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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttagtggctgtgagaaatttatattttgttgttaccaagaattttcccagtgttttttttaagttcattatttgcttagttgtatatcatttgcttactttcacaattgcaaatgtttggcagCCCTTGTTTCCTGGAGAGAGTGCAGTAGACCAACTTGTTGAAATTATAAAG

Basic information

species Vitis vinifera
transcript Vv12s0028g01810.t01
intron # 7
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|110711443|gb|EE087924.1|EE087924
EST:     TTGATATTTGGTCAGCTGGTTGTGTTTTTGCTGAGCTTCTACTAGGCCAG                         CCCTTGTTTCCTGGAGAGAGTGCAGTAGACCAACTTGTTGAAATTATAAAG
genomic: TTGATATTTGGTCAGCTGGTTGTGTTTTTGCTGAGCTTCTACTAGGCCAGgttagtggct ... tgtttggcagCCCTTGTTTCCTGGAGAGAGTGCAGTAGACCAACTTGTTGAAATTATAAAG
EST: gi|110725002|gb|EE101323.1|EE101323
EST:     TTGATATTTGGTCAGCTGGTTGTGTTTTTGCTGAACTTCTACTAAGCCAC                         CCCTTGTTTTCTGGAAAGAGTGCA
genomic: TTGATATTTGGTCAGCTGGTTGTGTTTTTGCTGAGCTTCTACTAGGCCAGgttagtggct ... tgtttggcagCCCTTGTTTCCTGGAGAGAGTGCA
EST: gi|349830587|gb|FQ416885.1|FQ416885
EST:     TTGATATTTGGTCAGCTGGTTGTGTTTTTGCTGAGCTTCTACTAGGCCAG                         CCCCTTGTT-CCTGGAGAGAGTGCAGTAGACCAACTT
genomic: TTGATATTTGGTCAGCTGGTTGTGTTTTTGCTGAGCTTCTACTAGGCCAGgttagtggct ... tgtttggcagCCC-TTGTTTCCTGGAGAGAGTGCAGTAGACCAACTT
EST: gi|27582878|gb|CB005573.1|CB005573
EST:     TTGATATTTGGTCAGCTGGTTGTGTTTTTGCTGAGCTTCTACTAGGCCAG                         CCCTTGTTTCCTGGAGAGAGTGCAGTAGACCAACTTGTTGAAATTATAAAG
genomic: TTGATATTTGGTCAGCTGGTTGTGTTTTTGCTGAGCTTCTACTAGGCCAGgttagtggct ... tgtttggcagCCCTTGTTTCCTGGAGAGAGTGCAGTAGACCAACTTGTTGAAATTATAAAG
EST: gi|33402557|gb|CF208184.1|CF208184
EST:     TTGATATTTGGTCAGCTGGTTGTGTTTTTGCTGAGCTTCTACTACGCCAG                         CCCTTGTTTCCTGGAGAGAGTGCAGT-GATANAACTTGTTGAAATTATAAA
genomic: TTGATATTTGGTCAGCTGGTTGTGTTTTTGCTGAGCTTCTACTAGGCCAGgttagtggct ... tgtttggcagCCCTTGTTTCCTGGAGAGAGTGCAGTAGACC-AACTTGTTGAAATTATAAA
EST: gi|351020144|gb|FQ445751.1|FQ445751
EST:     TTGATATTTGGTCAGCTGGTTGTGTTTTTGCTGAGCTTCTACTAGGCCCG                         CCCCTTGTTTCCTGGAGAGAGTGCAGT
genomic: TTGATATTTGGTCAGCTGGTTGTGTTTTTGCTGAGCTTCTACTAGGCCAGgttagtggct ... tgtttggcagCCC-TTGTTTCCTGGAGAGAGTGCAGT
EST: gi|351036312|gb|FQ458687.1|FQ458687
EST:     TTGATATTTGGTCAGCTGGTTGTGTTTTTGCTGAGCTTCTACTAGGCCAG                         CCCTTGTTTCCTGGAGAGAGTGCAGTAGACCAA
genomic: TTGATATTTGGTCAGCTGGTTGTGTTTTTGCTGAGCTTCTACTAGGCCAGgttagtggct ... tgtttggcagCCCTTGTTTCCTGGAGAGAGTGCAGTAGACCAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatttgcttagttgtatatcatttgcttactttcacaattgcaaatgtttggcagCCCTTGTTTCCTGGAGAGAGTGCAGTAGACCAACTTGTTGAAATTATAAAG
                       tgcttac  putative branch site (score: 2)
              tatatcattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttagtggctgtgagaaatttatattttgttgttaccaagaattttcccagtgttttttttaagttcattatttgcttagttgtatatcatttgcttactttcacaattgcaaatgtttggcagCCCTTGTTTCCTGGAGAGAGTGCAGTAGACCAACTTGTTGAAATTATAAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA