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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTCCTGAGATTGAGCAGGGACTTTCAGATGCTGCACATGCAAAAGTGACTGTCAGCTTCACTCCTCACCTAATGCCAATGgtagtggttacattcagatgtataaaagtacttataatattgtcatttgtctctttactcacaaagcagttaaacattatattcatattatggtgtgacag

Basic information

species Vitis vinifera
transcript Vv03s0063g01110.t01
intron # 10
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv03s0063g01110.t01 (Vitis vinifera), 5'ss of exon 10
lower sequence: GRMZM2G038848_T02 (Zea mays), 5'ss of exon 11
TTCCTGAGATTGAGCAGGGACTTTCAGATGCTGCACATGCAAAAGTGACTGTCAGCTTCACTCCTCACCTAATGCCAATGgtagtggttacattcagatgtataaaagtacttataatattgtcatttgtctctttactcacaaagcagttaaacattatattcatattatggtgtgacag
| |||||||||||||| |||||| ||||||||||  |  ||||||| ||| ||||||| ||||| ||  | |||   ||||||       || | |  | ||   |    | | | |  |  | | ||   | |  |||        | ||  | | |  |||  || |    | | | ||
TGCCTGAGATTGAGCAAGGACTTACAGATGCTGCTGAATCAAAAGTTACTATCAGCTTTACTCCACATTTGATGTGTATGgtaa-----gcacttaattatacttat---cctttgacttgctaaattcagtatgcactttttgtaaaattcgataat-catttctactgctatttaatag
















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|110390116|gb|EC955007.1|EC955007
EST:     CTGCACATGCAAAAGTGACTGTCAGCTTCACTCCTCACCTAATGCCAATG                         AGCCGTGGTATGCAATCAACTATATACGTGGAAATGACCCCAGGAGTCACA
genomic: CTGCACATGCAAAAGTGACTGTCAGCTTCACTCCTCACCTAATGCCAATGgtagtggtta ... ggtgtgacagAGCCGTGGTATGCAATCAACTATATACGTGGAAATGACCCCAGGAGTCACA
EST: gi|30330207|gb|CD013469.1|CD013469
EST:     CTGCACATGCAAAAGTGACTGTCAGCTTCACTCCTCACNTAATGCCAATG                         AGCCGTGGTATGCAATCAACTATATACGTGGAAATGACCCCAGGAGTCACA
genomic: CTGCACATGCAAAAGTGACTGTCAGCTTCACTCCTCACCTAATGCCAATGgtagtggtta ... ggtgtgacagAGCCGTGGTATGCAATCAACTATATACGTGGAAATGACCCCAGGAGTCACA
EST: gi|30134557|gb|CB919895.1|CB919895
EST:     CTGCACATGCAAAAGTGACTGTCAGCTTCACTCCTCACCTAATGCCAATG                         AGCCGTGGTATGCAATCAACTATATACGTGGAAATGACCCCAGGAGTCACA
genomic: CTGCACATGCAAAAGTGACTGTCAGCTTCACTCCTCACCTAATGCCAATGgtagtggtta ... ggtgtgacagAGCCGTGGTATGCAATCAACTATATACGTGGAAATGACCCCAGGAGTCACA
EST: gi|30329402|gb|CD012664.1|CD012664
EST:     ACATGCAAAAGTGACTGTCAGCTTCACTCCTCACCTAATGCCAATG                         AGCCGTGGTATGCAATCAACTATATACGTGGAAATGACCCCAGGAGTCACA
genomic: ACATGCAAAAGTGACTGTCAGCTTCACTCCTCACCTAATGCCAATGgtagtggtta ... ggtgtgacagAGCCGTGGTATGCAATCAACTATATACGTGGAAATGACCCCAGGAGTCACA
EST: gi|30320747|gb|CD004009.1|CD004009
EST:     CTGCACATGCAAAAGTGACTGTCAGCTTCACTCCTCACCTAATGCCAATG                         AGCCGTGGTATGCAATCAACTATATACGTGGAAATGACCCCAGGAGTCACA
genomic: CTGCACATGCAAAAGTGACTGTCAGCTTCACTCCTCACCTAATGCCAATGgtagtggtta ... ggtgtgacagAGCCGTGGTATGCAATCAACTATATACGTGGAAATGACCCCAGGAGTCACA
EST: gi|27583381|gb|CB006076.1|CB006076
EST:     CTGCACATGCAAAAGTGACTGTCAGCTTCACTCCTCACCTAATGCCAATG                         AGCCGTGGTATGCAATCAACTATATACGTGGAAATGACCCCAGGAGTCACA
genomic: CTGCACATGCAAAAGTGACTGTCAGCTTCACTCCTCACCTAATGCCAATGgtagtggtta ... ggtgtgacagAGCCGTGGTATGCAATCAACTATATACGTGGAAATGACCCCAGGAGTCACA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TTCCTGAGATTGAGCAGGGACTTTCAGATGCTGCACATGCAAAAGTGACTGTCAGCTTCACTCCTCACCTAATGCCAATGgtagtggttacattcagatgtataaaagtacttataatattgtcatttgtctctttactcacaaagcagttaaacattatattcatattatggtgtgacag

- - - - - - - - - - - - - - - - - - - - - - - - -  TCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTCCTC