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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gtcttttcatattttacaaggctttaaagatcgatgtggcctaaaattatgggcctctttacgaaaaatgaaaatcttacagaaaatattgtacctctagGTTAAACCAGTCATCAAATTGCTGAAACAAACACTAGTTGGGACAGGAGTGTTACTTGTTACAGCAGTGACACTATTTATCTTTGCTACACCAGTGGAGG

Basic information

species Vitis vinifera
transcript Vv07s0129g00470.t01
intron # 5
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|349826186|gb|FQ415991.1|FQ415991
EST:     GTCCTGGCTCGTGATAGACTGTTGGGCTCTTATAAG                         GTTAAACCAGTCATCAAATTGCTGAAACAAACACTAGTTGGGGACAGGAGT
genomic: GTCCTGGCTCGTGATAGACTGTTGGGCTCTTATAAGgtaataacga ... gtacctctagGTTAAACCAGTCATCAAATTGCTGAAACAAACACTAGTTGGG-ACAGGAGT
EST: gi|28961127|gb|CB340571.1|CB340571
EST:     GTCCTGGCTCGTGATAGACTGTTGGGCTCTTATAAG                         GTTAAACCAGTCATCAAATTGCTGAAACAAACACTAGTTGGGACAGGAGTG
genomic: GTCCTGGCTCGTGATAGACTGTTGGGCTCTTATAAGgtaataacga ... gtacctctagGTTAAACCAGTCATCAAATTGCTGAAACAAACACTAGTTGGGACAGGAGTG
EST: gi|349828063|gb|FQ415391.1|FQ415391
EST:     GTCCTGGCTCGTGATAGACTGTTGGGCTCTTATAAG                         GTTAAACCAGTCATCAAATTGCTGAAACAAACACTAGTTGGGACAGGAGTG
genomic: GTCCTGGCTCGTGATAGACTGTTGGGCTCTTATAAGgtaataacga ... gtacctctagGTTAAACCAGTCATCAAATTGCTGAAACAAACACTAGTTGGGACAGGAGTG
EST: gi|351013296|gb|FQ425001.1|FQ425001
EST:     GTCCTGGCTCGTGATAGACTGTTGGGCTCTTATAAG                         GTTAAACCAGTCATCAAATTGCTGAAACAAACACTAGTTGGGACAGGAGTG
genomic: GTCCTGGCTCGTGATAGACTGTTGGGCTCTTATAAGgtaataacga ... gtacctctagGTTAAACCAGTCATCAAATTGCTGAAACAAACACTAGTTGGGACAGGAGTG
EST: gi|26257651|gb|CA808714.1|CA808714
EST:     GTCCTGGCTCGTGATAGACTGTTGGGCTCTTATAAG                         GTTAAACCAGTCATCAAATTGCTGAAACAAACACTAGTTGGGACAGGAGTG
genomic: GTCCTGGCTCGTGATAGACTGTTGGGCTCTTATAAGgtaataacga ... gtacctctagGTTAAACCAGTCATCAAATTGCTGAAACAAACACTAGTTGGGACAGGAGTG
EST: gi|71873447|gb|DT022502.1|DT022502
EST:     GTCCTGGCTCGTGATAGACTGTTGGGCTCTTATAAG                         GTTAAACCAGTCATCAAATTGCTGAAACAAACACTAGTTGGGACAGGAGTG
genomic: GTCCTGGCTCGTGATAGACTGTTGGGCTCTTATAAGgtaataacga ... gtacctctagGTTAAACCAGTCATCAAATTGCTGAAACAAACACTAGTTGGGACAGGAGTG
EST: gi|351016512|gb|FQ423939.1|FQ423939
EST:     GTCCTGGCTCGTGATAGACTGTTGGGCTCTTATAAG                         GTTAAACCAGTCATCAAATTGCTGAAACAAACACTAGTTGGGACAGGAGTG
genomic: GTCCTGGCTCGTGATAGACTGTTGGGCTCTTATAAGgtaataacga ... gtacctctagGTTAAACCAGTCATCAAATTGCTGAAACAAACACTAGTTGGGACAGGAGTG
EST: gi|351040537|gb|FQ434670.1|FQ434670
EST:     GTCCTGGCTCGTGATAGACTGTTGGGCTCTTATAAG                         GTTAAACCAGTCATCAAATTGCTGAAACAAACACTGGTTGGGACAGG
genomic: GTCCTGGCTCGTGATAGACTGTTGGGCTCTTATAAGgtaataacga ... gtacctctagGTTAAACCAGTCATCAAATTGCTGAAACAAACACTAGTTGGGACAGG
EST: gi|110424500|gb|EC990863.1|EC990863
EST:     GTCCTGGCTCGTGATAGACTGTTGGGCTCTTATAAG                         GTTAAACCAGTCATCAAATTGCTGAAACAAACACTAGTTGGGACAGGAGTG
genomic: GTCCTGGCTCGTGATAGACTGTTGGGCTCTTATAAGgtaataacga ... gtacctctagGTTAAACCAGTCATCAAATTGCTGAAACAAACACTAGTTGGGACAGGAGTG
EST: gi|349830224|gb|FQ420484.1|FQ420484
EST:     GTCCTGGCTCGTGATAGACTGTTGGGCTCTTATAAG                         GTTAAACCAGTCATCAAATTGCTGAAACAAACACTAGTTGGGACAGGAGTG
genomic: GTCCTGGCTCGTGATAGACTGTTGGGCTCTTATAAGgtaataacga ... gtacctctagGTTAAACCAGTCATCAAATTGCTGAAACAAACACTAGTTGGGACAGGAGTG
EST: gi|349830039|gb|FQ420299.1|FQ420299
EST:     GTCCTGGCTCGTGATAGACTGTTGGGCTCTTATAAG                         GTTAAACCAGTCATCAAATTGCTGAAACAAACACTAGTTGGGACAGGAGTG
genomic: GTCCTGGCTCGTGATAGACTGTTGGGCTCTTATAAGgtaataacga ... gtacctctagGTTAAACCAGTCATCAAATTGCTGAAACAAACACTAGTTGGGACAGGAGTG
EST: gi|351019540|gb|FQ439357.1|FQ439357
EST:     GTCCTGGCTCGTGATAGACTGTTGGGCTCTTATAAG                         GTTAAACCAGTCATCAAATTGCTGAAACAAACACTAGTTGGGACAGGAGTG
genomic: GTCCTGGCTCGTGATAGACTGTTGGGCTCTTATAAGgtaataacga ... gtacctctagGTTAAACCAGTCATCAAATTGCTGAAACAAACACTAGTTGGGACAGGAGTG
EST: gi|349828064|gb|FQ415392.1|FQ415392
EST:     GTCCTGGCTCGTGATAGACTGTTGGGCTCTTATAAG                         GTTAAACCAGTCATCAAATTGCTGAAACAAAC
genomic: GTCCTGGCTCGTGATAGACTGTTGGGCTCTTATAAGgtaataacga ... gtacctctagGTTAAACCAGTCATCAAATTGCTGAAACAAAC
EST: gi|110385759|gb|EC950311.1|EC950311
EST:     GTCCTGGCTCGTGATAGACTGTTGGGCTCTTATAAG                         GTTAAACCAGTCATCAAATTGCTGAAACAAACACTAGTTGGGACAGGAGTG
genomic: GTCCTGGCTCGTGATAGACTGTTGGGCTCTTATAAGgtaataacga ... gtacctctagGTTAAACCAGTCATCAAATTGCTGAAACAAACACTAGTTGGGACAGGAGTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attatgggcctctttacgaaaaatgaaaatcttacagaaaatattgtacctctagGTTAAACCAGTCATCAAATTGCTGAAACAAACACTAGTTGGGACAGGAGTGTTACTTGTTACAGCAGTGACACTATTTATCTTTGCTACACCAGTGGAGG
                            atcttac  putative branch site (score: 3)
                                              tacctct  putative PPT
                  aaaaatgaaaatctta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtcttttcatattttacaaggctttaaagatcgatgtggcctaaaattatgggcctctttacgaaaaatgaaaatcttacagaaaatattgtacctctagGTTAAACCAGTCATCAAATTGCTGAAACAAACACTAGTTGGGACAGGAGTGTTACTTGTTACAGCAGTGACACTATTTATCTTTGCTACACCAGTGGAGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG
- - - - - - - - - - - - - - - - - - - - - aaaatta
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gaaaaat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gaaaatc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - agaaaat