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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...agtttgggttttctattttttttccaatgttttctagtgaaacaaactgaggttttggttgttcctttttgatgggtttgtgttttgtttatgtgttcagATCTAAATCGAAGGGAGACGTTTTTCCGATAAGCCATGGCTCTG

Basic information

species Vitis vinifera
transcript Vv12s0035g01130.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|351055139|gb|FQ440478.1|FQ440478
EST:     CTGCCGCTCCCACTTCTCGTGTGCGTTCGGAAGAACTCTCCTGGTCAAAG                         ATCTAAATCGAAGGGAGGCGTTTTTCCGATAAGCCATGGCTCTG
genomic: CTGCCGCTCCCACTTCTCGTGTGCCTTCGGAAGAACTCTCCTGGTCAAAGgtactctctc ... atgtgttcagATCTAAATCGAAGGGAGACGTTTTTCCGATAAGCCATGGCTCTG
EST: gi|110368464|gb|EC932441.1|EC932441
EST:     TCTCGTGTGCCTTCGGAAGAACTCTCCTGGTCAAAG                         ATCTAAATCGAAGGGAGACGTTTTTCCGATAAGCCATGGCTCTG
genomic: TCTCGTGTGCCTTCGGAAGAACTCTCCTGGTCAAAGgtactctctc ... atgtgttcagATCTAAATCGAAGGGAGACGTTTTTCCGATAAGCCATGGCTCTG
EST: gi|161719271|gb|FC068941.1|FC068941
EST:     CTGCCGCTCCCACTTCTCGTGTGCCTTCGGAAGAACTCTCCTGGTCAAAG                         ATCTAAATCGAAGGGAGACGTTTTTCCGATAAGCCATGGCTCTG
genomic: CTGCCGCTCCCACTTCTCGTGTGCCTTCGGAAGAACTCTCCTGGTCAAAGgtactctctc ... atgtgttcagATCTAAATCGAAGGGAGACGTTTTTCCGATAAGCCATGGCTCTG
EST: gi|110727170|gb|EE103626.1|EE103626
EST:     CACTTCTCGTGTGCCTTCGGAAGAACTCTCCTGGTCAAAG                         ATCTAAATCGAAGGGAGACGTTTTTCCGATAAGCCATGGCTCTG
genomic: CACTTCTCGTGTGCCTTCGGAAGAACTCTCCTGGTCAAAGgtactctctc ... atgtgttcagATCTAAATCGAAGGGAGACGTTTTTCCGATAAGCCATGGCTCTG
EST: gi|110385087|gb|EC949579.1|EC949579
EST:     CCCACTTCTCGTGTGCCTTCGGAAGAACTCTCCTGGTCAAAG                         ATCTAAATCGAAGGGAGACGTTTTTCCGATAAGCCATGGCTCTG
genomic: CCCACTTCTCGTGTGCCTTCGGAAGAACTCTCCTGGTCAAAGgtactctctc ... atgtgttcagATCTAAATCGAAGGGAGACGTTTTTCCGATAAGCCATGGCTCTG
EST: gi|351042107|gb|FQ456317.1|FQ456317
EST:     CTGCCGCTCCCACTTCTCGTGTGCGTTCGGAAGAACTCTCCTGGTCAAAG                         ATCTAAATCGAAGGGAGACGTTTTTCTGATAAGCCATGGCTCTG
genomic: CTGCCGCTCCCACTTCTCGTGTGCCTTCGGAAGAACTCTCCTGGTCAAAGgtactctctc ... atgtgttcagATCTAAATCGAAGGGAGACGTTTTTCCGATAAGCCATGGCTCTG
EST: gi|351017433|gb|FQ435786.1|FQ435786
EST:     CTGCCGCTCCCACTTCTCGTGTGCGTTCGGAAGAACTCTCCTGGTCAAAG                         ATCTAAATCGAAGGGAGACGTTTTTCCGATAAGCCATGGCTCTG
genomic: CTGCCGCTCCCACTTCTCGTGTGCCTTCGGAAGAACTCTCCTGGTCAAAGgtactctctc ... atgtgttcagATCTAAATCGAAGGGAGACGTTTTTCCGATAAGCCATGGCTCTG
EST: gi|110381916|gb|EC937999.1|EC937999
EST:     GTGCCTTCGGAAGAACTCTCCTGGTCAAAG                         ATCTAAATCGAAGGGAGACGTTTTTCCGATAAGCCATGGCTCTG
genomic: GTGCCTTCGGAAGAACTCTCCTGGTCAAAGgtactctctc ... atgtgttcagATCTAAATCGAAGGGAGACGTTTTTCCGATAAGCCATGGCTCTG
EST: gi|37183445|gb|CF602799.1|CF602799
EST:     CTCCTGGTCAAAG                         ATCTAAATCGAAGGGAGACGTTTTTCCGATAAGCCATGGCTCTG
genomic: CTCCTGGTCAAAGgtactctctc ... atgtgttcagATCTAAATCGAAGGGAGACGTTTTTCCGATAAGCCATGGCTCTG
EST: gi|351028342|gb|FQ427238.1|FQ427238
EST:     CTGCCGCTCCCACTTCTCGTGTGCGTTCGGAAGAACTCTCCTGGTCAAAG                         ATCTAAATCGAAGGGAGACGTTTTTCCGATAAGCCATGGCTCTG
genomic: CTGCCGCTCCCACTTCTCGTGTGCCTTCGGAAGAACTCTCCTGGTCAAAGgtactctctc ... atgtgttcagATCTAAATCGAAGGGAGACGTTTTTCCGATAAGCCATGGCTCTG
EST: gi|110381825|gb|EC935490.1|EC935490
EST:     TCTCGTGTGCCTTCGGAAGAACTCTCCTGGTCAAAG                         ATCTAAATCGAAGGGAGACGTTTTTCCGATAAGCCATGGCTCTG
genomic: TCTCGTGTGCCTTCGGAAGAACTCTCCTGGTCAAAGgtactctctc ... atgtgttcagATCTAAATCGAAGGGAGACGTTTTTCCGATAAGCCATGGCTCTG
EST: gi|110392524|gb|EC958004.1|EC958004
EST:     CTTCGGAAGAACTCTCCTGGTCAAAG                         ATCTAAATCGAAGGGAGACGTTTTTCCGATAAGCCATGGCTCTG
genomic: CTTCGGAAGAACTCTCCTGGTCAAAGgtactctctc ... atgtgttcagATCTAAATCGAAGGGAGACGTTTTTCCGATAAGCCATGGCTCTG
EST: gi|351025275|gb|FQ434288.1|FQ434288
EST:     CTGCCGCTCCCACTTCTCGTGTGCGTTCGGAAGAACTCTCCTGGTCAAAG                         ATCTAAATCGAAGGGAGACGTTTTTCCGATAAGCCATGGCTCTG
genomic: CTGCCGCTCCCACTTCTCGTGTGCCTTCGGAAGAACTCTCCTGGTCAAAGgtactctctc ... atgtgttcagATCTAAATCGAAGGGAGACGTTTTTCCGATAAGCCATGGCTCTG
EST: gi|71855580|gb|DT004635.1|DT004635
EST:     CTGCCGCTCCCACTTCTCGTGTGCCTTCGGAAGAACTCTCCTGGTCAAAG                         ATCTAAATCGAAGGGAGACGTTTTTCCGATAAGCCATGGCTCTG
genomic: CTGCCGCTCCCACTTCTCGTGTGCCTTCGGAAGAACTCTCCTGGTCAAAGgtactctctc ... atgtgttcagATCTAAATCGAAGGGAGACGTTTTTCCGATAAGCCATGGCTCTG
EST: gi|71859460|gb|DT008515.1|DT008515
EST:     CTGCCGCTCCCACTTCTCGTGTGCCTTCGGAAGAACTCTCCTGGTCAAAG                         ATCTAAATCGAAGGGAGACGTTTTTCCGATAAGCCATGGCTCTG
genomic: CTGCCGCTCCCACTTCTCGTGTGCCTTCGGAAGAACTCTCCTGGTCAAAGgtactctctc ... atgtgttcagATCTAAATCGAAGGGAGACGTTTTTCCGATAAGCCATGGCTCTG
EST: gi|71858356|gb|DT007411.1|DT007411
EST:     CTGCCGCTCCCACTTCTCGTGTGCCTTCGGAAGAACTCTCCTGGTCAAAG                         ATCTAAATCGAAGGGAGACGTTTTTCCGATAAGCCATGGCTCTG
genomic: CTGCCGCTCCCACTTCTCGTGTGCCTTCGGAAGAACTCTCCTGGTCAAAGgtactctctc ... atgtgttcagATCTAAATCGAAGGGAGACGTTTTTCCGATAAGCCATGGCTCTG
EST: gi|294965707|gb|GW839162.1|GW839162
EST:     CTGCCGCTCCCACTTCTCGTGTGCCTTCGGAAGAACTCTCCTGGTCAAAG                         ATCTAAATCGAAGGGAGACGTTTTTCCGATAAGCCATGGCTCTG
genomic: CTGCCGCTCCCACTTCTCGTGTGCCTTCGGAAGAACTCTCCTGGTCAAAGgtactctctc ... atgtgttcagATCTAAATCGAAGGGAGACGTTTTTCCGATAAGCCATGGCTCTG
EST: gi|351027331|gb|FQ444580.1|FQ444580
EST:     CTGCCGCTCCCACTTCTCGTGTGCGTTCGGAAGAACTCTCCTGGTCAAAG                         ATCTAAATCGAAGGGAGACGTTTTTCCGATAAGCCATGGCTCTG
genomic: CTGCCGCTCCCACTTCTCGTGTGCCTTCGGAAGAACTCTCCTGGTCAAAGgtactctctc ... atgtgttcagATCTAAATCGAAGGGAGACGTTTTTCCGATAAGCCATGGCTCTG
EST: gi|161714380|gb|FC063221.1|FC063221
EST:     CACTTCTCGTGTGCCTTCGGAAGAACTCTCCTGGTCAAAG                         ATCTAAATCGAAGGGAGACGTTTTTCCGATAAGCCATGGCTCTG
genomic: CACTTCTCGTGTGCCTTCGGAAGAACTCTCCTGGTCAAAGgtactctctc ... atgtgttcagATCTAAATCGAAGGGAGACGTTTTTCCGATAAGCCATGGCTCTG
EST: gi|351016802|gb|FQ424229.1|FQ424229
EST:     CTGCCGCTCCCACTTCTCGTGTGCGTTCGGAAGAACTCTCCTGGTCAAAG                         ATCTAAATCGAAGGGAGACGTTTTTCCGATAAGCCATGGCTCTG
genomic: CTGCCGCTCCCACTTCTCGTGTGCCTTCGGAAGAACTCTCCTGGTCAAAGgtactctctc ... atgtgttcagATCTAAATCGAAGGGAGACGTTTTTCCGATAAGCCATGGCTCTG
EST: gi|352794288|gb|FQ479530.1|FQ479530
EST:     CTGCCGCTCCCACTTCTCGTGTGCGTTCGGAAGAACTCTCCTGGTCAAAG                         ATCTAAATCGAAGGGAGACGTTTTTCTGATAAGCCATGGCTCTG
genomic: CTGCCGCTCCCACTTCTCGTGTGCCTTCGGAAGAACTCTCCTGGTCAAAGgtactctctc ... atgtgttcagATCTAAATCGAAGGGAGACGTTTTTCCGATAAGCCATGGCTCTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

actgaggttttggttgttcctttttgatgggtttgtgttttgtttatgtgttcagATCTAAATCGAAGGGAGACGTTTTTCCGATAAGCCATGGCTCTG
                     ttttgat  putative branch site (score: 4)
                                     ttttgtttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
agtttgggttttctattttttttccaatgttttctagtgaaacaaactgaggttttggttgttcctttttgatgggtttgtgttttgtttatgtgttcagATCTAAATCGAAGGGAGACGTTTTTCCGATAAGCCATGGCTCTG

- - - - - - - - - - - -ccaatgt
- - - - - - - - - - - - - - - - - - - -aaacaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gggtttg