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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAACCAGTTTCCCATGTGGTTGCCCGCCCTTCCCCAAATGATATTCTTGAGTGGCgtaagttgcatctatctctatctctttgctttctacttcaattaaattttccttttagagaaactgaaccttttctagataaggctatactgtgattgat...

Basic information

species Vitis vinifera
transcript Vv09s0002g00280.t01
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv09s0002g00280.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: GLYMA07G05170.1 (Glycine max), 5'ss of exon 3
GAACCAGTTTCCCATGTGGTTGCCCGCCCTTCCCCAAATGATATTCTTGAGTGGCgtaagttgcatctat-ctctatctctttgctttctacttcaattaaattttccttttagagaaactgaaccttttctagataaggctatactgtgattgat
|| |||||||| ||||| || || || ||||| |||| ||||||||||||||||||||||||   |  || || |  |  ||    |  || ||    | |  | || | ||    ||   |||     |   | | |  |  | || |     | 
GAGCCAGTTTCTCATGTTGTGGCTCGTCCTTCTCCAAGTGATATTCTTGAGTGGCgtaagtttgtttcatactgttacatttcttatattatttatgctgagctctcatgttcagaaagaagaaaaagattatgttgaacccttgctatatcata-

upper sequence: Vv09s0002g00280.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: GLYMA16G01680.2 (Glycine max), 5'ss of exon 3
GAACCAGTTTCCCATGTGGTTGCCCGCCCTTCCCCAAATGATATTCTTGAGTGGCgtaagttgcatctatctctatctctttgctt---tctacttcaattaaattttccttttagagaaactgaaccttttctagataaggctatactgtgattgat
|| |||||||| ||||| || || || ||||| || | ||||||||||||||||||||||||   | |  | || |  | || |||   |  | ||   ||||  | |  | ||    ||   |||     |   | | |  || |  | |   | ||
GAGCCAGTTTCTCATGTTGTGGCTCGTCCTTCACCGAGTGATATTCTTGAGTGGCgtaagtt-tgtttcacactgttccatttcttatattaatttatgttaagctctaatgttcagcaagaagaaaaagattatgttgaacctttgatata--tcat

upper sequence: Vv09s0002g00280.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: AT1G17280.1 (Arabidopsis thaliana), 5'ss of exon 3
GAACCAGTTTCCCATGTGGTTGCCCGCCCTTCCCCAAATGATATTCTTGAGTGGCgtaagttgcatctatctctatctctttgctttctacttcaattaaattttccttttagagaaactgaaccttttctagataag-gctatactgtg-attgat-
|||||||| |||||||| ||||| || |||||||||||||| ||||| ||||||||||||      |||||| | | ||||    || || | |   |     ||||| | |         || | |||||| | |   | |||  |  | ||  || 
GAACCAGTCTCCCATGTTGTTGCTCGTCCTTCCCCAAATGACATTCTCGAGTGGCgtaagccttccctatctttttttcttaatctt-tattcctgctgg--cttcctgtaatcctgttgcaagcgtttctataaagatgttatgataagtatatatg

upper sequence: Vv09s0002g00280.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: AT5G50430.2 (Arabidopsis thaliana), 5'ss of exon 3
GAACCAGTTTCCCATGTGGTTGCCCGCCCTTCCCCAAATGATATTCTTGAGTGGCgtaagttgcatctatctctatctctttgctttctacttcaattaaattttccttttagagaaactgaaccttttctagataaggctatactgtgattgat-----
|||||||| || ||||| ||||| || |||||||||||||| |||||||| ||||||||||   ||||  || | |    || ||||   ||| | ||   | | | || |||  |  ||        | | | || ||  ||||||   ||        
GAACCAGTCTCGCATGTTGTTGCTCGTCCTTCCCCAAATGACATTCTTGAATGGCgtaagtcttatctggctatttaatgttcctttt--ctttattt---tctgctttctagttattctattgaaggtttggctatggggatactggctttaggtacat

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|34543477|gb|CF511709.1|CF511709
EST:     AGTTTCCCATGTGGTTGCCCGCCCTTCCCCAAATGATATTCTTGAGTGGC                         ATTATGTGCTGGAGGGAAGTGAGGGAACACCGTTTGCAG
genomic: AGTTTCCCATGTGGTTGCCCGCCCTTCCCCAAATGATATTCTTGAGTGGCgtaagttgca ... gatgtttcagATTATGTGCTGGAGGGAAGTGAGGGAACACCGTTTGCAG
EST: gi|161715609|gb|FC068353.1|FC068353
EST:     AGTTTCCCATGTGGTTGCCCGCCCTTCCCCAAATGATATTCTTGAGTGGC                         ATTATGTGCTGGAGGGAAGTGAGGGAACACCGTTTGCAG
genomic: AGTTTCCCATGTGGTTGCCCGCCCTTCCCCAAATGATATTCTTGAGTGGCgtaagttgca ... gatgtttcagATTATGTGCTGGAGGGAAGTGAGGGAACACCGTTTGCAG
EST: gi|110730040|gb|EE106668.1|EE106668
EST:     AGTTTCCCATGTGGTTGCCCGCCCTTCCCCAAATGATATTCTTGAGTGGC                         ATTATGTGCTGGAGGGAAGTGAGGGAACACCGTTTGCAG
genomic: AGTTTCCCATGTGGTTGCCCGCCCTTCCCCAAATGATATTCTTGAGTGGCgtaagttgca ... gatgtttcagATTATGTGCTGGAGGGAAGTGAGGGAACACCGTTTGCAG
EST: gi|294966722|gb|GW837741.1|GW837741
EST:     AGTTTCCCATGTGGTTGCCCGCCCTTCCCCAAATGATATTCTTGAGTGGC                         ATTATGTGCTGGAGGGAAGTGAGGGAACACCGTTTGCAG
genomic: AGTTTCCCATGTGGTTGCCCGCCCTTCCCCAAATGATATTCTTGAGTGGCgtaagttgca ... gatgtttcagATTATGTGCTGGAGGGAAGTGAGGGAACACCGTTTGCAG
EST: gi|26257010|gb|CA808073.1|CA808073
EST:     AGTTTCCCATGTGGTTGCCCGCCCTTCCCCAAATGATATTCTTGAGTGGC                         ATTATGTGCTGGAGGGAAGTGAGGGAACACCGTTTGCAG
genomic: AGTTTCCCATGTGGTTGCCCGCCCTTCCCCAAATGATATTCTTGAGTGGCgtaagttgca ... gatgtttcagATTATGTGCTGGAGGGAAGTGAGGGAACACCGTTTGCAG
EST: gi|110728958|gb|EE104982.1|EE104982
EST:     AGTTTCCCATGTGGTTGCCCGCCCTTCCCCAAATGATATTCTTGAGTGGC                         ATTATGTGCTGGAGGGAAGTGAGGGAACACCGTTTGCAG
genomic: AGTTTCCCATGTGGTTGCCCGCCCTTCCCCAAATGATATTCTTGAGTGGCgtaagttgca ... gatgtttcagATTATGTGCTGGAGGGAAGTGAGGGAACACCGTTTGCAG
EST: gi|110713617|gb|EE089696.1|EE089696
EST:     AGTTTCCCATGTGGTTGCCCGCCCTTCCCCAAATGATATTCTTGAGTGGC                         ATTATGTGCTGGAGGGAAGTGAGGGAACACCGTTTGCAG
genomic: AGTTTCCCATGTGGTTGCCCGCCCTTCCCCAAATGATATTCTTGAGTGGCgtaagttgca ... gatgtttcagATTATGTGCTGGAGGGAAGTGAGGGAACACCGTTTGCAG
EST: gi|110726385|gb|EE102119.1|EE102119
EST:     AGTTTCCCATGTGGTTGCCCGCCCTTCCCCAAATGATATTCTTGAGTGGC                         ATTATGTGCTGGAGGGAAGTGAGGGAACACCGTTTGCAG
genomic: AGTTTCCCATGTGGTTGCCCGCCCTTCCCCAAATGATATTCTTGAGTGGCgtaagttgca ... gatgtttcagATTATGTGCTGGAGGGAAGTGAGGGAACACCGTTTGCAG
EST: gi|77587429|gb|DV222858.1|DV222858
EST:     AGTTTCCCATGTGGTTGCCCGCCCTTCCCCAAATGATATTCTTGAGTGGC                         ATTATGTGCTGGAGGGAAGTGAGGGAACACCGTTTGCAG
genomic: AGTTTCCCATGTGGTTGCCCGCCCTTCCCCAAATGATATTCTTGAGTGGCgtaagttgca ... gatgtttcagATTATGTGCTGGAGGGAAGTGAGGGAACACCGTTTGCAG
EST: gi|34543563|gb|CF511795.1|CF511795
EST:     AGTTTCCCATGTGGTTGCCCGCCCTTCCCCAAATGATATTCTTGAGTGGC                         ATTATGTGCTGGAGGGAAGTGAGGGAACACCGTTTGCAG
genomic: AGTTTCCCATGTGGTTGCCCGCCCTTCCCCAAATGATATTCTTGAGTGGCgtaagttgca ... gatgtttcagATTATGTGCTGGAGGGAAGTGAGGGAACACCGTTTGCAG
EST: gi|110732339|gb|EE107537.1|EE107537
EST:     AGTTTCCCATGTGGTTGCCCGCCCTTCCCCAAATGATATTCTTGAGTGGC                         ATTATGTGCTGGAGGGAAGTGAGGGAACACCGTTTGCAG
genomic: AGTTTCCCATGTGGTTGCCCGCCCTTCCCCAAATGATATTCTTGAGTGGCgtaagttgca ... gatgtttcagATTATGTGCTGGAGGGAAGTGAGGGAACACCGTTTGCAG
EST: gi|110721123|gb|EE097761.1|EE097761
EST:     AGTTTCCCATGTGGTTGCCCGCCCTTCCCCAAATGATATTCTTGAGTGGC                         ATTATGTGCTGGAGGGAAGTGAGGGAACACCGTTTGCAG
genomic: AGTTTCCCATGTGGTTGCCCGCCCTTCCCCAAATGATATTCTTGAGTGGCgtaagttgca ... gatgtttcagATTATGTGCTGGAGGGAAGTGAGGGAACACCGTTTGCAG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GAACCAGTTTCCCATGTGGTTGCCCGCCCTTCCCCAAATGATATTCTTGAGTGGCgtaagttgcatctatctctatctctttgctttctacttcaattaaattttccttttagagaaactgaaccttttctagataaggctatactgtgattgat

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aattaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - agagaaa