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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagaccactatttgtctatttgatataattacaggaaaaaaaaaaatctctaatctaagtttacagGTTGGAAAAGGACGAGATGTTGGACTCAATCAGATTGCTCTATTTGAAGGGAAAGTTGCTGGTGGTAATGGTGAACAAGTTCTCAGTCGAGACATTTACA

Basic information

species Vitis vinifera
transcript Vv06s0004g01200.t01
intron # 37
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv06s0004g01200.t01 (Vitis vinifera), 3'ss of exon 37
lower sequence: LOC_Os03g02756.1 (Oryza sativa), 3'ss of exon 6
-------------------------------gtaagaccactatttgtctatttgatataattacaggaa--aaaaaaaaatctctaatctaagtttacagGTTGGAAAAGGACGAGATGTTGGACTCAATCAGATTGCTCTATTTGAAGGGAAAGTTGCTGGTGGTAATGGTGAACAAGTTCTCAGTCGAGACATTTACA
                                ||  ||   |          ||| | |  || |  | |  | |   |  |  | ||  ||| | |  |||||||||| ||| |||| ||||| || ||||||||||| || || ||||| ||||||||||| || |||||||| ||||| ||||| || || || ||||
acttgttcgctgcaccatctactctagcattatataactgttgccaacactcttgctgtc-ttgcgagcattatattgatgttccaaacataattctgtagGTTGGAAAGGGAAGAGACGTTGGTCTTAATCAGATTGCACTGTTCGAAGGAAAAGTTGCTGGAGGAAATGGTGAGCAAGTGCTCAGCCGGGATATATACA

upper sequence: Vv06s0004g01200.t01 (Vitis vinifera), 3'ss of exon 37
lower sequence: GRMZM2G453794_T01 (Zea mays), 3'ss of exon 5
------------------------------gtaagacca--ctatttgtctatttgatataattacaggaaaaaaaaaaatctctaatctaagtttacagGTTGGAAAAGGACGAGATGTTGGACTCAATCAGATTGCTCTATTTGAAGGGAAAGTTGCTGGTGGTAATGGTGAACAAGTTCTCAGTCGAGACATTTACA
                                   || |    |   ||   | || |    |     ||| |      || |  ||  | | | |  ||||||| |||||  | ||||||||||| ||||||||||| ||||||||||| |||||||||||||| ||||||||||||||||| || |||||||| || |
ctttggatccctatttggcaattgctttccactgcactaactcaaccgtggttgtgctgctgtcttgtgaacactgttgatattaaacgttattctgtagGTTGGCAAAGGTAGGGATGTTGGACTTAATCAGATTGCACTATTTGAAGGAAAAGTTGCTGGTGGAAATGGTGAACAAGTTCTTAGCCGAGACATATATA

upper sequence: Vv06s0004g01200.t01 (Vitis vinifera), 3'ss of exon 37
lower sequence: GLYMA20G38860.1 (Glycine max), 3'ss of exon 42
gtaagaccactatttgtctatttgatataattacaggaaaaaaaaaaatctctaat-ctaagtttacagGTTGGAAAAGGACGAGATGTTGGACTCAATCAGATTGCTCTATTTGAAGGGAAAGTTGCTGGTGGTAATGGTGAACAAGTTCTCAGTCGAGACATTTACA
|| ||||   |  |||| || | |||     ||||    | |||    | ||||||  ||| ||||||||||||||| ||| |||||||||| |||||||||||||| ||||||||||| |||||| |||||||||| |||||||||||||||||||| ||  | ||||
gtgagac---ttgttgtttaat-gatgcctctaca----acaaatccttttctaatattaaatttacagGTTGGAAAGGGAAGAGATGTTGGGCTCAATCAGATTGCACTATTTGAAGGAAAAGTTTCTGGTGGTAACGGTGAACAAGTTCTCAGTCGTGATGTATACA

upper sequence: Vv06s0004g01200.t01 (Vitis vinifera), 3'ss of exon 37
lower sequence: GLYMA10G44150.1 (Glycine max), 3'ss of exon 40
gtaagaccactatttgtctatttgatataattacaggaaaaaaaaaaatctctaat-ctaagtttacagGTTGGAAAAGGACGAGATGTTGGACTCAATCAGATTGCTCTATTTGAAGGGAAAGTTGCTGGTGGTAATGGTGAACAAGTTCTCAGTCGAGACATTTACA
|| ||||   |  |||| |||| |||     ||||    | |||    | ||||||  ||| |||||||||||| || ||| |||||||||| |||||||||||||| ||||||||||| |||||| |||||||||| ||||||||||||||||| || ||  | ||||
gtgagac---ttgttgtttatt-gatccctctaca----acaaatcgttttctaatattaaatttacagGTTGGTAAGGGAAGAGATGTTGGGCTCAATCAGATTGCACTATTTGAAGGAAAAGTTTCTGGTGGTAACGGTGAACAAGTTCTCAGCCGTGATGTATACA

upper sequence: Vv06s0004g01200.t01 (Vitis vinifera), 3'ss of exon 37
lower sequence: AT3G07160.1 (Arabidopsis thaliana), 3'ss of exon 39
gtaagaccactatttgtctatttgatataattacaggaaaaaaaaaa-atctctaatctaa----gtttacagGTTGGAAAAGGACGAGATGTTGGACTCAATCAGATTGCTCTATTTGAAGGGAAAGTTGCTGGTGGTAATGGTGAACAAGTTCTCAGTCGAGACATTTACA
       |  || || |  | |   || ||||| |  || ||||| | || | |    |||    |||||||||| || ||||| ||||||||||| |||||||| || ||||| ||||||||||| ||||||||||| ||||||||||| ||||| ||||||||  | ||||
-----gtccgtactttttaactctttacaattaaaataataaaaatatatatatgcattaattctgtttacagGTGGGCAAAGGGCGAGATGTTGGGCTCAATCAAATAGCTCTGTTTGAAGGGAAGGTTGCTGGTGGGAATGGTGAACAGGTTCTTAGTCGAGATGTATACA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgtctatttgatataattacaggaaaaaaaaaaatctctaatctaagtttacagGTTGGAAAAGGACGAGATGTTGGACTCAATCAGATTGCTCTATTTGAAGGGAAAGTTGCTGGTGGTAATGGTGAACAAGTTCTCAGTCGAGACATTTACA
                                    ctctaat  putative branch site (score: 3)
     tatttgatataattac  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagaccactatttgtctatttgatataattacaggaaaaaaaaaaatctctaatctaagtttacagGTTGGAAAAGGACGAGATGTTGGACTCAATCAGATTGCTCTATTTGAAGGGAAAGTTGCTGGTGGTAATGGTGAACAAGTTCTCAGTCGAGACATTTACA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGTGG