTTCCTC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gcatgaaggaaatgtattatgtcacaaaaacttaactacttggagttttttgcagACATTTCAGAATAAAAAACTTGCTCATGCTGTCAAGGAGTCTACTCTTGACAGTCTTATCACTGAGCTTTTGCTTTGGCTTTTGGATGAAAGGGTTCCTC
                             acttaac  putative branch site (score: 3)
                                             ttttttgc  putative PPT
         aaatgtattat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ataaaaataaaaataaaaaatctggattcttgacaactgtactgtgcatgaaggaaatgtattatgtcacaaaaacttaactacttggagttttttgcagACATTTCAGAATAAAAAACTTGCTCATGCTGTCAAGGAGTCTACTCTTGACAGTCTTATCACTGAGCTTTTGCTTTGGCTTTTGGATGAAAGGGTTCCTC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCTT
- -aaaataa
- - - - - - - aaaaaat
- - - - - - - - - - - - - - - - - - - - - - -gcatgaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - acaaaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tacttgg