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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtagtgctcttggtcatggttagttttcctggaatgcaagaatgtgagaatctcatggtttctggctaatgcagAGATAATCTGAGGAACATCTTATTATCAATTTATGGGAATAAGGAATCAGTGGATGAAGATCTGCTACAG

Basic information

species Vitis vinifera
transcript Vv18s0089g01420.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|110376208|gb|EC941257.1|EC941257
EST:     TTGAAGCAACGAGGAATTGCTTCATCAATCTTTGAGCGTGTCAAACAAAG                         AGATAATCTGAGGAACATCTTATTATCAATTTATGGGAATAAGGAATCAGT
genomic: TTGAAGCAACGAGGAATTGCTTCATCAATCTTTGAGCGTGTCAAACAAAGgtagtgctct ... gctaatgcagAGATAATCTGAGGAACATCTTATTATCAATTTATGGGAATAAGGAATCAGT
EST: gi|351012301|gb|FQ429986.1|FQ429986
EST:     TTGAAGCAACGAGGAATTGCTTCATCAATCTTTGAGCGTGTCGAACAAAG                         AGATAATCTGAGGAACATCTTATTATCAATTTATGGGAATAAAGAATCAGT
genomic: TTGAAGCAACGAGGAATTGCTTCATCAATCTTTGAGCGTGTCAAACAAAGgtagtgctct ... gctaatgcagAGATAATCTGAGGAACATCTTATTATCAATTTATGGGAATAAGGAATCAGT
EST: gi|77584623|gb|DV221395.1|DV221395
EST:     TTGAAGCAACGAGGAATTGCTTCATCAATCTTTGAGCGTGTCAAACAAAG                         AGATAATCTGAGGAACATCTTATTATCAATTTATGGGAATAAGGAATCAGT
genomic: TTGAAGCAACGAGGAATTGCTTCATCAATCTTTGAGCGTGTCAAACAAAGgtagtgctct ... gctaatgcagAGATAATCTGAGGAACATCTTATTATCAATTTATGGGAATAAGGAATCAGT
EST: gi|110711535|gb|EE088128.1|EE088128
EST:     TTGAAGCAACGAGGAATTGCTTCATCAATCTTTGAGCGTGTCAAA-AAAG                         AGATAATCTGANGGA-CATCCTTAT-ATCAATT
genomic: TTGAAGCAACGAGGAATTGCTTCATCAATCTTTGAGCGTGTCAAACAAAGgtagtgctct ... gctaatgcagAGATAATCTGA-GGAACATC-TTATTATCAATT
EST: gi|110712201|gb|EE089554.1|EE089554
EST:     TGAAAGCA-CGAAGAATTGCTTCATCAATCTTTGAACGTGTCAAACAA-G                         AGATAATCTGAGGGACATCTTATTATCAATT
genomic: TGAA-GCAACGAGGAATTGCTTCATCAATCTTTGAGCGTGTCAAACAAAGgtagtgctct ... gctaatgcagAGATAATCTGAGGAACATCTTATTATCAATT
EST: gi|352798352|gb|FQ480377.1|FQ480377
EST:     TTGAAGCAACGAGGAATTGCTTCATCAATCTTTGAGCGTGTCAAACAAAG                         AGATAATCTGAGGAACATCTTATTATCAATTTATGGGAATAAGGAATC
genomic: TTGAAGCAACGAGGAATTGCTTCATCAATCTTTGAGCGTGTCAAACAAAGgtagtgctct ... gctaatgcagAGATAATCTGAGGAACATCTTATTATCAATTTATGGGAATAAGGAATC
EST: gi|351038339|gb|FQ461031.1|FQ461031
EST:     TTGAAGCAACGAGGAATTGCTTCATCAATCTTTGAGCGTGTCAAACAAAG                         AGATAATCTGAGGAACATCTTATTATCAAATTATGGGAATAAGGAATCA
genomic: TTGAAGCAACGAGGAATTGCTTCATCAATCTTTGAGCGTGTCAAACAAAGgtagtgctct ... gctaatgcagAGATAATCTGAGGAACATCTTATTATCAATTTATGGGAATAAGGAATCA
EST: gi|351048153|gb|FQ442123.1|FQ442123
EST:     TTGAAGCAACGAGGAATTGCTTCATCAATCTTTGAGCGTGTCAAACAAAG                         AGATAATCTGAGGAACATCTTATTATCAATTTATGGGAATAAGGAATCAGT
genomic: TTGAAGCAACGAGGAATTGCTTCATCAATCTTTGAGCGTGTCAAACAAAGgtagtgctct ... gctaatgcagAGATAATCTGAGGAACATCTTATTATCAATTTATGGGAATAAGGAATCAGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttagttttcctggaatgcaagaatgtgagaatctcatggtttctggctaatgcagAGATAATCTGAGGAACATCTTATTATCAATTTATGGGAATAAGGAATCAGTGGATGAAGATCTGCTACAG
                                            ggctaat  putative branch site (score: 3)
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtagtgctcttggtcatggttagttttcctggaatgcaagaatgtgagaatctcatggtttctggctaatgcagAGATAATCTGAGGAACATCTTATTATCAATTTATGGGAATAAGGAATCAGTGGATGAAGATCTGCTACAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA