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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaggatccatttgctctgctttatttgttttttttttttccggttccgtaatgaagttacgggcaacaaatactaaattctttccatttgtattttcagCCAGGGCCACGTGATGGGACTATCCAATGCTTCATCAAAAGGGATAAATCTAACTTAACTTACCACCTTTTTCTATGTCTTAGCCCTG

Basic information

species Vitis vinifera
transcript Vv12s0055g00460.t01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv12s0055g00460.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: LOC_Os12g06630.3 (Oryza sativa), 3'ss of exon 2
------------------------------------------------------------------------------gtaggatccatttgctctgctttatttgttttttttttttccg---------gttccgtaatgaagttacgggcaacaaatactaa-attctttcc--------atttgtattttcagCCAGGGCCACGTGATGGGACTATCCAATGCTTCATCAAAAGGGATAAATCTAACTTAACTTACCACCTTTTTCTATGTCTTAGCCCTG
                                                                               | |    | | | | | |||| || || |  ||| |  |  |          ||| |  ||  |  ||   |  |     | ||| || |||| |         |||   ||||||||| ||||| ||  ||||  | ||||| |||||||| |||||||||||||||| |  ||||||| |||| | ||||||||||||| | |
gtgatgatgatgctctcttgcttagtcttgtatttccgcgcttcgatttcagatttgtttaactaacatacatctttgatggttgtcgtatacacggcttaatatgctcatttatagtatgcgaaatgaaattctgatatagaaatatttgatatgttcattaatatgcttttcttgaccatgttttgtttttcagCCTGGGCCCCGGAATGGAGCCATCCAGTGCTTCATTAAAAGGGATAAATCTACCCAAACTTACAACCTATATCTATGTCTTAGCTCAG

upper sequence: Vv12s0055g00460.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GRMZM2G001272_T01 (Zea mays), 3'ss of exon 2
-----------------------------------------------gtaggatccatttgctctgctttatttgttttt---------tttttttccggttccgtaa--tgaagttacgggcaa-----------caaatactaaattctttccatttgt-attttcagCCAGGGCCACGTGATGGGACTATCCAATGCTTCATCAAAAGGGATAAATCTAACTTAACTTACCACCTTTTTCTATGTCTTAGCCCTG
                                                |   |    | || | |   | | |||| | |         | |||||        | ||    |   ||| |   |            | | | |||     ||   || |  || ||||||| ||||| || ||||  || |||||||||||||||||||||||||||||||    ||| ||| || | | ||| || |||||| | |
gtgatggtgctctctttgatccttatatgtttcatttccgtttttgtttcataattttatgttatatataacttgtatctgggaagcggtatttttaaaacaaagaaaaccaagaatacagatgaaccactttatctatacattaatactgttttgttggccatattcagCCTGGGCCTCGAGATGTAACCATCCAATGCTTCATCAAAAGGGATAAATCTACTCAAACCTACTACTTGTATCTGTGCCTTAGCACAG

upper sequence: Vv12s0055g00460.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA15G05490.1 (Glycine max), 3'ss of exon 3
-------------------------gtaggatccatttgctctgctttatttgttttttttttttccggtt--ccgtaat----gaagttacgggc---aacaaatactaaattcttt--ccatttgtattttcagCCAGGGCCACGTGATGGGACTATCCAATGCTTCATCAAAAGGGATAAATCTAACTTAACTTACCACCTTTTTCTATGTCTTAGCCCTG
                         |   | | || ||    |     |  | ||   ||| | |   | |  |  | ||    || |||| |||    | ||    |   ||| |||   | |||   ||||||||| |||||||| ||||| |  || ||||| || |||||||| ||||||||||| ||||| |||||||| || || ||||| |||||||
gttaggttcattatttttcatagcagactgtttcacttttattaaccaaactattacatttatgtggtgataacaatgatagttgatgttatgggttgaagcagcaccctgattgtttgctcctttcacttttcagCCTGGGCCACGGGATGGAATCATTCAATGTTTTATCAAAAGAGATAAATCTAATTTAACATACCACCTATTCCTTTGTCTCAGCCCTG

upper sequence: Vv12s0055g00460.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA08G19520.4 (Glycine max), 3'ss of exon 4
--------------------gtag--gatccatttgctctgctttatttgttttttttttttccggttccgtaa----------tgaagttacgggc---aacaaatactaaattcttt--ccatttgtattttcagCCAGGGCCACGTGATGGGACTATCCAATGCTTCATCAAAAGGGATAAATCTAACTTAACTTACCACCTTTTTCTATGTCTTAGCCCTG
                     |||  |||   ||  || |  || |      | ||   |||  |      |||          ||| |||| |||    | |||   |   ||| |||   | |||   ||||||||| |||||||| ||||| |  || ||||| || |||||||| ||||||||||| ||||| |||||||| || || ||||| |||||||
gttaggttcattactttttcatagcagattgcttcacttttattaaccaaactattacatttatgtggtgataacaatgatagttgatgttatgggttgaagcaacaccctgattgtttgctcctttcgcttttcagCCTGGGCCACGGGATGGAATCATTCAATGTTTTATCAAAAGAGATAAATCTAATTTAACATACCACCTATTCCTTTGTCTCAGCCCTG

upper sequence: Vv12s0055g00460.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: AT1G76900.1 (Arabidopsis thaliana), 3'ss of exon 2
gtaggatccatttgctctgctttatttgttttttttttttccggttccgtaatgaagttacgggcaacaaatactaa-attctttccatttgtattttcagCCAGGGCCACGTGATGGGACTATCCAATGCTTCATCAAAAGGGATAAATCTAACTTAACTTACCACCTTTTTCTATGTCTTAGCCCTG
      |    || |  | ||||| |  | |  |  |        |      |    ||| |       | | | |  | | | | | |  || |||  |||| || ||| | ||||  || || |||||||| ||||||||||||||||||||||| ||||| ||  | | ||| ||||| || ||||
-----gttagatttcaattctttactaatgtcatcatcacatatgttttggttagtcttatgattggttatttcaagtaatttcttcttcggtgtttatagCCTGGACCAAGAGATGCAACAATGCAATGCTTTATCAAAAGGGATAAATCTAACTTGACTTATCATTTATATCTTTGTCTCAGTCCTG

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|161719261|gb|FC064814.1|FC064814
EST:     GAAGTCCAGAGTTTTGTGCCAAACTTACCTTTCCAGTGTCCCTGAAGCAG                         CCAGGGCCACGTGATGGGACTATCCAATGCTTCATCAAAAGGGATAAATCT
genomic: GAAGTCCAGAGTTTTGTGCCAAACTTACCTTTCCAGTGTCCCTGAAGCAGgtaggatcca ... gtattttcagCCAGGGCCACGTGATGGGACTATCCAATGCTTCATCAAAAGGGATAAATCT
EST: gi|71863069|gb|DT012124.1|DT012124
EST:     GAAGTCCAGAGTTTTGTACCAAACTTACCTTTCCAGTGTCCCTGAAGCAG                         CCAGGGCCACGTGATGGGACTATCCAATGCTTCATCAAAAGGGATAAATCT
genomic: GAAGTCCAGAGTTTTGTGCCAAACTTACCTTTCCAGTGTCCCTGAAGCAGgtaggatcca ... gtattttcagCCAGGGCCACGTGATGGGACTATCCAATGCTTCATCAAAAGGGATAAATCT
EST: gi|71859885|gb|DT008940.1|DT008940
EST:     CAGTGTCCCTGAAGCAG                         CCAGGGCCACGTGATGGGACTATCCAATGCTTCATCAAAAGGGATAAATCT
genomic: CAGTGTCCCTGAAGCAGgtaggatcca ... gtattttcagCCAGGGCCACGTGATGGGACTATCCAATGCTTCATCAAAAGGGATAAATCT
EST: gi|71864896|gb|DT013951.1|DT013951
EST:     GAAGTCCAGAGTTTTGTACCAAACTTACCTTTCCAGTGTCCCTGAAGCAG                         CCAGGGCCACGTGATGGGACTATCCAATGCTTCATCAAAAGGGATAAATCT
genomic: GAAGTCCAGAGTTTTGTGCCAAACTTACCTTTCCAGTGTCCCTGAAGCAGgtaggatcca ... gtattttcagCCAGGGCCACGTGATGGGACTATCCAATGCTTCATCAAAAGGGATAAATCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tccgtaatgaagttacgggcaacaaatactaaattctttccatttgtattttcagCCAGGGCCACGTGATGGGACTATCCAATGCTTCATCAAAAGGGATAAATCTAACTTAACTTACCACCTTTTTCTATGTCTTAGCCCTG
                          tactaaa  putative branch site (score: 1)
                                 ttctttccatttgt  CT-rich tract
                       aaatactaaattcttt  TA-rich tract