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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGGAGAGGTTGGAAAATGGATTGCTTTCATTGCAATTGTACTAAGGCTTTTCTTCCCTAGACATTTCCCAGgtatattctctatgcatgggtcgagtactgattgatgccatttttagttatttgcagcaataatgctgtgtatggaatttcatttttaaccaaacacttc...

Basic information

species Vitis vinifera
transcript Vv00s0207g00220.t01
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv00s0207g00220.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: GLYMA02G06850.1 (Glycine max), 5'ss of exon 3
AGGAGAGGTTGGAAAATGGATTGCTTTCATTGCAATTGTACTAAGGCTTTTCTTCCCTAGACATTTCCCAGgtatattctctatgcatgggtcgagtactgattgatgccatttttagttatttgca-gcaataatgctgtg-tatgga-atttcatttttaaccaaacacttc--
|||||| ||||||||||||||||| ||||| ||| | || || ||||||||||||||||||||||| || |||||  |     ||||   | | |  ||  ||| ||||   ||||| |||  |  |    ||| | | ||| |||| | |||||| ||    | |   | |||  
AGGAGAAGTTGGAAAATGGATTGCATTCATCGCAGTCGTGCTGAGGCTTTTCTTCCCTAGACATTTTCCTGgtatgcttaacttgca-atgcctaacac--atttatgca--ttttaattacctaaatatcatacttcagtggtatgaacatttcagttgggtcaatctaattcaa

upper sequence: Vv00s0207g00220.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: GLYMA16G25870.1 (Glycine max), 5'ss of exon 3
AGGAGAGGTTGGAAAATGGATTGCTTTCATTGCAATTGTACTAAGGCTTTTCTTCCCTAGACATTTCCCAGgtatattc------tctatgcatgggtcgagtactgattgatgccatttttagttatttgcagcaataatgctgtgtatggaatttcatttttaaccaaacacttc
|||||| ||||||||||||||||| ||||| ||| | ||  | ||||| || |||||||||||||| || |||||          | | |||||    |    |   |||||    ||||  | ||| ||  |  ||      ||| ||      |||||| |              
AGGAGAAGTTGGAAAATGGATTGCATTCATCGCAGTCGTGTTGAGGCTCTTTTTCCCTAGACATTTTCCCGgtatgcctaatacatttctgcattttacctaaataaattgaaaaaatttaaacttaatttta--aacttcattgtataacatggttcattgtgtgtttgggg----

upper sequence: Vv00s0207g00220.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: AT3G50830.1 (Arabidopsis thaliana), 5'ss of exon 3
AGGAGAGGTTGGAAAATGGATTGCTTTCATTGCAATTGTACTAAGGCTTTTCTTCCCTAGACATTTCCCAGgt-atattctctatgcatgggtcgagtactgattgatgccatttttagttatttgcagcaataatgctgtgtatggaatttc------atttttaaccaaacacttc-------------------------------------------------------------------------------
 ||||| ||||| ||||||||||||||| ||||  |||| || || |||||||||||||  |||||||||||| ||    |||    ||   ||  |   ||  |  |   ||| || || ||    | |  | | | ||| |   |||| |         ||| |  ||||    |                                                                                
TGGAGATGTTGGGAAATGGATTGCTTTCGTTGCGGTTGTTCTCAGACTTTTCTTCCCTAAGCATTTCCCAGgtgatgacatcttcatatcattcttgatttgtatctttgtattgtt-gtcataca-atcgctgaagatgtctcgagaatctttaaaatgctttgaggcaaatctatactaacattcaagtcagtgtaattgctgaaacaaaattaaagtctcacacttttgttattgtggttttcaaaatgtgcag

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|110385431|gb|EC949956.1|EC949956
EST:     TGCTTTCATTGCAATTGTACTAAGGCTTTTCTTCCCTAGACATTTCCCAG                         ACTGGCTGGAGATGCCCGGGTCCTTAATTCTTCTTCTGGTTGTGGCTCCCA
genomic: TGCTTTCATTGCAATTGTACTAAGGCTTTTCTTCCCTAGACATTTCCCAGgtatattctc ... ggtgatgcagACTGGCTGGAGATGCCCGGGTCCTTAATTCTTCTTCTGGTTGTGGCTCCCA
EST: gi|110364615|gb|EC927998.1|EC927998
EST:     TGCTTTCATTGCAATTGTACTAAGGCTTTTCTTCCCTAGACATTTCCCAG                         ACTGGCTGGAGATGCCCGGGTCATTAATTCTTCTTCTGGTTGTGGCTCCCA
genomic: TGCTTTCATTGCAATTGTACTAAGGCTTTTCTTCCCTAGACATTTCCCAGgtatattctc ... ggtgatgcagACTGGCTGGAGATGCCCGGGTCCTTAATTCTTCTTCTGGTTGTGGCTCCCA
EST: gi|110378448|gb|EC943581.1|EC943581
EST:     TGCTTTCATTGCAATTGTACTAAGGCTTTTCTTCCCTAGACATTTCCCAG                         ACTGGCTGGAGATGCCCGGGTCCTTAATTCTTCTTCTGGTTGTGGCTCCCA
genomic: TGCTTTCATTGCAATTGTACTAAGGCTTTTCTTCCCTAGACATTTCCCAGgtatattctc ... ggtgatgcagACTGGCTGGAGATGCCCGGGTCCTTAATTCTTCTTCTGGTTGTGGCTCCCA
EST: gi|110402069|gb|EC968702.1|EC968702
EST:     TGCTTTCATTGCAATTGTACTAAGGCTTTTCTTCCCTAGACATTTCCCAG                         ACTGGCTGGAGATGCCCGGGTCCTTAATTCTTCTTCTGGTTGTGGCTCCCA
genomic: TGCTTTCATTGCAATTGTACTAAGGCTTTTCTTCCCTAGACATTTCCCAGgtatattctc ... ggtgatgcagACTGGCTGGAGATGCCCGGGTCCTTAATTCTTCTTCTGGTTGTGGCTCCCA
EST: gi|110399404|gb|EC965908.1|EC965908
EST:     TGCTTTCATTGCAATTGTACTAAGGCTTTTCTTCCCTAGACATTTCCCAG                         ACTGGCTGGAGATGCCCGGGTCCTTAATTCTTCTTCTGGTTGTGGCTCCCA
genomic: TGCTTTCATTGCAATTGTACTAAGGCTTTTCTTCCCTAGACATTTCCCAGgtatattctc ... ggtgatgcagACTGGCTGGAGATGCCCGGGTCCTTAATTCTTCTTCTGGTTGTGGCTCCCA
EST: gi|110389361|gb|EC954190.1|EC954190
EST:     TGCTTTCATTGCAATTGTACTAAGGCTTTTCTTCCCTAGACATTTCCCAG                         ACTGGCTGGAGATGCCCGGGTCCTTAATTCTTCTTCTGGTTGTGGCTCCCA
genomic: TGCTTTCATTGCAATTGTACTAAGGCTTTTCTTCCCTAGACATTTCCCAGgtatattctc ... ggtgatgcagACTGGCTGGAGATGCCCGGGTCCTTAATTCTTCTTCTGGTTGTGGCTCCCA
EST: gi|110402082|gb|EC968715.1|EC968715
EST:     TGCTTTCATTGCAATTGTACTAAGGCTTTTCTTCCCTAGACATTTCCCAG                         ACTGGCTGGAGATGCCCGGGTCCTTAATTCTTCTTCTGGTTGTGGCTCCCA
genomic: TGCTTTCATTGCAATTGTACTAAGGCTTTTCTTCCCTAGACATTTCCCAGgtatattctc ... ggtgatgcagACTGGCTGGAGATGCCCGGGTCCTTAATTCTTCTTCTGGTTGTGGCTCCCA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGGAGAGGTTGGAAAATGGATTGCTTTCATTGCAATTGTACTAAGGCTTTTCTTCCCTAGACATTTCCCAGgtatattctctatgcatgggtcgagtactgattgatgccatttttagttatttgcagcaataatgctgtgtatggaatttcatttttaaccaaacacttc

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gcaataa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aaccaaa