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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTGTACGACTTATGGGGCGTGCAGCCTCACACATTACATTGGAGTGTGCTTTGCAAACTCATCCAAACATTACAATTATTGGTGAAGAGgtatctccatacattagttttgttcacttccaattacttgtgtgctttagttgcatgttttcagaagaaggtgcattttcactggtgatttggacttcatatttgcaactattacaatatgtttactacttaaattttgctgcag

Basic information

species Vitis vinifera
transcript Vv10s0116g00360.t01
intron # 8
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv10s0116g00360.t01 (Vitis vinifera), 5'ss of exon 8
lower sequence: LOC_Os06g13810.1 (Oryza sativa), 5'ss of exon 8
TTGTACGACTTATGGGGCGTGCAGCCTCACACATTACATTGGAGTGTGCTTTGCAAACTCATCCAAACATTACAATTATTGGTGAAGAGgtatctccatacattagttttgttcacttccaattacttgtgtgctttagttgcatgttttcagaagaaggtgcattttcactggtgatttggacttcatatttgcaactattacaatatgtttactacttaaattttgctgcag
||||  | |||||||| ||||| || || ||||||||||||||||||||| ||||||| ||||| ||  || || | ||||| |||||||| | |  |    |||  | || ||   | || | || ||    ||  |    | | |  |     |||      |    | |||||   |   ||    ||||                                         
TTGTGAGGCTTATGGGACGTGCTGCTTCTCACATTACATTGGAGTGTGCTCTGCAAACACATCCTAATGTTGCACTCATTGGAGAAGAGgtttgt--aattcttatatatgatcttctacattgacctg-acactccaac--cttttcctagcttgaatactgttccataatggtggaatcatctattcatttc----------------------------------------

upper sequence: Vv10s0116g00360.t01 (Vitis vinifera), 5'ss of exon 8
lower sequence: GRMZM2G143862_T01 (Zea mays), 5'ss of exon 1
-----------TTGTACGACTTATGGGGCGTGCAGCCTCACACATTACATTGGAGTGTGCTTTGCAAACTCATCCAAACATTACAATTATTGGTGAAGAGgta---tctccatacattagttttgttcacttccaattacttgtgtgctttagttgcatgttttcagaagaaggtgcattttcactggtgatttggacttcatatttgcaactattacaatatgtttactacttaaattttgctgcag
           ||||  | |||||||| ||||| || || |||||||||||||| || ||||||||||| || || ||   | || | ||||| ||||||||      | ||| ||  |||| | |  || |  |||||   |  ||      ||| |||||  |          || |||      ||   || |      ||  | |||    | ||| | ||                       
CGCTCTTGCAGTTGTGAGGCTTATGGGTCGTGCTGCTTCTCACATTACATTGGAATGCGCTTTGCAAACACACCCCAATGCTGCACTCATTGGGGAAGAGgttggtgttacatgcaa-agttctttctacatggaatta---gcatg-----attggatgttccc----------gcctttatttaagtagattagg-----tacatacaa----tgcaaaaggtcag--------------------

upper sequence: Vv10s0116g00360.t01 (Vitis vinifera), 5'ss of exon 8
lower sequence: GLYMA07G39380.1 (Glycine max), 5'ss of exon 8
TTGTACGACTTATGGGGCGTGCAGCCTCACACATTACATTGGAGTGTGCTTTGCAAACTCATCCAAACATTACAATTATTGGTGAAGAGgtatctccatacattagttttgttcacttccaattacttgtgtgctttagttgcatgttttcagaagaaggtgcattttcactggtgatttggacttcatatttgcaactattacaatatgtttactacttaaattttgctgcag
|||| || |||||||| |||||||| || ||||||||| |||| ||||||||||||||||||||||||||||| |||||||| |||||||| | || ||| ||  | |   || |  |    ||   |  ||      |||| |||   |||  | ||  |||||    | || |   |||   || |  |||                                         
TTGTTCGGCTTATGGGACGTGCAGCTTCGCACATTACACTGGAATGTGCTTTGCAAACTCATCCAAACATTACTATTATTGGAGAAGAGgtttgtc-ataaatctgatcattttatctagtgtttgatcagttaaggggttg-atgaaatcaagataaaatgcatccatagtgat--cttgtgattgaagttt-----------------------------------------

upper sequence: Vv10s0116g00360.t01 (Vitis vinifera), 5'ss of exon 8
lower sequence: GLYMA17G01360.1 (Glycine max), 5'ss of exon 6
TTGTACGACTTATGGGGCGTGCAGCCTCACACATTACATTGGAGTGTGCTTTGCAAACTCATCCAAACATTACAATTATTGGTGAAGAGgtatctccatacattagttttgttcacttccaattacttgtgtgctttagttgcatgttttcagaagaaggtgcattttcactggtgatttggacttcatatttgcaactattacaatatgtttactacttaaattttgctgcag
|||| || |||||||| |||||||| |||||||||||| |||| |||||||||||||||||||| |||||||| |||||||| |||||||| |  || |   | | ||||  |    | || | |  |||       ||     | || ||| ||          ||| | | |  || |  |  || ||||| ||                                      
TTGTTCGGCTTATGGGACGTGCAGCTTCACACATTACACTGGAATGTGCTTTGCAAACTCATCCGAACATTACTATTATTGGAGAAGAGgt-ttaccttgt-tcaatttttcttgtattcagtgaaatgt------cagggctctcttatcaaaaa---------tttgatttgacatgtaaatatcttattt-cag-------------------------------------

upper sequence: Vv10s0116g00360.t01 (Vitis vinifera), 5'ss of exon 8
lower sequence: GLYMA15G11890.1 (Glycine max), 5'ss of exon 8
TTGTACGACTTATGGGGCGTGCAGCCTCACACATTACATTGGAGTGTGCTTTGCAAACTCATCCAAACATTACAATTATTGGTGAAGAGgtatctccatacat--tagttttgttcacttc--caattacttgtgtgctttagttgcatgttttcagaagaaggtgcattttcactggtgatttgg-acttcatatttgcaactattacaatatgtttactacttaaattttgct--gcag
|||| || ||||||||||||||||| |||||||||||  |||| ||||| || |||||||||||||||||||| |||||||| ||||||||   ||  | | |  ||  |||||||| ||   | | |  ||||      |||  | |  |    | || ||       || || || | || |     || |  |||||   ||| | ||| || ||   ||  | | |   ||   |||
TTGTGCGGCTTATGGGGCGTGCAGCTTCACACATTACGCTGGAATGTGCCTTACAAACTCATCCAAACATTACTATTATTGGAGAAGAGgttcttcacttcctcatatatttgttcaatttatctagtgtttgtacatactaggggtagatgaaaaaaataaaaaatgcttcca-tgttaatctcatgattaaagtttgcttttatcaaaatttgatttaaacccataatacacttttcag

upper sequence: Vv10s0116g00360.t01 (Vitis vinifera), 5'ss of exon 8
lower sequence: GLYMA09G01050.1 (Glycine max), 5'ss of exon 8
TTGTACGACTTATGGGGCGTGCAGCCTCACACATTACATTGGAGTGTGCTTTGCAAACTCATCCAAACATTACAATTATTGGTGAAGAGgtatctccatacat--tagttttgttcacttc--caattacttgtg--tgctttagttgcatgttttcagaagaaggtgcattttcactggtgatttggacttcatatttgcaactattacaatatgtttactactta-aattttgct--gcag
|||| || ||||||||||| || || |||||||||||  |||| |||||||| |||||||||||||||||||| |||||||| ||||||||  |||  | | |  ||  |||||||| ||   | | |  ||||   |||||  | |  |||  || | || ||  ||| |      |  |    ||   || |  |||||   ||| | ||  || ||   ||  | || |   ||   |||
TTGTGCGGCTTATGGGGCGGGCGGCTTCACACATTACGCTGGAATGTGCTTTACAAACTCATCCAAACATTACTATTATTGGAGAAGAGgttcctcacttcctcatatatttgttcaatttatctagtgtttgtacatgcttggggtagatgaattaaaaaaaaaatgcttccgtgttaatatcatga--ttaaagtttgcttttataaaaaattgatttaaacccataaatacacttttcag

upper sequence: Vv10s0116g00360.t01 (Vitis vinifera), 5'ss of exon 8
lower sequence: AT1G12000.1 (Arabidopsis thaliana), 5'ss of exon 8
TTGTACGACTTATGGGGCGTGCAGCCTCACACATTACATTGGAGTGTGCTTTGCAAACTCATCCAAACATTACAATTATTGGTGAAGAGgtatctccatacattagttttgttcacttccaattacttgtgtgctttagttgcatgttttcagaagaaggtgcattttcactggtgatttggacttcatatttgcaactattacaatatgtttactacttaaattttgctgcag
||||| |||||||||| ||||| || || ||||||||  | ||||||||||| |||||||| |||||||| || |||||||| ||||||||| |    |    | |||   |||| ||| ||||||      | | |       |   |   | ||| | |  | ||  ||||   ||  |   ||||||||||                                        
TTGTAAGACTTATGGGTCGTGCTGCTTCCCACATTACGCTTGAGTGTGCTTTACAAACTCACCCAAACATAACCATTATTGGAGAAGAGgtaacgtttt----tggttgacttcaattcaaattaccgtaaagatatctgaatcttaatcgtgtagatgatagaattagactgcaaatcaga--ttcatatttgt---------------------------------------

upper sequence: Vv10s0116g00360.t01 (Vitis vinifera), 5'ss of exon 8
lower sequence: AT4G04040.1 (Arabidopsis thaliana), 5'ss of exon 8
TTGTACGACTTATGGGGCGTGCAGCCTCACACATTACATTGGAGTGTGCTTTGCAAACTCATCCAAACATTACAATTATTGGTGAAGAGgtatctccatacattagttttgttcacttccaattacttgtgtgctttagttgcatgttttcagaagaaggtgcattttcactggtgatttggacttcatatttgcaactattacaatatgtttactacttaaattttgctgcag
|||| || |||||||| ||||| || || ||||||||| | || || ||||||||||| |||||||||||||| |||||||| ||||||||| ||         |||        ||||   | | | |||   ||| |||   | | ||   || | |||        ||| |  |      |  ||||| ||||                                      
TTGTGCGTCTTATGGGTCGTGCTGCTTCTCACATTACACTTGAATGCGCTTTGCAAACCCATCCAAACATTACCATTATTGGAGAAGAGgtacctttg------agtcactcaagcttct--tcattcgtggtttttggtttgctatatttcaaatatggtttgaga--actagaaagc--accaacatatatgcag-------------------------------------

upper sequence: Vv10s0116g00360.t01 (Vitis vinifera), 5'ss of exon 8
lower sequence: EFJ13842 (Selaginella moellendorffii), 5'ss of exon 8
TTGTACGACTTATGGGGCGTGCAGCCTCACACATTACATTGGAGTGTGCTTTGCAAACTCATCCAAACATTACAATTATTGGTGAAGAGgtatctccatacattagttttgttcacttccaattacttgtgtgctttagttgcatgttttcagaagaaggtgcattttcactggtgatttggacttcatatttgcaactattacaatatgtttactacttaaattttgctgcag
|||| || |||||||| ||||||||||||||||| || || ||||||||| |||| || || |||||  |  |  |||| |||||||||||   || |      |    |    |  ||  ||   |||  |  || ||                                                                                               
TTGTCCGCCTTATGGGACGTGCAGCCTCACACATAACTTTAGAGTGTGCTCTGCAGACGCACCCAAATGTCGCTCTTATCGGTGAAGAGgtgcgtctactttcaacacatacggatgtcttatcctttgcctttttcag-----------------------------------------------------------------------------------------------

Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|161710861|gb|FC058565.1|FC058565
EST:     TGGAGTGTGCTTTGCAAACTCATCCAAACATTACAATTATTGGTGAAGAG                         GTTGCTGCTAAGAAGCTGACCCTGAAAAATGTTACAGACTACATTGTTGAT
genomic: TGGAGTGTGCTTTGCAAACTCATCCAAACATTACAATTATTGGTGAAGAGgtatctccat ... tttgctgcagGTTGCTGCTAAGAAGCTGACCCTGAAAAATGTTACAGACTACATTGTTGAT
EST: gi|37183710|gb|CF603064.1|CF603064
EST:     TGGAGTGTGCTTTGCAAACTCATCCAAACATTACAATTATTGGTGAAGAG                         GTTGCTGCTAAGAAGCTGACCCTGAAAAATGTTACAGACTACATTGTTGAT
genomic: TGGAGTGTGCTTTGCAAACTCATCCAAACATTACAATTATTGGTGAAGAGgtatctccat ... tttgctgcagGTTGCTGCTAAGAAGCTGACCCTGAAAAATGTTACAGACTACATTGTTGAT
EST: gi|110699977|gb|EE077493.1|EE077493
EST:     TGGAGTGTGCTTTGCAAACTCATCCAAACATTACAATTATTGGTGAAGAG                         GTTGCTGCTAAGAAGCTGACCCTGAAAAATGTTACAGACTACATTGTTGAT
genomic: TGGAGTGTGCTTTGCAAACTCATCCAAACATTACAATTATTGGTGAAGAGgtatctccat ... tttgctgcagGTTGCTGCTAAGAAGCTGACCCTGAAAAATGTTACAGACTACATTGTTGAT
EST: gi|110730531|gb|EE107719.1|EE107719
EST:     GGAGTGTGCTTTGCAAACTCATCCAAACATTACAATTATTTGGTGAAGAG                         GTTGCTGCTAAGAAGCTGACCCTGAAAAATGTTACAGACTACATTGTTGAT
genomic: GGAGTGTGCTTTGCAAACTCATCCAAACATTACAATTATT-GGTGAAGAGgtatctccat ... tttgctgcagGTTGCTGCTAAGAAGCTGACCCTGAAAAATGTTACAGACTACATTGTTGAT
EST: gi|71865073|gb|DT014128.1|DT014128
EST:     TGGAGTGTGCTTTGCAAACTCATCCAAACATTACAATTATTGGTGAAGAG                         GTTGCTGCTAAGAAGCTGACCCTGAAAAATGTTACAGACTACATTGTTGAT
genomic: TGGAGTGTGCTTTGCAAACTCATCCAAACATTACAATTATTGGTGAAGAGgtatctccat ... tttgctgcagGTTGCTGCTAAGAAGCTGACCCTGAAAAATGTTACAGACTACATTGTTGAT
EST: gi|110730571|gb|EE107799.1|EE107799
EST:     TGGAGTGTGCTTTGCAAACTCATCCAAACATTACAATTATTGGTGAAGAG                         GTTGCTGCTAAGAAGCTGACCCTGAAAAATGTTACAGACTACATTGTTGAT
genomic: TGGAGTGTGCTTTGCAAACTCATCCAAACATTACAATTATTGGTGAAGAGgtatctccat ... tttgctgcagGTTGCTGCTAAGAAGCTGACCCTGAAAAATGTTACAGACTACATTGTTGAT
EST: gi|161714537|gb|FC062987.1|FC062987
EST:     TGGAGTGTGCTTTGCAAACTCATCCAAACATTACAATTATTGGTGAAGAG                         GTTGCTGCTAAGAAGCTGACCCTGAAAAATGTTACAGACTACATTGTTGAT
genomic: TGGAGTGTGCTTTGCAAACTCATCCAAACATTACAATTATTGGTGAAGAGgtatctccat ... tttgctgcagGTTGCTGCTAAGAAGCTGACCCTGAAAAATGTTACAGACTACATTGTTGAT
EST: gi|71857501|gb|DT006556.1|DT006556
EST:     GGAGTGTGCTTTGAC-AACTCATCCAAACATTACAATTATTGGTGAAGAG                         GTTGCTGCTAAGAAGCTGACCCTGAAAAATGTTACAGACTACATTGTTGAT
genomic: GGAGTGTGCTTTG-CAAACTCATCCAAACATTACAATTATTGGTGAAGAGgtatctccat ... tttgctgcagGTTGCTGCTAAGAAGCTGACCCTGAAAAATGTTACAGACTACATTGTTGAT
EST: gi|161719694|gb|FC067068.1|FC067068
EST:     GGAGTGTGCTTTGCAAACTCATCCAAACATTACAATTATTGGTGAAGAG                         GTTGCTGCTAAGAAGCTGACCCTGAAAAATGTTACAGACTACATTGTTGAT
genomic: GGAGTGTGCTTTGCAAACTCATCCAAACATTACAATTATTGGTGAAGAGgtatctccat ... tttgctgcagGTTGCTGCTAAGAAGCTGACCCTGAAAAATGTTACAGACTACATTGTTGAT
EST: gi|27581975|gb|CB004670.1|CB004670
EST:     GCAAACTCATCCAAACATTACAATTATTGGTGAAGAG                         GTTGCTGCTAAGAAGCTGACCCTGAAAAATGTTACAGACTACATTGTTGAT
genomic: GCAAACTCATCCAAACATTACAATTATTGGTGAAGAGgtatctccat ... tttgctgcagGTTGCTGCTAAGAAGCTGACCCTGAAAAATGTTACAGACTACATTGTTGAT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TTGTACGACTTATGGGGCGTGCAGCCTCACACATTACATTGGAGTGTGCTTTGCAAACTCATCCAAACATTACAATTATTGGTGAAGAGgtatctccatacattagttttgttcacttccaattacttgtgtgctttagttgcatgttttcagaagaaggtgcattttcactggtgatttggacttcatatttgcaactattacaatatgtttactacttaaattttgctgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA