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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ACGTACGAGATCTCATTTACCGAGAGATTCTTGAGTACCATCCAAAGATGTTGAAAGAGTACTTAGAGGGAACCGAACCAACAAGCTTCATGTATCCAAGgtattgttatttgaaacttttaattgttaatttttaacccaacttctgggccaattactgtattgaacatctttttaatgttcatgacctcacctgatgc...

Basic information

species Vitis vinifera
transcript Vv05s0020g02530.t01
intron # 7
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv05s0020g02530.t01 (Vitis vinifera), 5'ss of exon 7
lower sequence: GRMZM2G017351_T01 (Zea mays), 5'ss of exon 6
ACGTACGAGATCTCATTTACCGAGAGATTCTTGAGTACCATCCAAAGATGTTGAAAGAGTACTTAGAGGGAACCGAACCAACAAGCTTCATGTATCCAAGgtattg--ttatttgaaacttttaattgttaa----tttttaacccaacttctgggccaattactgtattgaacatctttttaatgttcatgacctcacctgatgc
|| || | || || || ||  |||| ||||||||||| |||||||||||||||||||| |   | |||||||| ||  |||   | |||||||| ||||||| |     ||| |     |||| ||| || |     |||| ||| ||     | ||||| |   ||     |||  ||| | ||     | |    |  || |||
ACATAAGGGAACTTATATATAGAGAAATTCTTGAGTATCATCCAAAGATGTTGAAAGAATTTATTGAGGGAACTGAGTCAAGTGGTTTCATGTACCCAAGgtgtgtacctatgttgctgttttcattatttaacatcttttgaccgaaaa---gtgccaaatttagtccgagacagttttgtcatacctgttat---atatgttgc

upper sequence: Vv05s0020g02530.t01 (Vitis vinifera), 5'ss of exon 7
lower sequence: GLYMA13G28120.2 (Glycine max), 5'ss of exon 7
ACGTACGAGATCTCATTTACCGAGAGATTCTTGAGTACCATCCAAAGATGTTGAAAGAGTACTTAGAGGGAACCGAACCAACAAGCTTCATGTATCCAAGgtattgt-tatttgaaacttttaattgttaatttttaaccca--acttctgggccaattactgtattgaacatctttttaatgttcatgacctcacctgatgc
| |||||||| || || |||||||||||||| ||||| ||||||||||||||||| || |   |||||||| | || |||||| | ||||||||||||||||||||| ||  |     |   ||||  |  |||  | | ||  |   ||     ||  ||    |||    |   ||| |  || ||    |  ||| |   
ATGTACGAGAGCTTATATACCGAGAGATTCTGGAGTATCATCCAAAGATGTTGAAGGAATTTCTAGAGGGATCAGAGCCAACAGGTTTCATGTATCCAAGgtattgtctaaatctctatccaaatttctgttttgcacctcattagcacttcatgaacaacatatttgggggttggtttcac-ttgatattgttgcctaac--

upper sequence: Vv05s0020g02530.t01 (Vitis vinifera), 5'ss of exon 7
lower sequence: GLYMA17G02220.1 (Glycine max), 5'ss of exon 7
ACGTACGAGATCTCATTTACCGAGAGATTCTTGAGTACCATCCAAAGATGTTGAAAGAGTACTTAGAGGGAACCGAACCAACAAGCTTCATGTATCCAAGgtattgttatttgaaacttttaattgttaatttttaacccaacttctgggccaattac-tgtattgaacatctttttaatgttcatgacctca-cctgatgc--
|||| ||||| || || |||||||||||||| ||||||||||| |||||||| |||||  |  |||||||| |||| |||||| | ||||||||||||||||| | || |   ||   | | |     ||||| |    || |||||    |  || | ||  ||  |   |||  |    |  || |  ||| | |  |    
ACGTGCGAGAGCTTATATACCGAGAGATTCTGGAGTACCATCCGAAGATGTTAAAAGAACATCTAGAGGGAGCCGAGCCAACAGGATTCATGTATCCAAGgtactattgtccaaa---tctgaaccaaaatttctgtttca-cttctcattcttttgcatgagtttgaacacttgatgggatctatcaattcaacattgtttgg

upper sequence: Vv05s0020g02530.t01 (Vitis vinifera), 5'ss of exon 7
lower sequence: GLYMA07G38510.1 (Glycine max), 5'ss of exon 6
ACGTACGAGATCTCATTTACCGAGAGATTCTTGAGTACCATCCAAAGATGTTGAAAGAGTACTTAGAGGGAACCGAACCAACAAGCTTCATGTATCCAAGgtattgttatttgaaacttttaattgttaatttttaacccaacttctgggccaattac-tgtattgaacatctttttaatgttcatgacctca-cctgatgc--
| || ||||| || || |||||||||||||| |||||||||||||||||||| |||||  |  ||||||||   || |||||| | ||||||||||||||||| | || |   || ||   ||     || |||       ||||||    |  || | ||| ||  |   |||  |    |  || |  ||| | |  |    
ATGTGCGAGAGCTTATATACCGAGAGATTCTGGAGTACCATCCAAAGATGTTAAAAGAACATCTAGAGGGAGAAGAGCCAACAGGATTCATGTATCCAAGgtactattgtccaaacctg--aacca--aagtttctgtttcacttctcattcttttgcatgtgtttgaacacttgatgggatctataaattcaacattgtttga

upper sequence: Vv05s0020g02530.t01 (Vitis vinifera), 5'ss of exon 7
lower sequence: GLYMA15G10940.4 (Glycine max), 5'ss of exon 7
ACGTACGAGATCTCATTTACCGAGAGATTCTTGAGTACCATCCAAAGATGTTGAAAGAGTACTTAGAGGGAACCGAACCAACAAGCTTCATGTATCCAAGgtattgt-tatttgaaacttttaattgttaatttttaaccca--acttctgggccaattactgtattgaacatctttttaatgttcatgacctcacctgatgc
| |||||||| || || |||||||||| | | ||||||||||| ||||||||||| || |   |||| ||| | || |||||| | ||||||||||||||||||||| ||  |     |   |||| ||  |||  | | ||  |   ||     ||  ||    |||    |   ||| |   | ||    | || | |   
ATGTACGAGAGCTTATATACCGAGAGACTTTGGAGTACCATCCGAAGATGTTGAAGGAATTTCTAGAAGGAGCAGAGCCAACAGGTTTCATGTATCCAAGgtattgtctaaatctctatccaaatttttgttttgcaccgcattagcacttcatgaacaacatatttggttgttgctttcac-ctgatattgttacttcac--

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|110368230|gb|EC932201.1|EC932201
EST:     TTGAAAGAGTACTTAGAGGGAACCGAACCAACAAGCTTCATGTATCCAAG                         TGCTGTTGACCAGTTCAAGAAGCAATTCGCTT
genomic: TTGAAAGAGTACTTAGAGGGAACCGAACCAACAAGCTTCATGTATCCAAGgtattgttat ... ctctttttagTGCTGTTGACCAGTTCAAGAAGCAATTCGCTT
EST: gi|71863134|gb|DT012189.1|DT012189
EST:     TTGAAAGAGTACTTAGAGGGAACCGAACCAACAAGCTTCATGTATCCAAG                         TGCTGTTGACCAGTTCAAGAAGCAATTCGCTTATCTCGAGGAGCACTATGG
genomic: TTGAAAGAGTACTTAGAGGGAACCGAACCAACAAGCTTCATGTATCCAAGgtattgttat ... ctctttttagTGCTGTTGACCAGTTCAAGAAGCAATTCGCTTACCTCGAGGAGCACTACGG
EST: gi|294964202|gb|GW838005.1|GW838005
EST:     TTGAAAGAGTACTTAGAGGGAACCGAACCAACAAGCTTCATGTATCCAAG                         TGCTGTTGACCAGTTCAAGAAGCAATTCGCTTACCTCGAGGAGCACTACGG
genomic: TTGAAAGAGTACTTAGAGGGAACCGAACCAACAAGCTTCATGTATCCAAGgtattgttat ... ctctttttagTGCTGTTGACCAGTTCAAGAAGCAATTCGCTTACCTCGAGGAGCACTACGG
EST: gi|110690752|gb|EE068184.1|EE068184
EST:     TTGAAAGAGTACTTAGAGGGAACCGAACCAACAAGCTTCATGTATCCAAG                         TGCTGTTGACCAGTTCAAGAAGCAATTCGCTTACCTCGAGGAGCACTACGG
genomic: TTGAAAGAGTACTTAGAGGGAACCGAACCAACAAGCTTCATGTATCCAAGgtattgttat ... ctctttttagTGCTGTTGACCAGTTCAAGAAGCAATTCGCTTACCTCGAGGAGCACTACGG
EST: gi|161719505|gb|FC067398.1|FC067398
EST:     TTGAAAGAGTACTTAGAGGGAACCGAACCAACAAGCTTCATGTATCCAAG                         TGCTGTTGACCAGTTCAAGAAGCAATTCGCTTACCTCGAGGAGCACTACGG
genomic: TTGAAAGAGTACTTAGAGGGAACCGAACCAACAAGCTTCATGTATCCAAGgtattgttat ... ctctttttagTGCTGTTGACCAGTTCAAGAAGCAATTCGCTTACCTCGAGGAGCACTACGG
EST: gi|33404616|gb|CF210243.1|CF210243
EST:     TTGAAAGAGTACTTAGAGGGAACCGAACCAACAAGCTTCATGTATCCAAG                         TGCTGTTGACCAGTTCAAGAAGCAATTCGCTTACCTCGAGGAGCACTACGG
genomic: TTGAAAGAGTACTTAGAGGGAACCGAACCAACAAGCTTCATGTATCCAAGgtattgttat ... ctctttttagTGCTGTTGACCAGTTCAAGAAGCAATTCGCTTACCTCGAGGAGCACTACGG
EST: gi|156735426|gb|EV239547.1|EV239547
EST:     TTGAAAGAGTACTTAGAGGGAACCGAACCACCCTTCTTCATGTATCCAAG                         TGCTGTTGACCAGTTCAAGAAGCAATTCGCTTACCTCGAGGAGCACTACGG
genomic: TTGAAAGAGTACTTAGAGGGAACCGAACCAACAAGCTTCATGTATCCAAGgtattgttat ... ctctttttagTGCTGTTGACCAGTTCAAGAAGCAATTCGCTTACCTCGAGGAGCACTACGG
EST: gi|71860512|gb|DT009567.1|DT009567
EST:     TTGAAAGAGTACTTAGAGGGAACCGAACCAACAAGCTTCATGTATCCAAG                         TGCTGTTGACCAGTTCAAGAAGCAATTCGCTTATCTCGAGGAGCACTATGG
genomic: TTGAAAGAGTACTTAGAGGGAACCGAACCAACAAGCTTCATGTATCCAAGgtattgttat ... ctctttttagTGCTGTTGACCAGTTCAAGAAGCAATTCGCTTACCTCGAGGAGCACTACGG
EST: gi|37188545|gb|CF607894.1|CF607894
EST:     TTGAAAGAGTACTTAGAGGGAACCGAACCAACAAGCTTCATGTATCCAAG                         TGCTGTTGACCAGTTCAAGAAGCAATTCGCTTACCTCGAGGAGCACTACGG
genomic: TTGAAAGAGTACTTAGAGGGAACCGAACCAACAAGCTTCATGTATCCAAGgtattgttat ... ctctttttagTGCTGTTGACCAGTTCAAGAAGCAATTCGCTTACCTCGAGGAGCACTACGG
EST: gi|110730439|gb|EE107523.1|EE107523
EST:     TTGAAAGAGTACTTAGAGGGAACCGAACCAACAAGCTTCATGTATCCAAG                         TGCTGTTGACCAGTTCAAGAAGCAATTCGCTTACCTCGAGGAGCACTACGG
genomic: TTGAAAGAGTACTTAGAGGGAACCGAACCAACAAGCTTCATGTATCCAAGgtattgttat ... ctctttttagTGCTGTTGACCAGTTCAAGAAGCAATTCGCTTACCTCGAGGAGCACTACGG
EST: gi|110387017|gb|EC951656.1|EC951656
EST:     TTGAAAGAGTACTTAGAGGGAACCGAACCAACAAGCTTCATGTATCCAAG                         TGCTGTTGACCAGTTCAAGAAGCAATTCGCTTACCTCGAGGAGCACTACGG
genomic: TTGAAAGAGTACTTAGAGGGAACCGAACCAACAAGCTTCATGTATCCAAGgtattgttat ... ctctttttagTGCTGTTGACCAGTTCAAGAAGCAATTCGCTTACCTCGAGGAGCACTACGG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ACGTACGAGATCTCATTTACCGAGAGATTCTTGAGTACCATCCAAAGATGTTGAAAGAGTACTTAGAGGGAACCGAACCAACAAGCTTCATGTATCCAAGgtattgttatttgaaacttttaattgttaatttttaacccaacttctgggccaattactgtattgaacatctttttaatgttcatgacctcacctgatgc

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAAGCT