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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttagtttttctcttttctttttatatactagttatttcttttactgctcaatctcatttccatctaaaacatttacagGATATGAGTGTGGGTACATCATGGAACATATTGAGGCCCGAGACAGTTGAATCACTGTTTTACCTCTGGCGTTTAACTGGCAGCAAGACATACCAAGAGT

Basic information

species Vitis vinifera
transcript Vv09s0054g00230.t01
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv09s0054g00230.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: GRMZM2G128914_T01 (Zea mays), 3'ss of exon 12
--------------gttagtttttctcttttctttttatatactagttatttc----ttttactgctcaatctcatttccatctaaaacatttacagGATATGAGTGTGGGTACATCATGGAACATATTGAGGCCCGAGACAGTTGAATCACTGTTTTACCTCTGGCGTTTAACTGGCAGCAAGACATACCAAGAGT
               ||  |||||  || |||   | ||| |    || |  |      | | | || ||| | |||| | |   || |||    |||| ||||||||||| ||||| |||||||| ||||| || ||||| |||||||||||  | ||||| ||||| || || || |  |  ||||||||||| |
gtagtatggcacccctttattttttcctcttccaataataaaaatcttgtaccaaaccatcaattctgaatgttattttcctactaagcat----agGACATGAGTGTGGGCACATCGTGGAACATCTTGAGACCGGAGACTGTTGAATCACTTATGTACCTATGGCGCTTGACGGGGAATACAACATACCAAGATT

upper sequence: Vv09s0054g00230.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: GRMZM2G130889_T01 (Zea mays), 3'ss of exon 13
--------gttagtttttctcttttctttttatatactagttatttcttttactgctcaatctcatttccatctaaaacatttacagGATATGAGTGTGGGTACATCATGGAACATATTGAGGCCCGAGACAGTTGAATCACTGTTTTACCTCTGGCGTTTAACTGGCAGCAAGACATACCAAGAGT
           |   ||| | ||| || |||  ||| ||   || |  |  |   |   |    ||||||  || |      || |||| ||| ||||||| || || |||||||| ||||| || ||||| |||||||||||| | ||||| ||||| || || || |  || ||||||||||| |
gtagtatgacaaccctttatttttcctctttcaataataaaaatcttgtccaaaccatca----atttcctactga-----ctatagGACATGGGTGTGGGCACGTCGTGGAACATCTTGAGACCGGAGACTGTTGAATCACTGATGTACCTGTGGCGCTTGACGGGGAATAAAACATACCAAGATT

upper sequence: Vv09s0054g00230.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: GLYMA08G23730.1 (Glycine max), 3'ss of exon 12
gttagtttttctcttttctttttatatactagttatttcttttactgctcaatctcatttccatctaaaacatttacagGATATGAGTGTGGGTACATCATGGAACATATTGAGGCCCGAGACAGTTGAATCACTGTTTTACCTCTGGCGTTTAACTGGCAGCAAGACATACCAAGAGT
       ||  |  ||  ||| | | | | |  || ||     | ||    ||||||     || |   |   ||| |||| ||||||||||||||||||||||||||| ||||||| ||||||||||| || || |||||||| |||||| ||||||||| ||| ||||||||||| |
------gttagttattagtttatttgtgccatgtaatttgaaaattgtgtgatctcaaacttatttttgaatatta-agGACATGAGTGTGGGTACATCATGGAACATACTGAGGCCAGAGACAGTTGAGTCCCTCTTTTACCTTTGGCGTCTAACTGGCAACAAAACATACCAAGAAT

upper sequence: Vv09s0054g00230.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: GLYMA07G02290.1 (Glycine max), 3'ss of exon 11
gttagtttttctcttttctttttatatactagttatttcttttactgctcaatctcatttccatctaaaacatttacagGATATGAGTGTGGGTACATCATGGAACATATTGAGGCCCGAGACAGTTGAATCACTGTTTTACCTCTGGCGTTTAACTGGCAGCAAGACATACCAAGAGT
       ||  |  ||  ||| | | | ||    | ||     | ||   ||||| |  |  || |   |  |||| |||| ||||||||||||||||||||||||||| ||||||| ||||||||||| || || |||||||| |||||| ||||||||| ||| || |||||||| |
------gttagttattagtttatttgtgctgtgcaatttgaaaattgtgtaatctgaaatttatttttgaacttta-agGACATGAGTGTGGGTACATCATGGAACATACTGAGGCCAGAGACAGTTGAGTCCCTCTTTTACCTTTGGCGTCTAACTGGCAACAAAACGTACCAAGAAT

upper sequence: Vv09s0054g00230.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: AT1G51590.1 (Arabidopsis thaliana), 3'ss of exon 12
----gttagt--ttttctcttttctttttatatactagttatttcttttactgctcaatctcatttccatctaaaacatttacagGATATGAGTGTGGGTACATCATGGAACATATTGAGGCCCGAGACAGTTGAATCACTGTTTTACCTCTGGCGTTTAACTGGCAGCAAGACATACCAAGAGT
    || | |  ||||  |   ||| ||| |||  |||||  ||  ||   ||    ||| |||   ||  | |     || ||||| |||||||| || ||||| |||||||| || || || || || |||||||||||||||||||||||||| |||||||| | ||||||||| |||||||
gttggtaaatactttttgcgcatctgtttgtatgttagttggttggtta--tgtcgtatc-cataagcacatga--ttgtttcagGACATGAGTGTTGGCACATCTTGGAACATTTTAAGACCAGAAACCGTTGAATCACTGTTTTACCTCTGGCGATTAACTGGGAACAAGACATATCAAGAGT

upper sequence: Vv09s0054g00230.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: AT3G21160.1 (Arabidopsis thaliana), 3'ss of exon 12
gttagtttttctcttttctttttatatactagttatttcttttactgctcaatctcatttccatctaaaacatt-tacagGATATGAGTGTGGGTACATCATGGAACATATTGAGGCCCGAGACAGTTGAATCACTGTTTTACCTCTGGCGTTTAACTGGCAGCAAGACATACCAAGAGT
||  ||  ||  | | |||||||  | ||   || ||| |||||    | | |     ||   | || |  ||  | ||||| |||||||| || || || |||||||| ||||| || || || || ||||||||||||||||||||||| |||||||| | ||||||||| |||||||
gtatgtcatttgcctgtcttttt-caaacacattgtttattttatgcgttatttattgtttagtatacatgatgattcagGACATGAGTGTTGGAACGTCGTGGAACATCTTGAGACCAGAAACTGTCGAATCACTGTTTTACCTCTGGCGGTTAACTGGAAACAAGACATATCAAGAGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatactagttatttcttttactgctcaatctcatttccatctaaaacatttacagGATATGAGTGTGGGTACATCATGGAACATATTGAGGCCCGAGACAGTTGAATCACTGTTTTACCTCTGGCGTTTAACTGGCAGCAAGACATACCAAGAGT
                                      atctaaa  putative branch site (score: 3)
     tagttatttctttta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttagtttttctcttttctttttatatactagttatttcttttactgctcaatctcatttccatctaaaacatttacagGATATGAGTGTGGGTACATCATGGAACATATTGAGGCCCGAGACAGTTGAATCACTGTTTTACCTCTGGCGTTTAACTGGCAGCAAGACATACCAAGAGT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAGA