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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttgatagtgtcgacctggttgatggcatggtccatagttcatcatcactttattctatttatattgacagtgattaactgctttaattttcttttaccagATGATCCTGACATTCTCCATGCCCAACATCATCGTAATTTCCTAAAAGAGCATGTGGTTTTTAAGGAG

Basic information

species Vitis vinifera
transcript Vv05s0077g01200.t01
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv05s0077g01200.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: GLYMA07G37040.1 (Glycine max), 3'ss of exon 7
-ttgatagtgtcgacctggttgatggcatggtccatagttcatcatcactttattctatttatattgacagtgattaactgctttaattttcttttaccagATGATCCTGACATTCTCCATGCCCAACATCATCGTAATTTCCTAAAAGAGCATGTGGTTTTTAAGGAG
 ||     |    |||||  | || |     |   |      |  |   ||||    ||||   ||     |  | |||  |||   ||  |  |   |||||||||| ||  |||    ||  |||||||||||||| ||| |||| |||||||| ||||||||||||
tttagcctttcttacctg-ctaatagaggtttaagtttgatgtacttgatttagatgatttcatttcttcattctgaaccacttggtttagcaatatgcagATGATCCAGAGGTTCCTTGTGTTCAACATCATCGTAAATTCTTAAAGGAGCATGTTGTTTTTAAGGAG

upper sequence: Vv05s0077g01200.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: GLYMA17G03570.1 (Glycine max), 3'ss of exon 9
ttgatagtgtcgacctgg--ttgatg-gcatggtccatagttcatcatcactttattctatttatattgacagtgattaactgctttaattttcttttaccagATGATCCTGACATTCTCCATGCCCAACATCATCGTAATTTCCTAAAAGAGCATGTGGTTTTTAAGGAG
  | || |   |   |    || |||    || |  | |     ||||  ||| ||||| ||  |  |  |  |  | |||  |||   ||  |  |   |||||||||| ||  |||    ||  |||||||||||||| ||| |||| |||||||| ||||||||||||
--gctaatagaggtttaagttttatgtatttgatttagatgatttcatttcttcattct-ttccttctaccttttctgaaccacttgttttagcaatatgcagATGATCCAGAGGTTCCTTTTGTTCAACATCATCGTAAATTCTTAAAGGAGCATGTTGTTTTTAAGGAG
















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|32248391|gb|CD714210.1|CD714210
EST:     GGGTCACTTGAGT                         ATGATCCTGACATTCTCCATGCCCAACATCATCGTAATTTCCTAAAAGAGC
genomic: GGGTCACTTGAGTgtaagtagtt ... cttttaccagATGATCCTGACATTCTCCATGCCCAACATCATCGTAATTTCCTAAAAGAGC
EST: gi|32267561|gb|CD716524.1|CD716524
EST:     GGGTCACTTGAGT                         ATGATCCTGACATTCTCCATGCCCAACATCATCGTAATTTCCTAAAAGAGC
genomic: GGGTCACTTGAGTgtaagtagtt ... cttttaccagATGATCCTGACATTCTCCATGCCCAACATCATCGTAATTTCCTAAAAGAGC
EST: gi|30324963|gb|CD008225.1|CD008225
EST:     GGGTCACTTGAGT                         ATGATCCTGACATTCTCCATGCCCAACATCATCGTAATTTCCTAAAAGAGC
genomic: GGGTCACTTGAGTgtaagtagtt ... cttttaccagATGATCCTGACATTCTCCATGCCCAACATCATCGTAATTTCCTAAAAGAGC
EST: gi|110711495|gb|EE088040.1|EE088040
EST:     GAAATTATTTGGGGATGACTTGATCATGGATGTCATTGGGTCACTTGAGT                         ATGATCCTGACATTCTCCATGCCCAACATCATCGTAATTTCCTAAAAGAGC
genomic: GAAATTATTTGGGGATGACTTGATCATGGATGTCATTGGGTCACTTGAGTgtaagtagtt ... cttttaccagATGATCCTGACATTCTCCATGCCCAACATCATCGTAATTTCCTAAAAGAGC
EST: gi|32272042|gb|CD721201.1|CD721201
EST:     GTCACTTGAGT                         ATGATCCTGACATTCTCCATGGCCAACATCATCGTAATTTCCTAAAAGAGC
genomic: GTCACTTGAGTgtaagtagtt ... cttttaccagATGATCCTGACATTCTCCATGCCCAACATCATCGTAATTTCCTAAAAGAGC
EST: gi|32270535|gb|CD719694.1|CD719694
EST:     GGGTCACTTGAGT                         ATGATCCTGACATTCTCCATGCCCAACATCATCGTAATTTCCTAAAAGAGC
genomic: GGGTCACTTGAGTgtaagtagtt ... cttttaccagATGATCCTGACATTCTCCATGCCCAACATCATCGTAATTTCCTAAAAGAGC
EST: gi|32269076|gb|CD718235.1|CD718235
EST:     GGGTCACTTGAGT                         ATGATCCTGACATTCTCCATGCCCAACATCATCGTAATTTCCTAAAAGAGC
genomic: GGGTCACTTGAGTgtaagtagtt ... cttttaccagATGATCCTGACATTCTCCATGCCCAACATCATCGTAATTTCCTAAAAGAGC
EST: gi|30326297|gb|CD009559.1|CD009559
EST:     GGGTCACTTGAGT                         ATGATCCTGACATTCTCCATGCCCAACATCATCGTAATTTCCTAAAAGAGC
genomic: GGGTCACTTGAGTgtaagtagtt ... cttttaccagATGATCCTGACATTCTCCATGCCCAACATCATCGTAATTTCCTAAAAGAGC
EST: gi|30325174|gb|CD008436.1|CD008436
EST:     GGGTCACTTGAGT                         ATGATCCTGACATTCTCCATGCCCAACATCATCGTAATTTCCTAAAAGAGC
genomic: GGGTCACTTGAGTgtaagtagtt ... cttttaccagATGATCCTGACATTCTCCATGCCCAACATCATCGTAATTTCCTAAAAGAGC
EST: gi|30324365|gb|CD007627.1|CD007627
EST:     GGGTCACTTGAGT                         ATGATCCTGACATTCTCCATGCCCAACATCATCGTAATTTCCTAAAAGAGC
genomic: GGGTCACTTGAGTgtaagtagtt ... cttttaccagATGATCCTGACATTCTCCATGCCCAACATCATCGTAATTTCCTAAAAGAGC
EST: gi|30325851|gb|CD009113.1|CD009113
EST:     GGGTCACTTGAGT                         ATGATCCTGACATTCTCCATGCCCAACATCATCGTAATTTCCTAAAAGAGC
genomic: GGGTCACTTGAGTgtaagtagtt ... cttttaccagATGATCCTGACATTCTCCATGCCCAACATCATCGTAATTTCCTAAAAGAGC
EST: gi|30327653|gb|CD010915.1|CD010915
EST:     GGGTCACTTGAGT                         ATGATCCTGACATTCTCCATGCCCAACATCATCGTAATTTCCTAAAAGAGC
genomic: GGGTCACTTGAGTgtaagtagtt ... cttttaccagATGATCCTGACATTCTCCATGCCCAACATCATCGTAATTTCCTAAAAGAGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cactttattctatttatattgacagtgattaactgctttaattttcttttaccagATGATCCTGACATTCTCCATGCCCAACATCATCGTAATTTCCTAAAAGAGCATGTGGTTTTTAAGGAG
                                   ctttaattttctttt  CT-rich tract
     tattctatttatattg  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttgatagtgtcgacctggttgatggcatggtccatagttcatcatcactttattctatttatattgacagtgattaactgctttaattttcttttaccagATGATCCTGACATTCTCCATGCCCAACATCATCGTAATTTCCTAAAAGAGCATGTGGTTTTTAAGGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - -cctggtt
- - - - - - - - - - - - -catggtc
- - - - - - - - - - - - - - - - - - - -catcatc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctgcttt