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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGAGTTTGATGAGGAAGGAAAAGCTGTTGGTGTTACATCAGAAGGGGAAACTGCTAGGTGCAAGAAAGTTGTCTGTGATCCTTCCTATTTGCCCAACAAGgtaatttgtttgaatgccttgttgatattattccatagcggcttttaggcatacacaatataagtctgcttttagttacccattttatttgtaagagatt...

Basic information

species Vitis vinifera
transcript Vv05s0094g01550.t01
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv05s0094g01550.t01 (Vitis vinifera), 5'ss of exon 9
lower sequence: GLYMA08G13300.3 (Glycine max), 5'ss of exon 9
AGAGTTTGATGAGGAAGGAAAAGCTGTTGGTGTTACATCAGAAGGGGAAACTGCTAGGTGCAAGAAAGTTGTCTGTGATCCTTCCTATTTGCCCAACAAGgtaatttgtttgaatgccttgttgatattattccatagcggctttta-ggcatacacaatataagtctgcttttagttacccattttatttgtaagagatt--
||| ||||||||||||||||| | ||||||||| ||||| |||||||||||||| | |||||| |||||||| |||||||| || |||||||||  ||||||| |       ||   || |||   | ||||    | | | |     |      |||    ||   ||  |||  |||   | | ||   |  |     |  
AGAATTTGATGAGGAAGGAAAGGTTGTTGGTGTCACATCTGAAGGGGAAACTGCAAAGTGCAAAAAAGTTGTTTGTGATCCATCATATTTGCCCGGCAAGgtattagaaaccaacctctagtttg-actatttgcaaccagttcaggtgatggtgacagcgaaaaattg--tttgcttataaagtctaggagccatgctatgc

upper sequence: Vv05s0094g01550.t01 (Vitis vinifera), 5'ss of exon 9
lower sequence: GLYMA05G30140.2 (Glycine max), 5'ss of exon 9
AGAGTTTGATGAGGAAGGAAAAGCTGTTGGTGTTACATCAGAAGGGGAAACTGCTAGGTGCAAGAAAGTTGTCTGTGATCCTTCCTATTTGCCCAACAAGgtaatttgtttgaatgccttgttgatattattccatagcggcttttaggcatacacaatataagtctgcttttagttacccattttatttgtaagagatt------
||| ||||||||||||||||| | ||||||||||||||| |||||||||||||| | ||| || |||||||| |||||||| || ||||||||   ||||||| |       ||   || |||   | ||||  | | |  | || |||     |   |   |||      ||  || |   |    | |   ||  ||       
AGAATTTGATGAGGAAGGAAAGGTTGTTGGTGTTACATCTGAAGGGGAAACTGCAAAGTGTAAAAAAGTTGTTTGTGATCCATCATATTTGCCTGGCAAGgtattagaaaccaacctctagttt-cactattt-acaacc-cgttcaggtg---atggtgagagtgaaaaattgcttgcttctaaagtctaggagtcatgctatgt

upper sequence: Vv05s0094g01550.t01 (Vitis vinifera), 5'ss of exon 9
lower sequence: PP1S20_16V6.1 (Physcomitrella patens), 5'ss of exon 9
AGAGTTTGATGAGGAAGGAAAAGCTGTTGGTGTTACATCAGAAGGGGAAACTGCTAGGTGCAAGAAAGTTGTCTGTGATCCTTCCTATTTGCCCAACAAGgtaatttg----tttgaatg-ccttgttgatattattccatagcggcttttaggcatacacaatataagtctgct--tttagttacccattttatttgtaagagatt-------------
||| ||||||||    ||  ||| | | || ||||| || || ||||| || |  | |  |||||||||||| |||||||| || ||||||||||| |||||||||||    |||||| | |||| ||   | | | || ||  |  || ||| |     ||     | ||  ||    |    |||  | | |    |  ||                 
AGAATTTGATGAAATGGGTCAAGTTATGGGGGTTACTTCCGAGGGGGAGACCGTGAAGGCCAAGAAAGTTGTTTGTGATCCATCGTATTTGCCCAATAAGgtaatttgctgatttgaaggtccttattagcactgtgcc-tatggctttgtagactatatcacggcgaatcatctaacgtgtccacctttgtgaaacatgggatgccgttgctttctcag

upper sequence: Vv05s0094g01550.t01 (Vitis vinifera), 5'ss of exon 9
lower sequence: PP1S100_23V6.1 (Physcomitrella patens), 5'ss of exon 9
AGAGTTTGATGAGGAAGGAAAAGCTGTTGGTGTTACATCAGAAGGGGAAACTGCTAGGTGCAAGAAAGTTGTCTGTGATCCTTCCTATTTGCCCAACAAGgtaatttgtttgaat---gccttgttgatattattccatagcgg-cttttag-gcatacacaatataagtctgcttttagtt-acccattttatttgtaagagatt------------
 || |||||||||   ||  ||| ||| || || || || || || || || |  | |  |||||||||||| ||||| ||||| ||||||||||| |||||||||| | ||| |      |||||| ||  | || || | |  ||| ||| | |||       ||    || | |  ||| ||  ||   ||   ||| |                
TGAATTTGATGAGATGGGTCAAGTTGTGGGAGTCACCTCTGAGGGTGAGACCGTGAAGGCCAAGAAAGTTGTTTGTGACCCTTCATATTTGCCCAATAAGgtaatttttgtgatttgaaagttgttgctagcagtctatcgtgaacttgtagagaatagtaggcttacacatggtatgggttgacttatgcgatgcataaaaccacctgctcctccag

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|110701800|gb|EE079788.1|EE079788
EST:     CTGCTAGGTGCAAGAAAGTTGTCTGTGATCCTTCCTATTTGCCCAACAAG                         GTGAGGAAGGTTGGAAGGGTTGCTAGAGCAATCTGCATTATGAGCCACCCA
genomic: CTGCTAGGTGCAAGAAAGTTGTCTGTGATCCTTCCTATTTGCCCAACAAGgtaatttgtt ... attgcaccagGTGAGGAAGGTTGGAAGGGTTGCTAGAGCAATCTGCATTATGAGCCACCCA
EST: gi|110700674|gb|EE077534.1|EE077534
EST:     CTGCTAGGTGCAAGAAAGTTGTCTGTGATCCTTCCTATTTGCCCAACAAG                         GTGAGGAAGGTTGGAAGGGTTGCTAGAGCAATCTGCATTATGAGCCACCCA
genomic: CTGCTAGGTGCAAGAAAGTTGTCTGTGATCCTTCCTATTTGCCCAACAAGgtaatttgtt ... attgcaccagGTGAGGAAGGTTGGAAGGGTTGCTAGAGCAATCTGCATTATGAGCCACCCA
EST: gi|110371128|gb|EC934907.1|EC934907
EST:     CTGCTAGGTGCAAGAAAGTTGTCTGTGATCCTTCCTATTTGCCCAACAAG                         GTGAGGAAGGTTGGAAGGGTTGCTAGAGCAATCTGCATTATGAGCCACCCA
genomic: CTGCTAGGTGCAAGAAAGTTGTCTGTGATCCTTCCTATTTGCCCAACAAGgtaatttgtt ... attgcaccagGTGAGGAAGGTTGGAAGGGTTGCTAGAGCAATCTGCATTATGAGCCACCCA
EST: gi|33406671|gb|CF212298.1|CF212298
EST:     TTGCCCAACAAG                         GTGAGGAAGGTTGGAAGGGTTGCTAGAGCAATCTGCATTATGAGCCACCCA
genomic: TTGCCCAACAAGgtaatttgtt ... attgcaccagGTGAGGAAGGTTGGAAGGGTTGCTAGAGCAATCTGCATTATGAGCCACCCA
EST: gi|352782310|gb|FQ470212.1|FQ470212
EST:     GTGCAAGAAAGTTGTCTGTGATCCTTCCTATTTGCCCAACAAG                         GTGAGGAAGGTTGGAAGGGTTGCTAGAGCAATCTGCATTATGAGCCACCCA
genomic: GTGCAAGAAAGTTGTCTGTGATCCTTCCTATTTGCCCAACAAGgtaatttgtt ... attgcaccagGTGAGGAAGGTTGGAAGGGTTGCTAGAGCAATCTGCATTATGAGCCACCCA
EST: gi|110692608|gb|EE072046.1|EE072046
EST:     CTGCTAGGTGCAAGAAAGTTGTCTGTGATCCTTCCTATTTGCCCAACAAG                         GTGAGGAAGGTTGGAAGGGTTGCTAGAGCAATCTGCATTATGAGCCACCCA
genomic: CTGCTAGGTGCAAGAAAGTTGTCTGTGATCCTTCCTATTTGCCCAACAAGgtaatttgtt ... attgcaccagGTGAGGAAGGTTGGAAGGGTTGCTAGAGCAATCTGCATTATGAGCCACCCA
EST: gi|110731100|gb|EE108936.1|EE108936
EST:     CTGCTAGGTGCAAGAAAGTTGTCTGTGATCCTTCCTATTTGCCCAACAAG                         GTGAGGAAGGTTGGAAGGGTTGCTAGAGCAATCTGCATTATGAGCCACCCA
genomic: CTGCTAGGTGCAAGAAAGTTGTCTGTGATCCTTCCTATTTGCCCAACAAGgtaatttgtt ... attgcaccagGTGAGGAAGGTTGGAAGGGTTGCTAGAGCAATCTGCATTATGAGCCACCCA
EST: gi|110700715|gb|EE077610.1|EE077610
EST:     CTGCTAGGTGCAAGAAAGTTGTCTGTGATCCTTCCTATTTGCCCAACAAG                         GTGAGGAAGGTTGGAAGGGTTGCTAGAGCAATCTGCATTATGAGCCACCCA
genomic: CTGCTAGGTGCAAGAAAGTTGTCTGTGATCCTTCCTATTTGCCCAACAAGgtaatttgtt ... attgcaccagGTGAGGAAGGTTGGAAGGGTTGCTAGAGCAATCTGCATTATGAGCCACCCA
EST: gi|30137389|gb|CB922727.1|CB922727
EST:     CTGCTAGGTGCAAGAAAGTTGTCTGTGATCCTTCCTATTTGCCCAACAAG                         GTGAGGAAGGTTGGAAGGGTTGCTAGAGCAATCTGCATTATGAGCCACCCA
genomic: CTGCTAGGTGCAAGAAAGTTGTCTGTGATCCTTCCTATTTGCCCAACAAGgtaatttgtt ... attgcaccagGTGAGGAAGGTTGGAAGGGTTGCTAGAGCAATCTGCATTATGAGCCACCCA
EST: gi|33406756|gb|CF212383.1|CF212383
EST:     CTGCTAGGTGCAAGAAAGTTGTCTGTGATCCTTCCTATTTGCCCAACAAG                         GTGAGGAAGGTTGGAAGGGTTGCTAGAGCAATCTGCATTATGAGCCACCCA
genomic: CTGCTAGGTGCAAGAAAGTTGTCTGTGATCCTTCCTATTTGCCCAACAAGgtaatttgtt ... attgcaccagGTGAGGAAGGTTGGAAGGGTTGCTAGAGCAATCTGCATTATGAGCCACCCA
EST: gi|110371769|gb|EC935892.1|EC935892
EST:     AAAGTTGTCTGTGATCCTTCCTATTTGCCCAACAAG                         GTGAGGAAGGTTGGAAGGGTTGCTAGAGCAATCTGCATTATGAGCCACCCA
genomic: AAAGTTGTCTGTGATCCTTCCTATTTGCCCAACAAGgtaatttgtt ... attgcaccagGTGAGGAAGGTTGGAAGGGTTGCTAGAGCAATCTGCATTATGAGCCACCCA
EST: gi|37183843|gb|CF603197.1|CF603197
EST:     CTGCTAGGTGCAAGAAAGTTGTCTGTGATCCTTCCTATTTGCCCAACAAG                         GTGAGGAAGGTTGGAAGGGTTGCTAGAGCAATCTCCATTATGAGCCACCCA
genomic: CTGCTAGGTGCAAGAAAGTTGTCTGTGATCCTTCCTATTTGCCCAACAAGgtaatttgtt ... attgcaccagGTGAGGAAGGTTGGAAGGGTTGCTAGAGCAATCTGCATTATGAGCCACCCA
EST: gi|352768234|gb|FQ469409.1|FQ469409
EST:     TGATCCTTCCTATTTGCCCAACAAG                         GTGAGGAAGGTTGGAAGGGTTGCTAGAGCAATCTGCATTATGAGCCACCCA
genomic: TGATCCTTCCTATTTGCCCAACAAGgtaatttgtt ... attgcaccagGTGAGGAAGGTTGGAAGGGTTGCTAGAGCAATCTGCATTATGAGCCACCCA
EST: gi|71888788|gb|DT037843.1|DT037843
EST:     CTGCTAGGTGCAAGAAAGTTGTCTGTGATCCTTCCTATTTGCCCAACAAG                         GTGAGGAAGGTTGGAAGGGTTGCTAGAGCAATCTGCATTATGAGCCACCCA
genomic: CTGCTAGGTGCAAGAAAGTTGTCTGTGATCCTTCCTATTTGCCCAACAAGgtaatttgtt ... attgcaccagGTGAGGAAGGTTGGAAGGGTTGCTAGAGCAATCTGCATTATGAGCCACCCA
EST: gi|110418003|gb|EC984109.1|EC984109
EST:     GGTGCAAGAAAGTTGTCTGTGATCCTTCCTATTTGCCCAACAAG                         GTGAGGAAGGTTGGAAGGGTTGCTAGAGCAATCTGCATTATGAGCCACCCA
genomic: GGTGCAAGAAAGTTGTCTGTGATCCTTCCTATTTGCCCAACAAGgtaatttgtt ... attgcaccagGTGAGGAAGGTTGGAAGGGTTGCTAGAGCAATCTGCATTATGAGCCACCCA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGAGTTTGATGAGGAAGGAAAAGCTGTTGGTGTTACATCAGAAGGGGAAACTGCTAGGTGCAAGAAAGTTGTCTGTGATCCTTCCTATTTGCCCAACAAGgtaatttgtttgaatgccttgttgatattattccatagcggcttttaggcatacacaatataagtctgcttttagttacccattttatttgtaagagatt

- - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aagagat