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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ccaccttcaggtccatgcggattttacaaacaaacttttatgcattgtgcaagcatgattatccatatttcagctcattattcaatttgacatcttgcagCTGATTGGCACCCCATCAGAGGCTGAGTTGGGGTTTTTGAATGAAAATGCAAAGAGATACATTCGGCAACTTCCTATTTACCGTCGGCAGACATTCACTG

Basic information

species Vitis vinifera
transcript Vv05s0094g00900.t01
intron # 4
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|30131434|gb|CB916773.1|CB916773
EST:     CTTTATTTCCTGGCAGAGATCATGTGCATCAGCTACGTTTGCTTATGGAG                         CTGATTGGCACCCCATCAGAGGCTGAGTTGGGGTTTTTGAATGAAAATGCA
genomic: CTTTGTTTCCTGGCAGAGATCATGTGCATCAGCTACGTTTGCTTATGGAGgtgattcttt ... catcttgcagCTGATTGGCACCCCATCAGAGGCTGAGTTGGGGTTTTTGAATGAAAATGCA
EST: gi|34364337|gb|CF405922.1|CF405922
EST:     -TTGTTTCCCTGGCAGAGATCATGTGCATCAGCTACGTTTGCTTATGGAG                         CTGATTGGCACCCCATCAGAGGCTGAGTTGGGGTTTTTGAATGAAAATGCA
genomic: TTTGTTT-CCTGGCAGAGATCATGTGCATCAGCTACGTTTGCTTATGGAGgtgattcttt ... catcttgcagCTGATTGGCACCCCATCAGAGGCTGAGTTGGGGTTTTTGAATGAAAATGCA
EST: gi|110411727|gb|EC977450.1|EC977450
EST:     CTTTATTTCCTGGCAGAGATCATGTGCATCAGCTACGTTTGCTTATGGAG                         CTGATTGGCACCCCATCAGAGGCTGAGTTGGGGTTTTTGAATGAAAATGCA
genomic: CTTTGTTTCCTGGCAGAGATCATGTGCATCAGCTACGTTTGCTTATGGAGgtgattcttt ... catcttgcagCTGATTGGCACCCCATCAGAGGCTGAGTTGGGGTTTTTGAATGAAAATGCA
EST: gi|71876332|gb|DT025387.1|DT025387
EST:     CCTTGTTTCCTGGCAGAGATCATGTGCATCAGCTACGTTTGCTTATGGAG                         CTGATTGGCACCCCATCAGAGGCTGAGTTGGGGTTTTTGAATGAAAATGCA
genomic: CTTTGTTTCCTGGCAGAGATCATGTGCATCAGCTACGTTTGCTTATGGAGgtgattcttt ... catcttgcagCTGATTGGCACCCCATCAGAGGCTGAGTTGGGGTTTTTGAATGAAAATGCA
EST: gi|33404655|gb|CF210282.1|CF210282
EST:     TTTATTTCCTGGCAGAGATCATGTGCATCAGCTACGTTTGCTTGAT-CAG                         CTGATTGGCACCCCATCAGAGGCTGAGTTGGGGTTTTTGAATGAAAATGC
genomic: TTTGTTTCCTGGCAGAGATCATGTGCATCAGCTACGTTTGCTT-ATGGAGgtgattcttt ... catcttgcagCTGATTGGCACCCCATCAGAGGCTGAGTTGGGGTTTTTGAATGAAAATGC
EST: gi|110705998|gb|EE083484.1|EE083484
EST:     CTTTGTTTCCTGGCAGAGATCATGTGCATCAGCTACGTTTGCTTATGGAG                         CTGATTGGCACCCCATCAGAGGCTGAGTTGGGGTTTTTGAATGAAAATGCA
genomic: CTTTGTTTCCTGGCAGAGATCATGTGCATCAGCTACGTTTGCTTATGGAGgtgattcttt ... catcttgcagCTGATTGGCACCCCATCAGAGGCTGAGTTGGGGTTTTTGAATGAAAATGCA
EST: gi|34363900|gb|CF405485.1|CF405485
EST:     AGAGATCATGTGCATCAGCTACGTTGGCTTATGGAG                         CTGATTGGCACCCCATCAGAGGCTGAGTTGGGGTTTTTGAATGAAAATGCA
genomic: AGAGATCATGTGCATCAGCTACGTTTGCTTATGGAGgtgattcttt ... catcttgcagCTGATTGGCACCCCATCAGAGGCTGAGTTGGGGTTTTTGAATGAAAATGCA
EST: gi|110405255|gb|EC970794.1|EC970794
EST:     CTTTATTTCCTGGCAGAGATCATGTGCATCAGCTACGTTTGCTTATGGAG                         CTGATTGGCACCCCATCAGAGGCTGAGTTGGGGTTTTTGAATGAAAATGCA
genomic: CTTTGTTTCCTGGCAGAGATCATGTGCATCAGCTACGTTTGCTTATGGAGgtgattcttt ... catcttgcagCTGATTGGCACCCCATCAGAGGCTGAGTTGGGGTTTTTGAATGAAAATGCA
EST: gi|33408675|gb|CF214302.1|CF214302
EST:     CTTTATTTCCTGGCAGAGATCATGTGCATCAGCTACGTTTGCTTATGGAG                         CTGATTGGCACCCCATCAGAGGCTGAGTTGGGGTTTTTGAATGAAAATGCA
genomic: CTTTGTTTCCTGGCAGAGATCATGTGCATCAGCTACGTTTGCTTATGGAGgtgattcttt ... catcttgcagCTGATTGGCACCCCATCAGAGGCTGAGTTGGGGTTTTTGAATGAAAATGCA
EST: gi|33408416|gb|CF214043.1|CF214043
EST:     CTTTATTTCCTGGCAGAGATCATGTGCATCAGCTACGTTTGCTTATGGAG                         CTGATTGGCACCCCATCAGAGGCTGAGTTGGGGTTTTTGAATGAAAATGCA
genomic: CTTTGTTTCCTGGCAGAGATCATGTGCATCAGCTACGTTTGCTTATGGAGgtgattcttt ... catcttgcagCTGATTGGCACCCCATCAGAGGCTGAGTTGGGGTTTTTGAATGAAAATGCA
EST: gi|161716253|gb|FC068076.1|FC068076
EST:     CTTTGTTTCCTGGCAGAGATCATGTGCATCAGCTACGTTTGCTTATGGAG                         CTGATTGGCACCCCATC
genomic: CTTTGTTTCCTGGCAGAGATCATGTGCATCAGCTACGTTTGCTTATGGAGgtgattcttt ... catcttgcagCTGATTGGCACCCCATC
EST: gi|110715356|gb|EE093309.1|EE093309
EST:     CTTTGTTTCCTGGCAGAGATCATGTGCATCAGCTACGTTTGCTTATGGAG                         CTGATTGGCACCCCATCAGAGGCTGAGTTGGGGTTTTTGAATGAAAATGCA
genomic: CTTTGTTTCCTGGCAGAGATCATGTGCATCAGCTACGTTTGCTTATGGAGgtgattcttt ... catcttgcagCTGATTGGCACCCCATCAGAGGCTGAGTTGGGGTTTTTGAATGAAAATGCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgtgcaagcatgattatccatatttcagctcattattcaatttgacatcttgcagCTGATTGGCACCCCATCAGAGGCTGAGTTGGGGTTTTTGAATGAAAATGCAAAGAGATACATTCGGCAACTTCCTATTTACCGTCGGCAGACATTCACTG
                                       atttgac  putative branch site (score: 4)
                             tcattattcaattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ccaccttcaggtccatgcggattttacaaacaaacttttatgcattgtgcaagcatgattatccatatttcagctcattattcaatttgacatcttgcagCTGATTGGCACCCCATCAGAGGCTGAGTTGGGGTTTTTGAATGAAAATGCAAAGAGATACATTCGGCAACTTCCTATTTACCGTCGGCAGACATTCACTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGA
ccacctt
- - - - - -tccatgc
- - - - - - - - - - - - - -aaacaaa
- - - - - - - - - - - - - - - - - - - - tgcattg
- - - - - - - - - - - - - - - - - - - - - - - - gcaagca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cagctca