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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATTTCGAAATTGGCTGAGGCGGCATGGGAACAGCCAACCTGACTGGTTTGGCATCTCAAATCAAGGACCTTTGCCATCAACAGTCTTATCAAAACGCCAGgtttggcagaaagttacccttttatgagcattgctactatcttcccactagaataaatagtgactttcaattttcaaagcatttcagtgcaaaaattcaa...

Basic information

species Vitis vinifera
transcript Vv06s0061g00790.t01
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv06s0061g00790.t01 (Vitis vinifera), 5'ss of exon 6
lower sequence: GLYMA12G08740.1 (Glycine max), 5'ss of exon 6
ATTTCGAAATTGGCTGAGGCGGCATGGGAACAGCCAACCTGACTGGTTTGGCATCTCAAATCAAGGACCTTTGCCATCAACAGTCTTATCAAAACGCCAGgtttggcagaaag--ttacccttttatgagcattgctactatcttcccactagaataaatagtgacttt---caattttcaaagcatttcagtgcaaaaattcaa
||||||||| ||||| ||||||||||| ||  ||||||| || |||||||||| |   |   |   ||| ||||||||||| || ||||||||||| |||||     |  | |  | |   ||||         ||  ||   ||   || |  |  |||  | ||  |   || |||  ||  | |||   |  |  ||     
ATTTCGAAACTGGCTAAGGCGGCATGGCAATGGCCAACCAGAATGGTTTGGCAACAGCAGCGACCAACCATTGCCATCAACTGTTTTATCAAAACGTCAGgtacaataacatgattcatgattttcattttgaagccccttaatttgaacaacgaagaatgttaacaatacacactttctaactcttttttatcgattaa-----
















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|27579116|gb|CB001811.1|CB001811
EST:     GCATCTCAAATCAAGGACCTTTGCCATCAACAGTCTTATCAAAACGCCAG                         ATGTTGGATAGATTTGAGCAGCACACTCTTAACTGTTCATCCTGTAAAGGA
genomic: GCATCTCAAATCAAGGACCTTTGCCATCAACAGTCTTATCAAAACGCCAGgtttggcaga ... gatattgtagATGTTGGATAGATTTGAGCAGCACACTCTTAACTGTTCATCCTGTAAAGGA
EST: gi|32246416|gb|CD712235.1|CD712235
EST:     GCATCTCAAATCAAGGACCTTTGCCATCAACAGTCTTATCAAAACGCCAG                         ATGTTGGATAGATTTGAGCAGCACACTCTTAACTGTTCATCCTGTAAAGGA
genomic: GCATCTCAAATCAAGGACCTTTGCCATCAACAGTCTTATCAAAACGCCAGgtttggcaga ... gatattgtagATGTTGGATAGATTTGAGCAGCACACTCTTAACTGTTCATCCTGTAAAGGA
EST: gi|30299354|gb|CB976148.1|CB976148
EST:     GCATCTCAAATCAAGGACCTTTGCCATCAACAGTCTTATCAAAACGCCAG                         ATGTTGGATAGATTTGAGCAGCACACTCTTAACTGTTCATCCAGTAAAGGA
genomic: GCATCTCAAATCAAGGACCTTTGCCATCAACAGTCTTATCAAAACGCCAGgtttggcaga ... gatattgtagATGTTGGATAGATTTGAGCAGCACACTCTTAACTGTTCATCCTGTAAAGGA
EST: gi|110403176|gb|EC964455.1|EC964455
EST:     GCATCTCAAATCAAGGACCTTTGCCATCAACAGTCTTATCAAAACGCCAG                         ATGTTGGATAGATTTGAGCAGCACACTCTTAACTGTTCATCCTGTAAAGGA
genomic: GCATCTCAAATCAAGGACCTTTGCCATCAACAGTCTTATCAAAACGCCAGgtttggcaga ... gatattgtagATGTTGGATAGATTTGAGCAGCACACTCTTAACTGTTCATCCTGTAAAGGA
EST: gi|30322149|gb|CD005411.1|CD005411
EST:     GCATCTCAAATCAAGGACCTTTGCCATCAACAGTCTTATCANAACGCCAG                         ATGTTGGATAGATTTGAGCAGCACACTCTTAACTGTTCATCCTGTAAAGGA
genomic: GCATCTCAAATCAAGGACCTTTGCCATCAACAGTCTTATCAAAACGCCAGgtttggcaga ... gatattgtagATGTTGGATAGATTTGAGCAGCACACTCTTAACTGTTCATCCTGTAAAGGA
EST: gi|30299921|gb|CB976715.1|CB976715
EST:     GCATCTCAAATCAAGGACCTTTGCCATCAACAGTCTTATCAAAACGCCAG                         ATGTTGGATAGATTTGAGCAGCACACTCTTAACTGTTCATCCTGTAAGGGA
genomic: GCATCTCAAATCAAGGACCTTTGCCATCAACAGTCTTATCAAAACGCCAGgtttggcaga ... gatattgtagATGTTGGATAGATTTGAGCAGCACACTCTTAACTGTTCATCCTGTAAAGGA
EST: gi|110398498|gb|EC964901.1|EC964901
EST:     GCATCTCAAATCAAGGACCTTTGCCATCAACAGTCTTATCAAAACGCCAG                         ATGTTGGATAGATTTGAGCAGCACACTCTTAACTGTTCATCCTGTAAAGGA
genomic: GCATCTCAAATCAAGGACCTTTGCCATCAACAGTCTTATCAAAACGCCAGgtttggcaga ... gatattgtagATGTTGGATAGATTTGAGCAGCACACTCTTAACTGTTCATCCTGTAAAGGA
EST: gi|37183700|gb|CF603054.1|CF603054
EST:     GCATCTCAAATCAAGGACCTTTGCCATCAACAGTCTTATCAAAACGCCAG                         ATGTTGGATAGATTTGAGCAGCACACTCTTAACTGTTCATCCTGTAAAGGA
genomic: GCATCTCAAATCAAGGACCTTTGCCATCAACAGTCTTATCAAAACGCCAGgtttggcaga ... gatattgtagATGTTGGATAGATTTGAGCAGCACACTCTTAACTGTTCATCCTGTAAAGGA
EST: gi|71890869|gb|DT039924.1|DT039924
EST:     GCATCTCAAATCAAGGACCTTTGCCATCAACAGTCTTATCAAAACGCCAG                         ATGTTGGATAGATTTGAGCAGCACACTCTTAACTGTTCATCCTGTAAAGGA
genomic: GCATCTCAAATCAAGGACCTTTGCCATCAACAGTCTTATCAAAACGCCAGgtttggcaga ... gatattgtagATGTTGGATAGATTTGAGCAGCACACTCTTAACTGTTCATCCTGTAAAGGA
EST: gi|110359771|gb|EC921878.1|EC921878
EST:     GCATCTCAAATCAAGGACCTTTGCCATCAACAGTCTTATCAAAACGCCAG                         ATGTTGGATAGATTTGAGCAGCACACTCTTAACTGTTCATCCTGTAAAGGA
genomic: GCATCTCAAATCAAGGACCTTTGCCATCAACAGTCTTATCAAAACGCCAGgtttggcaga ... gatattgtagATGTTGGATAGATTTGAGCAGCACACTCTTAACTGTTCATCCTGTAAAGGA
EST: gi|22009482|gb|BQ794516.1|BQ794516
EST:     GCATCTCAAATCAAGGACCTTTGCCATCAACAGTCTTATCAAAACGCCAG                         ATGTTGGATAGATTTGAGCAGCACACTCTTAACTGTTCATCCTGTAAAGGA
genomic: GCATCTCAAATCAAGGACCTTTGCCATCAACAGTCTTATCAAAACGCCAGgtttggcaga ... gatattgtagATGTTGGATAGATTTGAGCAGCACACTCTTAACTGTTCATCCTGTAAAGGA
EST: gi|27586759|gb|CB009454.1|CB009454
EST:     GCATCTCAAATCAAGGACCTTTGCCATCAACAGTCTTATCAAAACGCCAG                         ATGTTGGATAGATTTGAGCAGCACACTCTTAACTGTTCATCCTGTAAAGGA
genomic: GCATCTCAAATCAAGGACCTTTGCCATCAACAGTCTTATCAAAACGCCAGgtttggcaga ... gatattgtagATGTTGGATAGATTTGAGCAGCACACTCTTAACTGTTCATCCTGTAAAGGA
EST: gi|30126733|gb|CB912072.1|CB912072
EST:     CATCTCAAATCAAGGACCTTTGCCATCAACANGTCTTATCAAAACGCCAG                         ATGTTGGATAGATTTGAGCAGCACACTCTTAACTGTTCATCCTGTAAAGGA
genomic: CATCTCAAATCAAGGACCTTTGCCATCAACA-GTCTTATCAAAACGCCAGgtttggcaga ... gatattgtagATGTTGGATAGATTTGAGCAGCACACTCTTAACTGTTCATCCTGTAAAGGA
EST: gi|30327325|gb|CD010587.1|CD010587
EST:     GCATCTCAAATCAAGGACCTTTGCCATCAACAGTCTTATCAAAACGCCAG                         ATGTTGGATAGATTTGAGCAGCACACTCTTAACTGTTCATCCTGTAAAGGA
genomic: GCATCTCAAATCAAGGACCTTTGCCATCAACAGTCTTATCAAAACGCCAGgtttggcaga ... gatattgtagATGTTGGATAGATTTGAGCAGCACACTCTTAACTGTTCATCCTGTAAAGGA
EST: gi|110393693|gb|EC959113.1|EC959113
EST:     GCATCTCAAATCAAGGACCTTTGCCATCAACAGTCTTATCAAAACGCCAG                         ATGTTGGATAGATTTGAGCAGCACACTCTTAACTGTTCATCCTGTAAAGGA
genomic: GCATCTCAAATCAAGGACCTTTGCCATCAACAGTCTTATCAAAACGCCAGgtttggcaga ... gatattgtagATGTTGGATAGATTTGAGCAGCACACTCTTAACTGTTCATCCTGTAAAGGA
EST: gi|30323198|gb|CD006460.1|CD006460
EST:     GCATCTCAAATCAAGGACCTTTGCCATCAACAGTCTTATCANAACGCCAG                         ATGTTGGATAGATTTGAGCAGCACACTCTTAACTGTTCATCCTGTANAGGA
genomic: GCATCTCAAATCAAGGACCTTTGCCATCAACAGTCTTATCAAAACGCCAGgtttggcaga ... gatattgtagATGTTGGATAGATTTGAGCAGCACACTCTTAACTGTTCATCCTGTAAAGGA
EST: gi|32270883|gb|CD720042.1|CD720042
EST:     GCATCTCAAATCAAGGACCTTTGCCATCAACAGTCTTATCAAAACGCCAG                         ATGTTGGATAGATTTGAGCAGCACACTCTTAACTGTTCATCCTGTAAAGGA
genomic: GCATCTCAAATCAAGGACCTTTGCCATCAACAGTCTTATCAAAACGCCAGgtttggcaga ... gatattgtagATGTTGGATAGATTTGAGCAGCACACTCTTAACTGTTCATCCTGTAAAGGA
EST: gi|71883737|gb|DT032792.1|DT032792
EST:     GCATCTCAAATCAAGGACCTTTGCCATCAACAGTCTTATCAAAACGCCAG                         ATGTTGGATAGATTTGAGCAGCACACTCTTAACTGTTCATCCTGT
genomic: GCATCTCAAATCAAGGACCTTTGCCATCAACAGTCTTATCAAAACGCCAGgtttggcaga ... gatattgtagATGTTGGATAGATTTGAGCAGCACACTCTTAACTGTTCATCCTGT
EST: gi|30299431|gb|CB976225.1|CB976225
EST:     GCATCTCAAATCAAGGACCTTTGCCATCAACAGTCTTATCAAAACGCCAG                         ATGTTGGATAGATTTGAGCAGCACACTCTTAACTGTTCATCCAGTAAAGGA
genomic: GCATCTCAAATCAAGGACCTTTGCCATCAACAGTCTTATCAAAACGCCAGgtttggcaga ... gatattgtagATGTTGGATAGATTTGAGCAGCACACTCTTAACTGTTCATCCTGTAAAGGA
EST: gi|352769380|gb|FQ471529.1|FQ471529
EST:     GCATCTCAAATCAAGGACCTTTGCCATCAACAGTCTTATCAAAACGCCAG                         ATGTTGGATAGATTTGAGCAGCACACTCTTAACTGTTCATCCTGTAAAGGA
genomic: GCATCTCAAATCAAGGACCTTTGCCATCAACAGTCTTATCAAAACGCCAGgtttggcaga ... gatattgtagATGTTGGATAGATTTGAGCAGCACACTCTTAACTGTTCATCCTGTAAAGGA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATTTCGAAATTGGCTGAGGCGGCATGGGAACAGCCAACCTGACTGGTTTGGCATCTCAAATCAAGGACCTTTGCCATCAACAGTCTTATCAAAACGCCAGgtttggcagaaagttacccttttatgagcattgctactatcttcccactagaataaatagtgactttcaattttcaaagcatttcagtgcaaaaattcaa

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gcagaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tcttccc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gaataaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gcaaaaa