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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gaaatatatttgtctttttggcatctttctgttccaatcttattatatcccaatgaccaattattgatgttttctcacatgactgtctttctctgaatagGGTGATCCTCTTCAAGTGAAAGTCAACAAGCTCTCATCTACAAAGACACAACTACCATATGATTACTATTACTTGAAGTGGTGTAAGCCCAAGAAGATCA

Basic information

species Vitis vinifera
transcript Vv09s0002g02140.t01
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv09s0002g02140.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: LOC_Os06g37160.1 (Oryza sativa), 3'ss of exon 1
--gaaatatatttgtctttttggcatctttctgttccaatcttattatatcccaatgaccaattattgatgttttctcacatgactgtctttctctgaatagGGTGATCCTCTTCAAGTGAAAGTCAACAAGCTCTCATCTACAAAGACACAACTACCATATGATTACTATTACTTGAAGTGGTGTAAGCCCAAGAAGATCA
  |   ||| |||||    ||  |  ||   | |||    || |    | |    |      | ||| || ||         |     | |||  |    ||| ||||   |||||||| |||||||||||||| || ||||| ||||||||||| |||||||| |||||||   |  | |  || || ||  ||   || |
atgctttatgtttgtgcgatt--cccctcattattctgcactgacagcagctattttgttgctaatttattttgaaaggtcagctaaccattcaatttgcagGATGATGAGCTTCAAGTTAAAGTCAACAAGCTTTCGTCTACGAAGACACAACTTCCATATGACTACTATTTTCTAGACTACTGCAAACCTGAGGCAATTA
















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|71862773|gb|DT011828.1|DT011828
EST:     CGGCGCACTCGTTTTACCTTCCTGGCGTCGCTCCTCGTGATTTTGAAAGG                         GGTGATCCTCTTCAAGTGAAAGTGAACAAGCTCTCGTCTACAAAGACACAA
genomic: CGGCGCACTCGTTTTACCTTCCTGGCGTCGCTCCTCGTGATTTTGAAAGGgtattttcga ... ctctgaatagGGTGATCCTCTTCAAGTGAAAGTCAACAAGCTCTCATCTACAAAGACACAA
EST: gi|351033128|gb|FQ446481.1|FQ446481
EST:     CGGCGCACTCGTTTTACCTTCCTGGCGTCGCTCCTCGTGATTTTGAAAGG                         GGTGATCCTCTTCAAGTGAAAGTCAACAAGCTCTCATCTACAAAGACACAA
genomic: CGGCGCACTCGTTTTACCTTCCTGGCGTCGCTCCTCGTGATTTTGAAAGGgtattttcga ... ctctgaatagGGTGATCCTCTTCAAGTGAAAGTCAACAAGCTCTCATCTACAAAGACACAA
EST: gi|71865270|gb|DT014325.1|DT014325
EST:     CGGCGCACTCGTTTTACCTTCCTGGCGTCGCTCCTCGTGATTTTGAAAGG                         GGTGATCCTCTTCAAGTGAAAGTCAACAAGCTCTCATCTACAAAGACACAA
genomic: CGGCGCACTCGTTTTACCTTCCTGGCGTCGCTCCTCGTGATTTTGAAAGGgtattttcga ... ctctgaatagGGTGATCCTCTTCAAGTGAAAGTCAACAAGCTCTCATCTACAAAGACACAA
EST: gi|351030399|gb|FQ432337.1|FQ432337
EST:     CGGCGCACTCGTTTTACCTTCCTGGCGTCGCTCCTCGTGATTTTGAAAGG                         GGTGATCCTCTTCAAGTGAAAGTCAACAAGCTCTCATCTACAAAGACACAA
genomic: CGGCGCACTCGTTTTACCTTCCTGGCGTCGCTCCTCGTGATTTTGAAAGGgtattttcga ... ctctgaatagGGTGATCCTCTTCAAGTGAAAGTCAACAAGCTCTCATCTACAAAGACACAA
EST: gi|349833072|gb|FQ416450.1|FQ416450
EST:     CGGCGCACTCGTTTTACCTTCCTGGCGTCGCTCCTCGTGATTTTGAAAGG                         GGTGATCCTCTTCAAGTGAAAGTCAACAAGCTCTCATCTACAAAGACACAA
genomic: CGGCGCACTCGTTTTACCTTCCTGGCGTCGCTCCTCGTGATTTTGAAAGGgtattttcga ... ctctgaatagGGTGATCCTCTTCAAGTGAAAGTCAACAAGCTCTCATCTACAAAGACACAA
EST: gi|34546863|gb|CF515095.1|CF515095
EST:     CGGCGCACTCGTTTTACCTTCCTGGCGTCGCTCCTCGTGATTTTGAAAGG                         GGTGATCCTCTTCAAGTGAAAGTGAACAAGCTCTCATCTACAAAGACACAA
genomic: CGGCGCACTCGTTTTACCTTCCTGGCGTCGCTCCTCGTGATTTTGAAAGGgtattttcga ... ctctgaatagGGTGATCCTCTTCAAGTGAAAGTCAACAAGCTCTCATCTACAAAGACACAA
EST: gi|161713929|gb|FC062883.1|FC062883
EST:     CGGCGCACTCGTTTTACCTTCCTGGCGTCGCTCCTCGTGATTTTGAAAGG                         GGTGATCCTCTTCAAGTGAAAGTGAACAAGCTCTCGTCTACAAAGACACAA
genomic: CGGCGCACTCGTTTTACCTTCCTGGCGTCGCTCCTCGTGATTTTGAAAGGgtattttcga ... ctctgaatagGGTGATCCTCTTCAAGTGAAAGTCAACAAGCTCTCATCTACAAAGACACAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatcccaatgaccaattattgatgttttctcacatgactgtctttctctgaatagGGTGATCCTCTTCAAGTGAAAGTCAACAAGCTCTCATCTACAAAGACACAACTACCATATGATTACTATTACTTGAAGTGGTGTAAGCCCAAGAAGATCA
                          ttctcac  putative branch site (score: 2)
                                     ctgtctttctct  putative PPT
             aattattgatgtttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gaaatatatttgtctttttggcatctttctgttccaatcttattatatcccaatgaccaattattgatgttttctcacatgactgtctttctctgaatagGGTGATCCTCTTCAAGTGAAAGTCAACAAGCTCTCATCTACAAAGACACAACTACCATATGATTACTATTACTTGAAGTGGTGTAAGCCCAAGAAGATCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGATCA
-aaatata
- - - - - - - - - - - - ctttctg
- - - - - - - - - - - - - - - - -ccaatct
- - - - - - - - - - - - - - - - - - - - - - - - cccaatg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - acatgac