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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGAAGGGACTTACTCTTGTTACAACATCATTTGACGGTTATTTGTACCTTATAGATGGACCCACATCATGTGCTGATGTTGTTGATATTGGTGAAACTTCgtaagttatcctccactactattcatgtttagttttactgtttaatttttcaaaatttgtttaaaatataaatgcctttattacag

Basic information

species Vitis vinifera
transcript Vv08s0007g01790.t01
intron # 10
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv08s0007g01790.t01 (Vitis vinifera), 5'ss of exon 10
lower sequence: GLYMA01G27250.2 (Glycine max), 5'ss of exon 10
AGAAGGGACTTACTCTTGTTACAACATCATTTGACGGTTATTTGTACCTTATAGATGGACCCACATCATGTGCTGATGTTGTTGATATTGGTGAAACTTCgtaagttatcctccactactattcatgtttagttttactgtttaatttttcaaaatttgtttaaaatataaatgcctttattacag
 ||||||| | ||| ||||||| ||||||||||| |||||||||||||| || |||||||| ||   |||||||||||||||||| |||||||||||||||||||  || ||  |       || ||  ||   || ||||   | |||    || || | |   ||          ||  |||||
GGAAGGGATTAACTATTGTTACCACATCATTTGATGGTTATTTGTACCTCATTGATGGACCTACTGGATGTGCTGATGTTGTTGACATTGGTGAAACTTCgtaagagattctttaacctgtctcttgaatatgctttctgtcctactttcttgaagttatgtgccat--------tctttctacag

upper sequence: Vv08s0007g01790.t01 (Vitis vinifera), 5'ss of exon 10
lower sequence: GLYMA03G14690.1 (Glycine max), 5'ss of exon 12
AGAAGGGACTTACTCTTGTTACAACATCATTTGACGGTTATTTGTACCTTATAGATGGACCCACATCATGTGCTGATGTTGTTGATATTGGTGAAACTTCgtaagttatcctcca-ctactat-tcatgtttagttttactgtttaatttttcaaaatttgtttaaaatataaatgcctttattacag
|||||||| | ||| ||||||| ||||||||||| |||||||||||||| || |||||||| ||   ||||||||||| |||||| |||||||||||||||||||  || ||  | ||  ||| ||  |  ||   || |||||  | |||    || || | |   ||         ||| ||||||
AGAAGGGATTAACTATTGTTACCACATCATTTGATGGTTATTTGTACCTCATTGATGGACCTACTGGATGTGCTGATGCTGTTGACATTGGTGAAACTTCgtaagagattctttaactgttatctctcggatatgctttctgttctactttcttgaagttatgtgccat--------tttttttacag

upper sequence: Vv08s0007g01790.t01 (Vitis vinifera), 5'ss of exon 10
lower sequence: AT3G09090.2 (Arabidopsis thaliana), 5'ss of exon 10
AGAAGGGACTTACTCTTGTTACAACATCATTTGACGGTTATTTGTACCTTATAGATGGACCCACATCATGTGCTGATGTTGTTGATATTGGTGAAACTTCgtaagttatcctccactactattcatgtttagt---tttactgtttaatttttcaaaatttgtttaaaatataaatgcctttattacag
||||||| || ||  | ||||| ||||| |||||||||||  |||| || |||||||||||||| || ||  |||| |||||||| ||||| |||||||||||||| |   |    | || |       || |   |||| | |||       |||  | | ||  |  || |                
AGAAGGGTCTCACCATCGTTACTACATCCTTTGACGGTTACCTGTATCTCATAGATGGACCCACCTCGTGCACTGACGTTGTTGACATTGGCGAAACTTCgtaagtcacttttgcttcctctcggcacgtaatatctttagtattttgaccaccaatgtct-ttcgagttacag---------------

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|351053644|gb|FQ440153.1|FQ440153
EST:     ATAGATGGACCCACATCGTGTGCTGATGTTGTTGATATTGGTGAAACTTC                         ATATAGCATGGTCCTGGCGGACAATGTTGATGGTGGAGATGATCTTGATCT
genomic: ATAGATGGACCCACATCATGTGCTGATGTTGTTGATATTGGTGAAACTTCgtaagttatc ... tttattacagATATAGCATGGTCCTGGCGGACAATGTTGATGGTGGAGATGATCTTGATCT
EST: gi|56409013|gb|CX017265.1|CX017265
EST:     ATAGATGGACCCACATCATGTGCTGATGTTGTTGATATTGGTGAAACTTC                         ATATAGCATGGTCCTGGCGGACAATGTTGATGGTGGAGATGATCTTGATCT
genomic: ATAGATGGACCCACATCATGTGCTGATGTTGTTGATATTGGTGAAACTTCgtaagttatc ... tttattacagATATAGCATGGTCCTGGCGGACAATGTTGATGGTGGAGATGATCTTGATCT
EST: gi|56409203|gb|CX017455.1|CX017455
EST:     ATAGATGGACCCACATCATGTGCTGATGTTGTTGATATTGGTGAAACTTC                         ATATAGCATGGTCCTGGCGGACAATGTTGATGGTGGAGATGATCTTGATCT
genomic: ATAGATGGACCCACATCATGTGCTGATGTTGTTGATATTGGTGAAACTTCgtaagttatc ... tttattacagATATAGCATGGTCCTGGCGGACAATGTTGATGGTGGAGATGATCTTGATCT
EST: gi|56409023|gb|CX017275.1|CX017275
EST:     ATAGATGGACCCACATCATGTGCTGATGTTGTTGATATTGGCGAAACTTC                         ATATAGCATGGTCCTGGCGGACAGTGTTGATGGTGGAGATGATCTTGATCT
genomic: ATAGATGGACCCACATCATGTGCTGATGTTGTTGATATTGGTGAAACTTCgtaagttatc ... tttattacagATATAGCATGGTCCTGGCGGACAATGTTGATGGTGGAGATGATCTTGATCT
EST: gi|56409288|gb|CX017540.1|CX017540
EST:     ATAGATGGACCCACATCATGTGCTGATGTTGTTGATATTGGTGAAACTTC                         ATATAGCATGGTCCTGGCGGACAATGTTGATGGTGGAGATGATCTTGATCT
genomic: ATAGATGGACCCACATCATGTGCTGATGTTGTTGATATTGGTGAAACTTCgtaagttatc ... tttattacagATATAGCATGGTCCTGGCGGACAATGTTGATGGTGGAGATGATCTTGATCT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGAAGGGACTTACTCTTGTTACAACATCATTTGACGGTTATTTGTACCTTATAGATGGACCCACATCATGTGCTGATGTTGTTGATATTGGTGAAACTTCgtaagttatcctccactactattcatgtttagttttactgtttaatttttcaaaatttgtttaaaatataaatgcctttattacag

- - - - - - - - - - - - - - - - - - - - - - - - - -  GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGAT