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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtagggtccttgtagctgtcccctttttcaaatttactagttgatcaatgatccaggtttatgtaaagtcatcctgtcaaatttttaatcattttatagGATAAAGCAACTGTTGAGATGGAATGCATGGAGGAAGGATATCTTGCTAAGATAGTACTTGGAGATGGGGCAAAAGAGATCAAAGTTGGGCAG

Basic information

species Vitis vinifera
transcript Vv11s0016g01870.t01
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv11s0016g01870.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: LOC_Os02g01500.1 (Oryza sativa), 3'ss of exon 7
------------------------gtagggtccttgtagctgtcccctttttcaaatttactagttgatcaatgatccaggttta--tgtaaagtcatcctgtcaaatttttaat-catttta------tagGATAAAGCAACTGTTGAGATGGAATGCATGGAGGAAGGATATCTTGCTAAGATAGTACTTGGAGATGGGGCAAAAGAGATCAAAGTTGGGCAG
                          | |     | | | |      | |||  | ||    ||||   || | |      || |  || |     | |     |   ||| ||| ||||         ||||||||||| ||||| |||||||| |||||||| || || ||||| ||||||||  | | ||||||||| || |||||||||||||||||  ||
gtaagttttctaatatgtaaggctacatgccatatattgtttagatttatttttagttatgcagttagccagttacttctattaagctgcagtagaagctaaatatcctttgaatgcattcctgctgactagGATAAAGCCACTGTAGAGATGGAGTGCATGGAAGAGGGCTATCTCGCTAAGATCATTCATGGAGATGGTGCCAAAGAGATCAAAGTTGGTGAG

upper sequence: Vv11s0016g01870.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: LOC_Os06g01630.6 (Oryza sativa), 3'ss of exon 6
gtagggt-ccttgtagctgtcc---------cctttttcaaatttactagttgatcaatgatccaggtttatgtaaagtcatcctgtcaaatttttaatcattttatagGATAAAGCAACTGTTGAGATGGAATGCATGGAGGAAGGATATCTTGCTAAGATAGTACTTGGAGATGGGGCAAAAGAGATCAAAGTTGGGCAG
||| | | | || |   ||| |         | |  || || ||  ||| || ||   | ||  |||   |     ||     |  ||||     |      |   ||||||||||| || || ||||||||||||||||||||||| || |||||||| ||  | | ||||||||| || ||||| || ||||||||  ||
gtaagttactttcttaatgtgcacaccaagacttgatttaatttccctactttatt--taattaaggagcaacagcagcttaaccatcaatcacatttatggtgattagGATAAAGCGACAGTGGAGATGGAATGCATGGAGGAAGGCTACCTTGCTAAAATTATCCATGGAGATGGTGCCAAAGAAATTAAAGTTGGTGAG

upper sequence: Vv11s0016g01870.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: LOC_Os07g22720.2 (Oryza sativa), 3'ss of exon 7
------------------------gtagggtccttgtagctgtcccctttt--------tcaaatttactagttgatcaatgatccaggtttatgtaaagtcatcctgtcaaatttttaatcattttatagGATAAAGCAACTGTTGAGATGGAATGCATGGAGGAAGGATATCTTGCTAAGATAGTACTTGGAGATGGGGCAAAAGAGATCAAAGTTGGGCAG
                        | |   || | ||   |      ||||        |||| | |  |  || ||  | | | || |   || ||||   ||||| |  |||   |      |   ||||||||||| || || || ||||| |||||||| || || ||||||||||||||  | | |||||||||  | |||||||||||||||||  ||
gtaagttttctgatctctaaggcagcaatatcttagttagtacttatttttagtggtgctcaattattttcttttatttaagctgcaagagaatctaaa--tatcct-ttgaatgcatttctgctgactagGATAAAGCCACCGTAGAAATGGAGTGCATGGAAGAGGGCTATCTTGCTAAGATCATTCATGGAGATGGTTCCAAAGAGATCAAAGTTGGTGAG

upper sequence: Vv11s0016g01870.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: GRMZM2G161969_T01 (Zea mays), 3'ss of exon 2
gtagggtccttgtagctgtcccctttttcaaatttac-tagttgatcaatgatccaggtttatgtaaagtcatcctgtcaaat----ttttaatcattttat-------agGATAAAGCAACTGTTGAGATGGAATGCATGGAGGAAGGATATCTTGCTAAGATAGTACTTGGAGATGGGGCAAAAGAGATCAAAGTTGGGCAG
||| | |||||  |  |||      | | ||| |||  |  ||  |   | ||     ||  |     ||        |||||    ||| | |   ||| |       |||||||||||||||| |||||||| |||||||| || || ||||||||||||||  | | ||||||||| ||||| ||||| ||||||||  ||
gtaagttcctta-atttgtagaagatatgaaacttatgttatttgtatttaattttacttattaagctgttgcagaaccaaataacctttgagttgatttctggtggtcagGATAAAGCAACTGTGGAGATGGAGTGCATGGAAGAGGGCTATCTTGCTAAGATTATTCATGGAGATGGTGCAAAGGAGATTAAAGTTGGTGAG

upper sequence: Vv11s0016g01870.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: GRMZM2G015132_T01 (Zea mays), 3'ss of exon 6
gtagggtccttgtagctgtcccctttttcaaatttac-tagttgatcaatgatccaggtttatgtaaagtc-atcctgtcaaatttttaatcattttat-------agGATAAAGCAACTGTTGAGATGGAATGCATGGAGGAAGGATATCTTGCTAAGATAGTACTTGGAGATGGGGCAAAAGAGATCAAAGTTGGGCAG
||| | | |||  |  |||     || |  ||  ||  |  ||  |   |  |     || |  |  ||   | |     || |||| | |   ||| |       |||| ||||| ||||| |||||||| |||||||| || || ||||||||||||||  | | ||||||||| || || ||||| ||||||||  ||
gtaagtttctta-atttgtagaagttatggaacatatgttatttgtatttatttttacttaagctgtagcagaacgaaataacttttgagttgatttttggtgatcagGACAAAGCCACTGTGGAGATGGAGTGCATGGAAGAGGGCTATCTTGCTAAGATTATTCATGGAGATGGTGCGAAGGAGATTAAAGTTGGTGAG

upper sequence: Vv11s0016g01870.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: EFJ13978 (Selaginella moellendorffii), 3'ss of exon 2
gtagggtccttgtagctgtcccctttttcaaatttactagttgatcaatgatccaggtttatgtaaagtcatcctgtcaaatttttaatcattttatagGATAAAGCAACTGTTGAGATGGAATGCATGGAGGAAGGATATCTTGCTAAGATAGTACTTGGAGATGGGGCAAAAGAGATCAAAGTTGGGCAG
                             | |  |  |  |||    |||||   | ||| || || | |   |   |||||||             ||||||||||||| ||||| |||||||||||||| || || ||  | |||||||| ||| ||   || || |||||||| || |||||||| |||
---------------------------gtagagcttttcattgg--gatgatt--gttttctggaatgcctgaccagcaaattt------------cagGATAAAGCAACAGTTGACATGGAATGCATGGAAGACGGCTACTTGGCTAAGATCGTATTTTCGGACGGTGCAAAAGACATAAAAGTTGGACAG

upper sequence: Vv11s0016g01870.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: EFJ28117 (Selaginella moellendorffii), 3'ss of exon 2
gtagggtccttgtagctgtcccctttttcaaatttactagttgatcaatgatccaggtttatgtaaagtcatcctgtcaaatttttaatcattttatagGATAAAGCAACTGTTGAGATGGAATGCATGGAGGAAGGATATCTTGCTAAGATAGTACTTGGAGATGGGGCAAAAGAGATCAAAGTTGGGCAG
                             | |  |  |  |||    |||||   | ||| || || | |   |   |||||||             ||||||||||||| ||||| |||||||||||||| || || ||  | |||||||| ||| ||   || || |||||||| || |||||||| |||
---------------------------gtagagcttttcattgg--gatgatt--gttttctggaatgcctaaccagcaaattt------------cagGATAAAGCAACAGTTGACATGGAATGCATGGAAGACGGCTACTTGGCTAAGATCGTATTTTCGGACGGTGCAAAAGACATAAAAGTTGGACAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcaatgatccaggtttatgtaaagtcatcctgtcaaatttttaatcattttatagGATAAAGCAACTGTTGAGATGGAATGCATGGAGGAAGGATATCTTGCTAAGATAGTACTTGGAGATGGGGCAAAAGAGATCAAAGTTGGGCAG
                                      ttttaat  putative branch site (score: 3)
                                            tcatttt  CT-rich tract
                              tgtcaaatttttaatc  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtagggtccttgtagctgtcccctttttcaaatttactagttgatcaatgatccaggtttatgtaaagtcatcctgtcaaatttttaatcattttatagGATAAAGCAACTGTTGAGATGGAATGCATGGAGGAAGGATATCTTGCTAAGATAGTACTTGGAGATGGGGCAAAAGAGATCAAAGTTGGGCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGATCA