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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...agatccttggaactaaaacagagtgatttaaattattatggaaagtcagaacactccttaattttttccagaccaaattatgattcttttatttccacagGTGGTCACTTGGTGCTATCATGTATGAAATGCTTGTGGGGTATCCACCTTTTTATTCTGATGATCCCATGTCAACATGTAGGAAG

Basic information

species Vitis vinifera
transcript Vv07s0005g03690.t01
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv07s0005g03690.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: LOC_Os10g33640.1 (Oryza sativa), 3'ss of exon 6
agatccttggaactaaaacagagtgatttaaattattatggaaagtcagaacactccttaattttttccagaccaaattatgattcttttatttccacagGTGGTCACTTGGTGCTATCATGTATGAAATGCTTGTGGGGTATCCACCTTTTTATTCTGATGATCCCATGTCAACATGTAGGAAG
                   ||  |  |||| || | |||     | ||     ||| | | |||     | |  |||||   ||  ||| |  |    |||||||||||||| || ||||||||||||||||| ||||| ||||| || || ||||||||||| || ||| |||| || || |||
----------------gtaagcatcgtttacataaatatctcgtgccatggacctcttgagtttgcagtaaag-aaattg-aataatttcaactatctagGTGGTCACTTGGAGCAATCATGTATGAAATGCTAGTGGGCTATCCCCCATTCTATTCTGATGAGCCTATGACAACTTGCAGAAAG

upper sequence: Vv07s0005g03690.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GRMZM2G088245_T01 (Zea mays), 3'ss of exon 6
agatccttggaactaaaacagagtgatttaaattattatggaaagtc-agaacactccttaattttttccagaccaaattatgattcttttatttccacagGTGGTCACTTGGTGCTATCATGTATGAAATGCTTGTGGGGTATCCACCTTTTTATTCTGATGATCCCATGTCAACATGTAGGAAG
                          |    ||     || |   || |   || |  | | | |  ||   | |||||       |   | ||||||  ||||||| |||||| ||||||||||||| ||||| ||||| ||||| || || |||||||| || || ||| | || ||  | |||
-------------------------gtaagcatctccttgcaccatcgatcgcattgatgagtctagtctcaaacaaat-------cccatgtttcca--gGTGGTCCCTTGGTTCTATCATGTATGAGATGCTAGTGGGTTATCCTCCATTCTATTCTGACGAGCCTATGACTACTTGCCGAAAG

upper sequence: Vv07s0005g03690.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA19G34920.1 (Glycine max), 3'ss of exon 6
----agatccttggaactaaaacagagtg-atttaaattattatggaaagtcagaacactccttaattttttccagaccaaattatgattcttttatttccacagGTGGTCACTTGGTGCTATCATGTATGAAATGCTTGTGGGGTATCCACCTTTTTATTCTGATGATCCCATGTCAACATGTAGGAAG
    | ||| ||         | ||  |  |  |||| | | | |   |   |  | |    | | |||    ||   |  ||| ||||      |  | || |||||||||||||| ||||| |||||||||||| | ||||| |||||||||||||||||||||||||| ||||||||||||||||||
aaaaaaatctttattttatgtatagtttataaataaactttaacgagtaaatattaaatatttaagtttgacacaatgctcattgtgata-----aaattcatagGTGGTCACTTGGAGCTATTATGTATGAAATGTTAGTGGGATATCCACCTTTTTATTCTGATGATCCAATGTCAACATGTAGGAAG

upper sequence: Vv07s0005g03690.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA03G32160.1 (Glycine max), 3'ss of exon 6
agatccttggaactaaaacagagtgatttaaattattatggaaagtca--gaacactccttaattttttccagaccaaattatgattcttttatt----tccacagGTGGTCACTTGGTGCTATCATGTATGAAATGCTTGTGGGGTATCCACCTTTTTATTCTGATGATCCCATGTCAACATGTAGGAAG
      ||| |  ||||| ||    ||  ||| | ||||| | | |    ||| |    |||| | |||       | |  ||| || ||||  |    |    |||||||||||||| ||||| |||||||||||| | ||||| |||||||||||||||||||||||||| ||||||||||| ||||||
-----tttgtatgtaaaa-aggcaaataaaaactcttatgtatattttatgaataaatattaaatatttaagtttaacacaatgtttgttttgataaaatttgtagGTGGTCACTTGGAGCTATTATGTATGAAATGTTAGTGGGATATCCACCTTTTTATTCTGATGATCCAATGTCAACATGCAGGAAG

upper sequence: Vv07s0005g03690.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA13G18670.2 (Glycine max), 3'ss of exon 6
agatccttggaactaaaacagagtgatttaaattattatggaaagtcagaacactcctta-attttttccagaccaaattatgattcttttatttc-cacagGTGGTCACTTGGTGCTATCATGTATGAAATGCTTGTGGGGTATCCACCTTTTTATTCTGATGATCCCATGTCAACATGTAGGAAG
|      | |   | |     | | || |  | | || |||| | | ||| ||      | ||||| |   ||   ||| ||| || ||  |   | |||||||||||||| || ||||| ||||| |||||| | ||||| |||||||||||||||||||||||||| |||| |||||||||||||
aagcttattgggtttagcttcatttatgtggaat-ttgtggaca-taagatcaggttacatattttgttttgatgcaatgatggttgttacaaaactcacagGTGGTCACTGGGAGCTATTATGTACGAAATGTTGGTGGGATATCCACCTTTTTATTCTGATGATCCAATGTTAACATGTAGGAAG

upper sequence: Vv07s0005g03690.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA10G04410.2 (Glycine max), 3'ss of exon 7
agatccttggaactaaaacagagtgatttaaattattatggaaagtcagaacactccttaattttttccagaccaaattatgattcttttatt-tccacagGTGGTCACTTGGTGCTATCATGTATGAAATGCTTGTGGGGTATCCACCTTTTTATTCTGATGATCCCATGTCAACATGTAGGAAG
||    |||    |         |   |  ||||  |||  | |     |    | | || ||| ||   ||   ||| ||| || ||  |   | ||||||||||||||||| ||||| ||||| |||||||| ||||| ||||| |||||||||||||||||||| |||| |||||| ||||||
agcatattgagttttgcttcatttatgtggaatttgtatatataaggtcagggttacatattttatttt-gatgcaatgatggttgttacaaaattcacagGTGGTCACTTGGAGCTATTATGTACGAAATGCTGGTGGGATATCCTCCTTTTTATTCTGATGATCCAATGTTAACATGCAGGAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcagaacactccttaattttttccagaccaaattatgattcttttatttccacagGTGGTCACTTGGTGCTATCATGTATGAAATGCTTGTGGGGTATCCACCTTTTTATTCTGATGATCCCATGTCAACATGTAGGAAG
          ccttaat  putative branch site (score: 4)
                                      ttcttttatttccac  putative PPT
                             aaattatgattctttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
agatccttggaactaaaacagagtgatttaaattattatggaaagtcagaacactccttaattttttccagaccaaattatgattcttttatttccacagGTGGTCACTTGGTGCTATCATGTATGAAATGCTTGTGGGGTATCCACCTTTTTATTCTGATGATCCCATGTCAACATGTAGGAAG

- -tccttgg
- - - - - aactaaa
- - - - - - - - - - - - - - - - - - tatggaaa
- - - - - - - - - - - - - - - - - - - - - - - cagaaca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -agaccaa