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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...attttgatatggctgagaattataacactgaaagttcataatttatatctttagaagctacttttttttccaaccatatttggtccctgttttgatgcagGATGATGCACATATCTTCTGCAGGGAATCCCAG

Basic information

species Vitis vinifera
transcript Vv01s0026g00340.t01
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv01s0026g00340.t01 (Vitis vinifera), 3'ss of exon 12
lower sequence: GLYMA01G03930.1 (Glycine max), 3'ss of exon 11
----attttgatatggctgagaattataacactgaaagttcataatttatatctttagaagctacttttttttccaaccatatttggtccctgttttgatgcagGATGATGCACATATCTTCTGCAGGGAATCCCAG
    |||  | |||       | | |    |     | ||  || ||| | | |    |   ||||  | ||   ||    ||||| |     | ||| | ||||||||||||||||| ||||||||||| ||||||
tgcaattcagttatctggatcattcaccttatctttaatttctattttctgtttgagtatcatactactatt---aatggcatttgctttaaatgttgct-cagGATGATGCACATATTTTCTGCAGGGAGTCCCAG
















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|30325956|gb|CD009218.1|CD009218
EST:     AAGCCAGTGGTGCACTTACTGGATTAACTCGTGTCAGGAGGTTTCAGCAG                         GATGATGCACATATCTTCTGCAGGGAATCCCAG
genomic: AAGCCAGTGGTGCACTTACTGGATTAACTCGTGTCAGGAGGTTTCAGCAGgtattctttt ... tttgatgcagGATGATGCACATATCTTCTGCAGGGAATCCCAG
EST: gi|30325105|gb|CD008367.1|CD008367
EST:     AAGCCAGTGGTGCACTTACTGGATTAACTCGTGTCAGGAGGTTTCAGCAG                         GATGATGCACATATCTTCTGCAGGGAATCCCAG
genomic: AAGCCAGTGGTGCACTTACTGGATTAACTCGTGTCAGGAGGTTTCAGCAGgtattctttt ... tttgatgcagGATGATGCACATATCTTCTGCAGGGAATCCCAG
EST: gi|32268540|gb|CD717699.1|CD717699
EST:     AAGCCAGTGGTGCACTTACTGGATTAACTCGTGTCAGGAGGTTTCAGCAG                         GATGATGCACATATCTTCTGCAGGGAATCCCAG
genomic: AAGCCAGTGGTGCACTTACTGGATTAACTCGTGTCAGGAGGTTTCAGCAGgtattctttt ... tttgatgcagGATGATGCACATATCTTCTGCAGGGAATCCCAG
EST: gi|30323442|gb|CD006704.1|CD006704
EST:     AAGCCAGTGGTGCACTTACTGGATTAACTCGTGTCAGGAGGTTTCAGCAG                         GATGATGCACATATCTTCTGCAGGGAATCCCAG
genomic: AAGCCAGTGGTGCACTTACTGGATTAACTCGTGTCAGGAGGTTTCAGCAGgtattctttt ... tttgatgcagGATGATGCACATATCTTCTGCAGGGAATCCCAG
EST: gi|32249386|gb|CD715205.1|CD715205
EST:     AAGCCAGTGGTGCACTTACTGGATTAACTCGTGTCAGGAGGTTTCAGCAG                         GATGATGCACATATCTTCTGCAGGGAATCCCAG
genomic: AAGCCAGTGGTGCACTTACTGGATTAACTCGTGTCAGGAGGTTTCAGCAGgtattctttt ... tttgatgcagGATGATGCACATATCTTCTGCAGGGAATCCCAG
EST: gi|156735898|gb|EV240019.1|EV240019
EST:     AAGCCAGTGGTGCACTTACTGGATTAACTCGTGTCAGGAGGTTTCAGCAG                         GATGATGCACATATCTTCTGCAGGGAATCCCAG
genomic: AAGCCAGTGGTGCACTTACTGGATTAACTCGTGTCAGGAGGTTTCAGCAGgtattctttt ... tttgatgcagGATGATGCACATATCTTCTGCAGGGAATCCCAG
EST: gi|30327091|gb|CD010353.1|CD010353
EST:     AAGCCAGTGGTGCACTTACTGGATTAACTCGTGTCAGGAGGTTTCAGCAG                         GATGATGCACATATCTTCTGCAGGGAATCCCAG
genomic: AAGCCAGTGGTGCACTTACTGGATTAACTCGTGTCAGGAGGTTTCAGCAGgtattctttt ... tttgatgcagGATGATGCACATATCTTCTGCAGGGAATCCCAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatctttagaagctacttttttttccaaccatatttggtccctgttttgatgcagGATGATGCACATATCTTCTGCAGGGAATCCCAG
                                            ttttgat  putative branch site (score: 4)
                                      tccctgtttt  CT-rich tract
             tactttttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
attttgatatggctgagaattataacactgaaagttcataatttatatctttagaagctacttttttttccaaccatatttggtccctgttttgatgcagGATGATGCACATATCTTCTGCAGGGAATCCCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGCAG
- - - - -tggctga
- - - - - - - - - - -ataacac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aaccata
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tccctgt