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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaattcctaagcttaatctgtttctgctttgaaaaactagtttttaactggttgggtttacatgaatggtagaatcctctgacttgtgttataggctggctgacgggcaagctttctgtttctgtaattctttctcagGAGTTGTTGGGACCAAAGAGAGCATCACTATGATACACAATCATGAATTCATGGGGTTCTTATCATTCTGTGACAGCCAATGATTTCTTGCAATGAAGAA

Basic information

species Vitis vinifera
transcript Vv08s0007g04230.t01
intron # 11
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|110718237|gb|EE094838.1|EE094838
EST:     TATCATATTCATCCTATCCGGTGTGATATTTGCCAGTGCTCTCACAATGG                         GAGTTGTTGGGACCAAAGAGAGCATCACTATGATACACAATCATGAATTCA
genomic: TATCATATTCATCCTATCCGGTGTGATATTTGCCAGTGCTCTCACAATGGgtaattccta ... tctttctcagGAGTTGTTGGGACCAAAGAGAGCATCACTATGATACACAATCATGAATTCA
EST: gi|110716984|gb|EE092443.1|EE092443
EST:     TATCATATTCATCCTATCCGGTGTGATATTTGCCAGTGCTCTCACAATGG                         GAGTTGTTGGGACCAAAGAGAGCATCACTATGATACACAATCATGAATTCA
genomic: TATCATATTCATCCTATCCGGTGTGATATTTGCCAGTGCTCTCACAATGGgtaattccta ... tctttctcagGAGTTGTTGGGACCAAAGAGAGCATCACTATGATACACAATCATGAATTCA
EST: gi|110720724|gb|EE096897.1|EE096897
EST:     TATCATATTCATCCTATCCGGTGTGATATTTGCCAGTGCTCTCACAATGG                         GGAGTTGTTGGGACCAA-GAAAGCATCACTATGATACACAATCATGAAATT
genomic: TATCATATTCATCCTATCCGGTGTGATATTTGCCAGTGCTCTCACAATGGgtaattccta ... tctttctcagG-AGTTGTTGGGACCAAAGAGAGCATCACTATGATACACAATCATGAA-TT
EST: gi|110714603|gb|EE091700.1|EE091700
EST:     TATCATATTCATCCTATCCGGTGTGATATTTGCCAGTGCTCTCACAATGG                         GAGTTGTTGGGACCAAAGAGAGCATCACTATGATACACAATCATGAATTCA
genomic: TATCATATTCATCCTATCCGGTGTGATATTTGCCAGTGCTCTCACAATGGgtaattccta ... tctttctcagGAGTTGTTGGGACCAAAGAGAGCATCACTATGATACACAATCATGAATTCA
EST: gi|110382176|gb|EC938689.1|EC938689
EST:     TATCATATTCATCCTATCCGGTGTGATATTTGCCAGTGCTCTCACAATGG                         GAGTTGTTGGGACCAAAGAGAGCATCACTATGATACACAATCATGAATTCA
genomic: TATCATATTCATCCTATCCGGTGTGATATTTGCCAGTGCTCTCACAATGGgtaattccta ... tctttctcagGAGTTGTTGGGACCAAAGAGAGCATCACTATGATACACAATCATGAATTCA
EST: gi|110716151|gb|EE090882.1|EE090882
EST:     TATCATATTCATCCTATCCGGTGTGATATTTGCCAGTGCTCTCACAATGG                         GAGTTGTTGGGACCAAAGAGAGCATCACTATGATACACAATCATGAATTCA
genomic: TATCATATTCATCCTATCCGGTGTGATATTTGCCAGTGCTCTCACAATGGgtaattccta ... tctttctcagGAGTTGTTGGGACCAAAGAGAGCATCACTATGATACACAATCATGAATTCA
EST: gi|32249989|gb|CD715808.1|CD715808
EST:     GATATTTGCCAGTGCTCTCACAATGG                         GAGTTGTTGGGACCAAAGAGAGCATCACTATGATACACAATCATGAATTCA
genomic: GATATTTGCCAGTGCTCTCACAATGGgtaattccta ... tctttctcagGAGTTGTTGGGACCAAAGAGAGCATCACTATGATACACAATCATGAATTCA
EST: gi|71883946|gb|DT033001.1|DT033001
EST:     TATCATATTCATCCTATCCGGTGTGATATTTGCCAGTGCTCTCACAATGG                         GAGTTGTTGGGACCAAAGAGAGCATCACTATGATACACAATCATGAATTCA
genomic: TATCATATTCATCCTATCCGGTGTGATATTTGCCAGTGCTCTCACAATGGgtaattccta ... tctttctcagGAGTTGTTGGGACCAAAGAGAGCATCACTATGATACACAATCATGAATTCA
EST: gi|71888381|gb|DT037436.1|DT037436
EST:     TATCATATTCATCCTATCCGGTGTGATATTTGCCAGTGCTCTCACAATGG                         GAGTTGTTGGGACCAAAGAGAGCATCACTATGATACACAATCATGAATTCA
genomic: TATCATATTCATCCTATCCGGTGTGATATTTGCCAGTGCTCTCACAATGGgtaattccta ... tctttctcagGAGTTGTTGGGACCAAAGAGAGCATCACTATGATACACAATCATGAATTCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgtgttataggctggctgacgggcaagctttctgtttctgtaattctttctcagGAGTTGTTGGGACCAAAGAGAGCATCACTATGATACACAATCATGAATTCATGGGGTTCTTATCATTCTGTGACAGCCAATGATTTCTTGCAATGAAGAA
              ggctgac  putative branch site (score: 3)
                                            ttctttctc  putative PPT
                                         taattcttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaattcctaagcttaatctgtttctgctttgaaaaactagtttttaactggttgggtttacatgaatggtagaatcctctgacttgtgttataggctggctgacgggcaagctttctgtttctgtaattctttctcagGAGTTGTTGGGACCAAAGAGAGCATCACTATGATACACAATCATGAATTCATGGGGTTCTTATCATTCTGTGACAGCCAATGATTTCTTGCAATGAAGAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA