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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatggaaaaacccgtgagcattctattctctcttcatgacattgattactataaacagtgaatttatgattttgtctttctccatcatttttagGTGGAAAACGCACATTAAAGCTCCCCCCAGAGCTCGGATATGGCACGAGAGGTGCTGGCTGTAGAGGAG

Basic information

species Vitis vinifera
transcript Vv01s0011g00930.t01
intron # 3
splice site 3'
intron type U2

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|349824721|gb|FQ414579.1|FQ414579
EST:     CTGGGACCAGGGGATTCTAGGAGGTGATGGGGTTCCCCCCATGCTTGCTG                         GTGGAAAACGCACATTAAAGCTCCCCCCAGAGCTCGGATATGGCACGAGAG
genomic: CTGGGACCAGGGGATTCTAGGAGGTGATGGGGTTCCCCCCATGCTTGCTGgtatggaaaa ... tcatttttagGTGGAAAACGCACATTAAAGCTCCCCCCAGAGCTCGGATATGGCACGAGAG
EST: gi|30298919|gb|CB975713.1|CB975713
EST:     CTGGGACCAGGGGATTCTAGGAGGTGATGGGGTTCCCCCCATGCTTGCTG                         GTGGAAAACGCACATTAAAGCTCCCCCCAGAGCTCGGATATGGCACGAGAG
genomic: CTGGGACCAGGGGATTCTAGGAGGTGATGGGGTTCCCCCCATGCTTGCTGgtatggaaaa ... tcatttttagGTGGAAAACGCACATTAAAGCTCCCCCCAGAGCTCGGATATGGCACGAGAG
EST: gi|22013355|gb|BQ798389.1|BQ798389
EST:     CTGGGACCAGGGGATTCTAGGAGGTGATGGGGTTCCCCCCATGCTTGCTG                         GTGGAAAACGCACATTAAAGCTCCCCCCAGAGCTCGGATATGGCACGAGAG
genomic: CTGGGACCAGGGGATTCTAGGAGGTGATGGGGTTCCCCCCATGCTTGCTGgtatggaaaa ... tcatttttagGTGGAAAACGCACATTAAAGCTCCCCCCAGAGCTCGGATATGGCACGAGAG
EST: gi|349827180|gb|FQ421453.1|FQ421453
EST:     CTGGGACCAGGGGATTCTAGGAGGTGATGGGGTTCCCCCCATGCTTGCTG                         GTGGAAAACGCACATTAAAGCTCCCCCCAGAGCTCGGATATGGCACGAGAG
genomic: CTGGGACCAGGGGATTCTAGGAGGTGATGGGGTTCCCCCCATGCTTGCTGgtatggaaaa ... tcatttttagGTGGAAAACGCACATTAAAGCTCCCCCCAGAGCTCGGATATGGCACGAGAG
EST: gi|351024975|gb|FQ433392.1|FQ433392
EST:     CTGGGACCAGGGGATTCTAGGAGGTGATGGGGTTCCCCCCATGCTTGCTG                         GTGGAAAACGCACATTAAAGCTCCCCCCAGAGCTCGGATATGGCACGAGAG
genomic: CTGGGACCAGGGGATTCTAGGAGGTGATGGGGTTCCCCCCATGCTTGCTGgtatggaaaa ... tcatttttagGTGGAAAACGCACATTAAAGCTCCCCCCAGAGCTCGGATATGGCACGAGAG
EST: gi|349815365|gb|FQ400520.1|FQ400520
EST:     CTGGGACCAGGGGATTCTAGGAGGTGATGGGGTTCCCCCCATGCTTGCTG                         GTGGAAAACGCACATTAAAGCTNNNNNNNAGAGCTCGGATATGGCACGAGA
genomic: CTGGGACCAGGGGATTCTAGGAGGTGATGGGGTTCCCCCCATGCTTGCTGgtatggaaaa ... tcatttttagGTGGAAAACGCACATTAAAGCTCCCCCC-AGAGCTCGGATATGGCACGAGA
EST: gi|110428480|gb|EC994954.1|EC994954
EST:     CTGGGACCAGGGGATTCTAGGAGGTGATGGGGTTCCCCCCATGCTTGCTG                         GTGGAAAACGCACATTAAAGCTCCCCCCAGAGCTCGGATATGGCACGAGAG
genomic: CTGGGACCAGGGGATTCTAGGAGGTGATGGGGTTCCCCCCATGCTTGCTGgtatggaaaa ... tcatttttagGTGGAAAACGCACATTAAAGCTCCCCCCAGAGCTCGGATATGGCACGAGAG
EST: gi|110398543|gb|EC964979.1|EC964979
EST:     CTGGGACCAGGGGATTCTAGGAGGTGATGGGGTTCCCCCCATGCTTGCTG                         GTGGAAAACGCACATTAAAGCTCCCCCCAGAGCTCGGATATGGCACGAGAG
genomic: CTGGGACCAGGGGATTCTAGGAGGTGATGGGGTTCCCCCCATGCTTGCTGgtatggaaaa ... tcatttttagGTGGAAAACGCACATTAAAGCTCCCCCCAGAGCTCGGATATGGCACGAGAG
EST: gi|26265214|gb|CA816277.1|CA816277
EST:     CTGGGACCAGGGGATTCTAGGAGGTGATGGGGTTCCCCCCATGCTTGCTG                         GTGGAAAACGCACATTAAAGCTCCCCCCAGAGCTCGGATATGGCACGAGAG
genomic: CTGGGACCAGGGGATTCTAGGAGGTGATGGGGTTCCCCCCATGCTTGCTGgtatggaaaa ... tcatttttagGTGGAAAACGCACATTAAAGCTCCCCCCAGAGCTCGGATATGGCACGAGAG
EST: gi|110421011|gb|EC987298.1|EC987298
EST:     CTGGGACCAGGGGATTCTAGGAGGTGATGGGGTTCCCCCCATGCTTGCTG                         GTGGAAAACGCACATTAAAGCTCCCCCCAGAGCTCGGATATGGCACGAGAG
genomic: CTGGGACCAGGGGATTCTAGGAGGTGATGGGGTTCCCCCCATGCTTGCTGgtatggaaaa ... tcatttttagGTGGAAAACGCACATTAAAGCTCCCCCCAGAGCTCGGATATGGCACGAGAG
EST: gi|349830135|gb|FQ420395.1|FQ420395
EST:     CCGGGACCAGGGGATTCTAGGAGGTGATGGGGTTCCCCCCATGCTTGCTG                         GTGGAAAACGCACATTAAAGCTCCCCCCAGAGCTCGGGTATGGCACGAGAG
genomic: CTGGGACCAGGGGATTCTAGGAGGTGATGGGGTTCCCCCCATGCTTGCTGgtatggaaaa ... tcatttttagGTGGAAAACGCACATTAAAGCTCCCCCCAGAGCTCGGATATGGCACGAGAG
EST: gi|110726886|gb|EE103061.1|EE103061
EST:     TGGGACCAGGGGATTCTAGGAGGGTGATGGGGTTCCCCCCATGCTTGCTG                         GTGGAAAACGCACATTAAAGCTCCCCCCAAAGCTCGGATATGGCACGAGAG
genomic: TGGGACCAGGGGATTCTAGGAGG-TGATGGGGTTCCCCCCATGCTTGCTGgtatggaaaa ... tcatttttagGTGGAAAACGCACATTAAAGCTCCCCCCAGAGCTCGGATATGGCACGAGAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cattgattactataaacagtgaatttatgattttgtctttctccatcatttttagGTGGAAAACGCACATTAAAGCTCCCCCCAGAGCTCGGATATGGCACGAGAGGTGCTGGCTGTAGAGGAG
 cattgat  putative branch site (score: 4)
                              ttttgtctttctccat  putative PPT
                   tgaatttatgatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatggaaaaacccgtgagcattctattctctcttcatgacattgattactataaacagtgaatttatgattttgtctttctccatcatttttagGTGGAAAACGCACATTAAAGCTCCCCCCAGAGCTCGGATATGGCACGAGAGGTGCTGGCTGTAGAGGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG