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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtctttgttatgcttatatatttactaatatatcgtacttcatttgattttgaattatcctgaatatgaatcatataaccttattgcatgtagGACTTTGGATAAAACTATTTCCAATTTAGAGATGGAATTAGCTGCTGCCAGAGCTGCACAAGAATCTATGGTAAACGGTTCTCCAATATCAGAAGACTTG

Basic information

species Vitis vinifera
transcript Vv12s0059g00640.t01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv12s0059g00640.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA12G31980.1 (Glycine max), 3'ss of exon 3
gtaagtctttgttatgcttatatatttactaatatatcgta-cttcatttgattttgaattatcctgaatatgaatcatataaccttattgcatgtagGACTTTGGATAAAACTATTTCCAATTTAGAGATGGAATTAGCTGCTGCCAGAGCTGCACAAGAATCTATGGTAAACGGTTCTCCAATATCAGAAGACTTG
       |  ||||| ||||||||        | | | |||  || |||| |||||    | | |    ||   ||  | ||||   || | |||||| ||  |||| ||||||||||| || || |||||||||||||||||||| | ||| || || || |||||   ||  ||| ||||  || |||||||  | 
------gtaagttatacttatataccattggttgtgttgtaattttattttatttttgtattttcatgctaaacat-gtgtaactgcatggaatgtagAACCCTGGACAAAACTATTTCAAACTTGGAGATGGAATTAGCTGCTGCAAAAGCAGCTCAGGAGTCTATACGAAGTGGTGCTCCGGTAGCAGAAGATATC

upper sequence: Vv12s0059g00640.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA06G46230.1 (Glycine max), 3'ss of exon 3
gtaagtctttgttatgcttatatatttactaatatatcgtacttcatttgattttga--attatcctgaatatgaatcatataacct-tattgcatgtagGACTTTGGATAAAACTATTTCCAATTTAGAGATGGAATTAGCTGCTGCCAGAGCTGCACAAGAATCTATGGTAAACGGTTCTCCAATATCAGAAGACTTG
   ||   |  ||  |  || |  | | | || |   | ||  || | | ||||| |  |||||  || || | || | |||      |||||  ||||| || ||||| || |||||||| || |||||||||||||| |||||||| || |   | || |||||| |   ||  ||| |||| || ||||| ||  | 
cctagaagtgcttccggataaacttatccgaacaagccctaagtcttgttatttttattattattttgcatgtcaaacttatgggaggtattgactgtagAACATTGGACAAGACTATTTCGAACTTAGAGATGGAATTGGCTGCTGCTAGGGTAACTCAGGAATCTCTACGAAGTGGTGCTCCTATTTCAGATGATATA
















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|110711717|gb|EE088518.1|EE088518
EST:     GACTCTAAAGACATTATTGGGGAAGTTCATAAAACTCATCATGCTATACA                         GACTTTGGATAAAACTATTTCCAATTTANAGATGGAATTAGCTGCTGCCAG
genomic: GACTCTAAGGACATTATTGGGGAAGTTCATAAAACTCATCATGCTATACAgtaagtcttt ... ttgcatgtagGACTTTGGATAAAACTATTTCCAATTTAGAGATGGAATTAGCTGCTGCCAG
EST: gi|37183584|gb|CF602938.1|CF602938
EST:     GACTCTAAGGACATTATTGGGGAAGTTCATAAAACTCATCATGCTATACA                         GACTTTGGATAAAACTATTTCCAATTTAGAGATGGAATTAGCTGCTGCCAG
genomic: GACTCTAAGGACATTATTGGGGAAGTTCATAAAACTCATCATGCTATACAgtaagtcttt ... ttgcatgtagGACTTTGGATAAAACTATTTCCAATTTAGAGATGGAATTAGCTGCTGCCAG
EST: gi|110367432|gb|EC931364.1|EC931364
EST:     GACTCTAAGGACATTATTGGGGAAGTTCATAAAACTCATCATGCTATACA                         GACTTTGGATAAAACTATTTCCAATTTAGAGATGGAATTAGCTGCTGCCAG
genomic: GACTCTAAGGACATTATTGGGGAAGTTCATAAAACTCATCATGCTATACAgtaagtcttt ... ttgcatgtagGACTTTGGATAAAACTATTTCCAATTTAGAGATGGAATTAGCTGCTGCCAG
EST: gi|110723286|gb|EE100428.1|EE100428
EST:     GACTCTAAGGACATTATTGGGGAAGTTCATAAAACTCATCATGCTATACA                         GACTTTGGATAAAACTATTTCCAATTTAGAGATGGAATTAGCTGCTGCCAG
genomic: GACTCTAAGGACATTATTGGGGAAGTTCATAAAACTCATCATGCTATACAgtaagtcttt ... ttgcatgtagGACTTTGGATAAAACTATTTCCAATTTAGAGATGGAATTAGCTGCTGCCAG
EST: gi|110693148|gb|EE069126.1|EE069126
EST:     TACTCTAAGGACATTATTGGGGAAGTTCATAAAACTCATCATGCTATACA                         GACTTTGGATAAAACTATTTCCAATTTAGAGATGGAATTAGCTGCTGCCAG
genomic: GACTCTAAGGACATTATTGGGGAAGTTCATAAAACTCATCATGCTATACAgtaagtcttt ... ttgcatgtagGACTTTGGATAAAACTATTTCCAATTTAGAGATGGAATTAGCTGCTGCCAG
EST: gi|110698839|gb|EE076793.1|EE076793
EST:     GACTCTAAGGACATTATTGGGGAAGTTCATAAAACTCATCATGCTATACA                         GACTTTGGATAAAACTATTTCCAATTTAGAGATGGAATTAGCTGCTGCCAG
genomic: GACTCTAAGGACATTATTGGGGAAGTTCATAAAACTCATCATGCTATACAgtaagtcttt ... ttgcatgtagGACTTTGGATAAAACTATTTCCAATTTAGAGATGGAATTAGCTGCTGCCAG
EST: gi|110720685|gb|EE096823.1|EE096823
EST:     GACTCTAAGGACATTATTGGGGAAGTTCATAAAACTCATCATGCTATACA                         GACTTTGGATAAAACTATTTCCAATTTAGAGATGGAATTAGCTGCTGCCAG
genomic: GACTCTAAGGACATTATTGGGGAAGTTCATAAAACTCATCATGCTATACAgtaagtcttt ... ttgcatgtagGACTTTGGATAAAACTATTTCCAATTTAGAGATGGAATTAGCTGCTGCCAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttcatttgattttgaattatcctgaatatgaatcatataaccttattgcatgtagGACTTTGGATAAAACTATTTCCAATTTAGAGATGGAATTAGCTGCTGCCAGAGCTGCACAAGAATCTATGGTAAACGGTTCTCCAATATCAGAAGACTTG
                                  atataac  putative branch site (score: 3)
                                        ccttatt  CT-rich tract
                        aatatgaatcatataa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtctttgttatgcttatatatttactaatatatcgtacttcatttgattttgaattatcctgaatatgaatcatataaccttattgcatgtagGACTTTGGATAAAACTATTTCCAATTTAGAGATGGAATTAGCTGCTGCCAGAGCTGCACAAGAATCTATGGTAAACGGTTCTCCAATATCAGAAGACTTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC