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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgaatattccattgttgatccggaagaatactatacaatttggaaatggtgttatcaactactaagctaaaaatgttttcgtttttttacagGAGCATCAATGCCTCTAGGAGGAACTTGGGCTATTTCTCTTGTGGAACAGGCAACCCTATCGACGATTGCTGGAGGTGCGACGCCAACTGGGACAAGAAC

Basic information

species Vitis vinifera
transcript Vv14s0219g00230.t01
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv14s0219g00230.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA19G07490.1 (Glycine max), 3'ss of exon 1
gtgaatattccattgttgatcc--ggaagaatactatacaatttggaaatggtgt-tatcaactac-taagctaaaaatgttttcgtttttt---tacagGAGCATCAATGCCTCTAGGAGGAACTTGGGCTATTTCTCTTGTGGAACAGGCAACCCTATCGACGATTGCTGGAGGTGCGACGCCAACTGGGACAAGAAC
 || ||  |  | | ||| ||   ||  | | | |||  || || | |    | | ||| ||  ||  || |    ||  ||||  |||| |   ||||| ||||||||||||||||| || |||||||| ||||| || || ||||||||||||||||| |||||||||||| | || ||  |||||||||| || |||
ttgtattatttactcttggtcttgggtggtaaaatatgtaacttaggacgactatatataaagcacacaaacatgtaacattttatttttctcattacagAAGCATCAATGCCTCTAGAAGAAACTTGGGTTATTTATCATGCGGAACAGGCAACCCTATTGACGATTGCTGGCGTTGTGAATCCAACTGGGAGAACAAC

upper sequence: Vv14s0219g00230.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA05G23950.1 (Glycine max), 3'ss of exon 1
gtgaatattccattgttga-tccggaagaatactatacaatttggaaatggtgttatcaactactaagctaaaaatgttttcgtttt-------tttacagGAGCATCAATGCCTCTAGGAGGAACTTGGGCTATTTCTCTTGTGGAACAGGCAACCCTATCGACGATTGCTGGAGGTGCGACGCCAACTGGGACAAGAAC
 |  | | |  ||| || | ||  | |   ||  ||| || | | |||      |||  || || ||     |||  ||||  ||||       ||| ||| ||||||||||||||||| || |||||||| ||||| || || |||||||||||||| || |||||||||||| | || ||| |||| ||||| || |||
-ttcacaatgaattatttactcttggatggtaaaatataagtggaaaaactatatatttacaacaaaaagtgaaacattttatttttctttgattttgcagAAGCATCAATGCCTCTAGAAGAAACTTGGGTTATTTATCATGCGGAACAGGCAACCCCATTGACGATTGCTGGCGATGTGACCCCAATTGGGAGAACAAC

upper sequence: Vv14s0219g00230.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: PP1S563_1V6.3 (Physcomitrella patens), 3'ss of exon 1
---gtgaatattccattgttgatccggaagaatactatacaatttggaaatggtgttatcaactactaagctaaaaatgttttcgtttttttacagGAGCAT--CAATGCCTCTAGGAGGAACTTGGGCTATTTCTC---TTGTGGAACAGGCAACCCTATCGACGATTGCTGGAGGTGCGACGCCAACTGGGACAAGAAC------
   ||   ||  || | |    | || | |    | |    |||  ||| || | ||    | |   ||||      || ||||     |  | ||| |||   ||    ||| |  || | |    ||| | |       |||||||||||||||||| | ||||| |||||||||||   |  ||| ||||| |  ||       
gcagtttgtagccc-tcgcctcttcgcatgg-cgccagtggattatgaactgatttttgagaatctaaagc-----gtgatttctaacgtagagaggtgcaatgcagCAGCTCCAACAGTACCCGCCGCTCTCTGGGAGGCTGTGGAACAGGCAACCCTGTGGACGACTGCTGGAGGTGTAGCAGCAATTGGGAAAGCAATCGTCAG

upper sequence: Vv14s0219g00230.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: PP1S563_1V6.1 (Physcomitrella patens), 3'ss of exon 1
gtgaatattccattgttgatccggaagaatactatacaatttggaaatggtgttatcaactactaagctaaaaatgttttcgtttttttacagGAGCAT--CAATGCCTCTAGGAGGAACTTGGGCTATTTCTC---TTGTGGAACAGGCAACCCTATCGACGATTGCTGGAGGTGCGACGCCAACTGGGACAAGAAC---------
||   ||  || | |    | || | |    | |    |||  ||| || | ||    | |   ||||      || ||||     |  | ||| |||   ||    ||| |  || | |    ||| | |       |||||||||||||||||| | ||||| |||||||||||   |  ||| ||||| |  ||          
gtttgtagccc-tcgcctcttcgcatgg-cgccagtggattatgaactgatttttgagaatctaaagc-----gtgatttctaacgtagagaggtgcaatgcagcagCTCCAACAGTACCCGCCGCTCTCTGGGAGGCTGTGGAACAGGCAACCCTGTGGACGACTGCTGGAGGTGTAGCAGCAATTGGGAAAGCAATCGTCAGGGC

upper sequence: Vv14s0219g00230.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: PP1S563_1V6.2 (Physcomitrella patens), 3'ss of exon 1
-----------gtgaatattccattgttgatccggaagaatactatacaatttggaaatggtgttatcaactactaagctaaaa-atgttttcgtttttttacagGAGCAT--CAATGCCTCTAGGAGGAACTTGGGCTATTTCTC---TTGTGGAACAGGCAACCCTATCGACGATTGCTGGAGGTGCGACGCCAACTGGGACAAGAAC
           |     | |   | |      |        |     | | | |   |||   | ||    |   || |||||   || ||||     |  | ||| |||   ||    ||| |  || | |    ||| | |       |||||||||||||||||| | ||||| |||||||||||   |  ||| |||         
acgatgtaactggaggcagtttgtagccctcgcctcttcgcatggcgccagtggattatgaactgattt-ttgagaatctaaagcgtgatttctaacgtagAGAGGTGCAATGCAGCAGCTCCAACAGTACCCGCCGCTCTCTGGGAGGCTGTGGAACAGGCAACCCTGTGGACGACTGCTGGAGGTGTAGCAGCAATTGG---------


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atttggaaatggtgttatcaactactaagctaaaaatgttttcgtttttttacagGAGCATCAATGCCTCTAGGAGGAACTTGGGCTATTTCTCTTGTGGAACAGGCAACCCTATCGACGATTGCTGGAGGTGCGACGCCAACTGGGACAAGAAC
                           agctaaa  putative branch site (score: 3)
                                    tgttttcgttttttt  putative PPT
                              taaaaatgttttcgtt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgaatattccattgttgatccggaagaatactatacaatttggaaatggtgttatcaactactaagctaaaaatgttttcgtttttttacagGAGCATCAATGCCTCTAGGAGGAACTTGGGCTATTTCTCTTGTGGAACAGGCAACCCTATCGACGATTGCTGGAGGTGCGACGCCAACTGGGACAAGAAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAC