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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGAAGTTTGGTGCCTTCTTTGCATCTATTCCTTTACCAATATTTGCTGCCATATACTGTGTTCTATTTGGCATTGTTGgtgagtgagtttggctttatttttgttttagtcttgttagttaatatccttttgatgggtgtagtgttgcttctctttcttttcctgcag

Basic information

species Vitis vinifera
transcript Vv18s0001g11260.t01
intron # 12
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv18s0001g11260.t01 (Vitis vinifera), 5'ss of exon 12
lower sequence: LOC_Os12g39420.4 (Oryza sativa), 5'ss of exon 13
GGAAGTTTGGTGCCTTCTTTGCATCTATTCCTTTACCAATATTTGCTGCCATATACTGTGTTCTATTTGGCATTGTTGgtgagt--gagtttggctttatttttgttttagtcttgttagtta-atatccttttgatgggtgtagtgttgcttctctttcttttcctgcag---------------
||||||||||||| ||||||||||||||||| || ||||| || || || || | |||| |  ||||||| |||||||||||||  || |||   ||  |    ||  | |  | | |   || ||||       |   |  | |||||  || | | |  |   |||                  
GGAAGTTTGGTGCTTTCTTTGCATCTATTCCATTGCCAATCTTCGCAGCAATTTTCTGTATCTTATTTGGTATTGTTGgtgagtccgaattttctttcttaagagtccttgcatcgatgaatatatatggccgcaacatg-attgtgttcattttatgttctaatctgttttttttggcatatcag

upper sequence: Vv18s0001g11260.t01 (Vitis vinifera), 5'ss of exon 12
lower sequence: GLYMA14G08690.1 (Glycine max), 5'ss of exon 12
GGAAGTTTGGTGCCTTCTTTGCATCTATTCCTTTACCAATATTTGCTGCCATATACTGTGTTCTATTTGGCATTGTTGgtgagtgagtttggctttatttttgttttagtcttgttagttaatatccttttgatgggtgtagtgttgcttctctttcttttcctgcag
|||| ||||| ||||| |||||||| |||||  |||| |||||||||||||||||||||||| ||||||| || || |||  |||    ||   |||||       |  |  | ||    ||||            |  |  | ||  |  | ||  ||||  |||||
GGAAATTTGGAGCCTTTTTTGCATCGATTCCCCTACCGATATTTGCTGCCATATACTGTGTTTTATTTGGTATCGTGGgtaggtgctgctgctattattacatagatgataattttgaccaataaat-----gcaagccttttatt-ttattgttaatttttttgcag

upper sequence: Vv18s0001g11260.t01 (Vitis vinifera), 5'ss of exon 12
lower sequence: GLYMA17G36440.1 (Glycine max), 5'ss of exon 12
-GGAAGTTTGGTGCCTTCTTTGCATCTATTCCTTTACCAATATTTGCTGCCATATACTGTGTTCTATTTGGCATTGTTGgtgagtgagtttggctttatttttgttttagtcttgttagttaatatccttttgatgggtgtagtgttgcttc--tctttcttttcctgcag
 |||| ||||| || || |||||||| |||||  |||| |||||||||||||| ||||||||| ||||||| ||||| |||  |||    ||    |||| |||  |   |     || ||  |  ||  | ||||   |   | ||  ||   | ||  ||||  |||| 
GGGAAATTTGGAGCTTTTTTTGCATCAATTCCCCTACCGATATTTGCTGCCATCTACTGTGTTTTATTTGGTATTGTGggtaggtg---ctgctgctattattgcatagattacaataattt-tgaccaatagatgcaagcctttttattttgttgttgatttttttgca-

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|110387805|gb|EC952502.1|EC952502
EST:     TCCTTTACCAATATTTGCTGCCATATACTGTGTTCTATTTGGCATTGTTG                         CTGCTACTGGGATCTCATTTCTTCAATTTGCTAACAGTAATTCCATGAGAA
genomic: TCCTTTACCAATATTTGCTGCCATATACTGTGTTCTATTTGGCATTGTTGgtgagtgagt ... tttcctgcagCTGCTACTGGGATCTCATTTCTTCAATTTGCTAACAGTAATTCCATGAGAA
EST: gi|22015462|gb|BQ800496.1|BQ800496
EST:     TCCTTTACCAATATTTGCTGCCATATACTGTGTTCTATTTGGCATTGTTG                         CTGCTACTGGGATCTCATTTCTTCAATTTGCAAACAGTAATTCCATGAGAA
genomic: TCCTTTACCAATATTTGCTGCCATATACTGTGTTCTATTTGGCATTGTTGgtgagtgagt ... tttcctgcagCTGCTACTGGGATCTCATTTCTTCAATTTGCTAACAGTAATTCCATGAGAA
EST: gi|27581681|gb|CB004376.1|CB004376
EST:     TCCTTTACCAATATTTGCTGCCATATACTGTGTTCTATTTGGCATTGTTG                         CTGCTACTGGGATCTCATTTCTTCAATTTGCTAACAGTAATTCCATGAGAA
genomic: TCCTTTACCAATATTTGCTGCCATATACTGTGTTCTATTTGGCATTGTTGgtgagtgagt ... tttcctgcagCTGCTACTGGGATCTCATTTCTTCAATTTGCTAACAGTAATTCCATGAGAA
EST: gi|46917625|gb|CN546954.1|CN546954
EST:     TCCTTTACCAATATTTGCTGCCATATACTGTGTTCTATTTGGCATTGTTG                         CTGCTACTGGGATCTCATTTCTTCAATTTGCTAACAGTAATTCCATGAGAA
genomic: TCCTTTACCAATATTTGCTGCCATATACTGTGTTCTATTTGGCATTGTTGgtgagtgagt ... tttcctgcagCTGCTACTGGGATCTCATTTCTTCAATTTGCTAACAGTAATTCCATGAGAA
EST: gi|110413208|gb|EC978987.1|EC978987
EST:     TCCTTTACCAATATTTGCTGCCATATACTGTGTTCTATTTGGCATTGTTG                         CTGCTACTGGGATCTCATTTCTTCAATTTGCAAACAGTAATTCCATGAGAA
genomic: TCCTTTACCAATATTTGCTGCCATATACTGTGTTCTATTTGGCATTGTTGgtgagtgagt ... tttcctgcagCTGCTACTGGGATCTCATTTCTTCAATTTGCTAACAGTAATTCCATGAGAA
EST: gi|30328659|gb|CD011921.1|CD011921
EST:     TCCTTTACCAATATTTGCTGCCATATACTGTGTTCTATTTGGCATTGTTG                         CTGCTACTGGGATCTCATTTCTTCAATTTGCTAACAGTAATTCCATGAGAA
genomic: TCCTTTACCAATATTTGCTGCCATATACTGTGTTCTATTTGGCATTGTTGgtgagtgagt ... tttcctgcagCTGCTACTGGGATCTCATTTCTTCAATTTGCTAACAGTAATTCCATGAGAA
EST: gi|110718405|gb|EE095198.1|EE095198
EST:     TCCTTTACCAATATTTGCTGCCATATACTGTGTTCTATTTGGCATTGTTG                         CTGCTACTGGGATCTCATTTCTTCAATTTGCAAACAGTAATTCCATGAGAA
genomic: TCCTTTACCAATATTTGCTGCCATATACTGTGTTCTATTTGGCATTGTTGgtgagtgagt ... tttcctgcagCTGCTACTGGGATCTCATTTCTTCAATTTGCTAACAGTAATTCCATGAGAA
EST: gi|110717478|gb|EE093371.1|EE093371
EST:     TCCTTTACCAATATTTGCTGCCATATACTGTGTTCTATTTGGCATTGTTG                         CTGCTACTGGGATCTCATTTCTTCAATTTGCTAACAGTAATTCCATGAGAA
genomic: TCCTTTACCAATATTTGCTGCCATATACTGTGTTCTATTTGGCATTGTTGgtgagtgagt ... tttcctgcagCTGCTACTGGGATCTCATTTCTTCAATTTGCTAACAGTAATTCCATGAGAA
EST: gi|22013116|gb|BQ798150.1|BQ798150
EST:     TCCTTTACCAATATTTGCTGCCATATACTGTGTTCTATTTGGCATTGTTG                         NTGCTANTGGGATCTCATTTCTTCAATTTGCTAACAGTAATTCCATGAGAA
genomic: TCCTTTACCAATATTTGCTGCCATATACTGTGTTCTATTTGGCATTGTTGgtgagtgagt ... tttcctgcagCTGCTACTGGGATCTCATTTCTTCAATTTGCTAACAGTAATTCCATGAGAA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGAAGTTTGGTGCCTTCTTTGCATCTATTCCTTTACCAATATTTGCTGCCATATACTGTGTTCTATTTGGCATTGTTGgtgagtgagtttggctttatttttgttttagtcttgttagttaatatccttttgatgggtgtagtgttgcttctctttcttttcctgcag

- - - - - - - - - - - - - - - - - - - - -  TGCTGC