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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTTTCACTAAAAGTACCGGTGGTTGTTCGGCTTGAAGGCACCAATGTTGACCAAGGAAAAAGAATTCTGAAGgtaaatgcaaaacctttggatggaattcaatttatttcgagtgtttccaaaaaggaaaaaaaatcagaaacataatacgagttgttgatcacaaatgatattgcag

Basic information

species Vitis vinifera
transcript Vv07s0005g03790.t01
intron # 11
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv07s0005g03790.t01 (Vitis vinifera), 5'ss of exon 11
lower sequence: LOC_Os02g40830.1 (Oryza sativa), 5'ss of exon 11
GTTTCACTAAAAGTACCGGTGGTTGTTCGGCTTGAAGGCACCAATGTTGACCAAGGAAAAAGAATTCTGAAGgtaaatgcaaaacctttggatggaattcaatttatttcgagtgtttccaaaaaggaaaaaaaatcagaaacataatacgagttgttgatcacaaatgatattgcag
|||   || || || || || ||||||||| | ||||||||||||||||||||||| || || ||||| ||||||||    ||    ||| ||| | |    |||  |  || | | | | ||   |      | |   ||   |  |||  |    ||||      |  | ||||||
GTTGACCTGAAGGTGCCTGTTGTTGTTCGGTTGGAAGGCACCAATGTTGACCAAGGGAAGAGGATTCTAAAGgtaaa----aattacttgcatgcattctttttttgtaggaatatctgccaagtcgtccttcactggaaactttcgtacctgactgtgat-----gtcctgttgcag

upper sequence: Vv07s0005g03790.t01 (Vitis vinifera), 5'ss of exon 11
lower sequence: LOC_Os02g40830.2 (Oryza sativa), 5'ss of exon 11
GTTTCACTAAAAGTACCGGTGGTTGTTCGGCTTGAAGGCACCAATGTTGACCAAGGAAAAAGAATTCTGAAGgtaaatgcaaaacctttggatggaattcaatttatttcgagtgtttccaaaaaggaaaaaaaatcagaaacataatacgagttgttgatcacaaatgatattgcag
            || || || ||||||||| | ||||||||||||||||||||||| || || ||||| ||||||||    ||    ||| ||| | |    |||  |  || | | | | ||   |      | |   ||   |  |||  |    ||||      |  | ||||||
------------GTGCCTGTTGTTGTTCGGTTGGAAGGCACCAATGTTGACCAAGGGAAGAGGATTCTAAAGgtaaa----aattacttgcatgcattctttttttgtaggaatatctgccaagtcgtccttcactggaaactttcgtacctgactgtgat-----gtcctgttgcag

upper sequence: Vv07s0005g03790.t01 (Vitis vinifera), 5'ss of exon 11
lower sequence: GRMZM2G064695_T02 (Zea mays), 5'ss of exon 11
GTTTCACTAAAAGTACCGGTGGTTGTTCGGCTTGAAGGCACCAATGTTGACCAAGGAAAAAGAATTCTGAAGgtaaatgcaaaacctttggatggaattcaatttatttcgagtgtttccaaaaaggaaaaaaaatcagaaacataatacgagttgttgatcacaaatgatattgcag
|||   || ||||| || || ||||||||| | |||||||||||||| ||||||||||| || ||||| |||||||  ||      | |   |||       || ||      ||||         | |  |    |   |  | |    ||  | ||  ||     ||   |     
GTTGACCTGAAAGTTCCTGTTGTTGTTCGGTTGGAAGGCACCAATGTAGACCAAGGAAAGAGGATTCTTAAGgtaagagctgttgatattagtggtgcatgcttgatgcttc-tgttagtcttcccgtaggaggcccttgagtaaacccagatctattattcttgcctgtctt-----

upper sequence: Vv07s0005g03790.t01 (Vitis vinifera), 5'ss of exon 11
lower sequence: GLYMA10G04480.1 (Glycine max), 5'ss of exon 11
GTTTCACTAAAAGTACCGGTGGTTGTTCGGCTTGAAGGCACCAATGTTGACCAAGGAAAAAGAATTCTGAAGgtaaatgcaaaacctttggatggaattcaatttatttcgagtgtttccaaaaaggaaaaaaaatcagaaacataatacgagttgttgatcacaaatgatattgcag
||| |||| |||||||| || || ||||| || ||||||||||||||||| ||||||||||||||  ||||||||||||  | |  | |  ||  |||   ||  |   |||    ||          ||    | ||    | ||||| |  || |||||    ||||||    |||
GTTGCACTGAAAGTACCAGTTGTAGTTCGTCTGGAAGGCACCAATGTTGATCAAGGAAAAAGAATATTGAAGgtaaatgttagatttattaatataatcttatagaaaacgaagcatt----------aatgttagcaagtgcttaatatg--tttttgatactcaatgattcaacag

upper sequence: Vv07s0005g03790.t01 (Vitis vinifera), 5'ss of exon 11
lower sequence: GLYMA13G18730.1 (Glycine max), 5'ss of exon 11
GTTTCACTAAAAGTACCGGTGGTTGTTCGGCTTGAAGGCACCAATGTTGACCAAGGAAAAAGAATTCTGAAGgtaaatgcaaaacctttggatggaattcaatttatttcgagtgtttccaaaaaggaaaaaaaatcagaaacataatacgagttgttgatcacaaatgatattgcag
||| |||| |||||||| || || ||||| || ||||||||||||||||| || |||||||||||| ||||||||||||  | |  | |  ||  |||  |||  |||| ||   |       ||| || ||       |||          ||| ||| |    |||| |    |||
GTTGCACTGAAAGTACCCGTAGTAGTTCGTCTGGAAGGCACCAATGTTGATCATGGAAAAAGAATTTTGAAGgtaaatgtcagatttattaatt-aatataatc-atttagaaaat------gaagcaagaatttctgcaaatgcttattatgtttttggtactcaatgtttcaacag

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|32458077|gb|CD799251.1|CD799251
EST:     TTGTTCGGCTTGAGGGCACCAACGTTGACCAAGGAAAAAGAATTCTGAAG                         GAAAGTGGAATGGCATTGATAACAGCAGAAGATCTGGATGATGCAGCTGTG
genomic: TTGTTCGGCTTGAAGGCACCAATGTTGACCAAGGAAAAAGAATTCTGAAGgtaaatgcaa ... gatattgcagGAAAGTGGAATGGCATTGATAACAGCAGAAGATCTGGATGATGCAGCTGAG
EST: gi|34545859|gb|CF514091.1|CF514091
EST:     TTGTTCGGCTTGAAGGCACCAATGTTGACCAAGGAAAAAGAATTCTGAAG                         GAAAGTGGAATGGCATTGATAACAGCAGAAGATCTGGATGATGCAGCTGAG
genomic: TTGTTCGGCTTGAAGGCACCAATGTTGACCAAGGAAAAAGAATTCTGAAGgtaaatgcaa ... gatattgcagGAAAGTGGAATGGCATTGATAACAGCAGAAGATCTGGATGATGCAGCTGAG
EST: gi|71881691|gb|DT030746.1|DT030746
EST:     TTGTTCGGCTTGAAGGCACCAATGTTGACCAAGGAAAAAGAATTCTGAAG                         GAAAGTGGAATGGCATTGATAACAGCAGAAGATCTGGATGATGCAGCTGAG
genomic: TTGTTCGGCTTGAAGGCACCAATGTTGACCAAGGAAAAAGAATTCTGAAGgtaaatgcaa ... gatattgcagGAAAGTGGAATGGCATTGATAACAGCAGAAGATCTGGATGATGCAGCTGAG
EST: gi|110379096|gb|EC944270.1|EC944270
EST:     TTGTTCGGCTTGAAGGCACCAATGTTGACCAAGGAAAAAGAATTCTGAAG                         GAAAGTGGAATGGCATTGATAACAGCAGAAGATCTGGATGATGCAGCTGAG
genomic: TTGTTCGGCTTGAAGGCACCAATGTTGACCAAGGAAAAAGAATTCTGAAGgtaaatgcaa ... gatattgcagGAAAGTGGAATGGCATTGATAACAGCAGAAGATCTGGATGATGCAGCTGAG
EST: gi|46910485|gb|CN545860.1|CN545860
EST:     TTGTTCGGCTTGAAGGCACCAATGTTGACCAAGGTAAAAGAATTTTGAAG                         GAAAGTGGAATGGCATTGATAACAGCAGAAGATCTGGATGATGCAGCTGAG
genomic: TTGTTCGGCTTGAAGGCACCAATGTTGACCAAGGAAAAAGAATTCTGAAGgtaaatgcaa ... gatattgcagGAAAGTGGAATGGCATTGATAACAGCAGAAGATCTGGATGATGCAGCTGAG
EST: gi|30255821|gb|CB971953.1|CB971953
EST:     TTGTTCGGCTTGAAGGCACCAATGTTGACCAAGGAAAAAGAATTCTGAAG                         GAAAGTGGAATGGCATTGATAACAGCAGAAGATCTGGATGATGCAGCTGAG
genomic: TTGTTCGGCTTGAAGGCACCAATGTTGACCAAGGAAAAAGAATTCTGAAGgtaaatgcaa ... gatattgcagGAAAGTGGAATGGCATTGATAACAGCAGAAGATCTGGATGATGCAGCTGAG
EST: gi|110390462|gb|EC955371.1|EC955371
EST:     TTGTTCGGCTTGAAGGCACCAATGTTGACCAAGGAAAAAGAATTCTGAAG                         GAAAGTGGAATGGCATTGATAACAGCAGAAGATCTGGATGATGCAGCTGAG
genomic: TTGTTCGGCTTGAAGGCACCAATGTTGACCAAGGAAAAAGAATTCTGAAGgtaaatgcaa ... gatattgcagGAAAGTGGAATGGCATTGATAACAGCAGAAGATCTGGATGATGCAGCTGAG
EST: gi|110428351|gb|EC994820.1|EC994820
EST:     TTGTTCGGCTTGAAGGCACCAATGTTGACCAAGGAAAAAGAATTCTGAAG                         GAAAGTGGAATGGCA
genomic: TTGTTCGGCTTGAAGGCACCAATGTTGACCAAGGAAAAAGAATTCTGAAGgtaaatgcaa ... gatattgcagGAAAGTGGAATGGCA
EST: gi|110702283|gb|EE080823.1|EE080823
EST:     TTGTTCGGCTTGAAGGCACCAATGTTGACCAAGGAAAAAGAATTCTGAAG                         GAAAGTGGAATGGCATTGATAACAGCAGAAGATCTGGATGATGCAGCTGAG
genomic: TTGTTCGGCTTGAAGGCACCAATGTTGACCAAGGAAAAAGAATTCTGAAGgtaaatgcaa ... gatattgcagGAAAGTGGAATGGCATTGATAACAGCAGAAGATCTGGATGATGCAGCTGAG
EST: gi|22007633|gb|BQ792667.1|BQ792667
EST:     TTGTTCGGCTTGAAGGCCCCAATGTTGACCAAGGAAAAAGAATTTTGAAG                         GAAAGTGGAATGGCATTGATAACAGCAGAAGATTTGGATGATGCAGCTGAG
genomic: TTGTTCGGCTTGAAGGCACCAATGTTGACCAAGGAAAAAGAATTCTGAAGgtaaatgcaa ... gatattgcagGAAAGTGGAATGGCATTGATAACAGCAGAAGATCTGGATGATGCAGCTGAG
EST: gi|30256178|gb|CB972021.1|CB972021
EST:     TTGTTCGGCTTGAAGGCACCAATGTTGACCAAGGAAAAAGAATTCTGAAG                         GAAAGTGGAATGGCATTGATAACAGCAGAAGATCTGGATGATGCAGCTGAG
genomic: TTGTTCGGCTTGAAGGCACCAATGTTGACCAAGGAAAAAGAATTCTGAAGgtaaatgcaa ... gatattgcagGAAAGTGGAATGGCATTGATAACAGCAGAAGATCTGGATGATGCAGCTGAG
EST: gi|71883833|gb|DT032888.1|DT032888
EST:     TTGTTCGGCTTGAAGGCACCAATGTTGACCAAGGAAAAAGAATTCTGAAG                         GAAAGTGGAATGGCATTGATAACAGCAGAAGATCTGGATGATGCAGCTGAG
genomic: TTGTTCGGCTTGAAGGCACCAATGTTGACCAAGGAAAAAGAATTCTGAAGgtaaatgcaa ... gatattgcagGAAAGTGGAATGGCATTGATAACAGCAGAAGATCTGGATGATGCAGCTGAG
EST: gi|30256398|gb|CB972241.1|CB972241
EST:     TTGTTCGGCTTGAAGGCACCAATGTTGACCAAGGAAAAAGAATTCTGAAG                         GAAAGTGGAATGGCATTGATAACAGCAGAAGATCTGGATGATGCAGCTGAG
genomic: TTGTTCGGCTTGAAGGCACCAATGTTGACCAAGGAAAAAGAATTCTGAAGgtaaatgcaa ... gatattgcagGAAAGTGGAATGGCATTGATAACAGCAGAAGATCTGGATGATGCAGCTGAG
EST: gi|110714835|gb|EE092196.1|EE092196
EST:     TTGTTCGGCTTGAAGGCACCAATGTTGACCAAGGAAAAAGAATTCTGAAG                         GAAAGTGGAATGGCATTGATAACAGCAGAAGATCTGGATGATGCAGCTGAG
genomic: TTGTTCGGCTTGAAGGCACCAATGTTGACCAAGGAAAAAGAATTCTGAAGgtaaatgcaa ... gatattgcagGAAAGTGGAATGGCATTGATAACAGCAGAAGATCTGGATGATGCAGCTGAG
EST: gi|30132925|gb|CB918264.1|CB918264
EST:     AAAGAATTCTGAAG                         GAAAGTGGAATGGCATTGATAACAGCAGAAGATCTGGATGATGCAGCTGAG
genomic: AAAGAATTCTGAAGgtaaatgcaa ... gatattgcagGAAAGTGGAATGGCATTGATAACAGCAGAAGATCTGGATGATGCAGCTGAG
EST: gi|30305949|gb|CB982743.1|CB982743
EST:     TTGTTCGGCTTGAAGGCACCAATGTTGACCAAGGAAAAAGAATTTTGAAG                         GAAAGTGGAATGGCATTGATAACAGCAGAAGATCTGGATGATGCAGCTGAG
genomic: TTGTTCGGCTTGAAGGCACCAATGTTGACCAAGGAAAAAGAATTCTGAAGgtaaatgcaa ... gatattgcagGAAAGTGGAATGGCATTGATAACAGCAGAAGATCTGGATGATGCAGCTGAG
EST: gi|110362830|gb|EC926386.1|EC926386
EST:     TTGTTCGGCTTGAAGGCACCAATGTTGACCAAGGAAAAAGAATTCTGAAG                         GAAAGTGGAATGGCATTGATAACAGCAGAAGATCTGGATGATGCAGCTGAG
genomic: TTGTTCGGCTTGAAGGCACCAATGTTGACCAAGGAAAAAGAATTCTGAAGgtaaatgcaa ... gatattgcagGAAAGTGGAATGGCATTGATAACAGCAGAAGATCTGGATGATGCAGCTGAG
EST: gi|30256478|gb|CB972321.1|CB972321
EST:     TTGTTCGGCTTGAAGGCACCAATGTTGACCAAGGAAAAAGAATTCTGAAG                         GAAAGTGGAATGGCATTGATAACAGCAGAAGATCTGGATGATGCAGCTGAG
genomic: TTGTTCGGCTTGAAGGCACCAATGTTGACCAAGGAAAAAGAATTCTGAAGgtaaatgcaa ... gatattgcagGAAAGTGGAATGGCATTGATAACAGCAGAAGATCTGGATGATGCAGCTGAG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTTTCACTAAAAGTACCGGTGGTTGTTCGGCTTGAAGGCACCAATGTTGACCAAGGAAAAAGAATTCTGAAGgtaaatgcaaaacctttggatggaattcaatttatttcgagtgtttccaaaaaggaaaaaaaatcagaaacataatacgagttgttgatcacaaatgatattgcag

- - - - - - - - - - - - - - -  TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG