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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CAGGCCCTTGCAATGTCTATGGATGACCCTGCCACTAGCCTTGCCATGAGAGACACAGATATGTCTGAGGCAGCTGCAGATGATCAGGACTTGGCTCTTGgtgagtttgctcaatccctttttgttgtatgtagaggttttatggtctgtcccgcctctataactcatccttccattactggtggcctatcatgaatgcc...

Basic information

species Vitis vinifera
transcript Vv04s0023g03620.t01
intron # 7
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv04s0023g03620.t01 (Vitis vinifera), 5'ss of exon 7
lower sequence: GLYMA16G23590.1 (Glycine max), 5'ss of exon 7
CAGGCCCTTGCAATGTCTATGGATGACCCTGCCACTAGCCTTGCCATGAGAGACACAGATATGTCTGAGGCAGCTGCAGATGATCAGGACTTGGCTCTTGgtgagttt----gctcaatccctttttgtt-----gtatgtagaggttttatggtctgtcccgcctctataactcatcc--ttccattactggtggcctatcatgaatgcc
|||||||||||||||||||||||||| ||  | | || ||  | ||||||||| |||||||||||||| |||||||| || ||||  || |||||||| |||||||||    ||| ||||  | | | ||      | ||| || | ||| |  | | |   |  |  || | | |||   |||    | ||  |    ||          
CAGGCCCTTGCAATGTCTATGGATGATCCCACAATTAACCACGACATGAGAGATACAGATATGTCTGAAGCAGCTGCTGAAGATCCTGAGTTGGCTCTAGgtgagtttttatgcttaatcattctgtatttgaacatgtgtggatgctttctcatttatgttggttg-atgattgatctggttctggaattga-gaaaaatt---------

upper sequence: Vv04s0023g03620.t01 (Vitis vinifera), 5'ss of exon 7
lower sequence: GLYMA01G36990.1 (Glycine max), 5'ss of exon 7
CAGGCCCTTGCAATGTCTATGGATGACCCTGCCACTAGCCTTGCCATGAGAGACACAGATATGTCTGAGGCAGCTGCAGATGATCAGGACTTGGCTCTTGgtgagtt-----tgctcaatcc---ctttttgttgtatgtagaggttttatggtctgtcccgcctctataactcatccttccattactg-gtggcctatcatgaatgcc
||||| |||||||||||||||||||| ||||||| ||||| ||   | | ||| ||||||||||| || ||  |||||  |||||  ||||||||||| ||||||||     |  | ||| |   | |  | |   |   |||| | ||    |  |||  |        | |   |  | |||||| |       ||           
CAGGCGCTTGCAATGTCTATGGATGATCCTGCCATTAGCCATGATGTAAAAGATACAGATATGTCAGAAGCTTCTGCAAGTGATCCTGACTTGGCTCTGGgtgagttttatgttattaattcaatcctcatctaagaaacagagatattgacatgggtcatgatgtaggcaatggacactgcattacagtacaatttaag---------

upper sequence: Vv04s0023g03620.t01 (Vitis vinifera), 5'ss of exon 7
lower sequence: GLYMA02G05250.2 (Glycine max), 5'ss of exon 7
CAGGCCCTTGCAATGTCTATGGATGACCCTGCCACTAGCCTTGCCATGAGAGACACAGATATGTCTGAGGCAGCTGCAGATGATCAGGACTTGGCTCTTGgtgagttt----gctcaatccctttttgttgtatgtagaggttttatggtctgtcccgcctctataactcatccttccattactggtggcctatcatgaatgcc
||||||||||||||||| |||||||| ||  | | || || ||   ||||||| |||||||||||||| |||||||| || ||||  || |||||||| ||||||| |    ||| |||   | | | ||| |  | |  |  | |   |||        |   |   | ||   ||   | ||||     |   |  ||| | 
CAGGCCCTTGCAATGTCAATGGATGATCCCACAATTAACCATGAAGTGAGAGATACAGATATGTCTGAAGCAGCTGCTGAAGATCCCGAGTTGGCTCTAGgtgagtatttatgcttaattattctgtattgaacatgggtggat-actttctcatttatgttggtggatgattgatctggttctggaa--ttgagaaaaattc-

upper sequence: Vv04s0023g03620.t01 (Vitis vinifera), 5'ss of exon 7
lower sequence: GLYMA11G08290.1 (Glycine max), 5'ss of exon 7
CAGGCCCTTGCAATGTCTATGGATGACCCTGCCACTAGCCTTGCCATGAGAGACACAGATATGTCTGAGGCAGCTGCAGATGATCAGGACTTGGCTCTTGgtgagtt--tgctcaatccctttttgttgtatgtagaggttttatggtctgtcccgcctctataactcatccttccattactggtggcctatcatgaatgcc
||||| ||||||||||| ||||||||  |||| | ||||| ||   | | ||| |||||||||||||| ||| |||||  |||||  ||||||||||| ||||||||  |     || | ||     |  || ||        |     || |  |  || | ||   |  |  |  | ||||       |  |  | |   
CAGGCACTTGCAATGTCAATGGATGATTCTGCAATTAGCCATGATGTAAAAGATACAGATATGTCTGAAGCATCTGCAAGTGATCCTGACTTGGCTCTGGgtgagtttttatgttattcattcagtcttcatctaagaaacagagataatgacatgggtc-acaatgtaggcaacagtcactg-caatacagtacaatttaa

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|71884542|gb|DT033597.1|DT033597
EST:     AGACACGGATATGTCTGAGGCAGCTGCAGATGATCAGGACTTGGCTCTTG                         CTCTTCAATTATCTGTGCAGGACACTGGAAAAGATTCAACCAGTCAGACCG
genomic: AGACACAGATATGTCTGAGGCAGCTGCAGATGATCAGGACTTGGCTCTTGgtgagtttgc ... gtccttgcagCTCTTCAATTATCTGTGCAGGACACTGGAAAAGATTCAACCAGTCAGACCG
EST: gi|30137292|gb|CB922630.1|CB922630
EST:     GAGGCAGCTGCAGATGATCAGGACTTGGCTCTTG                         CTCTTCAA-TATCNTGTGCAGGACACTGGAAAAGATTCAACCAGTCAGACC
genomic: GAGGCAGCTGCAGATGATCAGGACTTGGCTCTTGgtgagtttgc ... gtccttgcagCTCTTCAATTATC-TGTGCAGGACACTGGAAAAGATTCAACCAGTCAGACC
EST: gi|30130168|gb|CB915507.1|CB915507
EST:     GGCAGCTGCAGATGATCAGGACTTGGCTCTTG                         CTCTTCAATTATCTGTGCAGGACACTGGAAAAGATTCAACCAGTCAGACCG
genomic: GGCAGCTGCAGATGATCAGGACTTGGCTCTTGgtgagtttgc ... gtccttgcagCTCTTCAATTATCTGTGCAGGACACTGGAAAAGATTCAACCAGTCAGACCG
EST: gi|110425434|gb|EC991819.1|EC991819
EST:     AGACACAGATATGTCTGAGGCAGCTGCAGATGATCAGGACTTGGCTCTTG                         CTCTTCAATTATCTGTGCAGGACACTGGAAAAGATTCAACCAGTCAGACCG
genomic: AGACACAGATATGTCTGAGGCAGCTGCAGATGATCAGGACTTGGCTCTTGgtgagtttgc ... gtccttgcagCTCTTCAATTATCTGTGCAGGACACTGGAAAAGATTCAACCAGTCAGACCG
EST: gi|110690274|gb|EE067240.1|EE067240
EST:     AGACACGGATATGTCTGAGGCAGCTGCAGATGATCAGGACTTGGCTCTTG                         CTCTTCAATTATCTGTGCAGGACACTGGAAAAGATTCAACCAGTCAGACCG
genomic: AGACACAGATATGTCTGAGGCAGCTGCAGATGATCAGGACTTGGCTCTTGgtgagtttgc ... gtccttgcagCTCTTCAATTATCTGTGCAGGACACTGGAAAAGATTCAACCAGTCAGACCG
EST: gi|351049150|gb|FQ449872.1|FQ449872
EST:     AGACACAGATATGTCTGAGGCAGCTGCAGATGATCAGGACTTGGCTCTTG                         CTCTTCAATTATCCGTGCAGGACACTGGAAAAGATTCAACCAGTCAGACCG
genomic: AGACACAGATATGTCTGAGGCAGCTGCAGATGATCAGGACTTGGCTCTTGgtgagtttgc ... gtccttgcagCTCTTCAATTATCTGTGCAGGACACTGGAAAAGATTCAACCAGTCAGACCG
EST: gi|110721698|gb|EE098992.1|EE098992
EST:     AGACACAGATATGTCTGAGGCAGCTGCAGATGATCAGGACTTGGCTCTTG                         CTCTTCAATTATCTGTGCAGGACACTGGAAAAGATTCA-CCAGTCAGACCG
genomic: AGACACAGATATGTCTGAGGCAGCTGCAGATGATCAGGACTTGGCTCTTGgtgagtttgc ... gtccttgcagCTCTTCAATTATCTGTGCAGGACACTGGAAAAGATTCAACCAGTCAGACCG
EST: gi|110684657|gb|EE062188.1|EE062188
EST:     AGACACGGATATGTCTGAGGCAGCTGCAGATGATCAGGACTTGGCTCTTG                         CTCTTCAATTATCTGTGCAGGACACTGGAAAAGATTCAACCAGTCAGACCG
genomic: AGACACAGATATGTCTGAGGCAGCTGCAGATGATCAGGACTTGGCTCTTGgtgagtttgc ... gtccttgcagCTCTTCAATTATCTGTGCAGGACACTGGAAAAGATTCAACCAGTCAGACCG
EST: gi|30137146|gb|CB922484.1|CB922484
EST:     AGACACAGATATGTCTGAGGCAGCTGCAGATGATCAGGACTTGGCTCTTG                         CTCTTCAATTATCTGTGCAGGACACTGGAAAAGATTCAACCAGTCAGACCG
genomic: AGACACAGATATGTCTGAGGCAGCTGCAGATGATCAGGACTTGGCTCTTGgtgagtttgc ... gtccttgcagCTCTTCAATTATCTGTGCAGGACACTGGAAAAGATTCAACCAGTCAGACCG
EST: gi|71882495|gb|DT031550.1|DT031550
EST:     GAGGCAGCTGCAGATGATCAGGACTTGGCTCTTG                         CTCTTCAATTATCTGTGCAGGACACTGGAAAAGATTCAACCAGTCAGACCG
genomic: GAGGCAGCTGCAGATGATCAGGACTTGGCTCTTGgtgagtttgc ... gtccttgcagCTCTTCAATTATCTGTGCAGGACACTGGAAAAGATTCAACCAGTCAGACCG
EST: gi|110693944|gb|EE070616.1|EE070616
EST:     AGACACGGATATGTCTGAGGCAGCTGCAGATGATCAGGACTTGGCTCTTG                         CTCTTCAATTATCTGTGCAGGACACTGGAAAAGATTCAACCAGTCAGACCG
genomic: AGACACAGATATGTCTGAGGCAGCTGCAGATGATCAGGACTTGGCTCTTGgtgagtttgc ... gtccttgcagCTCTTCAATTATCTGTGCAGGACACTGGAAAAGATTCAACCAGTCAGACCG
EST: gi|110689984|gb|EE066684.1|EE066684
EST:     AGACACGGATATGTCTGAGGCAGCTGCAGATGATCAGGACTTGGCTCTTG                         CTCTTCAATTATCTGTGCAGGACACTGGAAAAGATTCAACCAGTCAGACCG
genomic: AGACACAGATATGTCTGAGGCAGCTGCAGATGATCAGGACTTGGCTCTTGgtgagtttgc ... gtccttgcagCTCTTCAATTATCTGTGCAGGACACTGGAAAAGATTCAACCAGTCAGACCG
EST: gi|110384926|gb|EC949397.1|EC949397
EST:     AGACACGGATATGTCTGAGGCAGCTGCAGATGATCAGGACTTGGCTCTTG                         CTCTTCAATTATCTGTGCAGGACACTGGAAAAGATTCAACCAGTCAGACCG
genomic: AGACACAGATATGTCTGAGGCAGCTGCAGATGATCAGGACTTGGCTCTTGgtgagtttgc ... gtccttgcagCTCTTCAATTATCTGTGCAGGACACTGGAAAAGATTCAACCAGTCAGACCG
EST: gi|110386665|gb|EC951280.1|EC951280
EST:     AGACACGGATATGTCTGAGGCAGCTGCAGATGATCAGGACTTGGCTCTTG                         CTCTTCAATTATCTGTGCAGGACACTGGAAAAGATTCAACCAGTCAGACCG
genomic: AGACACAGATATGTCTGAGGCAGCTGCAGATGATCAGGACTTGGCTCTTGgtgagtttgc ... gtccttgcagCTCTTCAATTATCTGTGCAGGACACTGGAAAAGATTCAACCAGTCAGACCG
EST: gi|110409069|gb|EC974725.1|EC974725
EST:     AGACACAGATATGTCTGAGGCAGCTGCAGATGATCAGGACTTGGCTCTTG                         CTCTTCAATTATCTGTGCAGGACACTGGAAAAGATTCAACCAGTCAGACCG
genomic: AGACACAGATATGTCTGAGGCAGCTGCAGATGATCAGGACTTGGCTCTTGgtgagtttgc ... gtccttgcagCTCTTCAATTATCTGTGCAGGACACTGGAAAAGATTCAACCAGTCAGACCG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CAGGCCCTTGCAATGTCTATGGATGACCCTGCCACTAGCCTTGCCATGAGAGACACAGATATGTCTGAGGCAGCTGCAGATGATCAGGACTTGGCTCTTGgtgagtttgctcaatccctttttgttgtatgtagaggttttatggtctgtcccgcctctataactcatccttccattactggtggcctatcatgaatgcc

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tccttcc