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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tcccacactccaaggtttgttcggttaatttctatgttatctggtcatgttttatgtccttttcatggcctgttcttatgttatctatttttaatttcagGCTTCAAAAAGAGTTGATGGCCCTCATG

Basic information

species Vitis vinifera
transcript Vv13s0019g04090.t01
intron # 1
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|161721358|gb|FC070758.1|FC070758
EST:     CAGCTCAAAGCTGCGCCTAACCCCGTCGACACCAGTTCCGTTTCTCAGAG                         GCTTCAAAAAGAGTTGATGGCCCTCATG
genomic: CAGCTCAAAGCTGCGCCTAACCCCGTCGACACCAGTTCCGTTTCTCAGAGgtccatttcg ... ttaatttcagGCTTCAAAAAGAGTTGATGGCCCTCATG
EST: gi|161718960|gb|FC066380.1|FC066380
EST:     CAGCTCAAAGCTGCGCCTAACCCCGTCGACACCAGTTCCGTTTCTCAGAG                         GCTTCAAAAAGAGTTGATGGCCCTCATG
genomic: CAGCTCAAAGCTGCGCCTAACCCCGTCGACACCAGTTCCGTTTCTCAGAGgtccatttcg ... ttaatttcagGCTTCAAAAAGAGTTGATGGCCCTCATG
EST: gi|294965000|gb|GW838803.1|GW838803
EST:     CAGCTCAAAGCTGCGCCTAACCCCGTCGACACCAGTTCCGTTTCTCAGAG                         GCTTCAAAAAGAGTTGATGGCCCTCATG
genomic: CAGCTCAAAGCTGCGCCTAACCCCGTCGACACCAGTTCCGTTTCTCAGAGgtccatttcg ... ttaatttcagGCTTCAAAAAGAGTTGATGGCCCTCATG
EST: gi|161712977|gb|FC062103.1|FC062103
EST:     CAGCTCAAAGCTGCGCCTAACCCCGTCGACACCAGTTCCGTTTCTCAGAG                         GCTTCAAAAAGAGTTGATGGCCCTCATG
genomic: CAGCTCAAAGCTGCGCCTAACCCCGTCGACACCAGTTCCGTTTCTCAGAGgtccatttcg ... ttaatttcagGCTTCAAAAAGAGTTGATGGCCCTCATG
EST: gi|37186163|gb|CF605516.1|CF605516
EST:     CAGCTCAAAGCTGCGCCTAACCCCGTCGACACCAGTTCCGTTTCTCAGAG                         GCTTCAAAAAGAGTTGATGGCCCTCATG
genomic: CAGCTCAAAGCTGCGCCTAACCCCGTCGACACCAGTTCCGTTTCTCAGAGgtccatttcg ... ttaatttcagGCTTCAAAAAGAGTTGATGGCCCTCATG
EST: gi|110426829|gb|EC993253.1|EC993253
EST:     CAGCTCAAAGCTGCGCCTAACCCCGTCGACACCAGTTCCGTTTCTCAGAG                         GCTTCAAAAAGAGTTGATGGCCCTCATG
genomic: CAGCTCAAAGCTGCGCCTAACCCCGTCGACACCAGTTCCGTTTCTCAGAGgtccatttcg ... ttaatttcagGCTTCAAAAAGAGTTGATGGCCCTCATG
EST: gi|161720059|gb|FC065103.1|FC065103
EST:     CAGCTCAAAGCTGCGCCTAACCCCGTCGACACCAGTTCCGTTTCTCAGAG                         GCTTCAAAAAGAGTTGATGGCCCTCATG
genomic: CAGCTCAAAGCTGCGCCTAACCCCGTCGACACCAGTTCCGTTTCTCAGAGgtccatttcg ... ttaatttcagGCTTCAAAAAGAGTTGATGGCCCTCATG
EST: gi|110711177|gb|EE087407.1|EE087407
EST:     CAACTCAAAGCTGCGCCTAACCCCGTCGACACCAGTTCCGTTTCTCAGAG                         GCTTCAAAAAGAGTTGATGGCCCTCATG
genomic: CAGCTCAAAGCTGCGCCTAACCCCGTCGACACCAGTTCCGTTTCTCAGAGgtccatttcg ... ttaatttcagGCTTCAAAAAGAGTTGATGGCCCTCATG
EST: gi|30125638|gb|CB910977.1|CB910977
EST:     CAGCTCAAAGCTGCGCCTAACCCCGTCGACACCAGTTCCGTTTCTCAGAG                         GCTTCAAAAAGAGTTGATGGCCCTCATG
genomic: CAGCTCAAAGCTGCGCCTAACCCCGTCGACACCAGTTCCGTTTCTCAGAGgtccatttcg ... ttaatttcagGCTTCAAAAAGAGTTGATGGCCCTCATG
EST: gi|110686046|gb|EE063296.1|EE063296
EST:     CAGCTCAAAGCTGCGCCTAACCCCGTCGACACCAGTTCCGTTTCTCAGAG                         GCTTCAAAAAGAGTTGATGGCCCTCATG
genomic: CAGCTCAAAGCTGCGCCTAACCCCGTCGACACCAGTTCCGTTTCTCAGAGgtccatttcg ... ttaatttcagGCTTCAAAAAGAGTTGATGGCCCTCATG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

catgttttatgtccttttcatggcctgttcttatgttatctatttttaatttcagGCTTCAAAAAGAGTTGATGGCCCTCATG
                                           ttttaat  putative branch site (score: 3)
                                      tctattttt  CT-rich tract
                         tgttcttatgttatct  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tcccacactccaaggtttgttcggttaatttctatgttatctggtcatgttttatgtccttttcatggcctgttcttatgttatctatttttaatttcagGCTTCAAAAAGAGTTGATGGCCCTCATG

tcccaca
- - - -ctccaag
- - - - - - - - - - - - - - - - - - - - - ggtcatg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cctgttc