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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaccaattgatcttaagaaatgaaactgctgatccaagtgtgagccaaacacaataacatatttgatgttttgtgatgcagTTACTCTACCATTGCTTGGGGAGCTTCCGTGGATAAGGGCGTTCAGGACAATGTGGAGTATGGCTACAAAGCCAAGTCCACAGCAGGGACTGTCTTCAAC

Basic information

species Vitis vinifera
transcript Vv14s0171g00400.t01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv14s0171g00400.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA19G22590.1 (Glycine max), 3'ss of exon 3
----------gtaccaatt-gatcttaagaaatgaaactgctgatccaagtgtgagccaaacacaataacata---tttgatgttt----tgtgatgcagTTACTCTACCATTGCTTGGGGAGCTTCCGTGGATAAGGGCGTTCAGGACAATGTGGAGTATGGCTACAAAGCCAAGTCCACAGCAGGGACTGTCTTCAAC
             |   || |||  |   |  ||||   |   | |  |  |  |  ||||     |||  ||   ||  ||||||    | |  |||||||||||||| |||||||||| |||||| ||  ||||||| ||||| || |||||  | ||||| |||||||| |||   ||  ||||||| || || |||
gagaattgtcaagcggcttagattctgctagttgaatgagaataacacaccgaaatacaaaattgttaatttagtcttcaatgtttgcattttcctgcagTTACTCTACAATTGCTTGGGTAGCTTCTGTACATAAGGGTGTTCAAGAAAATGTACAATATGGTTACAAAGCTAAGAGTACTTCAGGGACAGTGTTTAAC
















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|161719199|gb|FC065732.1|FC065732
EST:     TTCAACTCCATCTCTGGTGTTTCTCTTGCAGCTGCAGTCATGTCCTTGAG                         TTACTCTACCATTGCTTGGGGAGCTTCCGTGGATAAGGGCGTTCAGGACAA
genomic: TTCAACTCCATCTCTGGTGTTTCTCTTGCAGCTGCAGTCATGTCCTTGAGgtaccaattg ... tgtgatgcagTTACTCTACCATTGCTTGGGGAGCTTCCGTGGATAAGGGCGTTCAGGACAA
EST: gi|161706673|gb|FC055876.1|FC055876
EST:     TTCAACTCCATCTCTGGTGTTTCTCTTGCAGCTGCAGTCATGTCCTTGAG                         TTACTCTACCATTGCTTGGGGAGCTTCCGTGGATAAGGGCGTTCAGGACAA
genomic: TTCAACTCCATCTCTGGTGTTTCTCTTGCAGCTGCAGTCATGTCCTTGAGgtaccaattg ... tgtgatgcagTTACTCTACCATTGCTTGGGGAGCTTCCGTGGATAAGGGCGTTCAGGACAA
EST: gi|161712409|gb|FC061714.1|FC061714
EST:     GTCATGTCCTTGAG                         TTACTCTACCATTGCTTGGGGAGCTTCCGTGGATAAGGGCGTTCAGGACAA
genomic: GTCATGTCCTTGAGgtaccaattg ... tgtgatgcagTTACTCTACCATTGCTTGGGGAGCTTCCGTGGATAAGGGCGTTCAGGACAA
EST: gi|161718440|gb|FC067297.1|FC067297
EST:     TTCAACTCCATCTCTGGTGTTTCTCTTGCAGCTGCAGTCATGTCCTTGAG                         TTACTCTACCATTGCTTGGGGAGCTTCCGTGGATAAGGGCGTTCAGGACAA
genomic: TTCAACTCCATCTCTGGTGTTTCTCTTGCAGCTGCAGTCATGTCCTTGAGgtaccaattg ... tgtgatgcagTTACTCTACCATTGCTTGGGGAGCTTCCGTGGATAAGGGCGTTCAGGACAA
EST: gi|32248067|gb|CD713886.1|CD713886
EST:     TTCAACTCCATCTCTGGTGTTTCTCTTGCAGCTGCAGTCATGTCCTTGAG                         TTACTCTACCATTGCTTGGGGAGCTTCCGTGGATAAGGGCGTTCAGGACAA
genomic: TTCAACTCCATCTCTGGTGTTTCTCTTGCAGCTGCAGTCATGTCCTTGAGgtaccaattg ... tgtgatgcagTTACTCTACCATTGCTTGGGGAGCTTCCGTGGATAAGGGCGTTCAGGACAA
EST: gi|110700407|gb|EE078411.1|EE078411
EST:     TTCAACTCCATCTCTGGTGTTTCTCTTGCAGCTGCAGTCATGTCCTTGAG                         TTACTCTACCATTGCTTGGGGAGCTTCCGTGGATAAGGGCGTTCAGGACAA
genomic: TTCAACTCCATCTCTGGTGTTTCTCTTGCAGCTGCAGTCATGTCCTTGAGgtaccaattg ... tgtgatgcagTTACTCTACCATTGCTTGGGGAGCTTCCGTGGATAAGGGCGTTCAGGACAA
EST: gi|32267566|gb|CD716529.1|CD716529
EST:     TTCAACTCCATCTCTGGTGTTTCTCTTGCAGCTGCAGTCATGTCCTTGAG                         TTACTCTACCATTGCTTGGGGAGCTTCCGTGGATAAGGGCGTTCAGGACAA
genomic: TTCAACTCCATCTCTGGTGTTTCTCTTGCAGCTGCAGTCATGTCCTTGAGgtaccaattg ... tgtgatgcagTTACTCTACCATTGCTTGGGGAGCTTCCGTGGATAAGGGCGTTCAGGACAA
EST: gi|32247418|gb|CD713237.1|CD713237
EST:     TTCAACTCCATCTCTGGTGTTTCTCTTGCAGCTGCAGTCATGTCCTTGAG                         TTACTCTACCATTGCTTGGGGAGCTTCCGTGGATAAGGGCGTTCAGGACAA
genomic: TTCAACTCCATCTCTGGTGTTTCTCTTGCAGCTGCAGTCATGTCCTTGAGgtaccaattg ... tgtgatgcagTTACTCTACCATTGCTTGGGGAGCTTCCGTGGATAAGGGCGTTCAGGACAA
EST: gi|161717137|gb|FC066560.1|FC066560
EST:     TTCAACTCCATCTCTGGTGTTTCTCTTGCAGCTGCAGTCCTGTCCTTGAG                         TTACTCTACCATTGCTTGGGGAGCTTCCGTGG
genomic: TTCAACTCCATCTCTGGTGTTTCTCTTGCAGCTGCAGTCATGTCCTTGAGgtaccaattg ... tgtgatgcagTTACTCTACCATTGCTTGGGGAGCTTCCGTGG
EST: gi|32271747|gb|CD720906.1|CD720906
EST:     TTCAACTCCATCTCTGGTGTTTCTCTTGCAGCTGCAGTCATGTCCTTGAG                         TTACTCTACCATTGCTTGGGGAGCTTCCGTGGATAAGGGCGTTCAGGACAA
genomic: TTCAACTCCATCTCTGGTGTTTCTCTTGCAGCTGCAGTCATGTCCTTGAGgtaccaattg ... tgtgatgcagTTACTCTACCATTGCTTGGGGAGCTTCCGTGGATAAGGGCGTTCAGGACAA
EST: gi|32271362|gb|CD720521.1|CD720521
EST:     TTCAACTCCATCTCTGGTGTTTCTCTTGCAGCTGCAGTCATGTCCTTGAG                         TTACTCTACCATTGCTTGGGGAGCTTCCGTGGATAAGGGCGTTCAGGACAA
genomic: TTCAACTCCATCTCTGGTGTTTCTCTTGCAGCTGCAGTCATGTCCTTGAGgtaccaattg ... tgtgatgcagTTACTCTACCATTGCTTGGGGAGCTTCCGTGGATAAGGGCGTTCAGGACAA
EST: gi|110724165|gb|EE099752.1|EE099752
EST:     TTCAACTCCATCTCTGGTGTTTCTCTTGCAGCTGCAGTCATGTCCTTGAG                         TTACTCTACCATTGCTTGGGGAGCTTCCGTGGATAAAGGCGTTCAGGACAA
genomic: TTCAACTCCATCTCTGGTGTTTCTCTTGCAGCTGCAGTCATGTCCTTGAGgtaccaattg ... tgtgatgcagTTACTCTACCATTGCTTGGGGAGCTTCCGTGGATAAGGGCGTTCAGGACAA
EST: gi|30328015|gb|CD011277.1|CD011277
EST:     TTCAACTCCATCTCTGGTGTTTCTCTTGCAGCTGCAGTCATGTCCTTGAG                         TTACTCTACCATTGCTTGGGGAGCTTCCGTGGATAAGGGCGTTCAGGACAA
genomic: TTCAACTCCATCTCTGGTGTTTCTCTTGCAGCTGCAGTCATGTCCTTGAGgtaccaattg ... tgtgatgcagTTACTCTACCATTGCTTGGGGAGCTTCCGTGGATAAGGGCGTTCAGGACAA
EST: gi|110703326|gb|EE080072.1|EE080072
EST:     TTCAACTCCATCTCTGGTGTTTCTCTTGCAGCTGCAGTCATGTCCTTGAG                         TTACTCTACCATTGCTTGGGGAGCTTCCGTGGATAAGGGCGTTCAGGACAA
genomic: TTCAACTCCATCTCTGGTGTTTCTCTTGCAGCTGCAGTCATGTCCTTGAGgtaccaattg ... tgtgatgcagTTACTCTACCATTGCTTGGGGAGCTTCCGTGGATAAGGGCGTTCAGGACAA
EST: gi|161716023|gb|FC069114.1|FC069114
EST:     TTCAACTCCATCTCTGGTGTTTCTCTTGCAGCTGCAGTCATGTCCTTGAG                         TTACTCTACCATTGCTTGGGGAGCTTCCGTGGATAAGGGCGTTCAGGACAA
genomic: TTCAACTCCATCTCTGGTGTTTCTCTTGCAGCTGCAGTCATGTCCTTGAGgtaccaattg ... tgtgatgcagTTACTCTACCATTGCTTGGGGAGCTTCCGTGGATAAGGGCGTTCAGGACAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgctgatccaagtgtgagccaaacacaataacatatttgatgttttgtgatgcagTTACTCTACCATTGCTTGGGGAGCTTCCGTGGATAAGGGCGTTCAGGACAATGTGGAGTATGGCTACAAAGCCAAGTCCACAGCAGGGACTGTCTTCAAC
                          aataacatatttgat  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
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---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaccaattgatcttaagaaatgaaactgctgatccaagtgtgagccaaacacaataacatatttgatgttttgtgatgcagTTACTCTACCATTGCTTGGGGAGCTTCCGTGGATAAGGGCGTTCAGGACAATGTGGAGTATGGCTACAAAGCCAAGTCCACAGCAGGGACTGTCTTCAAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG