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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...attaatatctataattgctatatttatactgaaattcatttttctgcttcaattttcaattaaagctcatttagtattttgtaccatcttaatgcatcagGTATTGGGGGGCAGACTGCATTGAAGCTCATCCGCCAACATGGCTCCATCGAGAATATATTGGAGAACATAAACAGAGAAAG

Basic information

species Vitis vinifera
transcript Vv14s0060g00210.t01
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv14s0060g00210.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: GLYMA20G22190.2 (Glycine max), 3'ss of exon 11
----attaatatctataattgctatatttatactgaaattcatttttctgcttcaattttcaattaaagctcattta-gtattttgtaccatc-----ttaatgcat----cagGTATTGGGGGGCAGACTGCATTGAAGCTCATCCGCCAACATGGCTCCATCGAGAATATATTGGAGAACATAAACAGAGAAAG
    |||  ||   ||   |   ||  ||   || |  ||  || |     | |  | |  | |  | |  ||| || |||| | |||  |        | |||  |    |||| |||||||| | ||| || ||||| ||||| || ||||||||||| || || |||||| |||||||| |||||| ||| ||
gtatatttttactcatttgtatgatgcttggtctaagtttggttctatgattgctgtatgaactctatgtgcatatatgtatatcgtataaataataaatgatgtgtggcacagGGATTGGGGGACTGACAGCTTTGAAACTCATACGTCAACATGGCTCTATTGAAAATATACTGGAGAACCTAAACAAAGAGAG

upper sequence: Vv14s0060g00210.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: GLYMA10G28200.1 (Glycine max), 3'ss of exon 11
--------------attaatatctata-attgctatatttatactgaaattcatt-tttctgcttcaattttcaattaaagc--tcatttagtat--tttgtaccatcttaatgcatcagGTATTGGGGGGCAGACTGCATTGAAGCTCATCCGCCAACATGGCTCCATCGAGAATATATTGGAGAACATAAACAGAGAAAG
              |||  ||| | ||   |||| | | ||   |    || ||  ||||||  | || | |   |  |     | || ||||||   |  ||     |   ||   |||| |||||||| | ||| || ||||| ||||| || ||||||||||| || || |||||| |||||||| |||||| ||| ||
gtatatttttagccatttttatttgtatgatgctttgtctaagtttggttttatgatttctgtatgaactctatgtgcatatatttatatagtataaatgataaatgatgtgtggtgcagGGATTGGGGGACTGACAGCTTTGAAACTCATACGTCAACATGGCTCTATTGAAAATATACTGGAGAACCTAAACAAAGAGAG
















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|110418849|gb|EC985030.1|EC985030
EST:     CATTGACCTGTGCATTCTTTCAGGGTGTGATTATTGTGACAGCATTCGAG                         GTATTGGGGGGCAGACTGCATTGAAGCTCATCCGCCAACATGGCTCCATCG
genomic: CATTGACCTGTGCATTCTTTCAGGGTGTGATTATTGTGACAGCATTCGAGgtattaatat ... aatgcatcagGTATTGGGGGGCAGACTGCATTGAAGCTCATCCGCCAACATGGCTCCATCG






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gcttcaattttcaattaaagctcatttagtattttgtaccatcttaatgcatcagGTATTGGGGGGCAGACTGCATTGAAGCTCATCCGCCAACATGGCTCCATCGAGAATATATTGGAGAACATAAACAGAGAAAG
                                         tcttaat  putative branch site (score: 3)
     aattttcaattaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
attaatatctataattgctatatttatactgaaattcatttttctgcttcaattttcaattaaagctcatttagtattttgtaccatcttaatgcatcagGTATTGGGGGGCAGACTGCATTGAAGCTCATCCGCCAACATGGCTCCATCGAGAATATATTGGAGAACATAAACAGAGAAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -aattaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ccatctt