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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagttgtctaaatatactcatgtttcatccatttttttgttaggcatcttctcattttattttaatgtgttcttataatttctagTGTGGGACCGATGCTCCAATTAGTGCTTCTCGAATGCTGGGGGAAGTGAGCAG

Basic information

species Vitis vinifera
transcript Vv13s0158g00120.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|349808350|gb|FQ405518.1|FQ405518
EST:     CAAAGGAACTCTTGATTCTTTAATG                         TGTGGGACCGATGCTCCAATTAGTGCTTCTCGAATGCTGGGGGAAGTGAGC
genomic: CAAAGGAACTCTTGATTCTTTAATGgtaagttgtc ... taatttctagTGTGGGACCGATGCTCCAATTAGTGCTTCTCGAATGCTGGGGGAAGTGAGC
EST: gi|110419752|gb|EC986001.1|EC986001
EST:     CAAAGGAACTCTTGATTCTTTAATG                         TGTGGGACCGATGCTCCAATTAGTGCTTCTCGGATGCTGGGGGAAGTAAGC
genomic: CAAAGGAACTCTTGATTCTTTAATGgtaagttgtc ... taatttctagTGTGGGACCGATGCTCCAATTAGTGCTTCTCGAATGCTGGGGGAAGTGAGC
EST: gi|110372637|gb|EC936821.1|EC936821
EST:     CAAAGGAACTCTTGATTCTTTAATG                         TGTGGGACCGATGCTCCAATTAGTGCTTCTCGGATGCTGGGGGAAGTAAGC
genomic: CAAAGGAACTCTTGATTCTTTAATGgtaagttgtc ... taatttctagTGTGGGACCGATGCTCCAATTAGTGCTTCTCGAATGCTGGGGGAAGTGAGC
EST: gi|351025482|gb|FQ435174.1|FQ435174
EST:     CAAAGGAACTCTTGATTCTTTAATG                         TGTGGGACCGATGCTCCAATTAGTGCTTCTCGGATGCTGGGGGAAGTAAGC
genomic: CAAAGGAACTCTTGATTCTTTAATGgtaagttgtc ... taatttctagTGTGGGACCGATGCTCCAATTAGTGCTTCTCGAATGCTGGGGGAAGTGAGC
EST: gi|351012117|gb|FQ429923.1|FQ429923
EST:     CAAAGGAACTCTTGATTCTTTAATG                         TGTGGGACCGATGCTCCAATTAGTGCTTCTCGAATGCTGGGGGAAGTGAGC
genomic: CAAAGGAACTCTTGATTCTTTAATGgtaagttgtc ... taatttctagTGTGGGACCGATGCTCCAATTAGTGCTTCTCGAATGCTGGGGGAAGTGAGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atttttttgttaggcatcttctcattttattttaatgtgttcttataatttctagTGTGGGACCGATGCTCCAATTAGTGCTTCTCGAATGCTGGGGGAAGTGAGCAG
                             ttttaat  putative branch site (score: 3)
                                       ttcttat  putative PPT
                       attttattttaatgtg  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagttgtctaaatatactcatgtttcatccatttttttgttaggcatcttctcattttattttaatgtgttcttataatttctagTGTGGGACCGATGCTCCAATTAGTGCTTCTCGAATGCTGGGGGAAGTGAGCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG